title: In vivo genome editing restores dystrophin expression in Duchenne muscular dystrophy patient muscle fibers [RNA-seq]

status: Public on Feb 28 2021

summary: Duchenne muscular dystrophy (DMD) is the most common fatal genetic disease. Clustered regularly interspaced short palindromic repeat (CRISPR)-mediated gene editing is a promising strategy for permanently curing DMD. In this study we developed a novel strategy for reframing DMD mutations by CRISPR-mediated large-scale excision of exons 46–54. We compared this approach to other DMD rescue strategies using DMD patient-derived primary muscle-derived stem cells (MDSCs) and found that it showed the highest efficiency in terms of restoring of dystrophin protein expression. We also confirmed that CRISPR from Prevotella and Francisella 1(Cpf1)-mediated genome editing could correct DMD mutation with higher specificity than CRISPR-associated protein 9 (Cas9). Furthermore, A patient-derived xenograft (PDX) DMD mouse model was established by transplanting DMD-MDSCs into immunodeficient mice. CRISPR gene editing components were intramuscularly delivered into the mouse model by adeno-associated virus vectors. Dystrophin expression levels were increased by 10%–30% in human DMD muscle fibers. The restored dystrophin in vivo was functional, as demonstrated by the expression of the dystrophin glycoprotein complex member β-dystroglycan. This study provides a sensitive indicator for in vivo efficacy of gene editing and lays the foundation for a clinical trial of DMD treatment with gene editing technology.

overall_design: 16 samples for RNA-seq, including 2 untreated samples as negative control, 4 normal samples as positive control, 2 mock transfected samples (PBS only),  2  only Cas9 transfected samples, 2 replicates for each treatment groups.

first: Menglong

last: Chen

first: Hui

last: Shi

first: Xiaomin

last: Wang

first: Han

last: Wu

first: Huili

last: Zhang

first: Yaqin

last: Li

first: Liang

first: Wenjing

last: Guo

first: Zhiwu

last: Jiang

first: Xiaoyu

last: Yang

first: Anding

last: Xu

first: Cheng

first: Xiaoping

first: Yuling

last: Zhu

first: Liangxue

last: Lai


title: RNA-seq gene expression profiling of protein coding and lncRNA genes in chromatin-bound RNA from livers of male and female mice, with or without exposure to TCPOBOP, a CAR (Nr1i3) agonist ligand [G178]

status: Public on Mar 01 2021

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

country: USA

institute: Boston University

type: Expression profiling by high throughput sequencing

summary: PolyA-selected RNA was isolated from the chromatin bound fraction of frozen liver tissue from adult male and female ICR/CD1 mice that were treated with 3 mg/kg TCPOBOP disolved in corn oil, or corn oil vehicle, for 27 hr. These samples are part of a study where we characterize global patterns of expression, maturation and localization for both lncRNA and protein coding gene transcripts in mouse liver, and where we identify candidate regulatory lncRNAs that may be important for a variety of hepatic functions, based on their co-localized within topologically associating domains, or their transcription divergent, antisense or intergenic to protein coding genes associated with key pathways linked to hepatic physiology and disease.

overall_design: Chromatin-bound liver RNA, polyA-selected, was isolated from frozen liver tissue from 7-8 week old male and female CD-1 mice treated with TCPOBOP or vehicle control for 27 hr. Each sample is derived from a single liver, with n=3-4 mice per treatment group.

first: Christine

last: Goldfarb

middle: J


title: In vivo genome editing restores dystrophin expression in Duchenne muscular dystrophy patient muscle fibers [WES]

city: Guangzhou

first: Shixue

last: Gou

address: No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou

country: China

institute: GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH,CHINESE ACADEMY OF SCIENCES

overall_design: 14 samples for Whole Exome Sequencing, including 2 untreated samples as control, 2 mock transfected samples (PBS only),  2  only Cas9 transfected samples, 2 replicates for each treatment groups.

first: Menglong


title: RNA-seq gene expression profiling of  protein coding and lncRNA genes in nucleoplasmic RNA from livers of male and female mice, with or without exposure to TCPOBOP, a CAR (Nr1i3) agonist ligand [G176]

summary: PolyA-selected RNA was isolated from the nucleoplasmic fraction of frozen liver tissue from adult male and female ICR/CD1 mice that were treated with 3 mg/kg TCPOBOP disolved in corn oil, or corn oil vehicle, for 27 hr. These samples are part of a study where we characterize global patterns of expression, maturation and localization for both lncRNA and protein coding gene transcripts in mouse liver, and where we identify candidate regulatory lncRNAs that may be important for a variety of hepatic functions, based on their co-localized within topologically associating domains, or their transcription divergent, antisense or intergenic to protein coding genes associated with key pathways linked to hepatic physiology and disease.

overall_design: Liver nucleoplasmicRNA, polyA-selected, was isolated from frozen liver tissue from 7-8 week old male and female CD-1 mice treated with TCPOBOP or vehicle control for 27 hr. Each sample is derived from a single liver, with n=3-4 mice per treatment group.


title: RNA-seq gene expression profiling of protein coding and lncRNA genes in nuclear RNA from livers of male and female mice, with or without exposure to TCPOBOP, a CAR (Nr1i3) agonist ligand [G175]

summary: PolyA-selected RNA was isolated from the nuclear fraction of frozen liver tissue from adult male and female ICR/CD1 mice that were treated with 3 mg/kg TCPOBOP disolved in corn oil, or corn oil vehicle, for 27 hr. These samples are part of a study where we characterize global patterns of expression, maturation and localization for both lncRNA and protein coding gene transcripts in mouse liver, and where we identify candidate regulatory lncRNAs that may be important for a variety of hepatic functions, based on their co-localized within topologically associating domains, or their transcription divergent, antisense or intergenic to protein coding genes associated with key pathways linked to hepatic physiology and disease.

overall_design: Liver nuclear RNA, polyA-selected, was isolated from frozen liver tissue from 7-8 week old male and female CD-1 mice treated with TCPOBOP or vehicle control for 27 hr. Each RNA sample is derived from a single liver, with n=3-4 mice per treatment group.


title: Small extracellular vesicles derived from interferon-γ pre-conditioned mesenchymal stromal cell(MSC)s effectively treat liver fibrosis

city: Niigata

first: Atsunori

last: Tsuchiya

state: %null%

address: 1-757, Asahimachi-dori, Chuo-ku, Niigata

country: Japan

institute: Niigata University

type: Non-coding RNA profiling by high throughput sequencing

summary: A novel therapeutic approach of IFN-γ-treated mesenchymal stromal cell-produced extracellular vesicles effectively treated a cirrhosis model.

overall_design: the miRNAs of small extracellular vesicles derived from MSCs (sEVs) and interferon-γ (IFN-γ) pre-conditioned MSCs (γ-sEVs)

first: Suguru

last: Takeuchi

first: Shuji

last: Terai


title: Circular RNA microarray analyses in hepatic ischemia-reperfusion injury with ischemic preconditioning prevention

city: Dalian

first: Yan

last: Hu

state: Liaoning

address: 467 Zhongshan Road

institute: Department of Pharmacy, Second Affiliated Hospital of Dalian Medical University

summary: The study for the first time systematically detect the dysregulated circRNAs and mRNAs in response to hepatic IRI and IPC intervention. Our profile and bioinformatic analysis provide numerous of novel clews on the understanding the pathophysiologic mechanism of IPC protection against hepatic IRI.

overall_design: Hepatic circRNAs expression profiles of sham, IRI and IPC mice were generated by microarray analysis in triplicate.

first: Xinyao

last: Tian


title: Real-time quantitative PCR analysis of Vegf knockdown on expression of extracellular matrix and adhension molecules in male and female primary murine osteoblasts

city: Southampton

first: Aikta

last: Sharma

state: Hampshire

address: Life Sciences Building 85, University Road

department: Biological Sciences

country: United Kingdom

institute: University of Southampton

summary: Primary murine osteoblasts, isolated from the long bones of 4-day old male and female Vegffl/fl mice, were cultured prior to transduction with adenovirus-Cre-GFP at an multiplicity of infection of 100, to knockdown Vegf expression (OBVEGFKO) in vitro for six days. Control cells were transduced with an adenovirus expressing GFP (WT). Following this, cells were stepped down in low serum media containing 1% FBS for 24 hours, after which the conditioned media was collected for knockdown validation using an VEGF ELISA. We used the Qiagen Extracellular Matrix and Adhension Molecule RT2 Profiler PCR Array to assay the sexually dimorphic effects of Vegf on the expression of genes associated with bone matrix formation and mineralisation, remodelling and angiogenesis.

overall_design: qPCR gene expression array. Osteoblasts isolated from 4-day old male and female Vegffl/fl mice were cultured prior to being transfected with adenovirus expressing Cre-recombinase-GFP to knockdown Vegf expression or adenovirus expressing GFP alone. Knockdown was validated using an VEGF ELISA. Equal amount total RNA (500 ng) was purified from each treatment group before reverse transcription and subsequent expression profiling.

first: Claire

middle: E

last: Clarkin


title: In vivo genome editing restores dystrophin expression in Duchenne muscular dystrophy patient muscle fibers [GUIDE-seq]

overall_design: The GUIDE-seq (Genome-wide, unbiased identification of DSBs enabled by sequencing) was applied to capture all the DNA double-stranded breaks (DSBs) generated by Cas9 and Cas12a. When the gRNA library is constructed, two libraries are generated of each gRNA sample, one is forward and the other is backward, which respectively correspond to N_R and P_R sequencing files. At the same time, each library will generate a corresponding index file, corresponding to the file containing N_I and P_I respectively

last: Chen

first: Hui

last: Shi

first: Xiaomin

last: Wang

first: Han

last: Wu

first: Huili

last: Zhang

first: Yaqin

last: Li

first: Liang

first: Wenjing

first: Zhiwu

first: Xiaoyu


title: In vivo genome editing restores dystrophin expression in Duchenne muscular dystrophy patient muscle fibers [Nanopore sequencing]

first: Shixue

overall_design: To understand the splicing changes mediated by large-scale excision, the long-read sequencing technology, nanopore sequencing was applied to inspect the spliced DMD fragments. About 2kb regions nearby the cutting sites were amplified from DMD- MDSCs edited by Cas9 or Cas12a with paired gRNAs.

first: Menglong

last: Guo

last: Jiang

last: Yang

first: Anding

last: Xu

first: Cheng

first: Xiaoping

first: Yuling

last: Zhu

first: Liangxue

last: Lai


title: Effects of biometals in regulating liver transcriptomes

status: Public on Feb 27 2021

city: Rochester

first: Zijuan

last: Liu

state: MI

address: 318 Meadow Brook Rd, Rochester, MI 48309

department: Biology

institute: Oakland University

summary: Four trace elements, Zn, Mn, Se and Fe were used to treat primary hepatocytes isolated from a ZIP8 liver-specific mouse line to study whether they can rescue the gene changes caused by loss of ZIP8 function.

overall_design:
Eight total samples were analyzed for the purpose of this study; there were four controls: two untreated WT primary hepatocytes (replicates) and two untreated ZIP8-liver specific knockout primary hepatocytes cultures (replicates). The other four samples were ZIP8-liver specific knockout hepatocytes treated with different divalent metals of interest (manganese, iron, selenium, zinc), which is added to a final concentrations of 2uM, for overnight treatment.
The total RNA was isolated from primary cultured hepatocytes and submitted for RNA-seq. The cDNA was synthesized by Genewiz. One-tail RNA-seq was performed at 500 million counts. All quality control analysis, read alignment, and read counting were performed on a high-performance computing environment on a Linux operating system hosted by The Institute for Cyber-Enabled Research at Michigan State University.

first: Michael

last: Powers

first: Liu

first: Dane

last: Deemer

first: Selina


title: In vivo genome editing restores dystrophin expression in Duchenne muscular dystrophy patient muscle fibers [Amplicon-seq]

last: Gou

overall_design: The targeting efficiency of gRNAs in DMD-MDSCs were detected by high-throughput sequencing the PCR products of edited DMD gene, three negative control (cas9 only, pbs mock, untreated) and one ontarget samples were produced, each sample has two replicates.

first: Hui

first: Xiaomin

first: Han

first: Huili

first: Yaqin


title: Chromatin accessibility analysis of CNS4-sufficient and defincient regulatory T cells, Treg cell precursors, and mature and semimature CD4 single positives

city: La Jolla

first: Stanislav

last: Dikiy

state: CA

address: 10550 North Torrey Pines Road

department: Immunology

institute: Scripps Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We have discovered that deletion of a conserved regulatory element upstream of the Foxp3 gene, termed CNS4, results in the abrogation of IL-2 mediated induction of Foxp3 expression during regulatory T cell development. However, the mice still harbor a reduced but functional population of Treg cells. To understand potential compensatory mechanisms driving the differentiation and expansion of regulatory T cells in the absence of CNS4, we profiled CNS4-deficient and -sufficient regulatory T cells, as well as related cell types, from the thymuses of male mice by ATAC-sequencing.

overall_design: Cells from 2 mice per genotype were analyzed, of the following genotypes: CNS4FL/YFoxp3GFP/Y; CNS4KO/YFoxp3GFP/Y. Cells were sorted from mechanically disrupted thymuses based on the following markers: Treg cells: Foxp3-GFP+CD4+CD8-TCRβ+; preTreg cells: CD25+Foxp3-GFP-CD4+CD8-TCRβ+; mSP cells: CD25-Foxp3-GFP-CD4+CD8-TCRβhiCD24lo; smSP cells: CD25-Foxp3-GFP-CD4+CD8-TCRβloCD24hi. 40,000 - 50,000 cells per replicate were used.

first: Rudensky

last: Alexander

first: Dikiy

last: Stanislav


title: Clinical and molecular differentiation between malignant rhabdoid tumor of normal tissue: A two-case report

status: Public on Feb 26 2021

city: Hefei

first: shuo

last: chen

address: Meishan Road#81

institute: Anhui Medical University

summary: Preoperative B-scan ultrasonography and Computed Tomography (CT) examination in 2 cases suggested that nephroblastoma . Treated with radical nephrectomy after general anesthesia. After operation,MRTK diagnosis by pathological examination. Regular chemotherapy 7 courses(Child 1) and 12 courses(Child 2),followed up for 2 years(Child 1) and 3 years and 1 month(Child 2), without symptoms. RNA-seq results showed 2203 differential genes (DEGs) in the kidney tissue of children with MRTK compared to normal tissue. GO analysis suggested that most DEGs participate in protein binding. KEGG results showed that the DEGs were mainly involved in the PI3K-Akt signaling pathway and microRNA-related proteins.

overall_design: Compare the expression of mRMA between MRTK and normal tissues to suggest new ideas for diagnosis and treatment.

first: Chenghao

last: Zhanghuang

first: Shuo

last: Chen

first: Li

first: Zhen

first: Yucheng

last: Xie

first: Jiwei

first: Haoyu

last: Tang

first: Xiaoli

last: He

first: Liuyi

last: Dong

first: Bing

last: Yan


title: Reorganization of 3D chromatin architecture of rice genomes during heat stress (ATAC-Seq)

city: Beijing

first: Xiaofeng

last: Gu

address: Zhongguancun south street

institute: Chinese Academy of Agricultrual Sciences

summary:
Background: The three-dimensional spatial organization of the genome plays important roles in chromatin accessibility and gene expression in multiple biological process, and has been reported to be altered in response to environmental stress. However, the functional changes in spatial genome organization during environmental changes in crop plants are poorly understood.
Results: Here we perform Hi-C, ATAC-seq and RNA-seq in two agronomically important rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica), to report a comprehensive profile of nuclear dynamics during heat stress (HS). We show that heat stress affects different levels of chromosome organization, including A/B compartment transition, increase in size of topologically associated domains, and loss of short-range interactions. The chromatin architectural changes were associated with chromatin accessibility and gene expression changes. Comparative analysis revealed that 93-11 exhibited more dynamic gene expression and chromatin accessibility changes, including of HS-related genes, consistent with observed higher HS tolerance in this cultivar.
Conclusions: Our data uncovered higher-order chromatin architecture as a new layer in understanding transcriptional regulation in response to heat stress in rice.

overall_design: ATAC-seq with two replicates

first: Zhe

last: Liang

first: Qian

last: Zhang

first: Qing

first: Changmian

last: Ji

first: Pingxian

first: Guihua

last: Hu

first: Yifan

last: Wang


title: Reorganization of 3D chromatin architecture of rice genomes during heat stress (HiC)

overall_design: Hi-C with two replicates

last: Liu


title: DOT1L inhibitors block abnormal self-renewal induced by cohesin loss

status: Public on Feb 25 2021

city: Miwaukee

first: Katelyn

middle: Elizabeth

last: Heimbruch

state: Wisconsin

address: 8727 Watertown Plank Road

institute: Medical College of Wisconsin

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

overall_design: Refer to individual Series


title: Loss of Prdm12 during development, but not in mature nociceptors, causes defects in pain sensation.

city: Dallas

first: Mark

last: Landy

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Prdm12 is a key transcription factor in nociceptor neurogenesis. Mutations of Prdm12 cause Congenital Insensitivity to Pain (CIP) due to failure of nociceptor development. However, precisely how deletion of Prdm12 during development or adulthood affects nociception is unknown. Here, we employ tissue- and temporal-specific knockout mouse models to test the function of Prdm12 during development and in adulthood. We find that constitutive loss of Prdm12 causes deficiencies in proliferation during sensory neurogenesis. We also demonstrate that conditional knockout from dorsal root ganglia (DRGs) during embryogenesis causes defects in nociception. In contrast, we find that in adult DRGs, Prdm12 is dispensable for most pain sensation and injury-induced hypersensitivity. Using transcriptomic analysis, we found mostly unique changes in adult Prdm12 knockout DRGs compared to embryonic knockout, and that PRDM12 is likely a transcriptional activator in the adult. Overall, we find that the function of PRDM12 changes over developmental time.

overall_design: Bulk mRNA profiles of dorsal root ganglia (DRGs) from  wild type (WT, n = 2) and Prdm12AvilERT2CKO (Mut, n = 2)

middle: A

first: Megan

last: Goyal

first: Katherin

middle: M

last: Casey

first: Chen

first: Helen

middle: C

last: Lai


title: Reorganization of 3D chromatin architecture of rice genomes during heat stress (RNA-Seq)

overall_design: RNA-seq with three replicates


title: Regulated sulfur sequestration promotes multicellularity during nutrient limitation

status: Public on Feb 24 2021

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University


title: A Combination of Epigenetic BET and CDK9 Inhibitors for Treatment of Human Melanoma

status: Public on Feb 23 2021

city: Camperdown

first: Stuart

last: Gallagher

state: NSW

address: Building 93, RPA Hospital

department: Melanoma Oncology

country: Australia

institute: Centenary Institute

summary: The transcriptome of 3 cutaneous melanoma cell lines treated with Control (DMSO), CDK9 inhibitor (CDKI73), BET/bromodomain and extra terminal inhibitors IBET151, or combination of both drugs was assessed using RNAseq.    Dysregulation of epigenetic modifiers is a frequent event in melanoma and underlies many aspects of melanoma biology including resistance to targeted and immunotherapies. Here we report that dual targeting of BET and CDK9 proteins have synergistic effects against melanoma cells in vitro and in vivo. The BET inhibitor (IBET151) and CDK9 inhibitor (CDKI73) synergistically killed melanoma cells in vitro independent of their BRAF or NRAS mutation status. The combination of drugs markedly inhibited the growth of human melanoma C002M cells in vitro in 3D spheroids and in vivo in NSG mice compared to vehicle control and the individual drugs (p<0.05). Cell death was associated with mitochondrial depolarisation and caspase dependent apoptosis with cleavage of PARP1 as well as downregulation of anti-apoptotic proteins BCL2, BCLXL and MCL1. GSEA revealed downregulation of hallmark gene-sets associated with E2F, G2M checkpoint and c-MYC.   Survival analysis showed worse prognosis with high G2M, E2F or c-MYC gene signatures suggesting biomarkers of response of BET and CDK9 inhibitors in melanoma. This novel combination of epigenetic inhibitors targets multiple downstream genes leading to cell death of melanoma cells in vitro and in vivo and warrant further investigation for treatment of melanoma in patients not responding to current therapies.

overall_design: RNAseq was performed on three melanoma cell lines treated for 24 h with the DMSO, BET inhibitor (IBET-151), CDK9 inhibitor (CDKI73), or combination. Experiments were performed in biological duplicates.

first: Jessamy

last: Tiffen

first: Abdullah

last: Al Emran


title: Regulated sulfur sequestration promotes multicellularity during nutrient limitation (RNA-Seq)

summary: Dictyostelium discoideum behavior depends on nutrients1. When sufficient food is present these amoebae exist in a unicellular state, but upon starvation they aggregate into a multicellular organism2,3. This unique biology makes D. discoideum an ideal model for investigating how fundamental metabolic pathways command cell differentiation and function. We show here that reactive oxygen species (ROS), generated as a consequence of nutrient limitation, lead to the sequestration of the amino acid cysteine in the antioxidant glutathione, limiting the use of its sulfur atom for processes such as protein translation and FeS cluster-containing enzyme activity that contribute to mitochondrial metabolism and cellular proliferation. Such regulated sulfur sequestration maintains D. discoideum in a non-proliferating state that paves the way for multicellular development. This new mechanism of ROS signaling highlights oxygen and sulfur as simple, early evolutionary signaling molecules dictating cell fate, with implications for responses to nutrient fluctuations in higher eukaryotes.

overall_design: Dictyostelium discoideum (D. discoideum) strain Ax4 was purchased from the Dictybase stock center. Vegetatively growing cells were axenically maintained in shaking culture in HL5 nutrient medium (14.3 g/L bacto peptone, 7.15 g/L yeast extract, 18 g/L maltose monohydrate, 0.641 g/L Na2HPO4, 0.49 g/L KH2PO4, supplemented with biotin, cyanocobalamin, folic acid, lipoic acid, riboflavin and thiamine-HCl). Starvation and consequent aggregation were induced by washing D. discoideum four times in development buffer (DB; 5 mM Na2HPO4, 5 mM KH2PO4, 1 mM CaCl2, 2 mM MgCl2 in autoclaved H2O) and plating at a density of 2 x 106 cells/ml in DB on tissue culture-treated plates, without shaking. As a control, vegetatively growing cells were plated at a density of 2 x 106 cells/ml in HL5 on tissue culture-treated plates, without shaking. Cells were starved for different lengths of time with or without treatment with reduced glutathione (1 – 20 mM) with 3 biological replicates per treatment

first: Beth

last: Kelly

first: Gustavo

last: Carrizo

first: Joy

last: Edwards-Hicks

first: David

last: Sanin

first: Michal

last: Stanczak

first: Chantal

last: Priesnitz

first: Lea

last: Flachsmann

first: Jonathan

middle: D

last: Curtis

first: Gerhard

last: Mittler

first: Yaarub

last: Musa

first: Joerg

last: Buesscher

first: Erika

middle: L

last: Pearce


title: DOT1L inhibitors block abnormal self-renewal induced by cohesin loss [RNA-seq]

first: Katelyn

last: Heimbruch

summary: Acute myelogenous leukemia (AML) is a high-risk malignancy characterized by a diverse spectrum of somatic genetic alterations. The mechanisms by which these mutations contribute to leukemia development and how this informs the use of targeted therapies is critical to improving outcomes. Importantly, how to target loss-of-function mutations has been a critical challenge in precision medicine. Heterozygous inactivating mutations in cohesin complex genes contribute to AML by increasing the self-renewal capacity of hematopoietic stem and progenitor cells (HSPCs) by altering PRC2 targeting to induce HOXA9 expression, a key self-renewal transcription factor. Here we sought to delineate the mechanism underpinning the enhanced self-renewal conferred by cohesin haploinsufficiency. Using primary (HSPCs) as a model we demonstrate that a reduction in a core cohesin subunit is associated with decreased H3K27me3 and increased H3K79me2, along with increased self-renewal capacity and a leukemic transcriptional profile. Inhibition of DOT1L in cohesin-depleted HSPCs restored normal self-renewal, H3K27me3 and H3K79me2 levels, and gene expression, identifying DOT1L as a potential therapeutic target in cohesin haploinsufficient AML. Together our data further characterizes the mechanism by which cohesin mutations contribute to AML and identifies DOT1L as a potential therapeutic target for AML patients harboring cohesin mutations.

overall_design: RNA-sequencing and ChIP-sequencing of 4 conditions, with 2-3 replicates per condition.

middle: H

first: Sridhar

last: Rao


title: RNA-seq data of aortas with atherosclerotic or medial calcification

city: BEIJING

first: YINGCHUN

last: HAN

state: BEIJING

address: CHAOYANG DISTRICT

institute: Anzhen Hospital

summary: Vascular calcification is the ectopic deposition of calcium hydroxyapatite minerals in arterial wall. However, the underlying molecular mechanisms regulating vascular calcification remain incompletely understood. In this study, we applied RNA sequencing to explore the mechanism of vascular calcificaiton in both medial and atherosclerotic vascular calcification models.

overall_design: mRNA profiles of aortas from 2-month old wild type, 16-month old ApoE-/-(atherosclerotic calcificaiton) and chronic kidney diseased mice(medial calcification).

first: Yingchun

last: Han


title: Regulated sulfur sequestration promotes multicellularity during nutrient limitation (scRNA-Seq)

first: Immunometabolism

last: Department

overall_design: Dictyostelium discoideum (D. discoideum) strain Ax4 was purchased from the Dictybase stock center. Vegetatively growing cells were axenically maintained in shaking culture in HL5 nutrient medium (14.3 g/L bacto peptone, 7.15 g/L yeast extract, 18 g/L maltose monohydrate, 0.641 g/L Na2HPO4, 0.49 g/L KH2PO4, supplemented with biotin, cyanocobalamin, folic acid, lipoic acid, riboflavin and thiamine-HCl). Starvation and consequent aggregation were induced by washing D. discoideum four times in development buffer (DB; 5 mM Na2HPO4, 5 mM KH2PO4, 1 mM CaCl2, 2 mM MgCl2 in autoclaved H2O) and plating at a density of 2 x 106 cells/ml in DB on tissue culture-treated plates, without shaking. As a control, vegetatively growing cells were plated at a density of 2 x 106 cells/ml in HL5 on tissue culture-treated plates, without shaking. Single cells were sequenced using the 10x Chromium controller. One sample per treatment was used.


title: Mapping of p300/CBP binding sites in MDA-MB-231 cells transfected with a control siRNA or a siRNA directed against Fra-1(FOSL1)

city: Montpellier

first: Isabelle

last: Jariel-Encontre

state: Montpellier Cedex5

address: 208 Avenue des Apothicaires

country: France

institute: IRCM-U1194- INSERM

summary: In the article "Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers"  by Bejjani et al., we mapped p300/CBP binding sites in MDA-MB-231 cells transfected with a control siRNA or a siRNA directed against Fra-1(FOSL1) to study whether Fra-1 can modulate p300/CBP recruitment on MDA-MB-231 genome

overall_design: MDA-MB-231 cells were transfected with a control siRNA or a siRNA directed against Fra-1. ChIP-seq were carried out using an mouse monoclonal antibody specific of p300/CBP (sc-32244X from Santa Cruz Biotechnology)

first: Fabienne

last: Bejjani

first: Marc

last: Piechaczyk


title: Seq data of aortas


title: Chromatin accessibility dictates specific transcriptional response by different cells of the innate immune system

first: Edward

last: Wakeland


title: Human METTL18 is a histidine-specific methyltransferase that targets RPL3 and affects ribosome biogenesis and function

city: Bern

first: Yeji

last: Kim

address: Freiestrasse 3

department: Department of Chemistry and Biochemistry

country: Switzerland

institute: University of Bern

summary: Methylation is a common post-translational modification that occurs primarily on lysine and arginine, but also on some other residues, such as histidine. METTL18 is the last uncharacterized member of a group of human methyltransferases (MTases) that mainly exert lysine methylation, and here we set out to elucidate its function. We found METTL18 to be a nuclear protein that contains a functional  nuclear localization signal and accumulates in nucleoli. Recombinant METTL18 methylated a single protein in nuclear extracts and in isolated ribosomes from METTL18 knock-out (KO) cells. This protein was identified as 60S ribosomal protein L3 (RPL3), and we also performed an RPL3 interactomics screen and identified METTL18 as the most significantly enriched MTase. Protein mass spectrometry and amino acid analyses revealed that His-245 in RPL3 carries a 3-methylhistidine (3MH; also referred to as t-methylhistidine) modification, which was absent in METTL18 KO cells. In addition, both recombinant and endogenous METTL18 were found to be monomethylated at His-154, likely resulting from auto-methylation, and further corroborating METTL18 as a histidine-specific MTase. Finally, METTL18 KO cells displayed altered pre-rRNA processing, decreased polysomes formation and codon-specific changes in mRNA translation, indicating that METTL18-mediated methylation of RPL3 is important for optimal ribosome biogenesis and function. In conclusion, we have here established METTL18 as the second human histidine-specific protein MTase, and demonstrated its functional relevance.

overall_design: Identifying function and target of METTL18 in human haploid cells

first: Jędrzej

last: Małecki

first: Marie

middle: F

last: Odonohue

first: Magnus

last: Jakobsson

first: Luca

last: Gessa

first: Jie

last: Wu

first: Rita

last: Pinto

first: Erna

last: Davydova

first: Anders

last: Moen

first: Bernd

last: Thiede

first: Pierre

last: Gleizes

first: Sebastian

last: Leidel

first: Pål

middle: O

last: Falnes


title: IRF1 governs the differential Interferon-Stimulated Gene responses in human monocytes and macrophages by regulating chromatin accessibility (RNA-seq - TLR stimulation)

summary: Myeloid lineage cells use TLRs to recognize and respond to diverse microbial ligands. Although unique transcription factors dictate the outcome of specific TLR signaling, whether lineage-specific differences exist to further modulate the quality of TLR-induced inflammation remains unclear. Comprehensive analysis of global gene transcription in human monocytes, monocyte-derived macrophages and monocyte-derived dendritic cells stimulated with various TLR ligands identifies multiple lineage-specific, TLR-responsive gene programs. Monocytes are hyperresponsive to TLR7/8 stimulation that correlates with higher expression of the receptors. While macrophages and monocytes express similar levels of TLR4, macrophages, but not monocytes, upregulate Interferon-Stimulated Genes (ISGs) in response to TLR4 stimulation. We find that TLR4 signaling in macrophages uniquely engages transcription factor IRF1, which facilitates opening of ISG loci for transcription. This study provides a critical mechanistic basis for lineage-specific TLR responses and uncovers IRF1 as a master epigenetic regulator for the ISG transcriptional program in human macrophages.

overall_design: RNA-seq anlaysis of transcriptional changes in monocytes, MDMs and MDDCs from five healthy human donors unstimulated or stimulated with Pam3CSK4, LPS, R837 or R848 for 18 hours

first: Ran

last: Song

first: Igor

last: Dozmorov

first: Venkat

last: Malladi

first: Chaoying

last: Liang

first: Carlos

last: Arana

first: Benjamin

first: Chandrashekhar

last: Pasare

middle: K


title: Distinct properties and functions of CTCF revealed by a rapidly inducible degron system [PRO-Seq]

city: Philadelphia

first: Jing

last: Luan

address: 3615 Civic Center Blvd, ARC 315

institute: University of Pennsylvania

summary: We coupled an auxin-induced degron (AID) system with precision nuclear run-on (PRO-seq). Oriented CTCF motifs in gene bodies are associated with transcriptional stalling in a manner ostensibly independent of bound CTCF. CTCF binding sites display highly variable resistance to degradation, with persistent sites displaying architectural related features.

overall_design: Transient endogenous CTCF depletion coupled with genome wide CTCF binding site profiling (ChIP-seq) and nascent transcription quantification (PRO-seq)

first: Luan

last: Jing

first: Blobl

last: Gerd


title: Distinct properties and functions of CTCF revealed by a rapidly inducible degron system [ChIP-Seq]


title: Evaluation of gene expression changes in tcs09 single and double mutants in the pneumococcal strain D39

status: Public on Feb 22 2021

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

summary: In order to elucidate the regulatory role of pneumococcal TCS09, a transcriptomic approach was performed using RNA-seq from bacterial cultures in chemical defined medium of single and double tcs09 mutants. A total of 69 genes presenting significant expression changes were selected for further evaluation and discussion. These 69 genes were classified accordingly to their biochemical function.

overall_design: response regulator 09, histidine kinase 09 and a rr09-hk09 mutants were generated in a pneumococcal D39 background. Each individual mutant strain and its wild-type were cultivated in chemically defined medium until mid-log phase and collected for RNA isolation in quadruplicate

first: Stephanie

last: Hirschmann

first: Alejandro

last: Gómez-Mejia

first: Ulrike

last: Mäder

first: Julia

last: Karsunke

first: Dominik

last: Driesch

first: Manfred

last: Rohde

first: Susanne

last: Häußler

first: Gerhard

last: Burchhardt

first: Sven

last: Hammerschmidt


title: Autophagic monocytic myeloid-derived suppressor cells protect mice cardiac allografts

city: Shanghai

first: Jiawei

last: Li

address: 180 Fenglin Road

institute: Fudan University Zhongshan Hospital

summary:
Background: Myeloid-derived suppressor cells (MDSCs) could prevent allograft rejections and induce immune tolerance in transplantation models. Previous studies demonstrated that inhibition of mTOR signal could enhance MDSCs protective effect in cardiac transplantation model via promoting MDSCs expansion. And the inhibition of mTOR is related with autophagy. Herein, this study was designed to investigate the protective mechanism of mTOR deficiency M-MDSCs in cardiac transplantation model.
Methods: Myeloid-specific mTOR conditional knockout mice were generated to get mTOR deficiency M-MDSCs. The proliferation and immunosuppressive function of mTOR deficiency M-MDSCs were determined by flow cytometry and CFSE T cell proliferation assays. mTOR deficiency M-MDSCs intracellular autophagy levels were determined by western blot and Electron microscopy. RNAseq analysis was performed for WT and mTOR-deficient M-MDSC cells. Cervical cardiac transplantation model mice were generated. ELISA were performed for control mice, model mice, WT MDSCs infusion model mice and mTOR-deficient MDSCs infusion model mice to examine the inflammatory cytokines in the recipients mice serum. Flow cytometry and immunohistochemistry were performed to determine mTOR-deficient MDSCs induced immune tolerance.
Results: mTOR deficiency could promote M-MDSCs differentiation and enhance intracellular autophagy levels in vivo and in vitro. mTOR deficiency also enhance the immunosuppressive function of M-MDSCs. In addition, infusing mTOR deficiency M-MDSCs could also prolong cardiac allograft survival and establish immune tolerance in recipient mice by inhibiting T cell activation and inducing Tregs.
Conclusion: mTOR-deficiency enhances M-MDSCs cells autophagy and immunosuppressive function and prolongs mice cardiac allograft survival.

overall_design: Wild-type (WT) and mTOR-deficient (KO) M-MDSC cells were induced from WT mice and Lyz-mTOR mice (n=3). Total RNA was isolated by Trizol (Sigma). RNA quality was determined by the ratios of A260/A280 using Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific). RNAs were further tested using an Agilent 2100 Bioanalyzer (Agilent Technologies), and samples with RIN>7 were selected for sequencing library construction using the (Illumina). And the final library was sequenced on Illumina Novaseq 6000 sequencer. On average about 20 million 150bp paired end reads were generated per sample.

first: Juntao

last: Chen

first: Mingnan

last: Zhang

first: Chao


title: DOT1L inhibitors block abnormal self-renewal induced by cohesin loss [ChIP-seq]

first: Katelyn

last: Heimbruch

overall_design: ChIP-sequencing of 4 conditions, 3 replicates per condition.

first: Sridhar

last: Rao


title: RNA Sequencing for MKRN3 regulating genes identification in GT1-7 cells

first: Menghuan

address: 320 Yue Yang Road

department: Shanghai Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

summary:
Purpose: The deletion or loss-of-function of MKRN3 were genetically associated with human centeral precocious puberty (CPP).The goal of this study is to explore the global genes expression changes on MKRN3 overexpessing by high-throughput RNA sequencing analysis.
Methods: The mRNA profiles of wild-type (WT) and MKRN3 overexpressed  GT1-7 cells were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were aligned to mus musculus genomic reference (GRCm38) using HISAT2. Read counts were summarized at the gene level in each sample with HTSeq.
Results: Using an optimized data analysis workflow, we mapped about 19 million sequence reads per sample to the mouse genome (build mm10) and identified 13,041 transcripts in the GT1-7 cells of WT and MKRN3. Approximately 6% of the transcripts showed differential expression between the WT and MKRN3 overexpressed cells, with a fold change ≥2 and p-adjust value <0.05. 354 genes were up-regulated by MKRN3, while 395 genes were down-regulated by MKRN3 in this study.
Conclusions: Our study is the first effort to explore MKRN3 on gobal genes expression, and hundreds of different  expressed genes have been identified.

overall_design: The mRNA profiles of wild type (WT) and MKRN3 overexpressed GT1-7 cells

first: Ronggui

last: Hu

first: Chuanyin

first: Tianting

last: Han


title: Distinct properties and functions of CTCF revealed by a rapidly inducible degron system

first: Jing

last: Luan


title: Gene expression-subcuteneous right CFPAC-1 tumor (human pancreatic ductal adenocarcinoma (PDAC) line) in humanized mice

status: Public on Feb 20 2021

city: Houston

first: Masataka

last: Suzuki

state: Texas

address: 1102 Bates Ave

institute: Baylor College of Medicine

summary: Immunotherapy outcome prediction classifiers were successfully constructed through expression profiling of a total of 594 genes in PDAC right tumors from humanized mice treated with immunotherapy

overall_design: In the study presented here,humanized mice harboring 2 CFPAC-1 tumors (left and right) were treated with our immunotherapies (CAd, CART or combinaiton), and right tumors were harvested from each mouse to analyze human immune gene expression.

first: Caroline

last: Porter


city: Cold Spring Harbor

first: Jonathan

middle: James

last: Ipsaro

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: Asterix/Gtsf1 has been previously been shown to be involved in the silencing of retrotransposons in animal germ cells through the piRNA pathway. Using eCLIP and a custom informatic pipeline, we found that Asterix/Gtsf1 binds directly to RNAs and preferentially interacts with tRNAs as a class. Given the role of tRNAs as primers for Long Terminal Repeat (LTR) transposons, this work implicates Asterix/Gtsf1 as exploiting tRNA dependence to identify transposon transcripts and promote piRNA silencing.

overall_design: eCLIP of mouse Asterix/Gtsf1 transfected in mouse P19 embryonal teratoma cells. The protein was expressed with a C-terminal TEV-Strep tag from the vector pEF under the control of the EF-1alpha promoter.

first: Leemor

last: Joshua-Tor


title: Gene expression data from mouse melanocyte cell lines established in culture from 3-day old skin of wild-type and bcat* mutant C57BL/6J mice

city: Orsay

first: Lionel

last: Larue

address: Centre Universitaire Bat 110

institute: Institut Curie

summary: To investigate the mechanism underlying the altered localization of pigmented melanosomes in cells expressing activated beta-catenin, we extracted mRNA from WT and bcat* cell lines and performed microarray-based transcriptome analysis.

overall_design: We  previously studied the effect of beta-catenin on the melanocyte lineage by creating a transgenic mouse model containing a stable, transcriptionally active beta-catenin mutant protein specifically in the melanocyte lineage (bcat* mice; Delmas et al., Genes Dev 2007). Melanocytes from the skin of wild-type C57BL/6J and bcat* mice were isolated and different cell lines were established in culture. In this study, we performed Affymetrix transcription microarray experiments on two wild-type (9v and 14d) and two bcat* (10d and 13d) cell lines.

first: Zackie

last: Aktary

first: Florian

last: Rambow


title: eCLIP of Drosophila Asterix/Gtsf1 (endogenous promoter) in Drosophila ovarian somatic sheath (OSS) cells

overall_design: eCLIP of Drosophila Asterix/Gtsf1 in Drosophila ovarian somatic sheath (OSS) cells. The protein is under the control of its endogenous promoter is tagged with GFP-FRT-Precission-V5-3xFLAG-P2A at it C-terminus.


title: CDK7 inhibitor THZ1 induces the cell apoptosis of B-cell acute lymphocytic leukemia by perturbing cellular metabolism

first: xia

last: jing

address: 1678 Dongfang Road

institute: Shanghai Children’s Medical Center

summary:
Purpose:CDK7 is a potential drug target for the treatment of tumors. THZ1 is the first selective and covalent CDK7 inhibitor, which shows anti-tumor effects in various cancers by inhibiting cell proliferation and inducing apoptosis. However, whether THZ1 has an inhibitory effect on B-ALL cells and the underlying mechanism remains unclear. To address this question, we collected THZ1- and DMSO-treated cells for RNA sequencing
Methods:Nalm6 cells were seeded at a density of 1× 10e6 cells/ml and treated with 500nm THZ1or DMSO for 24h.
Results:THZ1 perturbed the cellular metabolic pathways of B-ALL cells in vitro.

overall_design: Nalm6 total mRNA profiles treated with 500nm THZ1 or DMSO for 24h.

first: Tuersunayi

last: Abudureheman

last: Xia

first: Ming-Hao

first: Kai

last: Qing

first: Cai-Wen

last: Duan


summary: Asterix/Gtsf1 has been previously been shown to be involved in the silencing of retrotransposons in animal germ cells through the piRNA pathway. During early stages of purification of mouse Gtsf1 protein in Sf9 cells for structural studies, we found that the protein was co-purifying with endogenous nucleic acids. We first characterized those RNAs by next-generation sequencing (this dataset) and then later investigated its RNA-binding in more relevant cell culture systems. In each case, we found Asterix/Gtsf1 was binding tRNAs. Given the role of tRNAs as primers for Long Terminal Repeat (LTR) transposons, this work implicates Asterix/Gtsf1 as exploiting tRNA dependence to identify transposon transcripts and promote piRNA silencing.

overall_design: RIP-seq of mouse Asterix/Gtsf1 expressed in Sf9 cells. The protein was expressed with a C-terminal TEV-Strep tag under the control of the polyhedrin promoter.


overall_design: eCLIP of Drosophila Asterix/Gtsf1 transfected in Drosophila ovarian somatic sheath (OSS) cells. The protein was expressed with a C-terminal TEV-Strep tag from the vector pAWG under the control of the act5c promoter.


title: Asterix/Gtsf1 links tRNAs and piRNA silencing of retrotransposons

summary:
This SuperSeries is composed of the SubSeries listed below.
For processing workflows and scripts, please refer to https://github.com/jonipsaro/asterix_gtsf1

sample_organism:
Spodoptera frugiperda
Drosophila melanogaster
Mus musculus

overall_design: Refer to individual Series


title: Evaluating the effect of spaceflight on the host-pathogen interaction between human intestinal epithelial cells and Salmonella Typhimurium

status: Public on Feb 19 2021

city: Tempe

first: Jennifer

last: Barrila

state: AZ

address: 1001 S McAllister Ave

department: Biodesign Center for Fundamental and Applied Microbiomics

institute: Arizona State University

summary: Spaceflight uniquely alters the physiology of both human cells and microbial pathogens, stimulating cellular and molecular changes directly relevant to infectious disease. However, the influence of this environment on host-pathogen interactions remains poorly understood. Here we report our results from the STL-IMMUNE pilot study flown aboard STS-131, which investigated multi-omic responses (transcriptomic, proteomic) of human intestinal epithelial cells to infection with Salmonella Typhimurium when both host and pathogen were simultaneously exposed to spaceflight. To our knowledge, this is the first in vitro in-flight infection and dual RNA-seq analysis using human cells.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Human colonic epithelial cells were cultured in hollow fiber bioreactors in space aboard Space Shuttle Discovery (mission STS-131). Synchronous ground controls were performed in the same hardware on Earth at Kennedy Space Center. On Flight Day 11, Salmonella Typhimurium (~1x10^7 CFU) was injected into a subset of the cultures while the remaining cultures served as time-matched uninfected controls. Six hours post-infection, cultures were fixed in RNAlater II for post-flight analysis.

first: Shameema

last: Sarker

first: Nicole

last: Hansmeier

first: Shanshan

last: Yang

first: Kristina

last: Buss

first: Natalia

last: Briones

first: Jin

last: Park

first: Richard

middle: R

last: Davis

first: Rebecca

last: Forsyth

first: C. Mark

last: Ott

first: Kevin

last: Sato

first: Cristine

last: Kosnik

first: Anthony

first: Cheryl

last: Shimoda

last: Rayl

first: Diana

last: Ly

first: Aaron

last: Landenberger

first: Stephanie

last: Wilson

first: Naoko

last: Yamazaki

first: Jason

last: Steel

first: Camila

last: Montano

first: Rolf

middle: U

last: Halden

first: Tom

last: Cannon

first: Sarah

last: Castro-Wallace

last: Nickerson


title: Interferon response in Huh7 cells

city: New York

first: Christopher

last: Mason

address: 1305 York Ave

department: Physiology and Biophysics

institute: Weill Cornell Medical College

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


title: MicroRNA-seq data of aortas from chronic kidney disease (CKD) induced vascualr calcification mouse model

first: YINGCHUN

last: HAN

summary: MicroRNAs (miRNAs) are short noncoding RNAs that impact protein expression, regulating a variety of physiological processes. To date, a few miRNAs have been implicated in the process of vascular calcification; however, our understanding of the miRNAs involved and their regulatory mechanisms remains incomplete.The analysis showed differences of microRNAs in the aortas after CKD induced vascular calcification.

overall_design: Examination of MicroRNA profiles of aortas induced by CKD induced vascualr calcification mouse model.

first: Yingchun

last: Han


title: Identification of Fra-1 and/or Fra-2 regulated genes in MDA-MB231 cells

first: Isabelle

last: Jariel-Encontre

summary:
In the paper "Fra-1 regulates its target genes via binding to remote enhancers without exerting major control on chromatin architecture in triple negative breast cancers" by Bejjani et al., we identified Fra-1 and/or Fra-2 target genes in MDA-MB-231 cells. si RNA against Fra-1 and against Fra-2 were transfected in MDA-MB-231 cells either independenlty or simultaneously to identify genes regulated specifically by Fra-1 or Fra-2 and genes regulated redundantly or complementarily by Fra-1 and Fra-2
total RNA were purified and biotinylated sense-strand cDNA were produced. cDNA targets were used to probe Affymetrix GeneChip Human Gene 2.0 ST arrays

overall_design:
transcriptome 1 : cells either non transfected (T1.NT) or transfected with control siRNA (T1.siCTL) ,  siRNA against Fra-1 (T.siFra1) or against Fra-2 (T1.siFra2). 3 independant replicates (A, B and C) for each condition were produced
transcriptome 2 : cells either non transfected (T2.NT) or transfected with control siRNA (T2.siCTL) , with siRNA against Fra-1 + siRNA against Fra-2 (T2.siFra1_siFra2). 3 independant replicates (A, B and C) for each condition were produced
to discard bias linked to siRNA transfection itself, as well as potential bias linked to control siRNA , we introduced another control, i.e. cells that received the transfection reagent but not transfected (NT) with  siRNA. Fold changes were calculated versus NT conditions for the different siRNA transfections

first: Fabienne

last: Bejjani

first: Claire

last: Tolza

first: Tony

last: Kaoma

first: Laurent

last: Vallar

first: Marc

last: Piechaczyk


title: Co-immunoprecipitation of the small DUF1127 protein RSP_6037xFLAG and pRK0557_3xFLAG for RNA interaction

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

country: Germany

institute: Justus-Liebig University Gießen

summary: Many protein domains are conserved among different classes and are found in numerous species, but their function remains obscure. Data bases list more than 17,000 DUF1127 proteins but to date no biological function could be assigned to any of these proteins. This study demonstrates that the 71 amino acid DUF1127 protein CcaF1 from the alphaproteobacterium Rhodobacter sphaeroides participates in the maturation of the CcsR sRNAs that are processed from the 3´ UTR of the ccaF mRNA and have a role in the oxidative stress defense. CcaF1 also affects the abundance of several other sRNAs but also of tRNAs, rRNAs and several mRNAs. Co-immunoprecipitation revealed direct binding of CcaF1 to many cellular RNAs of different type and an effect of CcaF1 on the stability of selected RNAs was demonstrated. Thus, the widely distributed DUF1127 domain can mediate RNA-binding and affect stability of its binding partners and consequently the bacterial transcriptome.

overall_design: Protein-RNA interaction was analyzed by co-immunoprecipitation. The strains Rhodobacter sphaeroides 2.4.1 pRK6037_3xFLAG (control pRK6037) and pRK0557_3xFLAG (control pRK0557) were used. RNA was isolated and sequenced.

first: Konrad

last: Förstner

first: Julian

last: Grützner


title: mRNA profiles of hematopoietic stem cells from p5 neonate and 4 weeks old mice.

status: Public on Feb 18 2021

city: kumamoto-city

first: Michihiro

last: Hashimoto

state: kumamoto

address: 2-2-1 honjyo, 3-10-15 kuhonji chuo-ku

department: IRCMS

institute: kumamoto university

summary: Purpose: The goals of this study are to elucidate the underlying charactristic difference of p5 neonatal and 4 weeks old hematopoietic stem cell.  Methods: p5 neonatal and 4 weeks old  100 cells of HSCs were sorted. Moreover, after HSCs were cultured for 1day, 100 cells of phenotypic HSCs were sorted. These cells were subjected to mRNA sequence using Next-seq. The sequence reads that passed quality filters were analyzed by CLC genomic workbench.

overall_design: p5 neonatal or 4 weeks old mice, HSCs (CD150+ CD48- EPCR+ Lineage-) were sorted were sorted, and subsequently mRNA profiles were generated by deep sequencing using Next-seq.  After culturing HSCs (CD150+ CD48- EPCR+ Lineage-) derived from untreated mice for 1 day, mRNA profiles were generated by deep sequencing using Next-seq .

last: Hahsimoto

first: Umemoto

last: Terumasa

first: Toshio

last: Suda


title: Reduction of Fibrosis and Immune Suppressive Cells in ErbB2-Dependent Tumorigenesis by an LXR Agonist

status: Public on Feb 17 2021

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

summary: One of the central challenges for cancer therapy is the identification of factors in the tumor microenvironment that increase tumor progression and prevent immune surveillance. One such element associated with breast cancer is stromal fibrosis, a histopathologic criterion for invasive cancer and poor survival. Fibrosis is caused by inflammatory factors and remodeling of the extracellular matrix that elicit an immune tolerant microenvironment. To address the role of fibrosis in tumorigenesis, we developed NeuT/ATTAC transgenic mice expressing a constitutively active NeuT/erbB2 transgene, and an inducible, fat-directed caspase-8 fusion protein, which upon activation results in selective and partial ablation of mammary fat and its replacement with fibrotic tissue.  Induction of fibrosis in NeuT/ATTAC mice led to more rapid tumor development and an inflammatory and fibrotic stromal environment.  In an effort to explore therapeutic options that could reduce fibrosis and immune tolerance, mice were treated with the oxysterol liver X receptor (LXR) pan agonist, N,N-dimethyl-3ꞵ-hydroxy-cholenamide (DMHCA), an agent known to reduce fibrosis in non-malignant diseases. DMHCA reduced tumor progression, tumor multiplicity and fibrosis, and improved immune surveillance by reducing infiltrating myeloid-derived suppressor cells and increasing CD4 and CD8 effector T cells.  These effects were associated with an LXR-dependent gene network coupled to reduction of PTGS2, CCL5, S100A9, SPP1, ANXA1 and CD14.  These findings suggest that the use of DMHCA may be a potentially effective approach to reduce desmoplasia and immune tolerance and increase the efficacy of cancer therapy.

overall_design: Mammary gland fibrosis was induced in female six-week-old NeuT/ATTAC mice by i.p. injection of 0.4 mg/kg AP20187 (MedChemExpress) dissolved in a vehicle (4% ethanol, 10% PEG-400 and 1.75% Tween-20 in water) three times per week, and are hereafter referred to as ‘NeuT/ATTAC+AP’ mice. AP20187 is a dimer analog of FK506 and serves as a selective FKBPv-caspase 8 dimerizer resulting in partial ablation of mammary fat and its replacement by fibrotic tissue. At eight weeks of age, NeuT/ATTAC+AP mice were administered ad libitum a diet (LabDiet 5053) supplemented with 0.05% (w/w) DMHCA (WuXi App Tec, China), which is equivalent to a dose of ~100 mg/kg.  No weight loss or overt toxicity resulted from AP21087 or DMHCA treatment.

first: Gao

last: Sheng

first: Hongyan

last: Yuan

first: Suman

last: Ranjit

first: Julia

last: Panov

first: Xun

last: Lu

first: Moshe

last: Levi

first: Robert

middle: I

last: Glazer


title: RNA-seq analysis of different reproductive tissues in the olive fruit fly

city: Larisa

first: Maria Eleni

last: Gregoriou

address: Viopolis

department: Biochemistry and Biotechnology

country: Greece

institute: University of Thessaly

summary: we used an integrated approach for the elucidation of the reproductive system and mating procedures of the olive fruit fly, Bactrocera oleae. Initially, we performed RNAseq analysis in reproductive tissues of virgin and mated insects. Comparison of the transcriptomes resulted in the identification of genes that are differentially expressed after mating.

overall_design: two biological replicates of the following samples: female lower reproductive tract and male accessory glands. Two different conditions: virgin, 7 day old flies and once mated.

first: Gregoriou

last: Eleni

first: Reczko

last: Martin

first: Kakani

middle: G

last: Evdoxia

first: Tsoumani

middle: T

last: Konstantina

first: Kostas

last: Mathiopoulos


title: Exosomal RNA expression profiles in umbilical cord blood from preeclampsia patients

city: Nanjing

first: Juan

last: Wen

address: Tianfei Xiang 123#

institute: Women’s Hospital of Nanjing Medical University

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

summary: We used microarray technology to establish the differential RNA expression profiles in umbilical cord blood exosomes from preeclampsia patients compared with normal controls.

overall_design: 6 umbilical cord blood samples were collected for microarray screening, 3 preeclampsia patients and 3 controls

first: Minkai

last: Cao


title: DNA methylation data throughout human muscle cell differentiation in individuals with type 2 diabetes and controls

status: Public on Feb 16 2021

city: Malmö

first: Charlotte

last: Ling

address: Jan Waldenströms gata 35, CRC 91:12

department: Clinical Sciences

country: Sweden

institute: Lund University

type: Methylation profiling by genome tiling array

summary: DNA methylation data throughout human muscle cell differentiation in n=14 individuals with type 2 diabetes and n=14 controls

overall_design: Comparison of DNA methylation in proliferating myoblasts versus differentiated myotubes in either individuals with type 2 diabetes (n=14) or controls (n=14). DNA methylation data were obtained using Infinium HumanMethylation450 BeadChip (Illumina). This array contains more than 450,000 CpG sites covering 99% of RefSeq genes.

first: Cajsa

last: Davegårdh

first: Johanna

last: Säll

first: Alexander

last: Perfilyev

first: Emma

last: Nilsson

first: Camilla

last: Scheele


title: Deep-sequencing of small RNAs from barley shoot and root growing in low-Pi and control condition.

city: Poznan

first: Andrzej

last: Pacak

address: Uniwersytetu Poznanskiego 6

country: Poland

institute: Adam Mickiewicz University, Poznan

summary: RNA was isolated from 23 old barley plants (shoots and roots), line Rolap. We used a modified method that allows for enrichment of small RNAs. Libraries were prepared using TruSeq Small RNA Library Preparation Kit (Illumina), followed by sequencing of NGS libraries.

overall_design: Total RNA isolation, libraries preparation, single-reads (50 cycles) sequencing, Illumina technology, HiSeq 4000, sequencing performed at Fasteris SA (Switzerland).

first: Paweł

last: Sega


title: DNA methylation profiles of Purified Blood Cell types

city: Exeter

last: Walker

address: RILD Barrack Rd

institute: University of Exeter

overall_design: DNA methylation profiles for whole blood, CD4 T cells, CD8 T cells, B cells, Monocytes, Granulocytes, nasal epithelial cells and buccal cells purified from 30 individuals (217 samples in total).

first: Jonathan

last: Mill

first: Eilis

last: Hannon

first: Joe

last: Burrage


title: TNFα and α-synuclein fibrils differently regulate human astrocyte immune reactivity and impair mitochondrial respiration

city: Lund

first: Laurent

last: Roybon

address: Solvegatan 19

department: Experimental Medical Science


title: Umbilical Cord Blood-derived Exosomes from Very Preterm Infants with Bronchopulmonary Dysplasia Impaired Endothelial Angiogenesis: Roles of Exosomal MicroRNAs

city: Guangzhou

first: Xinqi

last: Zhong

state: Guangdong

address: 35 Liwan Rd, Zhong Shan Qi Ba Lu, Liwan District, Guangzhou, Guangdong Province, China

department: Department of Neonatology

institute: The Third Affiliated Hospital of Guangzhou Medical University

summary: Premature infants have a high risk of bronchopulmonary dysplasia (BPD), which is characterized by abnormal development of alveoli and pulmonary vessels. Exosomes and exosomal miRNAs (EXO-miRNAs) from bronchoalveolar lavage fluid are involved in the development of BPD and might serve as predictive biomarkers for BPD. However, the roles of exosomes and EXO-miRNAs from umbilical cord blood of BPD infants in regulating angiogenesis are yet to be elucidated. In this study, we showed that umbilical cord blood-derived exosomes from BPD infants impaired angiogenesis in vitro. Next generation sequencing of EXO-miRNAs from preterm infants without (NBPD group) or with BPD (BPD group) uncovered a total of 418 differentially expressed (DE) EXO-miRNAs. These DE EXO-miRNAs were primarily enriched in cellular function-associated pathways including the PI3K/Akt and angiogenesis- related signaling pathways. Among those EXO-miRNAs which are associated with PI3K/Akt and angiogenesis-related signaling pathways, BPD reduced expression of hsa-miR-103a-3p and hsa-miR-185-5p exhibiting most significant reduction (14.3% and 23.1% of NBPD group, respectively); BPD increased hsa-miR-200a-3p expression by 2.64 folds of NBPD group. Furthermore, overexpression of hsa-miR-103a-3p and hsa-miR-185-5p in normal human umbilical vein endothelial cells (HUVECs) significantly enhanced endothelial cell proliferation, tube formation and cell migration, whereas overexpressing hsa-miR-200a-3p inhibited these cellular responses. This study demonstrates that exosomes derived from umbilical cord blood of BPD infants impair angiogenesis, possibly via DE EXO-miRNAs, which might contribute to the development of BPD.

overall_design: miRNA profiles in umbilical cord blood-derived exosomes from very preterm Infants with or without bronchopulmonary dysplasia

first: Qin

last: Yan

first: Zhuang-gui

last: Chen

first: Chun-hong

last: Jia

first: Xiu-hong

last: Li

first: Zi-yan

last: Liang

first: Jian

last: Gu

first: Hui-ling

last: Wei

first: Chang-yu

last: Lian

first: Jing

last: Zheng

first: Qi-liang

last: Cui


title: Transcriptome analysis of Rhodobacter sphaeroides 2.4.1 wildtype and the two overexpressing strains OE_RSP_6037 and OE_CcsR

first: Gabriele

last: Klug

overall_design: This data includes the transcriptome data of three different exponentially growing strains each in triplicates: Rhodobacter sphaeroides 2.4.1 (wildtype), R. sphaeroides 2.4.1 pRK4352_RSP_6037 (constitutively overexpression of RSP_6037) and R. sphaeroides 2.4.1 pRK4352_CcsR1-4 (constitutively overexpression of the sRNAs CcsR1-4). Total RNA of all strains was isolated and sequenced.

first: Julian

last: Grützner

first: Daniel-Timon

last: Spanka

first: Vivian

last: Monzon


title: The Transcriptomic Responses of Atlantic Salmon (Salmo salar) to High Temperature Stress Alone, or in Combination with Moderate Hypoxia

city: St. John's

first: Anne

last: Beemelmanns

address: 0 Marine Drive

department: Ocean Science

country: Canada

institute: Memorial University

summary: In this study, we employed a 44K microarray approach to analyse the hepatic transcriptomic response of post smolt Atlantic salmon subjected to control conditions (12°C, ~100% air saturation), an incremental increase in temperature (12°C to 20°C; 1°C per week) under normoxia (~100% air saturation) or moderate hypoxia (~70% air saturation). Significance Analysis of Microarrays (FDR < 5%) identified 1900 and 2105 differentially expressed probes (DEPs) in salmon exposed to either Warm&Normoxic (WN) or Warm&Hypoxic (WH) conditions as compared with those maintained under control conditions (CT). Further, we found that heat stress alone or in combination with hypoxia caused most similar transcriptional responses and 1,111 (38%) DEPs were shared between WN and WH treatment groups. Consequently, in this study a unique set of 2,894 DEPs was determined.

overall_design: Atlantic salmon were exposed to following treatments: (1) Control (CT) constant temperature of 12°C and 100 % air saturation; (2) Warm&Normoxic (WN) incremental temperature increase (1°C per week from 12 - 20°C)  at 100% air saturation; and (3) Warm&Hypoxic (WH) decrease in oxygen content of 70% air saturation over one week, followed by two weeks of acclimation to this oxygen level, and then incremental temperature increase (1°C per week from 12 - 20°C) at 70% air saturation. Liver samples were taken from 8 fish per treatment group (Ct,WN, and WH) at 20°C after 3 days. A universal reference design was used for the microarray experiment. For the test samples, RNA was used from individual livers of 6 fish from the 3 treatment groups. For each treatment group we used 6 biological replicates (3 fish from 2 tank replicates). All test samples were labeled with Cy5. The common reference was a pool of 18 RNA samples from livers of fish from all individuals involved in microarray experiment. The common reference was labeled with Cy3. Each individual test sample was hybridized together with the common reference sample on an array, so the experiment consisted of 18 arrays.

first: Fabio

middle: S

last: Zanuzzo

first: Xi

last: Xue

first: Rebeccah

last: Sandrelli

first: Anthony

last: Gamperl

first: Matthew

last: Rise


title: Single cell Transcriptome of In Vitro Meiosis in mouse spermaotogia with NRRA treatment

city: Kansas City

first: Sumedha

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

summary: Here we performed single cell RNA seq analysis of cultured spermatogonia with NRRA treatment using 10X Genomics Chromium platform. 5 cluster cell populations were identified.

overall_design:
Single cell RNA sequencing of cultured spermatogonia NRRA treatment were generated by deep sequencing using the 10x Genomics
Veh: complete spermatogonial culture medium
NRRA: nutrient restriction medium plus retinoic acid

first: Ning

last: Wang

first: Xiaoyu

last: Zhang

first: Gunewardena

last: Sumedha


title: MeRIP-seq mapping of m6A in the IFN-β induced transcriptome in Huh7 cells

first: Christopher

middle: E

last: Mason

summary: The RNA modification N6-methyladenosine (m6A) regulates gene expression through various transcript-specific effects. The goal of this experiment was to identify m6A-modified transcripts during the type I interferon response, with interest in determining which interferon-stimulated genes are modified by m6A. We found that a high percentage of ISGs are m6A-modified, and in follow-up experiments we determined the effects of m6A on the expression of interferon-stimulated genes. We found that m6A regulates the translation of a subset of ISGs, which in turn augments the antiviral effects of the type I interferon respnose.

overall_design: Huh7 cells were seeded in 15-cm plates and treated with IFN-β at 50 units/mL or mock treated for 8 hours prior to harvest and MeRIP-seq was performed. 3 biological replicates were performed for each condition.

first: Michael

last: McFadden

first: Alexa

last: McIntyre

first: Nandan

last: Gokhale

first: Stacy

last: Horner


title: RNA-seq Analysis of spermatogonia with NRRA treatment Transcriptomes [Veh.vs.NRRA]

summary:
Purpose: The goals of this study are to compare RA, NR and NRRA treatment in in vitro spermtogonia transcriptome profiling (RNA-seq)  and to evaluate protocols for in vitro induced meiosis system.
Methods: Spermatogonia mRNA profiles of Veh, RA, NR and NRRA were generated by deep sequencing, in duplicate.
Conclusions: Our study represents the first detailed analysis of induced meiosis spermatogonia transcriptomes, with biologic replicates, generated by RNA-seq technology.

overall_design:
Spermatogonia mRNA profiles of Veh, RA, NR and NRRA were generated by deep sequencing, in duplicate, using Illumina.
Veh: complete spermatogonial culture medium
RA: complete spermatogonial culture medium plus retinoic acid (RA)
NR: nutrient restriction medium, which is composed of 10% complete spermatogonial culture medium and 90% EBSS
NRRA: nutrient restriction medium plus retinoic acid
EBSS: Earle's Balanced Salt Solution


title: RNA-seq and Ribo-seq analysis of the effects of METTL3/14 depletion on gene expression during the interferon response in Huh7 cells

summary: The RNA modification N6-methyladenosine (m6A) regulates gene expression through various transcript-specific effects. The overall goal of these experiments was to determine the effects of the m6A methyltransferase complex proteins METTL3 and METTL14 on the expression of interferon stimulated genes. First, we depleted METTL3 and METTL14 in Huh7 cells using siRNAs and treated with Mock or IFN-β to analyze the regulatory effects of METTL3/14 on interferon-stimulated genes' transcript abundance. We then used Ribo-seq following METTL3/14 siRNA depletion and IFN treatment to quantify its effect on the translation of ISGs and other genes. Overall, we found that METTL3/14 exerts transcript-specific regulatory effects on a subset of interferon-stimulated genes. Overall, METTL3/14 appeared to enhance the translation of a subset of interferon-stimulated genes. We characterized the molecular effects of METTL3/14 and m6A on certain ISGs and determined that m6A augments the antiviral effects of the interferon response.

overall_design: siRNA transfections were performed for 36 hours in Huh7 cells prior to IFN-β treatment (50 units/mL) for 8 hours, after which cells were harvested and RNA-seq or Ribo-seq protocols were performed. For RNA-seq, 3 replicates of each condition were performed and for Ribo-seq, 4 replicates for each condition were performed.

first: Haralambos

last: Mourelatos


title: Spt4 promotes Pol I processivity and transcription elongation

city: Birmingham

first: Abigail

last: Huffines

address: 720 20th St S

institute: University of Alabama at Birmingham

summary: The goal of this study was to determine the effect of Spt4 on transcription by Pol I in vivo. Therefore, Native Elongating Transcript Sequencing (NET-seq) was used to evaluate the occupancy of Pol I in wild-type and spt4△ strains. We determined that in spt4△ yeast, there was a processivity defect and Pol I accumulated at the 5' end of the 35S gene. Additionally, we observed that there was an enrichment for G-rich sequences just downstream of a high A content in the spt4△ strain, indicating that perhaps Spt4 plays a role in helping to propel Pol I through these regions of the rDNA. Altogether, this study suggests that Spt4 is an important transcription factor for Pol I by promoting polymerase processivity.

overall_design: NET-seq was utilized to determine Pol I occupancy differences between wild-type and spt4△ yeast, with both strains in triplicate.

first: Yvonne

middle: J

last: Edwards

first: David

middle: A

last: Schneider


title: Transcriptional analysis of islets of Langerhans from organ donors of different ages

city: Uppsala

first: Peter

last: Seiron

address: Rudbecklaboratoriet

department: Department of Immunology, Genetics and Pathology

institute: Uppsala University

summary: Islet function diminishes with age and as such the incidence of type 2 diabetes increases. The cause of this is unknown. In this study whole islets were extracted with laser capture microdissection from organ donors 1-81 years of age. Increasing age was associated with a downregulation of pathways associated with the cell cycle and increase in markers of senescence e.g. CDKN2A. Among novel genes increasing with age was SPP1.

overall_design:
Ampliseq transcriptome analysis based on laser capture microdissection of islets from human organ donors aged 1-81 years of age.
*** Submitter declares raw data files have been lost for the ip_293* samples.

first: Anton

last: Stenwall

first: Anders

last: Hedin

first: Louise

last: Granlund

first: Jonathan

last: Esguerra

first: Petr

last: Volkov

first: Erik

last: Renström

first: Olle

last: Korsgren

first: Marcus

last: Lundberg

first: Oskar

last: Skog


title: Transcriptome analysis of barley shoot growing in low-Pi and control condition.

first: Andrzej

last: Pacak

summary: RNA was isolated from 23 old barley plants (shoots), line Rolap. Libraries were prepared using mRNA-Seq Library kit v2 (Lexogen), followed by sequencing of NGS libraries

overall_design: Total RNA isolation, libraries preparation, paired-reads (150 cycles) sequencing.  Sequencing by Fasteris SA (Switzerland).

first: Paweł

last: Sega


title: Deep-sequencing of degraded or cleaved RNAs from barley shoot and root growing in low-Pi condition.

summary: RNA was isolated from 23 old barley plants (shoots and roots), line Rolap. PARE libraries were constructed for both barley organs, followed by sequencing of NGS libraries.

overall_design: Total RNA isolation, PARE libraries preparation, single-reads (50 cycles) sequencing, Illumina technology, HiSeq 2500, sequencing performed at Fasteris SA (Switzerland).


title: Human liver tissues: cancer vs. control

status: Public on Feb 13 2021

city: Xiamen

first: Yong

last: Lin

state: Fujian

address: 201-205 Hubin South Road

department: School of Medicine

institute: Zhongshan Hospital, Xiamen University

summary: Complete lncRNA and mRNA expression profile of hepatocellular carcinoma (HCC) tissues and non-cancer liver tissues

overall_design: One condition experiment, HCC tissues vs. controls, 10 HCC replicates and 10 control replicates.

first: Zan

middle: X

last: Fang

first: Jian

last: Niu

first: Ping

last: Liu


title: DNA methylation data for human muscle cells from individuals with type 2 diabetes and controls

status: Public on Feb 12 2021

first: Charlotte

last: Ling

summary: DNA methylation data for both proliferating myoblasts and differentiated myotubes from n=14 individuals with type 2 diabetes and n=14 controls

overall_design: Comparison of DNA methylation in either proliferating myoblasts or differentiated myotubes from individuals with type 2 diabetes (n=14) versus controls (n=14). DNA methylation data were obtained using Infinium HumanMethylation450 BeadChip (Illumina). This array contains more than 450,000 CpG sites covering 99% of RefSeq genes.

first: Cajsa

last: Davegårdh

first: Johanna

last: Säll

first: Alexander

last: Perfilyev

first: Emma

last: Nilsson

first: Camilla

last: Scheele


title: Proteasome Stress in Skeletal Muscle Mounts a Long-Range Protective Response that Delays Retinal and Brain Aging [Drosophila]

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: The proteasome maintains protein quality during aging and disease. Challenges to proteasome function can be compensated by local proteasome stress responses. However, whereas proteasome stress is also sensed systemically is unknown. In Drosophila , we find that proteasome stress in skeletal muscle non-autonomously promotes the degradation of proteasome substrates in distant tissues during aging. Several muscle-secreted factors (myokines) are upregulated by proteasomal stress via C/EBP transcription factors, including the amylase Amyrel, which increases the circulating levels of the disaccharide maltose. Muscle-specific Amyrel overexpression promotes the degradation of proteasome substrates in the aging brain and retina via the transcriptional induction of chaperones and proteases. Conversely, RNAi for maltose transporters worsens proteostasis and reduces the expression of Amyrel-induced genes in the brain. Moreover, maltose preserves protein quality in cell culture and human cortical brain organoids challenged by thermal stress. Thus, proteasome stress in skeletal muscle mounts a systemic adaptive response via amylase/maltose signaling.

overall_design: mRNA profiles of Drosophila thoraces (muscle) from 10-day-old male flies with RNAi driven specifically in skeletal muscle, and heads (enriched from brains and retinas) from 10-day-old male flies with Amyrel overexpression driven specifically in skeletal muscle and isogenic controls.

first: Mamta

last: Rai

first: Zane

last: Coleman

first: Michelle

last: Curley

first: Anjana

last: Nityanandam

first: Anna

last: Platt

first: Maricela

last: Robles-Murguia

first: Jianqin

last: Jiao

first: David

last: Finkelstein

first: Beisi

last: Xu

first: Yiping

last: Fan

first: Fabio

last: Demontis


title: Proteasome Stress in Skeletal Muscle Mounts a Long-Range Protective Response that Delays Retinal and Brain Aging

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

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: Refer to individual Series


title: Control (healthy) iPSC-derived astrocytes treated with: Media (control) or aSYN F110 10uM

first: Laurent

last: Roybon

summary:
The overall goal was to identify changes in gene expression following treatment with aSYN F110 compared to control (untreated).
Alpha-synuclein (αSYN) protein has been observed in reactive astrocytes in PD patients’ brains, raising the question of how αSYN, neuroinflammation, and astrocytes interact in PD pathogenesis. Here, we examined the cellular changes triggered by tumor necrosis factor alpha (TNFα) and different αSYN species in astrocytes derived from induced pluripotent stem cells. Human astrocytes treated with TNFα displayed a strong reactive pro-inflammatory phenotype with upregulation of pro-inflammatory gene networks, activation of the NF-kB pathway, and release of pro-inflammatory cytokines, whereas those treated with high molecular weight αSYN fibrils acquired a reactive antigen (cross-)presenting phenotype with upregulation of MHC genes and increased HLA-DR/DQ/DP and HLA-F molecules at the cell surface. Surprisingly, cell surface location of MHC proteins was abrogated by larger F110 fibrils polymorph, despite the upregulation of MHC genes. A proteomics investigation further confirmed a direct interaction between astrocytic MHC proteins and αSYN fibril peptides. Interestingly, TNFα and αSYN fibrils competed to drive the astrocyte immune reactive response. The astrocyte immune responses were accompanied by an impaired ATP-generating mitochondrial respiration, which was exacerbated in PD astrocytes containing a PARK2-variant. Our data provide evidence for astrocytic involvement in PD pathogenesis and reveal their complex immune reactive responses to exogenous stressors.

overall_design: 4 samples were analyzed per condition from 2 different donors: 2 different differentations of 37R were used and 9A and 36D samples were the same donor reprogrammed using retro or sendai virus, respectively.

first: Kaspar

last: Russ

first: Gabriel

last: Teku

first: Luc

last: Bousset

first: Virginie

last: Redeker

first: Sara

last: Piel

first: Ekaterina

last: Savchenko

first: Jimmy

last: Savistchenko

first: Tina

middle: C

last: Stummann

first: Carla

last: Azevedo

last: Collin

first: Stefano

last: Goldwurm

first: Karina

last: Fog

first: Eskil

last: Elmer

first: Mauno

last: Vihinen

first: Ronald

last: Melki


title: Proteasome Stress in Skeletal Muscle Mounts a Long-Range Protective Response that Delays Retinal and Brain Aging [Human]

first: Yong-Dong

last: Wang

overall_design: mRNA profiles of humen cortical brain organoids between control and maltose treatment, and either with heat shock or not, were generated by RNA-seq, in triplicate, using Illumina sequencing platform.

first: Mamta

last: Rai

first: Zane

last: Coleman

first: Michelle

last: Curley

first: Anjana

last: Nityanandam

first: Anna

last: Platt

first: Maricela

last: Robles-Murguia

first: Jianqin

last: Jiao

first: David

last: Finkelstein

first: Beisi

last: Xu

first: Yiping

last: Fan

last: Demontis


title: Control (healthy) iPSC-derived astrocytes treated with: Media (control), TNFa 100ug/ml, Monomeric aSYN 10uM, or Fibril aSYN 10uM

first: Laurent

last: Roybon

summary:
The overall goal was to identify changes in gene expression following treatment with TNFa, monomeric, or fibril aSYN compared to control (untreated).
Alpha-synuclein (αSYN) protein has been observed in reactive astrocytes in PD patients’ brains, raising the question of how αSYN, neuroinflammation, and astrocytes interact in PD pathogenesis. Here, we examined the cellular changes triggered by tumor necrosis factor alpha (TNFα) and different αSYN species in astrocytes derived from induced pluripotent stem cells. Human astrocytes treated with TNFα displayed a strong reactive pro-inflammatory phenotype with upregulation of pro-inflammatory gene networks, activation of the NF-kB pathway, and release of pro-inflammatory cytokines, whereas those treated with high molecular weight αSYN fibrils acquired a reactive antigen (cross-)presenting phenotype with upregulation of MHC genes and increased HLA-DR/DQ/DP and HLA-F molecules at the cell surface. Surprisingly, cell surface location of MHC proteins was abrogated by larger F110 fibrils polymorph, despite the upregulation of MHC genes. A proteomics investigation further confirmed a direct interaction between astrocytic MHC proteins and αSYN fibril peptides. Interestingly, TNFα and αSYN fibrils competed to drive the astrocyte immune reactive response. The astrocyte immune responses were accompanied by an impaired ATP-generating mitochondrial respiration, which was exacerbated in PD astrocytes containing a PARK2-variant. Our data provide evidence for astrocytic involvement in PD pathogenesis and reveal their complex immune reactive responses to exogenous stressors.

first: Kaspar

last: Russ

first: Gabriel

last: Teku

first: Luc

last: Bousset

first: Virginie

last: Redeker

first: Sara

last: Piel

first: Ekaterina

last: Savchenko

first: Jimmy

last: Savistchenko

first: Tina

last: Stummann

first: Carla

last: Azevedo

last: Collin

last: Goldwurm


title: Mutant huntingtin stalls ribosomes and represses protein synthesis in a cellular model of Huntington disease (mRNA-Seq)

city: Jupiter

first: Srinivasa

last: Subramaniam

state: FL

address: 130 Scripps Way

institute: The Scripps Research Institute

summary: The polyglutamine expansion of huntingtin (mHtt) causes Huntington disease (HD) and neurodegeneration, but the mechanisms remain unclear. Here, we found that mHtt promotes ribosome stalling and suppresses protein synthesis. Depletion of mHtt enhances protein synthesis and increases the speed of ribosome translocation, while mHtt directly inhibits protein synthesis in vitro. We found interactions of ribosomal proteins and translating ribosomes with mHtt. High-resolution global ribosome footprint profiling (Ribo-Seq) and mRNA-Seq indicated a widespread shift in ribosome occupancy toward the 5’ and 3’ end and unique single-codon pauses on selected mRNA targets in HD cells, compared to controls. Thus, mHtt impedes ribosomal translocation during translation by promoting ribosome stalling, a novel mechanistic defect that can be exploited for HD therapeutics.

overall_design: To identify the ribosome-bound messages associated with the stalled ribosomes in HD-homozygous cells in comparison with control, we conducted a harringtonine-based ribosome run-off (RR) assay followed by mRNA-Seq (PS-RRA-mRNASeq).

first: Mehdi

last: Eshragh

first: Pabalu

last: Karunadharma

first: Juliana

last: Blin

first: Emilliano

last: Ricci


title: DNA methylation data for VPS39-silenced human muscle cells and controls

status: Public on Feb 11 2021

first: Charlotte

last: Ling

summary: DNA methylation data for VPS39-silenced myoblasts and controls at day 3 of differentiation (n=6 independent experiments).

overall_design: Comparison of DNA methylation in VPS39-silenced myoblasts and controls at day 3 of differentiation (n=6 independent experiments). DNA methylation data were obtained using Infinium MethylationEPIC BeadChip kit (Illumina) that covers approximately 850,000 CpG sites.

first: Cajsa

last: Davegårdh

first: Johanna

last: Säll

first: Alexander

last: Perfilyev

first: Emma

last: Nilsson

first: Camilla

last: Scheele


title: Identification of novel fusion transcripts in neuroblastoma

city: Solna

first: Johan

last: Holmberg

state: Stockholm

address: Solnavägen 9

department: CMB

institute: Karolinska Institute

summary: Detection of novel chimeric transcripts by paired-end RNA-seq in neuroblastoma cell lines

overall_design: Identification of novel fusion transcripts in 8 neuroblastoma cells available in our lab via paired-end RNA-seq followed by bioinformatic analysis

first: Yao

last: Shi

first: Isabelle

last: Westerlund


title: RNA-seq Analysis of CD1 background spermatogonia with NRRA treatment Transcriptomes

first: Sumedha

last: Gunewardena

summary: Purpose: The goals of this study are to compare CD1 background spermatogonia veh with NRRA treatment transcriptome profiling (RNA-seq)  and to evaluate protocols for in vitro induced meiosis system.Methods: CD1 background spermatogonia mRNA profiles of veh and NRRA treatment were generated by deep sequencing, in duplicate. Methods: CD1 background spermatogonia veh with NRRA treatment were generated by deep sequencing, in duplicate. Conclusions: Our study represents the first detailed analysis of induced meiosis spermatogonia transcriptomes, with biologic replicates, generated by RNA-seq technology.

overall_design:
CD1 background spermatogonia mRNA profiles Veh and NRRA treatment were generated by deep sequencing, in duplicate, using Illumina.
Veh: complete spermatogonial culture medium
NRRA: nutrient restriction medium plus retinoic acid

first: Ning

last: Wang

first: Xiaoyu

last: Zhang

first: Gunewardena

last: Sumedha


title: RNA-seq Analysis of WT, STRA8KO and SPO11KO spermatogonia with NRRA treatment Transcriptomes

summary:
Purpose: The goals of this study are to compare WT, STRA8KO and SPO11KO spermatogonia with NRRA treatment transcriptome profiling (RNA-seq)  and to evaluate protocols for in vitro induced meiosis system.
Methods: Spermatogonia mRNA profiles of WT, STRA8KO and SPO11KO spermatogonia with NRRA treatment were generated by deep sequencing, in duplicate.
Conclusions: Our study represents the first detailed analysis of induced meiosis spermatogonia transcriptomes, with biologic replicates, generated by RNA-seq technology.

overall_design:
Spermatogonia mRNA profiles of WT, STRA8KO and SPO11KO spermatogonia with NRRA treatment were generated by deep sequencing, in duplicate, using Illumina.
NRRA: nutrient restriction medium plus retinoic acid


title: Genome wide mRNA sequencing of induced pluripotent stem cell (iPSC) and their diffrentiated cardiomyocytes (CMs).

city: McAllen

first: Satish

last: Kumar

address: 5300 North L Street (MBMRF-2.219)

department: Division of Human Genetics & South Texas Diabetes and Obesity Institute, UTRGV School of Medicine

institute: University of Texas Rio Grande Valley

summary: The cardiomyocytes (CMs) differentiation of 12 validated iPSC lines were induced using the Gibco PSC Cardiomyocyte Differentiation Kit and following manufacturer method with minor modifications (Thermo Fisher Scientific, Waltham, MA, USA). The differentiation kit consists of a set of serum-free and xeno-free media that enable efficient differentiation of human iPSCs into spontaneously contracting functional cardiomyocytes in 14 days. On day 14 of the differentiation, spontaneously contracting CMs were characterized by immunocytochemistry (ICC) analysis of cardiac mesoderm marker NKX2-5, and mature cardiomyocyte marker TNNT2 and genome-wide mRNA sequencing of the 12 iPSC lines and generated 12 CM lines were performed. The CMs differentiated from all the 12 iPSC lines expressed NKX2-5 and TNNT2 cardiomyocyte markers. Based on the criteria normalized read count (NRC) ≥ 20 in all 12 CM samples, a total of 12280 genes were found expressed. The average correlation coefficient at 95% CI between 12 CM samples, calculated based on all expressed genes, was 0.92 ± 0.02, suggesting a uniform differentiation of generated CMs across 12 samples. The expression of the well-known CMs genes/markers MYH6, MYL4, MYL3, MYL7, NPPA, NPPB, MYH7, NKX2-5, TBX5, TNNT2, ACTN2, TNNC1 and MB, was significantly up-regulated across all 12 CM samples (FDR corrected p-value ≤ 0.05 and fold change absolute (FC-abs) ≥ 2.0); whereas the expression of pluripotency markers and the ectodermal markers was significantly down regulated. The endodermal markers SOX17 and CLDN6 were below the expression threshold of NRC ≥ 20. A differential gene expression analysis of iPSC’s and CM’s expressed transcription identified 4,191 genes that were significantly differentially expressed (DE) between iPSCs and differentiated CMs. The 2,116 DE genes that were significantly up regulated in differentiated CMs showed significantly high enrichment in cardiovascular system development and functions (571 mRNAs; FDR adjusted p-value range: 1.75x10-66 – 1.61x10-14) and predicted activation of the functions associated with development of human heart and cardiovascular system.

overall_design: To better understand the functional profile and disease modeling potential of iPSC generated CMs. A genome wide mRNA sequencing analyses of iPSCs and their generated CMs were performed.

first: Joanne

last: Curran

first: John

last: Blangero


city: Koblenz

first: Andreas

last: Schüttler

address: Am Mainzer Tor 1

department: Department Biochemistry and Ecotoxicology

institute: German Federal Institute of Hydrology

summary:
Time and concentration dependent transcriptome signatures in the ZFE of a mixture consisting of diruon, diclofenac and naproxen. Mixture composition: diuron 11%; diclofenac 2.6%; naproxen 86.4%

Keywords: Expression profiling by array

overall_design: Wild-type adult zebrafish, originally received from OBI petshop (Leipzig, Germany) were kept in 120L fish tanks containing carbon-filtered tap water at 26°C under a 12h:12h dark-light cycle. Eggs were collected approximately 1 hour after light onset and inspected using a light microscope. Fertilized eggs were incubated at 26°C, while unfertilized eggs were discarded. For lethality experiments, which were conducted to find adequate exposure concentrations for transcriptome experiments, nine embryos per replicate were distributed into three 7.5ml glas vials, each containing 6ml exposure or control medium. Vials were sealed and incubated in a climate chamber shaking (Edmund Bühler SM-30 Control, 26°C, 75 rpm, 12h:12h light:dark) till 96 hours post fertilization (hpf). At 48 hpf, 72 hpf and 96 hpf sublethal and lethal effects were recorded. For transcriptome experiments 20 embryos per replicate were transfered to two 20ml GC-glas vials at 24 hpf. A volume of 18ml of exposure medium was added to each vial and vials were sealed and incubated in a climate chamber (same settings as above) until sampling. Embryos were exposed to a range of 5 different concentrations of toxicant and RNA was extracted at 6 different timepoints. The exposure concentrations were phenotypically anchored to the LC at 96 hpf/72 hpe. The LC25, modeled from experimental observations served as highest and the LC0.5 as lowest exposure concentration with 6 equal dilution steps in between, with dilution steps 1,2,4 and 6 chosen for exposure.

first: Janet

last: Krüger

first: Rolf

last: Altenburger

first: Gianina

last: Jakobs

first: Jelena

last: Fix

first: Wibke

last: Busch


title: PANDORA-seq: expanding the small RNA repertoire by overcoming RNA modifications

city: Riverside

first: Junchao

state: CA

address: 900 University Ave

department: Division of Biomedical Sciences, School of Medicine

institute: University of California, Riverside

summary: Small non-coding RNAs (sncRNAs) are key molecules regulating gene expression. High-throughput RNA-seq greatly advanced sncRNA discovery; however, traditional cDNA library construction protocols generate biased sequencing results, in part due to RNA modifications that interfere with adapter ligation and reverse transcription processes, preventing the detection of sncRNAs bearing these modifications. Here, we present PANDORA-seq (Panoramic RNA Display by Overcoming RNA modification Aborted Sequencing), employing a combination of enzymatic treatments to remove key RNA modifications that block adapter ligation and reverse transcription during cDNA library construction. PANDORA-Seq enables the discovery of thousands of modified sncRNAs previously undetected, mostly tRNA-derived small RNAs (tsRNAs) and rRNA-derived small RNAs (rsRNAs), which are tissue/cell-specifically detected across mouse brain, liver, spleen, sperm, mouse and human embryonic stem cells, and HeLa cells. Moreover, PANDORA-Seq reveals dynamic changes of tsRNAs and rsRNAs during reprogramming of induced pluripotent stem cells (iPSCs), pointing to future investigations on their potential regulatory functions.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Small RNA sequencing results of mouse/human tissues and cells under traditional, T4PNK treatment, AlkB treatment, or PANDORA-seq treatment.
We performed mESC RNA transfection of 7 types of tsRNA/rsRNA (i.e., rsRNA-28S-1, tsRNA-Ala, tsRNA-Arg, tsRNA-Glu, tsRNA-His, tsRNA-Lys, and a pool of the abovementioned five tsRNAs (tsRNA-pool)) followed by embryoid body (EB) formation and transcriptomic RNA-seq of EBs at Day1, Day3 and Day6 after transfection.

first: Tong

last: Zhou

first: Qi

last: Chen


title: Identifying CNS-colonizing T cells as potential therapeutic targets to prevent progression of multiple sclerosis

city: Hamburg

first: Manuel

last: Friese

address: Falkenried 94

department: Institut für Neuroimmunologie und Multiple Sklerose

institute: Universitätsklinikum Hamburg-Eppendorf

summary:
Background: Multiple sclerosis (MS), an autoimmune disease of the central nervous system (CNS), can be suppressed in its early stages but eventually becomes clinically progressive and unresponsive to therapy. Here we investigate whether the therapeutic resistance of progressive MS can be attributed to chronic immune cell accumulation behind the blood brain barrier.

Methods: We systematically track CNS-homing immune cells in the peripheral blood of 31 MS patients and 31 matched healthy individuals in an integrated analysis of 497,705 single cell transcriptomes and 355,433 surface protein profiles from 71 samples. Through spatial RNA-sequencing we localize these cells in post-mortem brain tissue of 6 progressive MS patients contrasted against 4 control brains (20 samples, 85,000 spot transcriptomes).

Findings: We identify a specific pathogenic CD161+/LTB+ T cell population that resides in brains of progressive MS patients. Intriguingly, our data suggest that the colonization of the CNS by these T cells may begin earlier in the disease course, as they can be mobilized to the blood by usage of the integrin-blocking antibody natalizumab in relapsing-remitting MS patients.

Conclusions: As a consequence, we lay the groundwork for a therapeutic strategy to deplete CNS-homing T cells before they can fuel treatment-resistant progression.

Funding: This study was supported by funding from the University Medical Center Hamburg-Eppendorf, the Stifterverband für die Deutsche Wissenschaft, the OAK Foundation, Medical Research Council UK and Wellcome.

overall_design:
In a primary cohort nine relapsing-remitting MS (RRMS) patients’ peripheral blood mononuclear cells (PBMC) were sampled longitudinally with and without natalizumab treatment. Two auxiliary cross-sectional cohorts consisting of eleven untreated RRMS and ten primary-progressive MS (PPMS) patients as well as 31 matched healthy individuals for all patients were included. Taken together, we performed multi-modal immunophenotyping by scRNA-seq and surface antibody staining in a total of 71 PBMC samples from 62 donors resulting in close to half a million single cell transcriptomes and around 360,000 surface protein profiles

**Raw data not provided due to patient privacy concerns**

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