Yovina Sontani

Comparison of predicted and actual consequences of missense mutations

Significance Computational tools applied to any human genome sequence identify hundreds of genetic variants predicted to disrupt the function of individual proteins as the result of a single codon change. These tools have been trained on disease mutations and common polymorphisms but have yet to be tested against an unbiased spectrum of random mutations arising de novo. Here we perform such a test comparing the predicted and actual effects of de novo mutations in 23 genes with essential functions for normal immunity and all possible mutations in the TP53 tumor suppressor gene. These results highlight an important gap in our ability to relate genotype to phenotype in clinical genome sequencing: the inability to differentiate immediately clinically relevant mutations from nearly neutral mutations. Each person’s genome sequence has thousands of missense variants. Practical interpretation of their functional significance must rely on computational inferences in the absence of exhaustive experimental measurements. Here we analyzed the efficacy of these inferences in 33 de novo missense mutations revealed by sequencing in first-generation progeny of N-ethyl-N-nitrosourea–treated mice, involving 23 essential immune system genes. PolyPhen2, SIFT, MutationAssessor, Panther, CADD, and Condel were used to predict each mutation’s functional importance, whereas the actual effect was measured by breeding and testing homozygotes for the expected in vivo loss-of-function phenotype. Only 20% of mutations predicted to be deleterious by PolyPhen2 (and 15% by CADD) showed a discernible phenotype in individual homozygotes. Half of all possible missense mutations in the same 23 immune genes were predicted to be deleterious, and most of these appear to become subject to purifying selection because few persist between separate mouse substrains, rodents, or primates. Because defects in immune genes could be phenotypically masked in vivo by compensation and environment, we compared inferences by the same tools with the in vitro phenotype of all 2,314 possible missense variants in TP53; 42% of mutations predicted by PolyPhen2 to be deleterious (and 45% by CADD) had little measurable consequence for TP53-promoted transcription. We conclude that for de novo or low-frequency missense mutations found by genome sequencing, half those inferred as deleterious correspond to nearly neutral mutations that have little impact on the clinical phenotype of individual cases but will nevertheless become subject to purifying selection.

Self-Renewal of the Long-Term Reconstituting Subset of Hematopoietic Stem Cells is Regulated by Ikaros

Hematopoietic stem cells (HSCs) are rare, ancestral cells that underlie the development, homeostasis, aging, and regeneration of the blood. Here we show that the chromatin‐associated protein Ikaros is a crucial self‐renewal regulator of the long‐term (LT) reconstituting subset of HSCs. Ikaros, and associated family member proteins, are highly expressed in self‐renewing populations of stem cells. Ikaros point mutant mice initially develop LT‐HSCs with the surface phenotype cKit+Thy1.1(lo)Lin(‐/lo)Sca1+Flk2‐CD150+ during fetal ontogeny but are unable to maintain this pool, rapidly losing it within two days of embryonic development. A synchronous loss of megakaryocyte/erythrocyte progenitors results, along with a fatal, fetal anemia. At this time, mutation of Ikaros exerts a differentiation defect upon common lymphoid progenitors that cannot be rescued with an ectopic Notch signal in vitro, with hematopoietic cells preferentially committing to the NK lineage. Althoughdispensable for the initial embryonic development of blood, Ikaros is clearly needed for maintenance of this tissue. Achieving successful clinical tissue regeneration necessitates understanding degeneration, and these data provide a striking example by a discrete genetic lesion in the cells underpinning tissue integrity during a pivotal timeframe of organogenesis. STEM CELLS 2009;27:3082–3092

A cell autonomous role for the Notch ligand Delta-like 3 in αβ T- cell development

Notch signalling is critical to help direct T‐cell lineage commitment in early T‐cell progenitors and in the development of αβ T‐cells. Epithelial and stromal cell populations in the thymus express the Notch DSL (Delta, Serrate and Lag2)ligands Delta‐like 1 (Dll1), Delta‐like 4 (Dll4), Jagged 1 and Jagged 2, and induce Notch signalling in thymocytes that express the Notch receptor. At present there is nothing known about the role of the Delta‐like 3 (Dll3) ligand in the immune system. Here we describe a novel cell autonomous role for Dll3 in αβ T‐cell development. We show that Dll3 cannot activate Notch when expressed in trans but like other Notch ligands it can inhibit Notch signalling when expressed in cis with the receptor. The loss of Dll3 leads to an increase in Hes5 expression in double positive thymocytes and their increased production of mature CD4+ and CD8+ T cells. Studies using competitive irradiation chimeras proved that Dll3 acts in a cell autonomous manner to regulate positive selection but not negative selection of autoreactive T cells. Our results indicate that Dll3 has a unique function during T‐cell development that is distinct from the role played by the other DSL ligands of Notch and is in keeping with other recent studies indicating that Dll1 and Dll3 ligands have non‐overlapping roles during embryonic development.

Up-regulation of LFA-1 allows liver-resident memory T cells to patrol and remain in the hepatic sinusoids

LFA-1 expression allows liver-resident CD8+ T cells to patrol hepatic sinusoids yet remain in the liver. LFA-1 helps T cells feel at home in the liver Liver-resident T cells are critical to defense against infections such as malaria and hepatitis B virus. To protect the hepatic sinusoids, these cells must enter circulation yet still remain in the liver. McNamara et al. now report that liver-resident CD8+ T cells up-regulate LFA-1 and that LFA-1–ICAM-1 (intercellular adhesion molecule–1) interactions are critical for T cell patrolling of the hepatic sinusoids. Moreover, in the absence of LFA-1, CD8 T cells do not form liver-resident memory populations, even after infection with either Plasmodium or lymphocytic choriomeningitis virus. Thus, LFA-1 expression acts as a sort of invisible fence, allowing the liver-resident memory T cells free reign within the boundaries of the liver. Liver-resident CD8+ T cells are highly motile cells that patrol the vasculature and provide protection against liver pathogens. A key question is: How can these liver CD8+ T cells be simultaneously present in the circulation and tissue-resident? Because liver-resident T cells do not express CD103—a key integrin for T cell residence in epithelial tissues—we investigated other candidate adhesion molecules. Using intravital imaging, we found that CD8+ T cell patrolling in the hepatic sinusoids is dependent on LFA-1–ICAM-1 (intercellular adhesion molecule–1) interactions. Liver-resident CD8+ T cells up-regulate LFA-1 compared with effector memory cells, presumably to facilitate this behavior. Last, we found that LFA-1–deficient CD8+ T cells failed to form substantial liver-resident memory populations after Plasmodium immunization or lymphocytic choriomeningitis virus infection. Collectively, our results demonstrate that it is adhesion through LFA-1 that allows liver-resident memory CD8+ T cells to patrol and remain in the hepatic sinusoids.

Zinc-finger protein ZFP318 is essential for expression of IgD, the alternatively spliced Igh product made by mature B lymphocytes

Significance Mammalian B lymphocytes make antibodies of five different heavy chain isotypes, IgM, IgD, IgG, IgE, and IgA. The different isotypes are produced at discrete stages in B-cell development from a single immunoglobulin heavy chain (Igh) gene, either by irreversible rearrangement of the gene to make IgG, IgE, or IgA or by alternative splicing of the RNA transcribed from the Igh gene to coexpress IgM and IgD. Developmentally regulated trans-acting factors have been hypothesized to control IgM and IgD expression from large Igh RNAs, but these factors have remained elusive for several decades. Here, using a genome-wide mutation screen in mice, we identify an obscure gene, Zfp318, as encoding a specific and essential factor promoting IgD expression in mature B cells. IgD and IgM are produced by alternative splicing of long primary RNA transcripts from the Ig heavy chain (Igh) locus and serve as the receptors for antigen on naïve mature B lymphocytes. IgM is made selectively in immature B cells, whereas IgD is coexpressed with IgM when the cells mature into follicular or marginal zone B cells, but the transacting factors responsible for this regulated change in splicing have remained elusive. Here, we use a genetic screen in mice to identify ZFP318, a nuclear protein with two U1-type zinc fingers found in RNA-binding proteins and no known role in the immune system, as a critical factor for IgD expression. A point mutation in an evolutionarily conserved lysine-rich domain encoded by the alternatively spliced Zfp318 exon 10 abolished IgD expression on marginal zone B cells, decreased IgD on follicular B cells, and increased IgM, but only slightly decreased the percentage of B cells and did not decrease expression of other maturation markers CD21, CD23, or CD62L. A targeted Zfp318 null allele extinguished IgD expression on mature B cells and increased IgM. Zfp318 mRNA is developmentally regulated in parallel with IgD, with little in pro-B cells, moderate amounts in immature B cells, and high levels selectively in mature follicular B cells. These findings identify ZFP318 as a crucial factor regulating the expression of the two major antibody isotypes on the surface of most mature B cells.

Delayed control of herpes simplex virus infection and impaired CD4(+) T-cell migration to the skin in mouse models of DOCK8 deficiency.

DOCK8 deficiency in humans and mice leads to multiple defects in immune cell numbers and function. Patients with this immunodeficiency have a high morbidity and mortality, and are distinguished by chronic cutaneous viral infections, including those caused by herpes simplex virus (HSV). The underlying mechanism of the specific susceptibility to these chronic cutaneous viral infections is currently unknown, largely because the effect of DOCK8 deficiency has not been studied in suitable models. A better understanding of these mechanisms is required to underpin the development of more specific therapies. Here we show that DOCK8‐deficient mice have poor control of primary cutaneous herpes simplex lesions and this is associated with increased virus loads. Furthermore, DOCK8‐deficient mice showed a lack of CD4+ T‐cell infiltration into HSV‐infected skin.

A Novel Mutation in Nucleoporin 35 Causes Murine Degenerative Colonic Smooth Muscle Myopathy.

Chronic intestinal pseudo-obstruction (CIPO) is a rare but life-threatening disease characterized by severe intestinal dysmotility. Histopathologic studies in CIPO patients have identified several different mechanisms that appear to be involved in the dysmotility, including defects in neurons, smooth muscle, or interstitial cells of Cajal. Currently there are few mouse models of the various forms of CIPO. We generated a mouse with a point mutation in the RNA recognition motif of the Nup35 gene, which encodes a component of the nuclear pore complex. Nup35 mutants developed a severe megacolon and exhibited a reduced lifespan. Histopathologic examination revealed a degenerative myopathy that developed after birth and specifically affected smooth muscle in the colon; smooth muscle in the small bowel and the bladder were not affected. Furthermore, no defects were found in enteric neurons or interstitial cells of Cajal. Nup35 mice are likely to be a valuable model for the subtype of CIPO characterized by degenerative myopathy. Our study also raises the possibility that Nup35 polymorphisms could contribute to some cases of CIPO.

Cooperation between somatic Ikaros and Notch1 mutations at the inception of T-ALL

To understand the interactions between Notch1 and Ikaros in the evolution of T cell acute lymphoblastic leukemia (T-ALL), we traced the evolution of T-ALL in mice with an inherited Ikaros mutation, Ikzf1(Plstc) which inactivates DNA binding. DNA-binding Ikaros repressed Notch1 response in transfected cell lines and in CD4(+)8(+) (DP) thymocytes from young pre-leukemic Ikzf1(Plstc) heterozygous mice. In DP thymocytes, a 50-1000 fold escalation in mRNA for Notch1 target genes Hes1 and Dtx1 preceded thymic lymphoma or leukemia and was closely correlated with the first detectable differentiation abnormalities, loss of heterozygosity (LOH) eliminating wild-type Ikzf1, and multiple missense and truncating Notch1 mutations. These findings illuminate the early stages of leukemogenesis by demonstrating progressive exaggeration of Notch1 responsiveness at the DP thymocyte stage brought about by multiple mutations acting in concert upon the Notch1 pathway.

Systems-guided forward genetic screen reveals a critical role of the replication stress response protein ETAA1 in T cell clonal expansion

Significance T cells are required for control of many intracellular infections, and a critical component of T cell immunity is the proliferative expansion of effector T cells upon stimulation. Using a forward-based genetic screen, we identify the mouse Etaa1 gene as critically important for T cell proliferative expansion after vaccination and during infection. Consistent with recent findings that ETAA1 prevents DNA damage during proliferation, our data demonstrate elevated DNA damage within Etaa1-deficient effector T cells, which likely leads to cell death. This phenotype is restricted to effector T cell proliferation, with T cell development and other immune parameters remaining normal. Thus, ETAA1 may represent a novel drug target to selectively suppress pathological T cell responses in transplantation or autoimmunity. T-cell immunity requires extremely rapid clonal proliferation of rare, antigen-specific T lymphocytes to form effector cells. Here we identify a critical role for ETAA1 in this process by surveying random germ line mutations in mice using exome sequencing and bioinformatic annotation to prioritize mutations in genes of unknown function with potential effects on the immune system, followed by breeding to homozygosity and testing for immune system phenotypes. Effector CD8+ and CD4+ T-cell formation following immunization, lymphocytic choriomeningitis virus (LCMV) infection, or herpes simplex virus 1 (HSV1) infection was profoundly decreased despite normal immune cell development in adult mice homozygous for two different Etaa1 mutations: an exon 2 skipping allele that deletes Gly78-Leu119, and a Cys166Stop truncating allele that eliminates most of the 877-aa protein. ETAA1 deficiency decreased clonal expansion cell autonomously within the responding T cells, causing no decrease in their division rate but increasing TP53-induced mRNAs and phosphorylation of H2AX, a marker of DNA replication stress induced by the ATM and ATR kinases. Homozygous ETAA1-deficient adult mice were otherwise normal, healthy, and fertile, although slightly smaller, and homozygotes were born at lower frequency than expected, consistent with partial lethality after embryonic day 12. Taken together with recently reported evidence in human cancer cell lines that ETAA1 activates ATR kinase through an exon 2-encoded domain, these findings reveal a surprisingly specific requirement for this ATR activator in adult mice restricted to rapidly dividing effector T cells. This specific requirement may provide new ways to suppress pathological T-cell responses in transplantation or autoimmunity.

Finding new immune regulatory genes by ENU mutagenesis

IntroductionThe Thousand Genomes Project has revealed the extraor-dinary scale of human genetic variation such as each per-son inherits ~12,000 protein-changing single nucleotidevariations (SNVs) including up to 100 premature STOPcodons creating an immense challenge to investigate thephysiological consequence of this type of genetic variationin experimental animals.AimTo develop a new strategy to meet this need by usingwhole exome capture, massively parallel DNA sequenc-ing and computational analysis to sensitively and specifi-cally identify 40-50 de novo mis-sense SNV mutationsspread across the genome of individual offspring fromENU-mutagenized C57BL/6 mice [1].ResultsIn this presentation we demonstrate how direct se-quencing of animals with indepe ndent defects in B celldevelopment resulted in the identification of the causa-tive mutation both in genes of previously known andunknown function without meiotic mapping. Thisapproach has resulted in the identification of a newphospholipid transport pathway that is crucial for nor-mal B cell development in the bone marrow [2] and therealization that an endopeptidase of previously unknownin vivo function is essential for normal processing ofMHC invariant chain and terminal B cell and DCmaturation.By sequencing animals from defined strains and alsofounder animals of ENU mutant pedigrees two generationsbefore the phenotypic screens we have started to build adatabase of missense mutations containing currently closeto 7000 mutations in mouse pedigrees actively breedingand immediately available for experimental analysis.All data is made available from the missense variant data-base (pb.apf.edu.au/phenbank).ConclusionThis approach transforms mammalian experimentalgenetics and opens up an unparalleled source for experi-mental models of human disease and validation of humandisease associated SNVs.