Wide Phenotypic Variability Research Articles

The microbiome and inborn errors of metabolism: Why we should look carefully at their interplay?

Research into the influence of the microbiome on the human body has been shedding new light on diseases long known to be multifactorial, such as obesity, mood disorders, autism, and inflammatory bowel disease. Although inborn errors of metabolism (IEMs) are monogenic diseases, genotype alone is not enough to explain the wide phenotypic variability observed in patients with these conditions. Genetics and diet exert a strong influence on the microbiome, and diet is used (alone or as an adjuvant) in the treatment of many IEMs. This review will describe how the effects of the microbiome on the host can interfere with IEM phenotypes through interactions with organs such as the liver and brain, two of the structures most commonly affected by IEMs. The relationships between treatment strategies for some IEMs and the microbiome will also be addressed. Studies on the microbiome and its influence in individuals with IEMs are still incipient, but are of the utmost importance to elucidating the phenotypic variety observed in these conditions.

Tuberous sclerosis complex: review based on new diagnostic criteria

Tuberous sclerosis complex is a multisystemic, autosomal dominant genetic disorder with complete penetrance, that can evolve with hamartomas in multiple organs, such as skin, central nervous system, kidney and lung. Due to the wide phenotypic variability, the disease is often not recognized. Tuberous sclerosis complex affects one in 10,000 newborns and most patients are diagnosed during the first 15 months of life. The diagnostic criteria for tuberous sclerosis were reviewed in 2012, at the second International Tuberous Sclerosis Complex Consensus Conference. The diagnosis is based on genetic criteria, by the identification of inactivating pathogenic mutation of tumor suppressor genes TSC1 and TSC2, and clinical criteria, including cutaneous, renal, pulmonary, cardiac and neurological manifestations. The treatment of tuberous sclerosis complex consists, mainly, in management of the symptoms caused by hamartomas and in prevention of organ failure. Multidisciplinary approach is recommended, in order to obtain better clinical outcomes.

Turner syndrome and spontaneous pregnancy

ABSTRACT The objective of this study is to describe patients with Turner syndrome (TS) who had spontaneous pregnancy and, when possible, to present the frequency of this outcome in this genetic condition. This is a literature review conducted in MedLine/PubMed, using the following English descriptors: Turner syndrome and spontaneous pregnancy. The following filters have been activated: articles with a publication date from the last 10 years that present the descriptors in the title/abstract. Twenty-nine articles were identified using the electronic search. After applying the inclusion and exclusion criteria, the number of articles selected was seven. However, two more articles were included after consulting the reference lists of these seven studies, totaling nine scientific articles. The frequency of spontaneous pregnancy ranged from 1.26% to 5.6%. Sixty-two TS patients who spontaneously became pregnant and 153 pregnancies were reported. There was a predominance of karyotype 45,X/46,XX (42 patients). Three patients were diagnosed with TS in adulthood and two of them after pregnancy. The minimum age at pregnancy was 21 years and the maximum 32. In the gestational outcome, an expressive number of children born, and abortions were observed, the latter with values of 54.9% and 34.6%. The present study described patients with TS and spontaneous pregnancy with mosaic (more frequent) and pure karyotype. It is believed that this value may be underestimated, since few studies have investigated primarily spontaneous pregnancy in this genetic condition, and many TS patients may not have been diagnosed because of the wide phenotypic variability associated with this chromosomal abnormality.

Genome-wide and gene-based association mapping for rice eating and cooking characteristics and protein content

Rice eating and cooking quality and protein content (PC) are important properties affecting consumers’ preferences, nutrition and health. Linkage QTL mapping and association studies are usually applied to genetically dissect related traits, which could be further facilitated by high density SNP markers and gene annotation based on reference genome to rapid identify candidate genes associated with interested traits. Here, we carried out an association study for apparent amylose content (AC), gel consistency (GC), gelatinization temperature (GT) and PC evaluated in two environments using a diverse panel of 258 accessions from 3 K Rice Genome Project. Wide phenotypic variations were observed in this panel. Genome-wide association study using 22,488 high quality SNPs identified 19 QTL affecting the four traits. Combining gene-based association study and haplotype analyses plus functional annotation allowed us to shortlist nine candidate genes for four important QTL regions affecting AC, GC and GT, including two cloned genes (Wx and ALK), and seven novels. The research suggested that GWAS and gene-based association analysis followed by haplotype analysis is an effective way to detect candidate genes. The identified genes and QTL provided valuable sources for future functional characterization and genetic improvement of rice eating and cooking quality and PC.

Strain profiling and epidemiology of bacterial species from metagenomic sequencing

Microbial communities are often composed by complex mixtures of multiple strains of the same species, characterized by a wide genomic and phenotypic variability. Computational methods able to identify, quantify and classify the different strains present in a sample are essential to fully exploit the potential of metagenomic sequencing in microbial ecology, with applications that range from the epidemiology of infectious diseases to the characterization of the dynamics of microbial colonization. Here we present a computational approach that uses the available genomic data to reconstruct complex strain profiles from metagenomic sequencing, quantifying the abundances of the different strains and cataloging them according to the population structure of the species. We validate the method on synthetic data sets and apply it to the characterization of the strain distribution of several important bacterial species in real samples, showing how its application provides novel insights on the structure and complexity of the microbiota.

Orthopaedic manifestations within the 22q11.2 Deletion syndrome: A systematic review.

The 22q11.2 Deletion Syndrome (22q11.2DS) is the most common microdeletion syndrome with an estimated prevalence of 1:4,000 live births. 22q11.2DS is known to have wide phenotypic variability, including orthopaedic manifestations. The purpose of this systematic review is to increase the awareness of orthopaedic manifestations associated with 22q11.2DS. This systematic review was performed according to the PRISMA Guidelines. Original epidemiological studies on the prevalence of orthopaedic manifestations within 22q11.2DS were systematically searched for in PubMed and EMBASE. The included articles were scored according to a risk-of-bias tool, a best-evidence synthesis was performed and the prevalence data was extracted. Sixty-nine published manuscripts described 58 orthopaedic manifestations in a total of 6,055 patients. The prevalence of at least one cervical or occipital anomaly is 90.5-100% (strong evidence). Fourteen studies (n = 2,264) revealed moderate evidence for a wide scoliosis prevalence of 0.6-60%. Two studies demonstrated that 5-6.4% of all 22q11.2DS patients required surgical scoliosis correction. Fifteen studies (n = 2,115) reported a 1.1-13.3% prevalence of clubfoot with moderate evidence. Other reported orthopaedic manifestations are patellar dislocation (10-20%), juvenile rheumatic arthritis (3.75%), impaired growth and skeletal anomalies like polydactyly (1.0-3.7%), syndactyly (11-11.8%), butterfly vertebrae (11.1%) and 13 ribs (2-19%). Orthopaedic findings are important manifestations of the 22q11.2DS, both in bringing patients to diagnostic attention and in requiring surveillance and appropriate intervention. Data on these manifestations are scattered and incomprehensive. Routinely screening for cervical anomalies, scoliosis, and upper and lower limb malformations is recommended in this vulnerable group of patients.

SaccharomycesIDentifier, SID: strain-level analysis of Saccharomyces cerevisiae populations by using microsatellite meta-patterns

Saccharomyces cerevisiae is a common yeast with several applications, among which the most ancient is winemaking. Because individuals belonging to this species show a wide genetic and phenotypic variability, the possibility to identify the strains driving fermentation is pivotal when aiming at stable and palatable products. Metagenomic sequencing is increasingly used to decipher the fungal populations present in complex samples such as musts. However, it does not provide information at the strain level. Microsatellites are commonly used to describe the genotype of single strains. Here we developed a population-level microsatellite profiling approach, SID (Saccharomyces cerevisiae IDentifier), to identify the strains present in complex environmental samples. We optimized and assessed the performances of the analytical procedure on patterns generated in silico by computationally pooling Saccharomyces cerevisiae microsatellite profiles, and on samples obtained by pooling DNA of different strains, proving its ability to characterize real samples of grape wine fermentations. SID showed clear differences among S. cerevisiae populations in grape fermentation samples, identifying strains that are likely composing the populations and highlighting the impact of the inoculation of selected exogenous strains on natural strains. This tool can be successfully exploited to identify S. cerevisiae strains in any kind of complex samples.

Bilateral clavicular hypoplasia and cleidocranial dysplasia: Case report

Clavicular hypoplasia or agenesis is common in patients with cleidocranial dysplasia (CCD). CCD is an uncommon congenital pathology with an autosomal dominant pattern affecting males and females equally. CCD presents with wide phenotypic variability, but there is no stable link between the genotype and phenotype. In addition to clavicular hypoplasia/agenesis, such patients present with thoracic deformities, iliac hypoplasia, cranial bone deformities, and delayed dentition. An early diagnosis is important to determine treatment options. However, there is no specific orthopedic treatment for this disease.

Early Onset Scoliosis within the 22q11.2 Deletion Syndrome (22q11.2DS)

22q11.2DS is the most common microdeletion syndrome. It is characterized by a wide phenotypic variability, including scoliosis. This is the first epidemiological study that shows that the prevalence of early onset scoliosis within this vulnerable group of patients is around 40%. A congenital heart defect (CHD) irrespective of surgery was an independent risk factor, with an Odd's Ratio of 12.09.

Multi-layered mutation in hedgehog-related genes in Gorlin syndrome may affect the phenotype.

Gorlin syndrome is a genetic disorder of autosomal dominant inheritance that predisposes the affected individual to a variety of disorders that are attributed largely to heterozygous germline patched1 (PTCH1) mutations. PTCH1 is a hedgehog (Hh) receptor as well as a repressor, mutation of which leads to constitutive activation of Hh pathway. Hh pathway encompasses a wide variety of cellular signaling cascades, which involve several molecules; however, no associated genotype–phenotype correlations have been reported. Recently, mutations in Suppressor of fused homolog (SUFU) or PTCH2 were reported in patients with Gorlin syndrome. These facts suggest that multi-layered mutations in Hh pathway may contribute to the development of Gorlin syndrome. We demonstrated multiple mutations of Hh-related genes in addition to PTCH1, which possibly act in an additive or multiplicative manner and lead to Gorlin syndrome. High-throughput sequencing was performed to analyze exome sequences in four unrelated Gorlin syndrome patient genomes. Mutations in PTCH1 gene were detected in all four patients. Specific nucleotide variations or frameshift variations of PTCH1 were identified along with the inferred amino acid changes in all patients. We further filtered 84 different genes which are closely related to Hh signaling. Fifty three of these had enough coverage of over ×30. The sequencing results were filtered and compared to reduce the number of sequence variants identified in each of the affected individuals. We discovered three genes, PTCH2, BOC, and WNT9b, with mutations with a predicted functional impact assessed by MutationTaster2 or PolyPhen-2 (Polymorphism Phenotyping v2) analysis. It is noticeable that PTCH2 and BOC are Hh receptor molecules. No significant mutations were observed in SUFU. Multi-layered mutations in Hh pathway may change the activation level of the Hh signals, which may explain the wide phenotypic variability of Gorlin syndrome.

Testing the face shape hypothesis in twins discordant for nonsyndromic orofacial clefting.

Nonsyndromic orofacial clefts (OFCs) are complex traits characterized by multifactorial inheritance and wide phenotypic variability. Numerous studies have shown subtle differences in the faces of unaffected relatives from cleft families compared to controls, the implication being that such outward differences are an incomplete expression reflecting an underlying genetic predisposition. Twins discordant for OFCs provide a unique opportunity to further test this idea, as the unaffected co-twin shares on average 50% (for dizygotic twins) and 100% (for monozygotic twins) of the genetic risk factors as the affected twin. We used 3D surface imaging and spatially-dense morphometry to compare facial shape in a sample of 44 unaffected co-twins and age- and sex-matched unaffected controls (n = 241). Unaffected co-twins showed statistically significant differences in the midface, lateral upper face, and forehead regions, compared to controls. Furthermore, co-twins were characterized by a distinct pattern of midfacial retrusion, broader upper faces, and greater protrusion of the mandible and brow ridges. This same general facial pattern was shown in both unaffected monozygotic and dizygotic co-twin subsets. These results provide additional support that altered facial shape is a phenotypic marker for OFC susceptibility.

The study of flavonolignan association patterns in fruits of diverging Silybum marianum (L.) Gaertn. chemotypes provides new insights into the silymarin biosynthetic pathway

Silymarin is the phytochemical with medicinal properties extracted from Silybum marianum (L.) Gaertn. fruits. Yet, little information is available about silymarin biosynthesis. Moreover, the generally accepted pathway, formulated thus far, is not in agreement with actual experimental measurements on flavonolignan contents. The present work analyses flavonolignan and taxifolin content in 201 S. marianum samples taking into consideration a wide phenotypic variability. Two stable chemotypes were identified: one characterized by both high silychristin and silybin content (chemotype A) and another by a high silydianin content (chemotype B). Through the correlation analysis of samples divided according to chemotype, it was possible to construct a simplified silymarin biosynthetic pathway that is sufficiently versatile in explaining experimental results responding to the actually unresolved questions about this process. The proposed pathway highlights that three separate and equally sized metabolite pools exist, namely: diastereoisomers A (silybin A plus isosilybin A), diastereoisomers B (silybin B plus isosilybin B) and silychristin. In both A and B diastereoisomers pools, isosilybin A and isosilybin B always represent a given amount of the metabolite flux through the specific metabolite pool suggesting the possible involvement of dirigent protein-like enzymes. We suggest that chemotype B possesses a complete silymarin biosynthetic pathway in which silydianin biosynthesis is enzymatically controlled. On the contrary, chemotype A is probably a natural mutant unable to biosynthesize silydianin. The present simplified pathway for silymarin biosynthesis will constitute an important tool for the further understanding of the reactions that drive flavonolignan biosynthesis in S. marianum.

The Lepidopteran Herbivores of the Model PlantMimulus guttatus

Mimulus guttatus is a widespread riparian plant native to western North America. Due to its wide distribution and phenotypic variation it has been the subject of many studies incorporating genetic information into ecological and life history evolution studies. Mimulus guttatus defends itself from herbivory with physical defenses (e.g. trichomes) as well as a suite of phytochemical defenses; phenylpropanoid glycosides (PPGs). Despite its importance as a model organism little has been done on the herbivores that feed on this plant. We used literature records as well as field observations to construct a list of the Lepidoptera that utilize M. guttatus as a food plant. Sixteen species of Lepidoptera within five families were recorded as feeding on M. guttatus. Six of these species are classified as generalist herbivores, while the rest have varying degrees of host plant specialization.

The antioxidant potential of dominant macroalgae species from the Sea of Japan

The range of variation in the key components of enzymatic and low-molecular-weight antioxidant systems (AOSs) is determined for 17 dominant species of macroalgae from the Sea of Japan waters that are exposed to minimal anthropogenic pressure, during the period of their active vegetative growth. The maximum activity of superoxide dismutase, glutathione reductase, ascorbate peroxidase, and the highest content of glutathione and carotenoids are observed in members of the phylum Chlorophyta. The studied algae display a wide phenotypic variability in terms of catalase activity and ascorbate abundance in their tissues. Differences between species in the constitutive capacity of AOS are found within the systematic phyla. It is shown for the first time that warm-water algae of temperate latitudes have a lower content of low-molecular-weight antioxidants and a higher activity of key antioxidant enzymes compared to those recorded for cold-temperate species.

Long-lasting response to oral therapy in a young male with monogenic diabetes as part of HNF1B-related disease.

Mutations in hepatocyte nuclear factor 1β gene (HNF1B) are responsible for a multisystemic syndrome where monogenic diabetes (classically known as MODY 5) and renal anomalies, mostly cysts, are the most characteristic findings. Urogenital malformations, altered liver function tests, hypomagnesemia or hyperuricemia and gout are also part of the syndrome. Diabetes in these patients usually requires early insulinization. We present the case of a young non-obese male patient with a personal history of renal multicystic dysplasia and a debut of diabetes during adolescence with simple hyperglycemia, negative pancreatic autoimmunity and detectable C-peptide levels. He also presented epididymal and seminal vesicle cysts, hypertransaminasemia, hyperuricemia and low magnesium levels. In the light of these facts we considered the possibility of a HNF1B mutation. The sequencing study of this gene confirmed a heterozygous mutation leading to a truncated and less functional protein. Genetic studies of his relatives were negative; consequently, it was classified as a de novo mutation. In particular, our patient maintained good control of his diabetes on oral antidiabetic agents for a long period of time. He eventually needed insulinization although oral therapy was continued alongside, allowing reduction of prandial insulin requirements. The real prevalence of mutations in HNF1B is probably underestimated owing to a wide phenotypical variability. As endocrinologists, we should consider this possibility in young non-obese diabetic patients with a history of chronic non-diabetic nephropathy, especially in the presence of some of the other characteristic manifestations.Learning points:HNF1B mutations are a rare cause of monogenic diabetes, often being a part of a multisystemic syndrome.The combination of young-onset diabetes and genitourinary anomalies with slowly progressive nephropathy of non-diabetic origin in non-obese subjects should rise the suspicion of such occurrence. A family history may not be present.Once diagnosis is made, treatment of diabetes with oral agents is worth trying, since the response can be sustained for a longer period than the one usually described. Oral treatment can help postpone insulinization and, once this is necessary, can help reduce the required doses.

The Sirenomelia Sequence: a Case Report

Sirenomelia or mermaid syndrome is a rare congenital condition with a wide phenotypic variation . It was originally named as caudal regression syndrome but it is now known that organs do not regress, they just do not form. An abnormal abdominal and umbilical vascular arrangement of affected individuals, and a primary abnormality in the generation of the mesoderm are two theories suggested for its genesis. Affected individuals show hypoplastic and fused lower limbs, vertebral abnormalities, and agenesis of the renal system, imperforated anus, and genital organs anomalies. Antenatal diagnosis in the first trimester is critical. We report a case of the mermaid syndrome associated with severe oligohydramnios, Potter’s facies, unilateral renal agenesis, and absent external genitalia.

Inter-familial and intra-familial phenotypic variability in three Sicilian families with Anderson-Fabry disease.

BackgroundAnderson-Fabry disease (AFD) is an inborn lysosomal enzymopathy resulting from the deficient or absent activity of the lysosomal exogalactohydrolase, α-galactosidase A. This deficiency, results in the altered metabolism of glycosphingolipids which leads to their accumulation in lysosomes, thus to cellular and vascular dysfunction. To date, numerous mutations (according to recent data more than 1000 mutations) have been reported in the GLA intronic and exonic mutations. Traditionally, clinical manifestations are more severe in affected hemizygous males than in females. Nevertheless, recent studies have described severe organ dysfunction in women.The aim of the studyThis study reports clinical, biochemical, and molecular findings of the members of three Sicilian families. The clinical history of these patients highlights a remarkable interfamilial and intrafamilial phenotypic variability which characterizes Fabry disease relative to target organs and severity of clinical manifestations.DiscussionOur findings, in agreement with previous data, report a little genotype-phenotype correlation for the disease, suggesting that the wide phenotypic variability of Anderson-Fabry disease is not completely ascribable to different gene mutations but other factors and mechanisms seem to be involved in the pathogenesis and clinical expression of the disease. Moreover, this study emphasies the importance of pedigree analysis in the family of each proband for identifying other possibly affected relatives.

Cognitive reserve and TMEM106B genotype modulate brain damage in presymptomatic frontotemporal dementia: a GENFI study.

Frontotemporal dementia is a heterogeneous neurodegenerative disorder with around a third of cases having autosomal dominant inheritance. There is wide variability in phenotype even within affected families, raising questions about the determinants of the progression of disease and age at onset. It has been recently demonstrated that cognitive reserve, as measured by years of formal schooling, can counteract the ongoing pathological process. The TMEM106B genotype has also been found to be a modifier of the age at disease onset in frontotemporal dementia patients with TDP-43 pathology. This study therefore aimed to elucidate the modulating effect of environment (i.e. cognitive reserve as measured by educational attainment) and genetic background (i.e. TMEM106B polymorphism, rs1990622 T/C) on grey matter volume in a large cohort of presymptomatic subjects bearing frontotemporal dementia-related pathogenic mutations. Two hundred and thirty-one participants from the GENFI study were included: 108 presymptomatic MAPT, GRN, and C9orf72 mutation carriers and 123 non-carriers. For each subject, cortical and subcortical grey matter volumes were generated using a parcellation of the volumetric T1-weighted magnetic resonance imaging brain scan. TMEM106B genotyping was carried out, and years of education recorded. First, we obtained a composite measure of grey matter volume by graph-Laplacian principal component analysis, and then fitted a linear mixed-effect interaction model, considering the role of (i) genetic status; (ii) educational attainment; and (iii) TMEM106B genotype on grey matter volume. The presence of a mutation was associated with a lower grey matter volume (P = 0.002), even in presymptomatic subjects. Education directly affected grey matter volume in all the samples (P = 0.02) with lower education attainment being associated with lower volumes. TMEM106B genotype did not influence grey matter volume directly on its own but in mutation carriers it modulated the slope of the correlation between education and grey matter volume (P = 0.007). Together, these results indicate that brain atrophy in presymptomatic carriers of common frontotemporal dementia mutations is affected by both genetic and environmental factors such that TMEM106B enhances the benefit of cognitive reserve on brain structure. These findings should be considered in evaluating outcomes in future disease-modifying trials, and support the search for protective mechanisms in people at risk of dementia that might facilitate new therapeutic strategies.

Identifying signatures of positive selection in pigmentation genes in two South Asian populations.

Skin pigmentation is a polygenic trait showing wide phenotypic variations among global populations. While numerous pigmentation genes have been identified to be under positive selection among European and East populations, genes contributing to phenotypic variation in skin pigmentation within and among South Asian populations are still poorly understood. The present study uses data from the Phase 3 of the 1000 genomes project focusing on two South Asian populations-GIH (Gujarati Indian from Houston, Texas) and ITU (Indian Telugu from UK), so as to decode the genetic architecture involved in adaptation to ultraviolet radiation in South Asian populations. Statistical tests included were (1) tests to identify deviations of the Site Frequency Spectrum (SFS) from neutral expectations (Tajima's D, Fay and Wu's H and Fu and Li's D* and F*), (2) tests focused on the identification of high-frequency haplotypes with extended linkage disequilibrium (iHS and Rsb), and (3) tests based on genetic differentiation between populations (LSBL). Twenty-two pigmentation genes fall in the top 1% for at least one statistic in the GIH population, 5 of which (LYST, OCA2, SLC24A5, SLC45A2, and TYR) have been previously associated with normal variation in skin, hair, or eye color. In comparison, 17 genes fall in the top 1% for at least one statistic in the ITU population. Twelve loci which are identified as outliers in the ITU scan were also identified in the GIH population. These results suggest that selection may have affected these loci broadly across the region.

Poor phenotype-genotype association in a large series of patients with Type III Bartter syndrome.

IntroductionType III Bartter syndrome (BS) is an autosomal recessive renal tubule disorder caused by loss-of-function mutations in the CLCNKB gene, which encodes the chloride channel protein ClC-Kb. In this study, we carried out a complete clinical and genetic characterization in a cohort of 30 patients, one of the largest series described. By comparing with other published populations, and considering that 80% of our patients presented the p.Ala204Thr Spanish founder mutation presumably associated with a common phenotype, we aimed to test the hypothesis that allelic differences could explain the wide phenotypic variability observed in patients with type III BS.MethodsClinical data were retrieved from the referral centers. The exon regions and flanking intronic sequences of the CLCNKB gene were screened for mutations by polymerase chain reaction (PCR) followed by direct Sanger sequencing. Presence of gross deletions or duplications in the region was checked for by MLPA and QMPSF analyses.ResultsPolyuria, polydipsia and dehydration were the main common symptoms. Metabolic alkalosis and hypokalemia of renal origin were detected in all patients at diagnosis. Calciuria levels were variable: hypercalciuria was detected in 31% of patients, while 23% had hypocalciuria. Nephrocalcinosis was diagnosed in 20% of the cohort. Two novel CLCNKB mutations were identified: a small homozygous deletion (c.753delG) in one patient and a small deletion (c.1026delC) in another. The latter was present in compound heterozygosis with the already previously described p.Glu442Gly mutation. No phenotypic association was obtained regarding the genotype.ConclusionA poor correlation was found between a specific type of mutation in the CLCNKB gene and type III BS phenotype. Importantly, two CLCNKB mutations not previously described were found in our cohort.