Impact of Holocene environmental change on the evolutionary ecology of an Arctic top predator

The Arctic is among the most climatically sensitive environments on Earth, and the disappearance of multiyear sea ice in the Arctic Ocean is predicted within decades. As apex predators, polar bears are sentinel species for addressing the impact of environmental variability on Arctic marine ecosystems. By integrating genomics, isotopic analysis, morphometrics, and ecological modeling, we investigate how Holocene environmental changes affected polar bears around Greenland. We uncover reductions in effective population size coinciding with increases in annual mean sea surface temperature, reduction in sea ice cover, declines in suitable habitat, and shifts in suitable habitat northward. Furthermore, we show that west and east Greenlandic polar bears are morphologically, and ecologically distinct, putatively driven by regional biotic and genetic differences. Together, we provide insights into the vulnerability of polar bears to environmental change and how the Arctic marine ecosystem plays a vital role in shaping the evolutionary and ecological trajectories of its inhabitants.

A Canadian guideline on the use of next-generation sequencing in oncology

Rapid advancements in next-generation sequencing (ngs) technology have created an unprecedented opportunity to decipher the molecular profile of tumours to more effectively prevent, diagnose, and treat cancer. Oncologists now have the option to order molecular tests that can guide treatment decisions. However, to date, most oncologists have received limited training in genomics, and they are now faced with the challenge of understanding how such tests and their interpretation align with patient management. Guidance on how to effectively use ngs technology is therefore needed to aid oncologists in applying the results of genomic tests. The Canadian guideline presented here describes best practices and unmet needs related to ngs-based testing for somatic variants in oncology, including clinical application, assay and sample selection, bioinformatics and interpretation of reports performed by laboratories, patient communication, and clinical trials.

The risk of breast cancer in BRCA1 and BRCA2 mutation carriers without a first-degree relative with breast cancer

The objective of this study was to estimate the lifetime risk of breast cancer in women with a BRCA1 or BRCA2 mutation with and without at least 1 first-degree relative with breast cancer. A total of 2835 women with a BRCA1 or BRCA2 mutation were followed. Age- and gene-specific breast cancer rates were calculated. The relative risks of breast cancer for subjects with a family history of breast cancer, compared to no family history were calculated. The mean age at baseline was 41.1 years, and they were followed for a mean of 6.0 years. The estimated penetrance of breast cancer to age 80 years was 60.8% for BRCA1 and 63.1% for BRCA2. For all BRCA carriers, the penetrance of breast cancer to age 80 for those with no first-degree relative with breast cancer was 60.4% and 63.3% for those with at least 1 first-degree relative with breast cancer. The risk of breast cancer for BRCA carriers with no first-degree relative with breast cancer is substantial, and as a result, clinical management for these women should be the same as those for women with an affected relative.

Abstract P3-09-05: Clinical outcome of patients with advanced triple negative breast cancer with germline and somatic variants in homologous recombination gene

Background: Variants in homologous recombination (HR) genes other than BRCA1/2 may cause a BRCA-like phenotype triple negative breast cancer (TNBC), which includes the sensitivity to platinums and DNA repair inhibitors. Evaluation of HR proficiency may influence the clinical management of TNBC. Our aim was to evaluate germline and somatic HR gene variants in advanced TNBC patients (pts) and clinical outcome.

Methods: Our cohort included advanced TNBC pts unselected for family history or age at diagnosis, enrolled in an institutional molecular screening program (NCT01505400). DNA from matched blood and FFPE tumor samples was assessed using a lab developed next generation sequencing Hereditary Cancer Panel (NGS-HCP) that includes all exons of 52 cancer predisposition genes, with 20 HR genes (Illumina MiSeq/NextSeq, germline coverage 100x, somatic coverage 500x). Medical records were reviewed for clinical outcome, pathology and prior germline BRCA1/2 testing results. All pts consented for research on banked samples and return of pathogenic germline variants was optional. Log rank test was used to determine time from surgery with curative intent to relapse (TTR) and overall survival from diagnosis to death (OS) differences based on presence of HR variants.

Results: We included 32 pts who consented for return of pathogenic germline variants and had sufficient DNA for NGS-HCP analysis. Median age at diagnosis was 45 years (range 21-80). Initial stages at diagnosis were: I (12.5%), II (62.5%), III (19%) and IV (6%). Germline HR variants were detected in 17 pts (53%) with a median number of variants per patient of 1 (range 0-6). Five pts had likely pathogenic or pathogenic variants in HR genes: BRCA1 (2), BRCA2 (1) FANCC (1) and FANCC + BML (1). Another patient had a BRCA1 pathogenic variant previously detected by Multiplex Ligation-dependent Probe Amplification but was not detected by NGS-HCP. 26 variants of unknown significance (VUS) were identified in 13 HR genes, including FANCA (6), FANCF (3) and BRCA1 (3). Only one patient had a somatic HR variant in FANCA not found in the germline. 30 pts (94%) had somatic TP53 variants. Sporadic somatic BRCA1/2 variants were not seen. BRCA1/2 variants present in the tumor were equivalent to those detected in blood of BRCA1/2 carriers. Median (m) TTR was 17 months (range 1-119) and mOS was 49 months (range 8-123). Presence of likely pathogenic or pathogenic germline variants was not associated with TTR (p=0.78) and OS (p=0.23). Presence of germline VUS, likely pathogenic or pathogenic variants also did not correlate with TTR (p=0.72) and OS (p=0.47)

Conclusions: In our cohort of pts with advanced TNBC, 12% had germline pathogenic variants in BRCA1/2, similar to the previously reported rate in early stage TNBC pts. Prevalence of likely pathogenic or pathogenic variants in non-BRCA HR genes was 6%. The presence of germline variants in HR genes was not associated with clinical outcome, however, the number of patients included was small and we had limited power to detect survival differences.Background: Variants in homologous recombination (HR) genes other than BRCA1/2 may cause a BRCA-like phenotype triple negative breast cancer (TNBC), which includes the sensitivity to platinums and DNA repair inhibitors. Evaluation of HR proficiency may influence the clinical management of TNBC. Our aim was to evaluate germline and somatic HR gene variants in advanced TNBC patients (pts) and clinical outcome.

Methods: Our cohort included advanced TNBC pts unselected for family history or age at diagnosis, enrolled in an institutional molecular screening program (NCT01505400). DNA from matched blood and FFPE tumor samples was assessed using a lab developed next generation sequencing Hereditary Cancer Panel (NGS-HCP) that includes all exons of 52 cancer predisposition genes, with 20 HR genes (Illumina MiSeq/NextSeq, germline coverage 100x, somatic coverage 500x). Medical records were reviewed for clinical outcome, pathology and prior germline BRCA1/2 testing results. All pts consented for research on banked samples and return of pathogenic germline variants was optional. Log rank test was used to determine time from surgery with curative intent to relapse (TTR) and overall survival from diagnosis to death (OS) differences based on presence of HR variants.

Results: We included 32 pts who consented for return of pathogenic germline variants and had sufficient DNA for NGS-HCP analysis. Median age at diagnosis was 45 years (range 21-80). Initial stages at diagnosis were: I (12.5%), II (62.5%), III (19%) and IV (6%). Germline HR variants were detected in 17 pts (53%) with a median number of variants per patient of 1 (range 0-6). Five pts had likely pathogenic or pathogenic variants in HR genes: BRCA1 (2), BRCA2 (1) FANCC (1) and FANCC + BML (1). Another patient had a BRCA1 pathogenic variant previously detected by Multiplex Ligation-dependent Probe Amplification but was not detected by NGS-HCP. 26 variants of unknown significance (VUS) were identified in 13 HR genes, including FANCA (6), FANCF (3) and BRCA1 (3). Only one patient had a somatic HR variant in FANCA not found in the germline. 30 pts (94%) had somatic TP53 variants. Sporadic somatic BRCA1/2 variants were not seen. BRCA1/2 variants present in the tumor were equivalent to those detected in blood of BRCA1/2 carriers. Median (m) TTR was 17 months (range 1-119) and mOS was 49 months (range 8-123). Presence of likely pathogenic or pathogenic germline variants was not associated with TTR (p=0.78) and OS (p=0.23). Presence of germline VUS, likely pathogenic or pathogenic variants also did not correlate with TTR (p=0.72) and OS (p=0.47)

Conclusions: In our cohort of pts with advanced TNBC, 12% had germline pathogenic variants in BRCA1/2, similar to the previously reported rate in early stage TNBC pts. Prevalence of likely pathogenic or pathogenic variants in non-BRCA HR genes was 6%. The presence of germline variants in HR genes was not associated with clinical outcome, however, the number of patients included was small and we had limited power to detect survival differences.

Citation Format: Stjepanovic N, Kim RH, Wilson M, Mandilaras V, Berman H, Amir E, Cescon D, Elser C, Randall Armel S, McCuaig J, Volenik A, Demsky R, Chow H, Misyura M, Wang L, Oza AM, Kamel-Reid S, Stockley T, Bedard PL. Clinical outcome of patients with advanced triple negative breast cancer with germline and somatic variants in homologous recombination gene [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-09-05.

The sooner the better: Genetic testing following ovarian cancer diagnosis

OBJECTIVE

As treatment based genetic testing becomes a reality, it is important to assess the attitudes and preferences of women newly diagnosed with ovarian cancer regarding genetic testing. The objective of this study was to determine when women with a diagnosis of high grade serous ovarian cancer would prefer to undergo genetic testing and factors that influence this preference.

METHODS

Women over 18years of age with a known diagnosis of high grade serous ovarian cancer diagnosed between October 2010-2013 were identified via the Princess Margaret Cancer Center Registry. Participants completed a questionnaire, which obtained preferences and attitudes towards genetic testing, cancer history, and demographic information.

RESULTS

120 of the 355 women identified (33.8%) completed the questionnaires. The median age at time of ovarian cancer diagnosis was 57years (range 35-84). The majority of participants in this study were offered (94.6%) and pursued (84.8%) genetic testing. In this cohort, testing was most frequently offered at diagnosis (41.8%) or during treatment (19.1%). In this study, women with high grade serous ovarian cancer felt that genetic testing should be offered before or at the time of diagnosis (67.8%). Having a family history of breast or ovarian cancer was significantly (p=0.012) associated with preferring genetic testing at an earlier time point in the disease course.

CONCLUSIONS

Our results demonstrate that women with high grade serous ovarian cancer acknowledge the personal and clinical utility of genetic testing and support test implementation at the time of cancer diagnosis.

Keeping it simple: genetics referrals for all invasive serous ovarian cancers

OBJECTIVE

In the province of Ontario, all women diagnosed with invasive serous ovarian cancer are eligible for genetic testing for mutations in the BRCA1 and BRCA2 genes. This study aimed to determine the proportion of these women who are seen for genetic counseling and to identify potential predictors and barriers to having genetic counseling.

METHODS

All women who were diagnosed with invasive serous ovarian cancer and had genetic counseling at Princess Margaret Hospital (PMH) between 2002 and 2009 were identified. Logistic regressions and trend analyses explored age at diagnosis, year at diagnosis, and the time between diagnosis and genetic counseling. Genetic counseling outcomes were also examined.

RESULTS

Of 623 women diagnosed with invasive serous ovarian cancer, 144 (23%) were seen for genetic counseling. As age at diagnosis increased, the likelihood of genetic counseling decreased (p=0.005). With a more recent date of diagnosis, the probability of having genetic counseling increased (p=0.032) while the time to genetic counseling decreased (p=0.001). Of women who pursued genetic testing, 31% were found to have a BRCA1 or BRCA2 mutation, 16% of whom had no family history of breast or ovarian cancer.

CONCLUSIONS

Despite the availability of genetic testing, only a small proportion of women with invasive serous ovarian cancer were seen for genetic counseling. Over time, an improvement in the proportion of women being seen for genetic counseling was noted; however barriers to seeing women with a later age at diagnosis or those with no family history of breast or ovarian cancer clearly exist.

Differential activation of protein kinase B and p70(S6)K by glucose and insulin-like growth factor 1 in pancreatic beta-cells (INS-1)

It has been shown that IGF-1-induced pancreatic beta-cell proliferation is glucose-dependent; however, the mechanisms responsible for this glucose dependence are not known. Adenoviral mediated expression of constitutively active phosphatidylinositol 3-kinase (PI3K) in the pancreatic beta-cells, INS-1, suggested that PI3K was not necessary for glucose-induced beta-cell proliferation but was required for IGF-1-induced mitogenesis. Examination of the signaling components downstream of PI3K, 3-phosphoinositide-dependent kinase 1, protein kinase B (PKB), glycogen synthase kinase-3, and p70-kDa-S6-kinase (p70(S6K)), suggested that a major part of glucose-dependent beta-cell proliferation requires activation of mammalian target of rapamycin/p70(S6K), independent of phosphoinositide-dependent kinase 1/PKB activation. Adenoviral expression of the kinase-dead form of PKB in INS-1 cells decreased IGF-1-induced beta-cell proliferation. However, a surprisingly similar decrease was also observed in adenoviral wild type and constitutively active PKB-infected cells. Upon analysis of extracellular signal-regulated protein kinase 1 and 2 (ERK1/ERK2), an increase in ERK1/ERK2 phosphorylation activation by glucose and IGF-1 was observed in kinase-dead PKB-infected cells, but this phosphorylation activation was inhibited in the constitutively active PKB-infected cells. Hence, there is a requirement for the activation of both ERK1/ERK2 and mammalian target of rapamycin/p70(S6K) signal transduction pathways for a full commitment to glucose-induced pancreatic beta-cell mitogenesis. However, for IGF-1-induced activation, these pathways must be carefully balanced, because chronic activation of one (PI3K/PKB) can lead to dampening of the other (ERK1/2), reducing the mitogenic response.

Sequencing and expression analysis of the serine protease gene cluster located in chromosome 19q13 region

The human kallikrein gene cluster, located in the chromosome band 19q13, contains several tissue-specific serine protease genes including the prostate-specific KLK2, KLK3 and prostase genes. To further characterize the gene cluster, we have mapped, sequenced, and analyzed the genomic sequence from the region. The results of EST database searches and GENSCAN gene prediction analysis reveal 13 serine protease genes and several pseudogenes in the region. Expression analysis by RT-PCR indicates that most of these protease genes are expressed only in a subset of the 35 different normal tissues that have been examined. Several protease genes expressed in skin show higher expression levels in psoriatic lesion samples than in non-lesional skin samples from the same patient. This suggests that the imbalance of a complex protease cascade in skin may contribute to the pathology of disease. The proteases, excluding the kallikrein genes, share approximately 40% of their sequences suggesting that the serine protease gene cluster on chromosome 19q13 arose from ancient gene duplications.