Distinct Genomic Profiles Are Associated with Treatment Response and Survival in Ovarian Cancer

Association of pituitary neuroendocrine tumors and neurofibromatosis type 1: assessing causation versus coincidence. Case report

Introduction

Patients with neurofibromatosis type 1 (NF1) are at risk for developing various neoplasms. Since the early twentieth century, multiple cases of pituitary neuroendocrine tumors (PitNETs) occurring in this context have been published. Yet, the role of NF1 (17q11.2) loss-of-function (LOF) variants in pituitary tumorigenesis remains unclear.

Aim

We report the clinical and molecular characterization of a case of PitNET diagnosed in a patient with NF1. We also review the available data for and against a causal association between NF1 defects and pituitary tumors.

Methods

Our patient was recruited via an ongoing prospective study of individuals with neuroendocrine neoplasms. Genetic testing was carried out by means of targeted next generation sequencing (NGS) and Sanger sequencing in blood and tumor DNA, respectively. NF1 expression was analyzed via quantitative polymerase chain reaction (qPCR) in blood and tumor cDNA. Similar cases were searched in the literature.

Results

A 54-year-old-man was incidentally diagnosed with a clinically non-functioning PitNET via brain imaging. He had a personal and family history of NF1 and carried the germline pathogenic variant NF1 (NM_001042492.3): c.147C>A, p.Y49*. Via transsphenoidal surgery, a 16 mm lesion was resected, showing strong granular cytoplasmic immunoreactivity with patchy distribution for NF1 and preserved heterozygosity for the NF1 defect. Additional NGS ruled out germline defects in PitNET-associated genes. By qPCR, NF1 was significantly overexpressed in the tumor when compared with another NF-PitNET, but not when compared with a corticotropinoma. We reviewed twenty-three case reports of PitNETs occurring in patients with either clinical NF1 without genetic study, individuals with NF1 germline variants with or without clinical NF1 or associated with somatic NF1 defects. Predominance of GH-secreting and large PitNETs, with young-onset in around half of the cases, were noticed. Two individuals developed multiple endocrine neoplasia-like phenotypes but tested negative for other relevant genetic defects.

Conclusions

Although the association of NF1 and PitNETs could be coincidental, the clinical characteristics of the reviewed cases differ from those of typical incidentalomas. NF1 could drive pituitary tumorigenesis via haploinsufficiency, but this hypothesis requires further research. Additional clinical and molecular data from large cohorts of affected individuals should help clarify this question.

Evolutionary states and trajectories characterized by distinct pathways stratify patients with ovarian high grade serous carcinoma

Ovarian high-grade serous carcinoma (HGSC) is typically diagnosed at an advanced stage, with multiple genetically heterogeneous clones existing in the tumors long before therapeutic intervention. Herein we integrate clonal composition and topology using whole-genome sequencing data from 510 samples of 148 patients with HGSC in the prospective, longitudinal, multiregion DECIDER study. Our results reveal three evolutionary states, which have distinct features in genomics, pathways, and morphological phenotypes, and significant association with treatment response. Nested pathway analysis suggests two evolutionary trajectories between the states. Experiments with five tumor organoids and three PI3K inhibitors support targeting tumors with enriched PI3K/AKT pathway with alpelisib. Heterogeneity analysis of samples from multiple anatomical sites shows that site-of-origin samples have 70% more unique clones than metastatic tumors or ascites. In conclusion, these analysis and visualization methods enable integrative tumor evolution analysis to identify patient subtypes using data from longitudinal, multiregion cohorts.

Whole-exome sequencing of epithelial ovarian carcinomas differing in resistance to platinum therapy

Exploration of the prognostic and predictive significance of exome variation in epithelial ovarian carcinoma patients, with TP53, Hippo, homologous recombination genes, and the SBS6 signature as the most interesting results.

Epithelial ovarian carcinoma (EOC) is highly fatal because of the risk of resistance to therapy and recurrence. We performed whole-exome sequencing of blood and tumor tissue pairs of 50 patients with surgically resected EOC. Compared with sensitive patients, platinum-resistant patients had a significantly higher somatic mutational rate in TP53 and lower in several genes from the Hippo pathway. We confirmed the pivotal role of somatic mutations in homologous recombination repair genes in platinum sensitivity and favorable prognosis of EOC patients. Implementing the germline homologous recombination repair profile significantly improved the prediction. In addition, distinct mutational signatures, for example, SBS6, and overall mutational load, somatic mutations in PABPC1, PABPC3, and TFAM co-segregated with the resistance status, high-grade serous carcinoma subtype, or overall survival of patients. We generated germline and somatic genetic landscapes of prognostically different subgroups of EOC patients for further follow-up studies focused on utilizing the observed associations in precision oncology.

Interpatient Heterogeneity in Drug Response and Protein Biomarker Expression of Recurrent Ovarian Cancer

Recurrent ovarian-cancer patients face low 5-year survival rates despite chemotherapy. A variety of guideline-recommended second-line therapies are available, but they frequently result in trial-and-error treatment. Alterations and adjustments are common in the treatment of recurrent ovarian cancer. The drug response of 30 lesions obtained from 22 relapsed ovarian cancer patients to different chemotherapeutic and molecular agents was analyzed with the patient-derived ovarian-cancer spheroid model. The profile of druggable biomarkers was immunohistochemically assessed. The second-line combination therapy of carboplatin with gemcitabine was significantly superior to the combination of carboplatin with PEGylated liposomal doxorubicin (p < 0.0001) or paclitaxel (p = 0.0007). Except for treosulfan, all nonplatinum treatments tested showed a lesser effect on tumor spheroids compared to that of platinum-based therapies. Treosulfan showed the highest efficacy of all nonplatinum agents, with significant advantage over vinorelbine (p < 0.0001) and topotecan (p < 0.0001), the next best agents. The comparative testing of a variety of treatment options in the ovarian-cancer spheroid model resulted in the identification of more effective regimens for 30% of patients compared to guideline-recommended therapies. Recurrent cancers obtained from different patients revealed profound interpatient heterogeneity in the expression pattern of druggable protein biomarkers. In contrast, different lesions obtained from the same patient revealed a similar drug response and biomarker expression profile. Biological heterogeneity observed in recurrent ovarian cancers might explain the strong differences in the clinical drug response of these patients. Preclinical drug testing and biomarker profiling in the ovarian-cancer spheroid model might help in optimizing treatment management for individual patients.