Center for Data Driven Discovery in Biomedicine
Dr. Mateusz Koptyra is a Senior Scientist responsible for initiation, coordination and implementation of scientific projects around the Center’s research units. His team identifies the research demands at the clinical level and creates pipelines for projects to test the research proposals at a pre-clinical level, with a primary focus on quality data generation in genomic, transcriptomic and proteomic tumor profiling for the biomarker search. Mateusz is also responsible for exploration and validation of the platforms to be utilized for Center’s pipelines, and improvements of sample collection, handling and storage methods to empower the Children’s Brain Tumor Tissue Consortium pipeline. His research focuses on non-invasive diagnostics in pediatric brain tumors, biomarker search, cell-free DNA/RNA, and extra-cellular vesicles, including the development of non-invasive medulloblastoma tumor profiling using circulating in blood tumor material (cell-free DNA).
Prior to joining CHOP in September of 2011, Mateusz worked as a research assistant to explore diagnostic utilities for breast cancer at the Center of Oncology in Warsaw, Poland. Additionally, he worked as a research scholar at Temple University where he studied mechanisms for therapy resistance to small molecule inhibitors in chronic myeloid leukemia, before completing a post-doctoral fellowship at Thomas Jefferson University to explore the role of Stat5 transcription factors in prostate cancer models.
Mateusz earned an MS degree from Warsaw University and completed his PhD from the Medical University of Warsaw in Warsaw, Poland. He is committed to empowering non-invasive diagnostics for pediatric brain tumors. He aims to bring a small chunk of meaningful quality research data which will lead to improvement in clinic for any child in need.
Children’s Hospital of Philadelphia
Proteomic Analysis of CBTN Cell Lines
Using cell lines provided by the Children’s Brain Tumor Network, researchers will attempt to build resources used to develop effective treatments and predict the treatment outcomes of pediatric brain tumor patients.
Functional Dependency Mapping in Paediatric Brain Cancers
The treatment of pediatric high grade gliomas could be improved and enhanced with a deeper understanding of their genetic and molecular characteristics. Using specimens from the Children’s Brain Tumor Network, researchers are exploring new therapeutic opportunities for pHGG.
Gene Expression Analysis Platform Evaluation for FFPE Specimen Material-Based Studies
Newly developed technology is advancing the ability of researchers to gain important insight from small clinical specimens.
Evaluation of Immunosignature Profile in Medulloblastoma
Medulloblastoma is a tumor with many subtypes and noninvasive diagnostic tools are needed to accelerate diagnosis. Using rare samples made available through the Children’s Brain Tumor Network, researchers will analyze the use of noninvasive methods for tumor classification.
Pediatric Brain Tumor miRNA Profiling for the Cohort of Children’s Brain Tumor Network Specimens
Many pediatric brain tumors are unable to be removed in surgery, requiring the development of new effective therapies. Using RNA samples provided by CBTN, researchers are producing important characterization of the tumors and biomarker data to be used by researchers around the world in the pursuit of such new approaches.
Craniopharyngioma, Medulloblastoma, HGG, (AT/RT), LGG, Ependymoma, Ganglioglioma, DNET, Schwannoma
CBTN Cell Lines High-Throughput Drug Screening Study (NCATS)
A robust resource on the drug response across pediatric cancer types will be helpful to guide clinical decisions. Using samples provided by the Children’s Brain Tumor Network, researchers will create and share this important data resource.
Medulloblastomas comprises the vast majority of pediatric embryonal tumors and by definition arise in the posterior fossa, where they constitute approximately 40% of all posterior fossa tumors. Other forms of embryonal tumors each make up 2% or less of all childhood brain tumors.The clinical feature
BloodPAC Quarterly Meeting
BloodPAC Quarterly Meeting
Mateusz Koptyra and Allison Heath
Children's Brain Tumor Network - Accelerating Research Through Collaboration and Open Science
This presentation highlights the impact and importance of the collaborative and open source nature of CBTN databases and samples.
Jena Lilly, Jennifer Mason, Elizabeth Appert, Allison Heath, Yuankun Zhu, Bo Zhang, Mateusz Koptyra, Mariarita Santi, Ian Pollack, Stewart Goldman, Sarah Leary, Anna Buccoliero, Mirko Scagnet, David Haussler, Derek Hanson, Jiangguo Zhang, Weiqing Wan, Chunde Li, Ron Firestein, Jason Cain, Joanna Phillips, Nalin Gupta, Sabine Mueller, Gerald Grant, Michelle Monje-Deisseroth, Sonia Partap, Jeffrey Greenfield, Brian Rood, Javad Nazarian, Eric Raabe, Eric Jackson, Stacie Stapleton, Robert Lober, David Kram, Phillip Storm, Rishi Lulla, Michael Prados, Adam Resnick, and Angela Waanders
Telomere Length Analysis of CNS Tumors in the Pediatric Brain Tumor Atlas
Through analysis of data provided through the Pediatric Brain Tumor Atlas, researchers analyze the lengths of telomeres (structures that cap the ends of chromosomes) found in pediatric brain tumors as a way to identify therapeutic needs for various tumor types.
Rokita JL, Gaonkar K, Ijaz H, Miller D, Karras T, Santi M, Martinez D, Koptyra M, De Raedt T, Mason J, Appert E, Lilly J, Zhu Y, Waanders A, Resnick A, Storm J, Cole K.
Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer
We report a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA sequencing, and proteomics and phosphoproteomics profiling, of 218 tumors across 7 histological types of childhood brain cancer: low-grade glioma (n = 93), ependymoma (32), high-grade glioma (25), medulloblasto
Francesca Petralia, Nicole Tignor, Boris Reva, Mateusz Koptyra, Shrabanti Chowdhury, Dmitry Rykunov, Azra Krek, Weiping Ma, Yuankun Zhu, Jiayi Ji, Anna Calinawan, Jeffrey R. Whiteaker, Antonio Colaprico, Vasileios Stathias, Tatiana Omelchenko, Xiaoyu Song, Pichai Raman, Yiran Guo, Miguel A. Brown, Richard G. Ivey, John Szpyt, Sanjukta Guha Thakurta, Marina A. Gritsenko, Karl K. Weitz, Gonzalo Lopez, Selim Kalayci, Zeynep H. Gümüş, Seungyeul Yoo, Felipe da Veiga Leprevost, Hui-Yin Chang, Karsten Krug, Lizabeth Katsnelson, Ying Wang, Jacob J. Kennedy, Uliana J. Voytovich, Lei Zhao, Krutika S. Gaonkar, Brian M. Ennis, Bo Zhang, Valerie Baubet, Lamiya Tauhid, Jena V. Lilly, Jennifer L. Mason, Bailey Farrow, Nathan Young, Sarah Leary, Jamie Moon, Vladislav A. Petyuk, Javad Nazarian, Nithin D. Adappa, James N. Palmer, Robert M. Lober, Samuel Rivero-Hinojosa, Liang-Bo Wang, Joshua M. Wang, Matilda Broberg, Rosalie K. Chu, Ronald J. Moore, Matthew E. Monroe, Rui Zhao, Richard D. Smith, Jun Zhu, Ana I. Robles, Mehdi Mesri, Emily Boja, Tara Hiltke, Henry Rodriguez, Bing Zhang, Eric E. Schadt, D.R. Mani, Li Ding, Antonio Lavarone, Maciej Wiznerowicz, Stephan Schürer, Xi S. Chen, Allison P. Heath, Jo Lynne Rokita, Alexey I. Nesvizhskii, David Fenyö, Karin D. Rodland, Tao Liu, Steven P. Gygi, Amanda G. Paulovich, Adam C. Resnick, Phillip B. Storm, Brian R. Rood, Pei Wang, Children’s Brain Tumor Network, Clinical Proteomic Tumor Analysis Consortium
An Integrated Set of Pediatric High Grade Glioma Resources for Translational Studies
In an effort to better support researchers around the world looking to understand pediatric high grade glioma, researchers have created a HGG resource that includes data and samples processed and provided by CBTN.
Heba Ijaz, Valerie Baubet, Mateusz Koptyra, Pichai Raman, Lamiya Tauhid, Krutika Gaonkar, Yuankun Zhu, Bo Zhang, Namrata Choudhari, Jamie Galanaugh, Elizabeth Appert, Jennifer Mason, Linnea Cripe, Taylor Lis, Maria Rita Santi, Jay Storm, Angela Waanders, Adam Resnick, and Kristina Cole