Pediatric Atypical Teratoid/Rhabdoid Tumors of the Brain: Identification of Metabolic Subgroups Using In Vivo 1H-MR Spectroscopy

Identifying reproducible transcription regulator coexpression patterns with single cell transcriptomics

The proliferation of single cell transcriptomics has potentiated our ability to unveil patterns that reflect dynamic cellular processes such as the regulation of gene transcription. In this study, we leverage a broad collection of single cell RNA-seq data to identify the gene partners whose expression is most coordinated with each human and mouse transcription regulator (TR). We assembled 120 human and 103 mouse scRNA-seq datasets from the literature (>28 million cells), constructing a single cell coexpression network for each. We aimed to understand the consistency of TR coexpression profiles across a broad sampling of biological contexts, rather than examine the preservation of context-specific signals. Our workflow therefore explicitly prioritizes the patterns that are most reproducible across cell types. Towards this goal, we characterize the similarity of each TR's coexpression within and across species. We create single cell coexpression rankings for each TR, demonstrating that this aggregated information recovers literature curated targets on par with ChIP-seq data. We then combine the coexpression and ChIP-seq information to identify candidate regulatory interactions supported across methods and species. Finally, we highlight interactions for the important neural TR ASCL1 to demonstrate how our compiled information can be adopted for community use.

Identifying Reproducible Transcription Regulator Coexpression Patterns with Single Cell Transcriptomics

The proliferation of single cell transcriptomics has potentiated our ability to unveil patterns that reflect dynamic cellular processes such as the regulation of gene transcription. In this study, we leverage a broad collection of single cell RNA-seq data to identify the gene partners whose expression is most coordinated with each human and mouse transcription regulator (TR). We assembled 120 human and 103 mouse scRNA-seq datasets from the literature (>28 million cells), constructing a single cell coexpression network for each. We aimed to understand the consistency of TR coexpression profiles across a broad sampling of biological contexts, rather than examine the preservation of context-specific signals. Our workflow therefore explicitly prioritizes the patterns that are most reproducible across cell types. Towards this goal, we characterize the similarity of each TR's coexpression within and across species. We create single cell coexpression rankings for each TR, demonstrating that this aggregated information recovers literature curated targets on par with ChIP-seq data. We then combine the coexpression and ChIP-seq information to identify candidate regulatory interactions supported across methods and species. Finally, we highlight interactions for the important neural TR ASCL1 to demonstrate how our compiled information can be adopted for community use.

Pediatric neuro-oncology: Highlights of the last quarter-century

The last quarter century has heralded dramatic changes in the field of pediatric neuro-oncology, with the era defined by profound developments in the understanding of the biological underpinnings of childhood central nervous system (CNS) tumors and translational therapeutics. Although there have been momentous strides forward in biologic, diagnostic, therapeutic, and experimental domains, considerable challenges remain and CNS tumors remain the leading cause of pediatric cancer-related mortality. Here, we review the significant advances in the field of pediatric neuro-oncology over the last 25 years and highlight ongoing hurdles facing future progress.

Advanced imaging techniques and non-invasive biomarkers in pediatric brain tumors: state of the art

In the pediatric age group, brain neoplasms are the second most common tumor category after leukemia, with an annual incidence of 6.13 per 100,000. Conventional MRI sequences, complemented by CT whenever necessary, are fundamental for the initial diagnosis and surgical planning as well as for post-operative evaluations, assessment of response to treatment, and surveillance; however, they have limitations, especially concerning histopathologic or biomolecular phenotyping and grading. In recent years, several advanced MRI sequences, including diffusion-weighted imaging, diffusion tensor imaging, arterial spin labelling (ASL) perfusion, and MR spectroscopy, have emerged as a powerful aid to diagnosis as well as prognostication; furthermore, other techniques such as diffusion kurtosis, amide proton transfer imaging, and MR elastography are being translated from the research environment to clinical practice. Molecular imaging, especially PET with amino-acid tracers, complement MRI in several aspects, including biopsy targeting and outcome prediction. Finally, radiomics with radiogenomics are opening entirely new perspectives for a quantitative approach aiming at identifying biomarkers that can be used for personalized, precision management strategies.

Current state of pediatric neuro-oncology imaging, challenges and future directions

Imaging plays a central role in neuro-oncology including primary diagnosis, treatment planning, and surveillance of tumors. The emergence of quantitative imaging and radiomics provided an uprecedented opportunity to compile mineable databases that can be utilized in a variety of applications. In this review, we aim to summarize the current state of conventional and advanced imaging techniques, standardization efforts, fast protocols, contrast and sedation in pediatric neuro-oncologic imaging, radiomics-radiogenomics, multi-omics and molecular imaging approaches. We will also address the existing challenges and discuss future directions.

Proton MR Spectroscopy of Pediatric Brain Disorders

In vivo MR spectroscopy is a non -invasive methodology that provides information about the biochemistry of tissues. It is available as a “push-button” application on state-of-the-art clinical MR scanners. MR spectroscopy has been used to study various brain diseases including tumors, stroke, trauma, degenerative disorders, epilepsy/seizures, inborn errors, neuropsychiatric disorders, and others. The purpose of this review is to provide an overview of MR spectroscopy findings in the pediatric population and its clinical use.

Proton and Multinuclear Spectroscopy of the Pediatric Brain

Magnetic resonance spectroscopy (MRS) is a valuable adjunct to structural brain imaging. State-of-the-art MRS has benefited greatly from recent technical advancements. Neurometabolic alterations in pediatric brain diseases have implications for diagnosis, prognosis, and therapy. Herein, the authors discuss MRS technical considerations and applications in the setting of various pediatric disease processes including tumors, metabolic diseases, hypoxic/ischemic encephalopathy/stroke, epilepsy, demyelinating disease, and infection.