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.

 

04_Frequency_Chart

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.

 

05_Pan-Cancer-Chart

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.

cgi-viruses

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

patient-family

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.

Intraoperative-Radiation-Therapy-For-Breast-Cancer-1-550x330

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

pexels-photo-267596

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.

allan breast hp

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

Forensic-Pathology-Blog-Post-Header

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.

 

 

 

 

 

 

Hormone Replacement Therapy does not Increase Risk of Breast Cancer in Women with BRCA Mutation after BSO Treatment

By Anthony M Magliocco MD

In a large multicenter international prospective study reported in JAMA Oncology, Kotsopoulos et al found that use of hormone replacement therapy overall did not appear to increase risk the of breast cancer among women with BRCA1-mutation after prophylactic bilateral salpingo-oophorectomy; however, use of estrogen-progesterone hormone replacement therapy appeared to be associated with increased risk vs estrogen alone.

Study Specifics

The study was a prospective, longitudinal cohort study of BRCA1- and BRCA2-mutation carriers from 80 centers in 17 countries which was conducted between 1995 and 2017. There was a mean follow-up of 7.6 years. The study participants had undergone BRCA1 or BRCA2 testing for familial or other reasions.

The current study included a total of 872 BRCA1-mutation carriers with no personal history of cancer with a mean postoophorectomy follow-up of 7.6 years. Patients had a mean age of 43.4 years. the questionnaires were administered every 2 years for information on hormone replacement therapy use.

The investigators concluded,

“These findings suggest that use of estrogen after oophorectomy does not increase the risk of breast cancer among women with a BRCA1 mutation and should reassure BRCA1 mutation carriers considering preventive surgery that [hormone replacement therapy] is safe. The possible adverse effect of progesterone-containing [hormone replacement therapy] warrants further study.”

However the study also revealed that use of estrogen plus progesterone was associated with higher risk vs use of estrogen-alone hormone replacement therapy.

Understanding the Biology and Treatment Options for Breast Cancer

by Anthony M Magliocco MD

Breast cancer is a common disease with up to 1 in 8 women receiving this diagnosis in her lifetime. It is more common in older women but it certainly can strike the young and even can occur in men at about 1/100 the rate seen in women.

We have learned a lot about the biology of breast cancer over the years and the condition is becoming easier to detect at an earlier stage and fortunately more effective therapies are now being developed.

We now know that breast cancer is complex and has multiple molecular and biological subtypes. The main types are called Luminal A, Luminal B, HER2 positive, and Triple Negative.

Luminal Cancers – Endocrine responsive tumors

The Luminal types of breast cancer are defined by expressing estrogen receptor. They tend to have better differentiation and generally a more indolent course. The standard treatment is surgery, potentially radiation, and endocrine treatment (an anti estrogen agent) for 5 to 10 years. If the tumor appears more aggressive- ie involves lymph nodes, or has higher grade, chemotherapy may be added to the treatment in an adjuvant way. One of the problems with luminal type breast cancer is it can recur many years after the original cancer has been treated. Its thought the cancer cells can spread and remain dormant in distant organs or bone for many years with some mysterious events causing them to become reactivated.

 

The HER2 positive breast cancers

A subset of breast cancers, about 15% seem driven by the oncogene ERBB2 (which produces the protein HER2).  For some reason this gene can become “amplified” – ie many copies are made in a single cell leading to vast over production of the HER2 protein. This over production seems to drive the cancer cell to proliferate and metastasize.

Fortunately, therapies have been designed for HER2 cancer, these include Trastuzumab and Pertuzumab – antibodies that react and block the function of the HER2 gene. These treatments appear to be able to halt the grow of the cancer and prevent metastases from occurring.

The Triple Negative Breast Cancers (TNBC)

The third main type of breast cancer are the Triple Negative Cancers or TNBC. This group is actually a mixed group of tumors defined by lack of expression of estrogen receptor or HER2.  They frequently occur in younger women, they may be familial, are over represented in African American women and often progress more quickly. Some of them seem to have a high immune infiltrate, some carry the BRCA gene mutation, and some show strange growth characteristics such as bone formation or “metaplasia”.

 

 

The problem with TNBC is they are a generally a diagnosis by exclusion. However there are certain tests a pathologist can order to help prove that a cancer is TNBC such as Nestin.

Because the TNBC is diagnosed by exclusion there is a significant possibility of error. For example some tumors are heterogenous, and only a small portion might be sampled. If the portion is ER negative or HER2 negative the tumor might be erroneously classified as TNBC.

In other cases, TNBC cancers with very low false expression of HER2 or ER may end up being misclassified as HER2 positive or ER positive which could lead to erroneous use of potentially toxic and ineffective anti -HER2 therapy

Use of Second opinion Expert Review Pathology 

A second opinion pathology review by an expert pathologist can help a patient and her oncology be confident that a tumor is indeed a TNBC. The pathologist may order a repeat immunohistochemical stain on additional case material which frequently changes a diagnosis of TNBC to ER positive or HER2 positive. Occasionally a ER positive or HER2 positive will be reclassified as TNBC also.

TNBC is a unique form of breast cancer with subtypes. further classification of TNBC into tumors with BRCA mutation will help with selection of Parp inhibitor or chemotherapy with carboplatinum.

Further, some TNBC tumors have been shown to be sensitive to immunotherapy.

Some TNBC also seem to express androgen receptor, which could be a therapeutic target.

 

Use of Liquid Biopsy

In some patients a liquid biopsy could also be helpful. If a patient has metastatic disease the cancer cells can be isolated and analyzed from a blood sample.  ER and HER2 status can be measured in these circulating tumor cells. In addition fragments of DNA from disintegrating cancer cells can also be measured and classified providing further evidence as to the amount of cancer and whether the cancer is changing or responding to therapy.

Of interest, it seems that breast cancers may undergo biomarker change as they progress or metastasize. for example an ER positive tumor might change and become ER negative or switch to HER2 overexpression.

Patients should seek second opinion pathology review if they have concern regarding the accuracy of their diagnosis or want to ensure that all treatment opportunities are properly considered.

 

 

As treatment options continue to expand, and testing methods improve, it is important that patients with breast cancer have access to the highest quality pathology services and they should also not hesitate to seek second opinion if there is concern regarding the accuracy of diagnosis.

BRCA Mutation Predicts Carboplatinum Response in Women with TNBC

Anthony M Magliocco MD

 

A recent study published in Nature Medicine reports that women with triple negative breast cancer with a BRCA mutation were much more likely to respond to treatment with carboplatin compared to treatment with docetaxel, which is the current treatment recommendation for these patients.

https://www.nature.com/articles/s41591-018-0009-7

Triple negative breast cancer remains a difficult disease to treat as standard anti-estrogen or anti-HER2 treatments are not considered.

In this study there were 376 women with advanced triple-negative breast cancer across the trial, regardless of BRCA gene status, the researchers found the 2 drugs worked similarly well. But among the 43 women in the study who also had BRCA gene mutations those who received carboplatin were twice as likely to respond to therapy as those given docetaxel.

The researchers have reported an observed resesponse of 68% of the patients treated with carboplatin, but only in 33% of the women on docetaxel.

 

 

 

Furthermore Carboplatin also appeared to cause fewer side effects along with prolonged tumor progression for longer in women with BRCA mutations—with a progression free survival of  7 months compared with 4 months for those treated with standard docetaxel.

The researchers believe carboplatin is more effective for this patient group because it works by damaging tumor DNA, and BRCA mutations impair the ability of cancer cells to repair the type of DNA damage created by this kind of platinum drug.

This study further highlights the need for availability of BRCA gene testing in women with breast cancer.

This study further highlights the need for NGS gene testing in women with breast cancer for the purpose of appropriate therapy selection

 

One curious feature of the study was women with BRCA1 gene methylation, low BRCA1 mRNA expression, or Myriad HRD analysis was not clearly associated with benefit of treatment with platinum based agents.

 

A study at the Moffitt Cancer Center recently showed many triple negative breast cancers may actually be misclassified due to errors in primary pathology biomarker analysis.

Second opinion analysis should be considered for women diagnosed with triple negative breast cancer as the original biomarker analysis may frequently be flawed and an actionable target such as estrogen receptor or HER2 is identified on reanalysis

 

TRIPLE NEGATIVE BREAST CANCER IS OVER DIAGNOSED

 

Morsani Molecular Lab at Moffitt Cancer Center is Central to its Personalized Oncology Mission

By Anthony M Magliocco MD

Moffitt Cancer Center, the largest and only NCI designated comprehensive cancer center in Florida and one of the largest in the country has been rapidly expanding its capabilities in molecular diagnostics with a clear focus on supporting its burgeoning personalized oncology programs which are led by internationally recognized expert Dr Howard McLeod.

It became clear several years ago that a huge revolution was coming in the area of personalized oncology and cancer treatments. That revolution is now here.

Explosive advances and numerous FDA approvals for new targeted therapies have emerged for treating and controlling once universal killers such as metastatic melanoma and advanced lung cancer.

These targeted therapy medicines, include vemurafenib targeting mutant BRAF, Erlotinib for EGFR mutant lung cancer, and crizontinib targeting ALK translocations. Further truly dramatic results have been seen with immunotherapy treatments such as the anti PDL-1 immune checkpoint inhibitor pembrolizumab for treatment of a variety of advanced cancers that over express the protein PDL-1 or carry MSI. More recently approvals of NTRK inibitors Larotrectinib and the PARP inhibitor Olaparib for BRCA mutant cancer have further increased demand for specialized testing as both of these treatments have companion diagnostic requirements

 

Immune cells (red and blue) surround a invasive cancer cells (green)

The approval of many new targeted treatments requiring companion biomarker evaluation is providing impetus to develop more advanced diagnostic technology including new cellular imaging methods

These rapid advances in treatment options hinge on the availability of routine, high quality, clinical grade, molecular analysis and diagnosis to properly identify patients who will be most likely to benefit from these costly and frequently toxic treatments.

The Morsani Molecular Laboratories were created to facilitate the rapid development and implementation of new molecular diagnostic assays into the routine CLIA laboratory at Moffitt

Moffitt leadership and its generous philanthropic doners and foundation laid the important cornerstone of the Moffitt Morsani Molecular Laboratories. Under the direction of Dr Magliocco, the laboratories had a singular mission to rapidly develop and deploy the advanced clinical grade diagnostic services necessary to support Moffitts rapidly maturing personalized medicine program.

The Laboratories were initially opened in 2012 and were first equipped with Mass array instruments and conventional Sanger sequencing, pyrosequencing and routine PCR ability. The decision was made to recruit PhD scientists who would help develop the new assays to a CLIA standard and then launch them into a “routine” production laboratory.

The demand from the Moffitt clincal services was high, especially from thoracic oncology, a ground breaking team offering a multitude of clinical trail options for Moffitt patients. This demand required that the assays be CLIA grade, complex and delivered in a rapid way.

This was very challenging. Launching a highly multiplex assay into a CLIA lab is not a trivial matter. The assay must be calibrated to show sensitivity, specificity, analytical performance, range, precision, accuracy and many other technical components. Further, any new assay must also be put through its paces to show its robustness and reproducibility when handled by different scientists and technologists.

Launching new assays into CLIA labs is not trivial and requires extensive expertise and investments

We initially chose to launch the LungCarta (TM) Mass Array Panel from Sequenom. This was very challenging to validate as it contained individual assays run in multiplex to assay over 213 distinct mutations. as these were separate mutations and assays, the decision was made to only validate the most clinically important ones, namely BRAF V600E, KRAS, EGFR, and PIK3CA. The next issue was obtaining appropriate clinical reference materials to validate these assays. Fortunately with Moffitt’s very high clinical volume, previous experience with single-plex testing, and availability of Total Cancer Care Protocol tumor bank which houses data and specimens from over 400,000 patients it was possible to obtain the necessary control and case materials to validate and launch the assays into clinical service.

The development of a CLIA assay requires access to appropriately characterized reference materials to enable clinical validation of the process and assay results.

Although the complete 213 mutation panel was run, only the CLIA validated assay results were reported to the treating physician. The remaining results were ported into Moffitt’s data warehouse for storage and use in properly approved research studies. Following the launch of the LungCarta assay, the Morsani Molecular laboratory also launched assays for melanoma, and a specially constructed Glioma panel assay.

 

In 2014, clinical demands for even more complex sequencing arose for proper management of Myelodysplastic Syndrome (MDS) mounted. The hematology team needed access to over 30 genes and potentially thousands of mutations. It was time for the big guns, time for next generation sequencing. At the same time Moffitt molecular pathologists also saw increasing needs for more complex sequencing for solid tumors as well. After careful discussions and further evaluations it was decided to begin next generation sequencing. Following some debate, the consensus was to start with Illumina, given their long history in next gen sequencing and also the experience with the technology in Moffitt’s core genetic research laboratory. It was decided to develop an off the shelf 26 gene panel TST26 that covered most of the key mutations in lung cancer and in melanoma. In addition Moffitt CLIA scientists, molecular pathologists, and clinicians worked with Illumina to design a 32 gene myeloid NGS panel.

Bringing on NGS brought new challenges of a complex wet lab and also a very complex bioinformatics dry lab. At Moffitt we worked with PierianDx who helped design bioinformatics pipelines and an efficient validation program for both the wet and dry lab as well as an information system – a genome workbench- which allows molecular pathologists to rapidly review cases and access a knowledge database to enable rapid sign out. We also required access to numerous control samples to validate the assays. Again these came from Moffitts vast biospecimen resources and also Horizon Discovery, a company specializing the the provision of reference materials for clinical validations. To date Moffitt has run over 10,000 NGS assays.

By 2017, clinical demands continued to mount for even more complex testing. There were new drugs approved that needed to evaluate fusions, “exon skipping” mutations, and even MSI and tumor mutational burden. With these demands, we turned to illuminas TST170 assay, a new type of sequencing assay that had both DNA and RNA. In addition the assay was designed with “actionable targets” in mind. Meaning, that targeted agents in clinical trials were scrutinized to determine the collection of genes and mutations that would likely be most informative for treatment selection in solid tumor oncology. This approach makes the assay very useful and practical for deployment in a busy cancer center where multiple trials are underway and complex patients with unusual cancers are presenting. Moffitts Morsani molecular team worked hard and spent several months validating the assay to bring it to acceptable CLIA standard finally launching it as “Moffitt STAR” an assay to screen for actionable mutations.

Since its launch, demand has been exceptionally high with hundreds of physician orders in the first week alone.

 

Moffitt laboratories continue to work closely with the worlds leading oncologists and pharma and technology companies to ensure that Moffitt Patients always have access to the latest diagnostic tools to enable them access to the most current treatment options.

That is what makes Moffitt an exceptional hospital for cancer patients seeking innovative treatments and explains why Moffitt has some of the best cancer outcome response rates in the country.

 

Loxo Oncology work with Illumina to develop Cdx NGS assay for Larotrectinib (NTRK) and LOXO-292 (RET)

Anthony Magliocco MD

In an important announcement Industry sequencing leader Illumina and LOXO Oncology, released that they are working on developing a companion diagnostic for larotrectinib, a NTRK inhibitor and LOXO-292 which targets ret.

 

It appears that they intend to use the TST170 as a basis and perhaps a DX version of the Nexseq 500

This is an important development for 2 reasons. The first is the molecular alterations in question are relatively rare, but they can occur in any tumor type regardless of the tissue of origin. The second is the identification of a standard instrument platform and multi-gene assay panel that is already in clinical use (Moffitt has recently deployed a version of TST170 for patient care as Moffitt STAR) will undoubtedly expedite the capability to scale this test for widespread deployment accross laboratories

The fact that TST170 is so comprehensive potentially offers the opportunity for other oncology drug developers to consider using this versatile assay as a companion diagnostic as well.

https://ir.loxooncology.com/press-releases/loxo-oncology-and-illumina-to-partner-on-developing-next-generation-sequencing-based-pan-cancer-companion-diagnostics

STAMFORD, Conn. and SAN DIEGO, April 10, 2018 (GLOBE NEWSWIRE) —  Loxo Oncology (Nasdaq:LOXO) and Illumina, Inc. (Nasdaq:ILMN) today announced a global strategic partnership to develop and commercialize a multi-gene panel for broad tumor profiling, resulting in a distributable, next-generation sequencing (NGS) based companion diagnostic (CDx) with a pan-cancer indication. The co-development partnership will seek approval for a version of the Illumina TruSight Tumor 170 as a companion diagnostic (CDx) for Loxo Oncology’s larotrectinib, which targets NTRK gene fusions, and LOXO-292, which targets RET gene alterations, across tumor types.

TruSight Tumor 170 is a comprehensive, state-of-the-art, next-generation sequencing test that interrogates point mutations, fusions, amplifications and splice variants in 170 genes associated with common solid tumors. The CDx version of TruSight Tumor 170 will allow local laboratories to provide referring physicians with comprehensive genomic information, so that patients can be matched to the most appropriate therapeutic options. This version of TruSight Tumor 170 will run on the NextSeq 550Dx platform.

“We are leveraging our leadership in next-generation sequencing to deliver in-vitro diagnostic solutions to improve the management of cancer patients in the clinic,” said Garret Hampton, Ph.D., executive vice president of clinical genomics at Illumina. “To this end, we are partnering with leading biotechnology companies, such as Loxo Oncology, to develop companion diagnostics for best-in-class therapeutics. Distributable diagnostic solutions, such as a CDx version of TruSight Tumor 170, in combination with the NextSeq 550Dx platform, will enable labs to perform precision medicine testing in-house.”

Under the partnership, the companies will collaborate to validate a CDx version of TruSight Tumor 170 for NTRK fusions and RET fusions/mutations as a Class III FDA-approved diagnostic in conjunction with larotrectinib and LOXO-292, respectively. The companies are also planning to broaden the clinical utility of the full panel by obtaining regulatory approval for the other assay content, to be marketed as a tumor profiling test. Illumina will lead regulatory activities related to the Class III plans for NTRK and RET, the Class II plans for the tumor profiling content, and CE marking.

“We are very excited to announce this collaboration with Illumina, the world’s leader in NGS technology,” said Jacob Van Naarden, chief business officer of Loxo Oncology. “We have piloted numerous NGS assays, and the Illumina TruSight Tumor 170 assay has consistently demonstrated robust performance with its assessment of both DNA and RNA, including highly sensitive gene fusion detection. The broad 170-gene assay content has the potential to deliver meaningful insights from a single tumor specimen, identifying patients with NTRK fusions, RET fusions, RET mutations, and many other actionable tumor alterations. Furthermore, we believe that this collaboration will improve patient access to high-quality NGS testing because pathologists will be able to run TruSight Tumor 170 locally and receive reimbursement.”

Moffitt Cancer Center Pushing Frontier of Pathology with Advanced Multiplex IHC in Its Morsani CLIA Laboratory

By Anthony M Magliocco MD

Next generation sequencing NGS has begun to revolutionize the capabilities of molecular pathologists to analyze the molecular foundation of cancer specimens offering improved diagnosis, classification and treatment selection.

Not to be outdone, similar remarkable advances are impacting tissue pathology as well. Immunohistochemistry is a powerful technique that allows pathologists to visualize and measure protein in routine formalin fixed, paraffin embedded tissue sections.

Moffitt Cancer Center is pushing the boundaries of tissue analysis using digital image analysis and multispectral immunohistocemistry in the Morsani Molecular Laboratories directed by Dr Magliocco.  The Advanced CLIA Analytical Microscopy laboratory at Moffitt is led by Susan McCarthy, an expert in molecular analysis and histotechnology. The fact that the laboratory is also certified by CLIA and CAP is important, as the new complex imaging methods can then easily be translated to patient care under a CLIA LDT regulatory mechanism.

Classically, Immunohistochemistry involves applying a primary antibody which will bind to an antigen and then detecting it with a tagged secondary antibody (essentially an antibody against the first antbody). Typically this binding is visualized using a brown dye (or chromogen) such as DAB.

The result allows the pathologist to assess the presence of a target protein and approximately its concentration. This method is very common and hundreds of different proteins can be analyzed. in the example above, an invasive breast cancer is stained with an antibody against estrogen receptor. The intense brown staining of the nuclei of cancer cells indicate that the cancer is strongly expressing the estrogen receptor and is likely being driven by estrogenic processes. The blue staining cells in the background are mostly lymphocytes stained with a blue counter stain to allow visualization of the tissue.  Breast cancers like this are considered to be estrogen receptor positive. It is known that estrogen receptor positive cancers are most likely to respond to hormonal treatments such as tamoxifen or aromatase inhibitors.

While single marker IHC is a powerful tool it presents challenges in that only one marker at a time and accurate quantification tools are lacking. Further, the assays are usually pushed to enable high sensitivity without proper dynamic range, so it can be difficult to accurately quantify expression in strongly expressing cells.

“Next Generation IHC” or multiplex IHC is a technique where more than one antibody can be applied to a tissue section at the same time and then visualized with secondary antibodies attached to different fluorescing tags. This produces a multiplex image which can be “deconvoluted” into separate channels for direct analysis

 

In this image the separate proteins Progesterone receptor and Cytokeratin can be isolated using filters to isolate the red and green fluorescence (the colors are actually false but help visualization for the human eye) the DAPI is a stain the stains nuclei. 

Once the various channels of image are acquired using a digital scanning microscope such as Aperio FL, computer software such as AQUA can isolate components of the images to define areas of interest on the tissue also called “masks”. These areas could be tumor nuclei, tumor cytoplasm,  lymphocytes, etc. Once masks are defined the signal from the target protein can then be accurately measured.

This ability to accurately localize and measure the protein semi-automatically produces very reproducible and precise data. Much like running an elisa on the slide

Some assays like estrogen receptor can be problematic to quantify, and this can lead to misclassification and mistreatment of patients causing serious risks to patients. A region of Canada unfortunately experienced problematic testing for many years which affected the quality and treatment of hundreds of breast cancer patients

http://www.cbc.ca/news/canada/newfoundland-labrador/lab-mistakes-poor-oversight-flagged-in-n-l-breast-cancer-inquiry-1.793504

ALso different approved method to measure hormone receptor in breast tissue may produce different results

https://www.nature.com/articles/modpathol2016151?WT.feed_name=subjects_cancer

Perkin Elmer is pushing multispectral imaging and quantification even further with their Vectra imaging systems and new Opal chemistries facilitating high multiplex staining.

http://www.perkinelmer.com/category/quantitative-pathology-research?gclid=CjwKCAjw75HWBRAwEiwAdzefxD-_DAE27g95aS1n9Jdyv3uLksY4AKWwRVIJs-W0fqyaJxjJbQ3JuBoCoSsQAvD_BwE

This elegant system allows 6 or more separate antibodies to be evaluated on a single tissue section.

 

This powerful, and stunningly beautiful, method enables multiple cell types to be visualized in a single tissue section.

In the above image  of a lung cancer produced by Susan McCarthy at Moffitt the orange areas are PDL1 and PD1 expression, the green are CD3 cells, the yellow CD8 and the red FOXP3. The cancer cells are highlighted in light blue and the dark blue identify nuceli.

Analysis like this preserve the rich complexity of the tumor microenvironment and allow direct visualization of not only the types of cells present, but their localization in respect to cancer cells and other immune cells.  This method has produced excitement amongst oncologists and immunologists seeking improved tools and clues into which tumors may be most susceptible to immune checkpoint treatment.

Challenges still remain in bringing assays like this into routine care. Its critical that the assay can meet quality and CLIA standards which include development of standard operating procedures, and delineation of the performance characteristics of the assay such as sensitivity, precision, performance, detectable range, and robustness.

Another layer of complexity is approach to the digital analysis of the data or “dry lab” as there can be many approaches such as counting cells or measuring areas of signal. Sources of variation could include different approaches to segmenting images and normalization. Despite these challenges I remain optimistic that these technologies will provide powerful new insights into the biology of cancer, and provide pathologists with compelling new way to microscopically examine human tissue.

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.