Computational anatomy and geometric shape analysis enables analysis of complex craniofacial phenotypes in zebrafish

Abstract

Due to the complexity of fish skulls, previous attempts to classify craniofacial phenotypes have relied on qualitative features or sparce 2D landmarks. In this work we aim to identify previously unknown 3D craniofacial phenotypes with a semiautomated pipeline in adult zebrafish mutants. We first estimate a synthetic ‘normative’ zebrafish template using microCT scans from a sample pool of wildtype animals using the Advanced Normalization Tools (ANTs). We apply a computational anatomy (CA) approach to quantify the phenotype of zebrafish with disruptions in bmp1a, a gene implicated in later skeletal development and whose human ortholog when disrupted is associated with Osteogenesis Imperfecta. Compared to controls, the bmp1a fish have larger otoliths, larger normalized centroid sizes, and exhibit shape differences concentrated around the operculum, anterior frontal, and posterior parietal bones. Moreover, bmp1a fish differ in the degree of asymmetry. Our CA approach offers a potential pipeline for high-throughput screening of complex fish craniofacial shape to discover novel phenotypes for which traditional landmarks are too sparce to detect. The current pipeline successfully identifies areas of variation in zebrafish mutants, which are an important model system for testing genome to phenome relationships in the study of development, evolution, and human diseases.

Examining craniofacial variation among crispant and mutant zebrafish models of human skeletal diseases

“…In two of the four model systems ( plod2 and meox1 ) our pseudolandmark pipeline identified areas of variation in the skull. These results lend support to our pseudolandmark pipeline enabling more efficient data collection, higher consistency and repeatability, and denser morphometric analysis than manual landmarking pipelines (Diamond et al, 2022).…”

“…With the exception of plod2 , in which the average of all landmarks was used as our manual gold standard, all genes were landmarked by a single author. Next, we transferred the set of 308 pseudolandmark points using the normative atlas of wildtype individuals that we previously published (Diamond et al, 2022) using the ALPACA module (Porto et al, 2021) of the SlicerMorph extension (Rolfe et al, 2021) in 3D Slicer (Fedorov et al, 2012). Pseudolandmark points were created using the PseudoLMGenerator module of the SlicerMorph package in 3D Slicer.…”

“…In this study we tested a previously developed semiautomated pipeline (Diamond et al, 2022) to identify areas of craniofacial variation in four zebrafish models of skeletal disease. Our results suggest that regardless of the type of fish used in a study (somatic vs. germline), there is a strong clutch effect in zebrafish.…”

“…In this study, we build on a previously developed semiautomated pipeline (Diamond et al, 2022) to identify areas of craniofacial variation in four different zebrafish models of skeletal disease: plod2 , meox1 , sost and wnt16 . Zebrafish models of plod2 are associated with Bruck Syndrome, a rare form of Osteogenesis Imperfecta (Lv et al, 2018).…”

First person – Kelly Diamond

“… ABSTRACT First Person is a series of interviews with the first authors of a selection of papers published in Biology Open, helping early-career researchers promote themselves alongside their papers. Kelly Diamond is first author on ‘ Computational anatomy and geometric shape analysis enables analysis of complex craniofacial phenotypes in zebrafish ’, published in BiO. Kelly is a postdoc in the lab of Dr Murat Maga at the Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, USA, investigating which combination of factors contribute to organismal morphology.…”