Tumor Mutational Burden a New Pan Cancer Marker for Immuno-Oncology?

By Anthony M Magliocco MD

A new molecular marker “Tumor Mutational Burden” is rapidly emerging in the immuno-oncology world. New trials are showing that TMB may be superior to PDL1 IHC analysis to determine a patients probability of responding to costly and potentially toxic immuno-therapy treatments such as immune checkpoint inhibitors.

Tumor Mutational Burden

The Cancer Genome Atlas (TCGA) has shown that cancers have significant variation in the burden of genomic mutations they carry.  Some tumors such as melanoma have extremely high burdens whereas others such as thyroid cancer have very low loads.

 

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FREQUENCY OF TMB ACROSS TUMOR HISTOLOGY TYPES

 

Some tumors have exceptionally high mutational loads which probably represents an underlying DNA repair deficiency such as POLE or MSI abnormalities. It may also reflect the mechanism of oncogenesis as UV induced tumors such as melanoma have very high burdens.

 

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THE NEOANTIGEN BURDEN IS DIRECTLY RELATED TO TMB

It is thought that TMB actually results in the development of neo-antigens, which are essentially immunogenic.  The probability of neo-antigens emerging is proportional to the total tumor mutational burden. However, this is still a probability measurement, its possible that tumors with even low mutational loads might still generate neo-antigens of interest to the immune system.

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CANCER CELL WITH NEOANTIGENS STIMULATE IMMUNE CELLS

 

Recent Clinical Trials Point to TMB as an important pan-cancer marker

There have recently been three interesting trials in advanced lung cancer reported with a significant association between tumor mutational burden (TMB) and response to the PD-L1 inhibitor nivolumab (Opdivo).  CheckMate 012 trial, was a single-arm evaluation of the combination of the PD-1 inhibitor nivolumab (Opdivo) and the CTLA-4 inhibitor ipilimumab (Yervoy), reveled benefit in patients with high TMB independent of PDL-1 expression.

At AACR The CheckMate 568 trial,   used a TMB cutoff of ≥10 mutations per megabase of DNA (mut/Mb) as the definition of high TMB. Comparing TMB and response rate in 98 patients with untreated stage IV non-small cell lung cancer (NSCLC), investigators found a 44% response rate in association with TMB ≥10 mut/Mb and no further improvement in response with a higher TMB. The response rate fell dramatically with TMB <10 mut/Mb.  This finding is interesting as it may there is a “shelf” or a bimodal distribution of TMB

According to Dr Ramalingam  of Emory “PD-L1 and TMB identify distinct and independent populations of non-small cell lung cancer that independently are associated with enhanced objective response rate and progression-free survival.”

Investigators in the randomized CheckMate 227 trial prospectively applied the TMB cutoff of ≥10 mut/Mb.  There was aa threefold improvement in 12-month PFS (42.6% versus 13.2%) in the subgroup of patients with TMB ≥10 mut/Mb.

The PFS difference persisted across analyses of high and low PD-L1 expression and squamous versus nonsquamous histology.

“CheckMate 227 validates TMB as an important and independent biomarker to be routinely tested in treatment-naive, advanced non-small cell lung cancer,” said Matthew Hellmann, MD, of Memorial Sloan Kettering Cancer Center in New York City

“TMB should be a standard of care in the initial evaluation of the patient with non-small cell lung cancer,” said Naiyer Rizvi, MD, of Columbia University Medical Center in New York City. “PD-L1 as a biomarker remains as a standard of care in concert with TMB. a validated TMB platform needs to be used.”

Problems with TMB

TMB is definitely showing promise, but what are the drawbacks?

NGS is required

First, TMB calculations require that a significant portion of DNA be sequenced, to generate enough sequence information to determine the tumor mutational load. However, some recent studies suggest that even targeted sequencing panels may provide enough sequence information to determine if the load is high. Access to NGS sequencing remains a challenge. Due to low reimbursements and difficulty of implementing the technology many oncologists may have difficulty  accessing the technology

The calculation of TMB is currently non-standardized and non-trivial

Second, TMB calculation is not standardized. It is not a trivial bioinformatics process as the bioinformatifcs process needs to determine if a  DNA variation is “real” or an artifact of sequencing- this is non-trivial as filters need to be defined to define the criteria to make a “call” ie what the confidence of the read is, what the alleic fraction is and whether the mutation is somatic or germline. In addition it must be determined if the sequence affects the coding region of a gene.  Further complicating this is what the denominator might be in an assay- ie does the NGS sequence only coding regions or are there significant non-coding regions. If the non-coding regions are included in the calculation the number may be artifactually low.

Third, thinking from a biological and mechanistic approach, it may matter whether the mutation actually produces a neo-antigen. Again this cannot be easily measured. It involves factors such as whehter the mutation is actually transcribed into protein, and whether the protein conformation is actually altered and neo-antigenic. Further issues include whether the sequence is secreted or made available when the cells degenerate.

TMB are not the only source of neo-antigens

DNA mutations may only account for some of the neo-antigens that a cancer can create. Other sources of neo-antigens in neoplasia include microbes (ie HPV virus in HPV driven cancers such as cervical or head and neck cancer. Other sources include post-translational modifications in cancer such as glycosolation events etc.

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HPV VIRUSES ADD ANTIGENS TO TUMORS

 

Host Factors

Further complicating the impact of neo-antigens include the condition of the host immune system and its capacity to recognize and react to neo-antigens. For example in immune deficiency conditions, neo-antigens may be present but ignored by the immune systems. Or genetic variants in cellular receptors or MHC may affect how neo-antigens are presented to the immune system

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Neo-Antigens may be induced in tumors as a therapeutic strategy

Another interesting angle affecting therapy is the possibility that neo-antigens could be induced in a cancer to trigger immune response. This effect may be a side effect of some therapies such as temozolamide or radiation therapy.

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RADIATION THERAPY MAY INDUCE NEO-ANTIGENS

 

Dr Magliocco is Chair of Pathology and director of the Morsani Molecular Laboratories at the Moffitt Cancer Center

 

 

 

The Value of Pathology Review in Cancer Diagnosis

By Anthony M Magliocco MD

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Pathologists are amongst the most misunderstood of medical specialists.  They are perhaps one of the most important members of the cancer care team, especially now in the age of precision oncology.

Pathologists are MDs who have gone on to undergo focused and specialized training in a 4 yr residency in pathology in either anatomic or clinical pathology.  Anatomic pathology is the study of tissues and includes the subspecialties of surgical pathology, cytopathology, and autopsy pathology. Clinical pathology covers blood based testing and microbiology.

Some pathologists go on to further super subspecialize in focused areas such as cancer, or research. When a surgeon or radiologist removes a tissue specimen from a lesion it is sent to the pathologist for review. This involves examining the specimen carefully and selecting regions for further microscopic examination.  This process involves “fixing” the specimen in formalin, removing the water from it, and embedding it in paraffin. Then thin slices are made to put the tissue on a glass slide for staining and further evaluation by the pathologist. The pathologist may also use advanced diagnostic methods such as immunohistochemistry or molecular analysis to further characterize the tissue.

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Image of high grade breast cancer with mitotic figures

Essentially, pathologists are often the first physicians to make a diagnosis of cancer in a patient and pathologists then perform the key further anlaysis to enable an oncologist to select the right treatment for a patient.

Taking breast cancer as an example, a pathologists role is to make the diagnosis of breast cancer, describe what histological type of cancer it might be- ie ductal or lobular. The pathologist must also evaluate the “grade” of the specimen which gives information of how biologically aggressive it might be, and whether the surgical margins and regional lymph nodes contain metastatic disease. This examination is critical to determine if further surgery is necessary or if other therapy such as endocrine therapy chemotherapy or a targeted therapy such as Trastuzumab.

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breast cancer with HER2 amplification a feature for selecting Trastuzumab

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As the treatments for breast cancer grow, and our knowledge increases we now know that breast cancer is a complicated disease with many subtypes and important features that help guide therapy. Consequently, the demands on pathologists are increasing this also means that non- specialist pathologists may have challenges keeping up with new advances in specialty areas of testing and treatment.

Consequently large cancer centers generally have a policy for all pathology to be reviewed by an expert cancer center subspecialist or team of subspecialists prior to selecting and initiating treatment.

This pathology review frequently adds new information to a case, or actually changes the diagnosis resulting in a change to the treatment plan. In some cases as many as 20% of community pathology diagnoses are changed or amended by central subspecialist pathologist review.

Consequently, a second opinion from a pathologist can be very valuable for a patient and their oncologist to ensure that the treatment course is the most appropriate for the condition.

Having the correct diagnosis and the complete biomarker profile of a cancer is essential to ensure that the most effective therapy is being used and the best chance for a good outcome is achieved.

 

 

 

 

 

 

HER2/HER3 and PIK3CA Mutations in Colorectal Cancer are Associated with Microsatellite Instability

By Anthony M Magliocco MD

 

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A recent study by Loree reported in the  Journal of the National Cancer Institute, found that ERBB2/ERBB3 mutations in colorectal cancer are associated with the presence of MSI microsatellite instability and PIK3CA mutation.

Study Details- Retrospective analysis of Colorectal Cancer Cases from two Cohorts

The study involved retrospective analysis of 419 patients from The University of Texas MD Anderson Cancer Center (MDACC) and 619 patients from the Nurses’ Health Study (NHS)/Health Professionals Follow-Up Study (HPFS) with stage I to IV disease, with tissue sequencing, clinicopathologic, mutational, and colorectal cancer consensus molecular subtype (CMS) profiles of patients with ERBB2/ERBB3 mutations. The circulating tumor DNA profile associated with ERBB2mutation was also investigated in an additional cohort of 1,623 patients with circulating tumor DNA assay results.

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Factors Associated With ERBB2/ERBB3 Mutation

Mutations were found in over 5% of cases and were not associated with age, location or stage of tumor. ERBB2 mutations were associated with shortend survival HR 1.82 but not ERBB3

The investigators concluded, “[Microsatellite instability] and PIK3CA mutations are associated with ERBB2/ERBB3 mutations. Co-occurring PIK3CA mutations may represent a second hit to oncogenic signaling that needs consideration when targeting ERBB2/ERBB3.”

 

The findings are interesting in that mutated ERBB2 is potentially an actionable target.

A Tale of 2 Biomarkers: CTCs and cfDNA are Key to Managing the Plethora of New Trial Options

By Anthony M Magliocco MD

 

We are currently living in revolutionary times when it comes to cancer therapy and treatment options. There are literally hundreds of clinical trials under way evaluating dozens of new therapeutic compounds and combinations of therapy. In fact there are so many trials that its difficult to always find enough patients for them and also to design them to produce the level of evidence expected in traditional multi-armed phase III trials.

There are hundreds of open clinical trials testing dozens of compounds and combinations of therapy

 

Indeed, we seem to be arriving at the point where cancer therapy really is being tailored and delivered to the individual. This shift from evidence based conventional cancer therapy clinical trials, to newer, matched and “N of One” trials creates new challenges for the oncologist and diagnostic laboratory industry.

In a traditional trial, selection and enrollment would depend on results of a key biomarker such as HER2 overexpression for Trastuzumab therapy

Traditionally a biomarker would be required to select a patient for a specific therapy. For example, in breast cancer, presence of HER2 over expression or amplification was a marker to help select patients for enrollment in a trial. Because the frequency of the biomarker was relatively common in a common disease, it was possible to build a well powered phase III trial to collect convincing evidence that on a population based setting that this was an effective strategy. This led to FDA approval and the development of companion diagnostics such as the Herceptin Test.

Fast forward twenty years or so. Now we have so called “basket trials” where cancers can be tested with complex genomic tests that will evaluate hundreds of genes, for example the Moffitt STAR assay that covers 170 actionable mutations and alterations resulting in detection of relatively rare, but still actionable mutations in many tumors. However the mutations are variable and the choices for treatment complex meaning that more than one combination of therapy could be considered. Whats an oncologist to do?

Going forward, it appears that if patients cannot be managed or enrolled in large trials, there will need to be an approach to effectively manage the so called “N of One” patient. In fact, it could be considered that almost every patient is a now unique in some way and could be classified as a rare disease

With a movement away from classical evidence based clinical trials toward n of one trials, off label therapy, and basket trials new approaches to companion diagnostics are urgently needed

In this situation, it appears that physicians will need to act on “best available evidence” or actual bioinformatics or other predictive models of possible response based on understanding the underlying molecular circuitry in the cancer in question. In this situation a “best guess” is made for assignment of therapy (either in a basket trial or in an off-label situation).

This approach can be problematic and has numerous complications such as the possibility of providing futile or toxic treatment. Fortunately, there are plenty of new advances in technology that might address this problem. The most help may come from the so-called “liquid biopsy”. Which is essentially usually a simple blood test evaluated with a exotic new technology.

Liquid Biopsy

The main components of a liquid Biopsy include circulating normal cells (WBC, Platelets, RBCs) possibly circulating living cancer cells (CTCs) and bits of dying cancer cells (cell free DNA, miRNA etc).

A Story of Two Biomarkers CTCs and cfDNA

CTCs Circulating Tumor Cells

The CTCs are very fragile, rare and hard to detect but give a window into the living cancer in the patient as treatment progresses. These cells can be further evaluated to determine if they are proliferating or if certain signalling pathways are active. In fact they can also be harvested, sequenced, and in some cases grown and expanded in culture.

Cell Free DNA cfDNA

Cell Free DNA or cfDNA gives a more stable read out of the tumor load, and mutation composition of the DNA, or at least the DNA leaking into the blood. It might be expected that when a new treatment begins, cancer cells in the host may undergo death and leak DNA into the blood. Consequently there could be an initial “Spike” in the amount of circulating DNA – this could be a positve signal. In other instances, cfDNA might indicate if there is residual cancer left in a patient after a surgery was completed that was initially intended to remove all disease giving a type of molecular staging. If a therapy is working well we would expect that CTCs and cfDNA would decrease and perhaps become immeasurable. On development of resistance there would be detection of new clones and expansion of the concentration of CTCs and cfDNA fragments.

Liquid biopsy provides a means to monitor tumor response to therapy in a dynamic and real time manner giving unprecedented opportunities to modulate treatment and truly personalize therapy for cancer patients

I expect that the twin technologies of CTC and cfDNA analysis will become more valued by oncologists, patients and payers as these tools will provide a way to dynamically monitor tumor response to treatment and provide immediate evidence of efficacy of a therapy or also of impending relapse potentially allowing a window of opportunity to adjust treatment.

 

New Mechanism Involving NFkappaB Drives Metastasis in Cancer with Chromosomal Instability

By Anthony M Magliocco MD

An interesting and important new study recently published in Nature gives new insights into possible targetable molecular mechanism linking chromosomal instability observed in some cancers and progession and metastasis.

https://www.nature.com/articles/nature25432

A subset of cancers develop chromosomal instability via disjunction errors during mitosis. This can lead to highly aneuploid and abnormal karyotypes more prevalent in certain cancers than other. For example, ovarian cancer is notorious for developing a  disrupted and unstable karyotype.

Metastatic Cancer

It appears that chromosomal instability in itself does not promote metastasis, however, in an intriguing observation it was noted that tumors with chromosomal instability also developed micronuclei when under mechanical stress.

These micronuclei are more prone to cytoplasmic rupture. Free DNA in the cytoplasm triggers a non-canonical NFkappaB cascade which may lead to mesenchymal transformation and a propensity to metastasis.

Interestingly cancers with high aneuploidy do not generally develop a high mutational burden such as cancers like melanoma. Nor do they tend to have targetable driver mutations.

“Cytosolic DNA from micronuclear rupture appears to trigger non-cannonical NFKappaB signaling which could lead to tumor metastasis”

 

DNA in the cytoplasm triggers NFKappaB as part of a host response to viral infection, but cancer may subvert this mechanism. In addition,  NFkappaB non-cannonical activation by cytosolic DNA from ruptured micronuclei may lead to a variety of effects immune activation which could assist with tumor metastasis.

These new insights into the consequences of chromosomal instability create opportunities for developing new therapeutic strategies for these types of cancer that lack specific driver mutations and significant neoantigen loads

 

MOFFITT NGS STAR* Enters Clinical Service

Moffitt’s latest NGS sequencing assay the Moffitt STAR (Solid Tumor Actionable Result) panel was validated by the Moffitt Morsani Molecular Laboratory and launched into service this month at the busy Florida Comprehensive Cancer Center in Tampa.

The assay is based on Illumina’s TruSight Tumor 170 assay which is a next-generation sequencing assay designed to cover 170 genes that are commonly designated as drivers in solid tumors. The assay evaluates both DNA and RNA and focuses on detecting actionable mutations which include SNV, dels, insertions, amplifications, and translocations. Such alterations are the target for many new targetable therapies including anti-EGFR agents, anti BRAF therapies and treatments targeting the Tropomyosin Receptor Kinase fusions (TRK) such as Larotrectinib.

Many key actionable mutations only occur rarely, making detection by single marker tests problematic and wasteful. However, the Moffitt STAR assay now allows the Moffitt molecular laboratory to screen patient tumors for multiple targetable mutations efficiently in a single test using a relatively small amount of nucleic acid extracted from routine formalin fixed, paraffin embedded tissues (FFPE). This important advance enables the Moffitt molecular diagnostic laboratory to effectively evaluate a patient for eligibility to receive treatment with a FDA approved targeted therapy, or be considered for clinical trial enrollment. Moffitt STAR is essentially an “All in one” test that can provide multiple functions.

Moffitt NGS STAR* is an exciting new “all in one” technology advance for Moffitt Cancer Center patients enabling rapid assessment of their tumors for presence of key mutations directing selection of effective approved targeted therapies or for qualification to enroll in the latest generation of clinical trials

Evidence is also emerging the assay, despite its mid size, Moffitt STAR could also reliably measure tumor mutational load and microsatellite instability. These molecular features are often associated with potential response to the latest immune check point inhibitors such as Pembrolizumab which has recently received FDA approval for use in tumors with high microsatellite instability.

Moffitt NGS STAR also provides information on tumor mutational burden and microsatellite instability- key features which may drive patient response to the latest immuno-oncology check point inhibitor therapies

Moffitt NGS STAR can also detect mutations in BRCA genes, a molecular feature that may predict response to parp inhibitors such as olaparib.

Moffitt NGS STAR can be performed on as little as 40ng of input nucleic acid.

Development and launch of Moffitt NGS STAR was made possible through collaboration with industry partners PierianDx and Illumina Inc.

The Moffitt Cancer center is one of the largest in the United States, is consistently ranked in the top cancer centers by U.S. News & World Report. Moffitt Cancer Center has a mission to “contribute to the prevention and cure of cancer” and the vision ” to transform cancer care through service, science, and partnership”

For further details contact anthony.magliocco@moffitt.org

TRIPLE NEGATIVE BREAST CANCER IS OVER DIAGNOSED

By Dr. Anthony Magliocco

Getting a second opinion for a cancer diagnosis is highly recommended, but even more so if you face triple negative breast cancer, which can be aggressive and difficult to treat.

A new study led by Moffitt Cancer Center pathologist Dr. Marilin Rosa shows that triple negative breast cancer may be frequently overdiagnosed and reclassified after expert review and biomarker retesting. Moffitt investigators presented the data at the 2018 United States & Canadian Academy of Pathology Annual Meeting in Vancouver.

Researchers reviewed over 560 cases of breast cancer referred to Moffitt and found that 113 were initially classified as triple negative by external evaluation. After biomarker retesting, about 28 percent of the triple negative cases were reclassified as hormone receptor positive.

Moffitt’s study demonstrates the value of biomarker retesting for triple negative breast cancers before selecting an appropriate treatment plan. A second opinion that changes your diagnosis can have a huge impact on survival.

In triple negative breast cancer, the three most common types of receptors known to fuel most breast cancer growth — estrogen, progesterone and the HER-2 gene — are not present. This makes common treatments such as hormone therapy and drugs that target the three missing receptors ineffective.

Up to 20 percent of breast cancer diagnoses are triple negative and are more likely to affect younger patients, blacks, Hispanics and those with a BRCA1 gene mutation. This disease is also more likely to spread and recur.

The takeaway: Having an accurate cancer diagnosis is critical to planning appropriate treatment. If you are diagnosed with triple negative breast cancer, consider getting a second opinion before starting a treatment plan.