The advent of preventive high-resolution structural histopathology by artificial-intelligence-powered cryogenic electron tomography

Abstract

Advances in cryogenic electron microscopy (cryoEM) single particle analysis have revolutionized structural biology by facilitating the in vitro determination of atomic- and near atomic-resolution structures for fully hydrated macromolecular complexes exhibiting compositional and conformational heterogeneity across a wide range of sizes. Cryogenic electron tomography (cryoET) and subtomogram averaging are rapidly progressing towards delivering similar insights for macromolecular complexes in situ, without requiring tags or harsh biochemical purification. Furthermore, cryoET allows visualizing cell and tissue phenotypes directly at molecular, nanometric resolution without chemical fixation or staining artifacts. This forward-looking review covers recent developments in cryoEM/ET and related technologies such as cryogenic focused ion beam milling scanning electron microscopy and correlative light microscopy, increasingly driven and boosted by artificial intelligence algorithms. Their potential application to emerging concepts is discussed, primarily the prospect of complementing medical histopathology analysis. Machine learning solutions are poised to address current challenges posed by 'big data' in cryoET of tissues, cells, and macromolecules, offering the promise of novel insights into disease processes translatable to the clinic in the near future in the form of improved diagnostics and targeted therapeutics.

Missing Wedge Completion via Unsupervised Learning with Coordinate Networks

“…Given the increasing popularity of cryoET [104] owing to its demonstrated applications in cellular structural characterization [105] and histopathological clinical diagnoses [32], we expect for artificial intelligence developments that enhance tomographic reconstruction to become an increasingly active and impactful field of research. Since cryoET can provide 3D views of individual macromolecules and complexes across a wide range of sizes, as well as their distributions within organelles, cells, and tissues, improving tomographic reconstruction quality may enable novel structure-based diagnostics at the molecular level and accelerate drug development by assessing the effects of molecular therapeutics on phenotype.…”

“…CryoET can also probe the structure of other clinically-relevant 2 of 19 samples ranging from individual organelles [16,17] and cells [18,19] to complex tissue sections [20][21][22][23][24]. Insights from cryoET data analysis can facilitate understanding dynamic molecular processes such as viral infections [25][26][27][28][29][30], enable pathology diagnosis [31,32], and reveal the impacts of potential therapeutic interventions [19], among other biomedical applications. A critical downstream technique, subtomogram averaging (STA) [33,34], further refines cryoET data to achieve subnanometer [35] to near-atomic [36] resolution of repeated structures within tomograms [37,38], underscoring the importance of precise cryoET reconstructions for accurate particle localization and structural analysis.…”