Cancer Research & Oncology 2019

Metastatic castration resistant prostate cancer (mCRPC) refractory to secondary hormonal treatments such as enzalutamide or abiraterone acetate are the most lethal of prostate cancers. In this setting, many resistance mechanisms exist, driven both through the androgen receptor (AR) and independent of AR. In this resistant setting, more molecular biomarkers are now available to guide treatment selection. Of these, the AR-v7 splice variant of the androgen receptor can guide selection for chemotherapy based on the PROPHECY study. Furthermore, patients with mutations in DNA damage repair genes (particularly BRCA2, CDK12, BRCA1, CHEK2, and ATM) are especially susceptible to PARP inhibitors. PROfound, a recent phase 3 trial of mCRPC patients previously treated with docetaxel randomized to olaparib vs secondary hormonal inhibitors, showed improved progression free survival and ORR for olaparib. Patients with CDK12 loss and microsatellite instability also respond well to pembrolizumab, an immune checkpoint inhibitor. Therefore, given these targeted treatments outside of standard of care options, there is more impetus to perform genomic testing to evaluate for molecular biomarkers for mCRPC patients. This talk highlights these molecular alterations and treatment options in mCRPC.

Tumor mutational burden (TMB) is an emerging biomarker that correlates with response to immunotherapeutic agents, such as checkpoint inhibitors. Recent studies indicate that a high mutation load increases the likelihood that immunogenic neoantigens expressed by tumor cells may induce a response to immunotherapy.  However, TMB estimation and reporting can be heavily influenced by differing working processes across clinical and research laboratories; primarily, the choice of assay, platform, and how the assay is implemented and interpreted. To streamline and standardize this process at scale, QIAGEN offers an end to end solution, from detection to interpretation of TMB and other somatic alterations.

In this webinar, we will provide insights into the implementation of the QIAseq Tumor Mutational Burden (TMB) Panel in the molecular diagnostics lab. This comprehensive cancer panel is capable of interrogating TMB, microsatellite instability (MSI), and other actionable alterations in a single assay, using specialized chemistry to remove false positives. Subsequently, we will discuss how QIAGEN Clinical Insight Interpret can streamline insights from comprehensive cancer profiles to deliver actionable information on detected variants and immunotherapy biomarkers, such as tumor mutational burden (TMB) and microsatellite instability (MSI). We will also discuss the concordance of the automatic implementation of the AMP/ASCO/CAP guidelines with manual expert classifications.

Osteosarcoma (OS) is the most common bone tumor in pediatric and adolescent/young adult patients. Over the past three decades, significant improvements in the survival rates or therapeutic approaches for these patients have not been made, especially in the context of metastatic disease. While immune checkpoint blockade has revolutionized the therapeutic landscape of various adult malignancies, its impact in OS has been largely underwhelming. Currently, it is unknown whether the lack of therapeutic benefit of immune checkpoint inhibition observed in patients with OS is truly due to treatment inefficacy rather than a limited understanding of the tumor microenvironment that supports this aggressive disease. To address this knowledge gap, we have profiled metastatic and non-metastatic osteosarcoma specimens using NanoString’s PanCancerIO360™ Gene Expression Panel. Our results show that metastatic specimens exhibit lymphocyte exclusion and immunohistochemistry confirms that T cells are confined to the periphery of the pulmonary lesions. Our data also provides evidence of vascular dysfunction in metastatic OS indicated by increased expression of VEGFA, an increased ANGPT2:ANGPT1 gene expression ratio, and decreased expression of SELE. Correlation analyses show an inverse relationship between lymphocyte abundance and markers of vascular dysfunction exclusively in the metastatic specimens. Together, our data shows that the non-metastatic OS specimens expressed increased levels of various immunotherapeutic targets in comparison metastatic specimens and identifies vascular dysfunction and lymphocyte exclusion as important processes for therapeutic intervention in metastatic disease.

FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.

Learning Objectives: 

1. Understand the complexity behind the response of osteosarcoma to immunotherapy
2. Learn the difference between the immune infiltrate of metastatic and non-metastatic osteosarcoma

Accumulation of structural variations (SVs) across the genome is a known trigger factor for oncogenesis. Structural mutations have been clearly implicated in a number of cancers, most notably translocations that result in druggable fusions involving genes such as NTRK, MPRSS2, RET, FGFR3, ALK, and ESR1.  Identifying these structural genomic alterations - accurately and comprehensively - is crucial for improving research and ultimately therapies for cancer patients, yet one of primary challenges when solely relied on short read sequencing and standard cytogenetic methods (e.g. karyotyping, FISH and chromosomal microarrays).
 
Whole genome imaging, enabled by the Bionano Saphyr® System, is quickly becoming established as a key method for detection of intractable types of structural variations. The Saphyr System images ultra-long, linearized DNA molecules labeled at specific sequence motifs. Comparative analysis of the label patterns over long contiguous reads across the whole genome, reveals structural variants (>500 bp), at sensitivities as high as 99%, with false positive rates below 2%, even at allele fractions as low as 5%. Whole genome imaging can accurately assemble and assay relevant regions for complex genomic disorders like cancer as well as for repeat expansion disorders, even those involving very large segmental duplications. Bioinformatics tools, an integral part of the Saphyr System, effectively prioritize the ~6000 structural variants based on the estimated frequency in a control population, whether it’s inherited germline or de novo, whether it’s somatic and also its proximity to a gene. As a case in point, whole genome imaging has to date unraveled a number of genes never implicated in cancer and shown how they are affected by structural variations, along with deciphering novel structural variants. Hence, combining whole genome imaging with whole genome sequencing offers a strong integrative approach to understand small and large genomic variations in cancers.

For Research Use Only. Not for use in diagnostic procedures.

Copy-number alterations and chromosomal translocations are widespread in cancer and frequently causing oncogenic mutations that drive tumorigenesis and therapy resistance. Despite their prevalence, how these alterations arise during tumor development remains a mystery. We have gained significant insight into this question by analyzing alterations in unstable genomes at the single-cell level over one and multiple generations. Our results indicate that even a single broken chromosome in an ancestor cell can cause highly dynamic evolution and generate extensive genetic diversity in the progeny population, giving rise to all forms of alterations in cancer genomes, including focal amplification and deletion, arm-level copy-number changes, and complex rearrangements. We hypothesize that such genetic diversity may fuel the transition from pre-malignancy to cancer and present preliminary evidence from the analyses of Barrett’s Esophagus as a precursor to esophageal adenocarcinoma. Together, our results suggest that a few simple mechanisms of chromosomal evolution may be sufficient to create the enormous complexity of cancer genomes and the evolution of unstable genomes may be not totally random after all.

Learning objectives:

1. What makes an unstable chromosome and how does it trigger genome evolution?
2. How does genome instability and genetic diversity promote tumor development?

Blockade of CTLA-4 and PD-1, members of the B7/CD28 family, have proven to be the most successful cancer immunotherapies to date. While the current therapeutic focus remains on B7/CD28 family members, novel immunoregulatory pathways are being uncovered as potential targets for oncology research and cancer immunotherapy. In this presentation, we discuss some of the next generation of novel immune checkpoint molecules, including Butyrophilins (BTNs), leukocyte immunoglobulin-like receptors (LILRs), and V-Set and Immunoglobulin domain containing (VSIGs). Specifically, we will present data demonstrating that bioactive recombinant Butyrophilin proteins (BTN1A1, BTN2A2, and BTN3A1) are T cell inhibitory modulators that inhibit cytokine secretion and cell proliferation on anti-CD3 activated T cells. We will also show data identifying ANGPTL proteins as novel LILR receptors and discuss a novel group of proteins termed V-Set And Immunoglobulin Domain-Containing (VSIG).

The Keynote Address will highlight eight actions that individuals can take to reduce their cancer risk. These recommendations span lifestyle modifications, cancer screening and molecular prevention. The evidence supporting these recommendations will be reviewed. The presentation will also describe the elements of a clinical cancer prevention program, using examples from MD Anderson’s Cancer Prevention Center.

Learning Objectives:

1. Identify evidence-based actions that can be recommended to individuals to reduce their cancer risk and understand the data supporting them.
2. Describe elements of building a clinical cancer prevention program.

In this webinar, we will be discussing some of our most recent testing using our Cas9 proteins, Cas9 RNP nickases in a variety of human cell types, including primary T-cells. Cas nucleases when delivered in protein format, pre-complexed with a single, modified guide RNA (gRNA), rather than encoded on a plasmid, allow researchers to bypass the historically limiting factors of using CRISPR in the therapeutic realm of off-targeting effects, low efficiency, and undesired cellular responses to foreign DNA. Modifying that Cas9 nuclease into a nickase with only a single active cutting domain, and then delivering two with proximal guide RNAs in a pair allows precise double stranded breaks, and provides hyper-specific and efficient genome editing in cell types that are more difficult to edit in.

CRISPR/Cas technologies have unlocked vast genome editing possibilities in human cell lines but have been historically limited in the therapeutic realm by off-targeting effects, low efficiency, and undesired cellular responses to foreign DNA plasmids. Recent advancements to combat these limitations include the direct delivery of ribonucleoproteins (RNPs) to cells. In this method, Cas nucleases are delivered in protein format, pre-complexed with a single, modified guide RNA (gRNA), rather than encoded on a plasmid. Another recent advancement is the use of paired Cas9 nickase systems. A nickase is a modified Cas9 nuclease with only one active cutting domain, allowing it to create single-stranded nicks in its target DNA. To achieve a double-stranded break (DSB), nickases must utilize two individual gRNAs targeting proximal DNA sequences, making an off-target DSB nearly impossible. Here, we combine these two innovations, enabling highly-efficient editing in human cells, without observable off-target effects, via the use of paired-nickase Cas9 RNPs. The improvements this system makes on previous methods lends to greater exploration of CRISPR technologies in the therapeutic domain

Learning Objectives:

1. Advantages of RNPs in Primary Cells

2. Nickase Design

3. Therapeutic Implications of this design

The quest to cure cancer through the manipulation the immune system has been at the forefront of science for the past half-decade. The result has been the emergence of a multitude of promising therapeutic approaches, many of which have been designed to promote the anti-tumorigenic activity of TILs in solid tumors.  In this webinar, we will discuss the necessary steps and considerations required for the consistent and reliable isolation and visualization of tumors and the immune cells they harbor.  Topics include:

1. Tumor storage and tissue dissociation
2. Automating target cell isolation
3. Activation, expansion and characterization of TILs
4. Whole tumor imaging using light sheet microscopy

This presentation will review the utility of multiparametric MRI (mpMRI) and genomic testing in the management of early stage prostate cancer and show when and if such tests should be used alone or in combination.
Prostate cancer (PCa) is the second most frequently diagnosed male malignancy worldwide. In the United States, approximately over 174,000 men are diagnosed with PCa and 31,000 men die of the disease per year.  The majority of PCa diagnosed, however, are low-risk indolent lesions which are not expected to increase disease-specific mortality.  Despite evidence demonstrating the lack of prostate cancer specific-survival benefit in this population, many patients receive immediate curative therapy.
 
Recently, active surveillance (AS), which monitors patients for disease progression, has been included in the National Comprehensive Cancer Network (NCCN) and American Urological Association (AUA) guidelines and is increasingly utilized as a treatment option for low- and favorable intermediate-risk patients.  Adoption of AS has been slow as current clinicopathological factors such as patient age, PSA, tumor grade (Gleason score) and tumor volume on biopsy do not adequately risk stratify patients.  
Newer tools for patient risk stratification such as mpMRI and genomic tests have substantially improved risk stratification so that clinicians can better optimize treatment selection between AS and immediate therapy such as radical prostatectomy or radiation.

The introduction of robot-assisted surgical technology into urological practice, has introduced new horizons for reducing the morbidity and enhancing the efficacy of surgery. Open radical cystectomy was the gold standard however over the years robot-assisted radical cystectomy has proven improved perioperative morbidity and similar oncologic outcomes. We investigate the status of RARC in 2019

MIBI is a powerful platform for identifying and analyzing multiple antigens in formalin-fixed paraffin-embedded tissues. This multiplexed methodology permits the identification of 40+ proteins at the same time in one single tissue section, with the ability to study various cell populations and their spatial distribution in different tissue specimens, including core needle biopsies, tissue microarrays, and whole sections at imaging resolution approaching 200nm.
During this presentation, we will show examples of cancer research using MIBI technology and provide an overview of the panel design and validation.
 
Learning Objectives:

1. Learn how MIBI technology is used in cancer research   

2. Learn how to design and optimize a MIBI panel for cancer research

A subset of women with ovarian cancer will present with an apparently isolated adnexal mass. Many of these women will have early stage ovarian cancer with a relatively good prognosis. Unfortunately, the majority of women with ovarian cancer present with advanced disease due to widespread intraperitoneal metastases. The surgical management of advanced ovarian cancer has undergone dramatic transformations over the past 20 years and that will be the focus of this presentation. A large body of retrospective data accumulated which indicated that women undergoing cytoreductive surgery for ovarian cancer did much better if all gross disease was resected (“R0”). Based on this, radical upper abdominal surgery to achieve R0 has been adopted into management. Many patients with advanced ovarian cancer are too ill or too advanced for surgery. Such patients are frequently do receive treatment with chemotherapy. It was recognized that many such patients respond well with subsequent improvement in performance status and operability. Based on this, data accumulated on management with neoadjuvant chemotherapy followed by interval cytoreductive surgery for selected patients. This data led to a series of prospective, randomized trials which demonstrated non-inferiority (when compared to primary cytoreductive surgery), along with a reduction in morbidity. Based on this, clinical practice guidelines (combined SGO/ASCO) were published in 2016 (Wright AA, et al.. Gynecol Oncol 2016; 143: 3-15) for primary management of women with advanced ovarian cancer that included evaluation by gynecologic oncologist, imaging with CT scan, utilization of neoadjuvant chemotherapy for women at high risk for surgery or low likelihood of achieving optimal cytoreduction, and histologic confirmation prior to initiation of neoadjuvant chemotherapy.

Learning objectives:

1. To gain an understanding of the evolution over the past 20 years in the surgical management of primary advanced ovarian cancer.
2. To gain insight into the technical aspects of cytoreductive surgery for advanced ovarian cancer.

Although about one in every seven men in the developed world will be diagnosed with prostate cancer in their lifetime, the mortality rate remains low with a 99% five-year survival rate for low to intermediate grade disease. Following diagnosis, surgery (radical prostatectomy), radiation therapy, hormonal therapy and chemotherapy either singly or in combinations are options for initial treatment. However, active surveillance - where disease progression is carefully monitored - may be a more appropriate option for less advanced and low grade disease.

At present a diagnosis of prostate cancer is initially and most commonly made on the basis of three investigations: the prostate specific antigen (PSA) test, digital rectal examination (DRE) and biopsy-based grading of the tumour by histopathology. It is accepted that these tests do not provide adequate information to support the decision of whether to pursue immediate treatment or active surveillance. Hence, there is a significant unmet need for specific and sensitive biomarkers to guide the decision between treatment and active surveillance, as well as for regular monitoring of disease progression in men on active surveillance.  

Despite a few decades of proteomics research and the apparent discovery of multiple protein biomarkers to support the diagnosis and treatment decisions, the number of protein biomarkers that have been developed to the stage of being used routinely is disappointingly low.  So, it's clear that whilst there’s a huge need to develop new protein biomarkers as yet biomarker development and delivery is proving very challenging.  Why is this?

This presentation will demonstrate how SRM/MRM on triple quadrupole mass spectrometers affords huge potential as a platform for the development of specific and sensitive 'biomarker signatures' comprising multiple proteins.   Strategies for the delivery and implementation of multiplexed protein biomarkers to support improved clinical decision making following prostate cancer diagnosis will be described.

Learning Objectives:

1. Appreciate the challenges faced in the management of prostate cancer
2. Recognise the need for authentic protein biomaker discovery and strategies to acheive it
3. Undertand how MRM can be used for the development of analytically validated protein biomarker signatures.
4. Appreciate the challenges associated with the delivery of biomarker signatures for routine use and improved prostate cancer patient outcomes.

For Research Use Only. Not for use in diagnostic procedures.

Acute lymphoblastic leukemia is the most common cancer in children and adolescents. While current treatments have resulted in 85-90% cure, the remaining 10-15% cases represent the leading causes of childhood cancer mortality. This is largely due to specific leukemia subtypes being resistant to treatment. One of these subtypes is hypodiploid B cell leukemia characterized by multiple chromosomal losses. For these patients, treatment options remain limited, and their prognosis is dim.

Learning Objectives:

1. How to integrate genomics and proteomics profiling with drug screens to identify potential therapeutic targets

2. How to move from in vitro to in vivo preclinical studies to inform new clinical trials.

3. The audience will learn about hypodiploidy: from cytogenetics to prognosis to drug response in the context of leukemia.

Introduction: Despite the current declines in prostate cancer mortality, African Americans (AA) continue to experience a 60% higher incidence and are twice as likely to die in comparison to men of other racial and ethnic groups. A host of factors have been postulated to explain this inequity, including access to care, patient-centered communication, concordance of patient and physician race, level of prostate cancer knowledge, attitudes and perceptions of care, socioeconomic differences, differences in biological manifestation, type and aggressiveness of treatment, diet, genetics, and lifestyle and environmental factors.  There has been no consistent strategy employed to address prostate cancer disparities, not withstanding an increased effort to provide prostate cancer screening.  Screening and early detection are likely to assist; however, the scientific evidence to date has been insufficient to definitively conclude screening for prostate cancer reduces deaths.  While the uncertainty of the effectiveness of the screening modalities for prostate cancer persists, patients are encouraged to participate in the informed decision making (IDM) process with their healthcare provider to effectively incorporate their values and preferences. However, the extent of the patient-provider interaction in general has been found to be a barrier to securing adequate healthcare among racial and ethnic groups.  Mistrust, fear, discrimination, and racism have all been cited as factors of concern, for African American men in particular, when interfacing with the healthcare system. Four patient mediating outcomes of IDM include: 1) individual risk assessment, 2) consideration of values and beliefs, 3) knowledge of the risk and benefits of screening, and 4) consideration of age and lifespan issues (i.e., existing co-morbidities).  The extent of IDM in clinical settings is unclear.  The goal of this study was to establish effective delivery practice strategies with current recommendations for IDM for prostate cancer screening among African American men.  The use of Community Navigation and digital technology in community based settings allow for the innovativeness of this study.  We conducted a community-based, Randomized Controlled Trial, to assess the effectiveness of community based education as compared to clinical setting usual care in the delivery of the IDM process. The design of the study allowed for the evaluation of the effectiveness of utilizing the Community Navigators and an enhanced Patient Decision Aid in community-based venues to disseminate IDM to AA men. The two study arms were: 1) control (usual care group) and 2) experimental (enhanced patient decision aide and lay health advisory). The eligibility criteria for the participants included: 1) have not been diagnosed or treated for any type of cancer, 2) self-identify as AA, 3) able to understand English (ability to repeat back in their own words), 4) in the age range 40-70, and 5) working telephone number.  Study findings will be presented related to the primary outcome, IDM, measured through four domains: Knowledge, Decisional Conflict, Control Preferences, and Decisional Self-Efficacy. The findings of this study have informed effective community-based strategies with current recommendations for IDM.