Discovery of serum biomarkers of ovarian cancer using complementary proteomic profiling strategies.

Ovarian cancer is a devastating disease and biomarkers for its early diagnosis are urgently required. Serum may be a valuable source of biomarkers that may be revealed by proteomic profiling. Herein, complementary serum protein profiling strategies were employed for discovery of biomarkers that could discriminate cases of malignant and benign ovarian cancer

Commercializing molecular diagnostics in oncology

Thesis (M.B.A.)--Massachusetts Institute of Technology, Sloan School of Management, 2012.Cataloged from PDF version of thesis.Includes bibliographical references (p. 69-81).Historically, the development of molecular companion diagnostics in oncology has underwhelmed the expectation of the medical field since the successful mapping of the human genome a decade ago. There have been several highly successful developments (Her2-neu, Genomic Health, etc.), but not the widespread revolution in clinical practice expected at the turn of the century. The primary goal of this document is to investigate the economics driving molecular diagnostics and its relationship with strategic decisions in developing a diagnostic technology. The document begins with a broad analysis of the funding environment for molecular and esoteric diagnostics in oncology. Following a discussion of funding sources and current trends, the second section reviews the nature of the projects that funding supports. This is accomplished through a set of detailed case studies of Genomic Health and Immunicon to compare and contrast the strategic decisions that led to value creation events for both companies. Finally, the third section abstracts away from specific cases to develop a strategic analytic framework for evaluating the potential risk-adjusted NPV for a new diagnostic technology. Sensitivity analyses are conducted in addition to a discussion of current events that may change the structure of the underlying decision tree. The conclusion revisits the topics discussed in the first three sections, connecting the implications of funding on different strategic decisions and chances of success. Areas for further investigation both for inputs to the current model proposed, as well as for more refined versions of the development model are discussed.by Joshua Copp.M.B.A

The impact of testosterone on murine models of infection and vaccination

In men, low testosterone is associated with an increased risk of all-cause and cardiovascular related mortality, and although its immunomodulatory properties have been well characterized, the impact of testosterone on both the severity of viral infection and the efficacy of vaccination remain poorly understood. The severity of influenza increases with age in men, and as circulating testosterone concentrations also decline with age in men, I hypothesized that reduced testosterone contributes to age-associated increases in influenza severity. A murine model was used, and consistent with in humans, young male mice had greater testosterone concentrations than did aged males. Following IAV infection, aged male mice experienced greater disease severity, mortality, and pulmonary inflammation than young males, while control of viral replication was delayed. Removal of testosterone in young males increased disease severity, and pulmonary inflammation independent of changes in viral replication. Because testosterone in young male mice reduced pulmonary inflammation, I further hypothesized that testosterone was altering the immune response to IAV infection. Testosterone reduced IAV severity not by changing pulmonary cytokine activity, but instead by accelerating pulmonary leukocyte contraction. To identify which immune cell types were persisting in testosterone-depleted males, we further characterized the composition of pulmonary cellular infiltrates. Testosterone depletion accelerated the contraction of IAV-specific CD8+ T cells, while inhibiting the influx of eosinophils into the lungs following clearance of virus from the lungs. The effects of testosterone on IAV-specific CD8+ T cells were mediated androgen receptor signaling and dependent on the environment in which they reside. In contrast with IAV infection where the immune suppressive effects of testosterone are protective, in the context of vaccination any reduction in immune response may be detrimental. Adult females tend to develop greater adaptive immune responses than males following vaccination in both preclinical animal studies and human clinical trials. Following vaccination with irradiated transgenic P. berghei sporozoites expressing the P. falciparum CSP protein, adult female mice mounted greater adaptive immune responses and were better protected against challenge than adult males. No sex differences in adaptive immune responses or protection were observed in mice vaccinated prior to puberty, suggesting a role for sex steroid hormones. Depletion of testosterone in males increased, whereas rescue of testosterone decreased, adaptive immune responses and protection in males following parasite challenge. Taken together, these data suggest that testosterone confers protection during IAV infection by modulating the immune response, while testosterone concentrations in males reduce adaptive immunity and contributes to reduced malaria vaccine efficacy

Ovarian cancer. Biomarkers, surgical outcome and survival.

Ovarian cancer is the eighth most common female cancer worldwide and the most lethal of the gynaecologic malignancies. Around 700 women are diagnosed in Sweden per year. Due to vague symptoms most of the patients are diagnosed with late-stage epithelial ovarian cancer (EOC) and prognosis is poor, with a five-year survival of 49%. However, for early-stage EOC the prognosis is excellent. Biomarkers for screening and early diagnosis have been sought for decades. To date, CA125 and HE4 are the only biomarkers in clinical use. Both lack sensitivity and specificity for early-stage EOC. The standard treatment for EOC is primary surgery with adjuvant chemotherapy. Centralisation of ovarian cancer care to high-volume hospitals with subspecialist surgeons and improved chemotherapy regimens have improved outcome and survival. Ovarian cancer surgery was centralised in Sweden in 2012.The aims of my thesis were to assess new biomarkers for their potential to improve the diagnostic performance of CA125 and HE4 in women with ovarian tumours (studies I and II), to evaluate ovarian cancer surgery after centralisation (study III) and to assess the incidence and survival in EOC in Sweden since the 1960s (study IV). Study I: CA125, HE4, B7-H4 and cleaved and intact suPAR were analysed in preoperative plasma samples from 350 women with ovarian tumours. Plasma levels of CA125, HE4 and suPAR(II-III) were found to increase from benign tumours to borderline, EOC type I and EOC type II while B7-H4 was only elevated in EOC II. Logistic regression models were fitted and a model combining CA125, HE4, suPAR(II-III) and age performed better (AUC=0.933) than the established ROMA algorithm (CA125, HE4 and menopause status) for discrimination of benign tumours from EOC in premenopausal women. The ROMA performed best in postmenopausal women (AUC=0.914). Furthermore, we correlated preoperative biomarker levels with survival after EOC diagnosis. High HE4, CA125 and suPAR(I) were prognostic for poor survival. At 12 months suPAR(I) was the only independent biomarker prognostic for poor short-term survival. In women above 75 years, high suPAR(I) indicated very poor prognosis in the first year after diagnosis (HR=8.9, p=0.01).Study II: 177 inflammation- and cancer-associated biomarkers were analysed in preoperative plasma samples from 180 women with ovarian tumour, using the proximity extension assay. HE4 was the best performing single biomarker for discrimination between benign tumours and EOC. Three-biomarker combinations of HE4, CA125 and one additional biomarker were compared to a reference model of HE4 and CA125. No biomarker significantly improved the diagnostic performance of HE4 and CA125. Study III: We analysed data from the GynOp Registry 2013-15. Out of 1108 cases of ovarian cancer surgery with curative intent, 30% were performed in regional hospitals with fewer than 20 cases per year. Four tertiary centres performed more than 25 surgeries per year. Compared with regional hospitals, tertiary centres perform more extensive surgery without an increased frequency of major complications. Large differences exist in patient selection for primary surgery and complete resection rates between the tertiary centres. Study IV: We identified all women with a diagnosis of epithelial ovarian, fallopian tube, and peritoneal cancers or undesignated abdominal/pelvic cancer from 1960 to 2014 in the Swedish Cancer Registry. Analyses of age-standardised incidence and relative survival (RS) were carried out and time trend graphs were modelled according to age, tumour site, and morphology. Since 1980 the age-standardised incidence of EOC has declined in Sweden. The age-standardised RS in EOC up to five years from diagnosis improved from 1960 to 2014. The 10-year RS has remained unchanged since 1960. In conclusion, CA125 plus HE4 continues to stand out as the best biomarker combination for assessment of cancer risk in a woman with ovarian tumours. CA125, HE4 and suPAR(I) are potential prognostic markers. Adding biomarkers to the preoperative assessment, especially in elderly women, could aid in the treatment decision on extensive primary surgery or neoadjuvant treatment. After centralisation of ovarian cancer surgery in Sweden, many women still have surgery at low-volume regional hospitals. The treatment for advanced EOC seems to differ considerably between the tertiary centres. Further centralisation as well as increased collaboration and exchange of knowledge between tertiary centres are needed to ensure equal access to care, regardless of region of living. Improved surgical and oncological treatment has prolonged life after EOC diagnosis. However, long-term survival remains poor. Most patients will die of their cancer. In order to cure EOC we need to find the patients at early stages. Better diagnostic tools are urgently needed

The Path to Clinical Proteomics Research: Integration of Proteomics, Genomics, Clinical Laboratory and Regulatory Science

Better biomarkers are urgently needed to cancer detection, diagnosis, and prognosis. While the genomics community is making significant advances in understanding the molecular basis of disease, proteomics will delineate the functional units of a cell, proteins and their intricate interaction network and signaling pathways for the underlying disease. Great progress has been made to characterize thousands of proteins qualitatively and quantitatively in complex biological systems by utilizing multi-dimensional sample fractionation strategies, mass spectrometry and protein microarrays. Comparative/quantitative analysis of high-quality clinical biospecimen (e.g., tissue and biofluids) of human cancer proteome landscape has the potential to reveal protein/peptide biomarkers responsible for this disease by means of their altered levels of expression, post-translational modifications as well as different forms of protein variants. Despite technological advances in proteomics, major hurdles still exist in every step of the biomarker development pipeline. The National Cancer Institute's Clinical Proteomic Technologies for Cancer initiative (NCI-CPTC) has taken a critical step to close the gap between biomarker discovery and qualification by introducing a pre-clinical "verification" stage in the pipeline, partnering with clinical laboratory organizations to develop and implement common standards, and developing regulatory science documents with the US Food and Drug Administration to educate the proteomics community on analytical evaluation requirements for multiplex assays in order to ensure the safety and effectiveness of these tests for their intended use

2004 Little International Agricultural Exposition Catalog

https://openprairie.sdstate.edu/little_international/1060/thumbnail.jp

Non-Coding RNAs in Ovarian Cancer

Ovarian cancer (OC) is the most lethal form of gynaecological cancer, with high- grade serous ovarian carcinoma (HGSOC) being the most common and the deadliest subtype. Non-coding RNAs are a recently discovered species of RNAs that do not code for proteins, yet play a crucial role in both normal physiology and disease. The overall goal of this thesis was to apply the power of non-coding RNAs to OC with the following aims: (1) to identify novel small non-coding RNAs present in serum that could separate patients with HGSOC from healthy women as well as predict their surgical outcome, (2) to assess the role of long non-coding RNAs (lncRNAs) in promoting cisplatin resistance in cell line models of OC, and (3) to study the effects of mutant-p53 on mRNAs and lncRNAs using a small compound known as APR-246 as well as investigating the drug’s mechanisms of action. Firstly, the lethality of OC could partially be attributed to the lack of specific symptoms, leading this disease to be termed the ‘silent killer’, as well as low inci- dence rate of 9.4 cases per 100,000 individuals, both requiring a highly accurate test for population screening that remains an ongoing challenge. Measuring the levels of small non-coding RNAs, known as microRNAs, in serum, experiments described in this thesis aimed to identify novel microRNAs that could separate pa- tients with HGSOC from healthy women as well as predict their surgical outcome, one of the most important factors influencing overall patient survival. Because serum microRNAs can be affected by pre-analytical factors such as haemolysis, the sensitivity of four methodologies to detect low levels of haemolysis was first determined. This work is published in Plos One. The work described in this thesis identified a novel serum microRNA, miR-375, that could improve the accuracy of CA-125, a routinely used biomarker in diagnosing OC, in separating patients with HGSOC from healthy women. Next, serum microRNA miR-34a-5p was found to predict the surgical outcome of patients with HGSOC. In fact, miR-34a-5p was found to be superior to CA-125 for this purpose. Although the standard therapy for treating OC consists of surgical removal of the tumour followed by chemotherapy containing platinum/taxane agents, this regimen may be too aggressive for a sub- set of patients who might benefit from neoadjuvant chemotherapy, i.e. chemother- apy followed by the surgery. A pre-operative expectation of the the surgical out- come could help surgeons decide on optimal timing for surgery. Both miR-375 and miR-34a-5p were also unaffected by haemolysis. Secondly, although OC is initially sensitive to chemotherapy, most patients develop resistance within two years, resulting in recurrent disease that is difficult to treat. To identify novel lncRNAs that could promote drug resistance, expression of ninety lncRNAs was profiled in cell line models of cisplatin resistance. Five lncRNAs were found to have the potential to promote cisplatin resistance in vitro, and lncRNA Urothelial Cancer Associated 1 (UCA1) was selected for further investigations. Despite its role in promoting cisplatin resistance in bladder cancer, UCA1 was not found to promote cisplatin resistance in cell line models of OC. Lastly, the tumour suppressor TP53 plays a central role in the biology of cancer and it is almost universally mutated in HGSOC. Recent evidence suggests that p53, the protein encoded by TP53, can significantly influence the expression of both small and long non-coding RNAs. Experiments described in this thesis aimed to investigate the effect of mutant-p53 on protein-coding and non-coding RNAs by using a small compound known as APR-246 which has been reported to restore wild-type p53 activities in multiple cancers by stabilising the structure of mutant- p53. Despite currently undergoing a phase Ib/II clinical trial for potential treatment of recurrent HGSOC, the ability of APR-246 to restore wild-type p53 activities in HGSOC has not been tested. A global transcriptomic analysis conducted in this thesis discovered that p53-responsive mRNAs and lncRNAs were not robustly induced following APR-246 treatment in two cell line models of HGSOC, but indicated that APR-246 could function by inducing high levels of reactive oxidative species (ROS). Overall, data presented in this thesis demonstrated the utility of small non- coding RNAs in identifying patients with HGSOC from healthy women as well as predicting their surgical outcome. This thesis also implicated that lncRNAs, in general, could have a role in promoting cisplatin resistance in OC as well as suggested that APR-246 could, based on evidence obtained from the expression of p53-responsive mRNAs and lncRNAs, act independently of mutant-p53. Together, this research raises novel ways for clinical management of patients with HGSOC and addresses the challenge of drug resistance using non-coding RNAs, as well as questions the assumed mechanisms of action of the ‘p53-activating’ drug APR- 246