Bendszus, M. | bioRxiv Science

bioRxiv2023

An AI-based segmentation and analysis pipeline for high-field MR monitoring of cerebral organoids

BackgroundCerebral organoids simulate the structure and function of the developing human brain in vitro, offering a large potential for personalized therapeutic strategies. The enormous growth of this research area over the past decade with its capability for clinical translation makes a non-invasive, automated analysis pipeline of organoids highly desirable. PurposeThis work presents the first application of magnetic resonance imaging (MRI) for the non-invasive quantification and quality assessment of cerebral organoids using an automated analysis tool. Three specific objectives are addressed, namely organoid segmentation to investigate organoid development over time, global cysticity classification, and local cyst segmentation. MethodsNine wildtype cerebral organoids were imaged over nine weeks using high-field 9.4T MRI including a 3D T2*-w and 2D diffusion tensor imaging (DTI) sequence. This dataset was used to train a deep learning-based 3D U-Net for organoid and local cyst segmentation. For global cysticity classification, we developed a new metric, compactness, to separate low- and high-quality organoids. ResultsThe 3D U-Net achieved a Dice score of 0.92{+/-}0.06 (mean {+/-} SD) for organoid segmentation in the T2*-w sequence. For global cysticity classification, compactness separated low- and high-quality organoids with high accuracy (ROC AUC 0.98). DTI showed that low-quality organoids have a significantly higher diffusion than high-quality organoids (p < .001). For local cyst segmentation in T2*-w, the 3D U-Net achieved a Dice score of 0.63{+/-}0.15 (mean {+/-} SD). ConclusionWe present a novel non-invasive approach to monitor and analyze cerebral organoids over time using high-field MRI and state-of-the-art tools for automated image analysis, offering a comparative pipeline for personalized medicine. We show that organoid growth can be monitored reliably over time and low- and high-quality organoids can be separated with high accuracy. Local cyst segmentation is feasible but could be further improved in the future.

developmental biology↗

bioRxiv2021

Reversible brain edema in experimental cerebral malaria is associated with transcellular blood-brain barrier disruption and delayed microhemorrhages

Brain swelling occurs in cerebral malaria (CM) and may either reverse or result in fatal outcome. It is currently unknown how brain swelling in CM reverses, as investigations have been hampered by inadequate animal models. In this study, we show that reversible brain swelling in experimental murine cerebral malaria (ECM) can be induced reliably after single vaccination with radiation-attenuated sporozoites as revealed by in vivo high-field (9.4T) magnetic resonance imaging. Our results provide evidence that parenchymal fluid increase and consecutive brain swelling results from transcellular blood-brain barrier disruption (BBBD), as revealed by electron microscopy. This mechanism enables reversal of brain swelling but does not prevent persistent focal brain damage, evidenced by microhemorrhages, in areas of most severe BBBD. In a cohort of 27 pediatric and adult CM patients (n=4 fatal, n=23 non-fatal) two out of four fatal CM patients (50%) and 8 out of 23 non-fatal CM patients (35%) showed microhemorrhages on MRI at clinical field strength of 1.5T, emphasizing the translational potential of the experimental model. Our data suggest that targeting transcellular BBBD may represent a promising adjunct therapeutic approach in cerebral brain swelling to reduce edema and may ultimately lead to a reduced permanent brain damage and a better longtime neurological outcome. Author summaryBrain swelling, which occurs in diseases such as cerebral malaria, is not necessarily fatal, and may reverse. Even upon reversal of brain swelling, neurological sequelae can still occur. The factors contributing to the reversibility of brain edema are not known, and treatment options remain therefore limited. Identifying the mechanisms leading to such reversibility could inform clinical management aimed at decreasing brain swelling and consecutive brain injury. Here we introduce a reproducible and simple animal model that allows comprehensive in vivo studies of reversible brain swelling in cerebral malaria at the peak of disease and upon recovery. We identify a specific type of blood-brain barrier disruption (BBBD) as a mechanism that occurs in brain swelling. We show that BBBD can reverse, but also highlight remaining brain damage in areas of most severe BBBD. As the ECM model introduced here bares crucial similarities to the CM in humans, our findings open strategies to study new therapeutic avenues and point to compounds that specifically target transcellular BBBD to reduce brain edema, and increase survival rates.

neuroscience↗