Early-Onset Breast Cancer in a Family with Neurofibromatosis Type 1 Associated with a Germline Mutation in BRCA1

Mutation spectrum of the NF1 gene and genotype-phenotype correlations in Turkish patients: Seventeen novel pathogenic variants

OBJECTIVE

Neurofibromatosis type 1 is one of the most common autosomal dominant diseases caused by heterozygous mutation in the NF1 gene. Wide spectrum of NF1-related clinical manifestations and mutation distribution makes genetic counselling difficult.

METHODS

The study enrolled 58 unrelated Turkish patients with clinically suspected NF1 referred to the Department of Medical Genetics. Individuals were eligible if they 1) met at least two of the main National Institutes of Health criteria or 2) had multiple café-au-lait macules as a child.

RESULTS

Fourty-one different disease-causing variants were identified in 42 (72.4%) individuals, including 17 novel variants. Twenty-four (58.2%) of the NF1 patients had de novo variants. Café-au-lait macules were observed in all patients (100%). Intracranial hamartoma was the second most common phenotype, found in 52.3% (22/42) of the patients. Other common manifestations were neurofibromas (35.7%), axillary or inguinal freckling (28.5%), and Lisch nodules (28.5%). Additionally, one patient had intra-abdominal malignant peripheral nerve sheath tumours and another patient underwent surgery for serous papillary ovarian cancer.

CONCLUSION

In conclusion, this study is one of the largest studies from Turkey to investigate the NF1 mutation spectrum and genotype-phenotype correlations.

MEScan: a powerful statistical framework for genome-scale mutual exclusivity analysis of cancer mutations

MOTIVATION

Cancer somatic driver mutations associated with genes within a pathway often show a mutually exclusive pattern across a cohort of patients. This mutually exclusive mutational signal has been frequently used to distinguish driver from passenger mutations and to investigate relationships among driver mutations. Current methods for de novo discovery of mutually exclusive mutational patterns are limited because the heterogeneity in background mutation rate can confound mutational patterns, and the presence of highly mutated genes can lead to spurious patterns. In addition, most methods only focus on a limited number of pre-selected genes and are unable to perform genome-wide analysis due to computational inefficiency.

RESULTS

We introduce a statistical framework, MEScan, for accurate and efficient mutual exclusivity analysis at the genomic scale. Our framework contains a fast and powerful statistical test for mutual exclusivity with adjustment of the background mutation rate and impact of highly mutated genes, and a multi-step procedure for genome-wide screening with the control of false discovery rate. We demonstrate that MEScan more accurately identifies mutually exclusive gene sets than existing methods and is at least two orders of magnitude faster than most methods. By applying MEScan to data from four different cancer types and pan-cancer, we have identified several biologically meaningful mutually exclusive gene sets.

AVAILABILITY AND IMPLEMENTATION

MEScan is available as an R package at https://github.com/MarkeyBBSRF/MEScan.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Chronic Lymphocytic Leukemia in Neurofibromatosis Type 1 Patients: Case Report and Literature Review of a Rare Occurrence

Neurofibromatosis type 1 (NF1) is an autosomal dominant genodermatosis that may also occur as the result of a spontaneous mutation. The diagnosis can be established by the presence of two of the seven National Institutes of Health (NIH) diagnostic criteria; several dermatologic manifestations are NIH criteria used to establish the diagnosis: axillary and inguinal freckling, café-au-lait macules, and neurofibromas. Mucosal evaluation of the eyes may detect a fourth criteria: pigmented iris hamartomas (Lisch nodules). The remaining NIH criteria include optic path glioma, distinctive osseus lesions, and a positive family history of the condition. A breast cancer 2 (BRCA2) positive woman with NF1 and chronic lymphocytic leukemia is described. Patients with NF1 have an increased lifetime risk to develop breast cancer, gastrointestinal stromal tumor, malignant glioma, malignant peripheral nerve sheath tumor, and rhabdomyosarcoma. Chronic lymphocytic leukemia occurring in NF1 patients is rare; including my female patient reported in this paper, chronic lymphocytic leukemia has only been reported in three individuals with NF1--two women and one man. The man and the other woman presented with advanced chronic lymphocytic leukemia and treatment with antineoplastic therapy at diagnosis; the man achieved clinical remission and the woman passed away from complications associated with therapy-refractory progression of her leukemia. My female patient required treatment 41 months after diagnosis and had a good clinical response; she has been without significant disease progression for 34 months. Similar to NF1, breast cancer 1 (BRCA1) and BRCA2 mutations are associated with an increased lifetime risk of developing cancer--particularly breast and ovarian carcinoma. An increased risk of chronic lymphocytic leukemia has also been demonstrated in patients with mutations of either BRCA1 or BRCA2. Also, albeit uncommon, either BRCA1 or BRCA2 mutation has been detected in women with NF1 who develop breast cancer. In conclusion, the development of chronic lymphocytic leukemia in NF1 patients may be coincidental and not associated with the underlying genodermatosis; however, the occurrence of chronic lymphocytic leukemia in my patient with NF1, in part, may be related to her BRCA2 positivity.

Contralateral Breast Cancer With Multiple Primary Neoplasms in a Patient With Neurofibromatosis Type 1: A Case Report and Review of the Literature

Neurofibromatosis type 1 (NF1) is an autosomal dominant neuroectodermal disorder associated with increased risk for several neural and non-neural malignancies. The link between NF1 and breast cancer has recently been established, with patients with NF1 being at higher risk for developing breast cancer, more likely to get breast cancer at a younger age, and more likely to have their breast cancer present with more adverse prognostic factors. Although rare, several cases of NF1 patients with contralateral breast cancer have been mentioned in the literature. We report the case of one such patient who developed contralateral breast cancer 40 years after her initial breast cancer diagnosis.

Pancreatic Gastrinoma, Gastrointestinal Stromal Tumor (GIST), Pheochromocytoma, and Hürthle Cell Neoplasm in a Patient with Neurofibromatosis Type 1: A Case Report and Literature Review

BACKGROUND Neurofibromatosis type 1 (NF1) is a multi-tumor syndrome in which affected patients develop malignancies that are rare in the overall population, such as tumors of neural or endocrine origin. CASE REPORT A 67-year-old woman with a clinical diagnosis of NF1 presented with abdominal pain and pneumoperitoneum. She underwent small-bowel resections for a perforated jejunal lesion and a second lesion in the ileum; pathology showed a neurofibroma at the site of the perforation and a 1-cm low-grade GIST, respectively. Additional staging with cross-sectional imaging identified a 3.7-cm pancreatic head mass and a 1.7-cm left adrenal mass; biochemical studies revealed elevated serum gastrin and urinary free metanephrines and catecholamines consistent with pheochromocytoma. Initial surgical management was a left posterior retroperitoneoscopic adrenalectomy. Postoperatively, gallium-68-DOTATOC PET/CT showed uptake in the pancreatic head and a 28-mm left thyroid nodule. Months later, she had an open pancreaticoduodenectomy. Pathology showed pheochromocytoma and a low-grade (G1) gastrinoma involving 2/8 peripancreatic lymph nodes (pT3pN1M0), respectively. Fine-needle aspiration biopsy of the thyroid nodule showed features consistent with a Hürthle cell neoplasm. Genetic testing identified a pathogenic mutation in NF1 and no mutations in BRCA1/2, CDC72, MEN1, or PALB2. The patient continues surveillance, with no evidence of recurrent disease. CONCLUSIONS We report the fifth case of gastrinoma associated with NF1 and the first to arise from the pancreas. This case of a pancreatic neuroendocrine tumor was associated with multiple additional neoplasms. Neuroendocrine tumors found in NF1 should raise suspicion of other malignancies.

Early-onset malignant phyllodes breast tumor in a patient with germline pathogenic variants in NF1 and BRCA1 genes

We present a 24-year-old female patient affected by neurofibromatosis type 1 (NF1) who developed a malignant phyllodes tumor of the breast. The molecular studies showed that the patient carried a heterozygous inactivating deleterious variant in BRCA1 inherited from the father associated with a germline de novo pathogenic alteration in NF1; the tumor presented a biallelic inactivation of both genes. Therefore, tumor analyses helped to establish that the germline NF1 and BRCA1 variants were in cis on the paternal chromosome. This last information is important to provide adequate genetic counselling regarding the risk of recurrence in the offspring, as well as opportunity for early intervention. In conclusion, we present the first case of a malignant phyllodes tumor of the breast in patient carrying pathogenic variants in NF1 and BRCA1. Further studies will be necessary to understand if the phyllodes histotype represents a very rare component of NF1-associated breast cancer.

Increased breast cancer risk in women with neurofibromatosis type 1: a meta-analysis and systematic review of the literature

BACKGROUND

Neurofibromatosis type 1 (NF1) is a cancer predisposing syndrome. Studies suggest that women < 50 years old (y.o.) with NF1 have an increased breast cancer (BC) incidence and BC associated mortality. However, this has not been widely recognized secondary to small study populations.

METHODS

A systematic literature review was conducted through database searches for BC and NF1: 3456 articles identified, 166 reviewed, 58 used for descriptive analysis and 4 utilized for meta-analysis. Fisher's exact tests, Kaplan-Meier curves and random-effects meta-analysis models were used for analysis.

RESULTS

Two hundred eighty-six cases of NF1 and female BC were identified with a median age of 46 years at diagnosis; 53% were <  50. Peak age of BC diagnosis was between 34 to 44 years. Women < 50 y.o. presented with more advanced disease vs. those ≥50 (56% vs. 22% stage III-IV, respectively; p = 0.005). Median survival for the entire cohort was 5 years vs. the reported median BC survival of over 20 years in the general population using the SEER database. Median age at BC death was 48.5 years; 64% of deceased patients were <  50. Meta-analysis of a total of 4178 women with NF1 revealed a BC standardized incidence ratio (SIR) of 3.07 (95%CI 2.16-4.38) for women with NF1 vs. the general population. Women < 50 y.o. demonstrated a higher SIR of 5.08 (95%CI 3.77-6.81) compared to 1.92 (95%CI 1.40-2.63) if ≥50 y.o.

CONCLUSIONS

This systematic literature review and meta-analysis suggests that women with NF1 <  50 y.o. have a five-fold increased risk of BC, present with more advanced disease, and may have an increased BC related mortality. Increased awareness and implementation of recent National Comprehensive Cancer Network early BC screening guidelines for this high-risk patient population is essential. Additional evaluation on the influence of NF1 gene mutations identified in patients undergoing hereditary cancer genetic testing on breast cancer risk in individuals without clinical evidence of NF1 is needed.

Metachronous bilateral triple-negative breast cancer associated with neurofibromatosis type 1: A case report

The present study reports a case of metachronous bilateral breast cancer associated with neurofibromatosis type 1 (NF1). A 67-year-old female, who had undergone a radical mastectomy of the left breast 34 years ago due to breast cancer, presented with a tumor of the right breast. The clinical stage of the original breast cancer was T2N0M0 stage IIA and adjuvant chemotherapy had not been not administered. With regard to the right-sided breast tumor, on physical examination, multiple neurofibromas and café-au-lait spots were found to be scattered over the skin. A 2-cm tumor was palpable. The preoperative histopathological diagnosis of the right-sided breast tumor was invasive ductal carcinoma, T2N0M0 stage IIA, with negative results for hormone receptors and human epidermal growth factor receptor 2. The patient underwent a modified radical mastectomy and axillary node dissection, and received adjuvant chemotherapy. The bilateral tumors were similar in histology and immunophenotype, each being histological grade 3, triple-negative and with a basal-like subtype. Based on a literature review of 90 breast cancers in 84 patients with NF1 (84 patients, 90 breasts), younger age onset, advanced clinical stage and hormone receptor negativity were characteristic features. Bilateral cancer occurred in 8.3% of patients and was characterized by ER negativity, earlier stage and younger age compared with patients with unilateral cancer.

Clonal lineage of high grade serous ovarian cancer in a patient with neurofibromatosis type 1

Neurofibromatosis type 1 (NF1) is caused by mutations in the NF1 gene encoding neurofibromin, which negatively regulates Ras signaling. NF1 patients have an increased risk of developing early onset breast cancer, however, the association between NF1 and high grade serous ovarian cancer (HGSOC) is unclear. Since most NF1-related tumors exhibit early biallelic inactivation of NF1, we evaluated the evolution of genetic alterations in HGSOC in an NF1 patient. Somatic variation analysis of whole exome sequencing of tumor samples from both ovaries and a peritoneal metastasis showed a clonal lineage originating from an ancestral clone within the left adnexa, which exhibited copy number (CN) loss of heterozygosity (LOH) in the region of chromosome 17 containing TP53, NF1, and BRCA1 and mutation of the other TP53 allele. This event led to biallelic inactivation of NF1 and TP53 and LOH for the BRCA1 germline mutation. Subsequent CN alterations were found in the dominant tumor clone in the left ovary and nearly 100% of tumor at other sites. Neurofibromin modeling studies suggested that the germline NF1 mutation could potentially alter protein function. These results demonstrate early, biallelic inactivation of neurofibromin in HGSOC and highlight the potential of targeting RAS signaling in NF1 patients.

Breast cancer risk and germline genomic profiling of women with neurofibromatosis type 1 who developed breast cancer

NF1 mutations predispose to neurofibromatosis type 1 (NF1) and women with NF1 have a moderately elevated risk for breast cancer, especially under age 50. Germline genomic analysis may better define the risk so screening and prevention can be applied to the individuals who benefit the most. Survey conducted in several neurofibromatosis clinics in the United States has demonstrated a 17.2% lifetime risk of breast cancer in women affected with NF1. Cumulated risk to age 50 is estimated to be 9.27%. For genomic profiling, fourteen women with NF1 and a history of breast cancer were recruited and underwent whole exome sequencing (WES), targeted genomic DNA based and RNA-based analysis of the NF1 gene. Deleterious NF1 pathogenic variants were identified in each woman. Frameshift mutations because of deletion/duplication/complex rearrangement were found in 50% (7/14) of the cases, nonsense mutations in 21% (3/14), in-frame splice mutations in 21% (3/14), and one case of missense mutation (7%, 1/14). No deleterious mutation was found in the following high/moderate-penetrance breast cancer genes: ATM, BRCA1, BRCA2, BARD1, BRIP1, CDH1, CHEK2, FANCC, MRE11A, NBN, PALB2, PTEN, RAD50, RAD51C, TP53, and STK11. Twenty-five rare or common variants in cancer related genes were discovered and may have contributed to the breast cancers in these individuals. Breast cancer predisposition modifiers in women with NF1 may involve a great variety of molecular and cellular functions.

Neurofibromatosis type-1 is a prognostic indicator in human gastric carcinoma

We investigated whether the Neurofibromatosis type-1(NF1) gene was of prognostic relevance to gastric cancer (GC) patients. Immunohistochemical staining of 160 matched GC tumor and adjacent normal tissue samples showed that 58.1% (93/160) of GC samples were NF1-positive as compared to 94.4% (151/160) of normal tissue samples (χ²=58.05, P <0.001). qRT-PCR analysis revealed that NF1 mRNA expression is lower in GC tissues than normal tissues (χ²=34.23, P <0.001). Moreover, NF1 protein and mRNA levels were associated with T stage (P <0.05) and TNM (P <0.001). No association was observed with other clinicopathological parameters, including gender, age, tumor size, lymph-node metastasis, cancer differentiation and distant metastasis (all P >0.05). Kaplan-Meier analysis revealed that negative or low NF1 were associated with poor overall survival (OS) in gastric cancer patients (P<0.001). Further univariate and multivariate cox regression analysis also showed that NF1 expression was an independent risk factor of survival of GC patients. These data show that NF1 has prognostic relevance to clinical outcomes in gastric cancer patients.

Unilateral gynaecomastia in a 16-month-old boy with neurofibromatosis type 1 - case report and brief review of the literature

Neurofibromatosis type 1 (NF1) is an autosomal dominant disease that shows high penetrance with a wide variability in the phenotype. Prepubertal enlargement of the breast in male subjects affected by this condition is well known, but rarely reported. The present case report describes diagnosis and therapy of unilateral gynaecomastia in a toddler showing integumental stigmata of NF1. Furthermore, the report provides a brief review of the literature concerning this finding in NF1. According to this review, the present case appears to be one of the youngest NF1-affected males affected by gynaecomastia that has been reported.

Association between Neurofibromatosis Type 1 and Breast Cancer: A Report of Two Cases with a Review of the Literature

Neurofibromatosis type 1 (NF1) is one of the most common genetic diseases in humans and is associated with various benign and malignant tumors, including breast cancer. However, an increased risk of breast cancer in NF1 patients has not been widely recognized or accepted. Here, we report two cases of breast cancer in NF1 patients and review the literature on the association between NF1 and breast cancer.