Splicing analysis of 24 potential spliceogenic variants in MMR genes and clinical interpretation based on refined ACMG/AMP criteria

Lynch syndrome (LS) is a common hereditary cancer syndrome caused by heterozygous germline pathogenic variants in DNA mismatch repair (MMR) genes. Splicing defect constitutes one of the major mechanisms for MMR gene inactivation. Using RT-PCR based RNA analysis, we investigated 24 potential spliceogenic variants in MMR genes and determined their pathogenicity based on refined splicing-related American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) criteria. Aberrant transcripts were confirmed in 19 variants and 17 of which were classified as pathogenic including 11 located outside of canonical splice sites. Most of these variants were previously reported in LS patients without mRNA splicing assessment. Thus, our study provides crucial evidence for pathogenicity determination, allowing for appropriate clinical follow-up. We also found that computational predictions were globally well correlated with RNA analysis results and the use of both SPiP and SpliceAI software appeared more efficient for splicing defect prediction.

A case of community-acquired spondylodiscitis caused by Achromobacter xylosoxidans

Achromobacter xylosoxidans is a Gram-negative, aerobic, non-fermenting bacillus mainly responsible for nosocomial infections. We report the first case of community-acquired spondylodiscitis caused by Achromobacter xylosoxidans in a 61-year-old woman, immunocompromised with necrotizing dermohypodermitis of the right lower limb successfully treated with ertapenem and ciprofloxacin.

PMS2 or PMS2CL? Characterization of variants detected in the 3' of the PMS2 gene

PMS2 germline pathogenic variants are one of the major causes for Lynch syndrome and constitutional mismatch repair deficiencies. Variant identification in the 3' region of this gene is complicated by the presence of the pseudogene PMS2CL which shares a high sequence homology with PMS2. Consequently, short-fragment screening strategies (NGS, Sanger) may fail to discriminate variant's gene localization. Using a comprehensive analysis strategy, we assessed 42 NGS-detected variants in 76 patients and found 32 localized on PMS2 while 6 on PMS2CL. Interestingly, four variants were detected in either of them in different patients. Clinical phenotype was well correlated to genotype, making it very helpful in variant assessment. Our findings emphasize the necessity of more specific complementary analyses to confirm the gene origin of each variant detected in different individuals in order to avoid variant misinterpretation. In addition, we characterized two PMS2 genomic alterations involving Alu-mediated tandem duplication and gene conversion. Those mechanisms seemed to be particularly favored in PMS2 which contribute to frequent genomic rearrangements in the 3' region of the gene.

From variant of unknown significance to likely pathogenic: Characterization and pathogenicity determination of a large genomic deletion in the MLH1 gene

BACKGROUND

The MLH1 gene is one of the DNA mismatch repair genes (MMR), implicated in Lynch syndrome (LS), an autosomal dominant hereditary tumor susceptibility disease. The advent of next-generation sequencing (NGS) technologies has accelerated the diagnosis of inherited diseases and increased the percentage of diagnosis of inherited cancers. However, some complex genomic alterations require the combination of several analytical strategies to allow correct biological interpretations. Here, we describe a novel MLH1 deletion and its pathogenicity determination in a patient suspected of LS.

METHODS

The index case was a French 73-year-old man diagnosed with colorectal cancer displaying microsatellite instability and the loss of MLH1 and PMS2 expression. NGS analysis was used as the primary method for MMR genes screening. Long-range PCR and reverse transcriptase polymerase chain reaction (RT-PCR) were used for breakpoints and pathogenicity determinations.

RESULTS

A large genomic deletion was detected which removed the last six nucleotides of MLH1 exon 11 together with a large part of intron 11. It was initially considered as a variant of unknown significance (VUS). Genomic breakpoints were subsequently characterized defining the deletion as c.1033_1039-248del. Further RNA analysis demonstrated that this variant activated a cryptic donor splice site at the 5' of the breakpoint, leading to a premature truncated protein: p.Thr345Alafs*13.

CONCLUSION

Our finding suggested that although NGS technologies have increased variant detection yield, combined approaches were still needed for complex variant characterization and pathogenicity assessment.

Overview of the Genetic Causes of Hereditary Breast and Ovarian Cancer Syndrome in a Large French Patient Cohort

The use of multigene panel testing for patients with a predisposition to Hereditary Breast and Ovarian Cancer syndrome (HBOC) is increasing as the identification of mutations is useful for diagnosis and disease management. Here, we conducted a retrospective analysis of BRCA1/2 and non-BRCA gene sequencing in 4630 French HBOC suspected patients. Patients were investigated using a germline cancer panel including the 13 genes defined by The French Genetic and Cancer Group (GGC)-Unicancer. In the patients analyzed, 528 pathogenic and likely pathogenic variants (P/LP) were identified, including BRCA1 (n = 203, 38%), BRCA2 (n = 198, 37%), PALB2 (n = 46, 9%), RAD51C (n = 36, 7%), TP53 (n = 16, 3%), and RAD51D (n = 13, 2%). In addition, 35 novel (P/LP) variants, according to our knowledge, were identified, and double mutations in two distinct genes were found in five patients. Interestingly, retesting a subset of BRCA1/2-negative individuals with an expanded panel produced clinically relevant results in 5% of cases. Additionally, combining in silico (splicing impact prediction tools) and in vitro analyses (RT-PCR and Sanger sequencing) highlighted the deleterious impact of four candidate variants on splicing and translation. Our results present an overview of pathogenic variations of HBOC genes in the southeast of France, emphasizing the clinical relevance of cDNA analysis and the importance of retesting BRCA-negative individuals with an expanded panel.

Identification and Characterization of New Alu Element Insertion in the BRCA1 Exon 14 Associated with Hereditary Breast and Ovarian Cancer

Hereditary breast and ovarian cancer syndrome (HBOC) is an autosomal dominant cancer predisposition syndrome characterized by an increased risk of breast and ovarian cancers. Germline pathogenic variants in BRCA1 are found in about 7–10% of all familial breast cancers and 10% of ovarian cancers. Alu elements are the most abundant mobile DNA element in the human genome and are known to affect the human genome by different mechanisms leading to human disease. We report here the detection, by next-generation sequencing (NGS) analysis coupled with a suitable bioinformatics pipeline, of an AluYb8 element in exon 14 of the BRCA1 gene in a family with HBOC history first classified as BRCA-negative by Sanger sequencing and first NGS analysis. The c.4475_c.4476insAluYb8 mutation impacts splicing and induces the skipping of exon 14. As a result, the produced mRNA contains a premature stop, leading to the production of a short and likely non-functional protein (pAla1453Glyfs*10). Overall, our study allowed us to identify a novel pathogenic variant in BRCA1 and showed the importance of bioinformatics tool improvement and versioning.

Classification of 101 BRCA1 and BRCA2 variants of uncertain significance by cosegregation study: A powerful approach

Up to 80% of BRCA1 and BRCA2 genetic variants remain of uncertain clinical significance (VUSs). Only variants classified as pathogenic or likely pathogenic can guide breast and ovarian cancer prevention measures and treatment by PARP inhibitors. We report the first results of the ongoing French national COVAR (cosegregation variant) study, the aim of which is to classify BRCA1/2 VUSs. The classification method was a multifactorial model combining different associations between VUSs and cancer, including cosegregation data. At this time, among the 653 variants selected, 101 (15%) distinct variants shared by 1,624 families were classified as pathogenic/likely pathogenic or benign/likely benign by the COVAR study. Sixty-six of the 101 (65%) variants classified by COVAR would have remained VUSs without cosegregation data. Of note, among the 34 variants classified as pathogenic by COVAR, 16 remained VUSs or likely pathogenic when following the ACMG/AMP variant classification guidelines. Although the initiation and organization of cosegregation analyses require a considerable effort, the growing number of available genetic tests results in an increasing number of families sharing a particular variant, and thereby increases the power of such analyses. Here we demonstrate that variant cosegregation analyses are a powerful tool for the classification of variants in the BRCA1/2 breast-ovarian cancer predisposition genes.

Impact of rifampicin dose in bone and joint prosthetic device infections due to Staphylococcus spp: a retrospective single-center study in France

BACKGROUND

Prosthetic joint infections (PJI) are a major cause of morbidity and mortality burden worldwide. While surgical management is well defined, rifampicin (RIF) dose remains controversial. The aim of our study was to determine whether Rifampicin dose impact infection outcomes in PJI due to Staphylococcus spp.

METHODS

single-center retrospective study including 411 patients with PJI due to Rifampicin-sensitive Staphylococcus spp. Rifampicine dose was categorized as follow: < 10 mg/kg/day, 10-20 mg/kg/day or > 20 mg/kg/day. The primary endpoint was patient recovery, defined as being free of infection during 12 months after the end of the initial antibiotic course.

RESULTS

321 (78%) received RIF for the full antibiotic course. RIF dose didn't affect patients recovery rate with 67, 76 and 69% in the < 10, 10-20 and > 20 mg/kg/day groups, respectively (p = 0.083). In univariate analysis, recovery rate was significantly associated with gender (p = 0.012) but not to RIF dose, or Staphylococcus phenotype (aureus or coagulase-negative). In multivariate analysis, age (p = 0.01) and treatment duration (p <  0.01) were significantly associated with recovery rate.

CONCLUSION

These data suggest that lower doses of RIF are as efficient and safe as the recommended high-dose French regimen in the treatment of PJI.

5-aminolevulinic acid photodynamic therapy for the treatment of high-grade gliomas

INTRODUCTION

Photodynamic therapy (PDT) is a two-step treatment involving the administration of a photosensitive agent followed by its activation at a specific light wavelength for targeting of tumor cells.

MATERIALS/METHODS

A comprehensive review of the literature was performed to analyze the indications for PDT, mechanisms of action, use of different photosensitizers, the immunomodulatory effects of PDT, and both preclinical and clinical studies for use in high-grade gliomas (HGGs).

RESULTS

PDT has been approved by the United States Food and Drug Administration (FDA) for the treatment of premalignant and malignant diseases, such as actinic keratoses, Barrett's esophagus, esophageal cancers, and endobronchial non-small cell lung cancers, as well as for the treatment of choroidal neovascularization. In neuro-oncology, clinical trials are currently underway to demonstrate PDT efficacy against a number of malignancies that include HGGs and other brain tumors. Both photosensitizers and photosensitizing precursors have been used for PDT. 5-aminolevulinic acid (5-ALA), an intermediate in the heme synthesis pathway, is a photosensitizing precursor with FDA approval for PDT of actinic keratosis and as an intraoperative imaging agent for fluorescence-guided visualization of malignant tissue during glioma surgery. New trials are underway to utilize 5-ALA as a therapeutic agent for PDT of the intraoperative resection cavity and interstitial PDT for inoperable HGGs.

CONCLUSION

PDT remains a promising therapeutic approach that requires further study in HGGs. Use of 5-ALA PDT permits selective tumor targeting due to the intracellular metabolism of 5-ALA. The immunomodulatory effects of PDT further strengthen its use for treatment of HGGs and requires a better understanding. The combination of PDT with adjuvant therapies for HGGs will need to be studied in randomized, controlled studies.

Recent concepts in the management of thoracolumbar spine metastasis

As patient with cancer live longer, spine metastasis is a growing problem. Untreated, it can cause pain, instability and neurologic deficit, which can severely alter the patient's ability and quality of life. When the diagnosis is established, scoring systems help the physician to best define the objective of treatment by evaluating the life expectancy. Except in rare circumstances, treatment is palliative. Over the past 2 decades, remarkable evolution in surgical techniques provided to patients valuable therapeutic options to perform circumferential decompression and stabilization of the affected level. More recently, minimally invasive techniques allowed a significant reduction of morbidity. The parallel development of stereotactic radiosurgery offers new therapeutic options in particular for patients ineligible for surgery.

Design, synthesis, and evaluation of conformationally constrained tongs, new inhibitors of HIV-1 protease dimerization

The active form of human immunodeficiency virus type 1 protease (HIV-1 PR) is a homodimeric structure in which two subunits are linked through a two-stranded antiparallel beta-sheet consisting of the N- and C-termini of each monomer. To inhibit the dimerization process or disrupt the dimeric interface leading to inactive enzyme, conformationally constrained "molecular tongs" have been designed and synthesized to interfere with one monomer end in a beta-sheet fashion. These molecules are based on two peptidic strands attached to an aromatic scaffold. Inhibitions (submicromolar range) were obtained with molecular tongs containing tripeptidic or tetrapeptidic arms attached to a pyridinediol- or naphthalenediol-based scaffold (Kid = 0.56-4.5 microM at pH 4.7 and 30 degrees C). Kinetic studies are in agreement with an interface inhibition mechanism.

Month of birth and sensitization to dust mites in New England

Charts from 908 patients born in New England and seen at the Lahey Clinic because of allergic rhinitis or asthma or both were reviewed to ascertain whether or not a relationship existed between month of birth and subsequent development of allergy to house dust mites. Prick/puncture and intradermal skin tests for aeroallergens were performed on all patients. Skin tests for Dermatophagoides farinae (Df) mite were scored very positive (VP) in 451 patients (49.7%), mildly positive (MP) in 234 patients (25.7%), and negative (NEG) in 223 patients (24.6%). No discernible difference in frequency of birth could be identified for any single month for either Df-sensitive or Df-negative patients. Comparisons of 4-month periods (May through August, September through December, and January through April) failed to show a seasonal predilection for month of birth. During the 6-month period of February through July, a slight difference was observed for the overall group of 908 patients: 240 of the VP patients (53.2%), 111 of the MP patients (47.4%), and 105 of the NEG patients (47.1%) were born within this period compared with 211 VP patients (46.8%), 123 MP patients (52.6%), and 118 NEG patients (52.9%) who were born within the period of August through January. The difference among the groups was not statistically different (P = 0.20). Of the 225 children and adolescents who were either VP or MP, 125 patients (55.6%) were born within the period of February through July; of the 83 children and adolescents who were NEG, 37 patients (44.6%) were born within that same period. Although dust-mite allergic patients and, in particular, children and adolescents with asthma or rhinitis or both tended to be born within the period of February through July, no clear-cut statistically significant predilection in month of birth or season could be identified for New England-born adult or pediatric mite-allergic patients with rhinitis or asthma or both.

[Imaging in pediatrics. Strategy and economic implications for the Third World]

The cost of acquiring medical imaging equipment is too high for many Third World nations. Ultrasonography and conventional roentegenography provide adequate data in most pediatric patients in tropical countries, for a low maintenance cost. Special training of practitioners in the use of these investigations is essential, before even performing the necessary choices among available equipment.

The value of computed tomography in osseous hydatid disease (echinococcosis)

The authors report three cases of osseous hydatid disease (echinococcosis) in which examination by computed tomography (CT) was found to be helpful in establishing the diagnosis. Recognition of this rare bone infection in orthodox radiographs is notoriously difficult, but is aided by knowledge of the patient having lived in an area in which the disease is endemic. In two instances, one involving the shoulder and the other the thoracic spine, radiological abnormalities had been attributed at first to tuberculosis. In the third case, in which a destructive lesion in the sacrum had been interpreted correctly, CT studies provided confirmation of a recurrence. CT has proved to be an effective and sensitive method of demonstrating these destructive lesions in bone, of determining their spread, and of establishing the presence of other hydatid cysts in adjacent soft tissues. This technique has been found to be of value in preoperative planning of the surgical approach to hydatid lesions of the skeleton.