Improved clinical utility of preimplantation genetic testing through the integration of ploidy and common pathogenic microdeletions analyses.

STUDY QUESTION: Can chromosomal abnormalities beyond copy-number aneuploidies (i.e. ploidy level and microdeletions (MDs)) be detected using a preimplantation genetic testing (PGT) platform? SUMMARY ANSWER: The proposed integrated approach accurately assesses ploidy level and the most common pathogenic microdeletions causative of genomic disorders, expanding the clinical utility of PGT. WHAT IS KNOWN ALREADY: Standard methodologies employed in preimplantation genetic testing for aneuploidy (PGT-A) identify chromosomal aneuploidies but cannot determine ploidy level nor the presence of recurrent pathogenic MDs responsible for genomic disorders. Transferring embryos carrying these abnormalities can result in miscarriage, molar pregnancy, and intellectual disabilities and developmental delay in offspring. The development of a testing strategy that integrates their assessment can resolve current limitations and add valuable information regarding the genetic constitution of embryos, which is not evaluated in PGT providing new level of clinical utility and valuable knowledge for further understanding of the genomic causes of implantation failure and early pregnancy loss. To the best of our knowledge, MDs have never been studied in preimplantation human embryos up to date. STUDY DESIGN, SIZE, DURATION: This is a retrospective cohort analysis including blastocyst biopsies collected between February 2018 and November 2021 at multiple collaborating IVF clinics from prospective parents of European ancestry below the age of 45, using autologous gametes and undergoing ICSI for all oocytes. Ploidy level determination was validated using 164 embryonic samples of known ploidy status (147 diploids, 9 triploids, and 8 haploids). Detection of nine common MD syndromes (-4p=Wolf-Hirschhorn, -8q=Langer-Giedion, -1p=1p36 deletion, -22q=DiGeorge, -5p=Cri-du-Chat, -15q=Prader-Willi/Angelman, -11q=Jacobsen, -17p=Smith-Magenis) was developed and tested using 28 positive controls and 97 negative controls. Later, the methodology was blindly applied in the analysis of: (i) 100 two pronuclei (2PN)-derived blastocysts that were previously defined as uniformly euploid by standard PGT-A; (ii) 99 euploid embryos whose transfer resulted in pregnancy loss. PARTICIPANTS/MATERIALS, SETTING, METHODS: The methodology is based on targeted next-generation sequencing of selected polymorphisms across the genome and enriched within critical regions of included MD syndromes. Sequencing data (i.e. allelic frequencies) were analyzed by a probabilistic model which estimated the likelihood of ploidy level and MD presence, accounting for both sequencing noise and population genetics patterns (i.e. linkage disequilibrium, LD, correlations) observed in 2504 whole-genome sequencing data from the 1000 Genome Project database. Analysis of phased parental haplotypes obtained by single-nucleotide polymorphism (SNP)-array genotyping was performed to confirm the presence of MD. MAIN RESULTS AND THE ROLE OF CHANCE: In the analytical validation phase, this strategy showed extremely high accuracy both in ploidy classification (100%, CI: 98.1-100%) and in the identification of six out of eight MDs (99.2%, CI: 98.5-99.8%). To improve MD detection based on loss of heterozygosity (LOH), common haploblocks were analyzed based on haplotype frequency and LOH occurrence in a reference population, thus developing two further mathematical models. As a result, chr1p36 and chr4p16.3 regions were excluded from MD identification due to their poor reliability, whilst a clinical workflow which incorporated parental DNA information was developed to enhance the identification of MDs. During the clinical application phase, one case of triploidy was detected among 2PN-derived blastocysts (i) and one pathogenic MD (-22q11.21) was retrospectively identified among the biopsy specimens of transferred embryos that resulted in miscarriage (ii). For the latter case, family-based analysis revealed the same MD in different sibling embryos (n = 2/5) from non-carrier parents, suggesting the presence of germline mosaicism in the female partner. When embryos are selected for transfer based on their genetic constitution, this strategy can identify embryos with ploidy abnormalities and/or MDs beyond aneuploidies, with an estimated incidence of 1.5% (n = 3/202, 95% CI: 0.5-4.5%) among euploid embryos. LIMITATIONS, REASONS FOR CAUTION: Epidemiological studies will be required to accurately assess the incidence of ploidy alterations and MDs in preimplantation embryos and particularly in euploid miscarriages. Despite the high accuracy of the assay developed, the use of parental DNA to support diagnostic calling can further increase the precision of the assay. WIDER IMPLICATIONS OF THE FINDINGS: This novel assay significantly expands the clinical utility of PGT-A by integrating the most common pathogenic MDs (both de novo and inherited ones) responsible for genomic disorders, which are usually evaluated at a later stage through invasive prenatal testing. From a basic research standpoint, this approach will help to elucidate fundamental biological and clinical questions related to the genetics of implantation failure and pregnancy loss of otherwise euploid embryos. STUDY FUNDING/COMPETING INTEREST(S): No external funding was used for this study. S.C., M.F., F.C., P.Z., I.P., L.G., C.P., M.P., D.B., J.J.-A., D.B.-J., J.M.-V., and C.R. are employees of Igenomix and C.S. is the head of the scientific board of Igenomix. A.C. and L.P. are employees of JUNO GENETICS. Igenomix and JUNO GENETICS are companies providing reproductive genetic services. TRIAL REGISTRATION NUMBER: N/A.

Measurement of the Positive Muon Anomalous Magnetic Moment to 0.46 ppm.

We present the first results of the Fermilab National Accelerator Laboratory (FNAL) Muon g-2 Experiment for the positive muon magnetic anomaly a_{µ}≡(g_{µ}-2)/2. The anomaly is determined from the precision measurements of two angular frequencies. Intensity variation of high-energy positrons from muon decays directly encodes the difference frequency ω_{a} between the spin-precession and cyclotron frequencies for polarized muons in a magnetic storage ring. The storage ring magnetic field is measured using nuclear magnetic resonance probes calibrated in terms of the equivalent proton spin precession frequency ω[over ˜]_{p}^{'} in a spherical water sample at 34.7 °C. The ratio ω_{a}/ω[over ˜]_{p}^{'}, together with known fundamental constants, determines a_{µ}(FNAL)=116 592 040(54)×10^{-11} (0.46 ppm). The result is 3.3 standard deviations greater than the standard model prediction and is in excellent agreement with the previous Brookhaven National Laboratory (BNL) E821 measurement. After combination with previous measurements of both µ^{+} and µ^{-}, the new experimental average of a_{µ}(Exp)=116 592 061(41)×10^{-11} (0.35 ppm) increases the tension between experiment and theory to 4.2 standard deviations.

Influence of variable salinity and low light on copper accumulation in the potential seagrass bioindicator, Zostera muelleri.

Utilising a potential coastal trace element bioindicator requires understanding its accumulation patterns under varying environmental scenarios. The present study aimed to understand, from two experiments, the influence and effect of low light (15.3 µmol photons m-2 s-1) and variable salinity (normal 36 and reduced 29) on Zostera muelleri accumulating variable Cu concentrations (control, low 5 µg L-1 and high 50 µg L-1) in order to determine its capability as a potential trace element bioindicator. Initial (24 h) leaf Cu concentration was in proportion to exposure Cu concentrations, irrespective of manipulated environmental conditions, suggesting passive accumulation. Final below-ground Cu concentrations, during the low light experiment, significantly increased over time, suggesting active Cu accumulation. Zostera muelleri leaves could act as a Cu bioindicator at times of reduced light and salinity while further interpretation is required of below-ground Cu concentrations. It is recommended that Z. muelleri could be utilised as a Cu bioindicator.

Aip regulates cAMP signalling and GH secretion in GH3 cells.

Mutations in the aryl hydrocarbon receptor-interacting protein (AIP) gene have been linked to predisposition to pituitary adenomas. However, the mechanism by which this occurs remains unknown. AIP interacts with a number of interesting proteins, including members of the cAMP signalling pathway that has been shown to be consistently altered in pituitary tumours. The functional role of Aip was investigated using both over-expression and knock down of Aip in GH3 cells. cAMP signalling and its downstream effectors, including GH secretion, were then investigated. cAMP signalling was analysed using cAMP assays, cAMP-response element-promoter luciferase reporter assays, real-time PCR and finally secreted GH quantification. Over-expression of wild-type (WT)-Aip reduced forskolin-induced cAMP signalling at the total cAMP level, luciferase reporter activity and target gene expression, when compared with empty vector and the non-functional R304X mutant. Additionally, GH secretion was reduced in WT-Aip over-expressing GH3 cells treated with forskolin. Knock down of endogenous Aip resulted in increased cAMP signalling but a decrease in GH secretion was also noted. Inhibition of phosphodiesterase activity using general and selective inhibitors did not completely ablate the effect of Aip on forskolin-augmented cAMP signalling. A mechanism by which Aip acts as a tumour suppressor, by maintaining a low cAMP signalling and concentration, is suggested. Mutations of Aip render the protein incapable of such activity. This effect appears not to be mediated by the AIP-PDE interaction, suggesting the involvement of other interacting partners in mediating this outcome.

Frequency of the CCR5-Delta32 polymorphism in the Maltese population at birth.

In this study, the frequency of the CCR5-Delta32 polymorphism was estimated in the human population of Malta. The frequency of the CCR5-Delta32 allele was found to be 1.1% which was similar to that of other island populations, and agree with the north to south gradient observed across Europe.

No effects of a synonymous variant within the CD59 gene on its protein product in duodenal biopsies of coeliac individuals.

A novel rare variant within the CD59 gene was linked with coeliac disease in a family with high incidence of disease. Functional analyses of this variant were performed using complementary DNA analysis and protein analysis in paraffin-embedded duodenal biopsies from affected individuals and controls. No effects on pre-mRNA or size of linear protein were observed, although these results do not exclude the possible effects of this variant on co-translational protein folding.

Variants within protectin (CD59) and CD44 genes linked to an inherited haplotype in a family with coeliac disease.

Coeliac disease (CD) is an autoimmune disorder characterised by inflammation, villous atrophy and hyperplasia of the small intestinal mucosa that affects genetically susceptible individuals. A genome-wide scan was performed in 17 family members with high incidence of CD. Highest nonparametric linkage (NPL) and logarithm of odds (LOD) scores were of 6.21 (P = 0.0107) and 2.57, respectively, to a region on chromosome 11p13-12. Following fine mapping, NPL and LOD scores did not change, but the linkage interval on chromosome 11 was narrowed to a region that is approximately 50.94 cM from pTer. Two inherited haplotypes on chromosomes 11p13-12 and 9q21 were observed in all affected members but not in the majority of clinically normal individuals. Sequencing of genes at region 11p13-12 showed a number of sequence variants, two of which were linked with the inherited haplotype. One of these variants in the CD59 gene was found at a very low frequency in the population and could possibly affect pre-messenger RNA splicing. This study is of particular importance for the identification of novel genes that might be responsible for CD other than human leukocyte antigen.

Decolorization and detoxication of reactive industrial dyes by immobilized fungi Trametes pubescens and Pleurotus ostreatus.

Trametes pubescens and Pleurotus ostreatus, immobilized on polyurethane foam cubes in bioreactors, were used to decolorize three industrial and model dyes at concentrations of 200, 1000 and 2000 ppm. Five sequential cycles were run for each dye and fungus. The activity of laccase, Mn-dependent and independent peroxidases, lignin peroxidase, and aryl-alcohol oxidase were daily monitored during the cycles and the toxicity of media containing 1000 and 2000 ppm of each dye was assessed by the Lemna minor (duckweed) ecotoxicity test. Both fungi were able to efficiently decolorize all dyes even at the highest concentration, and the duckweed test showed a significant reduction (p < or = 0.05) of the toxicity after the decolorization treatment. T. pubescens enzyme activities varied greatly and no clear correlation between decolorization and enzyme activity was observed, while P. ostreatus showed constantly a high laccase activity during decolorization cycles. T. pubescens showed better decolorization and detoxication capability (compared to the better known P. ostreatus). As wide differences in enzyme activity of the individual strains were observed, the strong decolorization obtained with the two fungi suggested that different dye decolorization mechanisms might be involved.

TNFRSF11B gene variants and bone mineral density in postmenopausal women in Malta.

UNLABELLED: A number of polymorphisms in various genes have been identified and associated with bone mineral density (BMD) and with an increased risk of osteoporosis. OBJECTIVE: In this study, three single nucleotide polymorphisms (SNPs) within the TNFRSF11B gene were studied for association with an increased risk of osteoporosis in postmenopausal Maltese women (n=126). METHODOLOGY: Analysis was performed by PCR restriction fragment length polymorphism (RFLP) while BMD at the lumbar spine, femoral neck, Ward's triangle and trochanter was measured by DEXA. RESULTS: No significant association was observed between genotypes and BMD for all polymorphisms studied within this gene. Homozygotes CC (T(950)-C) were observed to have the highest BMD at all anatomical sites although statistical significance was not reached when comparing the three genotypes. A statistical significant difference was observed in the distribution of genotype frequencies for this polymorphism between normal individuals and those that were either osteopenic or osteoporotic at one or both anatomical sites, with the TT genotype associated more frequently with low BMD. The T(950)-C and G(1181)-C polymorphisms were in strong linkage disequilibrium with each other but not with the A(163)-G polymorphism further upstream in the OPG promoter. Statistical significance was reached when constructing haplotypes, where the A-T-G haplotype was found to be more frequent in individuals with low BMD. CONCLUSIONS: These results indicate the possible role of TNFRSF11B gene variants in postmenopausal bone loss in women in Malta.

Use of foot-to-foot bioelectrical impedance analysis in children.

The aim of this study was to compare two methods of measuring body composition in children aged 6-10 years: with a traditional bioelectrical impedance analyser and a foot-to-foot impedance device. In 117 subjects (55 girls, 62 boys), bioelectrical impedance was measured using a Xitron 4000 device and a foot-to-foot impedance instrument (Rowenta); body fat mass and fat-free mass were then calculated and comparisons between means were performed using appropriate statistical tests.

Associations of polymorphisms in the vitamin D receptor gene (BsmI and FokI) with bone mineral density in postmenopausal women in Malta.

Previous studies have suggested that variations in the vitamin D receptor (VDR) gene are related to bone mineral density (BMD). In this study, the T-->C transition in the start codon and the G-->A polymorphism at the 3' end of the VDR gene, identified by endonucleases FokI and BsmI, respectively, were analysed and correlated with BMD in postmenopausal Maltese women ( n=104). Genotype frequencies observed for the VDR start codon polymorphism (SCP) were CC: 60.4%; CT: 30.7% and TT: 8.9%, while those observed for the 3' in this study were GG: 16.4%; GA: 51.9%; AA: 31.7%. In postmenopausal women, both lumbar and femoral BMD were observed to be highest in CC homozygotes for the FokI genotype and in GG homozygotes for the BsmI genotype, although in both groups the difference between the genotypes was not statistically significant, even after adjusting BMD for age, BMI and years since menopause. No evidence of linkage disequilibrium between the two alleles was observed.

Novel antitenascin antibody with increased tumour localisation for Pretargeted Antibody-Guided RadioImmunoTherapy (PAGRIT).

The Pretargeted Antibody-Guided RadioImmunoTherapy (PAGRIT) method is based on intravenous, sequential administration of a biotinylated antibody, avidin/streptavidin and (90)Y-labelled biotin. The hybridoma clone producing the monoclonal antitenascin antibody BC4, previously used for clinical applications, was found not suitable for further development because of the production of an additional, nonfunctional light chain. In order to solve this problem, the new cST2146 hybridoma clone was generated. The monoclonal antibody ST2146, produced by this hybridoma, having the same specificity as BC4 but lacking the nonfunctional light chain, was characterised. ST2146 was found able to bind human tenascin at an epitope strictly related, if not identical, to the antigenic epitope of BC4. It showed, compared to BC4, higher affinity and immunoreactivity and similar selectivity by immunohistochemistry. Biodistribution studies of biotinylated ST2146 and three other monoclonal antitenascin antibodies showed for ST2146 the highest and more specific tumour localisation in HT29-grafted nude mice. On the overall, ST2146 appears to be a good alternative to BC4 for further clinical development of PAGRIT.

Laparoscopic gastric resections.

The impressive breakthrough in laparoscopic surgery has pushed surgeons to perform gastric resection through such an approach. Laparoscopy reduces the surgical stress and the postoperative pain and has a positive impact on the rehabilitation time, the hospital stay, and return to work and social activities. Laparoscopic partial gastrectomy for benign diseases and for palliation has been accepted as an effective surgical option: they are reproducible operations performed worldwide at a more and more rapid pace. Laparoscopic gastric resections and laparoscopically assisted gastric resections for malignancy deserve a word of caution. Nevertheless, the investigators report their series of laparoscopic subtotal and distal gastrectomies for cancer with medium and long-term results comparable with those of open surgery. Furthermore, new and less invasive surgical options have been recently introduced. Full and partial thickness local resections may be accomplished through intragastric procedures, for treatment of small benign tumors and early stage gastric cancer.

Pyridinium crosslinks excretion in patients with rheumatoid arthritis. Correlation with disease activity and glucocorticoid treatment.

In patients with rheumatoid arthritis, significant positive correlations were found between urinary pyridinium crosslinks and C-reactive protein (CRP), erythrocyte sedimentation rate (ESR) and articular index. Also an inverse correlation was observed between pyridinium crosslinks excretion and grip strength. Glucocorticoid therapy, equivalent to daily doses of 7.5 mg of prednisolone or less, did not appear to have deleterious effect on bone metabolism in these patients as measured by urinary pyridinium crosslinks.

Aerobiological analysis in a salami factory: a possible case of extrinsic allergic alveolitis by Penicillium camembertii.

A 39-year-old man was hospitalized with a history of fatigue, dyspnoea and low grade fever which seemed to be related to his working environment. The patient was employed in a salami factory, working near the area where the salami are seasoned with fungal inocula. Chest X-ray showed diffuse initial changes of reticulonodular pattern that disappeared after a brief course of steroids therapy. Precipitating antibodies to Penicillium notatum and Aspergillus fumigatus were found both in plasma and bronchoalveolar lavage fluid. This, together with the finding of a lymphocytic alveolitis with CD4+ depletion and CD8+ increase, suggested the possibility of extrinsic allergic alveolitis of fungal aetiology. Qualitative and quantitative monitoring with an impinger of both the working and outside environment for aerial fungal concentration demonstrated a very high level of contamination (up to 1.14x10(9) fungal propagules m-3 of air) and an inside/outside ratio from 21 to about 2000. Penicillium camembertii was the most common species found in all the indoor sites (60-100% of the fungal load). The patient's BALF and serum both displayed precipitating antibodies to P. camembertii from the powder used for the inoculum and the air samples. These results together with the patient's working history gave some evidence of relationship between the indoor P. camembertii concentration and the patient's symptoms.

Production and characterisation of a recombinant single-chain anti ErbB2-clavin immunotoxin.

We generated a recombinant immunotoxin, named scFv(MGR6)-Cla, composed of the Fv region of an anti ErbB2 monoclonal antibody (MGR6) fused to clavin, a type 1 ribosome-inactivating protein (RIP) from Aspergillus clavatus. ErbB2 is a tyrosine kinase receptor which is overexpressed in most adenocarcinomas; clavin is a 17 kDa ribonuclease which inhibits protein synthesis by inactivating ribosomes. A recombinant DNA construct containing the cDNA of the single chain Fv fragment (scFv) of the MGR6 antibody fused to the clavin cDNA, was expressed at high levels in Escherichia coli as an insoluble fusion protein containing an N-terminal affinity tag of six consecutive histidine residues. Inclusion bodies were denatured and the recombinant fusion protein was purified under denaturing conditions by single-step purification using immobilised metal ion affinity chromatography (IMAC). The purified immunotoxin was renatured at high yield and histidine tag removed by digestion with enterokinase. The purity of the immunotoxin obtained after refolding was confirmed by SDS-PAGE, RP-HPLC, GPC-HPLC and N-terminal sequence analysis. Cell-free protein synthesis inhibition and binding assays showed that both clavin and scFv(MGR6) maintained their properties after refolding.

Restorative proctocolectomy or rectum-preserving surgery in patients with familial adenomatous polyposis: results of a prospective study.

Surgical treatment of familial adenomatous polyposis (FAP) is still controversial. From 1984 we carried out a prospective evaluation of total colectomy with ileorectal anastomosis (IRA) and restorative proctocolectomy with ileal pouch-anal anastomosis (IPAA) to determine differences in postoperative complications, functional results, occurrence of desmoids, and recurrence of polyps in the rectal stump. IRA was performed below the peritoneal reflection and was indicated in the absence of rectal cancer and in the presence of fewer than 10 polyps or minute polyposis in the last 10 cm of the rectal mucosa. IRA patients underwent a regular endoscopic follow-up and prolonged sulindac administration (100 mg twice daily). When criteria for IRA were absent, IPAA was performed adopting a manual anastomosis at the pectinate line. Fourteen patients were operated with IRA and 24 with IPAA. There was no difference in sex and age between the two groups of patients. The number of rectal polyps was significantly different in the two groups. Immediate postoperative complications were observed in only five IPAA patients, three of whom (12%) required reoperation. Late postoperative complications occurred more frequently in IRA patients (14%) than in IPAA patients (4%). Desmoids developed in both groups (five in the IRA group and four in IPAA group). The number of bowel movements was similar in both groups, but 25% of IPAA patients complained of nocturnal fecal soiling. Fulguration or polypectomy for recurrent polyps was necessary in all but two IRA patients at follow-up. The rectal stump was easily eradicated by polyps in all but four patients with minute polyps at surgery. In the latter patients a diffuse or carpeting rectal polyposis occurred. IPAA can give optimum control of colorectal polyposis in FAP patients with an acceptable incidence of postoperative complications and satisfactory functional results. This type of surgical procedure is indicated in most FAP patients, and IRA should be reserved for patients without polyps or with fewer than 10 polyps in the rectal stump; otherwise growth of polyps cannot be adequately controlled.

Aberrant crypt foci in human colon carcinogenesis.

We developed a procedure for the endoscopic visualization in humans of aberrant crypt foci (ACF), preneoplastic lesions of the colon mucosa, and we determined the frequency of ACF in resected sections of human colon. For the endoscopy we studied 12 consenting adults (6 controls and 6 colon cancer cases) by dyeing colon mucosa with 0.5% methylene blue and searching ACF with a magnifying endoscope. ACF of varying dimensions were visualized in all subjects. We also studied colon surgical specimens from patients with colon cancer or diverticulitis. After staining the mucosa with 2% methylene blue, we found approximately the same density of ACF in the colon mucosa of the patients with colon cancer as in that of patients with diverticulitis (ACF/cm2 were 0.124 +/- 0.143 [N = 14] and 0.108 +/- 0.210 [N = 4], respectively [mean +/- SD]). In conclusion, the visualization of ACF with methylene blue in humans does not identify groups at low and high risk of colon cancer.