Significant phenotypic variability in a multigenerational family with an NFIA missense mutation: Case series and review of the literature

We report the first multigenerational family with NFIA-related disorder from a missense variant. This case highlights the condition's phenotypic variability and the need for genetic testing when an initial diagnosis fails to explain all symptoms.

Prevalence of Frontotemporal Dementia in Females of 5 Hispanic Families With R159H VCP Multisystem Proteinopathy

Background and Objectives

Missense variants of the valosin-containing protein (VCP) gene cause a progressive, autosomal dominant disease termed VCP multisystem proteinopathy (MSP1). The disease is a constellation of clinical features including inclusion body myopathy (IBM), Paget disease of bone (PDB), frontotemporal dementia (FTD), and amyotrophic lateral sclerosis (ALS), typically reported at a frequency of 90%, 42%, 30%, and 9%, respectively. The Hispanic population is currently underrepresented in previous reports of VCP myopathy. We expand our genotype-phenotype studies in 5 Hispanic families with the c.476G>A, p.R159H VCP variant.

Methods

We report detailed clinical findings of 11 patients in 5 Hispanic families with the c.476G > A, p.R159H VCP variant. In addition, we report frequencies of the main manifestations in 28 additional affected members of the extended family members. We also compared our findings with an existing larger cohort of patients with VCP MSP1.

Results

FTD was the most prevalent feature reported, particularly frequent in females. PDB was only seen in 1 patient in contrast to the earlier reported cohorts. The overall frequency of the different manifestations: myopathy, PDB, FTD, and ALS in these 5 families was 39%, 3%, 72%, and 8%, respectively. The atypical phenotype and later onset of manifestations in these families resulted in a noticeable delay in the diagnosis of VCP disease.

Discussion

Studying each VCP variant in the context of ethnic backgrounds is pivotal in increasing awareness of the variability of VCP-related diseases across different ethnicities, enabling early diagnosis, and understanding the mechanism for these genotype-phenotype variations.

Human rDNA copy number is unstable in metastatic breast cancers

Chromatin-mediated silencing, including the formation of heterochromatin, silent chromosome territories, and repressed gene promoters, acts to stabilize patterns of gene regulation and the physical structure of the genome. Reduction of chromatin-mediated silencing can result in genome rearrangements, particularly at intrinsically unstable regions of the genome such as transposons, satellite repeats, and repetitive gene clusters including the rRNA gene clusters (rDNA). It is thus expected that mutational or environmental conditions that compromise heterochromatin function might cause genome instability, and diseases associated with decreased epigenetic stability might exhibit genome changes as part of their aetiology. We find the support of this hypothesis in invasive ductal breast carcinoma, in which reduced epigenetic silencing has been previously described, by using a facile method to quantify rDNA copy number in biopsied breast tumours and pair-matched healthy tissue. We found that rDNA and satellite DNA sequences had significant copy number variation - both losses and gains of copies - compared to healthy tissue, arguing that these genome rearrangements are common in developing breast cancer. Thus, any proposed aetiology onset or progression of breast cancer should consider alterations to the epigenome, but must also accommodate concomitant changes to genome sequence at heterochromatic loci.

Constitutive expression of AhR and BRCA-1 promoter CpG hypermethylation as biomarkers of ERα-negative breast tumorigenesis

Background

Only 5–10 % of breast cancer cases is linked to germline mutations in the BRCA-1 gene and occurs early in life. Conversely, sporadic breast tumors, which represent 90-95 % of breast malignancies, have lower BRCA-1 expression, but not mutated BRCA-1 gene, and tend to occur later in life in combination with other genetic alterations and/or environmental exposures. The latter may include environmental and dietary factors that activate the aromatic hydrocarbon receptor (AhR). Therefore, understanding if changes in expression and/or activation of the AhR are associated with somatic inactivation of the BRCA-1 gene may provide clues for breast cancer therapy.

Methods

We evaluated Brca-1 CpG promoter methylation and expression in mammary tumors induced in Sprague–Dawley rats with the AhR agonist and mammary carcinogen 7,12-dimethyl-benzo(a)anthracene (DMBA). Also, we tested in human estrogen receptor (ER)α-negative sporadic UACC-3199 and ERα-positive MCF-7 breast cancer cells carrying respectively, hyper- and hypomethylated BRCA-1 gene, if the treatment with the AhR antagonist α-naphthoflavone (αNF) modulated BRCA-1 and ERα expression. Finally, we examined the association between expression of AhR and BRCA-1 promoter CpG methylation in human triple-negative (TNBC), luminal-A (LUM-A), LUM-B, and epidermal growth factor receptor-2 (HER-2)-positive breast tumor samples.

Results

Mammary tumors induced with DMBA had reduced BRCA-1 and ERα expression; higher Brca-1 promoter CpG methylation; increased expression of Ahr and its downstream target Cyp1b1; and higher proliferation markers Ccnd1 (cyclin D1) and Cdk4. In human UACC-3199 cells, low BRCA-1 was paralleled by constitutive high AhR expression; the treatment with αNF rescued BRCA-1 and ERα, while enhancing preferential expression of CYP1A1 compared to CYP1B1. Conversely, in MCF-7 cells, αNF antagonized estradiol-dependent activation of BRCA-1 without effects on expression of ERα. TNBC exhibited increased basal AhR and BRCA-1 promoter CpG methylation compared to LUM-A, LUM-B, and HER-2-positive breast tumors.

Conclusions

Constitutive AhR expression coupled to BRCA-1 promoter CpG hypermethylation may be predictive markers of ERα-negative breast tumor development. Regimens based on selected AhR modulators (SAhRMs) may be useful for therapy against ERα-negative tumors, and possibly, TNBC with increased AhR and hypermethylated BRCA-1 gene.

A Phase 3 Trial of Sebelipase Alfa in Lysosomal Acid Lipase Deficiency

BACKGROUND

Lysosomal acid lipase is an essential lipid-metabolizing enzyme that breaks down endocytosed lipid particles and regulates lipid metabolism. We conducted a phase 3 trial of enzyme-replacement therapy in children and adults with lysosomal acid lipase deficiency, an underappreciated cause of cirrhosis and severe dyslipidemia.

METHODS

In this multicenter, randomized, double-blind, placebo-controlled study involving 66 patients, we evaluated the safety and effectiveness of enzyme-replacement therapy with sebelipase alfa (administered intravenously at a dose of 1 mg per kilogram of body weight every other week); the placebo-controlled phase of the study was 20 weeks long and was followed by open-label treatment for all patients. The primary end point was normalization of the alanine aminotransferase level. Secondary end points included additional disease-related efficacy assessments, safety, and side-effect profile.

RESULTS

Substantial disease burden at baseline included a very high level of low-density lipoprotein cholesterol (≥190 mg per deciliter) in 38 of 66 patients (58%) and cirrhosis in 10 of 32 patients (31%) who underwent biopsy. A total of 65 of the 66 patients who underwent randomization completed the double-blind portion of the trial and continued with open-label treatment. At 20 weeks, the alanine aminotransferase level was normal in 11 of 36 patients (31%) in the sebelipase alfa group and in 2 of 30 (7%) in the placebo group (P=0.03), with mean changes from baseline of -58 U per liter versus -7 U per liter (P<0.001). With respect to prespecified key secondary efficacy end points, we observed improvements in lipid levels and reduction in hepatic fat content (P<0.001 for all comparisons, except P=0.04 for triglycerides). The number of patients with adverse events was similar in the two groups; most events were mild and were considered by the investigator to be unrelated to treatment.

CONCLUSIONS

Sebelipase alfa therapy resulted in a reduction in multiple disease-related hepatic and lipid abnormalities in children and adults with lysosomal acid lipase deficiency. (Funded by Synageva BioPharma and others; ARISE ClinicalTrials.gov number, NCT01757184.).

Abstract P3-07-05: Frequent BRCA1 and BRCA2 mutations are found in Mexican and Mexican-American women with breast cancer

Background: The Arizona Cancer Registry has shown that in Pima County, AZ, breast cancer diagnosed in young Latinas increased 40% from 2004-2008, compared to 1999-2003, and Latinas more likely to die of their cancer. This study seeks to characterize genetic variation in women of Mexican ancestry with breast cancer using next generation sequencing, with the goal of providing prevalence information to help guide screening and cancer prevention efforts.

Methods: The ELLA Binational Breast Cancer Study enrolled women of Mexican ancestry living in either U.S. or Mexico within 24 months of breast cancer diagnosis. Mexican women from the state of Jalisco were collected through collaboration with the Universidad de Guadalajara and women of Mexican ancestry were recruited from Tucson and Phoenix, AZ. Genomic DNA from 92 ELLA study participants (49 from the U.S. and 43 from Mexico) was enriched for breast cancer influencing gene sequence using the BROCA panel with standard techniques. Samples were sequenced with next generation sequencing and variants identified.

Results: Sequencing of breast cancer risk genes in 92 Mexican and Mexican-American women with breast cancer revealed the presence of deleterious mutations in 15% of women (14/92). Five carry mutations in BRCA1, 5 in BRCA2, 2 in CHEK2, 1 in PALB2 and 1 in RAD51C. An additional 9% of participants (8/92) carry rare mutations of unknown functional consequence in the same genes. Four carry mutations in BRCA1 or BRCA2 at sites predicted to alter splice enhancers and four carry missense mutations in CHEK2 that are predicted to damage to kinase function. None of these variants appear in public databases or are characterized functionally in gene-specific databases. Dozens of women carry VUS or novel variants.

Women carrying BRCA1 mutations are significantly more likely to have had triple negative pathology. Women carrying other mutations known or thought to be deleterious are also more likely to have been younger at diagnosis, to have more aggressive breast cancer or to report a family history of breast cancer.

Table 1. Deleterious MutationsGeneEffectTotalBRCA1185delAG1BRCA12569delC2BRCA1Del Complete Gene1BRCA1Del Exons 9-121BRCA2c.658delGT1BRCA2c.3264insT2BRCA2c.5195delT1BRCA2c.6024insG1CHEK2R160G2PALB2S779 Stop1RAD51CDel Exons 4-91

Conclusion: Deleterious BRCA1 and BRCA2 gene mutations are common among women of Mexican ancestry diagnosed with breast cancer. Within this cohort, the prevalence of BRCA1/2 mutations is 11%, and 4% of women carry mutations in other genes increasing breast cancer risk. This is higher than the 10% mutation prevalence estimated for Ashkenazi Jewish women with breast cancer. An additional 9% of women carry variants likely to disrupt gene function and dozens of VUS and novel variants are found in these women. Further analysis of samples from the remaining 942 women using genetic sequencing will help further elucidate the role of genetic risk factors in women of Mexican ancestry with breast cancer.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P3-07-05.

Abstract A018: Genomic evaluation of inherited predisposition to breast cancer in women from the University of Arizona Cancer Center High Risk Breast Cancer Genetics Clinic

Background: One in 8 women will develop breast cancer over the course of her lifetime, making it the most common cancer affecting women and the 2nd leading cause of cancer death. 20% of women with breast cancer have 1 or more family members who have also been diagnosed. In 25% of familial cases, cancer occurs in both the breast and ovaries and is attributable to deleterious mutations in BRCA1/BRCA2 DNA repair genes. A woman with a BRCA gene mutation has an 85% lifetime risk for developing breast cancer and 20-60% risk for ovarian cancer. The remaining 75% of susceptibility is polygenic in nature and a large number of low-penetrance genes are involved. This project builds on the discovery of new breast cancer influencing genes that interact with BRCA1 and BRCA2 to function in DNA repair. Here, we utilize next generation parallel sequencing techniques to determine if 89 genes of interest thought to play a role in breast cancer susceptibility are found in women with strong family histories of breast cancer enrolled in the University of Arizona Cancer Center High Risk Breast Cancer Genetics Clinic (UACC BCGC).

Methods: The UACC BCGC is a unique and well-developed resource that is vital to the success of this translational project. The purpose of the high risk breast cancer genetics clinic is to provide cancer risk assessment and to manage surveillance and risk-reduction strategies in a cohort of high-risk women. This University of Arizona IRB-approved registry for epidemiologic and medical record information has been accruing for the past five years, and 182 subjects are currently enrolled with additional women being regularly recruited. Fifty-one (28%) of current UACC BCGC registry participants have identified BRCA1 or BRCA2 mutations and this study seeks genetic risk factors for cancer in other registry participants. The 72% of participants in the UACC BCGC database without identified BRCA mutations fall into four categories: 1) untested for BRCA mutations, 2) affected relative tests negative for deleterious BRCA mutation, 3) unaffected participant tests negative for deleterious BRCA mutation, and 4) BRCA negative participant diagnosed with breast cancer or “pre cancer”. Participants in categories 1, 2, and 4 were recruited. Genomic DNA was captured from the initial cohort of BCGC samples using Agilent Technologies HaloPlex protocols to enable additional analysis of novel custom genes of interest in addition to the University of Washington developed BROCA panel. Captured library DNA was denatured and subjected to cluster amplification on a Paired End Flow Cell in paired-end libraries with ~200 bp insert size, and sequenced on an Illumina HiSeq2000 instrument with 100 bp read lengths.

Results: We expect that our preliminary analysis will show variation within these 89 genes may explain up to 50% of breast cancer risk in families with a strong pattern of breast cancer enrolled in the UACC BCGC. It is our hope that discovering the genetic risk factors at work in high risk families will help clarify individual risk and that this genetic information can be utilized to improve the management of at-risk women. Population frequency of variation is a major thrust of this project and future studies will probe penetrance. Long terms goals include expanding our recruitment of patients and their family members to allow prospective analysis to determine if these heritable mutations correlate with development of other types of cancer.

Discussion: Women with strong personal and family histories of breast cancer are routinely tested for mutations in the BRCA1 and BRCA2 genes, but other gene testing is not generally available or offered. Researchers continue to study the genetic basis of the remaining familial breast cancer cases, and mutations in more than a dozen additional breast cancer risk genes have been identified. Some of these genes are highly penetrant with effect sizes similar to BRCA1 and BRCA2 (&gt;5x increased lifetime risk), while others confer more moderate breast cancer risk (2-5x). Testing for most of these gene mutations is not yet available clinically and information in mutation status is difficult to interpret because we lack knowledge of the degree of risk conferred and/or the prevalence of these mutations in the general population. Discovering genetic risk factors at work in high risk families using our expanded panel at the UACC BCGC will help clarify individual risk and this genetic information can be utilized to improve the management of at-risk women. Identifying these patients is important because we can suggest specific cancer prevention options based on genetics. We can increase the chance of identifying cancer early and at a more treatable non-invasive stage by using intensive screening, recommending preventive medication, and/or risk reducing surgery to decrease the chance of developing invasive breast cancer in high risk individuals.

Citation Format: Ateefa Chaudhury, Corina Mauss, Joanne Jeter, Christina Laukaitis. Genomic evaluation of inherited predisposition to breast cancer in women from the University of Arizona Cancer Center High Risk Breast Cancer Genetics Clinic. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications; Oct 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2013;11(10 Suppl):Abstract nr A018.

Visualizing muscle cell migration in situ

BACKGROUND

Cell migration has been studied extensively by manipulating and observing cells bathed in putative chemotactic or chemokinetic agents on planar substrates. This environment differs from that in vivo and, consequently, the cells can behave abnormally. Embryo slices provide an optically accessible system for studying cellular navigation pathways during development. We extended this system to observe the migration of muscle precursors from the somite into the forelimb, their cellular morphology, and the localization of green fluorescent protein (GFP)-tagged adhesion-related molecules under normal and perturbed conditions.

RESULTS

Muscle precursors initiated migration synchronously and migrated in broad, rather than highly defined, regions. Bursts of directed migration were followed by periods of meandering or extension and retraction of cell protrusions. Although paxillin did not localize to discernible intracellular structures, we found that alpha-actinin localized to linear, punctate structures, and the alpha5 integrin to some focal complexes and/or vesicle-like concentrations. Alterations in the expression of adhesion molecules inhibited migration. The muscle precursors migrating in situ formed unusually large, long-lived protrusions that were polarized in the direction of migration. Unlike wild-type Rac, a constitutively active Rac localized continuously around the cell surface and promoted random protrusive activity and migration.

CONCLUSIONS

The observation of cellular migration and the dynamics of molecular organization at high temporal and spatial resolution in situ is feasible. Migration from the somite to the wing bud is discontinuous and not highly stereotyped. In situ, local activation of Rac appears to produce large protrusions, which in turn, leads to directed migration. Adhesion can also regulate migration.