Features Partner Sites Information LinkXpress hp
Sign In
Advertise with Us

Download Mobile App




Pediatric Ependymoma Single-Cell Analysis Signatures Linked to Outcomes

By LabMedica International staff writers
Posted on 30 Jul 2020
An ependymoma is a tumor that arises from the ependyma, a tissue of the central nervous system. More...
Usually, in pediatric cases the location is intracranial, while in adults it is spinal. The common location of intracranial ependymomas is the fourth ventricle.

Ependymomas make up about 5% of adult intracranial gliomas and up to 10% of childhood tumors of the central nervous system (CNS). Their occurrence seems to peak at age 5 years and then again at age 35. They develop from cells that line both the hollow cavities of the brain and the canal containing the spinal cord.

A team of Pediatric Oncologists based at the Dana-Farber Cancer Center (Boston, MA, USA) and their colleagues generated single-cell transcriptomic data on 20 fresh surgical tumor samples from 18 patients, as well as on eight patient-derived cell models and two patient-derived xenografts. At the same time, they performed single-nucleus RNA-seq on 14 snap-frozen ependymoma samples. In all, they analyzed 74,927 single tumor cells or nuclei, and, based on the samples' DNA methylation patterns, determined the tumors' molecular subgroups.

Tumor tissue was dissociated mechanically followed by papain-based enzymatic digestion for 30 min at 37°C using a Brain Tumor Dissociation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany). Single-cell sorting was performed on a SH700 cell sorter (Sony Biotechnology, San Jose, CA, USA) using 488 nm (calcein AM, 530/30 emission filter) and 633 nm (TO-PRO3, 665/30 emission filter) lasers. Whole transcriptome amplification, library preparation, and sequencing of single cells and single nuclei were performed following the Smart-seq2 modified protocol. Single nuclei were processed using the microfluidics-based 10X Chromium Single Cell 3’ Reagent Kits v3 (10X Genomics, Pleasanton, CA, USA).

The investigators reported that the transcriptomes of cells found within ependymomas, were similar to those of normal brain cells. However, they noted that the tumor cells appeared to have stopped at various points along the differentiation process. Within ependymomas, they uncovered three differentiation trajectories: ependymal-like, glial progenitor-like and neuronal-like cells. In posterior fossa ependymoma samples — posterior fossa group A (PF-A ) is the most aggressive of the subgroups and posterior fossa group B (PF-B) is linked to better patient prognosis — they uncovered nine recurrent transcriptional metaprograms. Two programs were linked with cell-cycle genes and were particularly found among PF-A samples. Other metaprograms were associated with mature cell types, astrocytes, or immature stem-like cells and neuronal or glial lineage precursors.

The team identified 10 transcriptional metaprograms, including two associated with cell-cycle genes and others linked to radial glial-like or neuronal precursor-like cell types, among eight supratentorial ependymoma samples. Undifferentiated cell states were also more common among tumors with poorer prognosis, such as the typically more aggressive PF-A tumors, the researchers found. The more benign groups like PF-B or PF-subependymoma had less proliferative and more differentiated cell populations. Within bulk RNA expression data, tumors' transcriptional signatures correlated with survival.

The authors concluded that this deconvolution of heterogeneous (ependymoma) subpopulations pinpoints key malignant transcriptomic signatures, and identify high-risk tumors and subsequently inform the development of more effective anti-ependymoma treatments. The study was published on July 13, 2020 in the journal Cancer Cell.



Gold Member
Serological Pipets
INTEGRA Serological Pipets
Portable Electronic Pipette
Mini 96
New
Gold Member
Immunochromatographic Assay
CRYPTO Cassette
New
Clinical Chemistry System
P780
Read the full article by registering today, it's FREE! It's Free!
Register now for FREE to LabMedica.com and get access to news and events that shape the world of Clinical Laboratory Medicine.
  • Free digital version edition of LabMedica International sent by email on regular basis
  • Free print version of LabMedica International magazine (available only outside USA and Canada).
  • Free and unlimited access to back issues of LabMedica International in digital format
  • Free LabMedica International Newsletter sent every week containing the latest news
  • Free breaking news sent via email
  • Free access to Events Calendar
  • Free access to LinkXpress new product services
  • REGISTRATION IS FREE AND EASY!
Click here to Register








Channels

Hematology

view channel
Image: New research points to protecting blood during radiation therapy (Photo courtesy of 123RF)

Pioneering Model Measures Radiation Exposure in Blood for Precise Cancer Treatments

Scientists have long focused on protecting organs near tumors during radiotherapy, but blood — a vital, circulating tissue — has largely been excluded from dose calculations. Each blood cell passing through... Read more

Immunology

view channel
Image: The VENTANA HER2 (4B5) test is now CE-IVDR approved (Photo courtesy of Roche)

Companion Diagnostic Test Identifies HER2-Ultralow Breast Cancer and Biliary Tract Cancer Patients

Breast cancer is the most common cancer in Europe, with more than 564,000 new cases and 145,000 deaths annually. Metastatic breast cancer is rising in younger populations and remains the leading cause... Read more

Technology

view channel
Image: Conceptual design of the CORAL capsule for microbial sampling in the small intestine (H. Mohammed et al., Device (2025). DOI: 10.1016/j.device.2025.100904)

Coral-Inspired Capsule Samples Hidden Bacteria from Small Intestine

The gut microbiome has been linked to conditions ranging from immune disorders to mental health, yet conventional stool tests often fail to capture bacterial populations in the small intestine.... Read more
Copyright © 2000-2025 Globetech Media. All rights reserved.