Targeted sequencing for hereditary breast and ovarian cancer in BRCA1/2-negative families from the Lynch Memorial Biobank reveals complex genetic architecture and phenocopies.

Approximately 20% of breast cancer cases are attributed to increased family risk; yet variation in BRCA1/2 can only explain 20-25% of cases. Historically, only single gene or single variant testing were common in at-risk family members, and further sequencing studies were rarely offered after negative results. In this study, we applied an efficient and inexpensive targeted sequencing approach to provide molecular diagnoses in 245 human samples representing 134 BRCA mutation negative (BRCAX) hereditary breast and ovarian cancer (HBOC) families recruited from 1973-2019 by Dr. Henry Lynch. Sequencing identified 391 variants, which were functionally annotated and ranked based on their predicted clinical impact. Known pathogenic CHEK2 breast cancer variants were identified in five BRCAX families in this study. While BRCAX was an inclusion criterion for this study, we still identified a pathogenic BRCA2 variant (p.Met192ValfsTer13) in one family. A portion of BRCAX families could be explained by other hereditary cancer syndromes that increase HBOC risk: Li-Fraumeni Syndrome (gene: TP53) and Lynch Syndrome (gene: MSH6). Interestingly, many families carried additional Variants of Undetermined Significance (VOUSs) that may further modify phenotypes of syndromic family members. Ten families carried more than one potential VOUS suggesting the presence of complex multi-variant families. Overall, nine BRCAX HBOC families in our study may be explained by known likely-pathogenic/pathogenic variants, and six families carried potential VOUSs, which require further functional testing. To address this, we developed a functional assay where we successfully re-classified one family's PMS2 VOUS as benign.

In vitro data suggest a role for PMS2 Kozak sequence mutations in Lynch syndrome risk.

Lynch syndrome (LS) is the most common hereditary cancer syndrome. Heterozygous loss-of-function variants in PMS2 are linked to LS. While these variants are not directly cancer causing, reduced PMS2 function results in the accumulation of somatic variants and increased cancer risk over time due to DNA mismatch repair dysfunction. It is reasonable that other types of genetic variation that impact the expression of PMS2 may also contribute to cancer risk. The Kozak sequence is a highly conserved translation initiation motif among higher eukaryotes and is defined as the nine base pairs upstream of the translation start codon through the first four bases of the translated sequence (5'-[GTT]GCATCCATGG-3'; human PMS2: NM_000535.7). While Kozak sequence variants in PMS2 have been reported in ClinVar in patients with suspected hereditary cancer, all variants upstream of the translation start site are currently classified as variants of undetermined significance (VUSs). We hypothesized that variants significantly disrupting the Kozak sequence of PMS2 would decrease PMS2 protein expression, contributing to increased cancer risk over time. Using a dual-luciferase reporter plasmid and site-directed mutagenesis, we generated the wild-type human PMS2 and the ClinVar VUSs within the PMS2 Kozak sequence. Besides the c.1A>C variant, which is already known to be pathogenic, we implicate six additional variants as American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) pathogenic supporting (PP) variants and classify ten as benign supporting (BP). In summary, we present a method developed for the classification of human PMS2 Kozak sequence variants that can contribute to the re-classification of VUSs identified in patients.

Characterization of Ag-Ion Releasing Zeolite Filled 3D Printed Resins.

There has been profound growth in the use of 3D printed materials in dentistry in general, including orthodontics. The opportunity to impart antimicrobial properties to 3D printed parts from existing resins requires the capability of forming a stable colloid incorporating antimicrobial fillers. The objective of this research was to characterize a colloid consisting of a 3D printable resin mixed with Ag-ion releasing zeolites and fumed silica to create 3D printed parts with antiviral properties. The final composite was tested for antiviral properties against SARS-CoV-2 and HIV-1. Antiviral activity was measured in terms of the half-life of SARS-CoV-2 and HIV-1 on the composite surface. The inclusion of the zeolite did not interfere with the kinetics measured on the surface of the ATR crystal. While the depth of cure, measured following ISO4049 guidelines, was reduced from 3.8 mm to 1.4 mm in 5 s, this greatly exceeded the resolution required for 3D printing. The colloid was stable for at least 6 months and the rheological behavior was dependent upon the fumed silica loading. The inclusion of zeolites and fumed silica significantly increased the flexural strength of the composite as measured by a 3 point bend test. The composite released approximately 2500 µg/L of silver ion per gram of composite as determined by potentiometry. There was a significant reduction of the average half-life of SARS-CoV-2 (1.9 fold) and HIV-1 (2.7 fold) on the surface of the composite. The inclusion of Ag-ion releasing zeolites into 3D-printable resin can result in stable colloids that generate composites with improved mechanical properties and antiviral properties.

Antiretroviral release from poly(DL-lactide-co-glycolide) nanoparticles in mice.

OBJECTIVES: Free ritonavir, lopinavir and efavirenz injected intraperitoneally were compared with antiretroviral (AR) nanoparticles (NPs). METHODS: This is a prospective study in BALB/c mice comparing the pharmacokinetics of free drugs with AR NPs. All animals received free drugs or AR NPs (20 mg/kg) in PBS. In vitro replication assays were used for determination of the anti-HIV efficacy of NP formulations. At specific times (free drugs 0.08, 0.125, 0.25, 0.33, 1, 2 and 3 days; AR NPs 0.125, 0.33, 1, 2, 4, 7, 14, 21, 28, 35 and 42 days) mice were euthanized and serum and organs were harvested for determination of AR concentrations by HPLC. Single treatment of monocyte-derived macrophages (MDMs) infected with HIV-1(ada) compared AR NPs (0.005-0.05 mg/mL) with free efavirenz or lopinavir/ritonavir (0.01-0.1 mg/mL), blank NPs and controls. Results are presented as means ± SEM. RESULTS: Serum free AR drug concentrations peaked 4 h post-injection (ritonavir 3.9 ± 3.05, lopinavir 3.4 ± 2.5 and efavirenz 1.8 ± 0.63 µg/mL) and were eliminated by 72 h. Poly(dl-lactide-co-glycolide) NP animals had detectable ritonavir, lopinavir and efavirenz concentrations in all tissues for 28 days. Treatment of MDMs with AR NPs resulted in sustained inhibition of HIV-1(ada) replication. CONCLUSIONS: AR drug concentrations from NPs are sustained for 28 days in vivo and anti-HIV inhibition was comparable to that of free drugs in vitro and could be a sustained treatment for delivery of AR drugs.