title: Time- and tissue-specific response of the mouse transcriptome after a short-term exposure to normoxia or intermittent hypoxia (IH)

first: Bala S. C.

last: Koritala

state: Ohio

address: 3333 Burnet Avenue

department: Division of Pediatric Otolaryngology

summary: To investigated the effects of early exposure to IH on tissue-specific transcriptome and biological processes, we evaluated differential gene expression of circadian rhythms and 24-hour mean expression in the lung, heart, liver, kidney, muscle, and cerebellum from mice after exposure to normoxic and IH conditions. The cardiopulmonary tissues were most affected by short-term exposure to IH in comparison with other organs.

overall_design: Eight-week-old C57BL/6J mice were exposed to either normoxia or intermittent hypooxia (21-8% O2) for seven days before it was released into constant normoxic darkness for two days. Multiple tissues (liver, lung, kidney, muscle, heart, and cerebellum) were harvested on the second day of constant darkness for 24 hours with three-hour intervals to assess changes in their transcriptome.

first: Bala

middle: S

first: Yin

middle: Y

last: Lee

first: David

last: Smith


title: Characterizing the tumor immune microenvironment of ependymomas using targeted gene expression profiles and RNA sequencing

status: Public on Oct 25 2022

city: Rotterdam

first: Willem

last: de Koning

state: Zuid-Holland

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus University Medical Center

summary: Defining the tumor immune microenvironment (TIME) of patients using transcriptome analysis is gaining more popularity. Here, we examined and discussed the pros and cons of using RNA -sequencing for Fresh Frozen (FF) samples and targeted gene expression immune profiles (NanoString) for Formalin-Fixed, Paraffin-Embedded (FFPE) samples to characterize the TIME of ependymoma samples.

overall_design: RNA was extracted from FFPE samples (ST n=2, PF-A n=4)

first: Fenna

middle: F

last: Feenstra

first: Friso

middle: J

last: Calkoen

first: Jasper

last: van der Lugt

first: Lennart

middle: A

last: Kester

first: Dana

middle: M

last: Mustafa


title: Single-cell analysis reveals dynamics of human B cell differentiation and identifies novel B and antibody-secreting cell intermediates

status: Public on Sep 27 2022

city: Amsterdam

first: Niels

last: Verstegen

address: Plesmanlaan 125

institute: Sanquin Research

type: Expression profiling by high throughput sequencing

summary: Differentiation of B cells into antibody-secreting cells (ASCs) is a key process to generate protective humoral immunity. A detailed understanding of the cues controlling ASC differentiation is important to devise strategies to modulate antibody formation. Here, we dissected differentiation trajectories of human naive B cells into ASCs using single-cell RNA sequencing. By comparing transcriptomes of B cells at different stages of differentiation from an in vitro model with ex vivo B cells and ASCs, we uncovered a novel pre-ASC population present ex vivo in lymphoid tissues. For the first time, a germinal-center-like population is identified in vitro from human naive B cells and possibly progresses into a memory B cell population through an alternative route of differentiation, thus recapitulating in vivo human GC reactions. Our work allows further detailed characterization of human B cell differentiation into ASCs or memory B cells in both healthy and diseased conditions.

overall_design: Human naive B cells (CD19+CD27-IgG-IgD+) are sorted from healthy donor PBMCs and cultured on a feeder layer of human CD40L-expressing mouse fibroblasts and restimulated after six days. Cytokines typically expressed by follicular T cells (Tfh) (IL-21, IL-4) are added to mimic Tfh help for B cell differentiation. The dynamics of human naive B cell differentiation were investigated in detail by single-cell RNA sequencing. Cultured cells were single-cell sorted on day 11 based on the expression of CD27 and CD38 to obtain a faithful representation of cells at varying stages of B cell to ASC differentiation. Next, cells were processed for single-cell RNA sequencing using the SMARTseq2 method.

first: N

first: S

last: Pollastro

first: P

last: Unger

first: C

last: Marsman

first: G

last: Elias

first: T

last: Jorritsma

first: M

last: Streutker

first: K

last: Baβler

last: Händler

last: Rispens

first: J

middle: L

last: Schultze

first: A

last: ten Brinke

last: Beyer

last: van Ham


title: Development of Xenopus Mucociliary Epithelium

city: Ulsan

first: Taejoon

last: Kwon

address: 50 Unist-gil

department: Department of Biomedical Engineering

country: South Korea

institute: Ulsan National Institute of Science and Technology

summary: Here we profile 10 distinct Xenopus MCE developmental stages throughout embryogenesis and characterise the expression patterns and state transition accompanying cell-fate decisions.

overall_design: We harvest holoblastic blastula stage embryos (Nieuwkoop and Faber, NF stage 8), culture the explants ex vivo (referred as organoids), and profile 10 MCE development stages spanning blastula (stage 8) to gastrulation (stage 10.5, 12), neurula (stage 13, 16, 18, 21) and early tailbud development (stage 22, 24, 27), (22, 23) . After quality control (doublet removal and normalization; methods), we obtain 33,990 single-cell transcriptomes with high sampling and representation across all developmental stages.

first: Andreas

last: Møller

first: Julie

last: Lee

first: Shinhyeok

last: Chae

first: Jakub

last: Sedzinski

first: Kedar

middle: N

last: Natarajan


title: Modelling human pre-gastulation development by 3D culture of blastoids generated from the primed-to-naive transitioning intermediates [scRNA-seq]

status: Public on Sep 24 2022

city: Shanghai

first: Tu

middle: zhi

last: fen

address: Tongji University Siping Road Campus

department: life science and technology

country: China

institute: Tongji University

summary: Our study provides an alternative strategy to generate human blastoids and model early embryogenesis up to pre-gastrulation stage, facilitating the insights into human embryonic development

overall_design: Single cell transcription profiling of blastoid generated from intermediates during human primed-to-naïve transition process .

first: Yan

last: Bi

first: Zhifen

last: Tu

first: Yixuan

last: Wang


title: Modelling human pre-gastulation development by 3D culture of blastoids generated from the primed-to-naive transitioning intermediates [RNA-seq]

overall_design: Transcription profiling of derived stem cell lines from blastoid.


title: Modelling human pre-gastulation development by 3D culture of blastoids generated from the primed-to-naive transitioning intermediates

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

overall_design: Refer to individual Series


title: 3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice [ChIA-PET]

status: Public on Sep 28 2022

city: Wuhan

first: yue

last: li

address: Shizishan Street

institute: HUAZHONG Agriculture University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Repressive epigenetic modification histone H3 lysine 27 tri-methylation (H3K27me3) marks many agronomically important genes in plants. However, H3K27me3-associated three-dimensional (3D) genome architecture and its regulatory functions in rice flowering time remain unclear. In this study, we map H3K27me3-associated genome topology using long-read ChIA-PET and reveal extensive chromatin loops among H3K27me3-marked regions in different rice varieties and tissues. Multiple H3K27me3-associated chromatin loops usually tether together and further form repressive chromatin interacting domains (RIDs), which provide structural bases for the regulation of the co-modification and co-expression of interacting genes. Surprisingly, we identified extensive chromatin loops between the rice florigen genes Hd3a and RFT1, and frequent chromatin interactions between the positive flowering regulator Ehd1 on the chromosome 10 and Hd3a/ RFT1 loci on the chromosome 6. These results suggest that flowering genes might form a Ehd1-Hd3a/RFT1-centered spatial gene cluster in rice. We also demonstrate the flowering regulator protein complexes comprising Ghd7, Ghd8, and Hd1 could bind to the Ehd1-Hd3a/RFT1 spatial gene cluster. In addition, liquid-liquid phase separation of Ghd7 and Hd1, as well as the essentially synchronous expression of Ehd1 and Hd3a suggest that this spatial gene cluster acts as a regulatory hub to coordinately regulates the expression of Ehd1-Hd3a. This work uncovers the frame of integrated cis and trans molecular mechanism underlying transcriptional regulation of florigen genes in rice.

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: H3K27me3-associated genome topology in different rice varieties and tissues (MH63-seedling, MH63-root, ZS97-seedling, ZS97-root, DJ-seedling, osemf2b-seedling)

first: Yue

last: Li

first: Zhanyi

last: Zhang


title: Regulation of synaptic connectivity in schizophrenia by mutual neuron-microglia interaction

status: Public on Sep 16 2022

city: Reutlingen

first: Hansjuergen

last: Volkmer

address: Markwiesenstr 55

country: Germany

institute: NMI at the University of Tuebingen

summary: The examination of post-mortem brain tissue suggests synaptic loss as a central pathological hallmark of schizophrenia spectrum (SCZ), which is potentially related to activated microglia and increased inflammation. Induced pluripotent stem cells serve as a source for neurons and microglia-like cells to address neuron-microglia interactions. Here, we present a co-culture model of neurons and microglia, both of human origin, to show increased susceptibility of neurons to microglia-like cells derived from SCZ patients. Analysis of IBA-1 expression, NFκB signaling, transcription of inflammasome-related genes, and caspase-1 activation shows that enhanced, intrinsic inflammasome activation in patient-derived microglia exacerbates neuronal deficits such as synaptic loss in SCZ. Anti-inflammatory pretreatment of microglia with minocycline specifically rescued aberrant synapse loss in SCZ and reduced microglial activation. These findings open up possibilities for further research in larger cohorts, focused clinical work and longitudinal studies that could facilitate earlier therapeutic intervention.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for healthy control- and schizophrenia patient-derived iPSC-based microglia

first: Ricarda

last: Breitmeyer

first: Sabrina

last: Vogel

first: Johanna

last: Heider

first: Richard

last: Wüst

first: Anna-Lena

last: Keller

first: Anna

last: Binner

first: Julia

middle: C

last: Fitzgerald

last: Fallgatter

first: Hansjürgen

first: Sophia-Marie

last: Hartmann


title: Effect of cardiac-specific FASTKD1 overexpression on gene expression in the heart

status: Public on Sep 12 2022

city: Columbia

first: Christopher

last: Baines

state: MO

address: 134 Research Park Dr

country: USA

institute: University of Missouri

summary:
We generated transgenic mice with cardiac myocyte-specific overexpression of the mitochondrial RNA regulating protein FASTKD1
We then harvested hearts from 3-month-old non-transgenic and transgenic mice (4 mice in each group) and conducted gene expression profiling using RNA seq

overall_design: Comparative gene expression profiling analysis of RNA-seq data for non-transgenic and FASTKD1 transgenic mouse hearts


title: Identifying Altered Developmental Pathways in Induced Pluripotent Stem Cell-Derived Neural Stem Cells From a Patients with Globoid Cell Leukodystrophy Using Transcriptome Profiling

status: Public on Sep 04 2022

city: yichang

first: yafeng

last: lv

address: No. 8, Daxue Road, Xiling District, Yichang City

institute: China Three Gorges University

summary: we identified gene-expression changes in induced pluripotent stem cells (iPSCs) and iPSC-derived neural stem cells (NSCs) from a patients with GLD (K-iPSCs/NSCs) and normal control (AF-iPSCs/NSCs), in order to investigate the potential mechanism underlying GLD pathogenesis. We identified 194 (K-iPSCs vs. AF-iPSCs) and 702 (K-NSCs vs. AF-NSCs) significantly dysregulated mRNAs when comparing the indicated groups. We also identified dozens of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway terms that were enriched for the differentially expressed genes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for induced pluripotent stem cells (iPSCs) and iPSC-derived neural stem cells (NSCs) from a patients with GLD

first: Yafeng

last: Lv

first: Wei


title: Carbon source availability drives nutrient utilization in CD8+ T cells

status: Public on Sep 01 2022

city: Grand Rapids

first: Russell

last: Jones

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

summary: Investigating the impact of physiological carbon source (PCS) availability on the transcriptional profile of activated CD8+ T cells proliferating in vitro

overall_design: Activated mouse CD8+ T cells were cultured for 24 hours in growth medium (IMDM or VIM, plus IL-2) supplemented with or lacking physiologic carbon sources (acetate, beta-hydroxybutyrate, citrate, lactate, and pyruvate).

first: Irem

last: Kaymak

first: Katarzyna

last: Luda

middle: G


title: mRNA profiles of Salmonella specific tissue resident memory CD4 T cells and effector memory CD4 T cells from the liver, and splenic effector memory CD4 T cells

status: Public on Sep 17 2022

city: Davis

first: Claire

last: Depew

state: CA

address: 4115 Primate Drive

institute: University of California Davis

summary: IFN𝛾-YFP reporter mice (Jax# 017580) were immunized intravenously with attenuated Salmonella enterica serovar Typhimurium intravenously. 45 days later, tissue resident memory CD4 T cells (CD69+ YFP+) in the liver, effector memory CD4 T cells (CD69- YFP+) in the liver, and effector memory CD4 T cells (CD69- YFP+) in the spleeen were sorted and RNA was sequenced

overall_design: Comparative gene expression profiling analysis of RNAseq data for Salmonella enterica serovar Typhimurium specific liver tissue resident memory CD4 T cells, liver effector memory CD4 T cells and splenic effector memory CD4 T cells at day 45 post infection

middle: E

first: Stephen

last: McSorley


title: Microbiota derived interlukin-35 producing B cells induce regulatory immune responses and supress colitis in mice

status: Public on Aug 31 2022

first: Minxiang

last: Xie

address: Dongan Road 130

institute: Fudan University

summary:
To investigate the immune regulatory role of microbiota derived interlukin-35 producing B cells in DSS-induced mice colitis.
We then performed gene expression profiling analysis using data obtained from RNA-seq of isolated B cells from patches of colitis mice at four different time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of B cells from patches of colitis mice at different time points (Day 0, Day 4, Day 7 and Day 10)

first: Luman

last: Wang


title: APOE modulates microglial immunometabolism in response to age, amyloid pathology, and inflammatory challenge [Bulk RNA-seq]

city: Lexington

first: Lance

last: Johnson

state: KY

address: 760 Press Ave, HKRB 135

department: Physiology/Sanders-Brown Center on Aging

institute: University of Kentucky

summary: The E4 allele of Apolipoprotein E (APOE) is associated with both metabolic dysfunction and a heightened pro-inflammatory response – two findings that may be intrinsically linked through the concept of immunometabolism. Here, we combined bulk, single-cell, and spatial transcriptomics with cell-specific and spatially resolved metabolic analyses to systematically address the role of APOE across age, neuroinflammation, and AD pathology. RNAseq highlighted immunometabolic changes across the APOE4 glial transcriptome, specifically in subsets of metabolically distinct microglia enriched in the E4 brain during aging or following an inflammatory challenge. E4 microglia display increased Hif1a expression, a disrupted TCA cycle, and are inherently pro-glycolytic, while spatial transcriptomics and MALDI mass spectrometry imaging highlight an E4-specific response to amyloid that is characterized by widespread alterations in lipid metabolism. Taken together, our findings emphasize a central role for APOE in regulating microglial immunometabolism.

overall_design: Mice were female mice aged 3 or 24 months of age, or female E3_5xFAD or E4_5xFAD mice (homozygous APOE transgenic mice crossed to the 5XFAD strain) 12 months of age


title: Combating pancreatic cancer with ovarian cancer cells

status: Public on Aug 30 2022

city: Beijing

first: Chunmei

last: Cui

state: Beijing

address: Xueyuan Road 38, Haidian district, eijing

institute: Peking University

summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly malignant tumor, and the five-year survival rate is still less than 5%. However, Gemcitabine, a first-line chemotherapy drug of PDAC, has serious side effects and chemotherapy resistance. It is imperative to find new therapies to treat patients with advanced pancreatic cancer. With the computational screening, we found the gene sginature of ovarian serous carcinoma is anti-correlated with that of PDAC. Then we established an animal model of pancreatic cancer xenografts and injected ovarian cancer cell SKOV3 into xenografts to observe whether the  SKOV3 could inhibit the growth of pancreatic cancer. We used RNA-sequencing to compare the tumor treated with SKOV3 to that with normal saline.

overall_design: bulk RNA-seq of mouse tumor from normal saline treatment, and SKOV3 treatment

first: Xiao

last: Lin


title: APOE modulates microglial immunometabolism in response to age, amyloid pathology, and inflammatory challenge [Spatial transcriptomics]

overall_design: Mice were female mice aged 3 or 24 months of age, or female E3_5xFAD or E4_5xFAD mice (homozygous APOE transgenic mice crossed to the 5xFAD strain) 12 months of age.


title: Single cell RNA-sequencing of pleural cavity macrophages naïve and nematode-infected C57BL/6 and BALB/c mice

city: Dublin

first: Conor

last: Finlay

address: Trinity Translational Medicine Institute, Trinity College Dublin, St. James' Hospital Campus, Trinity College Dublin, Dublin 8

department: School of Medicine

country: Ireland

institute: Trinity College Dublin

summary: The recent revolution in tissue-resident macrophage biology has resulted largely from murine studies performed in the C57BL/6 strain. Here, we provide a comprehensive analysis of immune cells in the pleural cavity using both C57BL/6 and BALB/c mice. Unlike C57BL/6 mice, naïve tissue-resident Large Cavity Macrophages (LCM) of BALB/c mice failed to fully implement the tissue residency programme. Following infection with a pleural-dwelling nematode these pre-existing differences were accentuated with LCM expansion occurring in C57BL/6 but not BALB/c mice. While infection drove monocyte recruitment in both strains, only in C57BL/6 mice were monocytes able to integrate into the resident pool. Monocyte to macrophage conversion required both T cells and IL-4Rα signalling. Host genetics are therefore a key influence on tissue resident macrophage biology, and during nematode infection Th2 cells control the differentiation pathway of tissue resident macrophages.

overall_design: For the input of the single cell RNA sequencing, we chose the day 35 p.i. timepoint as this is when worm killing begins in C57BL/6 mice and monocyte influx begins in infected BALB/c mice. Pleural cavity immune cells were isolated from naïve and day 35 post infection L. sigmodontis-infected C57BL/6 and BALB/c mice. Cells were sorted by FACS to select Live single, lineage-CD45.2+Ter-119-CD11b+ cells, where lineage cocktail contained TCR-b, CD20, CD19, Ly6G, Nk1.1, CD90.2, CD5, IgM, CD3e and Siglec-F antibodies. Samples were loaded separately on 10X Genomics Chromium controller. 4 Separate cDNA libraries were created using the Single Cell 3’ Library Version 2 Kit. Library preparation was performed by University of Manchester Genomics technology core facility. The pooled Library was sequenced with paired-end reads using a full S2 lane of a NovaSeq-6000 (Illumina) by Edinburgh Genomics yielding 1750 million reads. Original fastq files are included. Sequencing reads in fastq format were aligned to the mm10 mouse transcriptome using Cell Ranger v3.0 (10 X Genomics) count function, quantifing Unique Molecular Identifiers (UMI) for each gene associated with each cell barcode. Samples were integrated and normalised using the Cell Ranger aggr function producing a gene versus cell expression matrix. Supplementary files contain analysed R/Python objects.

first: James

last: Parkinson

first: Judith

last: Allen


title: Differential contributions of nuclear lamina association and genome compartmentalization to gene regulation

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: Tennessee

address: 1311 Cumberland Avenue

department: Department of Biochemistry & Cellular and Molecular Biology

institute: University of Tennessee Knoxville

summary: Purpose: A systematic analysis of how lamina association of chromosome regions influences their gene regulation in response to stimuli.  Here, Lamin associated domains (LADs) of prostate cancer cell lines LNCaP and VCaP were experimentally measured using Lamin B1 ChIP-Seq so that these could be compared to previously published expression data in these cell lines and published LAD data from other cell types.

overall_design: LNCaP and VCAP cells growing in culture were crosslinked with formaldehyde, chromatin was sonicated, and then lamin associated regions were immunoprecipitated with Lamin B1 antibody.  ChIP and INPUT (not treated with antibody) DNA samples were prepared and sequenced on an Illumina sequencing instrument.

first: Priyojit

last: Das

first: Rebeca

last: San Martin

last: Patton  McCord


title: Serum levels of iCAF-derived Osteoglycin predict favorable outcome in pancreatic cancer

status: Public on Aug 23 2022

first: Leandro

last: Moreno

address: Meibergdreef 9

institute: AmsterdamUMC

summary: Pancreatic ductal adenocarcinoma (PDAC) is characterized by abundant stroma, the main cellular constituents of which are cancer-associated fibroblasts (CAFs). Heterogeneity in the PDAC CAF population was recently delineated demonstrating that both tumor-promoting and -suppressive activities co-exist in the stroma. Here, we aimed to identify biomarkers for the CAF population that contribute to a favorable outcome. Osteoglycin (OGN) was identified as a candidate serum prognostic marker. Single-cell analysis in KPC mice indicated that OGN is derived from a subgroup of inflammatory CAFs. OGN-expressing fibroblasts are distinct from resident healthy pancreatic stellate cells and arise during pancreatitis. Serum OGN levels were prognostic for favorable overall survival in two independent PDAC cohorts.

overall_design: Examination of single cell RNA expression profiles of pancreatic cells and post induced pancreatitis

first: Mark

middle: P

last: Dings

first: Maarten

last: Bijlsma


title: APOE modulates microglial immunometabolism in response to age, amyloid pathology, and inflammatory challenge

status: Public on Sep 15 2022


title: Expression data from triple negative breast cancer-MDA-MB-231 cells treated with vehicle and salvia chinensia benth

status: Public on Aug 25 2022

city: Dalian

first: Man

last: Li

state: Liaoning Province

address: 467#, Zhongshan Road, Shahekou distinct

department: Department of Oncology

institute: The Second Hospital of Dalian Medical University

summary: To identify salvia chinensia benths induced transcriptional changes in triple negative breast cancer cell, RNA-sequencing of MDA-MB-231 cells after salvia chinensia benths treantmnent was performed. Differential gene expression analysis resulted in 7582 differentially expressed genes.

overall_design:
MDA-MB-231 cells were treated with vehicle or salvia chinensia benth for 24 hours, followed by RNA extraction and RNA sequencing analysis. Each has three biological repeats.

Please note that the raw data files (initially provided by the submitter) failed at SRA, and replacement files have been requested but not yet provided.

first: Kainan

first: Zuowei

last: Zhao


title: Genome wide identification of potential odontogenic genes involved in the dental epithelium-mesenchymal interaction during early odontogenesis

status: Public on Aug 22 2022

city: Guangzhou

first: Jiawen

last: Chen

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District, Guangzhou, Guangdong, China, 510515

institute: Southern Medical University

summary:
To explore the the gene profile during epithelium-mesenchymal interaction in early odontogenesis.
Weperformed gene expression profiling analysis using data obtained from RNA-seq of the dental mesenchymal and epithelium group at two different timepoints, E11.5 and E13.5 respectively.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the dental mesenchymal and epithelium group at two different timepoints, E11.5 and E13.5 respectively.

first: Tianyu

last: Sun

first: Yan

last: You

first: Binbin

first: Buling

last: Wu

first: Jingyi


title: RIP-seq of DDX5 in rhabdomyosarcoma cells

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

summary: Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma of childhood characterized by the inability to exit the proliferative myoblast-like stage. Here, we identified the DEAD box RNA helicase 5 (DDX5) as a potential therapeutic target to inhibit alveolar rhabdomyosarcoma (ARMS) growth. We show that DDX5 is overexpressed in alveolar RMS cells, demonstrating that its depletion drastically decreases ARMS viability and slows tumor growth in xenograft models. Mechanistically, we provide evidence that DDX5 functions upstream the G9a/AKT survival signalling pathway, by modulating G9a protein stability

overall_design: DDX5 RNA binding examination in rhabdomyosarcoma cells, three biological replicates

first: Alberto

last: Gualtieri

first: Chiara

last: Mozzetta


title: TCR profiling of COVID convalescent and healthy donor whole blood with nCounter

status: Public on Aug 21 2022

city: Bethesda

first: Mallikarjuna

middle: Rao

last: Gedda

state: MD

address: 6 Center Dr

institute: NEI

summary: This study investigated the cellular immune response in people who had recovered from SARS-CoV2 infection(COVID-19).

overall_design: 253 whole blood samples from 158 COVID convalescent donors and 40 from Healthy donors

first: Patrick

last: Danaher

first: Lipei

last: Shao

first: Martin

last: Ongkeko

first: Leonard

first: Anh

last: Dihn

first: Mame

last: Thioye Sall

first: Opal

last: Reddy

first: Christina

last: Bailey

first: Amy

last: Wahba

first: Inna

last: Dzekunova

first: Robert

last: Somerville

first: Valeria

last: DiGiorgi

first: Jin

last: Ping

first: Kamille

last: West

first: David

last: Stroncek

first: Sandhya

middle: R

last: Panch


title: APOE modulates microglial immunometabolism in response to age, amyloid pathology, and inflammatory challenge [scRNA-seq 1]

first: Lance

last: Johnson


title: Whole Blood profiling of COVID convalescent and Healthy donors with nCounter

first: Mallikarjuna

last: Gedda

summary: This study investigated the cellular immune response in people who had recovered from SARS-CoV2 infection (COVID-19).

overall_design: 264 Whole Blood samples from 160 COVID convalescent donors, and 40 from Healthy donors.

first: Patrick

last: Chen


title: ChIP-Seq for CFI-1 in C. elegans

status: Public on Aug 20 2022

city: Chicago

first: Paschalis

last: Kratsios

state: IL

department: Department of Neurobiology

institute: University of Chicago

summary: We performed ChIP-seq on endogenously tagged CFI-1::3xFLAG fusion proteins in C. elegans

overall_design: One ChIP and one input sample.

first: Kratsios

last: Paschalis

first: Li

last: Yinan


title: Comparison of Erythrocyte Differentiation Efficiency and Gene Expression Signatures of Human Induced Pluripotent Stem Cells Derived from Peripheral Blood, Umbilical Cord Blood, and Bone Marrow

status: Public on Sep 25 2022

city: Seoul

first: Youn Keong

last: Cho

address: 50-1 Yonsei-ro

department: Department of Laboratory Medicine

institute: Yonsei University College of Medicine

summary: To determine the best cell source for the development of hiPSCs, we established hiPSCs from three different hematopoietic stem cell sources, peripheral blood, cord blood and, bone marrow aspirates, and differentiated them into functional RBCs. We compared the characteristics of hiPSCs and hiPSC-derived erythroid cells using various time course studies. We then performed gene expression profiling analysis using samples obtained from RNA-seq at 4 time points for each source.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hiPSCs derived from three different hematopoietic sources and hiPSC-derived erythroid cells at different time points

first: Youn

middle: K

first: Hyun-Kyung

last: Kim

first: Sinyoung

first: Hyun

middle: O


title: Vascular Surgery Patients with Elevated Neutrophil Lymphocyte Ratios Have Downregulated Neutrophil Complement RNA Expression

status: Public on Aug 17 2022

city: Cleveland

first: Ernest

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

summary: Elevated NLR (neutrophil-lymphocyte ratio) in elective vascular surgery (EVS) patients is associated with increased mortality independent of perioperative surgical outcome. To understand why high NLR is associated with higher mortality, we investigated neutrophil and lymphocyte transcriptome expression in patients undergoing EVS.

overall_design: Blood samples were collected from patients undergoing EVS and healthy donors for NLR calculation. RNAs were isolated and from subjects’ isolated neutrophils and lymphocytes. Patients were divided into NLR_Low (<3) and NLR_High (≥3) groups (n=6 each).

first: Alvin

middle: H

last: Schmaier

first: Jae

middle: S

first: E


title: Genome-wide mapping implicates R-loops in lineage-specific processes and DNA break hotspot formation in neural stem/progenitor cells

status: Public on Aug 16 2022

city: San Francisco

first: Bjoern

last: Schwer

institute: University of California, San Francisco

summary: We elucidated the genome-wide landscape of RNA:DNA hybrid structures called "R-loops" in primary neural stem/progenitor cells to assess their contribution to recurrent classes of DNA break "hotspots".

overall_design: We performed genome-wide mapping of RNA-DNA hybrids in mouse primary neural stem/progenitor cells via DRIP-seq.

first: Supawat

last: Thongthip

first: Annika

last: Carlson

first: Magdalena

last: Crossley


title: RNAseq Analysis of TP53+/+ and TP53-/- HCT116 colon carcinoma cell lines after treatment with p53 or ATF4-activating compounds

city: Albany

first: Morgan

last: Sammons

state: NY

address: 1400 Washington Ave, Life Sciences 2075

department: Biological Sciences

institute: University at Albany - SUNY

summary: We examined the gene expression changes resulting from treatment of either "wild-type" or "p53-deficient" human cell lines with compounds known to activate either p53 (nutlin-3A,etoposide) or the integrated stress response (ISR) transcription factor ATF4 (histidinol,tunicamycin)

overall_design: Comparative gene expression profiling (polyA+ selected RNAseq) on three biological replicates


title: The Histone Variant H2A.Z C-terminal Domain Has Locus- Specific Differential Effects on H2A.Z Occupancy and Nucleosome Localization

status: Public on Aug 18 2022

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

type: Genome binding/occupancy profiling by genome tiling array

summary: The incorporation of histone variant H2A.Z, a conserved H2A variant, into nucleosomes creates specialized chromatin domains that regulate DNA-templated processes, including transcription. H2A.Z-containing nucleosomes may poise gene regulatory regions for transcription, but mechanistic details are lacking. In Saccharomyces cerevisiae, the diverging H2A.Z C-terminus is thought to provide the H2A.Z exclusive functions. To elucidate the roles of this H2A.Z C-terminus genome wide, we made use of derivatives where the C-terminus was replaced with the corresponding region of H2A (ZA protein), or the H2A region plus a transcriptional activating peptide, with the idea of regenerating the H2A.Z-dependent regulation globally. An assessment of the genome-wide distribution of these H2A.Z derivatives shows that the H2A.Z C-terminal region is crucial for both maintaining the occupation level of H2A.Z and the proper positioning of the targeted nucleosomes. Interestingly, the specific contribution on incorporation efficiency vs nucleosome positioning varies enormously, depending on loci analyzed. For the ZA protein, positioning changes most importantly near origins of replication and snoRNA gene promoters, while incorporation is affected on all other sites. Furthermore, the role of H2A.Z in global transcription regulation also depends on its C-terminal region. Remarkably however, the latter mostly involves genes without a H2A.Z nucleosome in the promoter.

overall_design: We profiled H2A.Z and chimeric proteins derived from H2A.Z that bear modified C-terminal regions, namely ZA and ZA-rII', all tagged with HA, in yeast Saccharomyces cerevisiae by ChIP-chip on tiling arrays. All H2A.Z derivatives ChIP samples were labeled with Cy5 and hybridized against H3 ChIPs or Input DNA (labeled with Cy3). The microarrays used were described before (Jeronimo and Robert, 2014). The data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005). Each experiment was done in duplicate.

first: Hannah

last: Neumann

first: Célia

last: Jeronimo

first: Jean-François

last: Lucier

first: François

first: Raymund

middle: J

last: Wellinger

first: Luc

last: Gaudreau


title: Precise genomic editing of a pathogenic RBM20 mutation rescues dilated cardiomyopathy

status: Public on Aug 11 2022

city: Dallas

first: Jiwoong

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: Mutations in RNA binding motif protein 20 (RBM20) are a common cause of dilated cardiomyopathy (DCM). Many RBM20 mutations cluster within an arginine/serine rich (RS-rich) domain, resulting in mis-localization of RBM20 to ribonucleoprotein granules within the cytoplasm, abnormal splicing of cardiac genes, and cardiomyocyte dysfunction. We used adenine base editing (ABE) and prime editing to correct pathogenic p.R634Q and p.R636S mutations in the RS-rich domain in human isogenic induced pluripotent stem cell-derived cardiomyocytes. We also created humanized Rbm20R636Q mutant mice, which succumbed to severe cardiac dysfunction, heart failure and premature death.  Systemic delivery of ABE components by adeno-associated virus in these mice restored cardiac function and extended life span. These findings demonstrate the potential of precise correction of genetic mutations as a promising therapeutic approach for DCM.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of iPSC-derived cardiomyocytes and hearts from mice.

first: Takahiko

last: Nishiyama

first: Eric

last: Olson


status: Public on Aug 14 2022

first: Miao

last: Cui

address: UT Southwestern Medical Center Department of Molecular Biology 6000 Harry Hines Blvd.

institute: UTSW

overall_design: We analyzed the transcriptome of single cardiac nulcei from the 6-month old heart of the following genotypes: WT, RBM20 homozygous mutation, RBM20 heterzygous mutation, and RBM20 homozygous mutation with gene editing correction.


title: Role of the extracytoplasmic function sigma factor SigE in the stringent response of Mycobacterium tuberculosis

city: Padova

first: Giacomo

last: Baruzzo

address: Via Gradenigo 6/a

department: Department of Information Engineering

institute: University of Padova

summary: Bacteria respond to nutrient starvation implementing the stringent response, a stress signalling system resulting in metabolic remodelling leading to decreased growth rate and energy requirements. A well-characterized model of stringent response in Mycobacterium tuberculosis is that one induced by growth in low phosphate. The extracytoplasmic function (ECF) sigma factor SigE was previously suggested having a key role in the activation of stringent response. In this study we challenge this hypothesis by analyzing the temporal dynamics of the transcriptional response of a sigE mutant and its wild-type parental strain to low phosphate using RNA sequencing. We found that both strains responded to low phosphate with a typical stringent response trait, including the downregulation of genes encoding ribosomal proteins and RNA polymerase. We also observed transcriptional changes that support the occurring of an energetics imbalance, compensated by a reduced activity of the electron transport chain, decreased export of protons and a remodelling of central metabolism. The most striking difference between the two strains was the induction in the sigE mutant of several stress-related genes. In particular, the genes encoding the ECF sigma factor SigH and the transcriptional regulator WhiB6. Since both proteins respond to redox unbalances, their induction suggests that the sigE mutant is not able to maintain redox homeostasis in response to the energetics imbalance induced by low phosphate. In conclusion, our data suggest that SigE is not directly involved in initiating stringent response, but in protecting the cell from stress consequent to the exposure to low phosphate and activation of stringent response.

overall_design: Comparative gene expression profiling analysis over time of M. tuberculosis of RNA-seq data for wild-type H37Rv strain (WT) and its isogenic sigE null mutant ST28 (MU) in which SigE is rendered non-functional. Triplicate WT and MU cultures grown in phosphate-rich substrate were washed and re-suspended in low-phosphate substrate at 0 hours. RNA extraction was performed at 0 hours (high phosphate) and 6, 12, and 24 hours (low phosphate).

first: Agnese

last: Serafini

first: Francesca

last: Finotello

first: Tiziana

last: Sanavia

last: Boldrin

first: Enrico

last: Lavezzo

first: Luisa

last: Barzon

first: Stefano

last: Toppo

first: Roberta

last: Provvedi

first: Riccardo

last: Manganelli

first: Barbara

last: Di Camillo


title: Transcriptomic analysis of gene expression in diosgenin producing yeast strains

city: Tianjin

first: Feiyu

last: Fan

state: Tianjin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

summary: To detect the true expression patterns of diosgenin (DSG) synthetic genes after pathway engineering as well as investigate the impact of the DSG accumulation on the physiological state of yeast cells, a global analysis of the transcriptomes of DSG producing strains was performed using mRNA sequencing (RNA-Seq). DSG producing strains include LP085-Vc (DSG titer of 8.0 mg/L), LP104-17 (24.6 mg/L), and LP118 (31.4mg/L) were grown in SD media (2% w/v glucose) and cell samples of the 6h and 24h fermentation time points were collected for transcriptome analyses.

overall_design: The mRNA profiles of  DSG producing strains include LP085-Vc, LP104-17, and LP118.

first: Liping

last: Xu

first: Dong

last: Wang

first: Jing

last: chen

first: Bo

last: Li

first: Qingyan

first: Pingping

last: Liu

first: Ying

last: Qin

first: Zhubo

last: Dai

first: Xueli

last: Zhang


title: Nodulin homeobox (NDX) is required for heterochromatin homeostasis in Arabidopsis [RNA-seq]

status: Public on Aug 09 2022

city: Debrecen

first: Márton

last: Miskei

address: Egyetem tér 1.

department: Department of Molecular Biotechnology and Microbiology

country: Hungary

institute: University of Debrecen

summary: Nodulin homeobox (NDX) is a nuclear protein described as the regulator of specific euchromatic genes that controls multiple aspects of Arabidopsis development. At the molecular level, NDX was shown to i) interact with the Polycomb repressive complex 1 (PRC1) to promote deposition of repressive histone marks at abscisic acid-responsive gene loci, and (ii) stabilize an R-loop structure within the Flowering Locus C (FLC) to control its expression. Herein, we aimed to understand the global role of NDX in chromatin-based gene regulation and comprehensively characterized its genomic binding sites and transcriptional relationships involving sRNA profiling, DNA methylation, and 3D chromatin structure. Using quantitative microscopic and genomics approaches we show that NDX is a highly immobile heterochromatic protein that localizes primarily to centromeres and pericentromeric regions. Most NDX binding sites coincide with heterochromatic sRNA loci that are known to mediate transcriptional gene silencing via the RNA-dependent DNA methylation (RdDM) pathway. NDX localization was antagonistic with R-loop structures that were prevalent in euchromatic chromosomal arms. Functional analysis revealed that the absence of NDX led to differential hypo- and hyper-methylation in the CG / CHG / CHH sequence context, of which hypo-CHH / CHG sites were co-localized with NDX chromatin binding sites. The identified hypo-CHH/CHGs were associated with increased heterochromatic sRNA production (predominantly 24nt sRNAs) and parallel transcriptional activation of pericentric transposons. Chromosome conformation capture (Hi-C) revealed significant chromatin structural changes in the ndx mutant, with decreased intra-chromosomal interactions (chromatin decompaction) at pericentromeric regions where NDX is enriched in wild type plants, and increased inter-chromosomal contacts between KNOT-forming regions. KNOT interactions involved de novo interchromosomal contacts similar to genome structural changes observed in DNA methylation mutants. We conclude that the main role of NDX is the functional regulation of heterochromatin, which is mechanistically coupled to the effector phase of the RdDM pathway.

overall_design: mRNA-seq

first: Zsolt

last: Karányi

first: Ágnes

last: Mosolygó-L

first: Orsolya

last: Feró

first: Adrienn

last: Horváth

first: Beáta

last: Boros-Oláh

first: Éva

last: Nagy

first: Szabolcs

last: Hetey

first: Imre

last: Holb

first: Miklós

last: Vecsernyés

first: Henrik

last: Szaker

first: Tibor

last: Csorba

first: Lóránt

last: Székvölgyi


title: Nodulin homeobox (NDX) is required for heterochromatin homeostasis in Arabidopsis [Bisulfite-seq]

type: Methylation profiling by high throughput sequencing

overall_design: BS-seq


title: Nodulin homeobox (NDX) is required for heterochromatin homeostasis in Arabidopsis [Hi-C]

overall_design: Hi-C


title: Exploration of the role of circRNAs as regulators of spinal cord injury through integrated analyses of patterns of circRNA and mRNA expression

status: Public on Aug 06 2022

city: Nanchang

first: Jian

last: Cao

state: Jiangxi

address: 1 Minde Road, East Laker District, Nanchang, Jiangxi, China

department: orthopaedics

institute: The Second Affiliated Hospital of Nanchang University

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

summary: Circular RNAs (circRNAs) exhibit diverse intracellular functions through their ability to bind to RNA, DNA, and protein structures, influencing biological processes at both transcriptional and post-transcriptional levels. To date, however, few studies have sought to profile circRNA expression in the epicentral regions of spinal lesions in the context of spinal cord injury (SCI). Accordingly, this study was designed to assess circRNA and mRNA expression profiles in this pathological setting so as to gain insight regarding the ability of circRNAs to influence SCI development and resolution. A microarray-based approach was thus used to simultaneously measure the levels of these RNAs, with qPCR, fluorescence in situ hybridization and Western immunoblotting being further used to expand on these analyses and associated regulatory mechanisms in a rat SCI model system. In total, SCI was found to be associated with the differential expression of 414 and 5337 circRNAs and mRNAs, respectively. Pathway enrichment analyses suggested that these abnormally expressed circRNAs and mRNAs were associated with key SCI-related pathways and processes, with the cytokine-cytokine receptor interaction and neuroactive ligand-receptor interaction pathways being most strongly enriched. GSEA analyses of all identified mRNAs revealed that those which were differentially expressed were primarily associated with inflammatory immune response activity. Further screening of these inflammation-associated genes was used to construct and analyze a competing endogenous RNA network. Overall, these results emphasize the critical roles that circRNAs are likely to play in the pathophysiology of SCI, highlighting multiple important genes that play regulatory roles in this setting and providing a robust foundation for further research exploring the mechanisms governing the pathogenesis and potential therapeutic targets of SCI.

overall_design: 6 SPF male SD rats were randomly divided into two groups, including 3 in spinal cord injury group and 3 underwent the same laminectomy procedure without subsequent damage to the spinal cord. Rats were anesthetized at 3 days post-SCI, and the T10 spinal cord segments centered on and enclosing the injured site were collected. Microarray analysis was performed to investigate the circRNA and mRNAs expression patterns in rat spinal cord three days after SCI.

first: Xigao

last: Cheng


title: Nodulin homeobox (NDX) is required for heterochromatin homeostasis in Arabidopsis

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Replication origin mapping in the malaria parasite P. falciparum

status: Public on Aug 04 2022

city: Cambridge

first: Michael

last: Boemo

address: Tennis Court Road

department: Department of Pathology

country: United Kingdom

institute: University of Cambridge

summary: Replication origin mapping in the malaria parasite Plasmodium falciparum

overall_design: Replication origin mapping

middle: A


title: Nodulin homeobox (NDX) is required for heterochromatin homeostasis in Arabidopsis [ChIP-seq]

overall_design: ChIP-seq


title: Nodulin homeobox (NDX) is required for heterochromatin homeostasis in Arabidopsis [DRIP-seq]

overall_design: DRIP-seq


title: Physically interacting cell sequencing of mouse embryonic endoderm at E7.5, E8.5, and E9.5

status: Public on Aug 03 2022

city: Dongjak-Gu

first: Junil

last: Kim

state: Seoul

address: 369 Sangdo-Ro

department: Department of Bioinformatics

institute: SOONGSIL UNIVERSITY

summary: Cells continuously communicate with the neighboring cells during development. Direct interaction of different cell types can induce molecular signals dictating lineage specification and cell fate decisions. The current single-cell RNAseq (scRNAseq) technology cannot study cell contact dependent (or niche specific) gene expression due to the loss of spatial information. To overcome this issue and determine cell contact specific gene expression during embryogenesis, we performed RNA sequencing of physically interacting cells (PICseq) and assessed alongside our single cell transcriptomes (scRNAseq) derived from developing mouse embryos between embryonic day (E) 7.5 and E9.5. Analysis of PICseq data identifies an interesting suite of gene expression signatures depending on neighboring cell types. For instance, neural progenitor (NP) cells expressed Nkx2-1 when interacting with definitive endoderm (DE) and DE cells expressed Gsc when interacting with NP. Based on the identified cell contact specific genes, we devised a means to predict the neighboring cell types from individual cell transcriptome. We further developed spatial-tSNE to show the pseudo-spatial distribution of cells in a 2-dimensional space. In sum, we suggest an approach to study niche specific gene regulation during embryogenesis.

overall_design: Mouse FOXA2Venus embryos were collected between embryonic days (E) 7.5 and 9.5. The E9.5 embryos were dissected in order to enrich the sample with gut endoderm cells. Multiplet cells were isolated from FOXA2Venus mouse embryos. Cells were sorted using a BD FACS Aria III. FSC/SSC gates were used to define a homogeneous population, FSC-H/FSC-W gates were used to include multiplets, remove singlets and dead cells were excluded based on DAPI inclusion.

first: Michaela

middle: M

last: Rothova

first: David

last: Eyal


title: Profiling system-wide variations between Acute Rheumatic Fever and Rheumatic Heart Disease

status: Public on Jul 29 2022

city: Bengaluru

first: Kalpana

last: SR

state: Karnataka

address: Jayanagar 9th block, Bannerghatta Road

country: India

institute: Sri Jayadeva Institute of Cardiovascular Sciences & Research

summary: Rheumatic heart disease (RHD) continues to affect developing countries with low income, due to the lack of resources and effective diagnostic techniques. Understanding the genetic basis of progression from its prequel disease state, acute rheumatic fever (ARF), would aid in developing predictive biomarkers and improving patient care. To gain system-wide molecular insights into possible causes for progression, we collected blood transcriptomes from ARF (5) and RHD (5) patients. Using an integrated transcriptome and network analysis, we identified a subnetwork comprising the most significantly differentially expressed genes and most perturbed pathways in RHD as compared to ARF. For example, the chemokine signaling pathway was seen to be upregulated while tryptophan metabolism was found to be downregulated in RHD. The subnetworks of variation between the two conditions provide unbiased molecular-level insights into the host processes that may be associated with the progression of ARF to RHD, which has the potential to inform future diagnostics and therapeutic strategies. We also found significantly raised neutrophil/lymphocyte ratio in both ARF and RHD cohorts. Activated neutrophils and inhibited NK cell gene signatures reflected the drivers of the inflammatory process being common to both the disease conditions.

overall_design: Whole blood from 5 RHD (A5, C39, C41, C42, C44), 5 ARF (A8, A9, A11, A12, A13), 5 CHD (N7, N8, N9, N12, N13) and 2 Healthy (P1, P2) samples was sequenced. The healthy samples served as the control.

first: Ranjitha

last: Guttapadu

first: Nandini

last: Prakash

first: M

last: Alka

first: Ritika

last: Chatterjee

first: S

last: Mahantesh

first: J

last: Jayranganath

last: Usha

first: R

last: Jayshree

first: Dipshikha

last: Chakravortty

last: Kalpana

first: Nagasuma

last: Chandra


title: Trans-cellular regulation of synaptic properties by neuron-specific alternative splicing

status: Public on Jul 30 2022

city: Basel

first: Geoffrey

last: Fucile

address: Spitalstrasse 41

department: sciCORE

country: Switzerland

institute: University of Basel

summary: Genome-wide mapping of ribosome-associated mRNAs to investigate cell type-specific loss of function of the nuclear RNA binding protein SLM2 in the mouse hippocampus

overall_design: Comparative gene expression and alternative splicing analysis between WT and conditional Slm2 KO mutants in CA1, CA3 excitatory and SST+ inhibitory populations

first: Peter

last: Scheiffele

first: Lisa

last: Traunmueller


title: The WGBS and ATAC-seq from human serum and amniotic cell

city: Xiamen

last: Miao

state: Fujian

address: School of Medicine and School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, Fujian

institute: Huaqiao University

summary: we constructed a genome-wide DNA methylation landscape of adult 47XXY males from blood, and ATAC-seq from amniotic cell

overall_design: We use three 47, XXY blood samples, three 46, XX and three 46, XY blood samples with the similar ages (20-year-old) for the DNA extraction for the further WGBS analysis. We selected two amniotic fluid cells with a karyotype identified as 47, XXY. The two 46, XY samples and two 46, XX samples were selected as the control groups.

first: Miao

first: Tao

last: Sun


title: Transcriptome study of age-related resistance associated with vegetative phase change in Arabidopsis

status: Public on Jul 27 2022

city: Athens

first: Lanxi

last: Hu

address: 120 Charlton street

institute: University of Georgia

summary: To identify transcriptomic signatures for the age-related resistance during vegetative phase change.

overall_design: Age-related resistance during vegetative phase change

first: Peng

last: Qi

first: Li

last: Yang


title: Proof of concept of blockmiR induced MBNL rescue in Myotonic dystrophy muscle cells

status: Public on Jul 31 2022

city: Burjassot

first: Ruben

last: Artero

state: Valencia

address: C/ Doctor Moliner, 50

department: Genetics

country: Spain

institute: Universidad de Valencia

summary: The symptoms of Myotonic Dystrophy Type 1 (DM1) are multi-systemic and life-threatening. The neuromuscular disorder is rooted in a non-coding CTG microsatellite expansion in the DMPK gene that is correctly transcribed and physically sequesters the MBNL family of proteins. The high-affinity binding occurring between the proteins and the repetitions disallows MBNL proteins from performing their post-transcriptional splicing regulation leading to downstream molecular effects directly related to disease symptoms such as myotonia and muscle weakness. In this study, we build off of previously demonstrated evidence showing that the silencing of miR-23b and miR-218 can increase MBNL1 and 2 protein in DM1 cells. Here we use blockmiR antisense technology to block the binding sites of these miRNAs in order to increase MBNL translation into protein without binding to the microRNAs in DM1 muscle cells. The blockmiRs show therapeutic effects with the rescue of mis-splicing, MBNL subcellular localization, and transcriptomic expression proving that this novel and highly specific strategy could be a potentially viable therapy in Vivo.

overall_design: We have 3 replicas of: Control, DM1, DM1 + antagomiR23b, DM1 + BlockmiR.

first: Sarah

last: Overby

first: Estefanía

last: Cerro-Herreros

first: Jorge

last: Espinosa-Espinosa

first: Irene

last: González-Martínez

first: Nerea

last: Moreno-Cervera

first: Manuel

last: Pérez Alonso

first: Thorleif

last: Møller

first: Beatriz

last: Llamusí

first: Rubén


title: A Comprehensive Survey of C. elegans Argonaute Proteins Reveals Organism-wide Gene Regulatory Networks and Functions [mutants]

status: Public on Jul 22 2022

city: Toronto

first: Uri

last: Seroussi

address: 661 University Ave.

department: Molecular Genetics

institute: University of Toronto

summary: Argonaute (AGO) proteins associate with small RNAs to direct their effector function on complementary transcripts. The nematode C. elegans contains an expanded family of 19 functional AGO proteins, many of which have not been fully characterized. In this work we systematically analyzed every C. elegans AGO, using CRISPR-Cas9 genome editing to introduce GFP::3xFLAG tags. We have characterized the expression patterns of each AGO throughout development, identified small RNA binding complements, and determined the effects of ago loss on small RNA populations and developmental phenotypes. Our analysis indicates stratification of subsets of AGOs into distinct regulatory modules, and integration of our data led us to uncover novel stress-induced fertility and pathogen response phenotypes due to ago loss.

overall_design: Comparative small RNA expression analysis of sRNA-seq data of C. elegans strains carrying loss of function mutations in Argonaute genes and small-RNA analysis of Argonaute bound sRNAs from immunoprecipitations of epitope tagged Argonaute proteins.

first: Andrew

last: Lugowski

first: Lina

last: Wadi

first: Robert

middle: X

last: Lao

first: Alexandra

last: Willis

first: Winnie

last: Zhao

first: Adam

last: Sundby

first: Amanda

last: Charlesworth

first: Aaron

middle: W

last: Reinke

first: Julie

last: Claycomb


title: Transcriptomic data from a gallbladder cancer cell line with acquired chemoresistance to gemcitabine [NOZ]

status: Public on Jul 21 2022

city: TEMUCO (CD)

first: Luis

last: Vergara

state: Araucania region

address: Alemania Avenue #0458, 4to Floor

department: Center of Excellence in Traslational Medicine (CEMT)

country: Chile

institute: Universidad de La Frontera

summary:
Gallbladder cancer (GBC) has few therapeutic options, being gemcitabine the first-line chemotherapeutic drug. However, this treatment shows poor clinical outcomes on patients. The acquired resistance phenomenon during of the treatment is one of the main factors that leads to insufficient therapeutic effects, and the molecular mechanisms carried out by tumor cells against gemcitabine are still poorly understood.
First, we established a GBC cell line with acquired resistance to gemcitabine (NOZ GemR) from parental cell line (NOZ). After, we used microarray hybridization in NOZ and NOZ GemR to characterize their transcriptional profile to identify differentially expressed genes and/or molecular pathways involved chemoresistant cell phenotype.

overall_design: NOZ, a GBC cell line sensitive to gemcitabine, was subjected to increasing concentrations of gemcitabine for six months until obtaining a cell subline with stable acquired resistance against gemcitabine (NOZ GemR). Then, total RNA extracted and purified from NOZ and NOZ GemR was analyzed by Affymetrix microarray to study the mRNA expression levels in both conditions. Differentially expressed genes were identified in NOZ GemR respect to NOZ to elucidate the transcriptional networks underlying gemcitabine resistance in GBC cells. Three independent replicates for each sample were used.

first: L

first: J

last: Zhong

last: Espinoza

first: P

last: Leal

first: F

last: Suárez

first: K

last: Buchegger

first: G

last: Repetto

first: C

last: Ili

first: H

last: Weber

last: Roa

last: Bizama

last: García


title: Chip-seq of H3K4me3, H3K4me1, H3K27ac and P300 in HCC cells

first: Heng

last: Zhang

address: 38 Rd.Tongyan

institute: Nankai University

summary: Considered as fundamental epigenetic regulators controlling many key cellular processes, histone modifications are a well-conserved and widely studied class of epigenetic modifications. Genome-wide studies have identified enhancers as DNA sequences that bind to H3K4me1 and H3K27ac and promoters as DNA sequences that bind to H3K4me3. To explore how the Twist1 complex (Twist1/YY1/p300) regulates miR-9 expression, we performed ChIP-seq in PLC-PRF-5 cells, providing a panorama of p300, H3K4me3, H3K4me1, and H3K27ac.

overall_design: ChIP-seq  of p300, H3K4me3, H3K4me1, and H3K27ac was performed in PLC-PRF-5 cells.

first: Luning

last: Qin

first: Ting

last: Wu

first: Jingxia

last: Han

first: Tao

last: Sun


title: Effects of polyploidization on gene expression in Eucalyptus urophylla leaves

status: Public on Jul 13 2022

city: Beijing

first: Jun

last: Yang

address: No.35, Tsinghua East Rd.

institute: Beijing Forestry University

summary: In order to study the effect of polyploidization on gene expression in the leaves of Eucalyptus urophylla, triploid obtained by sexual polyploidization and its diploid control were used as materials, and leaves at different growth stages of different ploidies were collected for transcriptome sequencing.

overall_design: Terminal buds, young leaves at the shoot tips, fully expanded mature leaves, and senescent leaves of different ploidies were randomly selected for transcriptome sequencing.

first: Zhao

last: Liu

first: Xiangyang

last: Kang


title: Transcriptome analysis using RNA sequencing conducted for wild type (Col-0), ahl10-1 and rrp6l1-2 mutant under control conditions and after 96 h at moderate low water potential (-0.7 MPa)

status: Public on Jul 15 2022

city: Taipei City

first: Paul

last: Verslues

address: No.128, Sec.2, Academia Rd., Nangang Dist.

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

summary: RNA sequencing was used to identify genes differentially expressed (DEG) in ahl10-1 mutants and rrp6l1-2 mutant compared to Col-0 wild type. Two treatments were analyzed for each genotype: unstressed control and a 96 hour low water potential (-0.7 MPa) treatment. Approximately 2000-3000 genes were found to be significantly up and down-regulated in the wild type stress versus control treatment using . rrp6l1-2 mutant shows around 500 and 250 genes up and down regulated respectively in control treated seedlings while 10 or less than 10 found in ahl10-1. In the stress treatment, rrp6l1-2 and ahl10-1 have less and 60 genes up and downregulated. ahl10-1 and rrp6l-2 have a common set of downregulated genes (24 genes) at stress treatment.

overall_design: Wild type (Col-0), ahl10-1 and rrp6l1-2 Arabidopsis thaliana seedlings were germinated on agar plates and after seven days of growth, seedlings were transferred either to fresh plates of control media or to moderate severity low water potential (-0.7 MPa) imposed using agar plates of the control media infiltrated with PEG-8000.  Samples were collected 96 h after transfer (Control and stress treatments). Three independent biological experiments and mRNA extractions were performed for each genotype/treatment. (18 mRNA extractions. After quality check and quantitation the 18 samples were used for sequencing

first: Min

last: Wong


title: A Comprehensive Survey of C. elegans Argonaute Proteins Reveals Organism-wide Gene Regulatory Networks and Functions [Argonaute IP]

first: Uri

last: Seroussi

first: Andrew

last: Lugowski

first: Lina

last: Wadi

first: Robert

last: Lao

first: Alexandra

last: Willis

first: Winnie

last: Zhao

first: Adam

last: Sundby

first: Amanda

last: Charlesworth

first: Aaron

last: Reinke

first: Julie

last: Claycomb


title: Mapping the cellular and molecular organization of mouse cerebral aging by single-cell transcriptome imaging

first: William

middle: Edward

last: Allen

state: MA

address: Naito 034, Zhuang Group, 12 Oxford St.

department: Chemistry and Chemical Biology

institute: Harvard University

summary: The enormous cellular diversity and complex tissue organization of the brain have hindered systematic characterization of its age-related changes in cellular and molecular architecture and mechanistic understanding of its functional decline and degeneration during aging. Here we generated a high-resolution cell atlas of brain aging within the frontal cortex and striatum using spatially resolved single-cell transcriptomics and quantified the changes in gene expression and spatial organization of major cell types in these regions over the lifespan of mice. We observed more pronounced changes in the composition, gene expression and spatial organization of non-neuronal cells over neurons. Our data revealed molecular and spatial signatures of glial and immune cell activation during aging, particularly within the white matter of the corpus callosum, and identified both similarities and differences in cell activation patterns induced by aging and systemic inflammatory challenge. These results provide critical insights into age-related decline and inflammation in the brain.

overall_design: Nuclei of 2 young (4 week old) and 2 aged (90 week old) mice were isolated by fluorescence-activated cell sorting (FACS) according to the presence of Hoeschst signal and analyzed using 10X Genomics snRNA-seq.

first: Timothy

last: Blosser

first: Zuri

last: Sullivan

first: Catherine

last: Dulac

first: Xiaowei

last: Zhuang


title: Mechano-epigenetic regulation of extracellular matrix homeostasis via Yap and Taz

status: Public on Jul 14 2022

city: Iowa City

first: Dakota

middle: L

last: Jones

state: IA

address: 51 Newton Road

department: Department of Anatomy and Cell Biology

institute: University of Iowa

summary: Cells integrate mechanical cues to direct fate specification to maintain tissue function and homeostasis. While disruption of these cues is known to lead to aberrant cell behavior and chronic diseases (e.g. tendinopathies), the underlying mechanisms by which mechanical signals maintain cell function is not well understood. Here, we show using a novel model of tendon de-tensioning that loss of tensile cues in vivo acutely changes nuclear morphology, positioning, and expression of catabolic gene programs. Using paired ATAC/RNAseq, we further identify that a loss of cellular tension rapidly reduces chromatin accessibility in the vicinity of Yap/Taz genomic targets while also increasing expression of genes involved in matrix catabolism. Overexpression of Yap resulted in a reduction of chromatin accessibility at these matrix catabolic genes, and their transcript levels. Concordantly, depletion of Yap/Taz elevated their expression. Finally, we demonstrate that overexpression of Yap not only prevents the induction of a broad catabolic program following a loss of cellular tension, but also preserves the underlying chromatin state from force induced alterations. Taken together, these results provide novel mechanistic details by which mechanical signals regulate tendon cell function to preserve matrix homeostasis through a Yap/Taz axis.

overall_design: Investigation of the role of mechanical cues and Yap/Taz on chromatin and transcriptional homeostasis

last: Mauck

first: Nathaniel

last: Dyment


title: Bioinformatic analysis of the mechanism by which metformin enhances chemosensitivity of head and neck squamous cell carcinoma cells

status: Public on Jul 03 2022

city: Huhhot

first: shanchun

last: hou

address: Xinhua Street

institute: inner Mongolia medical university

summary: Metformin is one of the first-line drugs for clinical treatment of type II diabetes, and recent studies have found that metformin can inhibit the development of multiple malignant tumors. When metformin is combined with chemotherapeutic drugs to treat head and neck squamous cell carcinoma（HNSCC）, it can effectively enhance the efficacy of chemotherapy. The aim of this study was to define the signaling pathways regulated by metformin in HNSCC, and the underlying mechanisms by which metformin sensitizes HNSCC chemotherapy. We used RNA sequencing (RNA-seq) to examine metformin regulated genes in the cal27, human tongue squamous carcinoma cell line, using RT-PCR to determine alterations in gene expression. Data from RNA-seq analysis showed that gene products involved in DNA replication, cell cycle, IL-17 signaling pathway, mismatch repair were all regulated by metformin. Our results suggest that metformin regulates multiple pathways associated with tumor growth and progression in HNSCC.

overall_design: CAL27 cells were plated in 10 cm dishes at a density of ~ 300,000 cells/dish in high glucose DMEM medium supplemented with 10% FBS and 1% penicillin / streptomycin，and allowed to attach for one day. The cells were then treated for 48 hours with either PBS or 30 mM metformin. Total RNA was extracted from treated cells using the Trizol reagent and further purified using the Qiagen miRNeasy Micro Kit and assessed with Bioanalyzer 4200. Then, next-generation libraries were prepared using the VAHTS mRNA-seq v2 Library prep kit. Sequence runs were performed on an Illumina HiSeq X 10 utilizing a 150-bp RNA-Seq protocol.

first: Qi

last: Li

first: Yajun

last: Geng

first: Shanchun

last: Hou


title: Nodulin homeobox (NDX) is required for heterochromatin homeostasis in Arabidopsis [sRNA-seq]

first: Márton

last: Miskei

address: Egyetem tér 1.

institute: University of Debrecen

summary: Nodulin homeobox (NDX) is a nuclear protein described as the regulator of specific euchromatic genes that controls multiple aspects of Arabidopsis development. At the molecular level, NDX was shown to i) interact with the Polycomb repressive complex 1 (PRC1) to promote deposition of repressive histone marks at abscisic acid-responsive gene loci, and (ii) stabilize an R-loop structure within the Flowering Locus C (FLC) to control its expression. Herein, we aimed to understand the global role of NDX in chromatin-based gene regulation and comprehensively characterized its genomic binding sites and transcriptional relationships involving sRNA profiling, DNA methylation, and 3D chromatin structure. Using quantitative microscopic and genomics approaches we show that NDX is a highly immobile heterochromatic protein that localizes primarily to centromeres and pericentromeric regions. Most NDX binding sites coincide with heterochromatic sRNA loci that are known to mediate transcriptional gene silencing via the RNA-dependent DNA methylation (RdDM) pathway. NDX localization was antagonistic with R-loop structures that were prevalent in euchromatic chromosomal arms. Functional analysis revealed that the absence of NDX led to differential hypo- and hyper-methylation in the CG / CHG / CHH sequence context, of which hypo-CHH / CHG sites were co-localized with NDX chromatin binding sites. The identified hypo-CHH/CHGs were associated with increased heterochromatic sRNA production (predominantly 24nt sRNAs) and parallel transcriptional activation of pericentric transposons. Chromosome conformation capture (Hi-C) revealed significant chromatin structural changes in the ndx mutant, with decreased intra-chromosomal interactions (chromatin decompaction) at pericentromeric regions where NDX is enriched in wild type plants, and increased inter-chromosomal contacts between KNOT-forming regions. KNOT interactions involved de novo interchromosomal contacts similar to genome structural changes observed in DNA methylation mutants. We conclude that the main role of NDX is the functional regulation of heterochromatin, which is mechanistically coupled to the effector phase of the RdDM pathway.

overall_design: sRNA-seq

first: Zsolt

last: Karányi

first: Ágnes

last: Mosolygó-L

first: Orsolya

last: Feró

first: Adrienn

last: Horváth

first: Beáta

last: Boros-Oláh

first: Éva

last: Nagy

first: Szabolcs

last: Hetey

first: Imre

last: Holb

first: Miklós

last: Vecsernyés

first: Henrik

last: Szaker

first: Tibor

last: Csorba

first: Lóránt

last: Székvölgyi


title: An autoregulatory feedback loop converging on H2AK119ub1 drives synovial sarcoma [CUT&RUN]

status: Public on Jun 30 2022

city: Edinburgh

first: Nezha

middle: Suzanne

last: Benabdallah

state: Midlothian

address: Crewe Road South

department: Institute of Genetics and Cancer

institute: University of Edinburgh

summary: The SS18-SSX fusion drives oncogenic transformation in synovial sarcoma by bridging SS18, a member of mSWI/SNF complex, to polycomb repressive complex 1 (PRC1) target genes. Here we show that the SSX C-terminus, via its SSXRD domain, directs SS18-SSX chromatin binding independently of SS18. SSXRD specific targeting is mediated by interaction with H2AK119ub1 and histone MacroH2A with which the fusion overlaps genome wide. Variant Polycomb Repressive Complex 1.1 (PRC1.1) acts as the main depositor of H2AK119ub1 and consequently is required for SS18-SSX occupancy. Importantly, SSX C-terminus not only depends on H2AK119ub1 for localization but also further promotes it and consequently, high H2AK119ub1 levels are acquired during synovial sarcoma development. These results reveal an SS18-SSX/PRC1 autoregulatory feedback-loop that enforces fusion binding and could play a role in a wide-range of cancers and physiological settings where SSX proteins are overexpressed.

overall_design: Chromatin profiles of endogenous SS18-SSX1/2, H2AK119ub1 in human synovial sarcoma cells and HA occupancy in osteosarcoma or synovial sarcoma cells expressing MSCV-HA-eGFP-SS18-PGK-Puro, MSCV-HA-eGFP-SS18-SSX1-PGK-Puro and MSCV-HA-eGFP- SSX-C-PGK-Puro

first: Ana

last: Banito


title: Bioinformatics prediction and experimental verification of a novel microRNA for myocardial fibrosis after myocardial infarction in rats

first: Qianqian

last: Guo

address: Dongcheng District, Hai Yun Cang on the 5th Zip

summary: MicroRNAs (miRNAs) are a class of highly conserved endogenous noncoding single-stranded small RNAs with a length of 18-22 nucleotides. They are involved in regulation at the posttranscriptional and translational levels through the degradation and translation inhibition of messenger RNA (mRNA). It is estimated that at least 60% of all mammalian genes may be regulated by miRNAs. MiRNAs can help uncover the mechanisms of diseases and provide new entry points into therapy. Accumulated evidence has revealed that miRNAs are involved in the pathological process of cardiovascular disease through specific signaling pathways. To investigate the potential miRNAs for myocardial fibrosis post myocardial infarction, rat models of acute myocardial infarction (AMI) were established by ligating the anterior descending branch of the left coronary artery, while sham-operated rats were only threaded without ligation as a control group. There were three rats in each group. Thirteen differentially expressed miRNAs between the two groups were screened and their expression levels in the model group were all higher than those in the control group. The expression of miR-199a-5p was significantly increased in the model group in qRT-PCR, which was consistent with the results of the gene chip. KEGG enrichment analysis showed that the target genes of miR-199a-5p were enriched in the insulin signaling pathway. Furthermore, dual-luciferase reporter assay indicated that miR-199a-5p could negatively regulate the expression of GSK-3β. After transfection, the expression of miR-199a-5p was increased in the miR-199a-5p mimics group. The protein expression of GSK-3β was decreased in CFs transfected with miR-199a-5p mimics. In summary, our study identified miR-199a-5p could promote the progression of myocardial fibrosis after myocardial infarction by targeting GSK-3β, which provides novel targets for diagnosis and treatment of MF. In summary, our research suggests that miR-199a-5p promotes the progression of myocardial fibrosis after myocardial infarction through the activation of the insulin-PI3K/Akt-GSK-3β signaling pathway.

overall_design: SPF male Sprague–Dawley (SD) rats weighing 200±20 g were purchased from Beijing Vital River Laboratory Animal Technology Co. Ltd. Raised in the Barrier Animal Laboratory of Dongzhimen Hospital, Beijing University of Chinese Medicine, with a 12 h light/dark cycle and ad libitum food and water. All protocols and applications of animals in this study were approved by The Animal Care and Welfare Committee of Dongzhimen Hospital, Beijing University of Chinese Medicine (No: 16-25). The rats were divided into model group and sham-operated group by random number table. Before surgery, the rat was anesthetized intraperitoneally with 1% sodium pentobarbital (40 mg/kg). The skin was cut laterally at the third and fourth ribs of the left chest, approximately 1.5 cm in length. The musculature was bluntly separated, the rib was braced with a thoracotomy and the thymus was fixed upward to fully enlarge the surgical field, and the pericardium was carefully torn open to expose the ligation site of the rat heart. The anterior descending branch of the left coronary artery was ligated with a 5/0 line approximately 2 mm below the left atrial appendage and the arterial cone. The anterior myocardial wall was quickly ischemic and whitening, and the electrocardiogram (ECG) revealed saddle-back-like ST-segment elevations. After 24 h, the ECG was conducted again, and pathological Q waves appeared in the chest leads and lead I and aVL, indicating that the model was successful. The sham-operated rats were only threaded without ligation as a control group. The rats were fed adequate food and deionized water for 4 successive weeks, subsequently euthanized and dissected to isolate the heart for the subsequent experiments. Left ventricular samples were obtained for RNA extraction and hybridization on Agilent miRNA Microarrays.

first: Dandan

last: Wu

first: Dongdong

last: Jia

first: Xinyue

last: Zhang

first: Aiming

first: Lixia

last: Lou

first: Mingjing

last: Zhao

first: Mengzhu

first: Yijie

last: Gao

first: Manman

last: Wang

first: Menghua

last: Liu

first: Meng

last: Chen

first: Dongmei


title: Single cell sequencing of splenocytes following T. gondii infection

status: Public on Jul 01 2022

city: Philadelphia

first: Christopher

last: Hunter

address: 380 S. University Ave #341

institute: University of Pennsylvania

summary: The spleen is a site of acute infection following challenge with the parasite Toxoplasma gondii. We utilized scRNA sequencing to analyze the immune response to this infection.

overall_design: Splenocytes from T. gondii infected mice were harvested 14dpi, red blood cells were lysed, and remaining cells were analyzed using scRNAseq.

first: Lindsey

last: Shallberg

first: Anthony

middle: T

last: Phan

first: Joseph

last: Clark

first: Zachary

last: Lanzar


title: IL-33 function on CD4-CD8- double negative T cells in vitro

status: Public on Jun 27 2022

first: sun

middle: xiao

last: jing

address: NO.95 yongan road

institute: Beijing friendship hospital

summary: Methods: RNA transcription profiling of double negative T cells was compared between control group and IL-33 treated group

overall_design: Examination of  different genes in control double negative T cells and IL-33 cocultured double negative Tcells

first: Xiaojing

last: Sun

first: Guangyong

first: Dong

first: Li

last: Li


title: A method for the factor-specific spatio-temporal control of splicing

status: Public on Jun 18 2022

city: Berlin

first: Marco

last: Preussner

address: Takustrasse 6

institute: FU berlin

summary: Precursor messenger RNA splicing is a highly regulated process, mediated by a complex RNA-protein machinery, the spliceosome, that encompasses several hundred proteins and five small nuclear RNAs in human. Emerging evidence suggests that the spatial organization of splicing factors and their spatio-temporal dynamics participate in the regulation of splicing. For instance, Cajal bodies and nuclear speckles function as centers for snRNP assembly and recycling or storage, respectively, whereas the assembly of spliceosomes on nascent pre-mRNAs predominantly occurs in peri-chromatin fibrils. So far, methods to manipulate the spatial distribution of splicing factors in a temporally defined manner in living cells are missing. Here, we describe such an approach that takes advantage of a reversible chemical dimerizer, and outline the requirements for efficient, reversible re-localization of splicing factors to selected sub-nuclear compartments. In a proof-of-principle study, the partial re-localization of the PRPF38A protein to the nuclear lamina induced a moderate increase in intron retention. Our approach allows fast and reversible re-localization of splicing factors, has few side effects and can be applied to any splicing factor by fusion of a protein tag through genome engineering. Apart from the systematic analysis of the spatio-temporal aspects of splicing regulation, the approach has a large potential for the fast induction and reversal of splicing switches and can reveal mechanisms of splicing regulation in native nuclear environments.

overall_design: HEK293T single-engineered control cells (ctr) with an N-terminal FKBP-tagged CRISPR knockin PRPF38A or doubly-engineered HEK293T cells with an N-terminal FKBP-tagged CRISPR knockin PRPF38A and stably expressing a lamin A-ECFP-SNAP fusion protein  (stbl) were treated with a reversible chemical dimerizer (6 µM rCD1; Treat) or with DMSO as control.

first: Florian

last: Heyd

first: Karen

last: Vester

first: Markus

middle: C

last: Wahl


title: Critical role of galectin-9 in EBV-driven transformation of human B-lymphocytes

city: Guangzhou

first: Jingxiao

last: Xu

state: Guangdong Province

address: Dongfengdong Road 651

institute: Sun Yet san university

summary:
Background: In several types of malignancies, especially EBV-associated nasopharyngeal carcinomas, high Galectin-9 (Gal-9) expression is indicative of an aggressive tumor phenotype. The contribution of Gal-9 to the oncogenesis of B-cell lymphomas (BCLs) has not yet been investigated.
Methods: The expression of Gal-9, STING, and EBNA1 was measured by immunohistochemical (IHC) staining on tumor sections from 66 BCL patients. Artificial EBV infection of normal primary B cells in vitro was used as an experimental model. The dynamic changes of the transcriptome of EBV-infected B cells undergoing transformation were investigated by bulk RNA-sequencing and bioinformatics analysis. The oncogenic role of Gal-9 was investigated in vitro by addition of recombinant Gal-9 to EBV-infected primary B-cells, and growth assays. The underlying molecular mechanisms were investigated by immunoblotting and immunofluorescent (IF) staining, CHIP and luciferase reporter assays.
Results: In clinical specimens of BCLs, Gal-9 expression was significantly associated with tumor stage, latent EBV infection and abundance of the viral latent protein EBNA1. Looking at the transcriptome changes occurring in vitro during EBV-driven B-cell transformation, we could identify a series of genes undergoing long term activation and remaining highly expressed in mature LCLs. The Gal-9 gene is one of them. Its expression is enhanced during the transformation process at the mRNA level and even more at the protein level. This up-regulation results at least in part from its transactivation by EBNA1 which can bind its promoter.  Reciprocally, we find that addition of extra-cellular Gal-9 promotes B-cell transformation and establishment of the latent phase of EBV-infection. Concomitantly, extra-cellular Gal-9 blocks STING signaling and enhances STAT3 phosphorylation. Inhibition of Sting signaling or STAT3 phosphorylation blocks B-cell transformation, even in the presence of Gal-9.
Conclusion: our data unveil a role of amplification and acceleration for Gal-9 in the process of EBV-driven B-cell transformation. This process might be relevant to the pathogenesis of EBV-associated BCLs.

overall_design: The primary B cells were selected by human anti-CD3 beads (eBioscience) from the peripheral blood of healthy donors. Then the selected cells infected in vitro by EBV collected at multiple time points including D0, 3, 7, 14 ,21 and mature LCL were subjected to serial bulk RNA-seq assessment.

first: Jing-xiao

first: Jiang


title: Next Generation Sequencing Facilitates Quantitative Analysis of U87MG Cell Transcriptomes

status: Public on Jun 22 2022

city: West Lafayette

first: Yun

last: Chang

state: IN

address: 480 Stadium Drive

department: Chemical Engineering

institute: Purdue University

summary: Next-generation sequencing (NGS) has significantly advanced the elucidation of developmental signaling mechanisms that are important for U87MG cells under differente treatment. We report here the application of RNA-sequencing technology for transcriptome profile of U87MG cells treated with CAR neutrophils, nanodrugs, and CAR neutrophils loaded nanodrugs. Six U87MG samples were performed in IIIumina HiSeq2500. The resulting sequence reads were mapped to human genome (hg19) using HISAT, and the RefSeq transcript levels (RPKMs) were quantified using the python script rpkmforgenes.py. Our RNA-seq data analyzed different cellular signal pathways under treatment. This study shows a detailed analysis of U87MG transcriptomes generated by RNA-seq technology, providing insight into the mechanisms underlying CAR neutrophils lysis the tumor cells.

overall_design: U87MG transcriptome profiles of different treatments were generated by RNA-seq technology using IIIumina NextSeq500

first: Xiaoping

last: Bao


title: Tonic TNF conditioning of macrophages safeguards stimulus-specific inflammatory responses

city: Los Angeles

first: Quen

last: Cheng

address: 10833 LeConte Ave

institute: UCLA

summary: TNF is a key inflammatory cytokine that warns recipient cells of a nearby infection or tissue damage. Acute exposure to TNF activates characteristic oscillatory dynamics of the transcription factor NFκB and induces a characteristic gene expression program; these are distinct from the responses of cells directly exposed to pathogen-associated molecular patterns (PAMPs). Here we report that tonic TNF exposure is critical for safeguarding TNF’s specific functions. In the absence of tonic TNF conditioning, acute exposure to TNF causes 1) NFκB signaling dynamics that are less oscillatory and more like PAMP-responsive NFκB dynamics, 2) immune gene expression that is more similar to the Pam3CSK4-response program, 3) broader epigenomic reprogramming that is characteristic of PAMP-responsive changes. We show that tonic TNF signaling effects subtle changes to TNF receptor availability and dynamics such that enhanced pathway activity results in non-oscillatory NFκB. Our results reveal tonic TNF signaling as a key tissue determinant of the specific characteristics of cellular responses to acute paracrine TNF exposure, and their distinction from responses to direct exposure to PAMPs.

overall_design: Sequencing data from murine bone marrow-derived macrophages stimulated with TNF or Pam3CSK, exploring the role of tonic TNF in immune responses. Fluidigm scRNA-seq (82 samples), H3K4me1 ChIP-seq (18 samples).

first: Stefanie

last: Luecke

first: Adwunmi

last: Adelaja

first: Xiaolu

last: Guo

first: Supriya

last: Sen

first: Roberto

last: Spreafico

first: Yi

last: Liu

first: Brooks

last: Taylor

first: Jessica

last: Diaz

first: Alexander

last: Hoffmann


title: A Comprehensive Survey of C. elegans Argonaute Proteins Reveals Organism-wide Gene Regulatory Networks and Functions

first: Uri

last: Seroussi

address: 661 University Ave.

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

overall_design: Refer to individual Series


title: Transcriptomic data from a gallbladder cancer cell line with acquired chemoresistance to gemcitabine [TGBC1]

first: Luis

last: Vergara

address: Alemania Avenue #0458, 4to Floor

summary:
Gallbladder cancer (GBC) has few therapeutic options, being gemcitabine the first-line chemotherapeutic drug. However, this treatment shows poor clinical outcomes on patients. The acquired resistance phenomenon during of the treatment is one of the main factors that leads to insufficient therapeutic effects, and the molecular mechanisms used by tumor cells against gemcitabine are still poorly understood.
First, we established a GBC cell line with acquired resistance to gemcitabine (TGBC1 GemR) from parental cell line (TGBC1). After, we used microarray hybridization in TGBC1 and TGBC1 GemR to characterize their transcriptional profile to identify differentially expressed genes and/or molecular pathways involved chemoresistant cell phenotype.

overall_design: TGBC1, a GBC cell line, was subjected to increasing concentrations of gemcitabine for six months until obtaining a cell subline with stable acquired resistance against gemcitabine (TGBC1 GemR). Then, total RNA extracted and purified from TGBC1 and TGBC1 GemR was analyzed by Affymetrix microarray to study the mRNA expression levels in both conditions. Differentially expressed genes were identified in TGBC1 GemR respect to parental cell to elucidate the transcriptional networks underlying gemcitabine resistance in GBC cells. Three independent replicates for each sample were used.

first: L

first: J

last: Zhong

last: Espinoza

first: P

last: Leal

first: F

last: Suárez

first: K

last: Buchegger

first: G

last: Repetto

first: C

last: Ili

first: H

last: Weber

last: Roa

last: Bizama

last: García


title: Multiplexed assessment of human glucokinase variant activity

status: Public on Jun 16 2022

city: Copenhagen N

first: Sarah

last: Gersing

address: Ole Maaløes vej 5

country: Denmark

institute: University of Copenhagen

summary: Diabetes is a complex genetic disease affecting millions of people worldwide. A common monogenic form of diabetes is glucokinase (GCK) maturity-onset diabetes of the young (GCK-MODY), which is caused by heterozygous inactivating variants in the gene encoding GCK. GCK catalyzes the phosphorylation of glucose and is known as the pancreatic glucose sensor. Patients with GCK-MODY, in contrast to other diabetics, often do not require treatment but are frequently misdiagnosed and treated unnecessarily. Genetic testing can prevent this, but is hampered by the challenge of interpreting genetic variants. To address this challenge, we generated a comprehensive map of human GCK variant activity. The activity map includes 97% of the possible missense and nonsense variants and correlate with in vitro catalytic efficiency, fasting glucose levels in patients and evolutionary conservation analysis. Activity scores include both hyper- and hypoactive variants.

overall_design: The codon-optimized human GCK sequence was divided into three regions (aa 2-171, 172-337, 338-466) that were separately mutagenized, assayed and sequenced. Regional plasmid libraries were transformed into yeast (hxk1Δhxk2Δglk1Δ). Yeast cells were used for plasmid extraction following 3 days of selection on 0.2% glucose medium. The GCK ORF was amplified in 14 tiles spanning the ORF before and after selection. The relative frequency of variants in each tile was determined using Illumina sequencing.

first: Rasmus

last: Hartmann-Petersen


title: Evaluation of ATAD2 as a potential target in hepatocellular carcinoma

status: Public on Jun 15 2022

city: balcova

first: umut

last: ekin

state: izmir

address: mithatpasa st.

country: Turkey

institute: Izmir Biomedicine and Genome Center

summary: We evaluated differentially expressed genes (DEGs) between hepatocellular carcinoma cell lines (Hep3B, SNU449, and PLC/PRF/5) treated with ATAD2 siRNA or control using Affymetrix array data whether ATAD2 could be potential target in hepatocellular carcinoma.

overall_design: Hep3B, SNU449 and PLC/PRF/5 cell lines treated with ATAD2 siRNA or control siRNA in triplicates

first: Mehmet

last: Ozturk


title: Age-associated suppression of exploratory activity during sickness is linked to meningeal lymphatic dysfunction and microglia activation

status: Public on Jun 12 2022

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis


title: Asparagine starvation on histone methylation and gene expression

city: Indianapolis

first: Ji

last: Zhang

address: 1044 W Walnut Street, R4-170

department: Pediatrics

institute: Indiana University

summary: We are determining the impact of asparagine starvation on histone H3K4 trimethylation deposition across the genome and how they may affect the gene expression.

overall_design: RS4;11 cells were cultured in complete medium, asparagine-free medium or asparagine-free medium supplemented with 10 uM ferric nitrate for 24 hours. Whole cell RNA was collrected for RNA-seq and nuclear extracts were subjected to H3K4me3 ChIP-seq.


title: Measuring the transcriptomic response to targeting kinases correlated with estrogen receptor activity in Breast Cancer

city: York

first: Andrew

middle: Nicholas

last: Holding

address: Wentwork Way

department: Biology

institute: University of York

summary:
We undertook a phosophotranscriptomic network analysis of published patient tumour RNA-seq and phosphoproteomic data to identify kinases that correltated with Estrogen Receptor activity in Breast Cancer. The most sucessful canidates were selected for targeting by siRNA and the effects monitored by RNA-seq.

The code for generation of the expression matrix is available from https://github.com/andrewholding/SimonaVIPER

overall_design: Expression data characterising the effects of siRNAs targeting CAMK2D, CDK8, CSNK1A1, ESR1, GRB2, HIPK4, KSR1, LIMK1, MKNK2, NEK9 in both MCF7 and T47D.

first: Simona

last: Schindler

first: Amy

last: Cullen

first: Helen

middle: V

last: Cook

first: Florian

last: Markowetz

middle: N


title: Age-associated suppression of exploratory activity during sickness is linked to meningeal lymphatic dysfunction and microglia activation [ablation]

summary: The objective of this study is to assess the contribution of meningeal lymphatic vessels to microglia response to peripheral inflammation.  To this end, we sequence CD11b+ cells sorted from whole brain of adult mice with intact meningeal lymphatic vessels or mice with experimental meningeal lymphatic ablation, two hours following 1μg IL-1β or saline vehicle intraperitoneal injection.  The two-hour timepoint was selected for analysis because that corresponds with the peak of the behavioral response as defined by a decrease in locomotor activity and the connection between behavior and microglia activation is of particular interest in this study.

overall_design: Mice were maintained under specific pathogen-free conditions, with controlled temperature and humidity, on 12 h light:dark cycles, and ad libitum access to food and water.  Experiments were all performed during light cycle.  Experimental lymphatic ablation or sham operation was performed on two-month old male C57BL/6J (Jax #000664) mice.  For lymphatic ablation, mice were anesthetized with ketamine (100 mg kg−1) and xylazine (10 mg kg−1), and secured on a stereotaxic frame.  5μL of Visudyne (Valeant Ophtalmics) solution or artificial CSF for sham surgery was delivered via intra-cisterna magna injection and 15 minutes later, the drug was then photoconverted through intact skull using a non-thermal 689-nm wavelength laser (Coherent Opal Photoactivator, Lumenis) at 5 points previously demonstrated to be effective.  Each point was photoconverted for 83 seconds to provide a light dose of 50 J/cm2 at an intensity of 600 mW/cm2.  The mice were then sutured and recovered on heating pad until fully awake.  Following 1-week recovery, Mice were injected i.p. with either 1μg IL-1β or saline vehicle (5 mice per group, 4 groups +/- Visudyne +/-IL-1β).  Two hours later mice were euthanized by lethal dose of anesthetic (Euthasol) and perfused with cold PBS.  One whole hemisphere of brain was collected from each mouse and biological replicates were pooled.  Brain tissue was dissociated in 5mL Hank’s buffering saline solution with DNaseI (50U/mL) and papain (4U/mL) at 37ºC for 45 minutes.  Cell suspension was then passed through a 70um strainer and CD11b+ cells were magnetically sorted using CD11b MicroBeads, human and mouse (Miltenyi) as per manufacturer’s instructions using AutoMACS (Miltenyi) and 2000 cells per condition were targeted for sequencing.

first: Dylan

last: Goldman


title: Characterising the chromatin dynamics upon HER2 overexpression

status: Public on Jun 09 2022

city: LONDON

first: Ateequllah

last: Hayat

address: CRANMER TERRACE

department: IMBE

institute: SGUL

summary: We performed ATAC-seq to cells isolated from 3D cell culture to understand their 3D conformational change. An indcuible HER2 expression was induced from 0-48 hours and their ATAC-seq performed to their acini. This allowed us to isolate their chomatin changes at the very earliest time-points, which has not been performed to date.

overall_design: Buenrostro et al., 2015


title: IFNa primes cancer cells for Fusicoccin-induced cell death via 14-3-3 PPI stabilization

status: Public on Jun 02 2022

city: Eindhoven

first: Blaž

last: Andlovic

address: Den Dolech 2

country: Netherlands

institute: Eindhoven University of Technology

summary: The natural product family of the fusicoccanes (FCs) has been shown to display anti-cancer activity, especially when combined with established therapeutic agents. FCs stabilize 14-3-3 protein-protein interactions (PPIs). Here, we tested combinations of a small library of FCs with interferon α (IFNα) on different cancer cell lines and report a proteomics approach to identify the specific 14-3-3 PPIs that are induced by IFNα and stabilized by FCs in OVCAR-3 cells. Among the identified 14-3-3 target proteins are THEMIS2, receptor interacting protein kinase 2 (RIPK2), EIF2AK2, and several members of the LDB1 complex. Biophysical and structural biology studies confirm these 14-3-3 PPIs as physical targets of FC stabilization, and transcriptome as well as pathway analyses suggest possible explanations for the observed synergistic effect of IFNα/FC treatment on cancer cells. This study elucidates the polypharmacological effects of FCs in cancer cells and identifies potential targets from the vast interactome of 14-3-3s for therapeutic intervention in oncology.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for OVCAR-3 cells treated with FC-A, IFNα and combination of FC-A and IFNα.

first: Geronimo

last: Heilmann

first: Sabrina

last: Ninck

first: Yusuke

last: Higuchi

first: Nobuo

last: Kato

first: Luc

last: Brunsveld

first: Michelle

last: Arkin

first: Sascha

last: Menninger

first: Axel

last: Choidas

first: Farnusch

last: Kaschani

first: Markus

last: Kaiser

first: Christian

last: Ottmann

first: Jan

last: Eickhoff

first: Alexander

last: Wolf

first: Federica

last: Centorrino

first: Sebastian

last: Andrei