ATM whole gene deletion in an Italian family with hereditary pancreatic cancer: Challenges to cancer risk prediction associated with an 11q22.3 microdeletion.

Hereditary pancreatic cancer has been attributed to variants of several cancer predisposition genes including ATM. While heterozygous pathogenic variants in the ATM gene are implicated as a cause of familial breast and pancreatic cancers to our knowledge ATM whole gene deletions have not been previously reported. We describe a contiguous gene deletion of the ATM locus in a multi-generation family of Italian descent with a strong family history of pancreatic cancer. A deletion of one copy of the entire ATM gene was identified by routine panel testing and further characterized by chromosomal microarray analysis. An 11q22.3 microdeletion of approximately 960 kb was identified that is predicted to result in loss of 10 genes including ATM. The deletion was identified in two additional family members including a presymptomatic daughter and an affected sibling. A normal disomic complement of the 11q22.3 region was detected in a third family member with a history of prostate and pancreatic cancer. Additional family members were not available for testing. Given available evidence that ATM haploinsufficiency can increase cancer risk, we predict that the observed copy number loss has likely contributed to hereditary cancer in this family. However, absence of the familial microdeletion in at least one affected family member suggests that ATM deletions are unlikely the sole contributing factor influencing tumor development in affected individuals. This case highlights 11q22.3 microdeletions of the ATM gene region as a possible risk factor for hereditary cancer, including pancreatic cancer. The same case provides a further cautionary tale for over interpretation of cancer risk associated tumor suppressor microdeletions and suggests that the variant may not be sufficient for tumor development or may modify the cancer risks associated with other, yet unidentified hereditary cancer genes.

Utility of the Edmonton Frail Scale in identifying frail elderly patients during treatment of colorectal cancer.

BACKGROUND: Frailty has been proposed by geriatricians as an indicator of functional age. The Edmonton Frail Scale (EFS) is a 15-point incremental scale; it is quick (<5 min), and simple to administer. We conducted an exploratory study to establish if the EFS add utility to clinician's expertise by determining if there was an association between EFS and receipt of chemotherapy in colorectal cancer (CRC) patients. METHODS: The EFS was administered to stage II-IV CRC patients ≥70 years. EFS assessment was completed by one of the investigators, with the treating oncology team blinded to the results. RESULTS: A total of 46 patients were enrolled, and the EFS was reproduced in 32 patients at two visits (r=0.81; 95% CI: 0.64-0.90, P<0.0001). There was no correlation between the EFS and receipt of chemotherapy for the study population as a whole; however, exclusion of stage II patients showed a reduced likelihood of receiving chemotherapy with higher EFS scores (odds ratio 0.56; 95% CI: 0.37-0.85, P<0.01 per unit increment). A similar effect was observed after multivariable analysis (adjusting for performance status, age, stage and gender, odds ratio 0.41 95% CI: 0.18-0.96, P<0.05 per unit increment). CONCLUSIONS: This exploratory study suggests that EFS can identify patients that oncologists may have thought were too frail for chemotherapy, independent of PS. Therefore, the EFS has the potential to add a reproducible, and quantifiable measure of frailty to the clinician's decision making toolset. A follow up study will employ the EFS in real-time, and determine if using the EFS can minimize complications and unplanned health care utilization in elderly cancer patients.

Germline mutations and variants in the succinate dehydrogenase genes in Cowden and Cowden-like syndromes.

Individuals with PTEN mutations have Cowden syndrome (CS), associated with breast, thyroid, and endometrial neoplasias. Many more patients with features of CS, not meeting diagnostic criteria (termed CS-like), are evaluated by clinicians for CS-related cancer risk. Germline mutations in succinate dehydrogenase subunits SDHB-D cause pheochromocytoma-paraganglioma syndrome. One to five percent of SDHB/SDHD mutation carriers have renal cell or papillary thyroid carcinomas, which are also CS-related features. SDHB-D may be candidate susceptibility genes for some PTEN mutation-negative individuals with CS-like cancers. To address this hypothesis, germline SDHB-D mutation analysis in 375 PTEN mutation-negative CS/CS-like individuals was performed, followed by functional analysis of identified SDH mutations/variants. Of 375 PTEN mutation-negative CS/CS-like individuals, 74 (20%) had increased manganese superoxide dismutase (MnSOD) expression, a manifestation of mitochondrial dysfunction. Among these, 10 (13.5%) had germline mutations/variants in SDHB (n = 3) or SDHD (7), not found in 700 controls (p < 0.001). Compared to PTEN mutation-positive CS/CS-like individuals, those with SDH mutations/variants were enriched for carcinomas of the female breast (6/9 SDH versus 30/107 PTEN, p < 0.001), thyroid (5/10 versus 15/106, p < 0.001), and kidney (2/10 versus 4/230, p = 0.026). In the absence of PTEN alteration, CS/CS-like-related SDH mutations/variants show increased phosphorylation of AKT and/or MAPK, downstream manifestations of PTEN dysfunction. Germline SDH mutations/variants occur in a subset of PTEN mutation-negative CS/CS-like individuals and are associated with increased frequencies of breast, thyroid, and renal cancers beyond those conferred by germline PTEN mutations. SDH testing should be considered for germline PTEN mutation-negative CS/CS-like individuals, especially in the setting of breast, thyroid, and/or renal cancers.

Cowden syndrome.

Cowden syndrome (CS), due to germline mutations of the PTEN tumor-suppressor gene, is an often overlooked cancer predisposition syndrome associated with an increased risk of breast, thyroid, and endometrial cancers, as well as benign manifestations. Germline PTEN mutations also are associated with syndromes that have not been historically connected to an increase in risk for malignancy. These disorders include Bannayan-Riley-Ruvalcaba syndrome (BRRS), Proteus syndrome (PS), and Proteus-like syndrome (PSL). These syndromes can be described under the umbrella of PTEN hamartoma tumor syndrome (PHTS). As one would expect in allelic disorders, there is broad phenotypic overlap in the PHTS; however, the syndromes are clinically distinct. As additional information is discovered about new syndromes of cancer predisposition and their concordant genes, oncologists and allied healthcare providers must maintain vigilance to appropriately identify, and screen, individuals at an increased risk. Although CS is the only PHTS with a clearly documented predisposition to malignancies, pending further data, for precautionary reasons all individuals with a germline PTEN mutation are recommended to follow the cancer surveillance recommendations for CS.

Hamartomatous polyposis syndromes.

The hamartomatous polyposis syndromes are a heterogeneous group of disorders that share an autosomal-dominant pattern of inheritance and are characterized by hamartomatous polyps of the gastrointestinal tract. These syndromes include juvenile polyposis syndrome, Peutz-Jeghers syndrome and the PTEN hamartoma tumor syndrome. The frequency and location of the polyps vary considerably among syndromes, as does the affected patient's predisposition to the development of gastrointestinal and other malignancies. Although the syndromes are uncommon, it is important for the clinician to recognize these disorders because they are associated with considerable morbidity and mortality, not only from malignancy but also from nonmalignant manifestations such as bleeding, intussusception, and bowel obstruction. Each hamartomatous polyposis syndrome has its own distinctive organ-specific manifestations and each requires a different surveillance strategy, which makes accurate diagnosis crucial for appropriate patient management. The availability of clinical genetic testing for these disorders means that appropriate recognition allows for timely referral for cancer genetic counseling, and often allows for predicative testing in at-risk family members. Promisingly, an understanding of the molecular pathogenesis of these disorders offers insights into the mechanisms underlying the development of sporadic malignancy, and enables rational selection of targeted therapies that warrant further investigation.

Germline mutations in PTEN and SDHC in a woman with epithelial thyroid cancer and carotid paraganglioma.

BACKGROUND: A 43-year-old woman presented to a cancer genetics clinic for a genetic risk assessment because of her personal history of multiple neoplasias. At 37 years of age, she was diagnosed with multifocal papillary thyroid cancer, and within a year was further diagnosed with a paraganglioma of the left common carotid artery. Two years later, she was diagnosed with a paraganglioma of the right carotid body. All three tumors were treated with surgical resection. There was no family history of malignancy. Past medical history includes uterine leiomyoma and fibrocystic breast disease. Physical examination revealed macrocephaly and papillomatous papules. INVESTIGATIONS: CT scan of the neck and thorax, 24-hour urine collection for measurement of metanephrines and catecholamines, MRI of the neck, thorax, and abdomen, metaiodobenzylguanidine scan, germline mutation analysis of PTEN, SDHB, SDHC and SDHD. DIAGNOSIS: Cowden syndrome due to a germline mutation of PTEN, and pheochromocytoma-paraganglioma syndrome due to a germline mutation of SDHC. MANAGEMENT: Clinical surveillance for breast, endometrial, thyroid, and renal cell carcinoma risks associated with Cowden syndrome according to the National Comprehensive Cancer Network guidelines, annual MRI of the neck, thorax, abdomen and pelvis, annual metabolic screening, and where available, annual 18-fluorodopamine PET scanning, predictive genetic testing of both PTEN and SDHC for the patient's daughter and parents.

Cowden syndrome-affected patients with PTEN promoter mutations demonstrate abnormal protein translation.

Germline mutations of PTEN (phosphatase and tensin homolog deleted on chromosome 10) are associated with the multihamartomatous disorder Cowden syndrome (CS). Moreover, patients with CS with germline PTEN promoter mutations have aberrant PTEN protein expression and an increased frequency of breast cancer. Here, we examined the downstream effect of five PTEN promoter variants (-861G/T, -853C/G, -834C/T, -798G/C, and -764G/A) that are not within any known cis-acting regulatory elements. Clinically, all five of these patients have been given diagnoses of breast, thyroid, and/or endometrial cancer. We demonstrated that protein binding to the PTEN promoter (-893 to -755) was not altered in the five variants when compared with the wild-type (WT) promoter. However, reporter assays indicated that three of the variants (-861G/T, -853C/G, and -764G/A) demonstrated an ~50% decrease in luciferase activity compared with the WT construct. PTEN messenger RNA (mRNA) levels were not altered in these variants, whereas secondary structure predictions indicated that different PTEN 5' untranslated region transcript-folding patterns exist in three variants, suggesting an inhibition of protein translation. This was confirmed by PTEN protein analysis. These data indicate that variants causing large mRNA secondary structure alterations result in an inhibition of protein translation and a decrease in PTEN protein expression. These data emphasize the importance of PTEN promoter nucleotide variations and their ability to lead to CS progression by a novel regulatory mechanism. Importantly, these patients have a high prevalence of breast, thyroid, and endometrial malignancies; thus, understanding of the mechanism of PTEN dysfunction in these patients will lead to more-sensitive molecular diagnostic and predictive testing and, ultimately, to rational targeted therapies to treat or prevent malignancy.

Comparative genomic and functional analyses reveal a novel cis-acting PTEN regulatory element as a highly conserved functional E-box motif deleted in Cowden syndrome.

Germline mutations in PTEN, encoding a phosphatase on 10q23, cause Cowden syndrome (CS) and Bannayan-Riley-Ruvalcaba syndrome (BRRS). Approximately, 10% of CS-related PTEN mutations occur in the PTEN promoter and 11% of BRRS-related mutations include large deletions, often favoring the gene's 5' end (exon 1, promoter). In order to better understand the mechanism(s) underlying the deregulation of PTEN in these syndromes, it is important that functional cis-regulatory elements be identified. We employed a comparative genomic approach combined with molecular genetic techniques to identify a highly conserved sequence upstream of the PTEN promoter, sharing 80% sequence identity among Homo sapiens, Mus musculus and Rattus norvegicus. Within this region, we identified a canonical E-box sequence (CACGTG) located at position -2181 to -2176, approximately 800 bp upstream of the PTEN core promoter and more than 1.1 kb upstream of its minimal promoter region (located at -958 to -821). In vitro assays suggest that this motif is recognized by members of the basic region-helix-loop-helix-leucine-zipper (bHLH-LZ) transcription factor family, USF1 and USF2, and reporter assays indicate that this novel E-box is involved in mediating PTEN transcriptional activation. Four of 30 CS/CS-like patients, without previously identified PTEN mutations, were found with germline deletions of the E-box element. Of the four, three had deletions stretching to exon 1, but not 3' of it; importantly, one classic CS patient harbored a germline deletion localizing to this E-box region, further affirming the role of this element in PTEN's regulation and deregulation, and its contribution to the pathogenesis of CS.

Cancer phenomics: RET and PTEN as illustrative models.

Cancer phenomics, the systematic acquisition and objective documentation of host and/or somatic cancer phenotypic data at many levels, is a young field compared with other molecular-based 'omics'. Two relatively advanced phenomic paradigms are associated with phosphatase and tensin homologue (PTEN) and rearranged during transfection (RET), genes that are associated with cancer predisposition syndromes in addition to developmental disorders. The phenomic characterization of PTEN and RET underscores the importance of incorporating robust phenomics into the host 'omic' profile, and shows that the evolution of phenomics will be crucial to the advancement of personalized medicine.