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.
Proteomic Analysis of CBTN Cell Lines (Procan)
Scientists at Children’s Medical Research Institute are analysing tens of thousands of examples of all types of cancer from all over the world to develop a library of information to advance scientific discovery and enhance clinical treatment worldwide.This database will mean doctors can ef
HGG, Atypical teratoid/rhabdoid tumor (AT/RT)
Gene Expression Analysis Platform Evaluation for FFPE Specimen Material-Based Studies
This project aims to validate a novel RNA analysis platform. FFPE tissue material will be processed by the HTG EdgeSeq technology pipeline for mRNA and/or miRNA profiling.The HTG EgdeSeq system is an automated chemistry and workflow solution based on the HTG Molecular Diagnostics’ (HTG) ex
Evaluation of immunosignature profile in medulloblastoma
Medulloblastoma is the most common malignant pediatric brain tumor. Current therapies consist of surgical resection, whole brain or spinal cord radiation or aggressive chemotherapy. While five year survival in pediatric patients rates at 60-70%, survivors face neurological, intellectual, and phys
Pediatric brain tumor miRNA profiling for the cohort of Children’s Brain Tumor Tissue Consortium specimens
Pediatric brain tumors are the leading cause of disease related death in children. Major factors contributing to treatment failures for children with brain tumors include: a) the lack of comprehensive molecular characterization involving integration of the DNA-RNA-protein profiling; b) comprehens
Craniopharyngioma, Medulloblastoma, HGG, Atypical teratoid/rhabdoid tumor (AT/RT), LGG, Ependymoma, Ganglioglioma, DNET, Schwannoma
CBTN cell lines high throughput drug screening study (NCATS)
Brain cancer has become the leading cause of death in children with cancer. Brain tumor research generated little advances that have translated into meaningful clinical benefit for pediatric patients. One of the main reasons which significantly slowed down the progress of the scientific developme
Atypical teratoid/rhabdoid tumor (AT/RT)
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 clinic
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), medullobla
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