4.6 Article

Single-Cell Sequencing Identifies Master Regulators Affected by Panobinostat in Neuroblastoma Cells

Related references

Note: Only part of the references are listed.
Review Pharmacology & Pharmacy

Methodological advances in the discovery of novel neuroblastoma therapeutics

Miguel F. Segura et al.

Summary: Neuroblastoma, a cancer affecting the sympathetic nervous system, accounts for a significant portion of childhood cancer-related deaths, with poor survival rates among high-risk patients. New technologies and therapies, such as molecular profiling and immunotherapy, show promise in providing more effective and safer treatment options for these patients.

EXPERT OPINION ON DRUG DISCOVERY (2022)

Review Oncology

Neuroblastoma-Telomere maintenance, deregulated signaling transduction and beyond

Sabine A. Stainczyk et al.

Summary: Neuroblastoma, a childhood malignancy, has limited treatment options for high-risk and relapsed cases. Recent molecular profiling has revealed promising molecularly targeted therapies, with a particular emphasis on understanding the importance of telomere maintenance mechanisms in tumor progression.

INTERNATIONAL JOURNAL OF CANCER (2022)

Review Oncology

Advancing therapy for neuroblastoma

Bo Qiu et al.

Summary: Neuroblastomas, tumors of sympathetic origin, have shown significant progress in treatment, resulting in improved survival rates for patients. Ongoing efforts are focused on personalizing therapy for high-risk disease and reducing treatment intensity for low-risk disease. The addition of immunotherapies, targeted therapies, and radiopharmaceuticals to standard induction regimens aims to further improve initial response rates in high-risk neuroblastoma patients. Precision medicine strategies are being explored for relapsed and refractory cases to enhance the immune response and prolong disease remission. This review highlights advancements in understanding the pathogenesis of neuroblastoma and the development of risk-adapted therapies.

NATURE REVIEWS CLINICAL ONCOLOGY (2022)

Review Biology

The R Language: An Engine for Bioinformatics and Data Science

Federico M. Giorgi et al.

Summary: This article reviews the development of the R programming language from its inception to the present day, describing its current features and capabilities, as well as its relationship with other programming languages. It also provides a detailed introduction to the major tools and applications of R, and discusses its role in science.

LIFE-BASEL (2022)

Review Cell Biology

Regulation of ribosomal protein genes: An ordered anarchy

Cyrielle Petibon et al.

Summary: Ribosomal protein genes are highly expressed in most cell types and are essential for cell growth and proliferation. Regulation of these genes involves both general and gene-specific mechanisms, allowing the cell to coordinate ribosome production while maintaining functional specialization and diversity. Posttranscriptional regulatory events play a key role in fine-tuning the expression of ribosomal protein genes and controlling potential variation in ribosome functions.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2021)

Article Biochemistry & Molecular Biology

A modular master regulator landscape controls cancer transcriptional identity

Evan O. Paull et al.

Summary: Using a network-based approach, 407 master regulator proteins were identified to canalize individual cancer samples into 112 transcriptionally distinct tumor subtypes. These proteins were organized into 24 pan-cancer master regulator block modules regulating key cancer hallmarks and predictive of patient outcome. Genomic alterations were predicted to induce aberrant MR activity, providing insight into mechanisms linking tumor genetics and transcriptional identity.
Review Biochemistry & Molecular Biology

Targeting Oncogenic Transcriptional Networks in Neuroblastoma: From N-Myc to Epigenetic Drugs

Roberto Ciaccio et al.

Summary: Neuroblastoma is controlled by gene expression dysregulation, resulting in a dependency on specific tuning of gene expression caused by genetic and epigenetic alterations. Multi-target therapies play a significant role in disrupting tumorigenic pathways.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Review Oncology

MYCN Function in Neuroblastoma Development

Jorg Otte et al.

Summary: Dysregulated expression of the transcription factor MYCN is frequently detected in nervous system tumors such as childhood neuroblastoma and is a strong predictor of poor prognosis. Increased MYCN expression is an early event in these cancers, leading to a peculiar dysregulation of cells that exhibit embryonal or cancer stem-like qualities.

FRONTIERS IN ONCOLOGY (2021)

Article Biochemistry & Molecular Biology

Single-Cell Gene Network Analysis and Transcriptional Landscape of MYCN-Amplified Neuroblastoma Cell Lines

Daniele Mercatelli et al.

Summary: The study investigated two cell lines, BE2C and Kelly, of neuroblastoma, showing distinct transcriptional network activities with BE2C having more mesenchymal characteristics compared to Kelly. Single-cell data revealed that MYCN is not constantly active in these cells, and highlighted higher variance in metallothionein transcripts in Kelly cells.

BIOMOLECULES (2021)

Article Oncology

Atypical Teratoid Rhabdoid Tumours Are Susceptible to Panobinostat-Mediated Differentiation Therapy

Wai C. Chong et al.

Summary: ATRT is an aggressive undifferentiated malignancy of the central nervous system in children, characterized by the loss of the SMARCB1 gene. Treatment with the histone deacetylate inhibitor, panobinostat, shows therapeutic potential by inhibiting tumor growth and promoting neuronal differentiation. This preclinical study supports the use of panobinostat-mediated differentiation therapy for ATRT.

CANCERS (2021)

Article Cell Biology

Broad-Spectrum HDAC Inhibitors Promote Autophagy through FOXO Transcription Factors in Neuroblastoma

Katharina Koerholz et al.

Summary: The study found that pan-HDAC inhibitors can induce autophagy in neuroblastoma, and their combination with autophagy modulating drugs suppresses tumor growth of high-risk neuroblastoma cells.

CELLS (2021)

Article Biochemical Research Methods

The Transcriptome of SH-SY5Y at Single-Cell Resolution: A CITE-Seq Data Analysis Workflow

Daniele Mercatelli et al.

Summary: CITE-seq is a multimodal single cell analysis technique that combines antibody labeling and single-cell RNA sequencing, which can reduce costs and increase efficiency. By studying the transcriptome of neuroblastoma cell line, insights into cell heterogeneity and identification of reference genes can be obtained.

METHODS AND PROTOCOLS (2021)

Article Biochemistry & Molecular Biology

UCell: Robust and scalable single-cell gene signature scoring

Massimo Andreatta et al.

Summary: UCell is an R package designed for evaluating gene signatures in single-cell datasets. It offers robust signature scores based on the Mann-Whitney U statistic, requiring less computing time and memory compared to other methods. UCell can handle large datasets in minutes and can interact directly with Seurat objects.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2021)

Review Biochemistry & Molecular Biology

Gene regulatory network inference resources: A practical overview

Daniele Mercatelli et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2020)

Article Biochemical Research Methods

corto: a lightweight R package for gene network inference and master regulator analysis

Daniele Mercatelli et al.

BIOINFORMATICS (2020)

Review Biochemistry & Molecular Biology

Current best practices in single-cell RNA-seq analysis: a tutorial

Malte D. Luecken et al.

MOLECULAR SYSTEMS BIOLOGY (2019)

Article Genetics & Heredity

Pan-Cancer and Single-Cell Modeling of Genomic Alterations Through Gene Expression

Daniele Mercatelli et al.

FRONTIERS IN GENETICS (2019)

Article Multidisciplinary Sciences

The art of using t-SNE for single-cell transcriptomics

Dmitry Kobak et al.

NATURE COMMUNICATIONS (2019)

Review Oncology

MALAT1: a druggable long non-coding RNA for targeted anti-cancer approaches

Nicola Amodio et al.

JOURNAL OF HEMATOLOGY & ONCOLOGY (2018)

Article Multidisciplinary Sciences

Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq

Mariella G. Filbin et al.

SCIENCE (2018)

Article Biotechnology & Applied Microbiology

Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics

Marlon Stoeckius et al.

GENOME BIOLOGY (2018)

Article Multidisciplinary Sciences

Data Descriptor: Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines

Jo Lynne Harenza et al.

SCIENTIFIC DATA (2017)

Article Multidisciplinary Sciences

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

Itay Tirosh et al.

SCIENCE (2016)

Review Oncology

Panobinostat: A Review in Relapsed or Refractory Multiple Myeloma

Sarah L. Greig

TARGETED ONCOLOGY (2016)

Article Medicine, Research & Experimental

Histone deacetylase inhibitor panobinostat induces calcineurin degradation in multiple myeloma

Yoichi Imai et al.

JCI INSIGHT (2016)

Article Biotechnology & Applied Microbiology

Patterns of ribosomal protein expression specify normal and malignant human cells

Joao C. Guimaraes et al.

GENOME BIOLOGY (2016)

Article Biotechnology & Applied Microbiology

Spatial reconstruction of single-cell gene expression data

Rahul Satija et al.

NATURE BIOTECHNOLOGY (2015)

Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

Molecular signatures database (MSigDB) 3.0

Arthur Liberzon et al.

BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers

Celine Lefebvre et al.

MOLECULAR SYSTEMS BIOLOGY (2010)

Article Biotechnology & Applied Microbiology

Differential expression analysis for sequence count data

Simon Anders et al.

GENOME BIOLOGY (2010)

Review Biochemistry & Molecular Biology

Critical pathways in cellular senescence and immortalization revealed by gene expression profiling

A. L. Fridman et al.

ONCOGENE (2008)

Article Multidisciplinary Sciences

Identification and functional significance of genes regulated by structurally different histone deacetylase inhibitors

MJ Peart et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Medicine, General & Internal

COX-1, COX-2, and COX-3 and the future treatment of chronic inflammatory disease

DA Willoughby et al.

LANCET (2000)