Kimberly A. McAllister

Brca1 and Brca2 expression patterns in mitotic and meiotic cells of mice

The mouse homologues of the breast cancer susceptibility genes, Brca1 and Brca2, are expressed in a cell cycle-dependent fashion in vitro and appear to be regulated by similar or overlapping pathways. Therefore, we compared the non isotopic in situ hybridization expression patterns of Brca1 and Brca2 mRNA in vivo in mitotic and meiotic cells during mouse embryogenesis, mammary gland development, and in adult tissues including testes, ovaries, and hormonally altered ovaries. Brca1 and Brca2 are expressed concordantly in proliferating cells of embryos, and the mammary gland undergoing morphogenesis and in most adult tissues. The expression pattern of Brca1 and Brca2 correlates with the localization of proliferating cell nuclear antigen, an indicator of proliferative activity. In the ovary, Brca1 and Brca2 exhibited a comparable hormone-independent pattern of expression in oocytes, granulosa cells and thecal cells of developing follicles. In the testes, Brca1 and Brca2 were expressed in mitotic spermatogonia and early meiotic prophase spermatocytes. Northern analyses of prepubertal mouse testes revealed that the time course of Brca2 expression was delayed in spermatogonia relative to Brca1. Thus, while Brca1 and Brca2 share concordant cell-specific patterns of expression in most proliferating tissues, these observations suggest that they may have distinct roles during meiosis.

Mitochondria, energetics, epigenetics, and cellular responses to stress

Background: Cells respond to environmental stressors through several key pathways, including response to reactive oxygen species (ROS), nutrient and ATP sensing, DNA damage response (DDR), and epigenetic alterations. Mitochondria play a central role in these pathways not only through energetics and ATP production but also through metabolites generated in the tricarboxylic acid cycle, as well as mitochondria–nuclear signaling related to mitochondria morphology, biogenesis, fission/fusion, mitophagy, apoptosis, and epigenetic regulation. Objectives: We investigated the concept of bidirectional interactions between mitochondria and cellular pathways in response to environmental stress with a focus on epigenetic regulation, and we examined DNA repair and DDR pathways as examples of biological processes that respond to exogenous insults through changes in homeostasis and altered mitochondrial function. Methods: The National Institute of Environmental Health Sciences sponsored the Workshop on Mitochondria, Energetics, Epigenetics, Environment, and DNA Damage Response on 25–26 March 2013. Here, we summarize key points and ideas emerging from this meeting. Discussion: A more comprehensive understanding of signaling mechanisms (cross-talk) between the mitochondria and nucleus is central to elucidating the integration of mitochondrial functions with other cellular response pathways in modulating the effects of environmental agents. Recent studies have highlighted the importance of mitochondrial functions in epigenetic regulation and DDR with environmental stress. Development and application of novel technologies, enhanced experimental models, and a systems-type research approach will help to discern how environmentally induced mitochondrial dysfunction affects key mechanistic pathways. Conclusions: Understanding mitochondria–cell signaling will provide insight into individual responses to environmental hazards, improving prediction of hazard and susceptibility to environmental stressors. Citation: Shaughnessy DT, McAllister K, Worth L, Haugen AC, Meyer JN, Domann FE, Van Houten B, Mostoslavsky R, Bultman SJ, Baccarelli AA, Begley TJ, Sobol RW, Hirschey MD, Ideker T, Santos JH, Copeland WC, Tice RR, Balshaw DM, Tyson FL. 2014. Mitochondria, energetics, epigenetics, and cellular responses to stress. Environ Health Perspect 122:1271–1278; http://dx.doi.org/10.1289/ehp.1408418

Gene-Environment Interplay in Common Complex Diseases: Forging an Integrative Model—Recommendations From an NIH Workshop

Although it is recognized that many common complex diseases are a result of multiple genetic and environmental risk factors, studies of gene‐environment interaction remain a challenge and have had limited success to date. Given the current state‐of‐the‐science, NIH sought input on ways to accelerate investigations of gene‐environment interplay in health and disease by inviting experts from a variety of disciplines to give advice about the future direction of gene‐environment interaction studies. Participants of the NIH Gene‐Environment Interplay Workshop agreed that there is a need for continued emphasis on studies of the interplay between genetic and environmental factors in disease and that studies need to be designed around a multifaceted approach to reflect differences in diseases, exposure attributes, and pertinent stages of human development. The participants indicated that both targeted and agnostic approaches have strengths and weaknesses for evaluating main effects of genetic and environmental factors and their interactions. The unique perspectives represented at the workshop allowed the exploration of diverse study designs and analytical strategies, and conveyed the need for an interdisciplinary approach including data sharing, and data harmonization to fully explore gene‐environment interactions. Further, participants also emphasized the continued need for high‐quality measures of environmental exposures and new genomic technologies in ongoing and new studies. Genet. Epidemiol. 35: 217‐225, 2011.  © 2011 Wiley‐Liss, Inc.

Next generation analytic tools for large scale genetic epidemiology studies of complex diseases.

Over the past several years, genome‐wide association studies (GWAS) have succeeded in identifying hundreds of genetic markers associated with common diseases. However, most of these markers confer relatively small increments of risk and explain only a small proportion of familial clustering. To identify obstacles to future progress in genetic epidemiology research and provide recommendations to NIH for overcoming these barriers, the National Cancer Institute sponsored a workshop entitled “Next Generation Analytic Tools for Large‐Scale Genetic Epidemiology Studies of Complex Diseases” on September 15–16, 2010. The goal of the workshop was to facilitate discussions on (1) statistical strategies and methods to efficiently identify genetic and environmental factors contributing to the risk of complex disease; and (2) how to develop, apply, and evaluate these strategies for the design, analysis, and interpretation of large‐scale complex disease association studies in order to guide NIH in setting the future agenda in this area of research. The workshop was organized as a series of short presentations covering scientific (gene‐gene and gene‐environment interaction, complex phenotypes, and rare variants and next generation sequencing) and methodological (simulation modeling and computational resources and data management) topic areas. Specific needs to advance the field were identified during each session and are summarized. Genet. Epidemiol. 36 : 22–35, 2012.

Environmental Epigenomics, Imprinting and Disease Susceptibility

On Tuesday, November 2, 2005 over 450 scientists representing 14 nations converged on the Washington Duke Inn, Durham, NC, USA to discuss, learn and exchange information on how environmental influences can exert impacts on health not only on the individual that has been exposed but also for up to four subsequent generations in some human and animal models tested. The meeting entitled “Environmental Epigenomics, Imprinting and Disease Susceptibility” was sponsored by the National Institute of Environmental Health Sciences (NIEHS) and the Duke Comprehensive Cancer Center. The meeting featured presentations from many of the leading authorities/experts in epigenomics in the world and approximately 70 poster presentations, of which twelve were selected for oral presentation. The meeting was organized into nine scientific sessions spread over two and a half days that addressed the fetal basis of disease, epigenetics and gene regulation, epigenetics and cancer, therapeutic and reproductive cloning, stem cell differentiation, epigenetics and chronic diseases and epigenetics and neurodevelopment. The opening session introduced the meeting co-organizers, Randy Jirtle of Duke University Medical Center and Frederick Tyson of NIEHS, to conference participants and included greetings from. Christopher Willett, Chair of Duke Radiation Oncology Department, and William Schlessinger, Dean of the Nicolas School of the Environment and Earth Sciences. David Schwartz, Director of the NIEHS, set the tone for the conference with an overview lecture that identified research priorities of the NIEHS and pointed out the intersections between the environmental genomics component of NIEHS priorities and the environmental epigenomics. He noted that NIEHS research priorities will emphasize and coordinate efforts aimed at the study of complex human diseases. The environmental genomics infrastructural resources developed by NIEHS including over 500 re-sequenced environmentally responsive genes, over 50 humanized mouse strains, and progress towards establishing gene expression standards are available for utilization in the integration of epigenomic studies and the analysis of complex human diseases. Just as epigenomics is becoming increasingly more important in Schwartz’s own asthma research, this conference identified additional opportunities for the integration of environmental epigenomics and complex human disease.

Mammary Tumor Induction and Premature Ovarian Failure in ApcMin Mice Are Not Enhanced by Brca2 Defi ciency

Inherited BRCA2 mutations predispose individuals to breast cancer and increase risk at other sites. Recent studies have suggested a role for the APC I1307K allele as a low-penetrance breast cancer susceptibility gene that enhances the phenotypic effects of BRCA1 and BRCA2 mutations. To model the consequences of inheriting mutant alleles of the BRCA2 and APC tumor suppressor genes, we examined tumor outcome in C57BL/6 mice with mutations in the Brca2 and Apc genes. We hypothesized that if the Brca2 and Apc genes were interacting to influence mammary tumor susceptibility, then mammary tumor incidence and/or multiplicity would be altered in mice that had inherited mutations in both genes. Female and male offspring treated with a single IP injection of 50 mg/kg N-ethyl-N-nitrosourea (ENU) at 35 days of age developed mammary adenoacanthomas by 100 days of age. The female Apc-mutant and Brca2/Apc double-mutant progeny had mean mammary tumor multiplicities of 6.7 ± 2.8 and 7.2 ± 2.7, respectively, compared to wild-type and Brca2-mutant females, which had mean mammary tumor multiplicities of 0.1 ±0.4 and 0.3 ± 0.5, respectively. Female ENU-treated Apc-mutant and Brca2/Apc double heterozygotes were also susceptible to premature ovarian failure. Thus, the inheritance of an Apc mutation predisposes ENU-treated female and male mice to mammary tumors and, in the case of female mice, to ovarian failure. These results indicate that mammary tumor development in Apc-mutant mice can progress independently of ovarian hormones. The Apc mutation-driven phenotypes were not modified by mutation of Brca2, perhaps because Brca2 acts in a hormonally dependent pathway of mammary carcinogenesis.

BRCA2-null embryonic survival is prolonged on the BALB/c genetic background.

Women who inherit mutations in the BRCA2 cancer susceptibility gene have an 85% chance of developing breast cancer. The function of the BRCA2 gene remains elusive, but there is evidence to support its role in transcriptional transactivation, tumor suppression, and the maintenance of genomic integrity. Individuals with identical BRCA2 mutations display a different distribution of cancers, suggesting that there are low‐penetrance genes that can modify disease outcome. We hypothesized that genetic background could influence embryonic survival of a Brca2 mutation in mice. Brca2‐null embryos with a 129/SvEv genetic background (129B2−/−) died before embryonic day 8.5. Transfer of this Brca2 mutation onto the BALB/cJ genetic background (BALB/cB2−/−) extended survival to embryonic day 10.5. These results indicate that the BALB/c background harbors genetic modifiers that can prolong Brca2‐null embryonic survival. The extended survival of BALB/cB2−/− embryos enabled us to ask whether transcriptional regulation of the Brca1 and Brca2 genes is interdependent. The interdependence of Brca1 and Brca2 was evaluated by studying Brca2 gene expression in BALB/cB1−/− embryos and Brca1 gene expression in BALB/cB2−/− embryos. Nonisotopic in situ hybridization demonstrated that Brca2 transcript levels were comparable in BALB/cB1−/− embryos and wild‐type littermates. Likewise, reverse transcriptase–polymerase chain reactions confirmed Brca1 mRNA expression in embryonic day 8.5 BALB/cB2−/− embryos that was comparable to Brca2‐heterozygous littermates. Thus, the Brca1 and Brca2 transcripts are expressed independently of one another in Brca1‐ and Brca2‐null embryos. Mol. Carcinog. 28:174–183, 2000.

Spontaneous and irradiation-induced tumor susceptibility in BRCA2 germline mutant mice and cooperative effects with a p53 germline mutation.

Mutations in both p53 and BRCA2 are commonly seen together in human tumors suggesting that the loss of both genes enhances tumor development. To elucidate this interaction in an animal model, mice lacking the carboxy terminal domain of Brca2 were crossed with p53 heterozygous mice. Females from this intercross were then irradiated with an acute dose of 5 Gy ionizing radiation at 5 weeks of age and compared to nonirradiated controls. We found decreased survival and timing of tumor onsets, and significantly higher overall tumor incidences and prevalence of particular tumors, including stomach tumors and squamous cell carcinomas, associated with the homozygous loss of Brca2, independent of p53 status. The addition of a p53 mutation had a further impact on overall survival, incidence of osteosarcomas and stomach tumors, and tumor latency. The spectrum of tumors observed for this Brca2 germline mouse model suggest that it faithfully recapitulates some human disease phenotypes associated with BRCA2 loss. In addition, these findings include extensive in vivo data demonstrating that germline Brca2 and p53 mutations cooperatively affect animal survivals, tumor susceptibilities, and tumor onsets.

Genetic Simulation Tools for Post‐Genome Wide Association Studies of Complex Diseases

Genetic simulation programs are used to model data under specified assumptions to facilitate the understanding and study of complex genetic systems. Standardized data sets generated using genetic simulation are essential for the development and application of novel analytical tools in genetic epidemiology studies. With continuing advances in high‐throughput genomic technologies and generation and analysis of larger, more complex data sets, there is a need for updating current approaches in genetic simulation modeling. To provide a forum to address current and emerging challenges in this area, the National Cancer Institute (NCI) sponsored a workshop, entitled “Genetic Simulation Tools for Post‐Genome Wide Association Studies of Complex Diseases” at the National Institutes of Health (NIH) in Bethesda, Maryland on March 11–12, 2014. The goals of the workshop were to (1) identify opportunities, challenges, and resource needs for the development and application of genetic simulation models; (2) improve the integration of tools for modeling and analysis of simulated data; and (3) foster collaborations to facilitate development and applications of genetic simulation. During the course of the meeting, the group identified challenges and opportunities for the science of simulation, software and methods development, and collaboration. This paper summarizes key discussions at the meeting, and highlights important challenges and opportunities to advance the field of genetic simulation.

Meeting report: Identification of biomarkers for early detection of mitochondrial dysfunction.

In addition to their central role in cellular bioenergetics, mitochondria also play a major role in apoptosis, control of cytosolic calcium concentrations, and metabolic cell signaling. Through normal energy production by oxidative phosphorylation and the electron transport chain, mitochondrial proteins and mtDNA are vulnerable to damage from reactive oxygen species (ROS). Mitochondria are also a target for over 60 natural and synthetic compounds that exert their toxicity by affecting the integrity of mtDNA, inhibiting complexes in the electron transport chain, altering membrane potential, affecting calcium homeostasis, and by modulating induction of apoptosis. Mitochondrial dysfunction is associated with numerous chronic diseases including Type II diabetes, neurodegenerative diseases, blindness, cardiovascular disease, and cancer. This may reflect, in part, the vulnerability of mitochondria to environmental influences. For example, the organic pesticide rotenone is a potent Complex I inhibitor, exhibits selective toxicity for dopaminergic neurons, and is associated in human studies with increased risk of Parkinson’s disease (PD). The identification of mitochondrial impairment in clinical settings is challenging. Acute exposure to mitochondrial poisons causes short-term and nonspecific clinical symptoms that include muscle weakness, fatigue, hypotension and shortness of breath. The effects of drugs or environmental mitochondrial toxicants are often detected by lactic acidosis in which a large percentage of mitochondria have already been affected. Such markers have limited utility for detecting individuals at risk of developing disease or in the early stages of a disease. There is an urgent need for reliable, informative markers of early mitochondrial dysfunction associated with environmental stressors, as these could enable intervention in the subclinical stages of disease. In the case of PD, such markers could enable interventions aimed at preserving dopamine neurons.