Base-editing mutagenesis maps alleles to tune human T cell functions

CRISPR-enabled screening is a powerful tool for the discovery of genes that control T cell function and has nominated candidate targets for immunotherapies1-6. However, new approaches are required to probe specific nucleotide sequences within key genes. Systematic mutagenesis in primary human T cells could reveal alleles that tune specific phenotypes. DNA base editors are powerful tools for introducing targeted mutations with high efficiency7,8. Here we develop a large-scale base-editing mutagenesis platform with the goal of pinpointing nucleotides that encode amino acid residues that tune primary human T cell activation responses. We generated a library of around 117,000 single guide RNA molecules targeting base editors to protein-coding sites across 385 genes implicated in T cell function and systematically identified protein domains and specific amino acid residues that regulate T cell activation and cytokine production. We found a broad spectrum of alleles with variants encoding critical residues in proteins including PIK3CD, VAV1, LCP2, PLCG1 and DGKZ, including both gain-of-function and loss-of-function mutations. We validated the functional effects of many alleles and further demonstrated that base-editing hits could positively and negatively tune T cell cytotoxic function. Finally, higher-resolution screening using a base editor with relaxed protospacer-adjacent motif requirements9 (NG versus NGG) revealed specific structural domains and protein-protein interaction sites that can be targeted to tune T cell functions. Base-editing screens in primary immune cells thus provide biochemical insights with the potential to accelerate immunotherapy design.

The pleiotropic deubiquitinase Ubp3 confers aneuploidy tolerance

In this study, Dodgson et al. used a genome-wide screen for gene deletions that impair the fitness of aneuploid yeast and identified the deubiquitinase Ubp3 as a key regulator of aneuploid cell homeostasis. They found that Ubp3 is a guardian of aneuploid cell fitness conserved across species.

Aneuploidy—or an unbalanced karyotype in which whole chromosomes are gained or lost—causes reduced fitness at both the cellular and organismal levels but is also a hallmark of human cancers. Aneuploidy causes a variety of cellular stresses, including genomic instability, proteotoxic and oxidative stresses, and impaired protein trafficking. The deubiquitinase Ubp3, which was identified by a genome-wide screen for gene deletions that impair the fitness of aneuploid yeast, is a key regulator of aneuploid cell homeostasis. We show that deletion of UBP3 exacerbates both karyotype-specific phenotypes and global stresses of aneuploid cells, including oxidative and proteotoxic stress. Indeed, Ubp3 is essential for proper proteasome function in euploid cells, and deletion of this deubiquitinase leads to further proteasome-mediated proteotoxicity in aneuploid yeast. Notably, the importance of UBP3 in aneuploid cells is conserved. Depletion of the human homolog of UBP3, USP10, is detrimental to the fitness of human cells upon chromosome missegregation, and this fitness defect is accompanied by autophagy inhibition. We thus used a genome-wide screen in yeast to identify a guardian of aneuploid cell fitness conserved across species. We propose that interfering with Ubp3/USP10 function could be a productive avenue in the development of novel cancer therapeutics.

Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast

Aneuploidy causes severe developmental defects and is a near universal feature of tumor cells. Despite its profound effects, the cellular processes affected by aneuploidy are not well characterized. Here, we examined the consequences of aneuploidy on the proteome of aneuploid budding yeast strains. We show that although protein levels largely scale with gene copy number, subunits of multi-protein complexes are notable exceptions. Posttranslational mechanisms attenuate their expression when their encoding genes are in excess. Our proteomic analyses further revealed a novel aneuploidy-associated protein expression signature characteristic of altered metabolism and redox homeostasis. Indeed aneuploid cells harbor increased levels of reactive oxygen species (ROS). Interestingly, increased protein turnover attenuates ROS levels and this novel aneuploidy-associated signature and improves the fitness of most aneuploid strains. Our results show that aneuploidy causes alterations in metabolism and redox homeostasis. Cells respond to these alterations through both transcriptional and posttranscriptional mechanisms.

DOI:http://dx.doi.org/10.7554/eLife.03023.001

Nearly all tumor cells contain abnormal number of chromosomes. This state is called aneuploidy, and can also cause embryos to be miscarried, or to be born with severe developmental disorders.

Proteins are produced from the genes contained within chromosomes, and so cells with too many chromosomes produce too many of some proteins. How do these cells cope with this excess? Previous work identified one strategy where a gene called UBP6 is mutated to prevent it from working correctly. The UBP6 gene normally encodes a protein that removes a small tag (called ubiquitin) from other proteins. This tag normally marks other proteins that should be degraded; thus, if UBP6 is not working, more proteins are broken down.

Dephoure et al. investigated the effect of aneuploidy on the proteins produced by 12 different types of yeast cell, which each had an extra chromosome. In general, the amount of each protein produced by these yeast increased depending on the number of extra copies of the matching genes found on the extra chromosome. However, this was not the case for around 20% of the proteins, which were found in lower amounts than expected. Dephoure et al. revealed that this was not because fewer proteins were made, but because more were broken down. These proteins may be targeted for degradation because they are unstable, as many of these proteins need to bind to other proteins to keep them stable—but these stabilizing proteins are not also over-produced.

Aneuploidy in cells also has other effects, including changing the cells' metabolism so that the cells grow more slowly and do not respond as well to stress. However, Dephoure et al. found that, as well as reducing the number of proteins produced, deleting the UBP6 gene also increased the fitness of the cells. Targeting the protein encoded by the UBP6 gene, or others that also stop proteins being broken down, could therefore help to reduce the negative effects of aneuploidy for a cell. Whether targeting these genes or proteins could also help to treat the diseases and disorders that result from aneuploidy, such as Alzheimer's and Huntington's disease, remains to be investigated.

DOI:http://dx.doi.org/10.7554/eLife.03023.002

Aneuploidy causes proteotoxic stress in yeast

Gains or losses of entire chromosomes lead to aneuploidy, a condition tolerated poorly in all eukaryotes analyzed to date. How aneuploidy affects organismal and cellular physiology is poorly understood. We found that aneuploid budding yeast cells are under proteotoxic stress. Aneuploid strains are prone to aggregation of endogenous proteins as well as of ectopically expressed hard-to-fold proteins such as those containing polyglutamine (polyQ) stretches. Protein aggregate formation in aneuploid yeast strains is likely due to limiting protein quality-control systems, since the proteasome and at least one chaperone family, Hsp90, are compromised in many aneuploid strains. The link between aneuploidy and the formation and persistence of protein aggregates could have important implications for diseases such as cancer and neurodegeneration.

Congenital hypothyroidism with goiter in Tenterfield terriers

BACKGROUND

A cluster of cases of congenital hypothyroidism with goiter (CHG) in Tenterfield Terriers was identified and hypothesized to be dyshormonogenesis of genetic etiology with autosomal recessive inheritance.

OBJECTIVES

To describe the phenotype, thyroid histopathology, biochemistry, mode of inheritance, and causal mutation of CHG in Tenterfield Terriers.

ANIMALS

Thyroid tissue from 1 CHG-affected Tenterfield Terriers, 2 affected Toy Fox Terriers, and 7 normal control dogs. Genomic DNA from blood or buccal brushings of 114 additional Tenterfield Terriers.

METHODS

Biochemical and genetic segregation analysis of functional gene candidates in a Tenterfield Terrier kindred. Thyroid peroxidase (TPO) iodide oxidation activity was measured, and TPO protein and SDS-resistant thyroglobulin aggregation were assessed on western blots. TPO cDNA was amplified from thyroid RNA and sequenced. Exons and flanking splice sites were amplified from genomic DNA and sequenced. Variant TPO allele segregation was assessed by restriction enzyme digestion of PCR products.

RESULTS

Thyroid from an affected pup had lesions consistent with dyshormonogenesis. TPO activity was absent, but normal sized immunocrossreactive TPO protein was present. Affected dog cDNA and genomic sequences revealed a homozygous TPO missense mutation in exon 9 (R593W) that was heterozygous in all obligate carriers and in 31% of other clinically normal Tenterfield Terriers.

CONCLUSIONS

The mutation underlying CHG in Tenterfield Terriers was identified, and a convenient carrier test made available for screening Tenterfield Terriers used for breeding.