Phenomics Australia

In vivo research is critical to the functional dissection of
\nmulti-organ systems and whole organism physiology, and
\nthe laboratory mouse remains a quintessential animal model
\nfor studying mammalian, especially human, pathobiology.
\nEnabled by technological innovations in genome sequencing,
\nmutagenesis and genome editing, phenotype analyses, and
\nbioinformatics, in vivo analysis of gene function and dysfunction
\nin the mouse has delivered new understanding of the
\nmechanisms of disease and accelerated medical advances.
\nHowever, many significant hurdles have limited the elucidation
\nof mechanisms underlying both rare and complex,
\nmultifactorial diseases, leaving significant gaps in our scientific
\nknowledge. Future progress in developing a functionally
\nannotated genome map depends upon studies in model organisms,
\nnot least the mouse. Further, recent advances in
\ngenetic manipulation and in vivo, in vitro, and in silico phenotyping
\ntechnologies in the mouse make annotation of the
\nvast majority of functional elements within the mammalian
\ngenome feasible. The implementation of a Deep Genome
\nProject—to deliver the functional biological annotation of all human orthologous genomic elements in mice—is an essential
\nand executable strategy to transform our understanding
\nof genetic and genomic variation in human health and disease
\nthat will catalyze delivery of the promised benefits of
\ngenomic medicine to children and adults around the world.

BACKGROUND: Microphthalmia, anophthalmia, and coloboma (MAC) spectrum disease encompasses a group of eye malformations which play a role in childhood visual impairment. Although the predominant cause of eye malformations is known to be heritable in nature, with 80% of cases displaying loss-of-function mutations in the ocular developmental genes OTX2 or SOX2, the genetic abnormalities underlying the remaining cases of MAC are incompletely understood. This study intended to identify the novel genes and pathways required for early eye development. Additionally, pathways involved in eye formation during embryogenesis are also incompletely understood. This study aims to identify the novel genes and pathways required for early eye development through systematic forward screening of the mammalian genome. RESULTS: Query of the International Mouse Phenotyping Consortium (IMPC) database (data release 17.0, August 01, 2022) identified 74 unique knockout lines (genes) with genetically associated eye defects in mouse embryos. The vast majority of eye abnormalities were small or absent eyes, findings most relevant to MAC spectrum disease in humans. A literature search showed that 27 of the 74 lines had previously published knockout mouse models, of which only 15 had ocular defects identified in the original publications. These 12 previously published gene knockouts with no reported ocular abnormalities and the 47 unpublished knockouts with ocular abnormalities identified by the IMPC represent 59 genes not previously associated with early eye development in mice. Of these 59, we identified 19 genes with a reported human eye phenotype. Overall, mining of the IMPC data yielded 40 previously unimplicated genes linked to mammalian eye development. Bioinformatic analysis showed that several of the IMPC genes colocalized to several protein anabolic and pluripotency pathways in early eye development. Of note, our analysis suggests that the serine-glycine pathway producing glycine, a mitochondrial one-carbon donator to folate one-carbon metabolism (FOCM), is essential for eye formation. CONCLUSIONS: Using genome-wide phenotype screening of single-gene knockout mouse lines, STRING analysis, and bioinformatic methods, this study identified genes heretofore unassociated with MAC phenotypes providing models to research novel molecular and cellular mechanisms involved in eye development. These findings have the potential to hasten the diagnosis and treatment of this congenital blinding disease.

The biomedical research community addresses reproducibility challenges in animal studies through standardized nomenclature, improved experimental design, transparent reporting, data sharing, and centralized repositories. The ARRIVE guidelines outline documentation standards for laboratory animals in experiments, but genetic information is often incomplete. To remedy this, we propose the Laboratory Animal Genetic Reporting (LAG-R) framework. LAG-R aims to document animals' genetic makeup in scientific publications, providing essential details for replication and appropriate model use. While verifying complete genetic compositions may be impractical, better reporting and validation efforts enhance reliability of research. LAG-R standardization will bolster reproducibility, peer review, and overall scientific rigor.

We searched a database of single-gene knockout (KO) mice produced by the International Mouse Phenotyping Consortium (IMPC) to identify candidate ciliopathy genes. We first screened for phenotypes in mouse lines with both ocular and renal or reproductive trait abnormalities. The STRING protein interaction tool was used to identify interactions between known cilia gene products and those encoded by the genes in individual knockout mouse strains in order to generate a list of "candidate ciliopathy genes." From this list, 32 genes encoded proteins predicted to interact with known ciliopathy proteins. Of these, 25 had no previously described roles in ciliary pathobiology. Histological and morphological evidence of phenotypes found in ciliopathies in knockout mouse lines are presented as examples (genes Abi2, Wdr62, Ap4e1, Dync1li1, and Prkab1). Phenotyping data and descriptions generated on IMPC mouse line are useful for mechanistic studies, target discovery, rare disease diagnosis, and preclinical therapeutic development trials. Here we demonstrate the effective use of the IMPC phenotype data to uncover genes with no previous role in ciliary biology, which may be clinically relevant for identification of novel disease genes implicated in ciliopathies.

Recent advances in the development of pre-clinical models based on non-animal technologies (NATs) have stimulated expectations that the use of animals in research may soon be phased out. The true value of innovations in NATs and their applications lies, however, in enabling an expanded and integrated portfolio of complementary animal and non-animal model systems to improve the accuracy and efficiency of pre-clinical research and therapeutic development. The term NATs covers a range of techniques spanning in silico, cell free, organ-on-chip as well as in vitro techniques including three-dimensional cell culture models termed organoids. Of these, in vitro systems are currently the most broadly used in biomedicine laboratories and are the first NATs for which Australia has invested in nationwide support. The focus of this commentary is the importance of understanding the strengths and limitations of in vitro and animal models such that an integrated portfolio of complementary genetic models continues to evolve to best support pre-clinical research and therapeutic development pipelines.

Research infrastructure is critical for advancing knowledge of health and disease, fostering innovation through world-class, cutting-edge facilities and technical expertise. Phenomics Australia is Australia's national research infrastructure provider responsible for accelerating advances in mammalian functional genomics and precision medicine through the development and delivery of services and expertise in engineered disease model production, phenotyping, and biobanking. These capabilities and resources are enabled by Australia's National Collaborative Research Infrastructure Strategy and primarily support health and medical research for significant healthcare and economic benefits. Priorities identified in the Australian Government's 2021 National Research Infrastructure Roadmap include the development and expansion of capabilities in digital research infrastructure, improved research translation, and enhanced management of biological collections, which are strongly aligned with Phenomics Australia's strategy to develop and enable access to high-quality national genetics resources at scale. Here, we comment on Phenomics Australia's response to these national strategy imperatives and the critical role of preclinical biological models research infrastructure in Australia.