Multicenter Validation and Automation of the NEOPROFILER-MB Prototype, a Molecular Test for Medulloblastoma Classification Based on RT-qPCR Technology and Artificial Intelligence.

• Grant number: 24/16668-5
• Support Opportunities: Research Grants - Innovative Research in Small Business - PIPE
• Start date: September 01, 2025
• End date: August 31, 2027
• Field of knowledge: Health Sciences - Medicine - Maternal and Child Health
• Principal Investigator: Ricardo Bonfim Silva
• Grantee: Ricardo Bonfim Silva
• Company: Neogenys Diagnóstico Molecular Ltda
• CNAE: Pesquisa e desenvolvimento experimental em ciências físicas e naturais ; Atividades de serviços de complementação diagnóstica e terapêutica
• City: Ribeirão Preto
• Pesquisadores principais: Gustavo Alencastro Veiga Cruzeiro
• Associated researchers: Camila Morais Melo ; Carlos Alberto Oliveira de Biagi Júnior ; Elvis Terci Valera ; Felipe D'Almeida Costa ; Maristella Bergamo Francisco dos Reis ; Rodrigo Farinaccio Lotrario
• Associated research grant: 18/26437-0 - Establishment of a molecular classification platform for medulloblastoma by qPCR in real time, AP.PIPE

Abstract

Medulloblastoma is the most common malignant central nervous system tumor in children, with an estimated 30,000 children affected worldwide each year. According to the World Health Organization (WHO), this tumor is molecularly subdivided into four subgroups: WNT, SHH (wild-type TP53 or mutated TP53), and Non-WNT/SHH (Group 3 and 4). These subgroups have distinct molecular and clinical characteristics and differ in patient prognosis, impacting risk stratification and treatment type. For instance, the WNT subgroup has the best prognosis compared to the others, with an overall survival rate of 95% in 5 years and a frequency of 1 in every 3 patients. Phase II clinical trials in the USA aim to de-escalate radiotherapy and/or chemotherapy in WNT medulloblastoma patients, reducing long-term sequelae mainly caused by radiation. For patients in the SHH and non-WNT/SHH (Group 3 and 4) subgroups, treatment protocols need to be adapted as they present intermediate and poor prognoses, respectively. Implementing this protocol in Brazil will positively impact patients' quality of life and reduce the budget of public hospitals, highlighting the importance of molecular classification for precision medicine to establish the "ideal" protocol for different tumor subtypes. In the PIPE - Phase 1 project, we achieved a significant milestone by developing the prototype for the molecular classification test for medulloblastoma, NEOPROFILER-MB, validating it in formalin-fixed, paraffin-embedded (FFPE) samples. The method is based on the Taqman Low Density Array (TLDA), an array card with 20 genes for 4 samples/patients. Concurrently, we identified a set of 6 genes with the potential to molecularly classify the 4 molecular subtypes of medulloblastoma with accuracy similar to TLDA. This method was named OnDemand, as it analyzes individual samples, reducing both the overall processing time of the test and the final cost per sample. Despite the excellent results achieved in Phase 1, we recognize that the validation had limitations due to the small number and low diversity of samples, all from a single center, the Hospital das Clínicas de Ribeirão Preto. Therefore, the objective of this PIPE-FAPESP Phase 2 project is to validate, in a larger number of FFPE samples and multicentrically, the prototype molecular classification test for medulloblastoma on the TLDA and OnDemand platforms and to develop an artificial intelligence-based molecular classifier software with a user-friendly interface for automated analysis and results reporting. To develop this proposal, NEOGENYS has the support of associated researchers and collaborators and an agreement to use the infrastructure of the Molecular Biology Laboratory of the Department of Pediatrics at HCFMRP-USP. For multicentric validation and sample expansion, NEOGENYS has partnered with international hospitals and institutes, such as the Federal University of Rio Grande do Sul, AC Camargo Hospital, the University of Guadalajara in Mexico, and Hospital San Juan Garrahan in Argentina. The expertise of NEOGENYS members and scientific and clinical collaborators/partners will position the molecular classification test for medulloblastoma as a reference in the field, offering advanced and reliable diagnostic solutions to doctors and patients. We believe this technological innovation is essential to further drive the growth and success of our startup, allowing us to achieve our goals of democratizing access to molecular tests in oncology, with international potential to impact public health and the quality of life of cancer patients, and continue contributing to the advancement of oncology and precision medicine. (AU)