PIGQ-Related Glycophosphatidylinositol Deficiency Associated with Nonprogressive Congenital Ataxia

The glycophosphatidylinositol (GPI) anchor pathway plays an essential role in posttranslational modification of proteins to facilitate proper membrane anchoring and trafficking to lipid rafts, which is critical for many cell functions, including embryogenesis and neurogenesis. GPI biosynthesis is a multi-step process requiring the activity of over 25 distinct genes, most of them belonging to the phosphatidylinositol glycan (PIG) family and associated with rare neurodevelopmental disorders. PIGQ encodes the phosphatidylinositol glycan class Q protein and is part of the GPI-N-acetylglucosaminyltransferase complex that initiates GPI biosynthesis from phosphatidylinositol (PI) and N-acetylglucosamine (GlcNAc) on the cytoplasmic side of the endoplasmic reticulum (ER). Pathogenic variants in the PIGQ gene have been previously reported in 10 patients with congenital hypotonia, early-infantile epileptic encephalopathy, and premature death occurring in more than half cases. We detected a novel homozygous variant in PIGQ (NM_004204.5: c.1631dupA; p.Tyr544fs*79) by WES trio-analysis of a male patient with a neurodevelopmental disorder characterized by nonprogressive congenital ataxia, intellectual disability, generalized epilepsy, and cerebellar atrophy. Flow cytometry confirmed deficiency of several GPI-anchored proteins on leukocytes (CD14, FLAER). Clinical features of this case broaden the phenotypic spectrum of PIGQ-related GPI deficiency, outlining the importance of glycophosphatidylinositol (GPI) anchor pathway in the pathogenesis of cerebellar ataxia.

Microarray application in prenatal diagnosis: a position statement from the cytogenetics working group of the Italian Society of Human Genetics (SIGU), November 2011

A precise guideline establishing chromosomal microarray analysis (CMA) applications and platforms in the prenatal setting does not exist. The controversial question is whether CMA technologies can or should soon replace standard karyotyping in prenatal diagnostic practice. A review of the recent literature and survey of the knowledge and experience of all members of the Italian Society of Human Genetics (SIGU) Committee were carried out in order to propose recommendations for the use of CMA in prenatal testing. The analysis of datasets reported in the medical literature showed a considerable 6.4% incidence of pathogenic copy number variations (CNVs) in the group of pregnancies with sonographically detected fetal abnormalities and normal karyotype. The reported CNVs are likely to have a relevant role in terms of nosology for the fetus and in the assessment of reproductive risk for the couple. Estimation of the frequency of copy number variations of uncertain significance (VOUS) varied depending on the different CMA platforms used, ranging from 0-4%, obtained using targeted arrays, to 9-12%, obtained using high-resolution whole genome single nucleotide polymorphism (SNP) arrays. CMA analysis can be considered a second-tier diagnostic test to be used after standard karyotyping in selected groups of pregnancies, namely those with single (apparently isolated) or multiple ultrasound fetal abnormalities, those with chromosomal rearrangements, even if apparently balanced, and those with supernumerary marker chromosomes.

Identification of de novo mutations and rare variants in hypoplastic left heart syndrome

Hypoplastic left heart syndrome (HLHS) is one of the most severe congenital heart malformations, characterized by underdevelopment of the structures in the left heart-aorta complex. The majority of cases are sporadic. Although multiple genetic loci have been tentatively implicated in HLHS, no gene or pathway seems to be specifically associated with the disease. To elucidate the genetic basis of HLHS, we analyzed 53 well-characterized patients with isolated HLHS using an integrated genomic approach that combined DNA sequencing of five candidate genes (NKX2-5, NOTCH1, HAND1, FOXC2 and FOXL1) and genome-wide screening by high-resolution array comparative genomic hybridization. In 30 patients, we identified two novel de novo mutations in NOTCH1, 23 rare patients inherited gene variants in NOTCH1, FOXC2 and FOXL1, and 33 rare patients mostly inherited copy-number variants. Some of the identified variations coexisted in the same patient. The biological significance of such rare variations is unknown, but our findings strengthen the role of NOTCH pathway in cardiac valve development, indicating that HLHS is, at least in part, a 'valve' disease. This is the first report of de novo mutations associated with isolated HLHS. Moreover, the coexistence of multiple rare variants suggests in some cases a cumulative effect, as shown for other complex disease.

Olfactory Receptor-Related Duplicons Mediate a Microdeletion at 11q13.2q13.4 Associated with a Syndromic Phenotype

By array-CGH, we identified a cryptic deletion of about 3.4 Mb involving the chromosomal region 11q13.2q13.4 in a child with speech and developmental delay. Highly homologous segmental duplications related to the well-known olfactory receptor (OR)-containing clusters at 8p and 4p are located at the breakpoints of the imbalance and may be involved in its occurrence. Although these structural features are known to promote recurrent chromosomal rearrangements and previous studies had included the 11q13.2q13.4 deletion region among those considered potentially more unstable, neither deletions nor duplications of this region had been reported until now. Among the deleted genes, SHANK2 might play a role in the phenotype of the patient since it encodes a postsynaptic scaffolding protein similar to SHANK3, whose haploinsufficiency is a well-known cause of severe speech delay and autistic-like behavior, and recently deletions and mutations of SHANK2 have been described in patients with an autistic spectrum disorder or mental retardation.

Inverted duplications deletions: underdiagnosed rearrangements??

Molecular techniques led to the discovery that several chromosome rearrangements interpreted as terminal duplications were in fact inverted duplications contiguous to terminal deletions. Inv dup del rearrangements originate through a symmetric dicentric chromosome that, after asymmetric breakage, generates an inv dup del and a deleted chromosome. In recurrent inverted duplications the dicentric chromosome is formed at meiosis through non-allelic homologous recombination. In non-recurrent inv dup del cases, dicentric intermediates are formed by non-homologous end joining or intrastrand annealing. Some authors hypothesized that in these cases the dicentric may have been formed directly in the zygote. Healing of the broken dicentric chromosomes can occur not only in a telomerase-dependent way but also through telomere capture and circularization thus creating translocated or ring inv dup del chromosomes. In all the cases reported up to now, the duplicated region was always longer than the deleted one, but we can safely assume that there is another group of rearrangements where the deleted region is longer than the duplicated portion. In general, in these cases, the cytogeneticist will suspect the presence of a deletion and confirm it by FISH with a subtelomeric probe, but he/she will almost certainly miss the duplication. It is likely that the conventional analysis techniques used until now have led to a substantial underestimate of the frequency of inv dup del rearrangements and that the widespread use of array-CGH in routine analysis will allow a more realistic estimate. Obviously, the concomitant presence of deletion and duplication has important consequences in genotype/phenotype correlations.

Clinical and molecular delineation of the 17q21.31 microdeletion syndrome

BACKGROUND

The chromosome 17q21.31 microdeletion syndrome is a novel genomic disorder that has originally been identified using high resolution genome analyses in patients with unexplained mental retardation.

AIM

We report the molecular and/or clinical characterisation of 22 individuals with the 17q21.31 microdeletion syndrome.

RESULTS

We estimate the prevalence of the syndrome to be 1 in 16,000 and show that it is highly underdiagnosed. Extensive clinical examination reveals that developmental delay, hypotonia, facial dysmorphisms including a long face, a tubular or pear-shaped nose and a bulbous nasal tip, and a friendly/amiable behaviour are the most characteristic features. Other clinically important features include epilepsy, heart defects and kidney/urologic anomalies. Using high resolution oligonucleotide arrays we narrow the 17q21.31 critical region to a 424 kb genomic segment (chr17: 41046729-41470954, hg17) encompassing at least six genes, among which is the gene encoding microtubule associated protein tau (MAPT). Mutation screening of MAPT in 122 individuals with a phenotype suggestive of 17q21.31 deletion carriers, but who do not carry the recurrent deletion, failed to identify any disease associated variants. In five deletion carriers we identify a <500 bp rearrangement hotspot at the proximal breakpoint contained within an L2 LINE motif and show that in every case examined the parent originating the deletion carries a common 900 kb 17q21.31 inversion polymorphism, indicating that this inversion is a necessary factor for deletion to occur (p<10(-5)).

CONCLUSION

Our data establish the 17q21.31 microdeletion syndrome as a clinically and molecularly well recognisable genomic disorder.

Cryptic deletions are a common finding in "balanced" reciprocal and complex chromosome rearrangements: a study of 59 patients

Using array comparative genome hybridisation (CGH) 41 de novo reciprocal translocations and 18 de novo complex chromosome rearrangements (CCRs) were screened. All cases had been interpreted as "balanced" by conventional cytogenetics. In all, 27 cases of reciprocal translocations were detected in patients with an abnormal phenotype, and after array CGH analysis, 11 were found to be unbalanced. Thus 40% (11 of 27) of patients with a "chromosomal phenotype" and an apparently balanced translocation were in fact unbalanced, and 18% (5 of 27) of the reciprocal translocations were instead complex rearrangements with >3 breakpoints. Fourteen fetuses with de novo, apparently balanced translocations, all but two with normal ultrasound findings, were also analysed and all were found to be normal using array CGH. Thirteen CCRs were detected in patients with abnormal phenotypes, two in women who had experienced repeated spontaneous abortions and three in fetuses. Sixteen patients were found to have unbalanced mutations, with up to 4 deletions. These results suggest that genome-wide array CGH may be advisable in all carriers of "balanced" CCRs. The parental origin of the deletions was investigated in 5 reciprocal translocations and 11 CCRs; all were found to be paternal. Using customized platforms in seven cases of CCRs, the deletion breakpoints were narrowed down to regions of a few hundred base pairs in length. No susceptibility motifs were associated with the imbalances. These results show that the phenotypic abnormalities of apparently balanced de novo CCRs are mainly due to cryptic deletions and that spermatogenesis is more prone to generate multiple chaotic chromosome imbalances and reciprocal translocations than oogenesis.

Duplications in addition to terminal deletions are present in a proportion of ring chromosomes: clues to the mechanisms of formation

BACKGROUND AND METHODS

Ring chromosomes are often associated with abnormal phenotypes because of loss of genomic material at one or both ends. In some cases no deletion has been detected and the abnormal phenotype has been attributed to mitotic ring instability. We investigated 33 different ring chromosomes in patients with phenotypic abnormalities by array based comparative genomic hybridisation (CGH) and fluorescence in situ hybridisation (FISH).

RESULTS

In seven cases we found not only the expected terminal deletion but also a contiguous duplication. FISH analysis in some of these cases demonstrated that the duplication was inverted. Thus these ring chromosomes derived through a classical inv dup del rearrangement consisting of a deletion and an inverted duplication.

DISCUSSION

Inv dup del rearrangements have been reported for several chromosomes, but hardly ever in ring chromosomes. Our findings highlight a new mechanism for the formation of some ring chromosomes and show that inv dup del rearrangements may be stabilised not only through telomere healing and telomere capture but also through circularisation. This type of mechanism must be kept in mind when evaluating possible genotype-phenotype correlations in ring chromosomes since in these cases: (1) the deletion may be larger or smaller than first estimated based on the size of the ring, with a different impact on the phenotype; and (2) the associated duplication will in general cause further phenotypic anomalies and might confuse the genotype-phenotype correlation. Moreover, these findings explain some phenotypic peculiarities which previously were attributed to a wide phenotypic variation or hidden mosaicism related to the instability of the ring.

Contiguous gene deletions involving EFNB1, OPHN1, PJA1 and EDA in patients with craniofrontonasal syndrome

Craniofrontonasal syndrome (CFNS [MIM 304110]) is an X-linked malformation syndrome characterized by craniofrontonasal dysplasia and extracranial manifestations in heterozygous females. In the majority of patients CFNS is caused by mutations in the EFNB1 gene (MIM 300035). We identified three girls with classical CFNS and mild developmental delay harboring de novo deletions of the EFNB1 gene. Applying haplotype analysis, Southern blot hybridization and array-comparative genomic hybridization, deletion of EFNB1 was found to be part of contiguous gene deletions in the patients. In one patient the deletion interval includes the genes for oligophrenin-1 (OPHN1 [MIM 300127]) and praja 1 (PJA1 [MIM 300420]). In the second patient the deletion includes OPHN1, PJA1 and the gene for ectodysplasin A (EDA [MIM 300451]). In the third patient EFNB1 gene deletion may include deletion of regulatory regions 5' of OPHN1. Previously, the OPHN1 gene has been shown to be responsible for recessive X-linked mental retardation. Although it is too early to predict the future cognitive performance of the two infant patients with contiguous gene deletions of OPHN1-EFNB1-PJA1, mild learning disabilities have been recognized in the older, third patient. It is important for genetic counseling to be aware that their male offspring may not only be carriers of CFNS but may also be affected by mental retardation and anhidrotic ectodermal dysplasia.

Inversion polymorphisms and non-contiguous terminal deletions: the cause and the (unpredicted) effect of our genome architecture

Molecular definition at the BAC level of an 8p dicentric chromosome and an 8p deleted chromosome is reported in a patient with two different cell lines. The dicentric, which differed from that generating the recurrent inv dup del(8p) for the location of its break point, originated during the paternal meiosis on the background of the classical 8p23.1 inversion polymorphism. The breakage of this dicentric gave rise to the 8p deleted chromosome which, as a result of the inversion, had two non-contiguous deletions. These findings confirm previous data on 1p distal deletions, showing that at least some of the deletions stem from the breakage of dicentric chromosomes. They suggest that non-contiguous deletions may be frequent among distal deletions. This type of rearrangement can easily be overlooked when two contiguous clones, one absent and the other present by FISH analysis, are taken as boundaries of the deletion break point; in this case only high resolution array-CGH will reveal their real frequency. The definition of such non-contiguous distal deletions is relevant for phenotype/karyotype correlations. There are historical examples of blunders caused by overlooking a second non-contiguous deletion. This paper shows how small scale structural variations, such as common polymorphic inversions, may cause complex rearrangements such as terminal deletions.

[Collaboration between traditional and modern medicines: prospectives of structuring a combined care system for traumatology cases]

The Italian NGO Terra Nuova (TN) is implementing a project with the aim of promoting collaboration between traditional and conventional medicines within orthopedic traumatology in Mali. The study is supporting the project to formulate rightly the proposal of a joint system of managing traumatology cases. It has the purpose of analysing the ability of the two healthcare systems and identifying the training needs of the respective operators in this field, in order to draw interventions that can improve their therapeutic practice. The research uses quantitative and qualitative methods for data collection and is structured in three under-studies. The study points out a great use of the traditional medicine for traumatology cases, a good ability of the traditional care system to manage such cases, even though some aspects need improvements, and a diffused availability of conventional health workers to collaborate with traditional ones, since the former recognise their own incapability in this field. The study suggest that valorizing strengths and emending weakness of both healthcare systems in managing traumatology cases, will allow the TN intervention to structure and test collaboration between the two medicines with effective prospects for public health.

Inhibitory effect of NO-releasing ciprofloxacin (NCX 976) on Mycobacterium tuberculosis survival

Here, we report the antimycobacterial activity of NCX 976, a new molecule obtained adding a NO moiety to the fluoroquinolone ciprofloxacin, on Mycobacterium tuberculosis H37Rv strain, both in a cell-free model and in infected human macrophages. Unlike unaltered ciprofloxacin, NCX976 displayed a marked activity also at low-nanomolar concentrations.

Internal mammary blood supply for ileo-colon interposition in esophagogastroplasty: a case report

We report on a clinical case where microsurgical techniques successfully supported traditional surgery in a wide reconstruction between the oropharynx and small bowel. Several years ago, the patient sustained a severe corrosive injury of the upper digestive tract with subsequent esophageal stricture and stiffening; at that time, an emergency gastrectomy was performed. In this case, the restoration of the defect could not rely on the classic colonic interposition. During the operation the ileo-colic flap, well-fitted for tension-free reconstruction, revealed the foreseen inadequacy of its vascularization based on the sole middle colic vascular pedicle. The blood supply to its proximal part was then increased by microanastomosis between the right internal mammary and ileo-colic vessels. The revascularization ensured the viability of the interposed tissue. Oral intake resumed after 3 weeks; nowadays the patient is able to maintain her ideal weight with adequate nutrition.

[Intravenous versus inhalation anesthetics in anesthesia for bone marrow harvest for transplantation]

It is well known that nitrous oxide and many volatile anaesthetic drugs possess a certain degree of myelodepressive activity. The authors' aim has been to evaluate the degree of proliferative activity after exposure to forane or propofol. Bone marrow samples have been cultured after general anaesthesia induced and maintained by the same agents; cultures have also been performed after samples exposure to forane and propofol. The results have not shown significative differences in the haemopoietic colonies growth of bone marrow harvested from patients underwent intravenous or inhalatory anaesthesia. In vitro study has shown a significative variation of the colonies growth at the forane higher concentration. Intravenous anaesthetic may be safer for bone marrow harvest for transplantation.

[Anesthesiologic management for lower pulmonary lobectomy intervention in patients with heart transplant. A clinical case]

The Authors describe the case of a patient who had undergone human allograft cardiac transplant seven months before inferior pulmonary lobectomy for neoplasia. The pulmonary neoplasia had been revealed by X-rays during the periodic check-up examinations. Because of the high risk of infection following corticosteroid and immunosuppressive therapy, sterile equipment for invasive monitoring and oro-tracheal intubation has been used. The denervated heart presents peculiar haemodynamic and pharmacological aspects that the anaesthetist must pay attention to in the conduction of a general anaesthesia; moreover, arrhythmias are common in the recently transplanted heart. Anaesthesia has been induced and maintained by an association propofol-fentanyl that showed a good cardiocirculatory stability; neither arrhythmias have happened, nor the need for drugs different from those of anaesthesia and resuscitation have occurred.

[Transendoscopic retrograde cholangiography in the diagnosis of primary sclerosing cholangitis. Study of 6 cases]

Primary sclerosing cholangitis (PSC) is a rare disease of unknown etiology characterized by severe chronic inflammation, fibrosis and stenosis of variable length of the extra and/or intrahepatic biliary ducts in the absence of recent operative trauma, biliary stones, cancer or infection. Diagnosis has been made only at operation. The introduction of endoscopic retrograde cholangiography (ERC) offers the possibility of preoperative diagnosis. Six cases of PSC diagnosed by ERC are presented. Characteristic roentgenologic findings include strictures of variable length of extra and intrahepatic biliary ducts, beaded appearance and decreased arborization of intrahepatic biliary tree. The roentgenological anatomy of biliary tree at ERC influence the subsequent therapy, i.e. surgical therapy is indicated if a drainage can be performed above the site of the stenosis, while medical therapy (steroids and/or immunosuppressive drugs) is the choice when intrahepatic biliary tree is involved.

[Evaluation of transendoscopic retrograde cholangio-pancreatography in 151 jaundiced patients]

Endoscopic retrograde cholangiopancreatography was performed for possible obstruction of the extra-hepatic bile ducts in 151 patients with jaundice. The endoscope findings (9 cases) and the retrograde cholangiopancreatogram (127 cases) provided a final diagnosis in 131 cases. A correct surgical indication was obtaines in a further 5 cases (90% diagnostic success overall). In 19 cases, unnecessary exploratory laparotomy was avoided by the demonstration of normal extrahepatic ducts. No complications were noted. It is concluded that this technique is virtually free from risks and offers prompt diagnosis in subjects with jaundice. This, of course, has a significant influence on the subsequent treatment.

Can Mirizzi syndrome be classified into acute and chronic form? An endoscopic retrograde cholangiography (ERC) study

Three cases of Mirizzi syndrome (partial mechanical obstruction of the common hepatic duct owing to compression by a stone impacted in the cystic duct or gallbladder neck, or due to the inflammatory reaction resulting from compression) are reported. The roentgen features at endoscopic retrograde cholangiography (ERC) are discussed. As there are two causes for obstruction, compression or chronic fibrosing reaction resulting from compression, two characteristic X-ray findings and two operating techniques, the authors contend that Mirizzi syndrome should be classified as acute or chronic.