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Investigating monogenic and complex diseases with pluripotent stem cells

Key Points

  • Human genetic studies have revealed the molecular basis of countless monogenic diseases but have been less successful in dissecting complex multigenic conditions.

  • Embryonic stem cells and induced pluripotent stem cells are new tools that offer promise for determining the functional consequences of genetic variation.

  • Pluripotent stem cells (PSCs) are inexhaustible, scalable and physiologically native material for experimentation.

  • Robust and efficient differentiation towards selected cell and tissue types is one of the largest barriers to studying diseases in specific tissues, but progress is being made at a rapid pace.

  • We review selected PSC disease models that have been successfully applied to the study of more complex diseases.

  • We describe the multiple ways in which the challenge of studying non-cell-autonomous phenotypes might be addressed, such as through the use of co-culture experiments, organoids and human–mouse chimaeras.

  • The advent of genomic and sequencing technology will prove useful in describing the genetic profile of large sets of patient-derived cells.

  • The contribution of environmental and epigenetic factors to complex diseases may be equal to or greater than the contribution of genetics. PSCs can be used to probe the contribution of these factors.

  • It is difficult to perform targeted genetic modifications in human PSCs; the use of less-sophisticated genetic reagents and naturally occurring mutations from patient-derived cells are thus required.

  • Low-penetrance, modest and late-onset phenotypes are major challenges when studying complex or polygenic factors in any setting, including stem cells.

Abstract

Human genetic studies have revealed the molecular basis of countless monogenic diseases but have been less successful in associating phenotype to genotype in complex multigenic conditions. Pluripotent stem cells (PSCs), which can differentiate into any cell type, offer promise for defining the functional effects of genetic variation. Here, we recount the advantages and practical limitations of coupling PSCs to genome-wide analyses to probe complex genetics and discuss the ability to investigate epigenetic contributions to disease states. We also describe new ways of using mice and mouse embryonic stem cells (ESCs) in tandem with human stem cells to further define genotype–phenotype relationships.

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Figure 1: Pluripotent stem cells are a hub for genetic interrogation.
Figure 2: Using embryonic stem cells to mechanistically analyse phenotypes from mouse models.
Figure 3: Testing for epigenetic contributions to disease.

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Acknowledgements

G.Q.D. is an investigator of the Howard Hughes Medical Institute and the Manton Center for Orphan Disease Research. G.Q.D. is supported by grants from the US National Institutes of Health (RO1-DK70055, RO1-DK59279 and UO1-HL100001, and special funds from the American Recovery and Reinvestment Act (ARRA) stimulus package (RC2-HL102815)), the Roche Foundation for Anaemia Research, Alex's Lemonade Stand Foundation and the Harvard Stem Cell Institute.

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Correspondence to George Q. Daley.

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G.Q.D. is a member of the scientific advisory boards of the following companies: Johnson & Johnson, Verastem, Epizyme, iPierian, Solasia KK and MPM Capital, LLP. The other authors declare no competing financial interests.

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Glossary

Genome-wide association study

A whole-genome examination of genetic variation and how it statistically correlates with traits and diseases. This technique has led to the discovery of associations of particular genes with diseases such as age-related macular degeneration and diabetes.

Synteny

In classical genetics, synteny describes the colocalization of genetic loci on the same chromosome between individuals or species.

Amyotrophic lateral sclerosis

A neurodegenerative disease associated with a dominant L144F substitution in the superoxide dismutase 1 (SOD1) gene.

Long QT syndrome

An inborn heart condition in which delayed repolarization of the heart increases the risk of ventricular arrhythmias.

Teratoma formation assay

A teratoma is a tumour with tissue components resembling normal derivatives of all three germ layers. Teratoma formation is a key criterion for evaluating the pluripotency of human pluripotent stem cells, which are capable of forming multi-lineage tumours in immunodeficient murine hosts.

Cell-autonomous phenotype

If a gene's activity affects only those cells that express it, its function is cell-autonomous; if it affects cells other than (or in addition to) those expressing it, its function is non-cell-autonomous.

Organoid

A complex three-dimensional cluster of tissues comprising multiple cell types that self-organize into an organ-like structure, as generated by non-adherent culturing of stem or progenitor cells.

RNA-seq

High-throughput sequencing of cDNA that aims to obtain information about RNA content. RNA-seq measures transcriptome data, provides information on how different alleles of a gene are expressed, detects post-transcriptional mutations and identifies gene fusions.

Padlock probe

A probe with two target-complementary segments, which on hybridization are brought close to each other so that they can be covalently linked. This results in a circularized probe that is amenable to locus amplification and direct sequencing.

Somatic cell nuclear transfer

(SCNT). This involves replacing the nucleus of an unfertilized egg cell with the nucleus from a differentiated 'somatic cell' (a skin cell, for example). Stimulating the resulting pseudo-zygote to begin dividing leads to the creation of a cloned blastocyst. Subsequent uterine transfer can lead to the birth of a cloned animal or, in a process sometimes called 'therapeutic cloning', donor-identical cells can be extracted from the blastocyst to generate embryonic stem cells for disease modelling.

Beckwith–Wiedemann syndrome

An overgrowth disorder characterized by an increased risk of childhood cancer. Common features include large birth weight and length, large tongue, abdominal wall defects, ear creases or ear pits, and neonatal hypoglycaemia.

Tetraploid complementation

This technique is used to test the pluripotency of pluripotent stem cells and to generate genetically modified animals. By combining cells from a tetraploid embryo with diploid embryonic stem cells (ESCs), the resultant fetus is entirely derived from ESCs, whereas the extra-embryonic tissues are exclusively derived from tetraploid cells.

Penetrance

The proportion of individuals carrying a particular variation of a gene that also express an associated trait or disease.

ROCK inhibitors

Y-27,632 is a selective inhibitor of p160-RHO-associated coiled-coil kinase (ROCK). Dissociation-induced apoptosis of human embryonic stem cells is reduced upon inhibitor treatment, and the resulting single-cell cloning efficiency is increased from 1% to 27%.

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Zhu, H., Lensch, M., Cahan, P. et al. Investigating monogenic and complex diseases with pluripotent stem cells. Nat Rev Genet 12, 266–275 (2011). https://doi.org/10.1038/nrg2951

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