# Dissecting the role of PTEN in human disease by testing the effects of thousands of variants on multiple cellular phenotypes

> **NIH NIH F30** · UNIVERSITY OF WASHINGTON · 2020 · $40,118

## Abstract

Project Summary/Abstract
Understanding the role of the tumor suppressor gene PTEN in human disease is challenging because its protein
product controls many aspects of cellular physiology, including cell division, DNA repair, and cytoskeletal
organization. This challenge is exemplified by the myriad of phenotypes observed in patients with germline PTEN
variants and the difficulty in classifying clinically-sequenced PTEN missense variants as pathogenic versus
benign. In light of these difficulties, this project aims to systematically catalogue the effect of thousands of PTEN
missense variants on multiple cellular phenotypes, with the goals of better understanding the role of PTEN in
disease and helping classify clinically-observed PTEN missense variants. To do this, three high-throughput
functional assays – testing for cell growth, resistance to genotoxic agents, and cellular morphology – will be
employed in cultured human cell lines. By examining the relationships between these cancer-related cellular
phenotypes, PTEN missense variation, and clinical outcomes, it will be possible, for the first time, to
comprehensively dissect the role of PTEN in germline inherited disease and somatic cancers.
First, a high-throughput, growth-based functional assay will be used to measure the effect of a library of nearly
all possible PTEN missense variants for their ability to inhibit cellular growth, the primary PTEN function thought
to be important for human disease. The growth assay will be repeated in the presence of genotoxic agents to
measure the effect of PTEN variants in protecting against DNA damage. Second, a microscope-based selection
for cell morphology will be performed using a new technology we developed that analyzes millions of cells and
separates them based on microscopic visual phenotypes. Each of these high-throughput assays will annotate
each missense variant with a quantitative score documenting the effect of that variant on the selected phenotype.
Third, once the data are collected, the relative contribution of each PTEN function to disease will be examined
by comparing which functions are lost in variants annotated as pathogenic in ClinVar and in variants commonly
found in tumors.
These high-throughput experiments will be completed under the supervision of Dr. Douglas Fowler, who
pioneered large-scale, sequencing-based functional assays. The lab has already published a paper quantifying
the effect of PTEN missense variants on a much simpler phenotype, protein abundance, and so already has the
tools and knowledge required for studying this critical tumor suppressor. Courses that focus on the responsible
conduct of research and the biometric statistical analyses will be pursued to ensure the reproducibility and proper
analysis of the data. Additional help with interpreting the findings’ clinical utility will be provided by Dr. Mary-
Claire King, who works with patients harboring PTEN variants, and by Dr. Colin Pritchard, who is the head of
La...

## Key facts

- **NIH application ID:** 9829487
- **Project number:** 5F30CA236335-02
- **Recipient organization:** UNIVERSITY OF WASHINGTON
- **Principal Investigator:** Nicholas Hasle
- **Activity code:** F30 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $40,118
- **Award type:** 5
- **Project period:** 2018-12-01 → 2022-11-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9829487

## Citation

> US National Institutes of Health, RePORTER application 9829487, Dissecting the role of PTEN in human disease by testing the effects of thousands of variants on multiple cellular phenotypes (5F30CA236335-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9829487. Licensed CC0.

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