Dissertation
Diagnostic, prognostic, and therapeutic biomarkers in neuroendocrine tumors
University of Iowa
Doctor of Philosophy (PhD), University of Iowa
Spring 2024
DOI: 10.25820/etd.007406
Abstract
Neuroendocrine tumors (NETs) are a heterogenous group of mainly epithelial neuroendocrine neoplasms with high metastatic potential. Up to 60% of patients have advanced metastatic liver disease at the time of diagnosis. Twelve to fifty percent of primary NETs in the abdomen are regularly missed due to small tumor size, body habitus, and abdominal gases. Of these, 50% originate in the pancreas (pNETs) and small bowel (sbNETs). Often located in close proximity, they are difficult to differentiate because of similar signs and symptoms, including abdominal pain, nausea, poor appetite, weight loss, and diarrhea. However, it is particularly important to differentiate between pNETs and sbNETs due to different treatment options and protocols.
Everolimus, a mammalian target of rapamycin (mTOR) inhibitor, was approved for use in pNETs after a RADIANT-3 trial reported an increase in progression free survival (PFS). Unfortunately, no increase in overall survival (OS) was observed, which alludes to acquired everolimus resistance and creates a real limit to patient therapy. In addition to everolimus resistance, up to 5% of NETs defy site of origin assignment after exhaustive immunohistochemical and radiologic evaluation. In this backdrop, the lead authors of the 2022 World Health Organization (WHO) NET Classification stated that there remains a critical need for additional biomarkers to better classify NETs. Here we identified functional copy number alterations (fCNAs) and gene mutations that may be used as (1) diagnostic, (2) prognostic, and (3) therapeutic NET biomarkers.
Biomarkers are any biological substance, structure, or process that can be quantified to influence or predict the outcome of a disease. fCNAs are DNA copy number changes with concordant differential gene expression, are less likely to be bystander genetic lesions, and could serve as robust and reproducible tumor biomarkers.
To identify candidate (1) diagnostic and (2) prognostic NET biomarkers, we identified fCNAs by integrating chromosomal microarray and RNA-seq differential gene expression data from 31 pNETs and 33 sbNETs. Tumors were resected from 47 early disease progression (<24 months) and 17 late disease progression (>24 months) patients. Candidate fCNAs that accurately differentiated these groups were replicated using fluorescence in situ hybridization (FISH) on formalin-fixed, paraffin-embedded (FFPE) tissues in a larger validation cohort of 60 pNETs and 82 sbNETs that consisted of 52 early and 65 late disease progression samples. Logistic regression analysis was performed to determine the predictive ability and quality performance metrics were established. Our results indicate that copy number changes at chromosomal loci 7q31.2, 9p21.3, 17q12, 18q21.2, and 19q12 may be used as diagnostic and prognostic NET biomarkers.
To identify candidate genes that may be used as (3) therapeutic biomarkers in everolimus resistance, we performed both spontaneous (experimental= 2, control= 3) and Sleeping beauty induced (experimental= 7, control= 10) resistant screens in BON1 cells. DNA and RNA were collected, and sequencing was performed to identify gene mutations while assessing their impact on gene expression. Our results indicate that mutations in Angiopoietin 1(ANGPT1), DAB Adaptor Protein 1 (DAB1), Dynein Axonemal Heavy Chain 12 (DNAH12), Fanconi-associated Nuclease 1 (FAN1), Genetic Suppressor Element (GSE1), Glutaminase (GLS), LINE1 Type Transposase Domain Containing 1 (L1TD1), and Synaptic Ras GTPase Activating Protein 1 (SYNGAP1) may be involved in everolimus resistance.
Taken together, these results provide a direct response to the 2022 WHO NET Classification that stated that there is a critical need for additional biomarkers to better classify NETs. We identified fCNAs that can be utilized as (1) diagnostic NET biomarkers to determine primary tumor site for patients with metastatic liver disease and (2) prognostic NET biomarkers to help guide risk stratification of GEP NETs. We also provide a comprehensive list of candidate genes that may contribute to everolimus resistance and serve as (3) therapeutic NET biomarkers. Overall, the thorough work of this thesis could greatly impact patient care in the future.
Details
- Title: Subtitle
- Diagnostic, prognostic, and therapeutic biomarkers in neuroendocrine tumors
- Creators
- Hayley Vaughn
- Contributors
- Benjamin Darbro (Advisor)Terry Braun (Committee Member)Adam Dupuy (Committee Member)Donna Hammond (Committee Member)Aislinn Williams (Committee Member)
- Resource Type
- Dissertation
- Degree Awarded
- Doctor of Philosophy (PhD), University of Iowa
- Degree in
- Genetics
- Date degree season
- Spring 2024
- Publisher
- University of Iowa
- DOI
- 10.25820/etd.007406
- Number of pages
- xiii, 145 pages
- Copyright
- Copyright 2024 Hayley Vaughn
- Language
- English
- Date submitted
- 04/12/2024
- Description illustrations
- illustrations, tables, graph
- Description bibliographic
- Includes bibliographical references (pages 136-145).
- Public Abstract (ETD)
- Neuroendocrine tumors (NETs) are a group of cancers that occur throughout the human body. Unfortunately, up to 60% of patients have advanced metastatic liver disease at the time of diagnosis. Fifty percent of abdominal NETs occur in the pancreas (pNETs) and small bowel (sbNETs) and are difficult to distinguish because of similar signs and symptoms. However, it is important to identify the primary tumor site for appropriate patient treatment. One such treatment, everolimus was approved for use in pNETs after a clinical trial showed promising results, but unfortunately, no increase in overall survival was observed. In this backdrop, the lead researchers in the field concluded that there is a need for biomarkers to help with NET classification. Biomarkers are biological substances that can be measured to influence or predict the outcome of disease. Here we identified genetic markers that may be used as (1) diagnostic, (2) prognostic, and (3) therapeutic NET biomarkers. This will help (1) determine primary tumor site for patients with metastatic liver disease, (2) guide risk assessment, and (3) combat against drug resistance. Overall, the comprehensive work of this thesis could greatly impact patient care in the future.
- Academic Unit
- Interdisciplinary Graduate Program in Genetics
- Record Identifier
- 9984647355802771
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