Rise of the planet

Despite early failures, somatic gene therapy has recently shown renewed promise. Howy suggests that the day may come when germline gene therapy needs also to be reconsidered.EMBO reports (2013) 14, 1; doi:10.1038/embor.2012.194Human gene therapy has a short but chequered history. The recognition, in the 1980s, that many human diseases were caused by recessive single gene mutations, led inevitably to the idea that such defects could be corrected by the same technology that facilitates the creation of transgenic animals.At an early stage, scientists and clinicians explicitly eschewed the idea of making genetic modifications to the germline, even in the case of fatal diseases. This was partly to assuage public concern that such technology could be misused for eugenic purposes widely considered unethical and tainted by association with the Nazi genocide. More prosaically, the techniques for engineering changes in the genome were so novel that their safety could not be assured. Even if such hurdles could be overcome, the unpredictable effects upon subsequent generations were considered a sufficient reason to observe a self-imposed moratorium on any such ‘playing with evolution''. Germline manipulation of the human genome remains largely a taboo subject, of greater interest to Hollywood than Bethesda [1]. Indeed, editing even plant and animal genomes remains highly controversial and tightly restricted, if not completely prohibited, in many jurisdictions.Three decades later, it is time to reassess the issue in the light of our greatly expanded knowledge of genetics, and the rather limited success of non-germline approaches to genetic therapy to date.With the route blocked to germline transgenesis, the era of somatic gene therapy was born. In outline, the method seeks to replace a defective gene in those cells whose function is compromised, thus overcoming the deficiency. Numerous variations on this theme seek to target the gene or its expression to specified cell types, control its integration into the genome, incorporate molecular ‘safety triggers'' or limit the immune response to the modified cells. The experimental nature of somatic gene therapy dictated that initial trials were conducted only in cases of severely debilitating and inevitably fatal diseases. The inherent difficulties of targeting tissues within the body also restricted it, at first, to cell types where an ex vivo approach could be employed, such as blood. But even this approach to treat diseases such as severe combined immunodeficiency met with only limited success. Therapeutic benefits were seen, but were typically temporary, and some patients succumbed to serious or even fatal side-effects, for example, through the oncogenic effects of random insertions in the genome.These tragic outcomes cast a long shadow over subsequent trials. For a long time, almost the only diseases for which such an approach was contemplated were end-stage cancers, where the risk of novel neoplasms can be considered a side issue, as for radiotherapy or treatment with genotoxic drugs. Unfortunately, gene therapy for cancer, even when cleverly targeted, suffers the same methodological flaw as these older, cruder therapies, namely the practical impossibility of zapping every single tumour cell, including quiescent progenitor-type cells that may be the primary reservoir of disease. Some remissions have, however, been reported.A few brave attempts to develop the field are now under way, but fundamental safety and efficacy problems remain. Even when a non-immunogenic delivery system can be employed, a replacement gene typically elicits an immune reaction against what is, to the patient''s immune system, a foreign gene product. To be permanently effective, any such therapy requires at least a partial disabling of the recipient''s immune system, thus replacing one disease with another. The oncogenic risk associated with random insertions, as well as the common problem of transgene silencing can, in theory, be overcome by the use of targeted insertion systems based on site-specific recombinases. This has proven to be a powerful tool for creating transgenic animals in research. However, to be effective, it requires a specific landing pad in the recipient genome, and thus implies the prior use of germline genetic manipulation. In the future, it should be possible to use customized recombinases with enhanced specificity to target only one or a few ‘benign'' insertion sites in the human genome, permissive for transgene expression. But this has not yet been achieved. In weighing the ethical objections against germline gene therapy, we need to take account of the persisting problems with its somatic cousin.In the case of recessive disorders, preimplantation diagnosis offers a simple and safe alternative approach, although many people have ethical or religious objections to this procedure as well. But what if it were to be ascertained that making a specific alteration to the human genome could protect against Alzheimer disease or malaria? What if adding just a few additional copies of a tumour suppressor gene such as p53 could provide lifetime resistance to most common cancers? Preimplantation diagnosis is clearly useless for diseases acquired through somatic mutation or via epigenetic errors during development. Would it be ethical to withhold prophylactic germline ‘therapy'' if it could ensure the alleviation of suffering on a massive scale? Germline manipulation is already marching towards approval in the UK for mitochondrial DNA disorders [2]. To some this is the thin end of the wedge: to others it is a chink of light in a dark landscape.At some point in the future, humanity will have to face such questions. I believe that the continuing rapid progress in elucidating the underlying basis of disease must lead to feasible preventative strategies based on genetic technologies that essentially exist already. We need to be ready with answers.     

NF2 mutation screening by denaturing high-performance liquid chromatography and high-resolution melting analysis

Neurofibromatosis type 2 (NF2) is an autosomal-dominant disorder caused by mutations in the NF2 gene and predisposing to the development of nervous system. Identification of germline mutations is essential to provide appropriate genetic counseling in NF2 patients, but it represents an extremely challenging task because the vast majority of mutations are unique and spread over the entire coding sequence. Moreover, about 30% of de novo patients are indeed mosaic, and direct sequencing can undetect mutated alleles present in a minority of cells. As most screening techniques do not meet the requirements for efficient NF2 testing, we have developed a semi-automated denaturing high-performance liquid chromatography (DHPLC) method for point mutation detection combined with a multiplex ligation-dependent probe amplification approach to screen for gene rearrangements. In addition, we have evaluated high-resolution melting analysis (HRMA) as an exon scanning procedure to identify point mutations in the NF2 gene. The results obtained in 92 NF2 patients expand the NF2 mutational spectrum and indicate DHPLC and HRMA as good systems to screen for point mutations in diseases with a heterogeneous spectrum of alterations.     

Increased radiation toxicity with germline ATM variant of uncertain clinical significance

BackgroundWhile patients with ataxia telangiectasia are known to have increased radiation sensitivity, patients with germline heterozygous ataxia telangiectasia mutated (ATM) mutations can have widely varying functional and clinical effects, which can make management decisions difficult. With an increased prevalence of gene panel-based testing for breast cancer patients, radiation oncologists are increasingly confronted with patients who carry germline ATM variants of uncertain clinical significance. This study describes the clinical courses and outcomes of 5 breast cancer patients with varying germline heterozygous ATM mutations undergoing radiation therapy at our institution in order to provide additional knowledge of the varying clinical effects to aid future decision making.Case SeriesWe identified 5 patients with breast cancer and varying germline heterozygous ATM mutations treated at the University of North Carolina Hospitals between 2015 and 2017. The median age at breast cancer diagnosis for the patient series was 46. Clinical effects of radiation treatment varied amongst the 5 patients. The one patient with a pathogenic ATM mutation had no increased radiation related toxicity. Of the 4 patients with ATM variants of uncertain significance, one patient had increased radiation sensitivity with Grade 3 dermatitis. All patients have remained recurrence free with a median duration of 18 months.ConclusionOur data illustrates that patients with germline heterozygous ATM mutations can have widely varying clinical effects with radiation therapy. Given the possibility of unpredictable deleterious effects, our study highlights the importance of caution and careful consideration when devising the multi-modality management strategy in these patients.     

Promoter hypermethylation of BRCA1 correlates with absence of expression in hereditary breast cancer tumors

Germline mutations in BRCA1 account for a low proportion of hereditary cases in diverse populations. Several efforts have been made to find new genes involved in the inheritance of breast cancer with no success until today. The participation of BRCA1 in the development of breast cancer has been proposed in several studies where hypermethylation of its promoter and a decrease in expression has been reported for sporadic cases and one study on familial cases. To explore the participation of BRCA1 in hereditary carcinogenesis through a different mechanism than the inheritance of germline mutations, we studied the methylation status of its promoter in breast tumors, from patients previously screened for BRCA1/BRCA2 germline mutations. We also determined the presence of the BRCA1 protein in these tumors and correlated both events with tumor grade, hormone receptors and ERBB2 presence. Promoter hypermethylation of the BRCA1 gene was detected in 51% of our biopsies, among which 67% did not express the respective protein. This result leads us to suggest that hypermethylation could be considered as an inactivating mechanism for BRCA1 expression, either as a first or second hit. Moreover, a number of biopsies with absence of expression on BRCA1 showed negative detection of estrogen and progesterone receptors, a similar phenotype to BRCA1 mutated breast tumors.     

Sexual antagonism and X inactivation--the SAXI hypothesis

X inactivation has evolved in the soma of mammalian females so that both sexes have the same ratio of X:autosomal gene expression. The X chromosome in the germ cells of XY males is also precociously inactivated for reasons that remain unclear. Unlike X inactivation in the soma, this germline X inactivation is not restricted to mammals but has evolved independently in several animal phyla. Thus, germline X inactivation might have been the precursor of somatic X inactivation in mammals. We now propose a hypothesis for the evolution of germline X inactivation. The hypothesis predicts a redistribution of late spermatogenic genes from the X chromosome to the autosomes, leading eventually to germline X inactivation as the X chromosome becomes 'demasculinized'. Sexual antagonism could be the mechanism driving this redistribution. Recent expression and genetic studies in mammals, nematodes and Drosophila support this hypothesis, and expression data on taxa that have not evolved germline X inactivation, such as birds and butterflies, should shed further light on it.     

Simple fluorescent PCR assay for discriminating FRAXA fully mutated females from normal homozygotes

Fragile X syndrome linked to the FRAXA locus is the most common inherited genetic disease accounting for mental retardation and is usually caused by the expansion of an unstable CGG repeat in the first exon of the FMR1 gene on the X chromosome. Despite its robustness, Southern blot is not suitable for large-scale routine screening as part of neuropediatric practice. PCR appears as an interesting alternative, and various protocols have been successfully applied to molecular screening in mentally retarded boys and girls. Unfortunately, as of this date these protocols are unable to detect the expanded allele in FRAXA females reliably, thereby failing to discriminate between fully mutated females from normal homozygotes. Therefore, we opted for an alternative approach in designing a semiquantitative PCR assay, based on the amplification of the sole wild-type allele. This method allowed us to detect the presence of one or two normal alleles with the same sizes, thereby discriminating between a FRAXA fully mutated female or a normal homozygote, respectively. A trial on 95 DNA samples from normal and mutated females demonstrated the reliability of the procedure. We believe this simple PCR assay is a powerful approach that would reduce the recourse to Southern blotting in females with mental retardation of unknown etiology.     

VDJ genes in VHa2 allotype-suppressed rabbits. Limited germline VH gene usage and accumulation of somatic mutations in D regions

In this study we investigate the molecular genetic basis for VHa- Ig. Knowing that the expression of VHa allotype Ig is suppressed by neonatal injection of rabbits with anti-VHa allotype antibody, and that the decreased level of VHa allotype Ig, VHa+, in the suppressed rabbits is compensated for by an increase in VHa- Ig, we determined the nucleotide sequences of 41 VDJ genes from a2/a2 rabbits neonatally suppressed for the expression of a2 Ig. We compared these nucleotide sequences to each other and identified two groups of VH sequences. We predict that the molecules of each group are encoded by one germline VH gene. Inasmuch as VHa+ Ig is encoded predominantly by one germline VH gene, VH1, it appears that more than 95% of the VDJ repertoire of rabbits may be encoded by as few as three germline VH genes. A genomic VDJ gene whose VH sequence was similar to those of group I molecules was expressed in vitro and was shown by ELISA to encode molecules of the VHa- allotype, y33. Analysis of the D regions in the VDJ gene indicated that germline D2b and D3 gene segments were preferentially used in the VDJ gene rearrangement. A comparison of sequences of D regions of the 41 VDJ gene rearrangements in 3-, 6-, and 9-wk-old rabbits to sequences of germline D gene segments showed an accumulation of mutations in the D region. Inasmuch as we have previously shown that V regions of rabbit VDJ genes are diversified, in part, by somatic gene conversion, it appears now that rabbit VDJ genes diversify by a combination of somatic mutation and somatic gene conversion.     

Germline alteration by gene therapy: assessing and reducing the risks

Developments in gene therapy are certain to lead to the treatment of an increasing variety of diseases, some of which will affect patients who might wish to have children following their gene therapy treatment. These circumstances raise the concern that germline integration of gene therapy vector DNA could occur. Although our current understanding of reproductive biology and of the biodistribution of gene therapy vectors administered to extragonadal sites indicate that this risk is low, animal experiments and clinical studies designed specifically to address this question are warranted; because of this risk, every gene therapy vector should be tested for its potential to integrate into germ cells and preimplantation embryos.     

Immunoglobulin heavy- and light-chain repertoire in splenic marginal zone lymphoma

The considerable heterogeneity in morphology, immunophenotype, genotype, and clinical behavior of splenic marginal zone lymphoma (SMZL) hinders firm conclusions on the origin and differentiation stage of the neoplastic cells. Immunoglobulin (IG) gene usage and somatic mutation patterns were studied in a series of 43 SMZL cases. Clonal IGHV-D-J rearrangements were amplified in 42/43 cases (4 cases carried double rearrangements). Among IGHV-D-J rearrangements, IGHV3 and IGHV4 subgroup genes were used with the highest frequency. Nineteen IGHV genes were unmutated (> 98% homology to the closest germline IGHV gene), whereas 27/46 were mutated. Clonal IGKV-J and IGLV-J gene rearrangements were amplified in 36/43 cases, including 31 IGKV-J (8/31 in lambda light-chain expressing cases) and 12 IGLV-J rearrangements; 9/31 IGKV and 6/12 IGLV sequences were mutated. IGKV-J and IGLV-J rearrangements used 14 IGKV and 9 IGLV different germline genes. Significant evidence for positive selection by classical T-dependent antigen was found in only 5/27 IGHV and 6/15 IGKV+IGLV mutated genes. These results provide evidence for the diverse B-cell subpopulations residing in the SMZ, which could represent physiologic equivalents of distinct SMZL subtypes. Furthermore, they indicate that in SMZL, as in other B cell malignancies, a complementarity imprint of antigen selection might be witnessed either by IGHV, IGKV, or IGLV rearranged sequences.     

How good is our genome?

Our genome has evolved to perpetuate itself through the maintenance of the species via an uninterrupted chain of reproductive somas. Accordingly, evolution is not concerned with diseases occurring after the soma's reproductive stage. Following Richard Dawkins, we would like to reassert that we indeed live as disposable somas, slaves of our germline genome, but could soon start rebelling against such slavery. Cancer and its relation to the TP53 gene may offer a paradigmatic example. The observation that the latency period in cancer can be prolonged in mice by increasing the number of TP53 genes in their genome, suggests that sooner or later we will have to address the question of heritable disease avoidance via the manipulation of the human germline.     

Pathogenic autoantibodies in systemic lupus erythematosus are derived from both self-reactive and non-self-reactive B cells

Previous studies have shown that both murine and human anti-double-stranded DNA (anti-dsDNA) antibodies can develop from non-DNA-reactive B cells and suggest a crucial role for somatic mutation in dsDNA binding. However, since only a limited number of human anti-dsDNA antibodies have been analyzed previously, we could not exclude other mechanisms for the generation of anti-dsDNA antibodies in patients with systemic lupus erythematosus (SLE). Therefore, we isolated IgM anti-dsDNA antibodies from peripheral blood B cells of a patient with SLE. Three somatically mutated IgM anti-DNA antibodies with pathogenic potential (glomerular binding) were reverted to their germline configuration. Although all three IgM anti-dsDNA antibodies came from the same lupus patient, they displayed different profiles. Reversion to the germline sequence of autoantibodies A9 and B5 resulted in decreased dsDNA binding. In contrast, the germline form of G3-recognized dsDNA as well as the mutated counterpart. These results suggest that mutated IgM anti-dsDNA antibodies may develop from both DNA- and non-DNA-reactive B cells. The implications are that B cell activation occurs in response to self and non-self antigens, while selection after activation may be mediated by self antigen in SLE. Moreover, ineffective tolerance checkpoints may exist before and after antigen activation in SLE.     

Many human immunoglobulin heavy-chain IGHV gene polymorphisms have been reported in error

The identification of the genes that make up rearranged immunoglobulin genes is critical to many studies. For example, the enumeration of mutations in immunoglobulin genes is important for the prognosis of chronic lymphocytic leukemia, and this requires the accurate identification of the germline genes from which a particular sequence is derived. The immunoglobulin heavy-chain variable (IGHV) gene repertoire is generally considered to be highly polymorphic. In this report, we describe a bioinformatic analysis of germline and rearranged immunoglobulin gene sequences which casts doubt on the existence of a substantial proportion of reported germline polymorphisms. We report a five-level classification system for IGHV genes, which indicates the likelihood that the genes have been reported accurately. The classification scheme also reflects the likelihood that germline genes could be incorrectly identified in mutated VDJ rearrangements, because of similarities to other alleles. Of the 226 IGHV alleles that have previously been reported, our analysis suggests that 104 of these alleles almost certainly include sequence errors, and should be removed from the available repertoire. The analysis also highlights the presence of common mismatches, with respect to the germline, in many rearranged heavy-chain sequences, suggesting the existence of twelve previously unreported alleles. Sequencing of IGHV genes from six individuals in this study confirmed the existence of three of these alleles, which we designate IGHV3-49*04, IGHV3-49*05 and IGHV4-39*07. We therefore present a revised repertoire of expressed IGHV genes, which should substantially improve the accuracy of immunoglobulin gene analysis.     

Retrospective study of the cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations in Guthrie cards from a large cohort of neonatal screening for cystic fibrosis

The cystic fibrosis transmembrane conductance regulator (CFTR) gene encodes a cAMP-activated chloride channel, and in individuals with both alleles of the gene mutated, symptoms of CF disease are manifest. With more than 300 mutations so far described in the gene the profile of mutant alleles in a population is specific to its ethnic origin. For an analysis with an unbiased recruitment of the CF alleles in neonates of similar origin (Normandy, France), we have retrospectively analyzed the Guthrie cards of affected newborns, diagnosed by the immunoreactive trypsinogen (IRT) assay. Analysis of the 27 exons of the CFTR gene using a GC clamp denaturing gradient gel electrophoresis (DGGE) assay has enabled us to identify over 96% of the mutated alleles. Two of these were novel mutations. We would like to propose this strategy as an efficient method of retrospective molecular genetic diagnosis that can be performed wherever Guthrie cards can be obtained. Knowledge of rare alleles could be a prerequisite for CF therapy in the future.     

A growing family: Adding mutated Erbb4 as a novel cancer target

As the upward spiral of novel cancer gene discoveries and novel molecular compounds continues to accelerate, a repetitive theme in molecular drug development remains the lack of activity of initially promising agents when given to patients in clinical trials. It is however invigorating that a few targeted agents directed against a select group of a few ‘cancer gene superfamilies’ have escaped this all to common fate, and have evolved into novel, clinically meaningful molecular therapy strategies. Targeting dysregulated signaling of the epidermal growth factor family of transmembrane receptors (Erbb family) has encompassed over the last decade an ever increasing role in personalized treatment approaches in an increasing number of human malignancies. Erbbs are receptor tyrosine kinases that are important regulators of several signaling pathways. Two of its family members (Erbb1/EGFR and Erbb2/HER2) have previously been shown to be somatically mutated in large fraction of human cancers. To determine if this family is somatically mutated in melanoma, its sequences were recently analyzed and one of its members, Erbb4, was found to be somatically mutated in 19% of melanoma cases. Functional analysis of seven of its mutations was shown to increase its catalytic and transformation abilities as well as providing essential survival signals. Similar to other Erbb family members, mutant Erbb4 seems to confer ‘oncogene addiction’ on melanoma cells, making it an attractive therapeutic target. Gaining further understanding into the oncogenic mechanism of Erbb4 may not only help in the development of targeted therapy in melanoma patients but might accelerate the acceptance of a novel taxonomy of cancer which is based on the genomic perturbations in cancer genes and cancer gene families and their response to targeted agents.     

Missense mutations in hMLH1 associated with colorectal cancer

One of the most prevalent hereditary syndromes associated with colorectal cancer is hereditary nonpolyposis colorectal cancer (HNPCC). The inherited gene defects in HNPCC have been shown to reside in DNA mismatch repair genes, mostly hMSH2 or hMLH1. Most HNPCC patients are heterozygous with regard to the relevant mismatch repair gene; they have one normal and one mutated allele, and mismatch repair in normal somatic cells is functional. Cancer predisposition in HNPCC is believed to be associated with the loss of the wild-type allele in somatic cells, resulting in defective DNA mismatch repair. This gives rise to DNA microsatellite instability (MSI), an increased somatic mutation rate, and eventually, to the accumulation of mutations in genes involved in colorectal carcinogenesis. In support of this theory, colorectal tumors in HNPCC patients and in mice deficient for hMSH2 or hMLH1 show MSI. Here, we describe two missense mutations in hMLH1 exon 16 associated with colorectal cancer. Interestingly, the tumors do not show MSI. This raises some potentially important issues. First, even microsatellite-negative colorectal tumors can be associated with germline mutations and these will be missed if an MSI test is used to select patients for mutation screening. Second, the lack of MSI in these cases suggests that the mechanism involved in carcinogenesis could be different from that generally hypothesized.