Hypothesis 1: A more favorable immunological response to tumor occurs in LTS with advanced-stage HGSC than in STS and MTS.

 HGSC is one of the most genomically unstable solid cancers with a high degree of intratumoral heterogeneity (ITH). Advanced carcinomas such as HGSC are composed of multiple subclones and the subclonal structure of cancers continually evolves in response to selective pressures, resulting in emergence of treatment-resistant variants in many cases. Yet at the same time, emerging tumor variants can express novel antigens that instigate new cycles of immune recognition and attack. For the immune system to successfully contend with advanced cancers, it must either eliminate all tumor subclones within the patient or deploy surveillance and effector mechanisms that continually respond to and control the evolving tumor. Understanding these mechanisms is essential for the development of immunotherapies. The most current research indicates that CD8+ Tumor Infiltrating Lymphocytes (TIL) are associated with improved survival. Additional studies have indicated important roles for other immune related genes as well, including Interleukin-18, Major Histocompatibility Complex (MHC) Class I and II, and other components of antigen processing machinery and tumor infiltrating B Cells.

The biological properties of TILs and their well-established association with patient survival provide compelling support for a role in promoting exceptional survival. Nonetheless, TIL patterns have not been assessed in a well-defined cohort of 10+ year survivors and could differ from those associated with short/mid-term survival. The primary aim of this project will be to analyze patterns of TIL and other immune cells using multi-color immunohistochemistry (mcIHC) on FFPE tissue microarrays (TMA).

Hypothesis 2: The germline, somatic genomic and/or epigenomic characteristics of the tumor genome differ in LTS with advanced stage HGSC compared to STS and MTS.

The homologous recombination (HR) DNA repair pathway is defective in approximately 50% of HGSC, owing to germline, somatic and epigenetic alterations in BRCA1 and BRCA2 and, to a lesser extent, other components of the HR pathway. It is possible that exceptional responders to treatment share certain unusual patterns of HR deficiency. For example, compound mutations in two or more HR pathway genes, may result in particularly profound responses to platinum-based therapy and reduce the likelihood of developing chemoresistance. With the exception of TP53, BRCA1 and BRCA2, point mutations in oncogenes or tumor suppressor genes are relatively uncommon in HGSC. Rather, HGSCs are characterized by genomic structural variation which results in inactivation of tumor suppressors. Using whole genome sequencing, we have shown recently that gene breakage is an important mechanism of inactivating the tumor suppressors. Four molecular subtypes of HGSC have been identified using these methods and are associated with differential clinical outcomes and microenvironmental features, such as immune and stromal activation.

There are three aims to this portion of the project:

1) The primary aim of this project is to quantitate the contribution of HR deficit caused
by germline or somatic loss-of-function mutations in HR pathway genes by sequencing the coding sequences and splice-sites of HR genes in 1800 tumors and matched germline DNA.

2) To use whole genome sequencing to analyze somatic and germline DNA alterations of tumor DNA and matched germline DNA of 30 patients.

3) To use a custom NanoString panel of 100 genes, including candidate genes identified during whole genome sequencing as well as those associated with survival in OTTA, to evaluate expression in 1800 tumors.

Hypothesis 3: Diet, exercise, common medications and other personal exposures contribute to long-term survival with advanced-stage HGSC.

 It is now recognized that lifestyle, environmental, and genetic exposures influence histotype-specific risk in very different ways. Relatively few studies have considered how such factors may influence survival and generally, histotype has not been taken into consideration. Dietary, nutritional, and physical health factors are among the most commonly analyzed exposures in relation to survival. Of the studies that have been conducted, the literature is generally inconsistent. Outside of diagnosis and surgical factors, there are no factors definitively known to influence survival. Importantly, there has been little research on actions ovarian cancer patients can take to influence their survival.

There are three primary aims associated with this project:

1) To understand the relationship between pre-diagnostic environmental exposures and survival. Specifically, we will analyze known or suspected risk factors of ovarian cancer including oral contraceptive use, parity, tubal ligation, body size, physical activity, smoking, alcohol consumption, medication use and medical conditions, and diet.

2) To analyze the association between pre- and post-diagnosis medication exposures. Previous research on use of metformin, beta-blockers, and statins have suggested associations with survival however the literature is inconsistent and timing of medication exposure was not always clear.

3) To identify self-care or behavioral actions after diagnosis that survivors feel may have aided in their treatment or survival.