Oncologists’ Guide to Genomics

Stay current on the latest trends in genomics and molecular diagnostics for oncology.

Wednesday, July 18, 2018

An international team of researchers including University of Southern California (USC) scientists has found scores of new genetic markers in DNA code that increase prostate cancer risk—powerful knowledge likely to prove useful to detect and prevent the disease.

Focusing on DNA of more than 140,000 men worldwide, researchers were able to identify 63 new genetic markers associated with prostate cancer risk. That greatly increases the number of genetic risk regions, bringing the total to more than 170 and moving scientists closer to using genetic information for clinical treatment.

The results will help bridge the gap between cancer research diagnosis and treatment, equipping physicians with tools to screen at-risk patients. The study, based at USC with collaborators worldwide, including the London-based Institute of Cancer Research (Nature Genet 2018;50:928-936).

"This is not a cure, but the information can help to identify men at high risk of developing prostate cancer who may benefit from enhanced screening and future targeted prevention," said Christopher A. Haiman, ScD, Professor of Preventive Medicine at the Keck School of Medicine of USC and a principal investigator for the project.

DNA Analysis

Prostate cancer is the second-most common cancer in American men, with one in nine men being diagnosed in their lifetime, and the third-leading cause of cancer death for men.

To identify genetic markers associated with prostate cancer risk, the researchers used OncoArray, a new DNA analysis, to compare more than half a million single-letter changes in the DNA code of nearly 80,000 men with prostate cancer and more than 61,000 men without the disease. The researchers identified 63 new variants in DNA, which when inherited increased a man's risk of prostate cancer. Each individually had only a small effect on risk, but the combined effect of inheriting multiple variants could be dramatic.

Study Results

The findings show that 1 percent of men at highest risk were 5.7 times more likely than the general population to develop prostate cancer—an increase in absolute risk from about one in 11 to one in two. The researchers were able to identify that high-risk population because it inherited many of the harmful genetic variants.

And the top 10 percent in the population risk distribution were 2.7 times more likely to develop the disease than the general population—corresponding to a risk of almost one in four.

With the addition of dozens more genetic markers to previously known markers, almost 30 percent of a man's inherited risk of prostate cancer has been accounted for—which may now be enough to start using the information in practical testing strategies, according to the study.

"We now have the ability to identify men at greater risk of prostate cancer," Haiman noted. "We now need to figure out how to use this genetic information to prevent the disease."

These genetic markers may also one day help guide treatment for prostate cancer. Many of the new genetic variants were found in the region of genes involved in communication among cells of the immune system and other cells in the body. This implies that genetic errors in immune pathways may be affecting prostate cancer risk, which could have important implications for potential future treatment of prostate cancer with immunotherapies.

The study comes with caveats. For example, it focuses on white males only. Haiman said parallel studies are underway to study other ethnic groups. For reasons unknown, African-American men face a 74 percent greater risk of prostate cancer than in non-Hispanic white men, according to ASCO.

The global scope of the project enabled researchers to collect massive amounts of DNA and compare genetic variants, which was key to achieving critical mass to make new discoveries. About 200 researchers worldwide participated, including experts from the U.S., U.K., Sweden, Canada, Germany, China, Finland, Belgium, Spain, Poland, Malaysia, and Croatia, among others.

Wednesday, June 20, 2018

By Catlin Nalley

How can oncologists address treatment resistance in brain cancer?

"This is one of the key questions the cancer research community is currently trying to solve," noted Damian A. Almiron Bonnin, MD-PhD candidate at the Geisel School of Medicine at Dartmouth. "High-grade gliomas are the most common and aggressive primary brain tumors in adults, and unfortunately, current medical therapies are largely ineffective against this type of tumor."

Initially, targeted therapy with receptor tyrosine kinase (RTK) inhibitors appeared like a promising approach in this type of tumor, he explained. "However, despite abundant evidence implicating RTKs, including the platelet-derived growth factor receptor (PDGFR), in the pathogenesis of glioblastoma, the clinical use of RTK inhibitors in this disease has been greatly compromised by the rapid emergence of therapeutic resistance.

"Despite the initial responsiveness of high-grade gliomas to these state-of-the-art therapies, these tumors virtually always become resistant and eventually recur," Almiron Bonnin continued. "This is one of the reasons why [high-grade gliomas] have one of the worst survival rates (less than 2 years)."

Mechanisms of Resistance

Researchers at Dartmouth's Norris Cotton Cancer Center, along with Almiron Bonnin, are looking for new approaches to prevent brain tumors from becoming resistant to anti-tumor drug treatment Almiron Bonnin and his team found that "insulin signaling functions as a 'tumor-growth signal' in brain cancer cells that have been treated with a targeted therapy, which allows the tumor to grow despite continued treatment (Mol Cancer Ther 2017;16(4):705-716).

"In this study, we have successfully identified a pathway that mediates the resistance of the most aggressive brain tumors, glioblastoma multiforme, to targeted anti-tumor drugs," Almiron Bonnin noted. "Importantly, there are drugs currently available that can block this pathway to resistance."

In order to study the mechanism of resistance to RTK inhibition in high-grade gliomas, researchers utilized a "mouse model of glioma that we develop in our lab to produce proneural glioblastomas as a direct result of inappropriate PDGF/PDGFR activation in glial cells," Almiron Bonnin explained. "We engineered this mouse model so that the PDGF/PDGFR could be turned on or off at the discretion of the investigator to mimic important aspects of the therapeutic activity of RTK inhibitors.

"We analyzed the response of these tumors to RTK inhibition utilizing different biomolecular techniques such as immunoblotting arrays, microarrays, western blotting, RT-PCR, cell culture, and immunohistochemical techniques," he elaborated. "To dissect large datasets produced by these experiments, we used several bioinformatics approaches. With the insights and knowledge we gained from these computational studies, we queried the cancer genome atlas database which contains clinical and genomic data of large cohorts of glioblastoma multiforme patients."

This study, according to Almiron Bonnin, "will lead to a better understanding of cancer mechanisms of drug resistance that will hopefully translate into improved clinical therapies for the treatment of high-grade gliomas."

The next step for researchers is to pursue a clinical trial to test the efficacy of this new approach on patients diagnosed with proneural glioblastoma with PDGF/PDGFR alterations.

"An important concept this study highlights was that when signaling from a specific secreted factor is blocked (such as PDGF), an alternative secreted factor can maintain the oncogenic functions of the secreted factor that was blocked (such as insulin and IGF1)," Almiron Bonnin added. "Multiple studies suggest that the capacity of cancer cells to secrete a wide range of soluble factors with redundant functions significantly limits the efficacy of current antineoplastic treatments including targeted therapies.

"Therefore, targeting the secretory mechanisms of cancer cells could potentially simultaneously reduce the levels of multiple prooncogenic secreted factors and, consequently, diminish cancer drug resistance and increase patient survival."

Glioma Stem Cells

The cancer stem cells within glioblastoma multiforme tumors are thought to be important drivers of resistance and recurrence.

"To put it simply, if you eliminate most of the tumor with standard treatments, but leave even one cancer stem cell behind, that cell could, in theory, give rise to an entire new tumor," explained Almiron Bonnin. "Therefore, making sure these cells are being effectively targeted is an important goal of cancer research."

According to Osuka, et al (J Clin Invest 2017;127(2):415-426), "certain glioma stem cell (GSC) populations display higher intrinsic chemo- and radioresistance than non-GSCs, indicating that a fraction of the primary tumor GSC population can survive the initial therapy and initiate recurrent tumor formation. GSCs can overcome the damage induced by chemotherapy and radiotherapy not only through innate properties (e.g., genetic heterogeneity), but also through adaptive resistance pathways.

"Because of their tumor-sustaining capacity and resistance to conventional therapies, GSCs represent an important target in the quest to find more effective therapies for GBM."

Almiron Bonnin's team recently uncovered a therapeutic approach that targets aggressive brain cancer stem cells (Oncogene 2018;37(8):1107-1118). "The presence of glioma stem cells within high-grade gliomas is one of the reasons they are so difficult to treat," noted Almiron Bonnin, in a statement. "In this study, we have successfully identified a secretion-mediated pathway that is essential for the survival of glioma stem cells within aggressive brain tumors."

"Several studies suggest that the initiation, progression, and recurrence of gliomas are driven, at least partly, by cancer stem-like cells. A defining characteristic of these cancer stem-like cells is their capacity to self-renew," study authors wrote. "We have identified a hypoxia-induced pathway that utilizes the Hypoxia Inducible Factor 1α (HIF-1α) transcription factor and the JAK1/2-STAT3 axis to enhance the self-renewal of glioma stem-like cells."

Pharmacological blockade of the identified pathway leads to a noticeable reduction in tumor growth, according to Almiron Bonnin. "Being able to target the cancer stem cells within these tumors, like we did here, could potentially improve response to current chemotherapies and prevent recurrences, which would translate into an increase in patient survival rates."

Looking forward, the team is finalizing the preclinical experiments needed to initiate the clinical trial that will test drugs targeting glioma stem cells of patients diagnosed with this type of tumor.

Ongoing Research

The oncology community continues its efforts to unlock a better understanding of treatment resistance in brain cancer and new ways to combat it.

"Studies like ours demonstrate that it is not enough to target primary drivers of tumorigenesis such as PDGFR in proneural glioblastomas, for example," Almiron Bonnin concluded. "Effective anticancer therapies will have to be thoughtfully designed to also target the appropriate mechanisms of resistance, which vary depending on specific tumor types and therapeutic agent utilized."

Catlin Nalley is associate editor.

Monday, May 21, 2018

By Catlin Nalley

A new study has been launched that aims to provide further insight into the role genetic mutations play in the management of multiple myeloma, including treatment response and patient outcomes.

"There are significant knowledge gaps about multiple myeloma, and among these gaps is the role of genetic mutations in response to treatment and the related outcomes for patients," noted Brian G.M. Durie, MD, International Myeloma Foundation Chairman, in a statement. "This study has the potential to provide valuable real-world evidence that can help advance care for patients."

Study Details

The primary objective of the research, which is spearheaded by the International Myeloma Foundation (IMF), is to determine the overall survival of patients with multiple myeloma and the t(11;14) translocation, which is present in an estimated 16-24 percent of FISH-tested multiple myeloma cases (Leukemia 2017;32:131-138, Blood 2016;127:2955-2962).

"The idea evolved over the last 2-4 years as we were looking more closely at the types of patients with multiple myeloma and particularly the patients who have the t(11;14) translocation," Durie told Oncology Times. "What became very clear is that these patients are identified as having increased levels of the protein Bcl-2 present in the myeloma cells." This is important, Durie noted, because Bcl-2 prevents apoptosis and as a result helps sustain the growth of myeloma.

Blocking Bcl-2 has proven to be an effective treatment for myeloma and there are a number of agents that can be utilized in this approach, including venetoclax, according to Durie. "There is evidence that venetoclax alone as a single therapy could be remarkably effective in patients who have the t(11;14) translocation, but also in combination in others who may have some increase in Bcl-2, but may not have the t(11;14) translocation.

"And so, because of the potential for the selective precision approach to therapy, it became necessary to better understand the natural history of myeloma patients with the t(11;14) translocation," he continued. This desire to fill in gaps in knowledge is the origin of the research project, Durie noted. "We want to improve our understanding of the t(11;14) translocation and its role in multiple myeloma therapy as a potentially new selective precision medicine approach."

The study will include IMF researchers from at least 30 participating sites worldwide who will retrospectively review and characterize outcomes of 1,500 multiple myeloma patients with the t(11;14) translocation identified on FISH.

Secondary objectives of the study include response rates, progression-free survival, time to progression, time to next treatment, duration of responses, and overall survival with different regimens among patients with the t(11;14) translocation. The research also aims to determine prognostic factors for overall survival as well as identify the range of co-existing genetic abnormalities in this patient population.

"Myeloma patients can have a variety of chromosomal abnormalities and the t(11;14) translocation is just one of them," noted Durie. "So, a key objective of the study is to see if patients who have this translocation also have a bad prognostic chromosomal factor, which can lead to poorer outcomes.

"Conversely, do these patients have good risk features, such as trisomies, which could make the potential outcome even better," he continued. "So, [this study] aims to understand the presence of the t(11;14) translocation not just in isolation, but as a part of the larger picture of the disease."

Researchers are currently in the data‑gathering phase, according to Durie, and several hundred of the patient materials have been collected. The anticipated timeline is for analysis to occur in May/June and investigators are hopeful that they "will have a data analysis that would allow for the submission of scientific abstract for the ASH Annual Meeting in December 2018," Durie noted. "At the same time, we will be preparing a full publication of the data."

Potential Impact

Given the gaps in understanding regarding multiple myeloma and the role of genetic mutations, this study has the potential to make a significant impact in the treatment of this patient population.

"Identification of the subset of patients with the t(11;14) translocation as the dominant chromosome abnormality who, in turn, could selectively benefit from this targeted approach of therapy is hugely important," Durie concluded. "This could be a proof-of-principle demonstrating that the identification and targeting of a molecular subgroup of patients can be a way forward for the future."

Catlin Nalley is associate editor.

Friday, April 20, 2018

By Catlin Nalley

The key to reducing cancer deaths is early detection. Researchers at the Johns Hopkins Kimmel Cancer Center in Baltimore are exploring how to use cancer gene discoveries to develop screening assays to improve survival rates among cancer patients. A series of gene-based tests have the potential to improve the early detection of cancer for a number of patient populations, which in turn could lead to a decline in the rates of cancer mortality.


Researchers developed CancerSEEK, a single test that screens for eight common cancer types that account for more than 60 percent of cancer deaths in the U.S. and helps identify the location of the cancer (Science 2018; doi:10.1126/science.aar3247). This noninvasive, multianalyte test "simultaneously evaluates levels of eight cancer proteins and the presence of cancer gene mutations from circulating DNA in the blood," according to researchers.

Investigators evaluated the test on 1,005 patients with non-metastatic, stages I-III cancers of the ovary, liver, stomach, pancreas, esophagus, colorectum, lung, or breast. They found that the median overall sensitivity was 70 percent and ranged from a high of 98 percent for ovarian cancer to a low of 33 percent for breast cancer. For ovarian, liver, stomach, pancreatic, and esophageal cancers—which have no screening tests—sensitivity ranged from 69-98 percent, researchers reported.

The study showed that the test had a specificity of greater than 99 percent. Among the 812 healthy controls, only seven false-positive results were produced.

"Very high specificity was essential because false-positive results can subject patients to unnecessary invasive follow-up tests and procedures to confirm the presence of cancer," said Kenneth Kinzler, PhD, Professor of Oncology and Co-Director of the Ludwig Center, in a statement.

Additionally, study authors found that "CancerSEEK localized the cancer to a small number of anatomic sites in a median of 83 percent of the patients."

"This test represents the next step in changing the focus of cancer research from late-stage disease to early disease, which I believe will be critical to reducing cancer deaths in the long-term," noted Bert Vogelstein, MD, Co-Director of the Ludwig Center, Clayton Professor of Oncology, and Howard Hughes Medical Institute investigator.


Another recently developed detection tool, UroSEEK, utilizes urine samples to identify mutations in 11 genes or the presence of abnormal numbers of chromosomes that would signal the presence of DNA associated with bladder cancer or upper tract urothelial cancer (UTUC) (Elife 2018; doi:10.7554/eLife.32143).

"Bladder cancer is a huge health care issue because, while it might not be the most common cancer, it is certainly the most expensive," George Netto, MD, a senior author on the UroSEEK paper, formerly at The Johns Hopkins University and currently Chair of Pathology at the University of Alabama-Birmingham, told Oncology Times. One of the reasons for this, he noted, is the lifelong journey of follow-up and surveillance required following diagnosis.

Given the lack of noninvasive approaches, researchers sought to develop a test for bladder and UTUC cancers that would detect disease sooner with a reduced financial burden. Netto and team studied 570 patients who were considered high-risk for bladder cancer. In this early detection cohort, investigators found that UroSEEK was 83 percent positive among patients who developed cancer. Sensitivity among patients who developed the disease increased to 95 percent when combined with cytology.

Additionally, UroSEEK, when utilized alongside cytology, detected mutations in 71 percent of patients (n=322) who had been treated for bladder cancer and were currently in the surveillance stage. Comparatively, recurrences were detected in only 25 percent of these patients when cytology was used alone.

Researchers also utilized UroSEEK on 56 patients with UTUC and found that 75 percent tested positive, including 79 percent of those with noninvasive tumors, Netto reported. Cytology alone detected UTUC in only 10 percent of these patients. The patients in this cohort were from Taiwan, an area where the incidence of UTUC is high due to environmental factors, including the medicinal use of herbs containing aristolochic acids. "This is truly an international study," Netto said. "We wanted to make sure we were including different populations because we want to help not just people in the U.S., but beyond."

Research to validate this test is ongoing and investigators plan to seek FDA approval. Given the added sensitivity of utilizing UroSEEK in combination with cytology, researchers believe this could improve the management of cancer patients and spare them from more invasive and expensive procedures such as cystoscopy.

"We do not want to replace cytology, which is the gold standard, but rather add UroSEEK to improve sensitivity," Netto emphasized. "[UroSEEK] has the potential to make a huge difference in the management of the disease in both the early detection and surveillance settings."


Gynecologic cancers, specifically endometrial and ovarian, were the focus of another screening assay, which utilizes cervical fluid samples gathered during routine Pap tests.

"More than 86,000 U.S. cases of endometrial and ovarian cancer were diagnosed in 2017. Treatment often involves radical surgery and, in some cases, chemotherapy and radiation," said Amanda Nickles Fader, MD, Director of the Johns Hopkins Kelly Gynecological Oncology Service, Department of Gynecology and Obstetrics, and a corresponding author on this study. "Approximately 25,000 women a year die of gynecological cancers.

"The problem is that, for these particular cancers, there is no approved screening test to detect disease at an earlier, more treatable or curable stage. Additionally, a good number of young women are diagnosed with these cancers and so, not only is survival an issue, but loss of fertility is also common," she continued. "If we can detect cancer earlier using detection or screening tools, the potential to achieve more cures and also preserve fertility in young women could be realized."

With PapSEEK, mutations in DNA that have been identified for specific cancers can be detected sooner. Researchers studied 1,958 samples from 1,658 women, including 658 endometrial or ovarian cancer patients and 1,002 healthy controls, Nickles Fader reported (Sci Transl Med 2018; doi:10.1126/scitranslmed.aap8793).

Utilizing the samples, the assay looked for mutations in 18 genes as well as aneuploidy, the presence of abnormal numbers of chromosomes in cells. Investigators collected Pap brush samples from 392 endometrial cancer patients and 245 ovarian cancer patients. "We found [PapSEEK] detected 81 percent of endometrial cancers and 33 percent of ovarian cancers," Nickles Fader told Oncology Times.

Additionally, researchers obtained cervical fluid samples using a Tao brush, which extends further into the cervical canal and collects cells closer to the source of the potential cancer, Nickles Fader explained. "Detection increased to 93 percent in endometrial cancer patients and 45 percent in women with ovarian cancer," she noted. There were no false-positive results.

Not satisfied with the detection rates among ovarian cancer patients, researchers hypothesized that "ovarian cancers that were inaccessible by Pap or Tao brush sampling due to anatomical or other factors might be detectable by the presence of circulating tumor DNA (ctDNA) in plasma."

Utilizing assays for ctDNA in plasma along with PapSEEK on Pap brush samples increased the sensitivity of detecting ovarian cancer to 63 percent, according to Nickles Fader.

Current diagnostics do not always reliably distinguish between benign conditions and cancer, which can lead to unnecessary procedures or an inability to detect cancer. "Because of the high mortality associated with some gynecologic malignancies, cancer screening and detection are a huge priority," Nickles Fader concluded. "The results demonstrate the overall potential of mutation-based diagnostics to detect these cancers, ideally at a stage when they are going to be more curable."

Catlin Nalley is associate editor.

Tuesday, March 20, 2018

By Catlin Nalley

"Immunotherapy has profoundly changed the management of multiple cancers," said Roger Sun, MD, PhD candidate under Eric Deutsch, MD, PhD, and Charles Ferté, MD, PhD, at the laboratory INSERM U1030 at Gustave Roussy in Villejuif, France. "However, most patients do not respond to this type of treatment. That is why we need to identify biomarkers that allow identification of patients who are most likely to respond to immunotherapy."

Studies utilizing biopsy samples of tumor tissues have confirmed the link between immune-cell infiltration into tumors and patients' treatment responses; however, Sun noted, because cancers are heterogeneous, biopsies only reflect the local aspect of the tumor.

"Medical computational imaging, also known as radiomics, is a new field of research that aims to translate standard imaging like CT, MRI, or PET into objective data and use them as biomarkers," he explained.

New data, presented at the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics, suggests a computational imaging-based signature of immune-cell infiltration in and around a tumor could predict patients' responses to treatment with anti-PD-1/PD-L1 immunotherapies (Abstract A051).

Study Details

The research, spearheaded by Deutsch, Head of the INSERM U1030 Research Unit at Gustave Roussy, and Ferté, a medical oncologist and computational biologist from Gustave Roussy, aimed to develop a radiomics-based imaging tool of tumor immune infiltrate and assess whether this tool could predict clinical outcomes of patients treated with anti-PD-1/PD-L1 therapy.

"We wanted to explore the potential of radiomics in the other emerging field of immunotherapy, for which there are no established biomarkers to predict patient responses," study author Sun told Oncology Times.

"Moreover, this imaging biomarker is non-invasive, cost-effective, can be applied on all the tumor localizations [to] evaluate the tumor heterogeneity, and can be repeated throughout the course of disease," he emphasized. "Development of such a tool would be of highest interest in improving patient care."

The researchers utilized radiomics to estimate the abundance of immune-cell infiltration in tumors and assess their potential to predict response to anti-PD-1/PD-L1 therapies. Data from the head and neck, liver, lung, and bladder cohorts of The Cancer Imaging Archive was used by the team to develop a radiomics-based model of tumor-infiltrating effector T cells (Teff).

Eighty radiomics features were extracted, according to investigators, and a radiomics score was built that could predict the abundance of tumor-infiltrating Teff estimated using RNA sequencing data.

"As tumor inflammation is known to be related with clinical response to immunotherapy, we used genomic data of tumors from The Cancer Genome Atlas to quantify tumor inflammation using a published gene expression signature," Sun explained. "We then trained a radiomic signature based on the CT images of the corresponding tumor using machine learning approaches to predict tumor inflammation."

The radiomics score was initially tested on the CT scans of a cohort of 134 patients who had RNA-seq data available, investigators reported. Data showed that the radiomics score of Teff correlated with the genomics-based score of Teff.

"We validated this radiomic signature in a prospective cohort from our center, the MOSCATO trial, a precision medicine program where genomic information was extracted upon CT-guided biopsy," Sun noted. "For these patients, both contrast-enhanced CT scan at the time of the biopsy and RNA-seq data were also available.

"A third cohort of patients treated with immunotherapy was used to assess the association between the radiomic signature and outcome of patients (overall survival)."

The radiomics score was applied on data from the entire cohort and used the median value to divide the cohort into two groups: patients whose scores were above the median and those whose scores were below the median. According to investigators, "at any given time point, patients with a high score were 1.5 times more likely to be alive compared with those who had a low score."

"A signature based on imaging features, learned on genomic data, can reflect the tumor phenotype (low or high level of immune cells) and the response to immunotherapy," Sun said.

However, he acknowledged there are research limitations to consider, "Cohorts of patients were heterogeneous, with different types of tumors and varying imaging protocols, which could have impacted the radiomic signature.

"Even so, this data reflects the quality of data one can expect in 'real life,'" he continued. "Moreover, having access to the tumors' genomic data and the corresponding images in a large cohort is seldom possible, hence the data obtained is very valuable and is a unique opportunity to assess whether the radiomics data could provide an estimate of immune infiltration (assessed by RNA-seq)."

Practice Implications

This study is a positive step forward to better understand the potential clinical implications of radiomics.

"We are very encouraged by our findings that a signature based on imaging features could reflect the tumor immune infiltration and could predict response to immunotherapy," Sun noted. "These results are preliminary, and we need further clinical studies to validate them.

"Ultimately, this score may be useful to drive immunotherapy trials allowing stratification of patients. For radiotherapy-immunotherapy combinations, this score can be useful to identify which lesions to irradiate, in order to get some abscopal effects," he continued. "Enhancing data sharing and facilitating patient recruitment in clinical trials are necessary. With further improvements to this field with multi-disciplinary working groups, radiomics can become a reliable part of the decision support system in oncology."

Image computing can help extract information of the molecular and cellular composition of tissues, according to Sun. "Given the vast amount of medical images generated in oncology, the potential of radiomics in oncology is very huge and efforts have to be made to develop this very promising field of research," he concluded.

Catlin Nalley is associate editor.