Oncologists’ Guide to Genomics

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

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.

CancerSEEK

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.

UroSEEK

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."

PapSEEK

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.

Tuesday, February 20, 2018

By Catlin Nalley

The investigational drug tazemetostat shows early promise among children with relapsed or refractory malignant rhabdoid tumors, epithelioid sarcomas, or poorly differentiated chordomas with a particular genetic defect.

Data from a phase I study found the drug was well-tolerated with some objective and durable responses, according to results presented at the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics (Abstract A175).

"Malignant rhabdoid tumors and atypical teratoid rhabdoid tumors [ATRT; which occur in the brain] and other INI1-deficient tumors such as epithelioid sarcomas and poorly differentiated chordomas are extremely rare tumors in childhood," said Susan N. Chi, MD, Director of the Pediatric Brain Tumor Clinical Trials Program at the Dana-Farber Cancer Institute and Boston Children's Hospital, and Assistant Professor of Pediatrics at the Harvard Medical School. "However, children with these tumors have a poor prognosis despite conventional treatment regimens and, because of their rarity, there are no uniform treatment approaches."

INI1-Deficient Tumors

"INI1 is a gene that is uniquely mutated in these types of tumors," Chi noted. "And these tumors are highly malignant and very rare aggressive tumors of childhood. They include patients with malignant rhabdoid tumors (MRTs, ATRTs), epithelioid sarcoma, and poorly differentiated chordomas."

This mutation results in deficiencies in DNA transcription and cell proliferation, so cancer cells use an alternate pathway to enable uncontrolled cell proliferation, according to Chi. "The protein EZH2 is a component of this alternate pathway. Tazemetostat targets EZH2, thus inhibiting the proliferative activity of cancer cells.

"INI1-negative tumors are rare, aggressive, and they afflict children to the youngest of ages, particularly for kids with MRT and ATRT," Chi continued. "Children with MRTs and their central nervous system counterpart, ATRTs, have historically poor overall survival, and for the youngest of children especially those under the age of 3 the survival has historically been less than 20 percent."

Patients with epithelioid sarcoma, a soft tissue sarcoma that is often resistant to therapy, also has a poor survival rate. According to Chi, children with metastatic disease have a 1-year survival rate of less than 50 percent. Additionally, Chi noted, "Poorly differentiated chordomas are skull- and spine-based tumors and they have a high mortality rate of approximately 50 percent due to local and metastatic disease."

Study Details

This multicenter phase I study enrolled patients from 6 months to 21 years old with INI1-negative tumors, including rhabdoid tumors, epithelioid sarcomas, poorly differentiated chordoma, and synovial sarcoma.

"This is the first clinical trial for children testing this class of drugs," Chi noted. "The purpose of this study is to determine the highest dose tolerated, characterize the side effects of this drug in children, and assess the efficacy of this drug in select tumor types.

"This is a rolling 6 design which allows six subjects to be concurrently enrolled into each cohort," she explained during her presentation. Enrolled patients received one of the seven dose levels of tazemetostat as an oral suspension twice daily, according to researchers. Objective responses were assessed every 8 weeks.

At the time of presentation, 46 patients have been enrolled in the seven dose cohorts. When discussing patient demographics, Chi noted the young age of participants. "Our median age was quite young at 3 years old," she reported. "The majority of children (greater than 60%) had either ATRT or malignant rhabdoid tumors.

"All of the children had metastatic disease at the time of study entry and all of these patients were pretreated, the majority having 1-2 regimens prior to their enrollment," she continued. "Due to their aggressive nature, generally speaking, their regimens are very intense upfront."

Key Findings

Of the 46 patients treated so far, three—one with poorly differentiated chordoma, one with epithelioid sarcoma, and one with ATRT—had complete responses, and one patient with poorly differentiated chordoma had a partial response, according to investigators. "The patient with the longest complete response remains in remission after more than a year on study," Chi noted.

At the time of presentation, five of the 46 patients remain on tazemetostat and they all remain on doses above 520 mg/m2, researchers reported. "The children on this study experienced objective responses to this investigational drug that are durable at doses that appear to be well-tolerated," noted Chi, in a statement. "In fact, children have tolerated even higher doses than that in adults, thus demonstrating that children are not just 'little adults' from the standpoint of drug dosing."

In terms of safety, researchers found the treatment was well-tolerated. "There were fewer grade ≥3 treatment emergent adverse events in the higher dose levels (≥520 mg/m2) versus those in a lower dose level (<520 mg/m2)," Chi said. "There was one DLT reported at 300 mg/m2 (grade 4 hypoxia and grade 3 dyspnea), but no other DLTs were noted in any other cohort.

"The most common side effects included vomiting, fatigue, and nausea, but overall it was a very well-tolerated medication," she continued. "These related AEs were not dose- or time-dependent, with the exception of asymptomatic hyperchloremia."

In addition, researchers performed pharmacokinetic studies at various time points, according to Chi. "Children achieved a mean steady-state AUC(0-12) increased in a dose-pro portional fashion at doses ≥520 mg/m2," she explained. "Mean steady-state AUC(0-12) was also four-fold greater as seen in the adults RP2D level of 800 mg BID. The mean AUC was lower at steady-state (day 15) relative to single dose (except at 1,200 mg/m2), consistent with induction of tazemetostat metabolism.

"When we looked at the pharmacodynamic relationship to the pharmacokinetic measurements, we were able to observe inhibition of H3K27M as measured by chromatin flow analysis on the pre- and post-dose levels of the peripheral blood in monocytes and granulocytes," Chi continued.

Based on the pharmacokinetic, pharmacodynamic, clinical safety, and efficacy results, Chi and her team established that the recommended phase II dose was 1,200 mg/m2 tazemetostat given twice daily.

"Tazemetostat was a single-agent generally well-tolerated in children and showed promising anti-tumor activity, including CRs in patients with INI1-negative," Chi noted. "Additionally, this efficacy result is consistent with that previously reported in the adult patients with INI1-negative tumors.

"We are encouraged by our findings that we may now have a novel agent that can be used to treat some of these very difficult-to-treat childhood cancers," she emphasized in a statement. "For the rarest of tumors, especially in pediatrics, where specific and singular mutations may be the driving trigger, advances in the treatment of these tumors may offer insight to other more common tumor types potentially in children or adults or both."

Continued Investigation

The study is currently in its dose expansion phase, according to Chi, which will include four cohorts based on tumor type: ATRT (Cohort 1), MRT and rhabdoid tumors of the kidney (Cohort 2), all other INI1-negative tumors (Cohort 3), and a tablet cohort of tumor types in cohorts 1-3 (Cohort 4).

"Tazemetostat is formulated as an oral liquid formulation and a very important consideration in pediatrics, especially in these young children who cannot swallow tablets," Chi explained. "Tazemetostat for the adults is formulated in a tablet, so we are also testing the tablet for children as well for the older group.

"While we are encouraged to see clinical activity in children, we should remember that large phase II/III studies will provide more definitive assessments of clinical activity for investigational drugs," Chi concluded.

Catlin Nalley is associate editor.

Friday, January 19, 2018

A specific genetic alteration that could allow cancer cells to escape the immune system was detected in 40 percent of non-small cell lung cancers (NSCLC) analyzed, according to data presented at the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics in October 2017. Data suggest that the alteration occurs late in tumor evolution (Cell 2017;171(6):1259-1271.e11).

"One hallmark of cancer is the ability of cancer cells to evade destruction by the immune system," said Rachel Rosenthal, a graduate student in the laboratory of Charles Swanton, PhD, at the UCL Cancer Institute at University College London, U.K. "Together with Nicholas McGranahan, PhD, we developed a method to analyze whether we observed one potential mechanism of immune evasion—loss of heterozygosity (LOH) at the human leukocyte antigen (HLA) locus—in lung cancers and, if we found it to occur, to investigate its frequency and how it might impact tumor evolution."

Rosenthal explained that the presence of HLA class I molecules on the surface of cancer cells is essential for cancer cell recognition and destruction by CD8-positive T cells, and most cells in a human body contain two sets of genes encoding the HLA class I molecules, one set inherited from the mother and one from the father. Sometimes, genetic alterations can occur that result in loss of one set of genes; when this LOH event occurs at the HLA locus, it has the potential to facilitate immune evasion, she said.

"We saw that HLA LOH was a highly frequent event, occurring late in lung tumor evolution and under strong selective pressure," added Rosenthal. "These data have implications for our understanding of how the tumor may evade the immune system and for the development of novel neoantigen-targeting immunotherapies."

Analyzing DNA Data

The researchers developed a computational tool called LOHHLA to analyze next-generation sequencing data from lung cancer samples and determine the number of HLA alleles present in the samples.

According to Rosenthal, because HLA genes are some of the most diverse in the human genome with thousands of alleles of some of the genes, very few HLA sequencing reads successfully match the human reference genome. This means it is not possible to identify heterozygous positions, which are required for LOH analysis, she said. LOHHLA gets around the problem of using the human reference genome by leveraging a patient's known HLA alleles to detect LOH.

The researchers used LOHHLA to analyze next-generation sequencing data from tumor samples obtained prior to treatment from 90 patients with NSCLC who were enrolled in the TRAcking Cancer Evolution through therapy (Rx) (TRACERx) study. HLA LOH was detected in 40 percent of patients. A similar frequency of HLA LOH was observed following analysis of The Cancer Genome Atlas next-generation sequencing data from 692 treatment-naïve patients with NSCLC and previously published next-generation sequencing data from 37 paired primary NSCLC/brain metastasis samples.

Further analysis showed that HLA LOH was associated with a high subclonal neoantigen burden, APOBEC-mediated mutagenesis, upregulation of cytolytic activity, and PD-L1 positivity, which Rosenthal said highlights that the immune system is actively sculpting the tumor and suggests that HLA LOH is a response to the selection pressure applied via immune activity.

She also explained that the subclonal frequencies of HLA LOH, their enrichment in metastatic sites, and occurrence as parallel events suggest that HLA LOH is an immune escape mechanism, selected later in NSCLC tumor evolution.

According to Rosenthal, the main limitation of the study is that currently only tumors from NSCLC patients have been considered.