Author Interviews, Biomarkers, Cancer Research, Genetic Research, Ovarian Cancer / 07.08.2023
Ovarian Cancer: Proteomics Study Allows Identification of Subtype Resistant to Chemotherapy
MedicalResearch.com Interview with:
Pei Wang, PhD
Professor, Department of Genetics and Genomic Sciences
Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Michael J. Birrer MD PhD
Director, Winthrop P. Rockefeller Cancer Institute
University of Arkansas for Medical Sciences
Little Rock, AR 72205
Amanda G. Paulovich MD PhD
Translational Science and Therapeutics Division
Fred Hutchinson Cancer Center
Seattle WA 98109
MedicalResearch.com: What is the background for this study? How common is serous ovarian cancer?
Response: Epithelial ovarian cancer accounts for >185,000 deaths/year worldwide. The most common subtype, high-grade serous ovarian cancer (HGSOC), accounts for 60% of deaths. Despite improvements in surgical and chemotherapeutic approaches, HGSOC mortality has not changed in decades. Five-year survival remains ~30% for the majority of patients.
Standard of care involves surgical debulking combined with adjuvant or neoadjuvant chemotherapy with carbo- or cisplatin in combination with a taxane. At diagnosis, HGSOC is among the most chemo-sensitive of all epithelial malignancies, with initial response rates of ~85%, presumably related to DNA repair defects. Platinum is thought primarily to drive the response rate, due to the lower single-agent response rate for taxanes.
Unfortunately, 10-20% of HGSOC patients have treatment-refractory disease at diagnosis, fail to respond to initial chemotherapy, and have a dismal prognosis. The poor response to subsequent therapy and median overall survival of ~12 months for these patients has not changed in 40 years.
Despite >30 years of literature studying platinum resistance in cancer, there currently is no way to distinguish refractory from sensitive HGSOCs prior to therapy. Consequently, patients with refractory disease experience the toxicity of platinum-based chemotherapy without benefit. Due to their rapid progression, they are commonly excluded from participating in clinical trials. Consequently, there is no ongoing clinical research that could identify effective therapeutic agents for these patients or provide insights into molecular mechanisms of refractory disease. “Right now, we can’t identify drug-resistant ovarian cancer patients up front,” said co-senior author Michael Birrer, MD, PhD, who directs UAMS’ Winthrop J. Rockefeller Cancer Institute. “We find them by default: They get sick and pass away so quickly that they can’t even be put on new clinical trials.”
To address this unmet clinical need, we performed proteogenomic analysis of treatment-naïve HGSOCs (chemo-sensitive and chemo-refractory) to identify molecular signatures of refractory HGSOC and to identify potential treatment targets.
Dr. Davis[/caption]
Prof. Jonathan Davis, MD,
Chief of Newborn Medicine
Tufts Medical Center and
[caption id="attachment_60599" align="alignleft" width="125"]
Response: We were broadly interested in discovering instances of bacterial genes that have been acquired by diverse animal genomes over millions of years of evolution by the process of horizontal gene transfer (HGT). Since these events are quite rare and most previous discoveries have been serendipitous, we developed computational methods to identify genes acquired by HGT in animals. One of the exciting discoveries from our work was that vertebrate IRBP appeared to have originated in bacteria and is now a critical component of the vertebrate visual cycle, so this paper focuses on that one discovery.
IRBP or interphotoreceptor retinoid binding protein is an important protein present in the space between two major cell types in our eyes, photoreceptor cells and RPE cells. Our ability to see involves an intricate set of steps where light is first sensed by causing a change (isomerization) in the chemical structure of molecules in the eye called retinoids. This sensing of light occurs in our photoreceptor cells. Following this change in the chemical structure, the retinoid needs to be recycled back to the chemical structure that can again sense light. This recycling occurs in RPE cells. IRBP performs the essential function of shuttling retinoids between the photoreceptors and the RPE cells, which allows the cycle of sensing and regeneration to work. Supporting its importance, mutations in IRBP (also known as retinol binding protein 3 or RBP3) can cause several severe human eye diseases.
Dr. Tauscher-Wisniewski,[/caption]
Sitra Tauscher-Wisniewski, MD
Vice President Clinical Development & Analytics
Novartis Gene Therapies
MedicalResearch.com: What is the background for this study? Would you briefly describe the condition of Spinal muscular atrophy (SMA)?
Response: At the 2023 Muscular Dystrophy Association Conference, we presented new data from two of our Long-Term Follow-Up (LTFU) studies, LT001 and LT002, which show the continued efficacy and durability of Zolgensma across a range of patient populations, with an overall benefit-risk profile that remains favorable. LT001 is a 15-year ongoing observational LTFU study following the Phase 1 START patients, who were the very first patients to receive our gene replacement therapy. LT-002 is a voluntary Phase 4 15-year ongoing follow-up safety and efficacy study of Zolgensma IV and investigational intrathecal (IT) OAV101 in patients previously treated in the Phase 3 IV studies (STR1VE-US, STR1VE-EU, STR1VE-AP, SPR1NT) and the Phase 1 IT study (STRONG).
Spinal muscular atrophy (SMA) is a rare, devastating genetic disease that leads to progressive muscle weakness, paralysis, and when left untreated in one of its most severe forms (SMA Type 1), permanent ventilation or death in 90% of cases by age 2. It is caused by a lack of a functional survival motor neuron 1 (SMN1) gene, and in the most severe forms results in the rapid and irreversible loss of motor neurons, affecting muscle functions, including breathing, swallowing and basic movement.
Dr. Levin[/caption]
Trevor Levin Ph.D.
Founder and CEO of Convergent Genomics that produces the Uroamp assay
San Francisco, CA
MedicalResearch.com: What is the background for this study?
Response: Bladder cancer is one of the most expensive and challenging to diagnose and treat. Therefore, identifying cost-effective urine bladder cancer biomarkers to complement or replace the gold-standard invasive and costly cystoscopy for the early detection and monitoring of this highly recurrent disease is crucial. At the international Agency for research on Cancer (IARC-WHO), we have developed a simple urine-based assay TERT promoter mutations, the most common mutations in bladder cancer, and showed that the urine biomarker could detect bladder cancer patients at diagnosis but many years prior to clinical diagnosis. However, in this study, we wanted to see whether a more comprehensive genomic profiling of urine samples collected years prior to clinical diagnosis of bladder cancer could identify even more patients before they develop any symptoms.
The study was based on the UroAmp test, a general urine test that identifies mutations in 60 genes, developed by the Oregon Health Science University spin out company, Convergent Genomics. Drawing on previous research to identify genetic mutations linked to bladder cancer, the research team narrowed the new test down to focus on mutations within just ten genes.
Working with colleagues from the Tehran University of Medical Sciences in Iran, they trialled the potential new test using samples from the Golestan Cohort Study, which has tracked the health of more than 50,000 participants over ten years, all of whom provided urine samples at recruitment. Forty people within the study developed bladder cancer during that decade, and the team were able to test urine samples from twenty-nine of them, along with samples from 98 other similar participants as controls.
Dr. Mosley[/caption]
Jonathan Mosley, MD, PhD
Associate Professor
Division of Clinical Pharmacology
Departments of Internal Medicine and Biomedical Informatics
Vanderbilt University Medical Center
MedicalResearch.com: What is the background for this study?
Response: Prostate cancer is an important source of morbidity and mortality among men. Earlier detection of disease is essential to reduce these adverse outcomes. Prostate cancer is heritable, and many single nucleotide polymorphisms (SNPs) associated with disease risk have been identified. Thus, there is considerable interest in using tools such as polygenic risk scores, which measure the burden of genetic risk variants an individual carries, to identify men at elevated risk of disease.
Dr. Mahdavi[/caption]
Dr. Sara Mahdavi, PhD
Clinical Scientist and Clinical Instructor
Research Appointment in the Faculty of Medicine
University of Toronto
Toronto, ON
MedicalResearch.com: What is the background for this study?
Response: This was a long-term study spanning 16 years and began with a population of young adults who were medically assessed on a regular basis. It was remarkable to see just how striking the effects of coffee were in the group that had the susceptible genetic variant, what we termed “slow caffeine metabolizers” yet no effect whatsoever in those who did not were termed “fast metabolizers”.
Dr. den Hoed[/caption]
Marcel den Hoed, PhD
Researcher,Department of Immunology, Genetics and Pathology
Uppsala University
MedicalResearch.com: What is the background for this study? What are the main findings?
Response: In this paper we performed a multi-ancestry meta-analysis of 51 genome-wide association studies, in data from over 700,000 individuals. This yielded 11 DNA regions that are robustly associated with self-reported moderate-to-vigorous intensity physical activity during leisure time (MVPA), and 88 DNA regions for self-reported leisure screen time (LST).
Around half of the identified DNA regions are also associated with objectively assessed physical activity traits in data from the UK Biobank. Causal inference using a Mendelian randomization approach subsequently showed bidirectional causal effects between LST and body mass index (BMI), with the effect of LST on BMI being 2-3-fold larger than vice versa. Less LST and more MVPA protect from diabetes, attention deficit hyperactivity disorder, depression, and earlier age at death, with all causal effects of MVPA and leisure screen time being mediated or confounded by BMI. Further analyses showed that DNA regions associated with LST are more often located close to genes whose expression in skeletal muscle is altered by strength training than expected by chance, suggesting that these genes may influence the likelihood of adopting an active lifestyle by influencing the response to training.
Dr. Ying-Hui Fu[/caption]
Ying-Hui Fu, PhD
Professor, Neurology
Weill Institute for Neurosciences
UCSF
MedicalResearch.com: What is the background for this study?
Response: Most people are aware that a lack of sleep is associated with all sorts of health issues. However, familial natural short sleeper (FNSS) individuals sleep 4-6.5 hours a night most of their live and stay healthy. We set out to determine whether natural short sleep mutations can offer protection from various diseases. We chose Alzheimer as an example to start.
Dr. Torkamani[/caption]
Ali Torkamani, Ph.D.
Director of Genomics and Genome Informatics
Scripps Research Translational Institute
Professor, Integrative Structural and Computational Biology
Scripps Research
La Jolla, CA 92037
MedicalResearch.com: What is the background for this study?
Response: Prior research has shown that people with higher polygenic risk for coronary artery disease achieve greater risk reduction with statin or other lipid lowering therapy. In general, adherence to standard guidelines for lipid lowering therapy is low - about 30% of people who should be on lipid lowering therapy are, with no correlation to their genetic risk. We set out to see whether communicating personalized risk, including polygenic risk, for coronary artery disease would drive the adoption of lipid lowering therapy.
Dr. Mapara[/caption]
Markus Y Mapara, MD
Professor of Medicine
Director of the Blood and Marrow Transplantation
Columbia University Medical Center
MedicalResearch.com: What is the background for this study? What are the main findings?
Response: Sickle cell disease is caused by a point mutation in the beta-globin gene of hemoglobin resulting in the production of abnormal hemoglobin which leads to formation of sickle-shaped RBC under conditions of low oxygen. Sickle cell disease affects about 100,000 patients in the US which are predominantly African American. The only curative approach is to perform an allogeneic bone marrow transplant which is however fraught with significant treatment-related risks if a matched sibling donor is not available.
The current study describes the successful application of a novel gene therapy to treat patients with sickle cell disease. The strategy is based on a gene-addition approach to introduce the genetic information for a Hemoglobin F-like molecule termed HgAT87Q into hematopoietic stem cells. The expression of this novel hemoglobin prevents polymerization of HgbS and has now been demonstrated to prevent the occurrence of vaso-occlusive pain crises in sickle cell disease patients.
Dr. Ulhas Nair[/caption]
Nishanth Ulhas Nair, Ph.D.
Affiliation: Staff Scientist at Cancer Data Science Laboratory, Center for Cancer Research
National Cancer Institute (NCI), National Institutes of Health (NIH)
Bethesda, Maryland, USA. Date: April 22, 2021
Dr. Raffit Hassan and Dr. Eytan Ruppin at the National Cancer Institute (NCI) are the senior authors of this study.
MedicalResearch.com: What is the background for this study?
Response: Malignant mesothelioma is an aggressive cancer with limited treatment options and poor prognosis. An in-depth knowledge of genetic, transcriptomic and immunogenic events involved in mesothelioma is critical for successful development of prognostics and therapeutic modalities. In this study we aim to address this by exploring a new large scale patient tumor dataset of 122 mesothelioma patients, called NCI mesothelioma patient data, along with their genomic, transcriptomic, and phenotypic information. Unlike previous large-scale studies which have been focused on malignant pleural mesothelioma patients, our dataset contains an approximately equal representation of malignant pleural and peritoneal mesothelioma patients which allows to identify any differences between them.