title: A single-cell comparison of adult and foetal human epicardium defines the age-associated changes in epicardial activity

status: Public on Oct 31 2022

city: Cambridge

first: Vincent

last: Knight-Schrijver

address: Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way

country: United Kingdom

institute: University Of Cambridge

summary: Re-activating quiescent adult epicardium represents a potential therapeutic approach for human  cardiac regeneration. However, the exact molecular differences between inactive adult and active  foetal epicardium are not known. Here, we combined foetal and adult human hearts for the first  time using single-cell and single-nuclei RNA sequencing, and compared epicardial cells from both  stages. We found a migratory fibroblast-like epicardial population only in the foetal heart and  foetal epicardium expressed angiogenic gene programs, while the adult epicardium was solely  mesothelial and immune-responsive. Furthermore, we predicted that adult hearts may still receive  foetal epicardial paracrine communication, including WNT-signalling with endocardium, reinforcing  the validity of regenerative strategies that administer or reactivate epicardial cells in situ. Finally,  we explained graft efficacy of our human embryonic stem-cell derived epicardium model, by noting  its similarity to human foetal epicardium. Overall, our study defines epicardial programs of  regenerative angiogenesis absent in adult hearts, contextualises animal studies, and defines  epicardial states required for effective human heart regeneration.

overall_design: Seven (F1-F7) foetuses were obtained following elective termination of pregnancy with full consent and were stored overnight in Hibernate-A Medium (Gibco) at 4 °C. The next day following collection, the apex and base of each heart was dissected, and dissociated. Cells were submitted for 10x library preparation for 3’ single cell sequencing on a NovaSeq 6000 (Illumina) using V3 chemistry at the Cancer Research UK (CRUK) Cambridge Institute. One sample F5 was collected as a pilot sample independently and prepared separately from the other foetal samples and only the apex attached to a careful epicardial peeling was taken and dissociated. Sample F5 was sequenced independently at the Sanger Institute using HiSeq 4000 (Illumina).

first: Hongorzul

last: Davaapil

first: Semih

last: Bayraktar

first: Alexander

last: Ross

first: Kazumasa

last: Kanemaru

first: James

last: Cranley

first: Monika

last: Dabrowska

first: Minal

last: Patel

first: Xiaoling

last: He

first: Ludovic

last: Vallier

first: Sarah

last: Teichmann

first: Laure

last: Gambardella

first: Sanjay

last: Sinha

first: Krzysztof

last: Polanski


title: Single-cell analysis of mouse pituitaries

status: Public on Oct 14 2022

city: Beijing

first: Yehua

last: Li

address: shengmingkexueyuanlu7hao, changping

country: China

institute: NIBS

type: Expression profiling by high throughput sequencing

summary: Using the single-cell sequencing technology, the authors aim to make a globally construction of a single-cell cell atlas covering young and old pituitary cells. Moreover, the sorted Ai6+ cells from pituitary of Igha-Cre; Ai6 were also analyzed by single-cell sequencing.

overall_design: The young and old mouse pituitary cells, as well as sorted Igha-Cre; Ai6+ pituitary cells were captured and analyzed using the 10× Chromium platform.

first: Jiawen

last: Wang

first: Rui

first: Xioadong


title: Metabolic profiling and transcriptome analysis provide insights into the accumulation of flavonoids in chayote fruit during storage

status: Public on Oct 05 2022

city: Gui Yang

first: Yuting

last: Pu

address: Huaxi District

institute: Guizhou University

summary: Chayote (Sechium edule) fruits are rich in flavonoids, folate, and low-calorie food. However, studies about the flavonoids and regulatory mechanism of flavonoid synthesis in chayote fruits was still unclear. In present study, a transcriptome analysis and metabolite profiling of chayote fruits at three different storage stages were conducted to explore the flavonoid compositions and gene expression associated with flavonoid synthesis. Through the UPLC-MS/MS analysis, a total of 57 flavonoid compounds were detected. Of these, 42 flavonoid glycosides were significantly differential accumulation in chayote fruits at three different storage stages. Many genes associated with flavonoid synthesis were differentially expressed in chayote fruits at three different storage stages through RNA-seq analysis, including structural genes and some TFs. There was a high correlation between RNA-seq analysis and metabolite profiling, and the expression level of candidate genes in the flavonoid synthesis pathway were consistent with the dynamic changes of flavonoids. In addition, one R2R3-MYB transcription factor, FSG0057100, was defined as the critical regulatory gene of flavonoid synthesis. Furthermore, we treated chayote fruits during storage with phenylalanine, and the results show exogenous phenylalanine applications might promote the flavonoid synthesis. Phenylalanine is a effective additive to maintain or improve the total content flavonoids in chayote fruit during storage, can apply the phenylalanine in the postharvest storage of chayote. The above results not only make us better understand the molecular mechanism of flavonoid synthesis in chayote fruits, but also contribute to the promotion and application of chayote products.

overall_design: In present study,we here performed metabolome and transcriptome profiling of chayote fruits during storage at room temperature to examine the dynamic changes of flavonoid compounds and the corresponding regulatory mechanism of flavonoid synthesis. A total of 57 flavonoid derivatives were detected in this study. Among them, 42 flavonoid glycosides were differentially accumulated in different storage stages. Moreover, the DEGs, including structural genes and transcriptional factors (TFs) for flavonoid synthesis were also identified, and the expression pattern of some DEGs were further verified using qRT-PCR. Correlation analysis between RNA-seq analysis and metabolite profiling had revealed that the identified structural genes and TFs displayed better correlation with the quantitative changes of flavonoids.

first: Chen

first: Yongwen

last: Jiang

first: Xiaojing

first: Yujie

last: Ai

first: Weibing

last: Zhuang


title: Comparing a timecourse of hESC-epicardium differentiation with single-cell adult and foetal human epicardium as part of the study: A single-cell comparison of adult and foetal human epicardium defines the age-associated changes in epicardial activity

first: Vincent

last: Knight-Schrijver

summary: This study is associated with the GEO accession GSE216019. Abstract from article: Re-activating quiescent adult epicardium represents a potential therapeutic approach for human cardiac regeneration. However, the exact molecular differences between inactive adult and active foetal epicardium are not known. Here, we combined foetal and adult human hearts for the first time using single-cell and single-nuclei RNA sequencing, and compared epicardial cells from both stages. We found a migratory fibroblast-like epicardial population only in the foetal heart and foetal epicardium expressed angiogenic gene programs, while the adult epicardium was solely mesothelial and immune-responsive. Furthermore, we predicted that adult hearts may still receive foetal epicardial paracrine communication, including WNT-signalling with endocardium, reinforcing the validity of regenerative strategies that administer or reactivate epicardial cells in situ. Finally, we explained graft efficacy of our human embryonic stem-cell derived epicardium model, by noting its similarity to human foetal epicardium. Overall, our study defines epicardial programs of regenerative angiogenesis absent in adult hearts, contextualises animal studies, and defines  epicardial endpoints required for effective human heart regeneration.

overall_design: Six time points were sampled from a 9-day hESC-epicardium differentiation for analysis of differentiation timecourse. Cells were collected on days 1, 2, 3, 4, 8, and 9 following the intermediate lateral mesoderm stage during the protocol by Iyer et al., (2015).

middle: R

first: Hongorzul

last: Davaapil

first: Semih

last: Bayraktar

first: Alexander

middle: D

last: Ross

first: Kazumasa

first: James

first: Monika

first: Minal


title: S. aureus biofilm transcriptome following G-MDSC or Macrophage co-culture

status: Public on Sep 19 2022

city: Omaha

first: Tammy

last: Kielian

state: NE

address: 985900 Nebraska Medical Center

department: Pathology & Microbiology

country: USA

institute: University of Nebraska Medical Center

summary: To investigate biofilm-leukocyte crosstalk, we performed RNA-seq to evaluate how the S. aureus biofilm transcriptome was altered following exposure to G-MDSCs or macrophages in vitro. Interestingly, each immune cell type elicited a distinct transcriptional response.

overall_design: RNA-sequencing was performed on biofilm co-cultured with G-MDSCs (3 replicates), macrophages (3 replicates), or G-MDSCs + macrophages (2 replicates). Biofilm only was also used as a control (2 replicates).

first: Blake

middle: P

last: Bertrand

first: Cortney

middle: E

last: Heim

first: Sean

middle: C

last: West

first: Sujata

middle: S

last: Chaudhari

first: Hesham

last: Ali

first: Vinai

last: Thomas


title: Common and distinct functions of mouse Dot1l in the regulation of endothelial transcriptome

status: Public on Oct 11 2022

city: Seoul

first: Kwonho

last: Hong

address: 120 Neungdong

country: South Korea

institute: Konkuk university

summary: Epigenetic mechanisms are mandatory for endothelial cells (ECs) during cardiovascular development. Dot1l-mediated gene transcription in mice is essential for development and function of lymphatic ECs (LECs). The role of Dot1l in development and function of blood ECs (BECs) is unclear. RNA-seq datasets from Dot1l-depleted or -overexpressing BECs and LECs were used to comprehensively analyze regulatory networks of gene transcription and pathways. Dot1l depletion in BECs changed the expression of genes involving cell-to-cell adhesion and immunity-related biological processes. Dot1l overexpression changed the expression of genes involved in different types of cell-to-cell adhesion and angiogenesis-related biological processes. Genes involved in specific tissue development-related biological pathways were altered in Dot1l-depleted BECs and LECs. Vascular endothelial growth factor production-related genes were specifically regulated in BECs by Dot1l. Dot1l overexpression  uniquely altered ion transportation-related genes in BECs and  immune response regulation-related genes in LECs. Importantly, Dot1l overexpression in BECs led to expression of many genes related to the angiogenesis and mitogen-activated protein kinase signaling pathways. The expression of these genes was unchanged in Dot1l-overexpressing LECs. The findings demonstrate the unique transcriptomic program of ECs and the differential functions of Dot1l in the regulation of gene transcription in BECs and LECs.

overall_design: High throughput transcriptome sequencing of Dot1l knock-out or control E15.5 mouse embryo skin BEC and cultured mouse embryonic yolk sac BEC and dermal LEC transduced with empty or Dot1l overexpression vector containing lentivirus.

first: Hyunjin

last: Yoo

first: Hyeonwoo

last: La

first: Chanhyeok

last: Park

first: Seonho

first: Hyeonji

last: Lee

first: Hyuk

last: Song

first: Jeong

middle: T

last: Do

first: Youngsok

last: Choi


title: Genome-wide identification and expression profiles of CsHIPP family genes under heavy metal stress in Camellia sinensis (L.)

status: Public on Sep 09 2022

city: Guiyang

first: yunfeng

last: wei

address: Huaxi District, Guiyang City

summary: HIPP (heavy metal associated isoprenylated plant protein) is a group of metal-binding metallochaperones, which plays crucial roles in metal homeostasis and detoxification. Up to now, little information of CsHIPP family genes in C. sinensis has been reported.   In present study, a total of 56 CsHIPP genes from C. sinensis were identified, which were unevenly distributed on 15 chromosomes. The CsHIPP family genes were divided into five groups based on the topology of phylogenetic tree and identified AtHIPPs and OsHIPPs. Motif and gene structure analysis showed that the members in the same group showed similar conserved motifs and intron/exon structure. The expression pattern of CsHIPP family genes in different organs of C. sinensis was investigated using the previous RNA-seq data. The expression level of CsHIPP genes in C. sinensis under Cd and As treatments was also explored based on our RNA-seq analysis. The results showed that 16 CsHIPP genes displayed the same expression pattern under Cd and As treatments, which were also verified by qRT-PCR. Among them, three CsHIPP genes (CsHIPP15, CsHIPP36, and CsHIPP4) were increased at both 10 d and 15 d after Cd and As treatments, and one gene (CsHIPP40) was increased to a maximum at 10 d, and decreased at 15 d of Cd and As treatments, indicating that these four CsHIPP genes in C. sinensis might be involved in the resistance to Cd and As stresses.  These results provide a basis for the functional characterization of CsHIPP genes and investigations on the molecular mechanisms of heavy metal homeostasis in C. sinensis.

first: Chen

last: Wang

first: Yunfeng

last: Wei

first: Xiaojing

first: Weibing

last: Zhuang


title: Effects of Conditional Egfr deletion on transcriptome of the mouse cerebral cortex

status: Public on Oct 02 2022

city: Raleigh

first: Troy

last: Ghashghaei

state: North Carolina

address: 1060 William Moore Drive

department: Molecular Biomedical Sciences

institute: North Carolina State University

summary: To investigate the role of Egfr in the cerebreal cortex and hippocampal formation we conditionally deleted it using a floxed allele in combination with the Nestin-cre transgene. Cortices at P5 post-natal stage were harvested and split into rostral and caudal halves and RNA extracted and sequenced

overall_design: Comparison of RNA-seq data between rostral and caudal cortices and hippocampal formation of control brains (EgfrF/+ gentoype) and brain-specific knock of Egfr (Nestin-EgfrF/F).

first: T

first: M

last: Oldham

first: R

last: Eliscu


title: HCT116_SMARCA4 CUT&Tag

status: Public on Sep 04 2022

city: Nanjing

first: Xiangwei

last: Zeng

state: Jiangsu

address: Xianlin avenue

institute: Nanjing university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To investigate the enrichment of SMARCA4-R1157W mutation on downstream target gene promoters, we performed CUT&Tag experiments in HCT116 cells.

overall_design: CUT&Tag  for SMARCA4 in HCT116_SMARCA4-Wildtype and HCT116_SMARCA4-R1157W mutant cells

first: Jianpeng

last: Liu


title: Effect of depletion of ALKBH5 on gene expression of HaCAT human keratinocyte cell line

status: Public on Aug 12 2022

city: Shanghai

first: Xin

last: Huang

state: China

address: zhizaoju Road 639

institute: Ninth People's Hospital affiliated to Shanghai Jiao Tong University School of Medicine

summary: To investigate the function of ALKBH5 in the regulation of keratinocyte cellular function, we established HaCAT cell lines in which ALKBH5 has been knocked down by siRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells from duplicate experiments.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HaCAT cells and its KD derivatives (siALKBH5).

first: Tao

last: Zan

first: Qingfeng

last: Li


title: Cytosolic immunity against Moraxella catarrhalis requires innate immune signalling pillars converging on inflammasome activation

status: Public on Aug 17 2022

city: Canberra

first: Daniel

last: Enosi Tuipulotu

address: Australian National University

country: Australia

institute: Australian National University

summary: RNA-sequencing of uninfected and Moraxella catarrhalis-infected bone marrow-derived macrophages (BMDMs) isolated from Ifnar1 knockout and wild-type mice.

overall_design: RNA-sequencing of 12 samples (n=4 conditions, n=3 replicates/condition), including uninfected WT BMDMs, M. catarrhalis-infected WT BMDMs, uninfected Ifnar1 knockout BMDMs and M. catarrhalis-infected Ifnar1 knockout BMDMs.

last: Enosi Tupulotu

first: Si Ming

last: Man


title: Methylated RNA immunoprecipitation sequencing (MeRIP-seq) of human epidermis and HaCAT cells with or without ALKBH5 knockdown

status: Public on Aug 18 2022

summary: We performed MeRIP-seq on (1) two human epidermis tissue and HaCAT (human keratinocyte cell line) cells; (2) HaCAT cell lines with or without ALKBH5 knockdown by siRNA in duplicate experiments.

overall_design: Comparative mRNA m6A modification profiling analysis of MeRIP-seq data for (1) normal human epidermis tissue and HaCAT cells; (2)  HaCAT cells and its KD derivatives (siALKBH5).


title: Single cell RNA seq of bone marrow cells from mouse MDS disease model and WT control

status: Public on Aug 01 2022

city: Chicago

first: Peng

last: Ji

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

summary: mDia1-miR146a double knockout (DKO) mice develop aging related MDS and eventually progress to AML at moribund stage. To investigate the rescue effect from IL6 deficiency, we created mDia1-miR146a-IL6 triple knockout (TKO) mice. Singel cell RNA seq was used to investigate the bone marrow cellularity change and pathway involved during the disease progression.

overall_design: Total bone marrow cells were isolated from femur and tibia of aged WT, DKO, TKO and IL6 KO mice, respectively. Red blood cells were depleted with RBC lysis buffer before single cell library construction.

first: Beatriz

last: Martinez Abad


title: Effect of caspase-3 and -7 knockout on doxorubicin treated B16 melanoma cells

status: Public on Aug 05 2022

city: Durham

first: Shane

last: Killarney

state: NC

address: 4 SCOTTISH LANE

institute: Duke University School of Medicine

summary: To measure the immunosuppressive effect of caspase-3 and -7 in apoptosis, we generated B16 sgCTRL and sgCasp3/7 cells and treated them with doxorubicin

overall_design: We performed gene expression analysis on B16 sgCTRL and sgCasp3/7 cells in triplicate after .5 μM of Doxorubicin treatment for 48hrs

first: Ryan

last: Soderquist

first: Jacob

last: Hoj

first: Kris

last: Wood


title: Molecular signatures of the Eagle effect induced by the artificial siderophore conjugate LP-600 in E. coli

status: Public on Jul 31 2022

city: Braunschweig

first: Yi-Hui

last: Lai

address: Inhoffenstr. 7

country: Germany

institute: Helmholtz Centre for Infection Research

summary: We investigated a paradoxical re-growth of E. coli upon treatment of a novel siderophore-conjugate, LP-600, at concentrations 16-32 times above  the minimum inhibitory concentration (MIC).Transcriptome analysis revealed that LP-600 induced the expression of genes involved in SOS response and e14 prophage upon regrowth conditions.

overall_design: E.coli mRNA profiles of siderophore-conjugate treatments at different concentrations and growth phases

first: Lukas

last: Pinkert

first: Raimo

last: Franke

first: Mark

last: Brönstrup


title: Quantitative Analysis of Wild Type and Crtc2 adipocyte-specific KO Epididymal primary adipocyte Transcriptomes

status: Public on Jul 09 2022

first: Seung-Hoi

last: Koo

address: 145 Anam-Ro, Seongbuk-Gu

department: Life Sciences

institute: Korea University

summary: We attempted to analyze the effect of adipocyte-specific knockout of Crtc2 in in aging. By analyzing the transcriptomics of epididymal primary adipocytes from male mice with wild type and adipocyte-specific Crtc2 knockout mice in response to aging, we provide the insight into the collective roles of Crtc2 in epididymal white adipose tissues upon aging.

overall_design: mRNA profiles of epididymal primary adipocytes from 3-month-old wild type (WT), 18-month-old wild type (WT), 3-month-old adipocyte-specific Crtc2 KO mice, and 18-month-old adipocyte-specific Crtc2 KO mice

first: Hye-Sook

last: Han


title: A Bidirectional Single-Cell Migration and Retrieval Chip for Quantitative Study of Dendritic Cell Migration

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

summary: We describe a microfluidics-based single-cell migration platform that enables high-throughput and precise bidirectional chemotaxis assays (BM-Chip), which allows controllable retrieval of cell subpopulations that have different migratory potentials. We investigated dendritic cell (DC) migration in response to different chemoattractants and inhibitors. We quantitatively described DC migration patterns and retrieved DC subpopulations of different migratory potentials for differential gene expression analysis.

overall_design: Dendritic cells were cultured inside BM-Chip under chemoattractant gradient. Single cells migrated to different locations were collected and combined for RNAseq analysis.

first: Shao

last: Ning

first: Zhou

last: Yufu

first: Yao

last: Jun

first: Zhang

last: Pengchao

first: Song

last: Yanni

last: Kai

first: Han

last: Xin

first: Wang

last: Bin

first: Liu

last: Xuewu


title: Circulating small non-coding RNA profiling as potential biomarkers of atherosclerotic plaque composition in Type 1 diabetes

status: Public on Jul 14 2022

city: Padova

first: Giulio

last: Ceolotto

address: Via Orus 2B

department: Medicine

country: Italy

institute: University of Padova

type: Non-coding RNA profiling by high throughput sequencing

summary: Cardiovascular disease (CVD) accounts for the majority of deaths in patients with type 1 diabetes (T1D); however, the determinants of plaque composition are unknown in this population. MicroRNAs (miRNAs), the most abundant class of circulating small non-coding RNA (sncRNAs) regulating gene expression, participate in the development of atherosclerosis and represent promising biomarkers of CVD.  This study analyzed the circulating miRNA expression profile in T1D with carotid calcified and fibrous plaque. We identified four upregulated (miR-503-5p, let-7d-5p, miR-106b-3p, miR-93-5p) and one downregulated (miR-10a-5p) miRNAs in patients with calcified plaque(s) compared to those with fibrous plaque(s). ROC curve analysis demonstrated that miR-503-5p and miR-10a-5p discriminate with good performance in the different plaque compositions. miR-503-3p inversely and miR-10a-5p directly correlate with LDL cholesterol concentrations. Pathway enrichment analysis of putative gene targets of selected miRNAs revealed involvement in apoptotic and inflammatory processes regulation, osteogenic differentiation, and vascular calcification. These findings comprehensively characterize miRNAs and their signature in the regulatory network, leading to different plaque compositions in T1D. These results could have important clinical implications for developing  novel therapeutic strategies to prevent CVD  in diabetes.

overall_design: miRNA profile in plasma from type 1 diabetes and atherosclerotic plaque

first: Alessandra

last: Giannella


title: A chemically-targetable transcription factor-chromatin remodeler interaction underlies SARS-CoV-2 susceptibility

city: Boston

first: Cigall

last: Kadoch

state: Massachusetts

address: 450 Brookline Avenue

institute: Broad Institute of MIT and Harvard, Harvard Medical School, Dana-Farber Cancer Institute

summary: Identification of host determinants of coronavirus infection informs mechanisms of viral pathogenesis and provides novel therapeutic targets. Here, we demonstrate that the mSWI/SNF chromatin remodeling complex promotes coronavirus infection and represents a host-directed therapeutic target. SMARCA4 catalytic activity is required for mSWI/SNF-driven chromatin accessibility at the ACE2 locus, which is essential for ACE2 expression and virus susceptibility. Recruitment of mSWI/SNF complexes to ACE2 is mediated by mSWI/SNF binding to the transcription factor, HNF1A, enabling complex occupancy and chromatin accessibility at sites containing high HNF1A motif density. Notably, small molecule inhibition of mSWI/SNF catalytic activity abrogates ACE2 expression confers resistance to SARS-CoV-2 variants and infection of primary human airway cells by 5-logs. These data highlight the role for mSWI/SNF-mediated chromatin remodeling activities in conferring SARS-CoV-2 susceptibility and identify a potential new class of inhibitors to combat COVID-19.

sample_organism:
Homo sapiens
Chlorocebus sabaeus

platform_organism:
Homo sapiens
Chlorocebus sabaeus

overall_design: CUT&Tag, RNA-seq, and ATAC-seq in wild type and SMARCA4 KO Vero E6 cells to investigate the mechanism behind SARS-CoV-2 resistance after BAF inhibition

first: Ajinkya

last: Patil

first: Jin

last: Wei

first: Clayton

middle: K

last: Collings

first: Craig

middle: B

last: Wilen


title: Single RNA-Seq on GBM cells from NPCTKO mouse models

status: Public on Jul 07 2022

city: Wuhan

first: Xuan

last: Liu

address: Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province, P.R. China

institute: Wuhan university

summary: Glioblastoma multiforme (GBM), a highly malignant and heterogeneous brain tumor, contains various types of tumor and non-tumor cells. Whether GBM cells can trans-differentiate into non-neural cell types, including mural cells or endothelial cells, to support tumor growth and invasion remains controversial. Here we generated two genetic GBM models de novo in immunocompetent mouse brains, mimicking essential pathological and molecular features of human GBMs. Single-cell RNA sequencing showed that patterns of copy-number variations (CNVs) of mural cells and endothelial cells were distinct from those of GBM cells, indicating discrete origins of GBM cells and vascular components. Furthermore, lineage tracing and transplantation studies demonstrated that, although blood vessels in GBM brains underwent drastic remodeling, GBM cells did not give rise to non-neural cell types in the brain. Intriguingly, GBM cells could randomly express mesenchymal markers, including those for mural cells, during gliomagenesis. Most importantly, single-cell CNV analysis of human GBM specimens also strongly suggested that GBM cells and vascular cells are separate lineages. Instead, non-neural cell types expanded by proliferation during tumorigenesis. Therefore, cross-lineage trans-differentiation of GBM cells is very unlikely to occur during gliomagenesis. Our findings advance understanding of cell lineage dynamics during gliomagenesis, and have implications for targeted treatment of GBMs.

overall_design: RNA profiles of individual cells from tumor sites in NPCTKO mouse models.

first: Fangyu

last: Wang

first: Shaowen

last: Li

first: Yan

last: Zhou


title: Bulk RNA-Seq on GBM cells from NPCTKO and NSCHRas-shp53 mouse models

overall_design: GBM cells mRNA profiles of NPCTKO and NSCHRas-shp53 mouse models were generated by deep sequencing, in duplicate, using Illumina NovaSeq 6000.


title: SREBP signaling is essential for effective B cell responses and memory formation

status: Public on Jun 30 2022

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

summary: To investigate the function of SREBP signaling in established germinal center B cells, we generated SCAP fl/fl AID-Cre-YFP mice. We then performed gene expression profiling analysis using data obtained from RNA-seq of sorted germinal center B cells from immunized control and SCAP fl/fl AID-Cre-YFP mice

overall_design: Comparison of gene expression of control vs KO drainging lymph node germinal center B cells isolated 14 days post subcutaneous NP-OVA+RIBI immunization.

first: Wei

last: Luo

first: Julia

middle: Z

last: Adamska

first: Chungeng

first: Florian

last: Wimmer

first: Thomas

last: Hagan


title: The effects of SCAP deletion on gene expression of activated B cells

summary: To investigate the role of SREBP signaling in B cell activation, we stimulated SCAP+/+CD19Cre/+ (WT) and SCAPfl/fl CD19Cre/+ (KO) B cells with LPS, anti-CD40 or anti-IgM for 24 hrs and performed RNA sequencing to identifiy the differences.

overall_design: We performed RNA seqencing comparing WT and KO B cell unstimulated (time 0) or stimualted with LPS, anti-CD40 or anti-IgM for 24 hrs

first: Shakti

last: Gupta


title: Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation

status: Public on Jul 01 2022

city: LA JOLLA

first: Carlos

last: Guzman

address: 9262 REGENTS RD

institute: UCSD

summary: Using a transcription start site-capturing massively parallel reporter assay (TSS-MPRA) that simultaneously measures the location and frequency of transcription initiation from synthetic sequences, we carefully characterize the degree to which plasmid-based MPRAs recapitulate endogenous initiation patterns.

overall_design: TSS-MPRA sequencing of insert libraries to characterize transcription initiation patterns (K562)

first: Sascha

last: Duttke

first: Camila

last: De Arruda Saldanha

first: Christopher

last: Benner

first: Sven

last: Heinz

first: Nicholas

middle: L

last: Downes


title: Exercise-acclimated microbiota improves skeletal muscle metabolism

city: Kyoto

first: Wataru

last: Aoi

address: 1-5 Hangicho Shimogamo, Sakyo-ku

country: Japan

institute: Kyoto Prefectural University

summary:
Habitual exercise modulates the composition of the intestinal microbiota. We examined whether transplanting fecal microbiota from trained mice improved skeletal muscle metabolism in high-fat diet-fed mice. The recipient mice that received fecal samples from trained donor mice for 1 week showed elevated levels of metabolic signalings in skeletal muscle. Glucose tolerance was improved by fecal microbiota transplantation after 8 weeks of HFD administration. Intestinal microbiota may mediate exercise-induced metabolic improvement in mice.
We performed a microarray analysis to compare the metabolic gene expression profiles in the skeletal muscle from each mouse.

overall_design: Male germ-free mice were administered fecal samples from sedentary or training donor mice. After 1 week, 6 mice from each recipient group were used for microarray analysis. Total RNA was extracted from the gastrocnemius muscle. cRNA and target hybridization preparations were performed according to the Affymetrix GeneChip Technical Protocol. Affymetrix GeneChip Mouse Gene 1.0 ST arrays were stained and washed in an Affymetrix Fluidics Station 450 and scanned using a GeneChip Scanner 3000.

first: Katsura

last: Mizushima

first: Tomohisa

last: Takagi

first: Yuji

last: Naito


title: Human islets exposed to conditions that induce or inhibit calcium signaling

status: Public on Jun 17 2022

city: Vancouver

first: Francis

last: Lynn

state: BC

address: 950 28th Ave W

department: Surgery

country: Canada

institute: University of British Columbia

summary: Pancreatic islets depend on cytosolic calcium to trigger the secretion of glucoregulatory hormones and the transcriptional regulation of genes important for islet response to stimuli. To date, there has not been an attempt to profile calcium-regulated gene expression in all islet cell types. To address this, we generated a large single cell transcriptomic dataset from healthy human islets exposed to conditions that would acutely induce or inhibit intracellular calcium signaling, while preserving biological heterogeneity. Our aim was to use this dataset to identify acutely calcium-regulated genes in each islet cell type, while simulataneously exploring markers of islet heterogeneity.

overall_design: Islets were obtained from 3 healthy, age-matched, BMI-matched, male human donors: R253, R282, and R317. Each islet prep was split into 3 experimental conditions designed to induce or inhibit calcium signalling pathways: Low, Positive, and Negative. Each experimental condition within each donor prep was handled as an individual "sample" throughout the library preparation and analysis, resulting in 9 samples composed of 3 biological replicates of 3 experimental conditions. For sequencing, all libraries generated from the 3 experimental conditions were pooled per donor, and sequenced on a single flow cell. For each donor's 3 libraries, sequencing was performed twice in order to meet an appropriate number of reads, resulting in 2 technical replicates of sequencing: run1 and run2. In total, there were 18 individual samples' sequencing data carried downstream for analysis, composed of the 9 individual samples, each sequenced across 2 sequencing runs.

first: Ji

last: Yoon

first: Shugo

last: Sasaki

first: Jane

last: Velghe

first: Michelle

middle: Y

last: Lee

first: Helena

last: Winata

first: Cuilan

last: Nian


title: Single-cell RNA sequencing for vascular cell-enriched cell populations in the liver-specific apoE inducible mouse models

status: Public on Jun 15 2022

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

summary: Vascular cell-enriched cells in the cortex of mice expressing apoE3 or apoE4 in the liver were isolated and subjected to the single-cell RNA seq to investigate the effects of peripheral apoE on the brain transcriptomic profiles. Our data revealed that liver-expressed apoE4 reduced astrocyte endfeet and promoted immune responses in the endothelial cells as welll as increases vessel-associated gliosis. Genes involved in IGF signaling, tight junction formation, actin cytoskeleton signaling, and maintenance of endothelial barrier function were up-regulated in the endothelial cells of mice expressing apoE3 in the liver.

overall_design: Four mice (2 males and 2 females) were analyzed for each of the four groups, including APOE3/Alb-Cre-, APOE3/Alb-Cre+, APOE4/Alb-Cre-, APOE4/Alb-Cre+.

first: Chia-Chen

last: Liu

first: Yuka

last: Martens

first: Yu

last: Yamazaki


title: Single-cell transcriptomics of staged oocytes and somatic cells reveal novel regulators of follicle activation

status: Public on Jun 29 2022

city: Somerville

first: Daniela

middle: Dolores

last: Russo

address: 5 Russell Rd

institute: Ragon Institute of MGH, MIT and Harvard

summary: Primordial follicles are the first class of follicles formed in the mammalian ovary and are comprised of an oocyte surrounded by a layer of squamous pre-granulosa cells. This developmental class remains in a non-growing state until individual follicles activate to initiate folliculogenesis. What regulates the timing of follicle activation and the upstream signals that govern these processes are major unanswered questions in ovarian biology. This is partly due to the paucity of data on staged follicle cells since isolating and manipulating individual oocytes and somatic cells from early follicle stages are challenging. To date, most studies on isolated primordial follicles have been conducted on cells collected from animal-age- or oocyte size-specific samples, which encompass multiple follicular stages. Here, we report a method for collecting primordial follicles and their associated oocytes and somatic cells from neonatal murine ovaries using liberase, DNase I, and Accutase. This methodology allows for the identification and collection of follicles immediately post-activation enabling unprecedented interrogation of the primordial-to-primary follicle transition. Molecular profiling by single-cell RNA sequencing (scRNA-seq) revealed that processes including organelle disassembly and cadherin binding were enriched in oocytes and somatic cells as they transitioned from primordial to the primary follicle stage. Furthermore, targets including WNT4, TGFβ, FOXO3, and a network of transcription factors were identified in the transitioning oocytes and somatic cells as potential upstream regulators that collectively may drive follicle activation. Taken together, we have developed a more precise characterization and selection method for studying staged-follicle cells, revealing several novel regulators of early folliculogenesis.

overall_design: Single oocytes and somatic cells from CD-1 mice at various stages of ovarian follicle development were collected. Eight to twelve P6 ovaries were used to obtain all oocytes and somatic cells. In this study we included samples from the the primordial , transitioning from primordial to primary, primary, and secondary stages of follicular development. For the single oocytes, we included 14 primordial stage, 19 transitioning to primary, 20 primary, and 7 secondary replicates. There were a greater number of replicates for somatic cells with 40 primordial, 47 tranisitioning to primary, 56 primary, and 51 secondary being included in our study.

first: Yu-Ying

last: Chen

first: Riley

last: Drake

first: Francesca

last: Duncan

first: Alex

last: Shalek

first: Brittany

last: Goods

first: Teresa

last: Woodruff


title: Peripherally-expressed apoE4 impairs brain functions and exacerbates amyloid pathogenesis by compromising cerebrovascular functions

summary: The apolipoprotein E4 (APOE4) gene is the strongest genetic risk factor for late-onset Alzheimer’s disease (AD). ApoE is a lipid carrier abundantly expressed in both brain and periphery. As peripheral apoE is separated from brain apoE by the blood-brain barrier, it remains unclear whether peripheral apoE impacts brain functions and AD pathogenesis. To investigate this, we developed novel mouse models that conditionally express human APOE3 or APOE4 only in the liver with no detectable apoE in the brain. We found that liver-expressed apoE4 compromised synaptic plasticity and cognitive behaviors likely by impairing cerebrovascular functions. Remarkably, liver-expressed apoE4 exacerbated brain amyloid pathology, whereas apoE3 reduced it. Our findings demonstrate a pathogenic effect of peripheral apoE4, providing strong rationale for targeting peripheral apoE to treat AD.

overall_design: Brain transcriptome profiles of mouse models expressing human apoE3 or apoE4 specifically in the liver

first: Yuanxin

last: Zhao

first: Minghui

last: Wang

first: Yuan

last: Fu

first: Lin

last: Jia

first: Jing

first: Wenhui

last: Qiao

first: Lindsey

last: Felton

first: Justin

last: Rogers

first: Cynthia

last: Linares

first: Joshua

last: Knight

first: Yixing

first: Aishe

last: Kurti

first: Takahisa

last: Kanekiyo

first: John

last: Fryer

first: Yan

middle: W

last: Asmann

first: Bin

last: Zhang

first: Betty

last: Kim

first: Guojun

last: Bu


title: A novel approach for studying mast cell-driven disorders: mast cells derived from induced pluripotent stem cells

status: Public on Aug 31 2022

city: Berlin

first: Yanyan

last: Luo

address: Luisenstrasse 2

institute: Department of Dermatology and Allergy Allergie-Centrum-Chari

summary: We developed a novel strategy for the rapid and efficient differentiation of MCs from human induced pluripotent stem cells (hiPSC). These hiPSC-derived MCs (hiPSC-MCs) exhibit phenotypic and functional characteristics of human skin MCs (hsMCs) and peripheral hematopoietic stem cell-derived MCs (PSCMCs). hiPSC-MCs display stable expression of MC-associated receptors such as CD117, FcεRIα and MRGPRX2, and degranulate by stimulation with IgE/anti-IgE and Substance. P.

overall_design: 3 replicates of each group, i.e. hiPSC, primary human skin mast cells (hsMC) and hiPSC derived mast cells (hiPSC-MC)

first: Valeria

last: Fernandez Vallone

first: Jiajun

last: He

first: Stefan

last: Frischbutter

first: Pavel

last: Kolkhir

first: Sherezade

last: Moñino-Romero

first: Harald

last: Stachelscheid

first: Viktoria

last: Streu-Haddad

first: Marcus

last: Maurer

first: Frank

last: Siebenhaar

first: Jörg

last: Scheffel


title: Gene expression profiling of hepatocyte-like cells from human mesenchymal stem cells

status: Public on Jun 09 2022

city: Shinjyuku-ku

first: Tomoki

last: Takashina

state: Tokyo

department: Department of Intractable Diseases

institute: National center for Global Health and Medicine

summary: We established a protein-based artificial transcription system and successfully engineered human hepatocyte-like cells from human umbilical cord-derived mesenchymal stem cells (MSC-UCs). We utilized four artificial transcription factors (ATFs) that targeted hepatocyte nuclear factor (HNF)1α, HNF3γ, HNF4α and GATA4 (4F), and found that treatment with 4F for 5 days converted MSC-UCs to hepatocyte-like cells (4F-Heps). We then examined gene expression profiles of 4F-Heps and compared them with those of non-treated MSC-UCs (NC) or MSC-UCs treated with NTP-EGFP protein as control protein (NE).

overall_design: Gene expression profiles of three different groupe (4F-treated MSC-Ucs (4F-Heps), NTP-EGFP(NE)-treated MSC-UCs and non-treated MSC-Ucs). 4F and NE were added to culture medium at 0.25 nM twice a day for 5 days. The cells were collected  after 2 days of the last treatment.   Three independent experiments were performed at each sample.

first: Akihiro

last: Matsunaga

first: Yukiko

last: Shimizu

first: Tetsushi

last: Sakuma

first: Tadashi

last: Okamura

first: Kunie

last: Matsuoka

first: Takashi

last: Yamamoto

first: Yukihito

last: Ishizaka


title: Reprogramming of cochlear supporting cells by MYC/NICD co-activation.

status: Public on Jun 03 2022

first: Volkan

last: Ergin

state: MA

address: 243 Charles St.

department: Otolaryngology, Harvard Medical School

institute: Massachusetts Eye and Ear

summary: Strategies to overcome irreversible cochlear hair cell (HC) damage and loss are of vital importance to develop a treatment for hearing loss. HC regeneration in adult cochlea relies on a two-phase process: 1) Reprogramming mature cochlear (SCs) to regain the properties of their younger selves; 2) Activating Atoh1, a gene responsible for HC fate-determining, in the reprogrammed adult SCs for HC regeneration. We have shown that, by transient co-activation of Myc and NICD (Notch1 intracellular domain), the adult mouse cochlea can be successfully reprogrammed to a relatively younger stage and regain progenitor capacity, with the regeneration of HCs following Atoh1 overexpression in vitro and in vivo. To identify molecules to reprogram mature cochlear SCs, we utilized single-cell RNA sequencing and uncovered the pathways and their target genes underlying MYC/NICD-mediated reprogramming. We used an in-house adult cochlea explant culture system and carried out single-cell RNA sequencing to examine the gene expression profiles of cochlear explants from a transgenic mouse model, rtTa/tet-Myc/-tet-NICD, in response to Dox-induced MYC/NICD co-activation. We have shown that a 4-day treatment by Dox in cultured adult rtTa/tetMyc/-tet-NICD cochleae was sufficient to reprogram adult SCs for HC regeneration.

overall_design: We treated whole adult cochlear explants (rtTa/tet-Myc/-tet-NICD) with Dox in vitro for four days before dissecting sensory epithelium to create cDNA libraries subjected to 10X Genomics pipeline barcoding, library preparation, and sequencing. (Control, sterile water, n=4; and Dox-administered, n=8)


title: Effects of Conditional Egfr deletion on transcriptome of the mouse cerebral cortex

city: Raleigh

first: Troy

last: Ghashghaei

address: 1060 William Moore Drive

institute: North Carolina State University

summary: To investigate the role of Egfr in the cerebreal cortex and hippocampal formation we conditionally deleted it using a floxed allele in combination with the Nestin-cre transgene.  Cortices at E17.5 embryonic stage were harvested and split into rostral and caudal halves and RNA extracted and sequenced

overall_design: Comparison of RNA-seq data between rostral and caudal cortices and hippocampal formation of control brains (EgfrF/+ gentoype) and brain-specific knock of Egfr (Nestin-EgfrF/F).

first: Michael

last: Oldham

first: Rebecca

last: Eliscu


title: Single-cell analysis implicates Th17 to Th2 cell plasticity in the pathogenesis of palmoplantar pustulosis [RNA-Seq]

status: Public on May 31 2022

city: London

first: Dan

last: McCluskey

address: Guy's Hospital

institute: King's College London

summary: Palmoplantar pustulosis (PPP) is a severe inflammatory skin disorder, characterised by eruptions of painful, neutrophil-filled pustules on the palms and soles. While PPP has a profound effect on quality of life, it remains poorly understood and notoriously difficult to treat. To investigate the immune pathways that underlie disease pathogenesis, we first undertook bulk RNA-sequencing in patient skin. We detected a pervasive and unexpected signature of T-cell activation, with a significant enrichment of Th2 pathways and evidence for a modest upregulation of Th17 genes. To further explore these findings, we carried out single-cell RNA-sequencing in peripheral blood mononuclear cells of healthy and affected individuals. We found that the memory CD4+T-cells of PPP patients were skewed towards a Th17 phenotype, a phenomenon that was particularly significant among CLA+ skin-homing cells. We also identified a subset of memory CD4+ T-cells which expressed both Th17 (KLRB1/CD161) and Th2 (GATA3) markers, with pseudo-time analysis suggesting that the population was the result of Th17 to Th2 plasticity. Interestingly, the GATA3+/CD161+ cells were over-represented among the PBMCs of affected individuals, both in the scRNA-seq dataset and in independent flow-cytometry experiments. Dual positive cells were also detected in patient skin by means of immune fluorescence microscopy.  These observations demonstrate that PPP is associated with complex T-cell activation patterns and may explain why biologics that target individual T-helper populations have shown limited therapeutic efficacy.

overall_design: Bulk RNA-sequencing on 3 lesional and 8 non-lesional (3 matched) PPP and 7 healthy control skin biopsies

first: Daniel

first: Natashia

last: Benzian-Olsson

first: Francesca

last: Capon


title: Single-cell analysis implicates Th17 to Th2 cell plasticity in the pathogenesis of palmoplantar pustulosis [scRNA-Seq]

overall_design: Single-cell RNA-sequencing on PBMCs isolated from 7 PPP patients and 4 healthy controls

first: Christian

last: Wohnhaas


title: Single-cell RNA-seq of UVB-radiated Skin Reveals Landscape of Photoaging-related Inflammation and Protection by Vitamin D

status: Public on May 16 2022

city: Shanghai

first: Yuanbin

last: Lin

address: 99 Shangda Road, Baoshan District, Shanghai

institute: Shanghai University

summary: Due to the destruction of the ozone layer, the ultraviolet radiation received by our skin has increased significantly. Continuous exposure to sunlight can cause damage to our skin, which can lead to photoaging and even skin cancer. We performed single-cell RNA sequencing on the skin of normal and UV-irradiated mice, and found that UV-irradiation caused an inflammatory response in the skin of mice. On the contrary, the inflammation of the mice injected with vitamin D was significantly reduced. Finally, we uncovered that Hmox1 and vitamin D is related to achieve the anti-inflammatory effect of vitamin D. This provides a strategy for skin anti-UV treatment

overall_design: Single cell sequencing of 9 weeks old normal and UV-irradiated mice

first: Zhanglei

last: Cao

first: Jianping

last: Zheng

first: Tianqi

last: Lv


title: Estrogen receptor α-mediated signaling  inhibits type I interferon response to promote breast cancer

status: Public on May 18 2022

first: Zilun

last: RUAN

state: Hubei

address: Donghu Road, No. 115, Wuchang District

department: Department of Infectious Diseases, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University

institute: Wuhan University

summary:
To investigate the molecular mechanisms by which estrogen receptor α (ERα) inhibits type I IFN-induced signaling.
We identified genes induced by ERα signaling using data obtained from RNA-seq of MCF7 cells treated or untreated with selective ERα agonist propyl pyrazole triol (PPT).

overall_design: Differential gene expression analysis of RNA-seq data for MCF7 cells treated or untreated with PPT (5 nM) for 16 hours.

first: Libo

last: Ruan

first: Yulin

last: Yang

first: Nianchao

last: Zhang

first: Chuan

last: Gao

first: Cheguo

last: Cai

first: Jing

first: Mingming

last: Hu

first: Hongbing

last: Shu


title: Transcriptomic characterization of heterogeneity in paired primary and recurrent HNSCC tumors

status: Public on Apr 08 2022

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

summary: Despite aggressive multi-modal treatment, advanced head and neck squamous cell carcinoma (HNSCC) patients are at high risk of recurrence. n=19 different selected areas of matched pairs (n=3) of primary/recurrent tumor specimens were subjected to RNA sequencing. Transcriptional subtyping (classical/CL, basal/BA, inflamed-mesenchymal/IMS) in matched primary and recurrent HNSCC specimens revealed heterogeneity.

overall_design: n=19 different tumor areas of n=3 paired primary and recurrent HNSCC tumor specimens

first: Claus

last: Belka

first: Julia

last: Hess


title: Multi-omics Analysis reveals novel therapeutic vulnerabilities in lung cancer

status: Public on May 04 2022

first: Randa

last: El-zein

address: 6670 Bertner Avenue

institute: Houston Methodist

summary: Non-small cell lung cancer (NSCLC) comprises the majority (~85%) of all lung tumors, with lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) being the most frequently diagnosed histological subtypes. Currently, multi-modal omics profiles had been carried out in NSCLC, but no studies reported yet a systems biology approach to provide a complete picture of molecular perturbations specifically for LUAD and LUSC.

overall_design: In this study, we integrated transcriptomics, metabolomics and adducteomics for the first time to analyze 30 paired human lung tumors and adjacent noncancerous tissues. We portrayed unique metabolite related gene signatures to distinguish LUAD from LUSC and several altered pathways aberrantly expressed at both transcriptional and metabolic levels. Additionally, the integration studies revealed a 28-metabolite gene signature in TCGA-LUAD cohort and demonstrated a significant association with survival, especially for 6 metabolite related genes as therapeutic targets. To further explore, we identified AZD-6482, a clinical trial drug from LINCS/connectivity map and found that it significantly inhibited 3 genes from the 28-gene signature. By integrating adducteomics, we found a differential expression of 307 genes correlated with 6 DNA adducts in LUSC although LUAD did not show much correlation. We found that γ-hydroxy-propanodeoxyguanosine (γ-OH-PdG) is the major DNA adduct formed in LUSC, but not in adjacent noncancerous tissue and significantly correlated with 295 modulated genes as well. We also have identified aberrant signaling pathways for each specific DNA adducts in LUSC compared to adjacent normal. Overall, we have provided a broad picture of integration of omics that can distinguish LUAD and LUSC, prediction of patient survival and identification of therapeutic targets and anticancer drugs. Ultimately, genes modulated by DNA adducts in LUSC could serve as biomarkers or therapeutic targets for cigarette smoke induced lung cancer.

first: Cristian

last: Coarfa

first: Jose

last: Thaiparambil

first: Dimuthu

last: Perera

first: Jianrong

last: Dong

first: Sandra

last: Grimm


title: Full-length transcriptome sequencing reveals gene expression signatures in human soft tissue sarcomas

status: Public on May 05 2022

city: Changsha

first: Lin

last: Qi

address: 139 Renmin Road

institute: The Second Xiangya Hospital, Central South University

summary: Soft tissue sarcomas (STSs) are heterogeneous malignancies derived from mesenchymal cells. Due to its rarity, heterogeneity, and limited overall response to chemotherapy, STSs represents a therapeutic challenge. Necroptosis is a novel therapeutic strategy for enhancing immunotherapy of cancer. Nevertheless, no research has explored the relationship between necroptosis-related genes (NRGs) and STSs.We performed full-length transcriptome analysis of four pairs of soft-tissue sarcomas and normal normal adjacent tissues. We further validated the expression level of necroptosis-related genes (NRGs) in these sample pairs.

first: Zhihong

last: Li

first: Chao

last: Tu


status: Public on Apr 22 2022

city: WUHAN

first: heng

middle: zhi

last: du

address: 1095 Jiefang Dadao, Wuhan City, Hubei Province, China

institute: Wuhan Tongji Hospital

summary: RNA immunoprecipitation sequencing (RIP seq) using anti-Argonaute2 (Ago2) antibody to identify the potential targets of kshv-miR-K12-1-5p in AC16 cells.

overall_design: We report the application of sequencing technology for high-throughput profiling of mRNA expressions in AC16 cells. AC16 cells were lysed and then incubated with anti-Ago2 antibody (Abnova Corporation, Taiwan, China) after transfected with kshv-miR-K12-1-5p mimics or miR-con for 24 h. After incubating at 4 °C overnight, protein A/G magnetic beads (Thermo Scientific, Shanghai, China) were added into the solution and incubated for another 2 h at 4 °C. Then, the beads were washed five times with PBST and the remaining products were extracted with TRIzol agent. In this project, rRNA was removed from the total RNA by ribosomal RNA removal kit, and the way of ion breaking were used to break the RNA into 200-300bp fragments. By using RNA as template, the first strand of cDNA was synthesized with 6 base random primers and reverse transcriptase. The first strand cDNA was used as the template to synthesize the second strand cDNA. When the second strand cDNA is synthesized, the base T is replaced by U to achieve the goal of a chain specific library. All of our RNA-seq projects used strand specific kits to construct the libraries. Finally, we show that mRNA different expression in AC16 cells. This study provides abundance of mRNA that may predict heart diseases.

first: Heng

last: Du


title: Transcriptome analysis of MazF6 overexpression in Mycobacterium tuberculosis

status: Public on Apr 01 2022

city: Bangalore

first: Munmun

last: Bhasin

state: Karnataka

address: CV Raman Rd

department: Molecular Biophysics Unit

country: India

institute: Indian Institute of Science

summary: We report the effects of MazF6 overexpression on Mycobacterium tuberculosis H37Rv strain. The total RNA was isolated from M. tuberculosis harboring either pTetR-int or pTetR-Int-mazF6 the expression was induced with 50 ng/ml anhydrotetracycline for 24 hrs.

overall_design: Experiments were repeated thrice for each overexpression strain.

first: Gopinath

last: Chattopadhyay

first: Shahbaz

last: Ahmed

first: Tannu

last: Gosain

first: Srivarshini

last: Ganesan

first: Sayan

last: Das

first: Chandrani

last: Thakur

first: Nagasuma

last: Chandra

first: Ramandeep

last: Singh

first: Raghavan

last: Varadarajan


title: Natural variation in phenotypic impact of Candida albicans cyclin gene HGC1

status: Public on Mar 21 2022

city: ATHENS

first: Aaron

last: Mitchell

state: GA

address: 120 EAST GREEN STREET

department: Microbiology

institute: University of Georgia

summary: Purpose: Studying the role of HGC1 in the strain variation among the clinical isolates of C.albicans

overall_design: Transcriptome of each hgc1 mutant vs. Transcriptome of the wild-type

first: Anupam

last: Sharma


title: Lack of xanthine dehydrogenase leads to a remarkable renal decline in a novel hypouricemic rat model

status: Public on Mar 17 2022

city: Tampa

first: Alexander

last: Starushchenko

address: 560 Channelside Dr

department: Molecular Pharmacology & Physiology

institute: University of South Florida, College of medicine

summary: The SSXdh-/- rat (SS-Xdhem1Mcwi, Rat Genome Database ID:14398479), created on the Dahl SS background, resulted in severe hypouricemia in the tissues. With the Xdh project, the overall hypothesis is that the Xdh gene ablation will result in kidney damage and perturbation of blood pressure control. We were interested in finding out if the gene ablation alternates the kidney development process. The deletion of Xdh protein produced dramatic changes in proteins related to the salvage pathway. The novel Xdh knockout rat model exhibited profound hypouricemia, which increased oxidative stress and crystal formation, leading to inflammation, renal cell proliferation, severe kidney damage, and a subsequent decline in renal function.

overall_design:
This study comprised of 3 conditions (homozygotes, heterozygotes, and wild-type littermates) with 4 replicates in each. The RNA was extracted from kidney cortex homogenates of the rats.
contributor: Genomic Sciences and Precision Medicine Center at the Medical College of Wisconsin

last: Staruschenko


title: Transcriptional effects of LXR on the differentiation of monocyte-derived macrophages by tumor ascitic fluids or rheumatoid arthritis synovial fluids

status: Public on Mar 16 2022

city: Madrid

first: Angel

last: Corbí

state: Madrid

address: Ramiro de Maeztu 9

department: Molecular Microbiology and Infection Biology

country: Spain

institute: Consejo Superior de Investigaciones Científicas

summary: Analysis of the role of LXR on the transcriptional signature of monocyte-derived macrophages generated in the presence of tumor ascitic fluids or rheumatoid arthritis synovial fluids.   Methods: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes from independent donors (0.5 x 106 cells/ml, >95% CD14+ cells) were treated with DMSO (vehicle), 1 micromolar GW3965 or 1 micromolar GSK2033 for 1 hour, and then cultured in RPMI 1640 10% FBS supplemented with either 50% Tumor-derived Ascitic Fluid (TAF) or 20% Synovial Fluid from patients with active Rheumatoid Arthritis (RASF), at 37°C in a humidified atmosphere with 5% CO2 and 21% O2. After 72 hours, cells were lysed and RNA isolated for transcriptional analysis.

overall_design: mRNA profiles of human monocyte-derived macrophages generated in the presence of tumor ascitic fluids or rheumatoid arthritis synovial fluids, and in the presence of LXR agonists or antagonists.

first: Arturo

last: González de la Aleja

first: Antonio

last: Castrillo

first: Miguel

last: Vega


title: Dedifferentiation of human adult Sertoli cells in cross talk with seminoma cells in vitro

status: Public on Mar 01 2022

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary: Germ cell neoplasia in situ (GCNIS) is the noninvasive precursor of testicular germ cell tumors type II   (TGCT), the most common cancer in young men. GCNIS originates from embryonic germ cells blocked in their maturation. The causes are unknown. GCNIS is associated with impaired Sertoli cells that   express fetal marker keratin 18 (KRT18) and pluripotency factor SOX2. According to the spread theory of the origin of GCNIS, these impaired Sertoli cells are prepubertal cells arrested in their maturation   due to genetic anomalies and/ or environmental anti-androgens. Thus, they are unable to support the development of germ cells, leading to their maturational block with further progression into GCNIS.   The alternative theory states that the impaired Sertoli cells are adult cells dedifferentiating secondarily due to the influence of GCNIS. To address this issue, we established a co-culture model of adult human   Sertoli cells (FS1) and a seminoma cell line similar to GCNIS (TCam-2). After 2 weeks of co-culture, FS1 cells showed progressive expression of KRT18 and SOX2. Interestingly, TCam-2 cells in co-culture   showed SOX2 expression and upregulation of further pluripotency- and reprogramming-associated genes (LEFTY1/2, GAL, DPPA5, NODAL, ZIC3, DND1, DPPA3, GDF3, BCAT1, JARID2, and DNMT3B),   suggesting a seminoma to embryonal carcinoma transition. Thus, our FS1/ TCam-2 co-culture model is a valuable tool to investigate interactions between Sertoli cells and tumor cells. Our studies of human   testicular biopsies with GCNIS further suggest that the impaired Sertoli cells associated to GCNIS represent adult cells undergoing progressive dedifferentiation.

overall_design: 4 independent samples each from 2 different cell types (FS1 and TCam2) kept either in monoculture or in co-culture (= total of 16 samples) hybridized on 16 microarrays.

first: Cornelia

last: Fink


title: Spatial transcriptomics of whole mouse lung cells

status: Public on Mar 02 2022

city: Nanjing

first: Chao

last: Jie

address: 87 Dingjiaqiao Rd

department: Department of Physiology

institute: Southeast University

summary: We report the distribution of mRNA in fibrotic lung sections on spatial trancriptomics sequencing.

overall_design: Examination of mouse lung samples of NS-7d, SiO2-7d, NS-7d, SiO2-56d

first: Mengling

last: Chen

first: Jie

last: Chao


title: Transcriptomic clustering of critically-ill COVID-19 patients [Day 1-miRNA-Seq]

status: Public on Feb 28 2022

city: Oviedo

first: Guillermo

middle: M

last: Albaiceta

address: Avenida de Roma s/n

institute: Instituto de Investigación Sanitaria del Principado de Asturias

summary: Infections caused by SARS-CoV-2 may cause a severe disease, termed COVID-19, with significant mortality. Host responses to this infection, mainly in terms of systemic inflammation, have emerged as key pathogenetic mechanisms, and their modulation is the only therapeutic strategy that has shown a mortality benefit. Herein, we used peripheral blood transcriptomes of critically-ill COVID-19 patients obtained at admission in an Intensive Care Unit, to identify two clusters that, in spite of no major clinical differences, have different gene expression profiles that reveal different underlying pathogenetic mechanisms and ultimately have different ICU outcome. A transcriptomic signature was used to identify these clusters in an external validation cohort, yielding a similar result. These results illustrate the potential of transcriptomic profiles to identify patient endotypes and point to relevant pathogenetic mechanisms in COVID-19.

overall_design: Data from 46 patients was analyzed. Serum microRNAs were sequenced and the corresponding RNA-miRNA pairs analyzed.

first: Laura

last: Amado-Rodríguez

first: Cecilia

last: López-Martínez

first: Inés

last: López-Alonso


title: RNA-seq data to study immune response to SARS-CoV-2 virus infection in COVID-19 Health Action Response for Marines (CHARM) study

status: Public on Mar 25 2022

city: New York

first: Yongchao

last: Ge

state: NY

address: One Gustave L Levy Place #1137

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

summary: RNA-seq data from blood from participants of the COVID-19 Health Action Response for Marines (CHARM) study was generated to study innate immune responses to SARS-CoV-2 infection. We investigate 1. gene expression difference between symptomatic and asymptomatic participants, 2. gene expression difference between male and female participants, 3. how the gene expression and methylation are correlated, 4. change in alternative splicing.

overall_design: RNA sequencing was performed on samples collected from 475 subjects at different time points as part of SARS-Cov-2 of initial outbreak and later surveillance on the Marine recruits. 1605 samples were sequenced, and some samples were sequenced in duplicates. In total, there are 1858 RNA-seq data sets in this submission.

first: Venugopalan

last: Nair

first: Mary

last: Amper

first: Mital

last: Vasoya

first: Nitish

last: Seenarine

first: Kristy

last: Guevara

first: Natalie

last: Sauerwald

first: Weigang

last: Mao

first: Zijun

last: Zhang

first: Irene

last: Ramos

first: Andrew

middle: G

last: Letizia

first: Stuart

last: Sealfon


title: Cell-type-specific whole-genome landscape of ΔFOSB binding in nucleus accumbens after chronic cocaine exposure

status: Public on Jul 08 2022

first: Eric

middle: J.

last: Nestler

address: 1425 Madison Ave L10-26

summary:
Background
The ability of neurons to respond to external stimuli involves adaptations of gene expression. Induction of the transcription factor, ΔFOSB, in the nucleus accumbens (NAc), a key brain reward region, is important for the development of drug addiction. However, a comprehensive map of ΔFOSB’s gene targets has not yet been generated.

Methods
We use CUT&RUN to map the genome-wide changes in ΔFOSB binding in the two main types of NAc neurons—D1 or D2 medium spiny neurons (MSNs)—after chronic cocaine exposure. To annotate genomic regions of ΔFOSB binding sites, we also examined the distributions of several histone modifications. Resulting datasets were leveraged for multiple bioinformatic analyses.

Results
The majority of ΔFOSB peaks occur outside of promoter regions, including intergenic regions, and are surrounded by epigenetic marks indicative of active enhancers. BRG1, the core subunit of the SWI/SNF chromatin remodeling complex, overlaps with ΔFOSB peaks, consistent with earlier studies of ΔFOSB’s interacting proteins. Chronic cocaine induces broad changes in ΔFOSB binding in both D1 and D2 NAc MSNs of male and female mice. In addition, in silico analyses predict that ΔFOSB cooperatively regulates gene expression with homeobox and T-box transcription factors.

Conclusions
These novel findings uncover key elements of ΔFOSB’s molecular mechanisms in transcriptional regulation at baseline and in response to chronic cocaine exposure. Further characterization of ΔFOSB’s collaborative transcriptional and chromatin partners specifically in D1 and in D2 MSNs will reveal a broader picture of the function of ΔFOSB and the molecular basis of drug addiction.

overall_design: Examination of ∆FOSB binding sites, BRG1 coverage, and 4 different histone modifications in nucleus accumbens D1- and D2-type medium spiny neurons after animal received chronic cocaine administration.

middle: J

first: Szu-Ying

last: Yeh


title: Characterization of chromatin accessibility changes in retinal ganglion cells (RGCs) following optic nerve crush

status: Public on May 06 2022

city: Los Angeles

first: Yuyan

last: Cheng

address: 695 Charles E Young Dr S Rm 2305

institute: UCLA

summary: In this study, we profiled epigenetic and transcriptional landscapes in injured RGCs to identify transcription factors driving critical chromatin state and gene expression changes in reponse to injury.

overall_design: We generated ATAC-seq and RNA-seq data on mouse RGCs at 0,1,3 days following optic nerve injury, with 3-6 replicates in each condition.

first: Feng

last: Tian

first: Daniel

last: Geschwind

first: Zhigang

last: He


title: HOTTIP reinforces CTCF-defined TAD boundaries by forming R-loops to drive Wnt/b-catenin target gene expression in AML leukemogenesis

status: Public on Feb 18 2022

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

summary: HOTTIP lncRNA is highly expressed in acute myeloid leukemia (AML) patients carrying MLL rearrangement and NPM1c+ mutations, and positively correlates with poor patient survival by facilitating formation of leukemic-specific topologically associated domains (TADs) to drive leukemic transcription program. However, the direct mechanism through which HOTTIP accesses and regulates leukemic genome topology remains unknown. Here, we showed that HOTTIP directly interacts and regulates a fraction of CTCF binding sites (CBSs) including key WNT/b-catenin target loci in the AML genome by forming R-loop structure that reinforces the CTCF boundary, WNT/b-catenin TADs and gene transcription. Importantly, either deleting CBSs or targeting RNaseH to eliminate R-loop structure in boundaries of the Wnt/b-catenin TADs resulted in inhibited Wnt target promoter interactomes and Wnt target expression, and mitigation of leukemogenesis of PDX mouse models with aberrant HOTTIP expression. Thus, HOTTIP reinforces CTCF-defined TAD boundaries by forming R-loops to drive Wnt/b-catenin aberration and pathogenesis of MLL-rearranged/NPM1c+ AML.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We have finished the RNA-SEQ, ATAC-seq, ChIP-seq, DRIP-seq, DRIPc-seq, NG-Capture-C and single cell RNA-seq and scATAC-seq for WT and HOTTIP-KO MOLM13 leukemia cells and Hottip Transgenic mice cells. LK cells (Lin- Kit+) and LSK cells (Lin- Sca1+ Kit+) were sorted by FACS from the bone marrow of  WT and Hottip transgenic mice for RNA-seq, ATAC-seq and single cell-RNA seq and scATAC-seq assay

first: Suming

last: Huang


title: Transcriptomic clustering of critically-ill COVID-19 patients [Day 1-RNA-Seq]

first: Guillermo

last: Albaiceta

overall_design: Data from 56 patients was analyzed. Using peripheral blood transcriptomes, two different groups were identified by hyerarchical clustering.

first: Laura

last: Amado-Rodríguez

first: Cecilia

last: López-Martínez

first: Inés

last: López-Alonso


title: Non-invasive tape-stripping of psoriatic skin with high-resolution RNA profiling

status: Public on Jan 20 2022

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

summary: The objective of this study was to provide a comprehensive evaluation of how well tape-stripping paired with high resolution RNA-sequencing captures the global transcriptomic changes in psoriasis.

overall_design: Tape stripping is a minimally invasive, non-scarring method that can be utilized to assess gene expression in skin but is infrequently used given technical constraints.  By comparing different tape stripping technologies and full thickness skin biopsy results of lesional and non-lesional psoriatic skin from the same patients, we demonstrate that tape stripping with optimized high-resolution transcriptomic profiling can be used to effectively assess and characterize inflammatory responses in skin.

first: Johann

middle: E

last: Gudjonsson


title: KMT2C/KMT2D (MLL3/MLL4) Histone Methyltranferase Activity Dependent Chromatin Organization at Enhancers during Embryonic Stem Cell Differentiation [RNA-seq]

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

summary: PLAC-seq, mRNA-seq, and ChIP-seq experiments in mouse embryonic stem cells and neural progenitor cells in the presence or absence of  Mll3/4 catalytic activity.

overall_design: mRNA-seq experiments in mouse embryonic stem cells and neural progenitor cells in the presence or absence of  Mll3/4 catalytic activity.

first: Naoki

last: Kubo


title: Integration of Epigenetic and Transcriptomic Signature reveals Key Transcription Factors involving in Renal Tubular Response to extracellular Stimuli

status: Public on Jan 01 2022

first: Yuexian

last: Xing

state: Jiangsu

address: Zhongshan Road No.305

institute: Jinling Hospital

summary: To understand the transcription regulation of renal tubular epithelial cells under stimuli, here we investigated transcriptome, chromatin accessibility and their dynamics through RNA-seq and ATAC-seq under the three types of treatments. We identified genome-wide functional regions which coordinated transcription regulation in human renal proximal tubule epithelial cells (HK2). Our results provide a cell type-specific landscape of chromatin dynamics under stimuli and discovered an important TF in renal tubular epithelial cells that mediated genomic response to different injury stimuli.

overall_design: HK2 cells  treated with DMEM/F12, DMSO, H2O2, TGF-B1 and FG4592 were subjected to ATAC-seq and RNA-seq.

first: Jingping

last: Yang


title: Laminar shear stress regulated gene expression in HUVECs

status: Public on Apr 07 2022

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: To identify genes whose expression is regulated by laminar flow in HUVECs.

overall_design:
HUVECs were subjected to laminar shear stress (12 dynes/cm2) or were kept under static conditions for 48 hours. Then total RNA was isolated from HUVECs and RNA-sequencing was performed.

**NOTE: PMID 35443807 incorrectly quoted GSE167024. GSE236871 is the dataset described in this publication**

first: Guozheng

last: Liang

first: Lei

last: Wang

last: Guenther


title: Identification and targeting of the developmental blockade in extranodal natural killer/T cell lymphoma [850K/EPIC DNA methylation]

status: Public on Jan 12 2022

city: Columbus

first: Christopher

last: OAKES

state: OH

address: 400 W. 12th Avenue, Wiseman Hall, Suite 455

institute: The Ohio State University

type: Methylation profiling by genome tiling array

summary: Extranodal natural killer/T cell lymphoma (ENKTL) is an aggressive, rare lymphoma of natural killer (NK) cell origin with very poor clinical outcomes and no effective targeted therapies. Improved understanding of the underlying biology of the disease is critical to design more effective treatment. Here we used phenotypic and molecular profiling including epigenetic analyses to investigate how ENKTL ontogeny relates to normal NK cell development. We demonstrate that neoplastic NK cells are stably but reversibly arrested at earlier stages of NK cell maturation. Genes downregulated in the tumors that demonstrated the most epigenetic immaturity were associated with polycomb silencing along with genomic gain and overexpression of EZH2. ENKTL cells exhibited a remarkable degree of genome-wide DNA hypermethylation. Tumor-specific DNA methylation gains were associated with polycomb-marked regions, involved the silencing of hundreds of genes (many involved in NK cell development), and loss of transcription factor binding. To investigate therapeutic targeting of the epigenetic developmental blockade, we treated novel PDX models of ENKTL with the DNA hypomethylating agent, 5-azacytidine. Treatment led to reduction of DNA methylation, re-expression of NK cell developmental genes, phenotypic NK cell differentiation, and prolongation of survival. These studies lay the foundation for epigenetic-directed therapy targeting the developmental blockade in ENKTL.

overall_design: Illumina 850K/EPIC DNA methylation was performed on 46 ENKTL tumor samples from derived from FFPE blocks.  From fresh/frozen cells we analyzed 24 samples from HSPC and NK developmental stages, 5 ENKTL ,3 NKLGL, and 26 samples derived from ENKTL PDX mice.

last: Oakes


title: Acute GenX exposure induces spinal deformations and arrhythmia, and alters expression of genes involved in cardiac, vascular, neural, and visual systems during zebrafish (Danio rerio) early development

status: Public on Mar 22 2022

city: San Diego

first: Goran

last: Bozinovic

address: 3030 Bunker Hill St

institute: Boz Life Science Research and Teaching Institute

summary: This study assessed the potential for GenX exposure to exert adverse effects during early development of zebrafish using morphological and physiological assessments, and further performed gene expression analysis on sublethal exposures to evaluate the underlying toxicogenomics. Zebrafish embryos exposed to GenX concentrations of 0.5 – 20000 mg/L were assessed at 24, 48, and 72 hours post-fertilization (hpf) for morphology, physiology, and survival.  Shallow RNA-sequencing analysis of 9465 transcripts identified 38 genes that were consistently differentially expressed at 0.5, 1, 2, and 10 mg/L GenX exposures (compared to control at 72 hpf). Downregulated genes are associated with neurotransmission (6 genes) and visual response (10 genes), and upregulated genes are expressed in or regulate the cardiovascular system (7 genes). Our results suggest acute adverse effects by the alternative PFAS, GenX, in early zebrafish development by altering expression of genes involved in or regulating the heart and vascular tissue, neurotransmission, and visual response.

overall_design: Examination of effects on GenX on zebrafish embryos.

first: Sylvia

last: Gong

first: Flannery

last: McLamb

first: Damian

last: Shea

first: Jeanne

middle: P

last: Vu

first: Miguel

middle: F

last: Vasquez

first: Zuying

last: Feng

first: Kesten

first: Ken

last: Hirata

first: Richard

last: Gersberg


title: Identification and targeting of the developmental blockade in extranodal natural killer/T cell lymphoma

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

overall_design: Refer to individual Series


title: Expression data from MZ Twins discordant for concussion

status: Public on Dec 31 2021

city: Rochester

first: Tyler

last: Stahl

address: 265 Crittenden Blvd, Box 655c

institute: University of Rochester

summary:
Researchers have long relied on gene expression changes identified in animal models to develop targeted therapy for traumatic brain injury (TBI), but so far these therapies have not proved effective in human trials. While these pre-clinical models have provided valuable mechanistic insights, they might not reflect the unique pathophysiology of concussion in humans. Identifying important and potentially modifiable gene expression changes in humans diagnosed with TBI can help facilitate effective therapies.
The objective of the current study was to identify important and potentially novel differences in mRNA expression among this single pair of MZ twins discordant for sport-related concussion (SRC).

overall_design: 19-year-old female MZ twins had baseline (T0) preseason peripheral blood drawn. One twin sustained an SRC, afterwards both twins had peripheral blood drawn at 6 hours (T1) and 7 days post-injury (T2). Cognitive performance and postural stability were assessed at T0, at 3-days post-injury, and at T2.

first: Jessica

last: Gill

first: Elizabeth

last: Sainoz

first: Kian

last: Merchant-Borna

first: Jeffery

last: Bazarian


title: Characterization of cis-regulatory elements of effector ISGs

status: Public on Apr 01 2022

city: Debrecen

first: Lajos

last: Széles

address: Egyetem tér 1.

country: Hungary

institute: University of Debrecen

summary: We investigated the transcriptional activation and cis-regulatory elements of effector ISGs in CD8+ murine dendritic cells (DCs) stimulated with IFN-beta. We analysed gene repression changes and characterized activated cis-regulatory regions. Binding of ISGF3 subunits (IRF9, Stat1, and Stat2) and other transcription factors, DNA motifs, and chromatin status were also determined.

overall_design: PRJNA706415, CD8-positive dendritic cells were left stimulated with 5 μg/ml poly(I:C) HMW or 1 mM class B CpG oligonucleotide 1826 (CpG)  or 10U IFN-beta for 90 min.

first: Mária

last: Csumita

first: Loránd

last: Göczi


title: An RNA sequencing data set revealing differentially expressed transcripts during ε-poly-L-lysine production in Streptomyces albulus.

status: Public on Jan 19 2022

city: Suita

first: Kazuya

last: Yamanaka

state: Osaka

address: 3-3-35 Yamate-cho

institute: Kansai University

summary:
Purpose: Streptomyces albulus is an industrial producer of ε-poly-L-lysine, an antimicrobial cationic homo poly-amino acid used practically as a natural food preservative. Here, we present RNA sequencing data set unveiling differentially expressed transcripts during ε-poly-L-lysine production in the most extensively studied poly-L-Lys producer, S. albulus NBRC14147.
Methods: During the poly-L-Lys fermentation, cells grown for 8 hours and 35 hours were harvested as growth phase cells and production phase cells, respectively, and total RNA were extracted individually. A 100-bp paired-end mRNA sequencing was performed for each sample on the Illumina HiSeq 2500 system.
Result: Using an optimized data analysis workflow, we were able to map more than 44 million sequence reads per sample to the reference genome (GenBank accession number ASM385166v1). Differential gene expression analysis was performed using the edgeR. The RNA-seq data revealed that a total of 2449 genes were considered to be differentially expressed during poly-L-Lys production using a fold change cutoff of log2 less than -1 and greater than 1 (equivalent to a ±2-fold change).
Conclusion: Our data will serve as a primary source for investigating the regulatory mechanism which govern poly-L-Lys production in S. albulus NBRC14147.

overall_design: mRNA profiles of growth phase and production phase cells.

first: Tadao

last: Oikawa

first: Yoshimitsu

last: Hamano


title: Drug resistance profiling of thousands of Src kinase mutants uncovers a regulatory network that couples autoinhibition to catalytic domain dynamics

status: Public on Dec 17 2021

city: Seattle

first: Douglas

last: Fowler

state: WA

address: 3720 15th Ave NE, Foege Building, S041

department: Genome Sciences

institute: University of Washington

summary: Protein kinase inhibitors are effective cancer therapies, but acquired resistance often limits clinical efficacy. Despite the cataloguing of numerous resistance mutations with model studies and in the clinic, we still lack a comprehensive understanding of kinase inhibitor resistance. Here, we measured the resistance of thousands of Src tyrosine kinase mutants to a panel of ATP-competitive inhibitors. We found that ATP-competitive inhibitor resistance mutations are distributed throughout Src’s catalytic domain. In addition to inhibitor contact residues, residues that participate in regulating Src’s phosphotransferase activity were prone to the development of resistance. Unexpectedly, a resistance-prone cluster of residues that are on the top face of the N-terminal lobe of the catalytic domain contributes to Src autoinhibition by reducing the dynamics of the catalytic domain, and mutations in this cluster led to resistance by lowering inhibitor affinity and promoting kinase hyperactivation. Together, our studies demonstrate how comprehensive profiling of drug resistance can be used to understand potential resistance pathways and uncover new mechanisms of kinase regulation.

sample_organism:
Escherichia coli
Saccharomyces cerevisiae

overall_design: A barcoded plasmid library of Src variants was expressed in S. cerevisiae, treated with different Src kinase inhibitors, and timepoints were sampled throughout growth. Plasmids were extracted and barcodes amplified and counted with Illumina sequencing. Barcodes were related back to their cognate variant using barcode-variant map.

first: Dustin

last: Maly


title: Lactate regulation of activation in CD8+ T cells

status: Public on Dec 15 2021

city: Cambridge

first: David

last: Bargiela

address: 4, 7 Downing Pl

institute: University of Cambridge

summary:
CD8+ T cells infiltrate virtually every tissue to find and destroy infected or mutated cells. They often traverse varying oxygen levels and nutrient-deprived microenvironments. High glycolytic activity in tissues can result in extended exposure of cytotoxic T cells to the metabolite lactate. Lactate can be immunosuppressive, at least in part due to its association with tissue acidosis. We show here that the lactate anion is well tolerated by CD8+ T cells in pH neutral conditions. We describe how lactate is taken up by activated CD8+ T cells and is capable of displacing glucose as a carbon source. Activation in the presence of a pH neutral form of lactate significantly alters the CD8+ T cell transcriptome, including the expression of key effector differentiation markers such as granzyme B and interferon-gamma. Our studies reveal the novel metabolic features of lactate utilization by activated CD8+ T cells, and highlight the importance of lactate in shaping the differentiation and activity of cytotoxic T cells.
Method: CD8+ T cells were purified from mouse splenocytes and activated for 72h with anti-CD3/CD28 dynabeads (Thermo Fisher, 11456D) and 10 U/ml recombinant human IL-2, in either plain media (RPMI 1640 supplemented with 10% Fetal Bovine Serum, 50 µM 2-mercaptoethanol, and 100 U/ml penicillin-streptomycin), or in the presence of 40 mM sodium lactate. After activation, cells were washed twice with PBS and cell pellets were snap-frozen in RLT Plus lysis buffer (Qiagen, #1053393). Total RNA was extracted with the Qiagen’s RNeasy kit according to the manufacturer's instructions. All samples were quality checked with Agilent Tapestation RNA screen tape. To construct libraries suitable for Illumina sequencing, the Illumina TruSeq Stranded mRNA Sample preparation protocol which includes cDNA synthesis, ligation of adapters, and amplification of indexed libraries was used. The yield and quality of the amplified libraries were analysed using Qubit by Thermo Fisher and the Agilent Tapestation. The indexed cDNA libraries were normalised and combined, and the pools were sequenced on the Nextseq 550 for a 50-cycle v2.5 sequencing run, generating 71 bp single-end reads (and 2*10 bp index reads). Fastq files were generated by demultiplexing with bcl2fastq (v2.20.0.422). STAR 2.7.5b was used to map the fastq files to the mouse reference genome (mm10/GRCm38) and to remove PCR duplicates. Uniquely mapped reads were counted in annotated exons using featureCounts v1.5.1. The gene annotations (Mus_musculus.GRCm38.99.gtf) and reference genome were obtained from Ensembl. The count table from featureCounts was imported into R/Bioconductor and differential gene expression was performed using the EdgeR package and its general linear models pipeline.

overall_design: A total of 12 samples (n = 4 naive, n = 4  media, n = 4 NaLac) were used for differential gene expression analysis of sodium lactate- relative to media-treated cells. These include: non-activated (naïve) CD8+ T cells, isolated from 4 distinct mouse donors (A,B C, and D); activated CD8+ T cells, isolated from 5 independent mouse donors and treated with either plain media or 40 mM sodium lactate (NaLac) during 72h of activation with IL-2 and anti-CD3/CD28 dynabeads. Naive cells were used a control for activation. Activated, media-treated, cells were used as a control for the treatment with NaLac. All samples had high RINs (RNA integrity number) and passed the QC for library prepariton and sequencing on Nextseq 550. Differential gene expression analysis comparing NaLac- and media-treated samples was performed with EdgeR and its general linear models pipeline.

first: Laura

last: Barbieri

first: Pedro

last: Velica

first: Paulo

last: Gameiro

last: Cunha

first: Iosifina

last: Foskolou

first: Helene

last: Rundqvist

first: Randall

middle: S

last: Johnson


title: A Congenital Anemia Dissociates the Pleiotropic Functions of Master Transcription Factor GATA1

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering


title: Comprehensive epigenomic profiling of human alveolar epithelial differentiation identifies key epigenetic states and transcription factor co-regulatory networks for maintenance of distal lung identity

status: Public on Oct 27 2021

city: Duarte

first: Crystal

middle: N

last: Marconett

email: cmarcone@usc.edu, cmarconett@coh.org

state: CA

address: 1500 E Duarte Rd

department: Integrative Translational Sciences

institute: City of Hope

type: Methylation profiling by high throughput sequencing

summary: Background: Disruption of alveolar epithelial cell (AEC) differentiation is implicated in implicated in distal lung diseases such as chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, and lung adenocarcinoma that impact morbidity and mortality worldwide. Elucidating underlying disease pathogenesis requires a mechanistic molecular understanding of AEC differentiation. Previous studies have focused on changes of individual transcription factors, and to date no study has comprehensively characterized the dynamic, global epigenomic alterations that facilitate this critical differentiation process in humans. We comprehensively profiled the epigenomic states of human AECs during type 2 to type 1-like cell differentiation, including the methylome and chromatin functional domains, and integrated this with transcriptome-wide RNA expression data.  Enhancer regions were drastically altered during AEC differentiation. Transcription factor binding analysis within enhancer regions revealed diverse interactive networks with enrichment for many transcription factors, including NKX2-1 and FOXA family members, as well as transcription factors with less well characterized roles in AEC differentiation, such as members of the MEF2, TEAD, and AP1 families. Additionally, associations among transcription factors changed during differentiation, implicating a complex network of heterotrimeric complex switching in driving differentiation. Integration of AEC enhancer states with the catalog of enhancer elements in the Roadmap Epigenomics Mapping Consortium and Encyclopedia of DNA Elements (ENCODE) revealed that AECs have similar epigenomic structures to other profiled epithelial cell types, including human mammary epithelial cells (HMECs), with NKX2-1 serving as a distinguishing feature of distal lung differentiation. Enhancer regions are hotspots of epigenomic alteration that regulate AEC differentiation. Furthermore, the differentiation process is regulated by dynamic networks of transcription factors acting in concert, rather than individually. These findings provide a roadmap for understanding the relationship between disruption of the epigenetic state during AEC differentiation and development of lung diseases that may be therapeutically amenable.

overall_design: RNA was isolated from 1 million cells for each timepoint using the GE triplePrep kit. RiboZero depletion was used as well as DNaseI to ensure RNA quality prior to library preparation. Library preparation was performed at the USC Epigenome Core. Barcodes used for multiplexed sequencing are indicated in the filename for each sample. Reads underwent paired-end sequencing and were aligned back to the hg19 genome. DNA was isolated from the same cells as RNA using the GE triplePrep kit. DNA underwent bisulfite treatment and sequencing at the USC Epigenome Core. Reads were mapped back to the bisulfite hg19 genome. BisSNP was used for SNP calling and generation of methylation calls. MethylSeekR was used for methylation domain calling. Chromatin immunoprecipitation was performed using antibodies against H3K27ac (Cat # 39133, Active Motif, Carlsbad CA), H3K4me1 (pAb-037-050, Diagenode, Denville NJ), CTCF (Cat #2899, Cell Signaling, Danvers MA), H3K27me3 (#07-449) and H3K9/14Ac (#06-599) from Millipore (Burlington, MA) and the Imprint Ultra Chromatin Immunoprecipitation Kit (Sigma-Aldrich, St Louis MO). Enrichment was verified at the previously identified GRAMD2 enhancer region prior to Next-generation sequencing library construction. Human GRAMD2 enhancer primer sequence: Forward 5’-GGT CTC CTG ATT TCC TGA TG -3’, Reverse 5’-AGG CTG ACT TCT CAC TAT TC-3’. FAIRE libraries were generated from the histone-depleted supernatants. Free DNA was isolated using an established protocol. Samples underwent library preparation and single end (SE) 50-cycle DNA sequencing using an Illumina HiSeq2000 (Illumina, San Diego CA) at the USC Epigenome Center (USC, Los Angeles CA).

first: Beiyun

last: Zhou

first: Theresa

middle: R

last: Stueve

first: Evan

last: Mihalakakous

first: Lin

last: Miao

first: Daniel

last: Mullen

first: Yinchong

last: Wang

first: Yixin

last: Liu

first: Jiao

last: Luo

first: Evelyn

last: Tran

first: Kimberly

middle: D

last: Siegmund

first: Sean

middle: K

last: Lynch

first: Amy

last: Ryan

first: Ite

last: Offringa

first: Zea

last: Borok


title: Mll3/Mll4 catalytic activity is necessary for de novo enhancer-promoter contacts during embryonic stem cell differentiation

first: Bing

last: Ren


title: Lactobacillus enrichment and its association with gene expression in ER negative breast tumor tissue

status: Public on Oct 08 2021

city: Shanghai

first: Enuo

address: 2140 Xietu Road

institute: Shanghai Institute for Biomedical and Pharmaceutical Technologies

summary: ER+ patients are treated with hormone inhibitors combined with radiotherapy and chemotherapy, while ER- patients especially triple negative breast cancer, there are few treatment options other than radiotherapy and chemotherapy. However, there are no reports on the analysis of microbiome and its association with cancer development.

overall_design: Sections of formalin-fixed paraffin embedded (FFPE) were prepared from breast tumors of 33 patients. FFPE samples of patients with ER+, which is determined by immunohistochemistry method, were subjected to microarray analysis to identify gene expression profiles.

first: Fan

last: Zhang

first: Tiansheng

last: Xu

first: Luyi

last: Ye

last: Qian Ma

first: Zai-Si

last: Ji


title: Next generation RNA sequencing of Aβ-treated primary cultured mouse astrocytes to study the effect of ODC1 inhibition on AD-like astrocytes

status: Public on Oct 16 2021

city: Daejeon

first: C Justin

last: Lee

address: 55, Expo-ro, Doryong-dong, Yuseong-gu

department: Center for Cognition and Sociality

institute: Institute for Basic Science

summary:
Purpose: The existence and role of the urea cycle has not been well studied in the astrocytes of Alzheimer's Disease (AD). In the past, ODC1-inhibitor DFMO (Diflouromethylornithine) has been shown to have a neuroprotective effect on AD-like pathology, but the biochemical mechanism of this effect remains largely unknown. In this study, we aim to compare the transcriptome of naive and Aβ-treated astrocytes and further study the effect of DFMO treatment in Aβ-treatment condition.
Methods: Primary astrocyte culture (from P0-P1 mouse pups) mRNA profiles were generated by high-throughput NGS in 3 treatment conditions in duplicate using HiSeq 2500. Sequence reads were analysed using Partek Genomics Suite, aligned using STAR and then quantified to the mouse genome assembly (mm10 Ensemble transcripts release 99), following which they were normalised to median ratio values and differentially analysed using the DeSeq2 algorithm. Finally, pathway analysis was carried out to study  the differential expression of biomolecular pathways, with reference to the KEGG database.
Results: Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the mouse genome (build mm10) and identified 18783 genes in the dataset. Differential analysis revealed upregulation of autophagy-related genes as well as switching-on of the genes involved in the cyclic metabolism of urea on Aβ treatment of astrocytes. ODC1 inhibition by DFMO induced upregulation of genes involved in the non-amyloidogenic processing of APP and downregulation of amyloidogenic genes. Pathway analysis revealed upregulation of urea cycle and urea metabolic process pathways, as well as selective autophagy and phagosome-lysosome fusion on Aβ treatment.
Conclusions: Our study represents the first detailed analysis of mouse astrocyte culture transcriptome on Aβ-treatment, and the effect of ODC1 inhibition on the same, with biological replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. From our results, we can conclude that the urea cycle is turned on in Alzheimer's Disease (AD)-like condition and that ODC1-inhibition can be a suitable therapeutic strategy to reduce the Aβ load in AD.

overall_design: RNA-seq of astrocytes untreated or treated with Aβ or Aβ with DFMO

first: Yeonha

last: Ju

first: Mridula

last: Bhalla

first: C


title: Chromatin accessibility profile of Tfh cells during intestinal helminth infection

status: Public on Oct 20 2021

city: CLAYTON

first: Aidil

last: Zaini

state: VICTORIA

address: LEVEL 3, BUILDING 77, MONASH UNIVERSITY

department: BIOCHEMISTRY AND MOLECULAR BIOLOGY

institute: MONASH UNIVERSITY

summary: The goal of this study was to define the regulation of Tfh cell response during intestinal helminth infection. Using the helminth Trichuris muris, we performed ATAC-seq analysis  on Tfh cells that develop during acute vs chronic helminth infection. We found that the epigenetic profile of acute vs chronic induced Tfh cells are distinct by adopting Th2 and Th1 cell phenotypes, respectively. For example, Th2-associated genes such as the Il4 locus was more accessible in acute-induced Tfh cells (and vice versa for Th1-associated genes in chronic-induced Tfh cells).

overall_design: Mice were infected with acute (high dose, HD) and chronic (low dose, LD) Trichuris muris. At d21 post infection, messentric lymph node (mLN)-derived Tfh cells (CD4+ CD44hi FOXP3- Ly6C- CD162- PD-1+ CXCR5+), as well as naive Th cells (CD4+ FOXP3- CD44lo CD62Lhi ) from uninfected mice were sorted and purified, followed by DNA extraction and ATAC-seq analysis. 2 replicates were included for each group (acute & chronic Tfh cells, as well as naive CD4 T cells).

first: Kirill

last: Tsyganov

first: Deanna

last: Lucas