Pericentriolar Material 1 (PCM1): predict the effects of missense changes in a zebrafish model

Challenge: PCM1 missense
Dataset description: public
Variant data: public
Last updated: 9 Nov 2017
This challenge closes at 9:00 PM PST (Pacific Standard Time) on 10 January 2018 .

[Summary] [Background] [Experiment] [Prediction Challenge] [Prediction Submission Format] [References] [Revision history]

Summary
The PCM1 (Pericentriolar Material 1) gene is a component of centriolar satellites occurring around centrosomes in vertebrate cells. Several studies have implicated PCM1 variants as a risk factor for schizophrenia. Ventricular enlargement is one of the most consistent abnormal structural brain findings in schizophrenia Therefore 38 transgenic human PCM1 missense mutations implicated in schizophrenia were assayed in a zebrafish model to determine their impact on the posterior ventricle area. The challenge is to predict whether variants implicated in schizophrenia impact zebrafish ventricular area.

Background
The PCM1 (Pericentriolar Material 1) gene is a component of centriolar satellites occurring around centrosomes in vertebrate cells. PCM1 can form a complex at the centrosome with DISC1 protein. In addition to containing centrosomal proteins, the centriolar satellites can move along microtubules. The centrosomal proteins help anchor the microtubules at the centrosome. The centrosome is essential for neurodevelopment (specifically cortical development). If PCM1 is mutated, localization of centrosomal proteins may be altered (not correctly localized). Thus, certain components of the PCM1 have been implicated in genetic susceptibility to cancers, schizophrenia, and other mental diseases. (Kamiya et al., 2008; Zoubovsky et al., 2015)

Several studies have implicated PCM1 variants as a risk factor for schizophrenia. PCM1 mutant mice have shown behavioral deficits (Moens, Ceulemans, et al., 2010). However, other studies have found low risk or no association. (Zoubovsky et al., 2015)

Experiment
The Katsanis lab assessed 38 missense mutations within PCM1 in a zebrafish model.

Native zebrafish embryo PCM1 protein was suppressed by injecting morpholino (MO) antisense oligonucleotides to inhibit translation of mRNA of the pcm1 gene. MOs are stable molecules that consist of a large, nonribose morpholine backbone with the four DNA bases pairing stably with mRNA at either the translation start site (to disrupt protein synthesis) or at intron-exon boundaries (to disrupt mRNA splicing).(Summerton & Weller, 1997) Morpholinos have been shown to bind to and block translation of mRNA in vitro, in tissue culture cells, and, in vivo. (Davis et al., 2014) Embryos deficient in pcm1 function show an absence of brain ventricle formation.

For each mutation, the Katsanis lab injected a group of embryos with MO and the mRNA of the human gene carrying the mutation (MO+VAR). The brain ventricle formation of the group of the (MO+VAR) animals was compared to the brain ventricle formation measured in a group of animals with MO alone and a group with MO+WT. In order to understand the process of ventricle formation, the ventricle space is filled with a fluorescent dye and imaged by brightfield and fluorescent microscopy (Niederriter et al., 2013; Gutzman & Sive, 2009). P values for statistically different brain ventricle formation between pairs of conditions (Lowery et al., 2009) were obtained using a Student’s t-test. When the p-value is:

  1. NOT statistically different from MO, but statistically significantly different from MO+WT, the variant is pathogenic or loss of function
  2. Statistically different from MO, but not from MO+WT, the variant is benign
  3. Statistically different from MO, and at the same time statistically significantly different from MO+W, the variant is hypomorphic or partially loss of function.

Prediction challenge
Participants are asked to submit the probability of the effect of the variants on zebrafish brain development.

Download dataset
5- PCM1_dataset.txt

Download submission template
5-PCM1_template.txt

Download validation script
5-PCM1_cagi-validate.R

Prediction submission format
The prediction submission is a tab-delimited text file. Organizers provide a file template, which must be used for submission. In addition, a validation script will be provided, and predictors must check the correctness of the format before submitting their predictions.

In the submitted file, each row should include the following tab-separated fields:

  1. Nucleotide position: DNA coding change of the variant (e.g., c.G17A) on the human genome.
  2. Variant: protein change of the variant (e.g. p.G6D).
  3. p-value relative of change from MO: The probability that this variant is statistically different from MO.
  4. Standard deviation: This defines the confidence of the prediction in column 3. Large SD means low confidence, while small SD means that the predictor is confident about the submitted prediction.
  5. p-value of change from MO+WT: The probability that this variant is statistically different from MO+WT
  6. Standard deviation: This defines the confidence of the prediction in column 5. Large SD means low confidence, while small SD means that the predictor is confident about the submitted prediction.
  7. Functional effect: pathogenic, hypomorphic, or benign
  8. Confidence: in the functional effect assignment ranges 0.0 to 1.0. (1.0 implies total confidence in the assignment)
  9. Comments: Optional brief comments based on the predictions.

In the template file, cells in columns 3-9 are marked with a "*". Submit your predictions by replacing the "*" with your value. No empty cells are allowed in the submission. If you choose not to enter a prediction leave the "*" in those cells. If you are not confident in a prediction for an individual, enter a large standard deviation for the prediction. Optionally, enter brief comments indicating the basis of the predictions; otherwise, leave the "*" in these cells. Please make sure you follow the submission guidelines strictly.

In addition, your submission must include a detailed description of the method used to make the predictions, similar in style to the Methods section in a scientific article. This information will be submitted as a separate file.

To submit predictions, you need to create or be part of a CAGI User group. Submit your predictions by accessing the link "All submission forms" from the front page of your group. For more details, please read the FAQ pagege.

Ethical approval
All animal experiments were approved by the Duke University Institutional Care and Use Committee.

Dataset provided by
Maria Kousi, Nicholas Katsanis, Duke University

References

  1. Davis EE, Frangakis S, Katsanis N. 2014. Interpreting human genetic variation with in vivo zebrafish assays. Biochim Biophys Acta 1842:1960-1970. PMCID:PMC4382103. doi:10.1016/j.bbadis.2014.05.024
  2. Gutzman JH, Sive H. 2009. Zebrafish brain ventricle injection. J Vis Exp. PMCID:PMC2791086. doi:10.3791/1218
  3. Kamiya A, Tan PL, Kubo K, Engelhard C, Ishizuka K, Kubo A, Tsukita S, Pulver AE, Nakajima K, Cascella NG, Katsanis N, Sawa A. 2008. Recruitment of PCM1 to the centrosome by the cooperative action of DISC1 and BBS4: a candidate for psychiatric illnesses. Arch Gen Psychiatry 65:996-1006. PMCID:PMC2727928. doi:10.1001/archpsyc.65.9.996
  4. Lowery LA, De Rienzo G, Gutzman JH, Sive H. 2009. Characterization and classification of zebrafish brain morphology mutants. Anat Rec (Hoboken) 292:94-106. PMCID:PMC2894611. doi:10.1002/ar.20768
  5. Niederriter AR, Davis EE, Golzio C, Oh EC, Tsai IC, Katsanis N. 2013. In vivo modeling of the morbid human genome using danio rerio. J Vis Exp:e50338. PMCID:PMC3856313. doi:10.3791/50338
  6. Summerton J, Weller D. 1997. Morpholino antisense oligomers: Design, preparation, and properties. Antisense Nucleic Acid Drug Dev 7:187-195. doi:10.1089/oli.1.1997.7.187
  7. Zoubovsky S, Oh EC, Cash-Padgett T, Johnson AW, Hou Z, Mori S, Gallagher M, Katsanis N, Sawa A, Jaaro-Peled H. 2015. Neuroanatomical and behavioral deficits in mice haploinsufficient for pericentriolar material 1 (pcm1). Neurosci Res 98:45-49. PMCID:PMC4522364. doi:10.1016/j.neures.2015.02.002

Revision history
9 Nov 2017 (v01): initial release