Evenflow project reposted this
Bioinformatics predoctoral researcher at the Barcelona Supercomputing Center and Universitat Pompeu Fabra #AI #bio Bluesky: @gprolcastelo.bsky.social
New Insights into Medulloblastoma! 🧠 I am very happy to announce the first paper in my Ph.D. thesis journey, now available as a preprint: Exploring the Boundaries of Medulloblastoma Subgroups with synthetic Data Generation (https://lnkd.in/dxW_ixix) Shout out to all the authors: Alejandro Tejada Lapuerta, Beatriz Urda, Iker Núñez Carpintero, Alfonso Valencia, and Davide Cirillo. Thanks to the Evenflow project, and my institution Barcelona Supercomputing Center. Let’s dive into our findings in this post! 🧵⤵️ (3 min read) 1. What is Medulloblastoma? Medulloblastoma (MB) is a childhood brain tumor that is classically divided into four molecular subgroups [1]: Wingless (WNT), Sonic Hedgehog (SHH), Group 3 (G3), and Group 4 (G4). It is a rare disease, with 5 cases per million in the pediatric population [2]. 2. Why study Medulloblastoma Subgroups? G3 and G4 subgroups tend to be closely clustered. This tight relationship is reflected in the latest consensus classification of MB, dividing the disease into WNT, SHH, and non-WNT/non-SHH subgroups [3]. Research has suggested the possibility to deem G3 and G4 as a continuum [4] but also the existence of an additional subgroup between G3 and G4 [5, 6] sometimes referred to as G3-G4. However, the limited number of patients in this intermediate case have made gaining relevant insights a challenge 3. How can we study a rare occurrence of a rare disease? We have obtained the data from the largest repository available on MB [7] and used the VAE's [8] generative ability to amplify the G3-G4 subgroup. This means we can learn from real patient data to generate new, synthetic patients. 4. What do we find? By identifying and augmenting the patients in the G3-G4 subgroup, we achieved high classification performance, reinforcing that this intermediate group displays distinct features in comparison to G3 and G4 (see first image attached) We have seen there are about 2,500 genes’ expressions that are unique to the G3-G4 subgroup, some of which are commonly mutated in MB: KMT2C, MYC, SNCAIP, SYNCRIP, and TP53 (see the other 5 images attached). 5. How is this helpful for MB research? We believe our contributions will help develop better treatments for MB: labeling patients’ subgroups leads to different treatment strategies, so elucidating the most adequate is essential for an optimal recovery. References [1] https://lnkd.in/d8jVZ8Ab [2] https://lnkd.in/dwfTUdcf [3] https://lnkd.in/dHhGMkEH [4] https://lnkd.in/dt_hMvNN [5] https://lnkd.in/dkY7W_pK [6] https://lnkd.in/dDq-GNDp [7] https://lnkd.in/dCnFBZ_r [8] https://lnkd.in/dNJtMgzj
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