A mosaic activating mutation in AKT1 associated with the Proteus syndrome

Microbial dysbiosis and colon carcinogenesis: could colon cancer be considered a bacteria-related disease?

Colorectal cancer (CRC) is posing an increasingly important burden on the health care system, with western countries seeing a growing incidence of the disease. Except for germline DNA mutations which have been attributed to less than 5% of patients, little is known about the main causes of CRC. However, environment factors such as food, lifestyle and medication are now suspected to have a major influence on inducing cancers. Today, exhaustive quantitative and qualitative evaluation of all environmental factors is not possible. Various environment-induced diseases have been characterized based on colon microflora, also called microbiota, analyses. Growing data have shown specific changes in microflora (i.e. dysbiosis) in the stools of patients with colon cancer or those adherent to the colonic mucosa. Thus, it appears that microbiota may be considered a platform offering host and environment interactions for studying CRCs. The hypothesis that colon cancer might be a bacteria-related disease is suggested and perspectives are discussed.

A mosaic PTEN mutation causing Cowden syndrome identified by deep sequencing

PURPOSE

Mosaic PTEN mutations are not well described in Cowden syndrome. We report a 40-year-old woman with a clinical diagnosis of Cowden syndrome including Lhermitte-Duclos disease, who had a mosaic PTEN mutation detected by next-generation deep sequencing.

METHODS

Complete PTEN gene sequencing by the Sanger method and deletion/duplication analysis performed on DNA extracted from blood leukocytes at a commercial clinical laboratory did not identify a mutation. Because of high suspicion of a PTEN mutation, we repeated testing by next-generation sequencing using the ColoSeq assay, which sequences the entire PTEN locus at >320-fold average coverage.

RESULTS

ColoSeq identified a frameshift PTEN mutation (c.767_768delAG) in 1.7% of sequencing reads from peripheral blood leukocytes (21/1,184 reads), which is below the limit of detection of most Sanger sequencing methods. The mutation was detected at full heterozygous levels in skin fibroblasts and a cerebellar tumor, and at approximately the 25% level in colonic and endocervical mucosa, confirming somatic mosaicism.

CONCLUSION

Our report highlights the power of deep next-generation sequencing to identify mosaic mutations that can be missed by traditional less sensitive approaches. We speculate that mosaic PTEN mutations are more common in Cowden syndrome than previously described.

Fibroproliferative Neuromas May Occur After Iatrogenic Injury for Lipomatosis of Nerve

BACKGROUND:

Lipomatosis of nerve (LN) is a condition associated with nerve-territory overgrowth. We have noted a unique type of neuroma at sites of LN injury; the neuroma extends beyond the epineurium, enhances, and appears to enlarge over time.

OBJECTIVE:

We sought to understand the relationship between fibroproliferative scarring and surgery performed on the nerve.

METHODS:

A review of the searchable records for LN at our institution found 52 cases, confirmed by pathology or pathognomonic appearance on magnetic resonance imaging (MRI). Clinical histories were reviewed to categorize the surgeries performed by the degree of iatrogenic injury to the nerve. Postoperative MRI was performed in 22 of the 46 patients who had surgery, which was then retrospectively reviewed for fibroproliferative neuromas.

RESULTS:

Complex and masslike neuromas were found on MRI, correlating with the degree of iatrogenic injury to the nerve. These fibrous neuromas proliferated beyond the epineurium, disrupted fascicular architecture, were contrast enhancing when contrast was administered, indicative they were unique and unlike stump or traction neuromas. Of the 8 patients who underwent surgery involving nerve decompression alone, none developed fibroproliferative neuromas. Of the 7 patients who underwent surgery involving nerve debulking, fibroproliferative neuromas developed in 4. Of the 11 patients who underwent surgery involving nerve transection, all developed fibroproliferative neuromas (P < .001). There was also a high incidence of hypertrophic scarring of the skin incision (21.3%).

CONCLUSION:

Surgical injury of LN appears to be strongly associated with the development of fibroproliferative neuromas. It is possible that the pathological overgrowth stimulus associated with LN promotes exuberant scar formation.

Molecular mechanisms of childhood overgrowth

This issue of the Seminar Series C is dedicated to the molecular mechanisms of childhood overgrowth and celebrates the last decade of unprecedented gene discovery. Constitutional gene disorders, somatic gene disorders and imprinting dysregulation are each considered. The constitutional overgrowth genes discussed include NSD1, EZH2, GPC3, DIS3L2, and PTEN whilst the somatic overgrowth genes include AKT3, PIK3R2, and PIK3CA. Abnormalities of imprinting, exemplified by disruption of the (epi)genetic regulation of the imprinted 11p15 gene cluster, constitutes the final section of this issue. Many of the genes discussed in this issue encode components of the PI3K/mTOR growth regulatory pathway. This signaling cascade consists of dual, parallel branches, anchored by the serine-threonine kinase, mTOR, and has diverse downstream effects including inhibition of apoptosis, activation of protein synthesis, and enhanced cell survival. Activation of the PI3K/mTOR pathway promotes growth whereas inhibition, or abrogation, results in decreased cellular growth. Despite the rapid advances of the last decade, there is still an enormous amount to discover. We hope that some of the work reviewed in this issue will facilitate the next decade's discoveries and we look forward to a 10 years as productive as the last.

Rare variants in complex traits: novel identification strategies and the role of de novo mutations

Following the limited success of linkage and association studies aimed at identifying the genetic causes of common neurodevelopmental syndromes like autism and schizophrenia, complex traits such as these have recently been considered under the 'common disease-rare variant' hypothesis. Prior to this hypothesis, the study of candidate genes has enabled the discovery of rare variants in complex disorders, and in turn some of these variants have highlighted the genetic contribution of de novo variants. De novo variants belong to a subcategory of spontaneous rare variants that are largely associated with sporadic diseases, which include some complex psychiatric disorders where the affected individuals do not transmit the genetic defects they carry because of their reduced reproductive fitness. Interestingly, recent studies have demonstrated the rate of germline de novo mutations to be higher in individuals with complex psychiatric disorders by comparison to what is seen in unaffected control individuals; moreover, de novo mutations carried by affected individuals have generally been more deleterious than those observed in control individuals. Advanced sequencing technologies have recently enabled the undertaking of massive parallel sequencing projects that can cover the entire coding sequences (exome) or genome of several individuals at once. Such advances have thus fostered the emergence of novel genetic hypotheses and ideas to investigate disease-causative genetic variations. The genetic underpinnings of a number of sporadic complex diseases is now becoming partly explained and more major breakthroughs for complex traits genomics should be expected in the near future.

Germline Mutations in RASA1 Are Not Found in Patients with Klippel-Trenaunay Syndrome or Capillary Malformation with Limb Overgrowth

The RASA1 gene encodes p120RASGAP, a multidomain cytoplasmic protein that acts as a negative regulator of the RAS signalling pathway. Heterozygous loss-of-function RASA1 mutations were identified in patients with Parkes Weber syndrome and multifocal capillary malformations. This syndrome is characterised by a capillary blush on an extremity, arteriovenous microfistulas, and bony and soft tissue hypertrophy. The aim of this study was to test RASA1 in 2 disorders characterised by asymmetric limb enlargement and vascular malformations, namely Klippel-Trenaunay syndrome and regional capillary malformation with overgrowth. We did not identify any clear pathogenic change in these patients. Thus, besides clinical and radiological criteria, RASA1 testing constitutes an additional tool to differentiate Parkes Weber syndrome of capillary malformation-arteriovenous malformation (CM-AVM) from overlapping disorders.

Many mosaic mutations

Steven Narod’s latest Countercurrents contribution to Current Oncology discusses a new breast and ovarian cancer susceptibility gene known as PPM1D. [...]

New findings in genodermatoses

New technologies are accelerating the pace at which genetic defects leading to inherited skin disease are elucidated. Translation of these genetic discoveries into new therapies for patients with inherited skin diseases has not been as rapid but the pace is now accelerating. This article summarizes recent findings in genetic skin diseases, the scope of advances being made, the role of new DNA analysis technologies in these discoveries, as well as highlighting some examples of how an understanding of the genetic cause of inherited skin diseases can lead to therapeutic interventions for patients.

Targeting activated Akt with GDC-0068, a novel selective Akt inhibitor that is efficacious in multiple tumor models

PURPOSE

We describe the preclinical pharmacology and antitumor activity of GDC-0068, a novel highly selective ATP-competitive pan-Akt inhibitor currently in clinical trials for the treatment of human cancers.

EXPERIMENTAL DESIGN

The effect of GDC-0068 on Akt signaling was characterized using specific biomarkers of the Akt pathway, and response to GDC-0068 was evaluated in human cancer cell lines and xenograft models with various genetic backgrounds, either as a single agent or in combination with chemotherapeutic agents.

RESULTS

GDC-0068 blocked Akt signaling both in cultured human cancer cell lines and in tumor xenograft models as evidenced by dose-dependent decrease in phosphorylation of downstream targets. Inhibition of Akt activity by GDC-0068 resulted in blockade of cell-cycle progression and reduced viability of cancer cell lines. Markers of Akt activation, including high-basal phospho-Akt levels, PTEN loss, and PIK3CA kinase domain mutations, correlate with sensitivity to GDC-0068. Isogenic PTEN knockout also sensitized MCF10A cells to GDC-0068. In multiple tumor xenograft models, oral administration of GDC-0068 resulted in antitumor activity ranging from tumor growth delay to regression. Consistent with the role of Akt in a survival pathway, GDC-0068 also enhanced antitumor activity of classic chemotherapeutic agents.

CONCLUSIONS

GDC-0068 is a highly selective, orally bioavailable Akt kinase inhibitor that shows pharmacodynamic inhibition of Akt signaling and robust antitumor activity in human cancer cells in vitro and in vivo. Our preclinical data provide a strong mechanistic rationale to evaluate GDC-0068 in cancers with activated Akt signaling.

Quantitative and sensitive detection of GNAS mutations causing mccune-albright syndrome with next generation sequencing

Somatic activating GNAS mutations cause McCune-Albright syndrome (MAS). Owing to low mutation abundance, mutant-specific enrichment procedures, such as the peptide nucleic acid (PNA) method, are required to detect mutations in peripheral blood. Next generation sequencing (NGS) can analyze millions of PCR amplicons independently, thus it is expected to detect low-abundance GNAS mutations quantitatively. In the present study, we aimed to develop an NGS-based method to detect low-abundance somatic GNAS mutations. PCR amplicons encompassing exons 8 and 9 of GNAS, in which most activating mutations occur, were sequenced on the MiSeq instrument. As expected, our NGS-based method could sequence the GNAS locus with very high read depth (approximately 100,000) and low error rate. A serial dilution study with use of cloned mutant and wildtype DNA samples showed a linear correlation between dilution and measured mutation abundance, indicating the reliability of quantification of the mutation. Using the serially diluted samples, the detection limits of three mutation detection methods (the PNA method, NGS, and combinatory use of PNA and NGS [PNA-NGS]) were determined. The lowest detectable mutation abundance was 1% for the PNA method, 0.03% for NGS and 0.01% for PNA-NGS. Finally, we analyzed 16 MAS patient-derived leukocytic DNA samples with the three methods, and compared the mutation detection rate of them. Mutation detection rate of the PNA method, NGS and PNA-NGS in 16 patient-derived peripheral blood samples were 56%, 63% and 75%, respectively. In conclusion, NGS can detect somatic activating GNAS mutations quantitatively and sensitively from peripheral blood samples. At present, the PNA-NGS method is likely the most sensitive method to detect low-abundance GNAS mutation.

Midbrain and hindbrain malformations: advances in clinical diagnosis, imaging, and genetics

Historically, the midbrain and hindbrain have been considered of secondary importance to the cerebrum, which has typically been acknowledged as the most important part of the brain. In the past, radiologists and pathologists did not regularly examine these structures-also known as the brainstem and cerebellum-because they are small and difficult to remove without damage. With recent developments in neuroimaging, neuropathology, and neurogenetics, many developmental disorders of the midbrain and hindbrain have emerged as causes of neurodevelopmental dysfunction. These research advances may change the way in which we treat these patients in the future and will enhance the clinical acumen of the practising neurologist and thereby improve the diagnosis and treatment of these patients.

R132C IDH1 mutations are found in spindle cell hemangiomas and not in other vascular tumors or malformations

Spindle cell hemangioma (SCH) is a rare, benign vascular tumor of the dermis and subcutis. The lesions can be multifocal and are overrepresented in Maffucci syndrome, in which patients also have multiple enchondromas. Somatic mosaic R132C IDH1 hotspot mutations were recently identified in Maffucci syndrome. We evaluated the presence of mutations in solitary and multiple SCHs in patients without multiple enchondromas and tested a range of other vascular lesions that enter into the differential diagnosis. The R132C IDH1 mutation was identified by hydrolysis probes assay and confirmed by Sanger sequencing in 18 of 28 (64%) SCHs; of the 10 negative cases, 2 harbored a mutation in IDH2 (R172T and R172M) by Sanger sequencing. None of 154 other vascular malformations and tumors harbored an IDH1 R132C mutation, and R132H IDH1 mutations were absent in all 182 cases. All 16 SCHs examined by immunohistochemistry were negative for expression of HIF-1α. In conclusion, 20 of 28 (71%) SCHs harbored mutations in exon 4 of IDH1 or IDH2. Given that mutations were absent in 154 other vascular lesions, the mutation seems to be highly specific for SCH. The mutation does not induce expression of HIF-1α in SCH, and therefore the exact mechanism by which mutations in IDH1 or IDH2 lead to vascular tumorigenesis remains to be established.

Pathogenic mutations in two families with congenital cataract identified with whole-exome sequencing

PURPOSE

Congenital cataract is one of the most frequent causes of visual impairment and childhood blindness. Approximately one quarter to one third of congenital cataract cases may have a genetic cause. However, phenotypic variability and genetic heterogeneity hamper correct genetic diagnosis. In this study, we used whole-exome sequencing (WES) to identify pathogenic mutations in two Korean families with congenital cataract.

METHODS

Two affected members from each family were pooled and processed for WES. The detected variants were confirmed with direct sequencing.

RESULTS

WES readily identified a CRYAA mutation in family A and a CRYGC mutation in family B. The c.61C>T (p.R21W) mutation in CRYAA has been previously reported in a family with congenital cataract and microcornea. The novel mutation, c.124delT, in CRYGC may lead to a premature stop codon (p.C42Afs*60).

CONCLUSIONS

This study clearly shows the efficacy of WES for rapid genetic diagnosis of congenital cataract with an unknown cause. WES will be the first choice for clinical services in the near future, providing useful information for genetic counseling and family planning.

Multiple congenital melanocytic nevi and neurocutaneous melanosis are caused by postzygotic mutations in codon 61 of NRAS

Congenital melanocytic nevi (CMN) can be associated with neurological abnormalities and an increased risk of melanoma. Mutations in NRAS, BRAF, and Tp53 have been described in individual CMN samples; however, their role in the pathogenesis of multiple CMN within the same subject and development of associated features has not been clear. We hypothesized that a single postzygotic mutation in NRAS could be responsible for multiple CMN in the same individual, as well as for melanocytic and nonmelanocytic central nervous system (CNS) lesions. From 15 patients, 55 samples with multiple CMN were sequenced after site-directed mutagenesis and enzymatic digestion of the wild-type allele. Oncogenic missense mutations in codon 61 of NRAS were found in affected neurological and cutaneous tissues of 12 out of 15 patients, but were absent from unaffected tissues and blood, consistent with NRAS mutation mosaicism. In 10 patients, the mutation was consistently c.181C>A, p.Q61K, and in 2 patients c.182A>G, p.Q61R. All 11 non-melanocytic and melanocytic CNS samples from 5 patients were mutation positive, despite NRAS rarely being reported as mutated in CNS tumors. Loss of heterozygosity was associated with the onset of melanoma in two cases, implying a multistep progression to malignancy. These results suggest that single postzygotic NRAS mutations are responsible for multiple CMN and associated neurological lesions in the majority of cases.

De novo truncating mutations in ASXL3 are associated with a novel clinical phenotype with similarities to Bohring-Opitz syndrome

Background

Molecular diagnostics can resolve locus heterogeneity underlying clinical phenotypes that may otherwise be co-assigned as a specific syndrome based on shared clinical features, and can associate phenotypically diverse diseases to a single locus through allelic affinity. Here we describe an apparently novel syndrome, likely caused by de novo truncating mutations in ASXL3, which shares characteristics with Bohring-Opitz syndrome, a disease associated with de novo truncating mutations in ASXL1.

Methods

We used whole-genome and whole-exome sequencing to interrogate the genomes of four subjects with an undiagnosed syndrome.

Results

Using genome-wide sequencing, we identified heterozygous, de novo truncating mutations in ASXL3, a transcriptional repressor related to ASXL1, in four unrelated probands. We found that these probands shared similar phenotypes, including severe feeding difficulties, failure to thrive, and neurologic abnormalities with significant developmental delay. Further, they showed less phenotypic overlap with patients who had de novo truncating mutations in ASXL1.

Conclusion

We have identified truncating mutations in ASXL3 as the likely cause of a novel syndrome with phenotypic overlap with Bohring-Opitz syndrome.

Cutaneous vascular anomalies in the neonatal period

Vascular birthmarks can be difficult to diagnose in the perinatal period due to varied growth characteristics and similar initial appearances. Location and type of birthmark can provide signals that extracutaneous involvement may be a concern. This article provides a baseline framework that can help diagnose, define associations and guide workup and treatment in these neonates.

Use of somatic mutations to quantify random contributions to mouse development

Background

The C. elegans cell fate map, in which the lineage of its approximately 1000 cells is visibly charted beginning from the zygote, represents a developmental biology milestone. Nematode development is invariant from one specimen to the next, whereas in mammals, aspects of development are probabilistic, and development exhibits variation between even genetically identical individuals. Consequently, a single defined cell fate map applicable to all individuals cannot exist.

Results

To determine the extent to which patterns of cell lineage are conserved between different mice, we have employed the recently developed method of “phylogenetic fate mapping” to compare cell fate maps in siblings. In this approach, somatic mutations arising in individual cells are used to retrospectively deduce lineage relationships through phylogenetic and—as newly investigated here—related analytical approaches based on genetic distance. We have cataloged genomic mutations at an average of 110 mutation-prone polyguanine (polyG) tracts for about 100 cells clonally isolated from various corresponding tissues of each of two littermates of a hypermutable mouse strain.

Conclusions

We find that during mouse development, muscle and fat arise from a mixed progenitor cell pool in the germ layer, but, contrastingly, vascular endothelium in brain derives from a smaller source of progenitor cells. Additionally, formation of tissue primordia is marked by establishment of left and right lateral compartments, with restricted cell migration between divisions. We quantitatively demonstrate that development represents a combination of stochastic and deterministic events, offering insight into how chance influences normal development and may give rise to birth defects.

Functional analysis of a duplication (p.E63_D69dup) in the switch II region of HRAS: new aspects of the molecular pathogenesis underlying Costello syndrome

Costello syndrome is a congenital disorder comprising a characteristic face, severe feeding difficulties, skeletal, cardiac and skin abnormalities, intellectual disability and predisposition to malignancies. It is caused by heterozygous germline HRAS mutations mostly affecting Gly(12) or Gly(13), which impair HRAS-GTPase activity and result in increased downstream signal flow independent of incoming signals. Functional analyses of rarer HRAS mutations identified in individuals with attenuated Costello syndrome phenotypes revealed altered GDP/GTP nucleotide affinities (p.K117R) and inefficient effector binding (p.E37dup). Thus, both phenotypic and functional variability associated with HRAS mutations are evident. Here, we report on a novel heterozygous HRAS germline mutation (c.187_207dup, p.E63_D69dup) in a girl presenting with a phenotype at the milder end of the Costello syndrome spectrum. The p.E63_D69dup mutation impaired co-precipitation of recombinant HRAS with NF1 GTPase-activating protein (GAP) suggesting constitutive HRAS(E63_D69dup) activation due to GAP insensitivity. Indeed, we identified strongly augmented active HRAS(E63_D69dup) that co-precipitated with effectors RAF1, RAL guanine nucleotide dissociation stimulator and phospholipase C1. However, we could not pull down active HRAS(E63_D69dup) using the target protein PIK3CA, indicating a compromised association between active HRAS(E63_D69dup) and PIK3CA. Accordingly, overexpression of HRAS(E63_D69dup) increased steady-state phosphorylation of MEK1/2 and ERK1/2 downstream of RAF, whereas AKT phosphorylation downstream of phosphoinositide 3-kinase (PI3K) was not enhanced. By analyzing signaling dynamics, we found that HRAS(E63_D69dup) has impaired reagibility to stimuli resulting in reduced and disrupted capacity to transduce incoming signals to the RAF-MAPK and PI3K-AKT cascade, respectively. We suggest that disrupted HRAS reagibility, as we demonstrate for the p.E63_D69dup mutation, is a previously unappreciated molecular pathomechanism underlying Costello syndrome.

Akt1 mediates neuronal differentiation in zebrafish via a reciprocal interaction with notch signaling

Akt1 is well known for its role in regulating cell proliferation, differentiation, and apoptosis and is implicated in tumors and several neurological disorders. However, the role of Akt1 in neural development has not been well defined. We have isolated zebrafish akt1 and shown that this gene is primarily transcribed in the developing nervous system, and its spatiotemporal expression pattern suggests a role in neural differentiation. Injection of akt1 morpholinos resulted in loss of neuronal precursors with a concomitant increase in post-mitotic neurons, indicating that knockdown of Akt1 is sufficient to cause premature differentiation of neurons. A similar phenotype was observed in embryos deficient for Notch signaling. Both the ligand (deltaA) and the downstream target of Notch (her8a) were downregulated in akt1 morphants, indicating that Akt1 is required for Delta-Notch signaling. Furthermore, akt1 expression was downregulated in Delta-Notch signaling-deficient embryos and could be induced by constitutive activation of Notch signaling. In addition, knockdown of Akt1 was able to nullify the inhibition of neuronal differentiation caused by constitutive activation of Notch signaling. Taken together, these results provide in vivo evidence that Akt1 interacts with Notch signaling reciprocally and provide an explanation of why Akt1 is essential for the inhibition of neuronal differentiation.

Diverse mechanisms of AKT pathway activation in human malignancy

AKT/PKB (Protein Kinase B) are central proteins mediating signals from receptor tyrosine kinases and phosphatidylinositol 3-kinase. AKT kinases are involved in a number of important cellular processes including cell proliferation and survival, cell size in response to nutrient availability, tumor invasion/metastasis, and angiogenesis.Various components of the AKT signaling pathway are encoded by tumor suppressor genes and oncogenes whose loss or activation, respectively, plays an important role in tumorigenesis. The growing body of evidence connecting deregulated AKT signaling with sporadic human cancers and inherited cancer predisposition syndromes is discussed. We also highlight new findings regarding the involvement of activating mutations of AKT1, AKT2, and AKT3 in somatic overgrowth disorders: Proteus syndrome, hypoglycemia with hypertrophy, and hemimegalencephaly, respectively. In addition, we review recent literature documenting the various ways the AKT signaling pathway is activated in human cancers and consequences for molecularly targeted therapies.

The Akt DUBbed InAktive

Akt is a central node in the phosphoinositide-3 kinase-Akt-mammalian target of rapamycin pathway and is activated by a multistep process in response to growth factor stimulation. An additional layer of posttranslational modification has emerged as a new paradigm in the regulation of Akt. The identification of an E3 ligase for Lys(63)-linked ubiquitination of Akt has now been complemented with the discovery of the tumor suppressor cylindromatosis as a deubiquitinating enzyme (DUB) for Akt. Thus, like phosphorylation and dephosphorylation, cycles of ubiquitination and deubiquitination provide additional on-off switches that keep Akt activity in balance, and disturbances in this balance have pathological consequences.

Further Evidence of Contrasting Phenotypes Caused by Reciprocal Deletions and Duplications: Duplication of NSD1 Causes Growth Retardation and Microcephaly

Microduplications of the Sotos syndrome region containing NSD1 on 5q35 have recently been proposed to cause a syndrome of microcephaly, short stature and developmental delay. To further characterize this emerging syndrome, we report the clinical details of 12 individuals from 8 families found to have interstitial duplications involving NSD1, ranging in size from 370 kb to 3.7 Mb. All individuals are microcephalic, and height and childhood weight range from below average to severely restricted. Mild-to-moderate learning disabilities and/or developmental delay are present in all individuals, including carrier family members of probands; dysmorphic features and digital anomalies are present in a majority. Craniosynostosis is present in the individual with the largest duplication, though the duplication does not include MSX2, mutations of which can cause craniosynostosis, on 5q35.2. A comparison of the smallest duplication in our cohort that includes the entire NSD1 gene to the individual with the largest duplication that only partially overlaps NSD1 suggests that whole-gene duplication of NSD1 in and of itself may be sufficient to cause the abnormal growth parameters seen in these patients. NSD1 duplications may therefore be added to a growing list of copy number variations for which deletion and duplication of specific genes have contrasting effects on body development.

Molecular dermatology comes of age

Groundbreaking advances on the molecular and cellular physiological and physiopathological skin processes, including the complete sequencing of the genome of several species and the increased availability of gene-modified organisms, paved the way to firmly establishing molecular approaches and methods in experimental, translational, and clinical dermatology. As a result, newly developed experimental ex vivo assays and animal models prove exquisite tools for addressing fundamental physiological cutaneous processes and pathogenic mechanisms of skin diseases. A plethora of new findings that were generated using these experimental tools serve as a strong basis for intense translational research efforts aiming at developing new, specific, and sensitive diagnostic tests and efficient "personalized" therapies with less side-effects. Consequently, a broad array of molecular diagnostic tests and therapies for a wide spectrum of skin diseases ranging from genodermatoses through skin neoplasms, allergy, inflammatory and autoimmune diseases, are already routinely used in the clinical dermatology practice. This article highlights several major developments in molecular experimental and clinical dermatology.

Genetics of neural crest and neurocutaneous syndromes

Neural crest progenitor cells are identified at the lateral margins of the neural placode at the time of gastrulation. With folding of the placode, these precursors are brought to the dorsal midline of the neural tube at the site of closure, become committed to neural crest lineage and almost immediately migrate peripherally to various predetermined sites in the body and then differentiate as a variety of cellular types in all three of the traditional "germ layers." All of these processes of migration and differentiation of neural crest are precisely genetically programed, temporally and spatially, by a variety of genes. Primary neurocutaneous syndromes are all very different diseases with different genetic mutations, but the unifying factor amongst them is that all are neurocristopathies and can be explained as such, including the tumor-suppressor function of several of these genes, especially those of neurofibromatosis 1 and 2 and tuberous sclerosis. This chapter reviews the principal genes that program neural crest development and also are documented, implicated, or suspected in the pathogenesis of neurocutaneous syndromes. Recent genetic discoveries are noted in epidermal nevus syndrome, including Proteus syndrome and their association with hemimegalencephaly and congenital infiltrating lipomatosis of the face.

Non-heritable genetics of human disease: spotlight on post-zygotic genetic variation acquired during lifetime

The heritability of most common, multifactorial diseases is rather modest and known genetic effects account for a small part of it. The remaining portion of disease aetiology has been conventionally ascribed to environmental effects, with an unknown part being stochastic. This review focuses on recent studies highlighting stochastic events of potentially great importance in human disease-the accumulation of post-zygotic structural aberrations with age in phenotypically normal humans. These findings are in agreement with a substantial mutational load predicted to occur during lifetime within the human soma. A major consequence of these results is that the genetic profile of a single tissue collected at one time point should be used with caution as a faithful portrait of other tissues from the same subject or the same tissue throughout life. Thus, the design of studies in human genetics interrogating a single sample per subject or applying lymphoblastoid cell lines may come into question. Sporadic disorders are common in medicine. We wish to stress the non-heritable genetic variation as a potentially important factor behind the development of sporadic diseases. Moreover, associations between post-zygotic mutations, clonal cell expansions and their relation to cancer predisposition are central in this context. Post-zygotic mutations are amenable to robust examination and are likely to explain a sizable part of non-heritable disease causality, which has routinely been thought of as synonymous with environmental factors. In view of the widespread accumulation of genetic aberrations with age and strong predictions of disease risk from such analyses, studies of post-zygotic mutations may be a fruitful approach for delineation of variants that are causative for common human disorders.

Epidermal nevus syndrome

Epidermal nevus syndrome (ENS) is an inclusive term for a heterogeneous group of congenital disorders characterized by the presence of epidermal nevi associated with systemic involvement. These disorders, as are all primary neurocutaneous syndromes, are neurocristopathies. The epidermal nevi that follow the lines of Blaschko and most systemic anomalies in skeletal, ocular, cardiovascular, endocrine, and orodental tissues, as well as lipomas, are due to defective neural crest. The most important and frequent anomaly in the brain in all forms of epidermal nevus syndromes (ENSs) is hemimegalencephaly (HME). This malformation often is not recognized, despite being the principal cause of neurological manifestations in ENSs. They consist mainly of epilepsy and developmental delay or intellectual disability. The onset of epilepsy in ENS usually is in early infancy, often as infantile spasms. Several syndromic forms have been delineated. I propose the term "Heide's syndrome" for those distinctive cases with the typical triad of hemifacial epidermal nevus, ipsilateral facial lipoma, and hemimegalencephaly. Most ENSs are sporadic. The mechanism is thought to be genetic mosaicism with a lethal autosomal dominant gene. Specific genetic mutations (PTEN, FGFR3, PIK3CA, and AKT1) have been documented in some patients. The large number of contributors for over more than a century and a half to the description of these disorders precludes the use of new author eponyms.

Next generation sequencing (NGS) strategies for the genetic testing of myopathies

Next generation sequencing (NGS) technologies offer the possibility to map entire genomes at affordable costs. This brings the genetic testing procedure to a higher level of complexity. The positive aspect is the ease to cope with the complex diagnosis of genetically heterogeneous disorders and to identify novel disease genes. Worries arise from the management of too many DNA variations with unpredictable meaning and incidental findings that can cause ethical and clinical dilemmas. The technology of enrichment makes possible to focus the sequencing to the exome or to a more specific DNA target. This is being used to provide insights into the genetics underlying Mendelian traits involved in myopathies and to set up cost-effective diagnostic tests. This huge potential of the NGS applications makes likely that these will soon become the first approach in genetic diagnostic laboratories.

Genodermatoses caused by genetic mosaicism

Genetic mosaicism is defined as the existence of at least two genetically distinct cell populations within one individual. Mosaic presentation of genetic disorders is common and is often particularly obvious in the skin, because there it will generate recognizable patterns. Recognizing those can frequently assist in establishing a diagnosis. In this review, we discuss the mechanisms that give rise to genetic mosaicism. We describe its most frequent cutaneous manifestations that are relevant to paediatric practice. While most mosaic genetic diseases are rare, it is important to recognize them so that patients and parents may receive appropriate genetic counselling. Moreover, recent developments are now resulting in novel, targeted treatments for such disorders that promise to considerably improve patients' lives.

Loss of heterozygosity is present in SEC63 germline carriers with polycystic liver disease

Polycystic liver disease (PCLD) is an autosomal dominant disorder characterised by multiple fluid filled cysts in the liver. This rare disease is caused by heterozygous germline mutations in PRKCSH and SEC63. We previously found that, in patients with a PRKCSH mutation, over 76% of the cysts acquired a somatic 'second-hit' mutation in the wild type PRKCSH allele. We hypothesise that somatic second-hit mutations are a general mechanism of cyst formation in PCLD which also plays a role in PCLD patients carrying a SEC63 germline mutation. We collected cyst epithelial cells from 52 liver cysts from three different SEC63 patients using laser microdissection. DNA samples were sequenced to identify loss of heterozygosity (LOH) mutations and other somatic mutations in cyst epithelial DNA. We discovered somatic SEC63 mutations in patient 3 (1/14 cysts), but not in patient 1 and 2 (38 cysts). Upon review we found that the germline mutation of patient 1 and 2 (SEC63 c.1703_1705delAAG) was present in the same frequency in DNA samples from healthy controls, suggesting that this variant is not causative of PCLD. In conclusion, as somatic second-hit mutations also play a role in cyst formation in patients with a SEC63 germline mutation, this appears to be a general mechanism of cyst formation in PCLD.

Disruption of PH-kinase domain interactions leads to oncogenic activation of AKT in human cancers

The protein kinase v-akt murine thymoma viral oncogene homolog (AKT), a key regulator of cell survival and proliferation, is frequently hyperactivated in human cancers. Intramolecular pleckstrin homology (PH) domain-kinase domain (KD) interactions are important in maintaining AKT in an inactive state. AKT activation proceeds after a conformational change that dislodges the PH from the KD. To understand these autoinhibitory interactions, we generated mutations at the PH-KD interface and found that most of them lead to constitutive activation of AKT. Such mutations are likely another mechanism by which activation may occur in human cancers and other diseases. In support of this likelihood, we found somatic mutations in AKT1 at the PH-KD interface that have not been previously described in human cancers. Furthermore, we show that the AKT1 somatic mutants are constitutively active, leading to oncogenic signaling. Additionally, our studies show that the AKT1 mutants are not effectively inhibited by allosteric AKT inhibitors, consistent with the requirement for an intact PH-KD interface for allosteric inhibition. These results have important implications for therapeutic intervention in patients with AKT mutations at the PH-KD interface.

Somatic gain-of-function mutations in PIK3CA in patients with macrodactyly

Macrodactyly is a discrete congenital anomaly consisting of enlargement of all tissues localized to the terminal portions of a limb, typically within a ‘nerve territory’. The classic terminology for this condition is ‘lipofibromatous hamartoma of nerve’ or Type I macrodactyly. The peripheral nerve, itself, is enlarged both in circumference and in length. It is not related to neurofibromatosis (NF1), nor is it associated with vascular malformations, such as in the recently reported CLOVES syndrome. The specific nerve pathophysiology in this form of macrodactyly has not been well described and a genetic etiology for this specific form of enlargement is unknown. To identify the genetic cause of macrodactyly, we used whole-exome sequencing to identify somatic mutations present in the affected nerve of a single patient. We confirmed a novel mutation in PIK3CA (R115P) present in the patient's affected nerve tissue but not in blood DNA. Sequencing PIK3CA exons identified gain-of-function mutations (E542K, H1047L or H1047R) in the affected tissue of five additional unrelated patients; mutations were absent in blood DNA available from three patients. Immunocytochemistry confirmed AKT activation in cultured cells from the nerve of a macrodactyly patient. Additionally, we found that the most abnormal structure within the involved nerve in a macrodactylous digit is the perineurium, with additional secondary effects on the axon number and size. Thus, isolated congenital macrodactyly is caused by somatic activation of the PI3K/AKT cell-signaling pathway and is genetically and biochemically related to other overgrowth syndromes.

Focal congenital lipoatrophy and vascular malformation: a mild form of inverse Klippel-Trenaunay syndrome?

A 2 year-and seven month-old male boy with vascular malformation and localized soft tissue hypotrophy is reported. Such presentation could represent the mildest end of the spectrum of 'inverse' Klippel-Trenaunay syndrome, a recently proposed disorder presenting with tissue hypotrophy as opposed to partial or complete limb overgrowth of classic Klippel-Trenaunay syndrome.

De novo mutations in neurological and psychiatric disorders: effects, diagnosis and prevention

Neurological and psychiatric disorders account for a considerable proportion of the global disease burden. Although there is a high heritability and a significant genetic component in these disorders, the genetic cause of most cases has yet to be identified. Advances in DNA sequencing allowing the analysis of the whole human genome in a single experiment have led to an acceleration of the discovery of the genetic factors associated with human disease. Recent studies using these platforms have highlighted the important role of de novo mutations in neurological and psychiatric disorders. These findings have opened new avenues into the understanding of genetic disease mechanisms. These discoveries, combined with the increasing ease with which we can sequence the human genome, have important implications for diagnosis, prevention and treatment. Here, we present an overview of the recent discovery of de novo mutations using key examples of neurological and psychiatric disorders. We also discuss the impact of technological developments on diagnosis and prevention.

A mutation in the 5'-UTR of IFITM5 creates an in-frame start codon and causes autosomal-dominant osteogenesis imperfecta type V with hyperplastic callus

Osteogenesis imperfecta (OI) is a clinically and genetically heterogeneous disorder associated with bone fragility and susceptibility to fractures after minimal trauma. OI type V has an autosomal-dominant pattern of inheritance and is not caused by mutations in the type I collagen genes COL1A1 and COL1A2. The most remarkable and pathognomonic feature, observed in ~65% of affected individuals, is a predisposition to develop hyperplastic callus after fractures or surgical interventions. To identify the molecular cause of OI type V, we performed whole-exome sequencing in a female with OI type V and her unaffected parents and searched for de novo mutations. We found a heterozygous de novo mutation in the 5'-untranslated region of IFITM5 (the gene encoding Interferon induced transmembrane protein 5), 14 bp upstream of the annotated translation initiation codon (c.-14C>T). Subsequently, we identified an identical heterozygous de novo mutation in a second individual with OI type V by Sanger sequencing, thereby confirming that this is the causal mutation for the phenotype. IFITM5 is a protein that is highly enriched in osteoblasts and has a putative function in bone formation and osteoblast maturation. The mutation c.-14C>T introduces an upstream start codon that is in frame with the reference open-reading frame of IFITM5 and is embedded into a stronger Kozak consensus sequence for translation initiation than the annotated start codon. In vitro, eukaryotic cells were able to recognize this start codon, and they used it instead of the reference translation initiation signal. This suggests that five amino acids (Met-Ala-Leu-Glu-Pro) are added to the N terminus and alter IFITM5 function in individuals with the mutation.

Overgrowth syndromes

PURPOSE OF REVIEW

Human growth ensues from a complex interplay of physiological factors, in the wider setting of varying genetic traits and environmental influences. Intensive research in these divergent areas, and particularly in the field of genetics, continues to clarify the molecular basis of disorders which result in overgrowth, and it is therefore timely to provide a review of these findings.

RECENT FINDINGS

This article provides an overview of the factors which regulate growth, followed by a discussion of the more commonly encountered overgrowth syndromes and their genetic basis as it is understood at the current time. There is also an added focus on recently discovered genetic associations in some conditions, such as Weaver, Perlman and Proteus syndromes.

SUMMARY

New discoveries continue to be made regarding the genetic basis for many overgrowth syndromes and the development of a much needed molecular classification system for overgrowth may become possible as the interlinking functions of these genes on growth are unravelled. As there exists a wide spectrum of syndromes, disorders resulting in overgrowth can represent a diagnostic and therapeutic challenge, from those causing prenatal overgrowth with a poor prognosis to less severe genetic aberrations which are identified in later childhood or adult life.

Synthetic spike-in standards improve run-specific systematic error analysis for DNA and RNA sequencing

While the importance of random sequencing errors decreases at higher DNA or RNA sequencing depths, systematic sequencing errors (SSEs) dominate at high sequencing depths and can be difficult to distinguish from biological variants. These SSEs can cause base quality scores to underestimate the probability of error at certain genomic positions, resulting in false positive variant calls, particularly in mixtures such as samples with RNA editing, tumors, circulating tumor cells, bacteria, mitochondrial heteroplasmy, or pooled DNA. Most algorithms proposed for correction of SSEs require a data set used to calculate association of SSEs with various features in the reads and sequence context. This data set is typically either from a part of the data set being “recalibrated” (Genome Analysis ToolKit, or GATK) or from a separate data set with special characteristics (SysCall). Here, we combine the advantages of these approaches by adding synthetic RNA spike-in standards to human RNA, and use GATK to recalibrate base quality scores with reads mapped to the spike-in standards. Compared to conventional GATK recalibration that uses reads mapped to the genome, spike-ins improve the accuracy of Illumina base quality scores by a mean of 5 Phred-scaled quality score units, and by as much as 13 units at CpG sites. In addition, since the spike-in data used for recalibration are independent of the genome being sequenced, our method allows run-specific recalibration even for the many species without a comprehensive and accurate SNP database. We also use GATK with the spike-in standards to demonstrate that the Illumina RNA sequencing runs overestimate quality scores for AC, CC, GC, GG, and TC dinucleotides, while SOLiD has less dinucleotide SSEs but more SSEs for certain cycles. We conclude that using these DNA and RNA spike-in standards with GATK improves base quality score recalibration.

Expression analysis of macrodactyly identifies pleiotrophin upregulation

Macrodactyly is a rare family of congenital disorders characterized by the diffuse enlargement of 1 or more digits. Multiple tissue types within the affected digits are involved, but skeletal patterning and gross morphological features are preserved. Not all tissues are equally involved and there is marked heterogeneity with respect to clinical phenotype. The molecular mechanisms responsible for these growth disturbances offer unique insight into normal limb growth and development, in general. To date, no genes or loci have been implicated in the development of macrodactyly. In this study, we performed the first transcriptional profiling of macrodactyly tissue. We found that pleiotrophin (PTN) was significantly overexpressed across all our macrodactyly samples. The mitogenic functions of PTN correlate closely with the clinical characteristics of macrodactyly. PTN thus represents a promising target for further investigation into the etiology of overgrowth phenotypes.

Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress

The pace of exome and genome sequencing is accelerating, with the identification of many new disease-causing mutations in research settings, and it is likely that whole exome or genome sequencing could have a major impact in the clinical arena in the relatively near future. However, the human genomics community is currently facing several challenges, including phenotyping, sample collection, sequencing strategies, bioinformatics analysis, biological validation of variant function, clinical interpretation and validity of variant data, and delivery of genomic information to various constituents. Here we review these challenges and summarize the bottlenecks for the clinical application of exome and genome sequencing, and we discuss ways for moving the field forward. In particular, we urge the need for clinical-grade sample collection, high-quality sequencing data acquisition, digitalized phenotyping, rigorous generation of variant calls, and comprehensive functional annotation of variants. Additionally, we suggest that a 'networking of science' model that encourages much more collaboration and online sharing of medical history, genomic data and biological knowledge, including among research participants and consumers/patients, will help establish causation and penetrance for disease causal variants and genes. As we enter this new era of genomic medicine, we envision that consumer-driven and consumer-oriented efforts will take center stage, thus allowing insights from the human genome project to translate directly back into individualized medicine.

The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions

Next generation exome sequencing (ES) and whole genome sequencing (WGS) are new powerful tools for discovering the gene(s) that underlie Mendelian disorders. To accelerate these discoveries, the National Institutes of Health has established three Centers for Mendelian Genomics (CMGs): the Center for Mendelian Genomics at the University of Washington; the Center for Mendelian Genomics at Yale University; and the Baylor-Johns Hopkins Center for Mendelian Genomics at Baylor College of Medicine and Johns Hopkins University. The CMGs will provide ES/WGS and extensive analysis expertise at no cost to collaborating investigators where the causal gene(s) for a Mendelian phenotype has yet to be uncovered. Over the next few years and in collaboration with the global human genetics community, the CMGs hope to facilitate the identification of the genes underlying a very large fraction of all Mendelian disorders; see http://mendelian.org.

A severe and rapidly progressive case of proteus syndrome in a neonate who presented with unilateral hydrocephalus apart from other typical features of the proteus syndrome

Proteus syndrome is a rare hamartomatous disorder affecting multiple tissues and manifesting itself in a variety of ways. The understanding of the complete spectrum of clinical features, the natural clinical course of the disease and the proper management of such a rare but highly variable syndrome depend heavily on experiences gathered by previously reported cases. We present an unusually severely affected and rapidly progressive case of proteus syndrome in a neonate who presented with craniofacial hemihypertrophy, subcutaneous masses, capillary hemangioma, varicose veins, epidermal nevi and macrodactyly. The cranial ultrasonogram revealed unilateral hydrocephalus with partial obstruction of the foramen of monro.