title: Gene expression of THP-1 macrophages co-cultured with F. nucleatum under iron-deficient and iron-overload conditions

city: Kumamoto

first: Taishi

last: Yamane

address: 1-1-1 Honjo

institute: 1.	Department of Cell Signaling and Metabolic Medicine, Faculty of Life Sciences, Kumamoto University

summary: Fusobacterium nucleatum (F. nucleatum) contributes to the development of colorectal cancer (CRC) by inducing chronic inflammation. We found that iron deposition in macrophages is associated with poor prognosis of CRC patients with high amount of F. nucleatum. To explore the impact of iron on macrophage properties in the presence of F. nucleatum, we conducted RNA sequencing of THP-1 macrophages pretreated with ferric anmonium citrate (FAC) or deferoxamine (DFO), followed by treatment with F. nucleatum. Several chemokine genes were differentially increased in FAC-treated cells when compared with DFO-treated cells, suggesting that iron is required for the efficient induction of tumor-promoting chemokines in macrophages upon F. nucleatum infection. Our results suggest a prognostic role for iron in F. nucleatum-positive CRC.

overall_design: RNA sequenscing of THP-1 macrophages pretreated with ferric anmonium citrate (FAC) or deferoxamine (DFO), followed by treatment with Fusobacterium nucleatum

first: Yohei

last: Kanamori

first: Shingo

last: Usuki

first: Toshiro

last: Moroishi


title: Gene profiling of endometrial cancer cells transfected with tRF-20-S998LO9D mimics or negative control

status: Public on Jul 23 2022

city: Nanjing

first: Shanliang

last: Zhong

address: Baiziting 42

country: China

institute: The Affiliated Cancer Hospital of Nanjing Medical University

type: Expression profiling by high throughput sequencing

summary: To identify the downstream genes of tRF-20-S998LO9D, we transfected HEC-1-A and RL-95-2 cells with tRF-20-S998LO9D mimics or negative control of mimics, and send the cells for RNA-Seq. Differentially expressed tsRNAs were identified using DESeq2.

overall_design: The gene expression in endometrial cancer cells transfected with tRF-20-S998LO9D mimics was compared to those transfected with negative control of mimics.


title: ADAR1-mediated RNA editing promotes hepatacellular carcinoma (HCC) stemness by mitophagy activation

city: Hong Kong

first: Jie

last: Luo

address: 21 Sassoon Road, Pokfulam, Hong Kong

department: Clinical Oncology

country: Hong Kong

institute: Li Ka Shing Faculty of Medicine, The University of Hong Kong

summary:
To investigate the role of ADAR1in HCC development and stemness maintenance, we established  HCC cell lines in which ADAR1 has been knocked down by shRNA or overexpressed.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 8 different cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PLC8024 and SUN-878 cells and their KD derivative (sh2ADAR1), or SNU-449 and SNU-878 cells and their OE derivative ( ADAR1p110)

first: Xin-Yuan

last: Guan


title: Ectopic expression of Ino80 complex subunit Actr5 in mouse heart

status: Public on Jul 24 2022

city: Wakayama

first: Tsuyoshi

last: Morita

address: Mikazura 580

department: Department of Biology

country: Japan

institute: Wakayama Medical University

summary: Actr5 is one of the subunits of the ATPase-dependent chromatin remodeling complex INO80. In muscle tissues such as skeletal muscle, heart, and aorta, the expression of Actr5 is much lower than that in non-muscle tissues. During skeletal and smooth muscle development, it interacts with transcription factors such as MyoD, MyoG, SRF, and myocardin to play a repressive role in muscle differentiation, but its physiological role in cardiac development is not entirely clear. To investigate the role of Actr5 in the heart, AAV6 expression vectors containing Actr5 gene were infected into mice, and total RNA were extracted from the heart, followed by DNA microarray analysis.

overall_design: Three-week-old mice were injected intraperitoneally with the Actr5-AAV6 vector. As a control, empty AAV6 vector was injected. Three weeks after injection, hearts were harvested and RNA was extracted from them.

first: Ken'ichiro

last: Hayashi


title: Gene expression profile of oligodendrocyte lineage cells isolated from lateral striatum 2 weeks after transient middle cerebral artery occlusion (MCAO) in postnatal day 10 (p10) mice

status: Public on Jul 14 2022

city: Aurora

first: ANDRA

last: DINGMAN

state: CO

department: Pediatrics

country: USA

institute: University of Colorado Anschutz Medical Campus

summary: Oligodendrocytes are key to normal developmental myelination after birth, and for myelin repair.  We used scRNA seq to evaluate gene expresison changes in oligodendrocytes in a mouse model of full term neoanatl arterial ischemic stroke.

overall_design: Male C57/BL6 Mice underwent 60 minutes of MCAO on p10, followed by 2 weeks of reperfusion.  Oligodendrocyte lineage cells were isolated from lateral striatum using FACS sorting for cells expresing A2B5 and/or O4 surface antigens.

first: Andra

last: Dingman

first: Katherine

last: Given


title: Gene expression of peripheral blood in healthy, moderate asthma, and severe asthma patients from the IMSA cohort

status: Public on Jul 11 2022

city: Boston

first: Scott

last: Ginebaugh

state: Massachusetts

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

summary: Identification and characterization of gene expression using Next Generation Sequencing (NGS) of mRNA sequence from whole peripheral blood obtained from asthma patients with varying clinical disease severity

first: Matt

last: Camiolo

first: Sally

last: Wenzel

first: Anuradha

last: Ray


status: Public on Aug 15 2022

city: Shenyang

first: li

last: bingwu

address: shenhe

institute: Shenyang Pharmaceutical University

summary: Autophagy-overactivated composite microbe engineered from oncolytic adenoviruses for the cascade enhancement of cancer immunotherapy

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq. Comparative gene expression profiling analysis of RNA-seq data for OMVs@P2O-Ads treated cell derived xenograft and PBS treated cell derived xenograft

first: Bingwu

last: Li

first: Wanxu

last: Huang


title: Downregulation of iNOS/NO Promotes Epithelial-Mesenchymal Transition and Metastasis in Colorectal Cancer

status: Public on Jul 13 2022

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: Metastasis is the major cause of cancer-related death in patients with colorectal cancer. Although inducible nitric oxide synthase (iNOS) is a crucial regulator of cancer development and progression, its roles in epithelial-mesenchymal transition (EMT) and the pathogenesis of metastatic colorectal cancer have not been fully investigated. Primary colorectal cancer and liver metastatic tissue specimens were analyzed showing 90% of liver metastatic colorectal cancer with reduced expressions of iNOS compared with 6% of primary colorectal cancer. The Cancer Genome Atlas database analyses via cBioPortal reveal that mRNA expression of iNOS negatively correlated with selected EMT markers in colorectal cancer in a cancer type-dependent manner. The transcriptomic profiling (RNA sequencing data) indicates that iNOS knockdown in SW480 colorectal cancer cells induced an EMT program with upregulated expression of selected stem-cell markers. iNOS knockdown did not alter E-cadherin mRNA expression but re-localized it from membrane to cytoplasm through iNOS-GATA4-Crb2-E-cadherin pathway. iNOS knockdown induced a change in cell morphology, and promoted cell invasion and migration in vitro, and metastasis in vivo.

overall_design: 2 independent shRNAs for NOS2 and one control shRNA were used in SW480 cells. The samples used in the RNA-seq analysis were in duplicates.

first: Qiang

last: Du

first: Silvia

first: Kun

last: Dong

first: Xiao

last: Cui

first: Jing

first: David

middle: A

last: Geller


title: Genome-wide methylation analysis of murine CD4+ Th1, Th2, and Th17 cells

status: Public on Jul 19 2022

city: Braunschweig

first: Stefan

last: Floess

address: Inhoffenstr. 7

department: Experimental Immunology

country: Germany

institute: Helmholtz-Centre for Infection Research

type: Methylation profiling by high throughput sequencing

summary: T helper cells play an essential role in supporting immune reactions as a part of the adaptive immune system. During activation, naive CD4+ T cells can differentiate into various types of effector T cells, each defined by the expression of lineage-specific transcription factors and secretion of specific cytokines. The three main effector/memory cells were classified as T helper 1 (Th1), 2 (Th2) or 17 (Th17) cells, expressing T-bet, Gata3 or Ror gamma t, respectively. Differentiation into a specific T helper lineage is accompanied with durable transcriptional changes partially regulated by epigenetic mechanisms like changes in DNA methylation. Comparing the methylomes of CD4+ memory T cells opens up the chance to identify accessible, functionally relevant gene loci that would have been overlooked in an RNA-seq approach because their transcription depends on inflammatory stimuli. Because studies have shown that in vitro induced T helper cells do not completely match in vivo generated cells, we sorted ex vivo Th1, Th2, and Th17 cells from spleen and lymph nodes of healthy mice, and performed a bisulfite sequencing (Bi-Seq). The pairwise comparison of the methylomes identified differential methylated regions (DMRs) in known epigenetically regulated genes like Tbx21, Ifng, Gata3, Il4, and Ccr6, as well as in loci not known to be epigenetically regulated like Ccr8, Lck or NfkB1.

overall_design: Spleens and lymph nodes of numerous healthy mice were prepared and pooled. Then, Th1, Th2 and Th17 cells were sorted by flow cytometry and used for Bi-seq. Differentially methylated regions were identified by pairwise comparison of the samples with the software metilene.

first: Chia-Wen

last: Lu

first: Susanne

last: Strahlendorff-Herppich

first: Michael

last: Beckstette

first: Matthias

last: Lochner


title: The effect of Kaposi's sarcoma herpesvirus infection on endothelial progenitor cell (EPC) gene expression profile

status: Public on Jul 10 2022

city: Helsinki

first: Krista

last: Tuohinto

address: Haartmaninkatu 8

department: Research Program Unit, CAN-PRO

country: Finland

institute: University of Helsinki

summary: The alterations induced by KSHV-infection of EPCs with lymphatic characterictics was investigated with gene expression profiling analysis using data from RNA-seq of EPCs 7 days post infection compared to non-infected cells, and from 3 biological replicates.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mock and KSHV-infected progenitor EPCs with lymphatic characteristics.

first: Päivi

middle: M

last: Ojala


title: Knockdown of IGFBP7 decreases FGF2 expression in GC.

status: Public on Jul 08 2022

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

summary: Our previous study reported that IGFBP7 plays a role in maintaining mRNA stability of oncogenic lncRNA UBE2CP3 by RNA-RNA interaction. Clinical cohort studies had implied an oncogenic role of IGFBP7 in GC. However, the molecular mechanism of IGFBP7 in driving gastric cancer (GC) progression remains unknown. In this study, clinical analysis based on two independent cohort showed that IGFBP7 was positively associated with poor prognosis and macrophage infiltration in GC. Loss-of-function studies confirmed the oncogenic properties of IGFBP7 in regulating GC cell proliferation and invasion. Mechanismly, IGFBP7 was induced by epithelial-to-mesenchymal transition (EMT) signaling, since its expression was increased by TGF-beta treatment and reduced by overexpression of OVOL2 in GC. RNA sequencing, qRT-PCR, ELISA assay showed that IGFBP7 positively regulating FGF2 expression and secretion. Transcriptome analysis revealed that FGFR1 was downregulated in M1 macrophages but upregulated in M2 macrophages. Exogenous recombinant IGFBP7 protein in macrophages and GC cells further identified that IGFBP7 promotes macrophage polarization towards to a M2/TAM phenotype via FGF2/FGFR1/PI3K/AKT axis. Our finding highlights that IGFBP7 promotes GC by enhancing TAM infiltration through FGF2/FGFR1/PI3K/AKT axis.

overall_design: To uncover the molecular mechanism of oncogenic role of IGFBP7 in GC, we conducted loss-of-function studies by silencing IGFBP7. Then, IGFBP7-depleted GC cells were identified by deep sequencing, using Illumina HiSeq 4000.

first: Shanshan

last: Qin

first: Dandan


title: PHGDH Arginine Methylation by PRMT1 Promotes Serine Synthesis and Represents a Therapeutic Vulnerability in Hepatocellular Carcinoma

city: Chengdu

first: Kui

last: Wang

address: No.17, Section 3, South Renmin Rd

institute: Sichuan University

summary: Serine synthesis is crucial for tumor growth and survival, but its regulatory mechanism in cancer remains elusive. Here, using integrative metabolomics and transcriptomics analyses, we show a heterogeneity between metabolite and transcript profiles. Specifically, the level of serine in HCC tissues is increased, whereas the expression of phosphoglycerate dehydrogenase (PHGDH), the first rate-limiting enzyme in serine biosynthesis pathway, is dramatically downregulated. Interestingly, the increased serine level is obtained by enhanced PHGDH catalytic activity due to protein arginine methyltransferase 1 (PRMT1)-mediated methylation of PHGDH at arginine 236. PRMT1-mediated PHGDH methylation and activation potentiates serine synthesis, ameliorates oxidative stress, and promotes HCC growth in vitro and in vivo. FBXO7, an E3 ubiquitin ligase which is downregulated in human HCC tissues, ubiquitinates and downregulates PRMT1 to suppress PHGDH methylation and serine synthesis, leading to the inhibition of HCC cell growth. Furthermore, PRMT1-mediated PHGDH methylation correlates with PHGDH hyperactivation and serine accumulation in human HCC tissues, and is predictive of poor prognosis of HCC patients. Notably, blocking PHGDH methylation with a TAT-tagged non-methylated peptide inhibits serine synthesis and restrains HCC growth, both in an HCC patient-derived xenograft (PDX) model and subcutaneous HCC cell-derived xenograft model. Overall, our findings reveal a novel regulatory mechanism of PHGDH activity and serine synthesis, and suggest PHGDH methylation as a potential therapeutic vulnerability in HCC.

overall_design: Total RNA from 27 human HCC samples and paired normal liver tissues was extracted and subjected to RNA sequencing with Illumina NovaSeq 6000 by Novogene Inc. (Tianjin, China).

first: Li

last: Luo

first: Shuyue

last: Fu

first: Canhua


title: Next Generation Sequencing of Wild Type and jmjd1c B KO germinal center B cells and activated B cells Transcriptomes

first: Yuchao

last: Jing

state: Jiangsu

address: 101 Longmian Ave Jiangning District

department: Immunology

institute: Nanjing Medical University

summary: The aim of our study is to find out the differential expression genes and differential enrichment pathways of wild type and Jmjd1c B cells specific knockout germinal center B cells and activated B cells, clarify the function of Jmjd1c in germinal center B cells and activated B cells

overall_design: Germinal center B cells and activaterd B cells mRNA profiles of wild type (WT) and Jmjd1c B KO mice

first: Xiaoming

first: Yuye

last: Yin

first: Yuliang


title: Multi-hallmark long noncoding RNA maps reveal non-small cell lung cancer vulnerabilities.

status: Public on Jul 05 2022

city: Dublin

first: Rory

last: Johnson

address: Belfield

country: Ireland

institute: UCD Conway Institute for Biomolecular and Biomedical Research

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

overall_design: Refer to individual Series


title: Genome-wide maps of H3K9me2 modification  in wild type and jmjd1c B KO Activated B  cells.

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This study aims to characterize the H3K9me2 modification in wild type and jmjd1c B KO activated B cells, and find the potential mechanism of the jmjd1c B KO in  activated B cells

overall_design: Activated B cells profiles from wild type and jmjd1c B KO mice


title: Multi-hallmark long noncoding RNA maps reveal non-small cell lung cancer vulnerabilities [ASOseries]

summary: Long noncoding RNAs (lncRNAs) are widely dysregulated in cancer, yet their functional roles in cellular disease hallmarks remain unclear. Here we employ pooled CRISPR deletion to perturb 831 lncRNAs detected in KRAS-mutant non-small cell lung cancer (NSCLC), and measure their contribution to proliferation, chemoresistance and migration across two cell backgrounds. Integrative analysis of this data outperforms conventional “dropout” screens in identifying cancer genes, while prioritising disease-relevant lncRNAs with pleiotropic and background-independent roles. Altogether 80 high-confidence oncogenic lncRNAs are active in NSCLC, the majority identified here for the first time, and which tend to be amplified and overexpressed in tumours. A follow-up antisense oligonucleotide (ASO) screen shortlisted two candidates, Cancer Hallmarks in Lung LncRNA 1 (CHiLL 1) and GCAWKR, whose knockdown consistently suppressed cancer hallmarks in a variety of two- and three-dimension tumour models. Molecular phenotyping reveals that CHiLL 1 and GCAWKR control cellular-level phenotypes via distinct transcriptional networks converging on common oncogenic pathways. In summary, this work reveals a multi-dimensional functional lncRNA landscape underlying NSCLC that contains potential therapeutic vulnerabilities.

overall_design: RNA sequencing of A549 and NCI-H460 cells treated with antisense oligonucleotides targeting two top lncRNA candidates.

first: Roberta

last: Esposito

first: Taisia

last: Polidori

first: Dominik

middle: F

last: Meise

first: Carlos

last: Pulido-Quetglas

first: Panagiotis

last: Chouvardas

first: Stefan

last: Forster

first: Paulina

last: Schaerer

first: Andrea

last: Kobel

first: Juliette

last: Schlatter

first: Erik

last: Kerkhof

first: Michaela

last: Roemmele

first: Emily

middle: S

last: Westemeier

first: Lina

last: Zhu

first: Andrés

last: Lanzós

first: Hugo

last: Guillen-Ramirez

first: Giulia

last: Basile

first: Irene

last: Carrozzo

first: Adrienne

last: Vancura

first: Sebastian

last: Ullrich

first: Alvaro

last: Andrades

first: Dylan

last: Harvey

first: Pedro

middle: P

last: Medina

first: Patrick

middle: C

last: Ma

first: Simon

last: Haefliger

first: Xin

first: Ivan

last: Martinez

first: Adrian

last: Ochsenbein

first: Carsten

last: Riether


title: Multi-hallmark long noncoding RNA maps reveal non-small cell lung cancer vulnerabilities [CRISPRseries]

first: Rory

last: Johnson

overall_design: High-throughput CRISPR/Cas9-deletion screens using a long noncoding RNA targeting paired-guide RNA library in two KRAS+ non-small cell lung cancer models, A549 and NCI-H460, performing proliferation, cisplatin drug response and migration based assays.

first: Roberta

last: Esposito

first: Taisia

last: Polidori

first: Dominik

last: Meise

first: Carlos

last: Pulido-Quetglas

first: Panagiotis

last: Chouvardas

first: Stefan

last: Forster

first: Paulina

last: Schaerer

first: Andrea

last: Kobel

first: Juliette

last: Schlatter

first: Erik

last: Kerkhof

first: Michaela

last: Roemmele

first: Emily

last: Wang


title: A single cell atlas of human glioma under therapy

city: San Francisco

first: Aaron

last: Diaz

state: CA

department: Neurological Surgery

institute: University of California, San Francisco

summary: Most clinical trials for glioblastoma (GBM) enroll patients at recurrence. However, most pre-clinical animal models are of primary disease. Most studies have used tissues from primary tumors. Knowledge of GBM cellular composition at recurrence is limited. We profiled 80 human IDH-wild-type GBM specimens via single-nucleus RNA sequencing, 40 primary tumors and 40 patient-matched recurrent tumors. Select cohorts were also profiled via single-cell assay for transposase-accessible chromatin, single-cell digital-spatial, and single-cell spatial-transcriptomic assays. All patients were treated only with standard-of-care therapy: temozolomide, radiation and surgical resection. The cohort had a 1.2 male/female ratio, ages 35–76. We found a significant increase at recurrence in cells with the Verhaak mesenchymal phenotype and fewer proneural cells. Although there was an increase in the percentage of cycling cells overall, the fraction of cycling proneural cells decreased while the fraction of cycling mesenchymal cells increased. These changes were concomitant with a significant increase in the percentage of tumor-infiltrating monocytic-lineage cells derived from the periphery. Taken together, these findings support a proneural-to-mesenchymal shift at recurrence due to an increase in the birth rate of mesenchymal cells, supported by an expansion of myeloid-derived cells from peripheral blood. Although the percentages of glioblastoma-infiltrating T-cells are generally low (~1% on average in our data), we found a statistically significant increase in T-cell abundance at recurrence. We identified a cohort of T-cell outliers that demonstrate 2-to-8-fold increases in T-cells over average levels. We validated that T-cells in these tumors have extravasated beyond the perivascular space and into the cellular tumor via immunohistochemistry and spatial profiling. We present our ongoing analysis of the paracrine signals, upstream transcription-factor expression, and cis-regulatory grammars utilized in immune-outlier GBMs. We describe how these programs change under therapy. These studies shed light on the effect of standard therapy in shaping GBM composition at recurrence.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
We performed bulk RNA sequencing (RNA-seq), single-nuclei RNA sequencing (snRNA-seq), single-cell assay for transposase-accessible chromatin using sequencing(scATAC-seq), and spatial transcriptomics and proteomics of specimens from untreated human gliomas. We integrated the public single cell GBM data and our data, which showed that proneural and mesenchymal cells resided on a single axis. We investigated the cell composition and showed that mesenchymal cells increased in recurrence compared with the primary GBM. We identified therapeutic targets gene via intergration of spatial data and cell-cell interction analysis from snRNA-seq daata. Lastly, we performed an in vitro screen of drug combinations that target genes identified from our single-cell analysisof GBM.

We profiled spatial proteomics (SP) for six formalin-fixed paraffin embedded (FFPE) slides from three recurrent outlier-cases and their matched primary cases by using the Nanostring GeoMx platform. We next performed spatial transcriptomics (ST) on 10 slides from five patient-matched primary-recurrent pairs.
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Authors state that the raw data is "not available due to privacy concerns".

first: Lin

first: Husam

last: Babikir

first: Jangham

last: Jung

first: Karin

last: Shamardani

first: Saket

last: Jain

first: Xi

last: Feng

first: Nalin

last: Gupta

first: Susanna

last: Rosi

first: Susan

last: Chang

first: David

last: Raleigh

last: Solomon

first: Joanna

middle: J

last: Phillips


title: Liver RNA sequencing data from wildtype and DKO mice during dietary leucine deprivation or control feeding

status: Public on Jul 01 2022

city: Cambridge

first: Andrew

last: Cangelosi

state: MA

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

summary: The goal of this project is to perform a systemic analysis of transcriptional responses in the liver of WT and Sestrin DKO mice during dietary leucine deprivation.

overall_design: Liver transcriptional profiles of WT and Sestrin DKO mice after 24 hours and 8 days of feeding with control or leucine-free food

middle: L

first: George

middle: W

last: Bell

last: Sabatini


title: Transcriptome Profiling Identified Candidate Genes Contributing to Male and Female Gamete Development in Synthetic Brassica Allohexaploids

status: Public on Jun 29 2022

city: Zhengzhou

first: Ji

last: Chengyan

address: 100 Science Avenue

institute: Zhengzhou University

summary: The aim of the present study was to explore commonly and preferentially expressed genes for male and female gamete development in synthetic Brassica allohexaploids. We performed differential expression analysis to identify precise genes that regulate developmental events during male and female gamete development of Brassica allohexaploids.

overall_design: The leaf, anther from meiosis to pollen maturation and ovule from meiosis to mature embryo sac formation of synthetic Brassica allohexaploids have three repetitions respectively, and the leaves are the control group.

first: Chengyan

last: Ji

first: Fang

last: Wei


title: Iron availability enhances the cellular energetics of aerobic Escherichia coli cultures by activating anaerobic respiratory chains

status: Public on Jun 30 2022

city: Bethesda

first: Ashish

middle: K

last: Sharma

state: MD

address: 14 Service Rd West Building 14A Room 176 MS-5522

department: National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)

institute: National Institute of Health

summary: Aerobic Escherichia coli growth at restricted iron concentrations (≤ 1.75 ± 0.04 mM) is characterized by lower biomass yield, higher acetate accumulation, and higher activation of the siderophore iron-acquisition systems. Although iron homeostasis in E. coli has been studied intensively, these studies focused only on understanding the regulation of the iron import systems and the iron-requiring enzymes. In this study, the effect of iron availability on the energy metabolism of E. coli was investigated. It was established that aerobic cultures growing at limiting iron conditions showed lower ATP yield per glucose, lower growth rate, and lower TCA cycle activity and respiration, and at the same time increased glucose consumption, acetate and pyruvate accumulation, practically mimicking microaerobic growth. However, at excess iron, independently of oxygen availability, the cultures showed high cellular energetics (5.8 ATP/mol of glucose) by using pathways requiring iron-rich complex proteins found in the TCA cycle and respiration chain. At conditions of iron excess, some iron requiring terminal reductases of the respiratory chain, that were supposed to be anaerobic, were used by the E. coli, when in aerobic conditions, to keep high respiration activity. This high respiration activity allowed E. coli to produce more biomass and more reactive oxygen species that were controlled by the higher activity of the antioxidant defenses (SOD, peroxidase, and catalase) and the iron-sulfur cluster repair systems.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of E. coli chemostat cultures grown in iron limiting and iron excess conditions. The samples were collected from the steady state cultures growing at three dissolved oxygen conditions i.e., 6.3, 21 and 63%.

first: Antonino

last: Baez

first: Andrey

last: Bryukhanov

first: Eric

middle: D

last: Anderson

first: Roberto

last: Olivares-Hernández

last: Quan

first: Joseph

last: Shiloach


title: KLF5 CUT&Tag of HBECs at ALI with and without IL-13 stimulation

last: Erle

address: 555 Mission Bay Blvd

institute: UCSF

summary: Using CUT&Tag, we examined KLF5-associated genomic regions in primary human bronchial epithelial cells (HBECs) cultured at air-liquid interface (ALI) with and without IL-13 stimulation.

overall_design: Examination of KLF5 binding profile in HBECs


title: T cells produce interleukin-22 to promote CD155-driven lung metastasis

city: Munich

first: Daria

last: Briukhovetska

address: Lindwurmstraße 2a

department: Division of Clinical Pharmacology

institute: Klinikum der Universität München

summary: T cells are key players in immunosurveillance and anti-tumor immunity. However, subsets of T helper cells producing high levels of interleukin-22 (IL-22) accumulate in primary breast and lung tumors and are linked to a more dismal outcome. Here, we demonstrate that such TH22 cells promote metastasis by abrogating NK cell-mediated immune surveillance. Using mouse models of metastatic lung and breast cancer, we find that secreted IL-22 acts directly on disseminated cancer cells expressing the IL-22 receptor (IL-22R). In turn, IL-22 induces cancer cell overexpression of CD155, which binds to activating receptor CD226 on the surface of NK cells and triggers its downregulation. This functionally impairs NK cells to promote lung metastases. Importantly, neutralization of IL-22 in vivo blocked the metastatic potential of cancer cells, suggestive of therapeutic exploitability. We confirmed the paramount role of IL-22 signaling that was associated with CD155 expression in human datasets and marked poor patient outcomes. This study reveals an immunosuppressive feedback loop activated by T cell-derived IL-22 in cancer progression, creating the rationale for the development of future targeted therapeutics.

overall_design: Assessment of differential gene expression of 4T1 cells after treatment with IL-22 in compatison to untreated cells. For each experimental condition, analysis was performed on three biological replicates.

first: Briukhovetska

last: Daria

first: Suarez-Gosalvez

last: Javier

first: Voigt

last: Cornelia

first: Markota

last: Anamarija

first: Schübel

last: Maryam

first: Jobst

last: Jakob

first: Dörr

last: Janina

first: Märkl

last: Florian

first: May

last: Peter

first: Gottschlich

last: Adrian

first: Tokarew

last: Nicholas

first: Giannou

last: Anastasios

first: Zhang

last: Tao

first: Lücke

last: Jöran

first: Oner

last: Arman

first: Schwerdtfeger

last: Melanie

first: Jie

last: Philipp

first: Grünmeier

last: Ruth

first: Seifert

last: Matthias

first: Hristov

last: Michael

first: König

last: Lars

first: Cadilha

last: Bruno Loureiro

first: Mikhaylov

last: Oleg

first: Anders

last: Hans-Joachim

first: Rothenfußer

last: Simon

first: Flavell

last: Richard

first: Cerezo-Wallis

last: Daniela

first: Tejedo

last: Cristina

first: Huber

last: Samuel

first: Soengas

last: María

first: Bald

last: Tobias

first: Endres

last: Stefan

first: Kobold

last: Sebastian


title: Clariom D assay data from four colorectal cancer patients with tumor, metastasis and normal

status: Public on Jun 26 2022

city: Lübeck

first: Axel

last: Künstner

address: Ratzeburger Allee 160

department: LIED

institute: University of Lübeck

summary: Colorectal cancer (CRC) is one of the most prevalent cancers, with more than one million new cases every year worldwide. The prognosis of CRC considerably depends on its disease stage and metastatic status. This study aimed to identify significant expression differences during colorectal progression using a unique set of paired patient samples concerning tumor heterogeneity.

overall_design: Total RNA was extracted and prepared for Clariom D arrays from 4 patients cases following the manufacturer protocol.

first: Hauke

last: Busch

first: Timo

last: Gemoll


title: The Central Circadian Clock Protein CCA1 Regulates Seedling Growth and Spike Development in wheat (Triticum aestivum L.)

city: Beijing

first: Zefu

last: Lu

state: Haidian

address: No.12 Zhongguancun South St.,Haidian District, Beijing, P.R.China

institute: Institute of Crop Sciences

summary: The biological functions of circadian clock on growth and development have been well elucidated in model plants, while its regulatory roles in crop species, especially the roles on yield-related traits are poorly understood. Here, we characterize the core clock gene CCA1 homoeologs in wheat and studied their biological functions in seedling growth and spike development. TaCCA1 homoeologs exhibit typical diurnal expression patterns which are positively regulated by rhythmic histone modifications (H3K4me3, H3K9ac and H3k36me3). TaCCA1s are preferentially located in the nucleus and tend to form both homo- and heterodimers. TaCCA1 overexpression (TaCCA1-OE) transgenic wheat plants show disrupted circadian rhythmicity coupling with reduced chlorophyll and starch content, as well as biomass at seedling stage, also decreased spike length, grain number per spike and grain size at the ripening stage. Further studies using DNA affinity purification followed by deep sequencing (DAP-seq) indicates that TaCCA1 preferentially binds to sequences similar to “evening elements” (EE) motif in the wheat genome, particularly genes associated with photosynthesis, carbon utilization and auxin homeostasis, and decreased transcriptional levels of these target genes are observed in TaCCA1-OE transgenic wheat plants. Collectively, our study provides novel insights into a circadian-mediated mechanism of gene regulation to coordinate photo synthetic and metabolic activities in wheat, which is important for optimal plant growth and crop yield formation.

overall_design: To explore the underlying regulation networks of TaCCA1s, the typical circadian rhythm-control transcription factor in wheat, we performed genome-wide TaCCA1-7D-binding profiles using DNA affinity purification followed by deep sequencing (DAP-seq).


title: PDGFRβ+ cells play a dual role as hematopoietic precursors and niche cells during mouse ontogeny

city: Edinburgh

first: Mihaela

last: Crisan

address: 5 Little France Drive

country: United Kingdom

institute: The University of Edinburgh

summary: Hematopoietic stem cell (HSC) generation in the aorta-gonads-mesonephros region requires HSC specification signals from the surrounding microenvironment. In zebrafish, PDGF-B/PDGFRβ signaling controls hematopoietic stem/progenitor cell (HSPC) generation and is required in the HSC specification niche. Little is known about murine HSPC specification in vivo and whether PDGF-B/PDGFRβ is involved.  Here we show that PDGFRβ is expressed in distinct perivascular stromal cell layers surrounding the mid-gestation dorsal aorta, and its deletion impairs hematopoiesis. We demonstrate that PDGFRβ+ cells play a dual role in murine hematopoiesis. They act in the aortic niche to support HSPCs, and in addition, PDGFRβ+ embryonic precursors give rise to a subset of HSPCs that persist into adulthood. These findings provide crucial information for the controlled production of these clinically important cells in vitro.

overall_design: Single-cell transcriptome profiling of E11 AGM samples from PDGFRB +/+ (WT) (n=1) and PDGFRB -/- (KO) (n=1) mice

first: Diana

last: Sá da Bandeira

first: Alastair

last: Kilpatrick

first: Madalena

last: Marques

first: Mario

last: Gomez-Salazar

first: Telma

last: Ventura

first: Zaniah

middle: N

last: Gonzalez

first: Dorota

last: Stefancova

first: Fiona

last: Rossi

first: Chris

last: Vink

first: Mariana

last: Beltran

first: Neil

last: Henderson

first: Bongnam

last: Jung

first: Reinier

last: van der Linden

first: Harmen JG

last: van de Werken

first: Wilfred FJ

last: van IJken

first: Christer

last: Betsholtz

first: Stuart

last: Forbes

first: Henar

last: Cuervo


title: Three distinct Atoh1 enhancers cooperate for sound receptor hair cell development

status: Public on Jul 21 2022

first: Du

last: Yi

state: Beijing

address: No. 1 West Beichen Road

institute: Institute of Genetics and Developmental Biology Chinese Academy of Sciences


title: MicroRNA (miRNA) expression from blood plasma of patients with a prostate cancer

status: Public on Jun 24 2022

city: Moscow

first: Anton

last: Zhiyanov

address: 20 Myasnitskaya ulitsa

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

summary: We investigated how microRNAs' expression profile changes in blood plasma depending on a prostate cancer aggresivness.

overall_design: Whole blood samples was collected from 5 healthy volunteers (“Control”), 40 patients of “Low” risk group, 16 “Intermediate” risk, and 91 “High” risk group rated according EAU-ESTRO-SIOG Guidelines on Prostate Cancer.

first: Evgeny

last: Knyazev

first: Maxim

last: Shkurnikov


title: RNA-sequencing data of mouse macrophages exposed to polyphenols or polyphenol-amino acid adducts

city: Frederiksberg C

first: Andrew

last: Williams

state: --- Select One ---

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

summary: We show here the transcriptional response in mouse macrophages stimulated with LPS alone, LPS together with caffeic acid or chlorogenic acid, or the corresponding polyphenol-cystiene adducts

overall_design: RNA was obtained from RAW264.7 macrophages following 6 hours of treatments

middle: R


title: Transcriptome profile of tra1 mutant in S. cerevisiae

status: Public on Jun 16 2022

city: London,

first: Khaleda Afrin

last: Bari

state: ON

address: 1151 Richmond St

department: Anatomy and Cell Biology

country: Canada

institute: Western University

summary: Tra1 is an essential component of both the yeast SAGA/SLIK and NuA4 complexes, where it recruits these complexes to acetylate histones at targeted promoters. Importantly, Tra1 regulates the transcriptional response to multiple stresses. This submission contains RNA sequencing data from Saccharomyces cerevisiae strains expressing a Tra1 mutant with three arginine to glutamine mutations in the PI3K domain (tra1Q3; Berg et al., 2018). Our goal was to identify how gene expression profile changes during the chronological aging process due to mutation in the PI3K domain of Tra1.

overall_design: mRNA of strains expressing tra1Q3 compared to strains expressing wild type TRA1

first: Khaleda

last: Afrin Bari

first: Matthew

last: Berg

first: Julie

last: Genereaux

first: Christopher

last: Brandl

first: Patrick

last: Lajoie


title: Shuffling the yeast genome using CRISPR/Cas9-generated DSBs that target the transposable Ty1 elements

status: Public on Jun 01 2022

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

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

summary: We explored how Cas9-induced double-strand breaks (DSBs) on Ty1 produce genomic alterations in the diploid yeast Saccharomyces cerevisiae. Following Cas9 induction, we observed a significant elevation of chromosome rearrangements (large deletions and duplications), loss of heterozygosity (gene conversions, crossovers, and break-induced replication), and aneuploidy. Almost all of the chromosomal rearrangements reflect the repairing of DSBs at Ty1 elements by homologous recombination.

overall_design: The goal of our experiments was to analyze genomic rearrangements induced in yeast by expression of a CRISPR/Cas9 system directed against a target in the repeated transposon Ty1. Using whole genome SNP microarrays, we analyzed genomic alterations in 18 yeast isolates. For each isolate, cells were under long-term or transient (2 hours or 4 hours) exposure of CRISPR/Cas9 for inducing double strand breaks on Ty1. MD741-3, -5, -6, -7 are from long-term exposure. We subcultured MD741-3, -5, -6, -7 for one time to analyze the ongoing instability. 2 colonies from each isolate were picked up for analyzing, named as MD741-3-S1, MD741-3-S2, MD741-5-S1, MD741-5-S2, MD741-6-S1, MD741-6-S2, MD741-7-S1, MD741-7-S2. MD704-2h-7, -26 are from 2 hours exposure. MD704-4h-1, -6P, -8, -12 are from 4 hours exposure.

first: Lei

last: Qi

first: Daoqiog

first: Thomas

last: Petes


title: OXPHOS Promotes Apoptotic Resistance and Persistence in TH17 cells

status: Public on Sep 08 2022

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

summary: Apoptotic cell death is a cell-intrinsic, immune tolerance mechanism that regulates the magnitude and resolution of T cell-mediated responses. Evasion of apoptosis is critical for the generation of memory T cells, as well as autoimmune T cells, and knowledge of the mechanisms that enable resistance to apoptosis will provide insight into ways to modulate their activity during protective and pathogenic responses. IL-17-producing CD4 T cells (TH17s) are long-lived, memory cells. These features enable their role in host defense, chronic inflammatory disorders, and anti-tumor immunity. A growing number of reports now indicate that TH17s in vivo require mitochondrial oxidative phosphorylation (OXPHOS), a metabolic phenotype that is poorly induced in vitro. To elucidate the role of OXPHOS in TH17 processes, we developed a system to polarize TH17s that metabolically resembled their in vivo counterparts. We discovered that directing TH17s to use OXPHOS promotes mitochondrial fitness, glutamine anaplerosis, and an anti-apoptotic phenotype marked by high BCL-XL and low BIM. Through competitive co-transfer experiments and tumor studies, we further revealed how OXPHOS protects TH17s from cell death while enhancing their persistence in the periphery and tumor microenvironment. Together, our work demonstrates a non-classical role of metabolism in regulating TH17 cell fate and highlights the potential for therapies that target OXPHOS in TH17-driven diseases.

overall_design: Mouse T helper 17 (TH17) cells differentiated from CD4+ T cells were cultured in glucose (GLC; glycolytic cells) or galactose (GAL; OXPHOS cells) and 3 replicates each were prepared for RNA-seq.

first: Hanna

last: Hong

first: Nneka

middle: E

last: Mbah

first: Mengrou

last: Shan

first: Kristen

last: Loesel

first: Lin

last: Lin

first: Peter

last: Sajjakulnukit

first: Anthony

last: Andren

first: Atsushi

last: Hayashi

first: Zhaoheng

last: Li

first: Yuying

last: Xie

first: Yu

last: Lei

first: Li

last: Zhang

last: Opipari

first: Ilona

last: Kryczek

first: Nobuhiko

last: Kamada

first: Weiping

last: Zou

first: Luigi

last: Franchi

first: Costas

last: Lyssiotis


title: Differential gene expression in murine lung cancer in vitro vs. in vivo

status: Public on May 29 2022

city: Aurora

first: Emily

last: Kleczko

state: Colorado

department: Medicine

institute: University of Colorado Anschutz Medical Campus

summary: The tumor microenvironment (TME) is incredibly important to the growth of tumors. To better understand the effect that the TME has on cancer cells, we assessed genes that were differentially expressed in murine lung tumors versus cells that were cultured in an incubator. We employed our orthotopic mouse model where murine lung cancer cells were implanted into the left lung of immunocompetent, syngeneic GFP-expressing mice of the C57BL/6 strain. After 3-4 weeks, tumors were harvested and a single cell suspension was prepared from the tumors. Using fluorescent-activated cell sorting, live (DAPI-negative), GFP-negative cells were isolated from the single cell suspensions. These GFP-negative cells constitute a pure population of tumor cells, excluding cells from the TME. RNA was isolated from these tumor cells, and submitted to RNA-seq. These are our “in vivo” samples. Concurrently, the cells from the same batch of cells that were initially injected into mice were cultured in vitro, and RNA was isolated from them and submitted to RNA-seq. These samples are our “in vitro” samples. Our study specifically utilizes 2 newly developed EML4-ALK fusion-driven murine lung cancer cell lines (EA1 and EA2 cells).

overall_design: The following conditions were analyzed: (1) EA1 in vitro. RNA was extracted from EA1 cells cultured in vitro. This condition has 5 independent replicates; (2) EA1 in vivo. EA1 cells were injected into the left lung of GFP-expressing mice C57BL/6 mice. Tumors grew for 3-4 weeks, were isolated, and prepared into a single cell suspension. Tumor cells were isolated by flow sorting for GFP-negative cells, and RNA was isolated. This condition has 5 independent replicates. Each replicate is a pool of tumors from 3-5 mice; (3) EA2 in vitro. RNA was extracted from EA2 cells cultured in vitro. This condition has 3 independent replicates; and (4) EA2 in vivo. EA2 cells were injected into the left lung of GFP-expressing mice C57BL/6 mice. Tumors grew for 3-4 weeks, were isolated, and prepared into a single cell suspension. Tumor cells were isolated by flow sorting for GFP-negative cells, and RNA was isolated. This condition has 5 independent replicates. Each replicate is a pool of tumors from 3-5 mice.

first: Joanna

last: Poczobutt

first: Natalia

last: Gurule

first: Lynn

last: Heasley

first: Raphael

last: Nemenoff


title: Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution

status: Public on Jun 19 2022

city: Ipswich

first: Bo

last: Yan

address: County Road

institute: New England Biolabs

summary:
We developed Methyl-SNP-seq, a technology that takes advantage of the redundancy of the double helix, to extract the methylation and sequence information from a single original DNA molecule
We demonstrate the usefulness of this technology on a broad spectrum of applications ranging from allele specific methylation analysis in humans to methylation identification in complex bacterial communities.

sample_organism:
Escherichia coli
Clostridium acetobutylicum
Homo sapiens

overall_design: Methyl-SNP-seq uses bisulfite conversion of one of the double strands to identify methylation while the other strand is left intact for sequencing. Both strands are locked together to link the dual readout on a single paired-end read.

first: Duan

last: Wang

first: Romas

last: Vaisvila

first: Zhiyi

last: Sun

first: Laurence

last: Ettwiller


title: Whole genome bisulfite sequencing data of cassava

status: Public on May 27 2022

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary: Cassava mosaic disease (CMD) suppresses cassava yields across the tropics. It has been reported that  landraces lose CMD resistance after regeneration through de novo morphogenesis.  We sequenced WGBS data of 14 samples.

overall_design: This dataset includes whole genome sequencing and WGBS data to understand DNA methylation in cassava.


title: ChIP-seq of HBECs at ALI with and without stimulation of IFN-a, IL-17, and IL-13

status: Public on May 24 2022

first: Walter

last: Eckalbar

address: 513 Parnassus Ave MSB-813

institute: University of California, San Francisco

summary: We used ChIP-seq to investigate epigenomic modifications in response to IFN-a, IL-17, and IL-13 in primary human bronchial epithelial cells (HBECs).

overall_design: Human HBE cells were treated with IL13, IL17 IFN alpha, IL13 + IFN alpha, or a no treatment control in order to identify asthma-associated cytokine responsive enhancers and promoters through H3K27ac ChIP-seq.

first: Kyung

last: Koh

first: Luke

last: Bonser

first: walter

first: David

last: Erle


title: Bulk RNA-seq of HBECs at ALI with and without stimulation of IFN-a, IL-17, and IL-13

summary: We used bulk cell RNA-seq to investigate transcriptional effects of IFN-a, IL-17, and IL-13 in primary human bronchial epithelial cells (HBECs).

overall_design: Bulk cell transcriptional effects of IFN-a, IL-17, and IL-13 in HBECs


title: scRNA-seq, bulk RNA-seq and ChIP-seq of HBECs at ALI with and without stimulation of IFN-a, IL-17, and IL-13

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

overall_design: Refer to individual Series


title: Expression data of pig pancreas from Oncopig tumor and normal pigs

status: Public on May 17 2022

city: Omaha

first: Hamid

last: Band

state: Nebraska

address: 42nd and Emile

department: Eppley

institute: University of Nebraska Medical Center

summary: In order to determine the difference in expression between pancreatic tumors generated from OCM or Oncopigs and wild type pig pancreas, we have harvested pancreatic tumors and normal pancreas from two OCM subjects and two normal pigs, respectively.

overall_design: Pancreatic tissue from two OCM pigs with pancreatic tumors and two normal pancreas from wild type pigs were used to extract total RNA and subjected to microarray analysis to identify differential expression.

first: Pinaki

last: Mondal

first: Katie

last: Baliey

first: Mark

last: Carlson


title: Transcriptome profiling reveals different expression pattern in baseline group, 0G group,and 5G group in ex vivo organ-cultured HFs.

status: Public on May 19 2022

city: Guangzhou

first: Damao

last: Dai

state: Guangdong

address: 1838 North Guangzhou AV

department: Department of Plastic and Aesthetic Surgery

institute: Nanfang Hospital of Southern Medical University

summary:
Transcriptome profiling reveals different expression pattern in baseline group(after isolated hair follicles---HFs,collect samples immediately), 0G group(sham irradiation, collect organ-cultured HFs for 3 days),and 5G group(5G dose irradiation, collect organ-cultured HFs for 3 days) in ex vivo organ-cultured HFs.
Hair greying or canities is one of the earliest phenomena in aging. A worldwide survey based on a large sample of human subjects showed that men grey faster than women, but in distinct scalp regions, and the populations of Asian and African descent had less grey hair than those of the same age of Caucasian descent. The average grey hair age of whites is 34 ± 9.6 years in Caucasians, while 43.9 ± 10.3 years in African. And then clinical observation demonstrates that by the age of 50 in 50% of all men in senile canities, 50% of all hair follicles (HFs) have lost their pigment. In addition, an increasing number of studies found that hair greying acts as an important predictor of aging-associated pathology, including Alzheimer’s disease,  Parkinson’s disease and cardiovascular disease, etc.     Grey hair is both visible and non-lethal, and it makes this phenotype a unique model system for investigating mechanisms that contribute to tissue aging and therapeutic strategies to combat this process. In humans and mice, age-related grey hair is attributed to the loss of melanocyte stem cells (MeSCs),  precursor cells, and melanocytes, or their reduced or restricted functions, which is induced by a multitude of exogenous and endogenous challenges, such as radiation, inflammation, psycho-emotional stress, or gene mutation (BCL-2 deficiency), etc. Of which, ionizing radiation (IR) produces multiple clusters of double-strand breaks that mediate cell cycle arrest, apoptosis, and DNA repair, and successfully induces grey hair in mice. The accelerating process of aging by IR may provide an avenue to create a grey hair model.  Although there is a mouse model of grey hair, the existence of species differences also limits the translational potential of the mice HF models for human applications. Recently, Rachmin et al demonstrated that IR could result to ectopically pigmented melanocytes (EPM) in outer root sheath (ORS) followed hair greying and speculated that this may provide a tool to prevent or reverse hair greying in humans. They proved that different genotoxicity can induce premature differentiation of MeSCs and/or amelanotic cells. However, they didn’t determine the appropriate dose of irradiation for creating the hair grey model and not discuss the mechanisms of forming the model.  Hence, this study focuses on establishing a suitable ex vivo human grey HF model by IR, demonstrating the series change of grey hair and exploring the possible mechanisms of the model.  In our study, parameters about senescence and melanotic features in our model are almost in line with essential traits of human grey hair in previous studies. In addition,to explore the profound mechanism of the irradiated model, we performed transcriptome analysis for baseline, 0G and 5G groups. Then, three pairwise comparisons were established---0G vs 5G, baseline vs 5G and baseline vs 0G. This profiling results be used to understand the different molecular mechanism of creating ex vivo grey HFs model,and those provided a possibility for anti-aging treatment.In summary, our results indicate that the ex vivo grey HFs by irradiation can perfectly replace elderly grey hair and establish a potential preclinical aging model for pharmacological and mechanism studies.

overall_design: hair follicle mRNA profiles from baseline group(after isolated HFs,collect samples immediately), 0G group(sham irradiation, collect organ-cultured HFs for 3 days),and 5G group(5G dose irradiation, collect organ-cultured HFs for 3 days) in ex vivo organ-cultured hair follicles.

first: Qian

last: Qu

first: Yong

last: Miao

first: Zhiqi

last: Hu


title: Single cell RNA-seq of HBECs at ALI with and without stimulation of IFN-a, IL-17, and IL-13

city: San Francisco

summary: We used scRNA-seq to investigate cell type-specific transcriptional effects of IFN-a, IL-17, and IL-13 in primary human bronchial epithelial cells (HBECs).

overall_design: Cell type-specific transcriptional effects of IFN-a, IL-17, and IL-13 in HBECs


title: Short tandem repeats are important contributors to silencer elements in T cells

status: Public on May 12 2022

city: Marseille

first: Nori

last: SADOUNI

address: 169 Avenue Luminy

country: France

institute: TAGC INSERM U1090

summary: Analysis of Dnase Hypersensitive Site (DHS) of P5424 mouse cell line using High-throughput reporter assay

first: Saadat

last: Hussain

last: Sadouni

first: Dominic

last: Van Essen

first: Lan

middle: T

last: Dao

first: Quentin

last: Ferre

first: Guillaume

last: Charbonnier

first: Magali

last: Torres

first: Charles-Henri

last: Lecellier

first: Tom

last: Sexton

first: Simona

last: Saccani

first: Spicuglia

last: Salvatore


title: Single-molecule chromatin architectures of human centromeres and telomeres

status: Public on May 10 2022

city: Seattle

first: Andrew

middle: Ben

last: Stergachis

state: WA

address: 1959 NE Pacific St

department: Medical Genetics

institute: University of Washington

summary: Centromeres and telomeres are essential structural components of eukaryotic genomes, and alterations in their structure and function contribute to various human diseases. Currently, our understanding of the chromatin architecture underlying centromeres and telomeres is limited owing to their highly repetitive DNA content. To overcome this, we applied long-read single-molecule chromatin fiber-sequencing (Fiber-seq) to a human cell line with a complete telomere-to-telomere (T2T) reference genome, resulting in single-nucleotide precise mapping of chromatin accessibility, nucleosome positioning, and transcription factor occupancy across 1.7 million intact ~16kb chromatin fibers - resolving the chromatin architecture for ~97% of human telomeric and centromeric DNA. We identify that the centromeric kinetochore binding region contains highly atypical chromatin that juxtaposes highly accessible and tightly compacted DNA - a feature unique to the kinetochore. This structure mirrors the alpha-satellite DNA repeat and appears driven via clustered CENP-B occupancy at hypo-CpG methylated repeats. In addition, telomeres often contain several kilobases of non-nucleosomal chromatin, and the transition between nucleosome-bound chromatin and the telomere cap is highly heterogeneous and often punctuated by CTCF-bound elements. Our findings uncover non-standard chromatin architectures as the predominant organizational structure of telomeres and the kinetochore binding region, and provide a framework for future studies of complete human epigenomes.

overall_design:
Single-molecule chromatin fiber-sequencing (Fiber-seq) of CHM13 cells using a complete reference genome.
Single-molecule chromatin fiber-sequencing (Fiber-seq) of GM12878 cells using a complete reference genome.

first: Danilo

last: Dubocanin

first: Adriana

last: Sedeño-Cortés

first: Jane

last: Ranchalis

first: Taylor

last: Real

middle: B


title: Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation [HiChIP]

status: Public on May 13 2022

city: Stanford

first: Howard

middle: Y

last: Chang

address: CCSR 2130, 269 Campus Drive

department: Center for Personal Dynamic Regulomes

institute: Stanford University

summary: Polycomb-group proteins play critical roles in gene silencing through the deposition of histone H3 lysine 27 trimethylation (H3K27me3) and chromatin compaction. This process is essential for embryonic stem cells (ESCs) pluripotency, differentiation, and development. Polycomb repressive complex 2 (PRC2) can both read and write H3K27me3, enabling processive spread of H3K27me3 on linear genome and epigenetic memory. Long-range Polycomb-associated DNA contacts have also been described, but their regulation and role in gene silencing remains unclear. Here, we develop H3K27me3 HiChIP and apply optical reconstruction of chromatin architecture to reveal long-range Polycomb-associated DNA loops that span tens to hundreds of megabases and across multiple topological associated domains in mouse ESCs and human induced pluripotent stem cells. H3K27me3 loop anchors are enriched for Polycomb nucleation points and coincide with key developmental genes, such as Hmx1, Wnt6 and Hoxa. Genetic deletion of H3K27me3 loop anchors causes spatially proximal partner chromosomal loci to break apart, and alters H3K27me3 deposition, both locally and megabases away on the same chromosome. A selective EZH2 mutant deficient in RNA binding but intact H3K27me3 enzymatic activity leads to global alteration in H3K27me3 loops, decreased spatial proximity, and failure to spread Polycomb from PRC2 nucleation points to partner loci at developmental genes. Together, these results suggest PRC2 acts as a “genomic wormhole”, using RNA binding to enhance long range chromosome folding and H3K27me3 spreading. Developmental gene loci have novel roles in Polycomb spreading, emerging as key architectural elements of the epigenome.

overall_design: H3K27ac and H3K27me3 HiChP of mouse embryonic stem cells (mESCs), wild-type and RNA-binding deficient EZH2 mutant human induced pluripotent stem cells (iPSCs).

first: Katerina

last: Kraft

first: Kathryn

last: Yost

first: Sedona

last: Murphy

first: Andreas

last: Magg

first: Yicheng

last: Long

first: M

last: Corces

first: Jeffrey

last: Granja

first: Stefan

last: Mundlos

first: Thomas

last: Cech

first: Alistair

last: Boettiger


title: Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation


title: Transcriptional profiling of sweet orange leaves infected with Xanthomonas citri and Xanthomonas aurantifolii pathotype C

status: Public on May 11 2022

city: Campinas

first: Celso

middle: Eduardo

last: Benedetti

state: SP

address: R. Giuseppe Maximo Scolfaro 10000

country: Brazil

institute: Laboratorio Nacional de Biociencias

summary: To compare the early transcriptional changes that occur in sweet orange leaves in response to Xanthomonas citri versus Xanthomonas aurantifolii pathotype C infection, plant leaves infiltrated with each bacterial pathogen were examined by RNAseq.

overall_design: Plant leaves were infiltrated with each bacterial pathogen, or water as control, and RNA samples extracted at 24 and 48 h after bacterial inoculation were used to prepare the cDNA libraries for sequencing.

first: Hugo

middle: M

last: Shimo


title: Transcriptome analysis revealed potential neuro-immune interaction in papillary thyroid carcinoma tissues

status: Public on May 08 2022

city: Shenzhen

first: SHAO

middle: MIN

last: YANG

state: guangdong

address: Nanshan

department: Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center

institute: Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine

summary:
We aimed to explore the potential interaction between neural markers and signatures of tumor microenvironment.
Comparative gene expression profiling analysis of Gene set variation analysis (GSVA) was conducted to calculate the enrichment scores of gene sets regarding tumor-infiltrating immune cells and tumor microenvironment.

overall_design: We then performed mRNA sequencing was conducted using 6 pairs of PTC and adjacent normal tissues.

first: Haibei

last: Hu


title: mRNAseq of murine qPSCs after culture with conditioned media

status: Public on May 09 2022

city: Marburg

first: Magdalena

last: Huber

address: Hans-Meerweinstr. 02

department: Mikrobiology

institute: University of Marburg

summary: we examined the influence of Tc17-CM from WT or from IL17A/F KO mice on the in vitro differentiation of quiescent pancreatic stellate cells (qPSC) towards an iCAF or myCAF phenotypes

overall_design: qpSCs were seeded as co-cultures for 48h in matrigel droplets. After that they were treated for 48 hours with conditioned media in quadruplicates.

first: F

middle: S

last: Picard

first: A

last: Brichkina

last: Klein

first: H

last: Chung

last: Neuhaus

last: Raifer


title: Colony stimulating factor-1 producing endothelial cells and mesenchymal stromal cells maintain monocytes within a perivascular bone marrow niche

status: Public on May 03 2022

city: Toronto

first: Clinton

middle: S.

last: Robbins

state: Ontario

address: 101 College Street

institute: University Health Network

summary: Macrophage colony stimulating factor-1 (CSF-1) plays a critical role in maintaining myeloid lineage cells. However, congenital global deficiency of CSF-1 (Csf1op/op) causes severe musculoskeletal defects that may indirectly affect hematopoiesis. Indeed, we show here that osteolineage-derived Csf1 prevented developmental abnormalities but had no effect on monopoiesis in adulthood. However, ubiquitous deletion of Csf1 conditionally in adulthood decreased monocyte survival, differentiation, and migration, independent of its effects on bone development. Bone histology revealed that monocytes reside near sinusoidal endothelial cells (ECs) and leptin receptor (Lepr)-expressing perivascular mesenchymal stromal cells (MSCs). Targeted deletion of Csf1 from sinusoidal ECs selectively reduced Ly6C- monocytes, whereas combined depletion of Csf1 from ECs and MSCs further decreased Ly6Chi cells. Moreover, EC-derived CSF-1 facilitated recovery of Ly6C- monocytes and protected mice from weight loss following induction of polymicrobial sepsis. Thus, monocytes are supported by distinct cellular sources of CSF-1 within a perivascular BM niche.

overall_design: We compared whole-transcriptome RNA sequencing (RNA-seq) of flow sorted mature CXCR4low Ly6Chigh and Ly6Cnegative monocytes isolated from the bone marrow between Ubc-CreERT2; Csf1fl/fl and control Csf1fl/fl mice.

first: Takuo

last: Emoto

first: Jessie

last: Lu

first: Tharini

last: Sivasubramaniyam

first: Hassaan

last: Maan

first: Aniqa

last: Khan

first: Amina

middle: A

last: Abow

first: Stephanie

last: Schroer

first: Sharon

last: Hyduk

first: Marwan

middle: G

last: Althagafi

first: Trevor

last: McKee

first: Fred

last: Fu

first: Shiva

last: Shabro

first: Antigona

last: Ulndreaj

first: Felix

last: Chiu

first: Elvira

last: Paneda

first: Shaun

last: Pacheco

first: Tao

last: Wang

first: Angela

last: Li

first: Jean

middle: X

last: Jiang

first: Peter

last: Libby

first: Mansoor

last: Husain

first: Bo

first: Barry

last: Rubin

first: Myron

middle: I

last: Cybulsky


title: The RNA-binding protein RBM46 is essential for gametogenesis and functions in post-transcriptional roles affecting meiotic cohesin subunits

status: Public on Apr 23 2022

city: Jinan

first: Yuling

last: Cai

state: Shandong

address: Qianfoshan Street

department: CCenter of reproductive medicine

institute: Shandong University

summary: RBM46 is a germ cell-specific RNA binding protein required for gametogenesis, but the targets and molecular functions of RBM46 remain unknown. Here, we demonstrate that RBM46 binds at specific motifs in the 3'UTRs of mRNAs encoding multiple meiotic cohesin subunits and show that RBM46 is required for normal synaptonemal complex formation during meiosis initiation. Using a recently reported, high-resolution technique known as LACE-seq and working with low-input cells, we profiled the targets of RBM46 at single-nucleotide resolution in gametes of specific meiotic stages leptotene and zygotene. We found that RBM46 preferentially binds target mRNAs containing GCCUAU/GUUCGA motifs in the 3 'UTRs region. In Rbm46 knock-out mice, the RBM46-target cohesin subunits displayed unaltered mRNA levels but had reduced translation, resulting in failed assembly of axial elements, synapsis disruption, and meiotic arrest. Overall, our study provides mechanistic insights into the molecular functions of RBM46 in gametogenesis and illustrates how the power of LACE-seq in the study of RBP functions using low-input materials.

overall_design: The antibody used for immunoprecipitation was: HA-Tag (C29F4) Rabbit mAb (Cell signaling technology, 3724) with 3μg for each test sample. And the IgG from rabbit was used for negative control.And two technical replicates were performed for each group.

first: Yue

last: Lv

first: Gang

last: Lu

first: Ruibao

last: Su


title: Dynamic states of cervical epithelia during pregnancy and epithelial barrier disruption

status: Public on May 02 2022

city: Dallas

first: Anne

last: Cooley

state: TX

address: 5323 Harry Hines Blvd

institute: UTSW

summary: The cervical epithelium undergoes continuous changes in proliferation, differentiation and function that is critical before pregnancy to ensure fertility and during pregnancy to provide a physical and immunoprotective barrier for pregnancy maintenance. Barrier disruption can lead to the ascension of pathogens that elicit inflammatory responses and preterm birth. Here we identify epithelial subtypes in the cervix of nonpregnant, pregnant and laboring mice using single cell- transcriptome and spatial analysis. We identify heterogeneous subpopulations of epithelia displaying spatial and temporal specificity in cell proliferation, turnover and transcriptional programs. Further we identify untimely proliferation and function of epithelial cells in a model of cervical epithelial barrier disruption. Together these data provide insights as to how the cervical epithelium undergoes a continuous remodeling to maintain a dynamically shifting state of homeostasis in pregnancy and labor and provide a framework by which to understand perturbations in epithelial cell health and host-microbe interactions that contribute to risk of premature birth.

overall_design: Single-cell sequencing of mouse cervices from six wild type timepoints: non-pregnant (diestrus (n=7) and estrus (n=2)), gestation day (GD) 6 (n=5), GD12 (n=4), GD15 (n=3), GD18 (n=3), and in-labor (n=3), and 2 HA KO timepoints: GD15 & GD18.

first: Gary

last: Hon

first: Mala

last: Mahendroo

first: ShanmugaPriyaa

last: Madhukaran


title: Spatial gene expression-based, non-small cell lung carcinoma patients with paired brain metastases

status: Public on Apr 25 2022

city: London

first: Rober

last: Abdo

address: 1151 Richmond St

department: Pathology

institute: The University of Western Ontario

summary: Spatial RNA-seq were successfully constructed through expression profiling of a total of 18,694 genes in non-small cell lung cancer (NSCLC) cases with paired brain metastases.

overall_design: In the study presented here, 35 cases from a well-defined cohort of 44 NSCLC cases with paired brain metastases was used to acquire expression profiles of a total of 18,694 unique genes.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type 、 ryhB-1、 ryhB-2、 ryhB-1/ryhB-2 Mutant Strains Transcriptomes

city: Yangzhou

first: Mengping

last: He

address: Shuangqiao Street

institute: Yangzhou university

summary:
Purpose:To investigate the effect of small RNA RyhB-1and RyhB-2 deletion of Salmonella enteritidis on genes expression of genome  under simulated intestinal conditions
Methods:S. Enteritidis wild type (WT) strain 50336 and mutants △ryhB-1, △ryhB-2, and △ryhB-1/ryhB-2 were grown overnight in 50 mL of the LB medium with 160 rpm shaking at 37°C under aerobic condition, washed thrice, and re-suspended with iron-limited and nutrient-limited medium. The above prepared bacterial cells were cultured for 2 h at 37°C in the anaerobic workstation. Each sample was analysed in triplicate. Total RNA of the above stains was extracted using TRIzol reagentwith DNase digestion according to the manufacturer’s instruction. Ribosome RNA was removed using a Ribo-Zero rRNA removal kit (Illumina) that leaves the mRNA. Sequencing libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB), sequenced on an Illumina Hiseq 2000 platform at Beijing Novogene Bioinformatics Technology。
Results: Analysis of the RNA-Seq data identified 496, 250, and 553 DEGs in △ryhB-1, △ryhB-2, and △ryhB-1△ryhB-2, respectively, compared to the WT strain.A total of 213 genes changed in  △ryhB-1, △ryhB-2, and △ryhB-1△ryhB-2 mutants. The transcriptional levels of 176 genes changed in △ryhB-1 and △ryhB-1△ryhB-2 but not in △ryhB-2.  Furthermore, 14 genes were only changed in RyhB-2, 96 DEGs were only identified in △ryhB-1, and 12 DEGs were only identified in △ryhB-2 but not in △ryhB-1△ryhB-2. Moreover, 150 DEGs were only identified in △ryhB-1△ryhB-2 but neither in △ryhB-1 nor in △ryhB-2.
Conclusions: A total of 213 genes could be regulated by △ryhB-1, △ryhB-2, and △ryhB-1△ryhB-2 mutants,  176 genes  are regulated only by RyhB-1, 14 genes were regulated only by RyhB-2.

sample_organism: Salmonella enterica subsp. enterica serovar Enteritidis

overall_design: Including 4 samples, Wild Type, ryhB-1, ryhB-2, ryhB-1/ryhB-2 Mutants, and each sample was analysed in triplicate. The RNA-Seq clean reads were aligned to the Salmonella Enteritidis str. P125109 genome from NCBI (https://www.ncbi.nlm.nih.gov/nuccore/NC_011294.1) using Bowtie2-2.2.3 (51). Rockhopper [13,14] was used for RNA-Seq data analysis (https://cs.wellesley.edu/~btjaden/Rockhopper/index.html), including differential gene expression detection, novel and reference-based transcript identification, and operon prediction. Gene expression was quantified as reads per kilobase of coding sequence per million reads (RPKM) algorithm. Genes with an adjusted q values < 0.01 and [log2(fold change)] >1 were assigned as differentially expressed genes (DEGs).

first: Xia

last: Meng

first: Binjie

last: Chen


title: Latent TGF β binding proteins 1 and 3 protect the larval zebrafish outflow tract   from aneurysmal dilatation

status: Public on Apr 19 2022

city: Cambridge

first: Vincent

last: Butty

state: MA

address: 77 Massachusetts Avenue Bldg 68-317A

department: Biology / Koch Institute / Bioengineering / CEHS

institute: Massachusetts Institute of Technology

summary: Aneurysm and dissection of the aortic root is a common cause of morbidity and mortality   in Loeys-Dietz Syndrome (LDS) and Marfan Syndrome (MFS), where perturbations in   TGF β signaling play a causal or contributory role, respectively. Despite the advantages   of cross-species disease modeling for mechanistic studies and pre-clinical drug   discovery, animal models of aortic root aneurysm are largely restricted to genetically   engineered mice. Here, we report that zebrafish larvae, homozygous for null mutations   in latent TGF β binding proteins (ltbps) 1 and 3, develop rapid and severe aneurysmal   dilatation of the aortic root equivalent, the outflow tract (OFT), after grossly unperturbed   cardiac morphogenesis. The ventricle also becomes significantly dilated and upregulates   stress-responsive genes, which likely reflects compensatory pathologic remodeling since   ltbp1 and ltbp3 co-expression is restricted to the OFT. Similar to aneurysm tissue from   LDS and MFS patients, the distended OFTs display evidence for hyperactivated TGF β     signaling. Moreover, RNA-sequencing revealed significant overlap between the   molecular signatures of diseased tissue from double knockout zebrafish and MFS mice.   Lastly, chemical inhibition of the TGF β Type I receptor in wild-type embryos evoked   similar OFT and ventricular dilation phenotypes, demonstrating that TGF β signaling is   protective against these pathologies. The disease relevance of the mutant phenotype is   further supported by recent family studies implicating genetic lesions in Ltbp3, and likely   Ltbp1, as heritable causes of aortic root aneurysm. Ultimately, our data demonstrate that   the unique advantages of zebrafish can now be leveraged to interrogate thoracic   aneurysmal disease and identify novel lead compounds through small molecule   suppressor screens.

overall_design: Dissected ventricles and outflow tracts from 5 days post-fertilization sibling control and ltbp1-/-; ltbp3-/- double knockout zebrafish were profiled by RNA-Seq

first: Maryline

last: Abrial

first: C

last: Burns

first: Caroline


title: Transcriptional analysis of bone morphogenetic protein 2 signaling in human placental trophoblast development and function

status: Public on Apr 13 2022

city: Vancouver

first: Yuyin

last: Yi

address: 4500 Oak St

institute: University of British Columbia, BC Children’s Hospital Research Institute

summary: Previous studies have demonstrated the pro-invasive action of BMP2 signaling in human trophoblast cells in vitro. In this study, we investigated downstream transcriptional targets of BMP2 signaling using mRNA-sequencing on control and BMP2-treated primary human trophoblast cells (n=5). Gene ontology annotations revealed that differentially expressed genes were involved in multiple organ development and cellular functions. Cell adhesion and extracellular matrix organization were among the significantly associated terms.

overall_design: Primary human trophoblasts were isolated from first-trimester placental villi. mRNA expression profiling was conducted on primary placental trophoblast cells from five first-trimester placentas (n=5) treated with vehicle control or 25 ng/ml BMP2 for 24 h.

first: Peter

middle: C

last: Leung


title: NLRP3 deficiency reverts intratumoral T cell exhaustion

status: Public on Apr 14 2022

first: Veronika

last: Lutz

state: D

institute: Philipps-University of Marburg

summary: CD8+ T cells derived from mice with intact NLRP3 signaling in the tumor microenvironment showed an increased expression of coinhibitory receptors PD-1, TIM-3, 2B4 and LAG-3 compared to CD8+ T cells from PancOVA-bearing Nlrp3-/- mice, indicating that NLRP3 inflammasome activation in the tumor microenvironment mediates IL-18 receptor signaling-induced T cell exhaustion. RNAseq was used to characterised molecular pathways involved in T cell plasticity in the presence and absence of intratumoral NLRP3.

overall_design: RNAseq of endogenous WT versus  Nlrp3-/- CTLs showed a distinct transcriptional program for WT and Nlrp3-/- CTLs, related to signaling pathways regulating T cell exhaustion

first: Christian

last: Bauer

first: Magdalena

last: Huber

first: Matthias

last: Klein

first: Hartmann

last: Raifer

first: Felix

last: Picard

first: Ho-Ryun

last: Chung


title: Bulk RNA-seq analysis of neutrophils primed with KPC and KPSC

status: Public on Apr 26 2022

city: Shanghai

first: Ningning

last: Niu

address: 160 Pu Jian Road, Shanghai

department: Clinical Stem Cell Research Center

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

summary: BM-derived neutrophils were isolated and cultured for 20hr in 20% supernatants of KPC, KPSC, and control, respectively.

overall_design: For RNA preparation, neutrophils were sorted from BM cells, freshly treated with 20% CM from KPC or KPSC, and harvested after 24 hours. RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit (Illumina) using 5 μg of total RNA, according to manufacturer’s instructions.

first: Niu

last: Ningning

first: Xue

last: Jing


title: The whole transcriptional landscape of circulating tumor cells compared to metastases in stage IV breast cancer

status: Public on May 01 2022

city: Los Angeles

first: Julie

last: Lang

state: CA

address: 1510 San Pablo Street, Suite 412

department: Deparment of Surgery

institute: University of Southern California

summary: Metastasis is responsible for the vast majority of breast cancer related deaths. Metastatic breast cancer (MBC) is inherently different than primary breast cancer (BC), evolving under selection pressure at different organ sites or during systemic therapy.   The current ASCO guidelines call for biopsy of a metastatic site to guide decision making for systemic therapy. Yet, biopsies of macro metastasis are  oftentimes not feasible in the clinical setting. Circulating tumor cells (CTCs) have been shown to be prognostic in MBC, but their use as clinical biomarker beyond CTC enumeration has been limited. A better understanding of CTC-biology compared to  metastasis may shed light on treatment opportunities and help advance the application of CTCs as liquid biopsies in clinical practice. The ANGLE Parsortix system is a microfluidics device that separates CTCs based on size and deformability, without the need for  cell-surface marker selection. Our lab has previously demonstrated the feasibility of gene expression profiling of rare CTCs. Here, we evaluated whether whole transcriptome sequencing (RNA Seq) gene expression profiling of ANGLE Parsortix isolated CTCs may serve as a surrogate for biopsies of macro metastases. CTCs from 21 MBC patients were enumerated and captured from 10mL peripheral blood (PB) via the ANGLE Parsortix system.  RNA Seq was  performed on fresh metastatic tumor biopsies (mets), CTCs and peripheral blood from all patients.  Biopsy sites included: skin (n=1), lung (n=1), pleural effusion (n=5), pericardial effusion (n=1), breast (n=3), lymph node (n=2), brain (n=4), liver (n=1), ascites (n=3), cerebrospinal fluid (n=2) and bone (n=1).  19/21 patients were included in subsequent data analysis. We present the whole transcriptomic landscape of CTCs with comparison to metastases and peripheral blood all acquired prior to treatment of  Stage IV breast cancer.  Multiple genes, including oncogenes, breast epithelial, mesenchymal genes and cancer stem cell genes were found with higher expression in CTCs versus metastases.  When focusing on 66 known potentially clinically actionable genes in breast cancer, represented by 7 molecular signaling pathways, CTCs did not show significantly different patterns of expression versus mets compared to PB.  RNA Seq of CTCs  may be utilized to identify alterations in MBC patients that are potentially clinically actionable.

overall_design:
For n=19 patients, fresh metastatic tissue biopsies were compared to circulating tumor cells (CTCs).  Both metastatic tissue biopsies and CTCs were compared to peripheral blood (PB) to control for the normal leukocyte population of each patient.
Please note that there are 21 MBC patients, but only 19 were included in subsequent data analysis. The other 2 patiens had very low coverage for either CTC, PB, or Met sample. In such cases, the patient was excluded in the intrapatient analysis but the samples with good coverage were included in the global analysis.  The other 5 patients (78534, 111951, 111956, 111958, 111961) are controls (with only blood samples).

This series includes 3 samples of PBS buffer for negative controls.

first: Daniel

last: Campo


title: Small RNA sequencing of in vitro Angiogenin-hydrolyzed tRNAs

status: Public on Apr 05 2022

city: Vienna

first: Schaefer

last: Matthias

state: AT

address: Schwarzspanierstrasse 17-I

department: Cell and Developmental Biology

country: Austria

institute: Medical University Vienna, Center for Anatomy & Cell Biology

type: Non-coding RNA profiling by high throughput sequencing

summary: Specific environmental insults cause the limited fragmentation of transfer RNAs (tRNAs) into tRNA-derived small RNAs (tsRNAs), which have been implicated in a wide range of biological processes. tRNA fragmentation results from endonucleolytic activities targeting single-stranded tRNA regions. However, how a tRNA with a single hydrolyzed phosphodiester bond in the anticodon loop (‘nicked’ tRNA) gives rise to distinct tsRNAs remains poorly understood. After identifying RNA helicases that were able to unwind ‘nicked’ tRNAs in vitro, the specificity of one of those enzymes, DDX3X, was determined by RNA helicase assays on tRNAs, which had been subjected to  recombinant Angiogenin. Both in vivo ‘nicked’ tRNAs, DDX3X-unwound ‘nicked’ tRNAs as well as heat-denatured ‘nicked’ tRNAs were subjected to small RNA sequencing.

overall_design: To understand DDX3X unwinding specificity towards specific cleaved tRNAs, we performed small RNA sequencing on input tracer tRNA duplexes, heat-denatured tsRNAs as well as tsRNAs displaced from tracer tRNA duplexes by DDX3X helicase.

first: Aleksej

last: Drino

last: Schaefer


title: IL-18R signaling affects transcriptional profile of intratumoral CTLs

status: Public on Apr 08 2022

summary: We report that intratumoral IL-18R-deficient T cells show decreased T cell exhaustion in a murine pancreatic cancer model

overall_design: Examination of wt versus Il18r-/- OT-1 T cells in an adoptive T cell transfer model of pancreatic carcinoma


title: Regulatory role of energy metabolism in skeletal development

status: Public on Apr 01 2022

city: Boston

first: Tatsuya

last: Kobayashi

address: 50 Blossom Street, Thier 1101

department: Endocrine Unit

institute: Massachusetts General Hospital

summary: To test the consequence of reduced glycolysis and reduced cytoplasimic acetyl-CoA in mouse skeletal devleopment.  To reduce glycolysis, Ldha was homozygously deleted in collagen 2 expressing chondrocytes using the Cre-lox sytem [Col2-Cre:Ldha(fl/fl)] on top of one allele germline deletion of Ldhb [Ldhb(+/-)].  To reduce cytoplasmic/nuclear acetyl-CoA, Acly that catalizes conversion of citreate into acetyl-CoA was deleted in chondrocytes using Col2-Cre.  Both mutant mice develop skeletal dysplasia, but former model survive postnatally, whereas Acly mutants die at birth.

overall_design: To test the consequence of reduced glycolysis and reduced cytoplasimic acetyl-CoA in mouse skeletal devleopment, we deleted Ldha and one allele of Ldhb, and Acly in chondrocytes.  Primary chondrocytes were isolated from P5 Col2-Cre:Ldha(fl/fl):Ldhb+/- mice, and from E18.5 Col2-Cre:Acly(fl/fl) mice.  Rib cartilage was digested with 0.2% collagenase in DMEM with 10% FCS.  Collagenase was removed and cells were plated at a confluent density. After overnight culture in vitro, RNA was extracted for RNA-seq analysis.


title: Progerin triggers a phenotypic switch  in VSMC that causes replication stress and an aging-associated secretory signature

status: Public on Mar 23 2022

city: St Louis

first: Susana

last: Gonzalo

state: MO

address: 1100 S Grand Blvd

department: Biochemistry and Molecular Biology

institute: Saint Louis University

summary: Hutchinson Gilford Progeria Syndrome is a premature aging disease caused by LMNA gene mutation and the production of a truncated lamin A protein “progerin” that elicits cellular and organismal toxicity. Progerin accumulates in the vasculature, being especially toxic for vascular smooth muscle cells (VSMC). Patients' autopsies show that vessel stiffening, and aortic atherosclerosis is accompanied by VSMC depletion in the medial layer, altered extracellular matrix (ECM), and thickening of the adventitial layer. Mechanisms whereby progerin causes massive VSMC loss and vessel alterations remain poorly understood. Mature VSMC retain phenotypic plasticity and can switch to a synthetic/proliferative phenotype. Here we show that progerin expression in human and mouse VSMC causes a switch towards the synthetic/proliferative phenotype. This switch elicits some level of replication stress in normal cells, which is exacerbated in the presence of progerin, leading to telomere fragility, genomic instability, and ultimately VSMC death. Importantly, calcitriol prevents replication stress, telomere fragility, and genomic instability, reducing VSMC death. In addition, RNAseq analysis shows induction of a profibrotic and proinflammatory aging-associated secretory phenotype upon progerin expression in human primary VSMC. Our data suggest that phenotypic switch-induced replication stress might be an underlying cause of VSMC loss in progeria, which together with loss of contractile features and gain of profibrotic and proinflammatory signatures contribute to vascular stiffness in HGPS. Preventing the phenotypic switch-induced replication stress with compounds such as calcitriol might ameliorate CVD in HGPS patients

overall_design: To determine the effects of progerin expression in VSMC, we lentivirally transduced human primary aortic VSM (AoSMC) with Flag-progerin (progerin) or only Flag (control). These cells were generated two independent times and each cell line was analyzed by RNAseq two independent times. Thus, we have a total of 4 repeats analyzed per sample. We performed bulk RNA-seq and GO analysis of differentially expressed (DE) genes was performed using functional annotation tools DAVID and STRING.

first: Nuria

last: Coll-Bonfill

first: Urvashi

last: Mahajan

first: Chien-Jung

last: Lin

first: Robert

middle: P

last: Mecham


title: Single cell deconstruction of murine volumetric muscle loss reveals inflammatory imbalances preventing muscle stem cell mediated regeneration

status: Public on Apr 04 2022

city: Ann Arbor

first: Carlos

middle: Andres

last: Aguilar

address: 2200 Bonisteel Blvd

department: Biomedical Engineering

institute: University of Michigan

summary: Volumetric muscle loss (VML) overwhelms the innate regenerative capacity of mammalian skeletal muscle (SkM), leading to numerous disabilities and reduced quality of life. Immune cells are critical responders to muscle injury and guide tissue resident stem cell and progenitor mediated myogenic repair. However, how immune cell infiltration and inter-cellular communication networks are altered following VML and drive pathological outcomes remains under-explored. Herein, we characterize the cellular and molecular mechanisms of VML injuries that result in fibrotic degeneration or regeneration of SkM. Following degenerative VML injuries, we observe heightened infiltration of a previously uncharacterized population of Natural Killer (NK) cells as well as persistence of neutrophils beyond two weeks post injury. Functional validation of NK cells revealed an antagonistic role on neutrophil accumulation in part via CCR1 mediated chemotaxis. The persistent infiltration of neutrophils in degenerative VML injuries was found to contribute to impairments in muscle stem cell regenerative function, which was also attenuated by transforming growth factor beta 1 (TGFb1). Blocking TGFb signaling antagonized neutrophil accumulation, reduced fibrosis, and improved muscle specific force. Collectively, these results enhance our understanding of immune cell-stem cell crosstalk that drives regenerative dysfunction and provide further insight into possible avenues for fibrotic therapy exploration.

overall_design: 8-10 week old C57B6J mice were uninjured or received bilateral 2mm or 3mm muscle loss defects to the rectus femoris and were humanely euthalized 7, 14, 28, or 42 days post injury. Quadriceps were dissected using sterile surgical instruments and enzymatically digested. Live cells were FACS-enriched using propidium iodide negative selection, then loaded into the 10X Genomics chromium single cell controler and single cells were captured into nanoliter-scale gel bead-in-emulsions. cDNAs were prepared using the second generation single cell 3? Protocol as per manufacturer?s instructions and sequenced on a Novaseq. Each sample is a pool of two mice (4 defects).

first: Jacqueline

last: Larouche

first: Sarah

middle: J

last: Kurpiers


title: Mst1-mediated phosphorylation of Nur77 is required for embryo implantation

status: Public on Mar 21 2022

city: Nanjing

first: Ruiwei

last: Jiang

address: No.321 Zhongshan Road

department: Drum Tower Hospital Affiliated to Medical School

institute: Nanjing University

summary: Our results indicated that a Nur77-derived phosphorylated peptide containing the phosphorylated T366 promotes epithelium-embryo adhesion both in vitro and in vivo, RNA-seq analysis was applied in the uterus samples from delayed implantation mouse model treated with pepetide-pThr366 or saline intrauterus injection.

overall_design: Mice were ovariectomized on the morning of D4 and maintained by Progesterone injections, then was terminated via the injection of a sufficient dose of Estrogen, and either saline or a peptide was then injected into the uterus. Uerine samples from peptide and saline groups were collected at 12 h after peptide injection for RNA sequencing.

first: Ruiweim


title: Functional Characterization of a Potent and Novel BET Inhibitor BBC1115 Identified from DNA-encoded Small Molecule Library Screening

status: Public on Mar 20 2022

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

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

overall_design: Refer to individual Series


title: S100a16 deficiency prevents liver fibrosis via inhibiting C-X-C motif chemokine receptor 4 expression

status: Public on Mar 25 2022

first: Wen-Song

last: Zhang

state: Jiangsu

address: 300 Guangzhou Road

institute: The First Affiliated Hospital of Nanjing Medical University

summary: Liver fibrosis has been implicated in the pathogenesis of various liver disease. Thus far, there is still no effective intervention means for this process. Recently, we have demonstrated that S100A16 participated in liver lipid accumulation and renal fibrosis. Therefore, we hypothesized that S100A16 took a critical role in liver fibrosis. S100a16 transgenic and knockdown mice were generated and stimulated with carbon tetrachloride, bile duct ligation and methionine choline deficiency diet. Alterations of gene expression in hepatic stellate cells from wild type and S100a16+/- mice were investigated by transcriptome sequencing. S100A16 expression levels in liver tissue of patients and rodent models of liver fibrosis were markedly increased. S100a16 transgenic mice showed spontaneous liver fibrosis after normal feeding for 6 months. On the contrary, silencing of S100a16 exhibited obvious protective effect against liver fibrosis caused by different stimulations. Meanwhile, results showed that deletion of S100a16 significantly inhibited hepatic stellate cells (HSCs) activation cultured in fetal bovine serum contained medium. RNA sequencing results revealed that mechanistically, C-X-C motif chemokine receptor 4 (Cxcr4) participated in the process of S100a16 in liver fibrosis. Knockdown of S100a16 inhibited Cxcr4 expression through augmenting P53 expression. SDF-1α/CXCR4-dependent extracellular signal-regulated kinase 1/2 and Akt phosphorylation mediated the effects of S100a16 on α-smooth muscle actin expression and HSCs activation. These data indicate that S100a16 deficiency prevents liver fibrosis by inhibiting Cxcr4 expression. Targeting S100A16 may provide insights into the pathogenesis of liver fibrosis and pave the way for developing strategies for liver fibrosis-related diseases prevention and treatment.

overall_design: HSCs were isolated from WT or S100a16+/- mice and cultured in FBS-containing medium for 7 days for full differentiation, and the genome-wide expression was determined by transcriptome sequencing.

first: Yun

last: Liu


title: CDK7 inhibition interdicts deregulated transcription and cell cycle control in multiple myeloma

city: Houston

first: Charles

middle: Yang

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine


title: ATAC-Seq of young and aged satellite cells

status: Public on Mar 15 2022

city: Montreal

first: Vahab

last: Soleimani

state: QC

address: 3640 rue University

department: Human Genetics

institute: McGill University

summary: The function of skeletal muscle stem cells (MuSC) declines during aging, contributing to the advent of age-related myopathies. However, whether this decline is the result of accumulating cellular damage, altered heterogeneity in stem cell populations or due to the effect of the changing niche environment remains largely unknown. By scRNA-Seq, we show that the age-related reduction in the MuSC pool is not stochastic, with different subpopulations being distinctly affected in aging. Using an in vivo allogeneic stem cell transplantation model, we show that exposure of MuSCs from old mice to a youthful niche environment significantly restores the gene expression of genes that are altered in aging. We show that age-related changes in the MuSC transcriptome are mainly driven by alterations in chromatin and transcription but are not due to posttranscriptional mechanisms affecting RNA stability. Furthermore, our data indicates that the portion of the genome that is activated in aging is significantly more responsive to restoration by niche factors compared to the repressed counterpart. Taken together, our data reveals that the niche environment plays a decisive role in controlling the transcriptional activity of MuSCs.

overall_design: 5000 satellite cells were isolated by Fluorescence-Activated Cell Sorting (FACS) from 2 young and 2 aged Pax7-eGFP male mice and sorted directly into ATAC-Seq Lysis buffer. Each sample was processed using a modified version of the OMNI ATAC-Seq protocol (Corces, M. R. et al. Nature Methods, 2017).

middle: D

first: Hamed

last: Najafabadi


title: scRNAseq RAT DIA WT and DMD 12months

status: Public on Mar 14 2022

city: CRETEIL

first: Valentina

last: TAGLIETTI

address: RUE GENERAL SERRAIL

institute: INSERM

summary: Duchenne muscular dystrophy (DMD) is a fatal muscle-wasting disorder caused by mutations in the Dystrophin gene with no therapeutic option. To bridge the gap between preclinical and therapeutic evaluation studies, we have generated a rat model for DMD that carries an exon 52 deletion (R DMDdel52) causing a complete lack of dystrophin protein. Here we show that R DMDdel52 animals recapitulated human DMD pathophysiological trajectory more faithfully than the mdx mouse model. We report that R DMDdel52 rats displayed progressive and severe skeletal muscle loss associated with fibrotic deposition, fat infiltration and fibre type switch. Early fibrosis was also apparent in the cardiac muscle. These histological modifications led to severe muscle, respiratory and cardiac functional impairments leading to premature death around one year. Moreover, DMD muscle exhibited systemic inflammation with a mixed M1/M2 phenotype. A comparative single cell RNAseq analysis of the diaphragm muscle was performed, revealing cellular populations alteration and molecular modifications in all muscle cell types. We show that DMD fibroadipogenic progenitors produced elevated levels of cartilage oligomeric matrix protein (COMP), a glycoprotein responsible for modulating homeostasis of extracellular matrix, and whose increased concentration correlated with muscle fibrosis both in R DMDdel52 rats and human patients. Fibrosis is a component of tissue remodelling impacting the whole musculature of DMD patients, at the tissue level but most importantly at the functional level. We therefore propose that this specific biomarker can optimize the prognostic monitoring of functional improvement of patients included in clinical trials.

overall_design: RAT Diaphragm WT and DMD 12months

last: Taglietti

first: Kaouthar

last: Kefi

first: Iwona

last: Bronisz-Budzyńska

first: Busra

last: Mirciloglu

first: Mathilde

last: Rodrigues

first: Nastasia

last: Cardone

first: Fanny

last: Coulpier

first: Baptiste

last: Periou

first: Christel

last: Gentil

first: Melissa

last: Goddard

first: François-Jérôme

last: Authier

first: France

last: Pietri-Rouxel

first: Edoardo

last: Malfatti

first: Peggy

last: Lafuste

first: Laurent

last: Tiret

first: Frederic

last: Relaix


title: Quantitative Transcriptome Analysis of RIPK1-KO CD4 T cells

status: Public on Feb 27 2022

city: Yokohama

first: Takayuki

last: Imanishi

address: 1-7-22 Suehiro-cho, Tsurumi-ku

institute: RIKEN Center for Integrative Medical Sciences (IMS)

summary: RIPK1 is a key signaling molecule controlling cell death and inflammation through both scaffold and kinase functions of RIPK1. Human RIPK1 deficiency causes immunodeficiency and inflammatory diseases. Here we analyzed the functional roles of RIPK1 in CD4 T cells.

overall_design: The transcriptome of CD4 T cells from T-cell-specific RIPK1-KO mice were analyzed using Illumina HiSeq1500.

first: Takashi

last: Saito