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Colorectal Cancer Stratification in the Routine Clinical Pathway

A District General Hospital Experience

Wedden, Sarah PhD*; Miller, Keith FIBMS*,†; Frayling, Ian M. FRCPath; Thomas, Teresa FRCPath§; Chefani, Alina MD§; Miller, Karolina MRes§; Hamblin, Angela FRCPath; Taylor, Jenny C. PhD; D’Arrigo, Corrado FRCPath*

Applied Immunohistochemistry & Molecular Morphology: July 2019 - Volume 27 - Issue 6 - p e54–e62
doi: 10.1097/PAI.0000000000000631
Online Articles: Research Article
Open

Colorectal cancer (CRC) has many subtypes with different prognoses and response to treatment. Patients must be characterized to access the most appropriate treatment and improve outcomes. An increasing number of biomarkers are required for characterization but are not in routine use. We investigated whether CRC can be stratified routinely within a small district general hospital to inform clinical decision making at local multidisciplinary team meeting/tumor board level. We evaluated mismatch repair (MMR) and EGFR signaling pathways using predominantly in-house immunohistochemical (IHC) tests (MSH2, MSH6, MLH1, PMS2, BRAF-V600E, Her2, PTEN, cMET) as well as send away PCR/NGS tests (NRAS, KRAS, and BRAF). We demonstrated that many of the tests required for personalized treatment of CRC can be done locally and timely. Send away tests need to be requested shortly after cut-up and this needs to be firmly established in the tissue pathways for the results to be considered at multidisciplinary team meeting/tumor board. We have shown that MMR IHC combined with BRAFV600E IHC is practical and easy to perform in a small district general hospital, has full concordance with DNA-based tests and satisfies the latest NICE requirements for the identification of potential Lynch syndrome patients. We provide a framework for the interpretation and presentation of test results. It is a practical classification that clinical pathologists can use to communicate effectively with the clinical team. It is broadly based on molecular subtyping, firmly focused on treatment decisions and dependent on the panel of molecular tests currently available.

*CADQAS CIC, Poundbury Cancer Institute

UK NEQAS Immunocytochemistry & In-Situ Hybridisation, London

Institute of Cancer & Genetics, Cardiff University

§Dorset County Hospital Foundation Trust

Molecular Diagnostics Centre, Oxford BRC Haematology Theme, Oxford University Hospitals NHS Foundation Trust

Wellcome Trust Centre for Human Genetics, University of Oxford and Oxford NIHR Biomedical Research Centre, UK

This study was the result of a collaboration between Roche Tissue Diagnostics, UK NEQAS ICC&ISH and Dorset County Hospital Foundation Trust and was funded by Roche Tissue Diagnostics. NGS panel was funded by Technology Strategy Board. J.C.T. was funded by Oxford Biomedical Research Centre. C.D. and K.M. have received honoraria from Roche Tissue Diagnostics and Roche Pharma. The remaining authors declare no conflict of interest.

Reprints: Sarah Wedden, PhD, CADQAS CIC, Poundbury Cancer Institute, Newborough House, 3 Queen Mother Square, Poundbury, Dorchester, Dorset DT1 3BJ, UK (e-mail: sarah@cadqas.org).

Received July 24, 2017

Accepted November 12, 2017

This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal. http://creativecommons.org/licenses/by-nc-nd/4.0/

Colorectal cancer (CRC) is one of the most common cancers worldwide (1.6 million new diagnoses per annum) and is the fourth most common cause of cancer death.1 The standard treatment for early stage disease has been surgery with or without adjuvant chemotherapy. Although the diverse nature of CRC has long been accepted, there has been little clinical reason to recognize this since treatment options have been few and historically determined predominantly by tumor stage and not by disease subtype.2 In the past decade, the therapeutic landscape has become complex with the emergence of numerous new targeted treatments (Fig. 1) that are only effective on selected cohorts of patients. Companion diagnostic tests are required to identify potential responders (eg, RAS mutational analysis for drugs targeting the EGFR pathway.3,4 Pathologists are now required to provide companion diagnostics and other prognostic and predictive tests to guide treatment choice and clinicians have to consider the significance of growing numbers of additional tests.

FIGURE 1

FIGURE 1

The Multidisciplinary team (MDT)/tumor board (TB) meeting is the forum where all test results are considered and the management of each cancer patient is agreed. Despite UK guidelines recommending the use of tests such as those for DNA mismatch repair (MMR) on all patients with CRC,5,6 at present only few are managed with the full knowledge of these results.7 The reasons for this noncompliance are unclear. The aim of our study was to understand whether high-quality, full-scale testing for CRC biomarkers can be delivered for all CRC patients in a timely manner, what practical obstacles may prevent implementation, and to provide a framework for laboratories wanting to comply with the guidance. The work was carried out in a small District General Hospital (DGH) to provide proof of principle that these service improvements are not dependent on facilities and expertise available only in large regional reference centers or teaching hospitals. Our goal was to develop a workflow plan to produce and present molecular pathology data for optimal personalized patient management in time for MDT/TB (within 2 wks from surgery). Our assessment included IHC for MMR together with BRAF V600E, as per NICE guidance6 and RAS mutation status (as a biomarker for EGF-R targeted therapy). In addition, we evaluated PTEN, HER-2, and c-MET. Although these are currently not in guidelines, there is evidence that they influence the effectiveness of EGF-R targeted therapy8,9 and can be evaluated easily by IHC.

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MATERIALS AND METHODS

This work was performed prospectively as part of a study to improve the colorectal histopathology service and, as such, required no ethics approval. The study included all patients at Dorset County Hospital who underwent surgical resection for CRC during 2013.

For each resection specimen, a tissue block suitable for the study was identified at cut-up (day 0). Ideally, this contained tumor plus normal colonic tissue (for control). Tissue was fixed in 10% neutral buffered formalin for 6 to 72 hours at room temperature (16 to 21°C) and paraffin-embedded following routine processing.

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Immunohistochemistry (IHC)

Eight different IHC tests were performed on each case (Table 1). Sections (3 μm) were cut from the selected block and placed on coated slides. Control tissue was also added to the slide if required. Where available, the patient’s initial endoscopic biopsy was identified, sectioned, and placed on the same slide. The slides were baked for 45 minutes at 60°C. We included endoscopic biopsies to assess whether they could provide robust molecular data for the patients who are treated before surgery. We used the resection data if there was discordance between endoscopic biopsy and resection in this study.

TABLE 1

TABLE 1

All the IHC was performed on either the Ventana BenchMark XT or Ventana BenchMark ULTRA following the protocols indicated in Table 1. Staining patterns were evaluated according to the criteria in Table 1 on resection specimens and, when available, endoscopic biopsies.

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Controls for IHC

Colorectal tissue contained sufficient internal positive and negative controls for most of the antibodies. An additional piece of known positive tissue was placed on each slide for the BRAF V600E mutation-specific antibody (VE1) and HER-2/neu antibody (4B5). For the MMR markers, appendix tissue can be used to facilitate validation and control for staining consistency (Fig. 2). Quality assurance of our MMR IHC was through the UK NEQAS ICC&ISH assessment scheme.

FIGURE 2

FIGURE 2

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Genomic Testing: Next Generation Sequencing (NGS) and Conventional Non-NGS Techniques

After taking all the sections necessary for the in-house IHC work, the tissue blocks were sent to a reference center (UCL Advanced Diagnostics) for RAS and BRAF mutation analyses. These requests followed the routine clinical pathways of the hospital and therefore were performed using PCR, pyrosequencing, and NGS, depending on the current method used by the reference laboratory. The concordance of some of the mutation data was later assessed using NGS (Ion Ampliseq Cancer Hotspot Panel v2, Thermo Fisher Scientific), as per manufacturer’s instructions10 through a research collaboration with Oxford Molecular Diagnostic Centre.

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RESULTS

A total of 111 patients underwent surgical resection for CRC at Dorset County Hospital during 2013. One patient with neuroendocrine tumor and 1 patient with no residual tumor after neoadjuvant radiotherapy were later excluded from the analyses, so we assessed 109 cases. Seven cases of rectal cancer and 1 of sigmoid cancer had neoadjuvant radiotherapy. Molecular data for our cohort are summarized in Table 2 and the staining patterns are illustrated in Figure 3.

TABLE 2

TABLE 2

FIGURE 3

FIGURE 3

IHC was performed routinely and was successful in all 109 cases. Routine mutational analyses were requested for KRAS (76), NRAS (27), and BRAF (56) and all carried out successfully. Retrospective NGS analysis was performed on 93 cases. The data obtained from resection specimens were comparable to that obtained from the respective endoscopic biopsy with the exception of PTEN, C-MET, and HER-2 (see below).

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MMR Status and BRAF V600E Mutation Status

There was complete concordance between endoscopic biopsy and resection specimen for MMR marker IHC (MSH2, MSH6, MLH1, and PMS2). All 4 MMR proteins were expressed in 93 cases, and classified as proficient for MMR (pMMR). In 16 cases, ≥1 MMR proteins were abnormal, that is, absent, and were classified as deficient for MMR (dMMR). Four of these had wild-type BRAF, raising the possibility of Lynch syndrome (LS). One had loss of MSH6 whereas the other 3 had loss of both MLH1 and PMS2.

BRAF mutation status was evaluated by IHC for all 109 cases. We verified these results in 101 cases using PCR only (n=8), NGS only (n=45), or both (n=48). We were unable to verify the IHC result for the remaining 8 cases because of repeated failure of NGS testing. IHC-based BRAF mutation status was concordant with NGS & PCR findings except for mutation c.1816G>A (p.Gly606Arg), which was identified with NGS. This is a Tier 3 mutation, of indeterminate significance, distal to codon 600, and was unsurprisingly not picked up by either PCR or IHC. Such cases were therefore deemed nonmutated. There was complete concordance between endoscopic biopsies and resection specimens for BRAF IHC.

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KRAS and NRAS Mutation Status

KRAS mutation status was determined successfully for a total of 105 cases. It was determined by PCR or pyrosequencing only (n=12), NGS only (n=29), or both (n=64). There were 2 cases where a mutation identified by NGS was not picked up by PCR (KRAS c.38G>A [p.Gly13Asp] and KRAS c.183A>C [p.Gln61His]). Both are Tier 1 mutations and therefore included as KRAS mutations within this study.

NRAS mutation status was determined successfully in a total of 98 cases by PCR or pyrosequencing only (n=5), by NGS only (n=71) or by both methods (n=22) with full concordance.

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PTEN Loss, HER-2, and c-MET Over Expression

Where available, these biomarkers were scored on the endoscopic biopsy as well as the resection specimen. There was discordance in PTEN expression between biopsy and resection in 8.3% of cases (7/84). In all discordant cases PTEN was present in the endoscopic biopsy but lost in the resection. Discordant c-MET expression occurred in 25% of cases with biopsy (7/28). These were not the same 7 cases as above. In 6 cases there was a decreased expression in the resection. Discordant HER-2 expression occurred in just 1 case (of 80 with biopsy), where focal 3+ expression was not seen in the biopsy.

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DISCUSSION

We wanted to understand if a DGH IHC laboratory, with support from a reference center, can carry out up-front/reflex testing to stratify CRC within the timeframe required for informing clinical decision making and we wanted to provide a framework for the production and presentation of this molecular pathology data. We evaluated whether it is possible to perform the selected tests (MMR status, BRAF mutation status, RAS mutation status, loss of PTEN, and overexpression of c-MET and HER-2) within a 2-week turnaround time (TAT) and in time for the local MDT.

We demonstrated that all slide-based tests were easily performed in-house within a 48-hour TAT. The mutation analyses were sent off-site to a reference center as part of the routine diagnostic pathway and had a TAT of 8 to 10 working days. It was therefore only possible to collate all the results in time for MDT if a suitable block was selected at the time of cut-up and sent away promptly, without waiting for the diagnostic report. If TAT of referral centers cannot be improved, the prompt dispatch of the tissue block is critical and needs to be inserted into the routine cut-up procedure. A recent study has shown that using a NGS panel approach achieves a median turn-around time of 7 days at a cost which is increasingly competitive compared to single gene testing as more targets are added.10

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MMR Deficiency and LS

Recent NICE guidance states that all CRC patients, regardless of their age, should have tumor-based testing to assess the risk of LS when first diagnosed.6 LS is the most common cause of hereditary bowel cancer and carries an increased risk of developing other cancers.11 LS is estimated to cause 1000 cases of bowel cancer each year in UK, yet fewer than 5% of people with this condition are currently identified.12

This guidance significantly increases the amount of testing required but our study demonstrates that testing all CRC patients for MMR using in-house IHC in a DGH is feasible. The addition of BRAF IHC allows the identification of BRAF V600E mutation-negative patients who require referral to genetic services for further investigations for LS. These IHC tests can be performed on either the endoscopic biopsy or resection specimen, as we demonstrated 100% concordance. NICE guidelines recommend that patients negative for both BRAF V600E mutation and MLH1 require an MLH1 promoter hypermethylation test.6 Only 3 patients in our cohort (2.8%) fell into this category, demonstrating that in-house IHC would be sufficient for the majority of cases.

MMR testing by IHC can be done quickly and reliably before treatment in order to support clinical decision making as patients with dMMR tumors may have better prognosis,13 may not benefit from adjuvant chemotherapy,14 may benefit from low dose aspirin15 and respond to immunomodulation through checkpoint inhibitors.16 The FDA has recently granted accelerated approval to Pembrolizumab in certain situations for patients with any type of dMMR solid tumor,17 emphasizing the importance of universal MMR testing.

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Implications for Targeted/Biological Therapies

Prompt identification of dMMR or LS patients is only one aspect of CRC biomarking. It is a rapidly growing and constantly evolving area, but we have demonstrated that a DGH can implement the necessary service improvements to take advantage of new biomarkers and provide high quality testing with adequate turnaround time for patient treatment in a local setting.

The targeting of the EGF-R signaling pathway is a major therapeutic option in CRC (Fig. 1) and the regulatory approval for drugs targeting this pathway is dependent on absence of activating mutations in the RAS genes. Although RAS mutation status was only immediately relevant for 4 of our patients (those presenting with advanced/metastatic disease), an estimated recurrence rate of 20% to 30% for stage II and 50% to 80% for stage III patients18 means that 75% of our cohort would need this data to inform treatment in the near future. This would provide ample justification for immediate reflex testing rather than on-demand at a later date. In fact, immediate reflex testing provides higher quality information in the pathology report that is, most importantly, rapidly accessible upon recurrence. In addition, as we have shown in the prostate setting, reflex testing allows more effective use of service resources thus paradoxically creating capacity (manuscript in preparation).

Evidence suggests that changes in many other molecules along the EGF-R signaling pathways may impact on response to inhibitors of these pathways. For example, the presence of BRAF activating mutations affect the response to EGF-R inhibitors such as cetuximab and panitumumab.19 Likewise, loss of PTEN, over-expression of c-MET or HER-2 have a negative effect on response to EGF-R inhibitors although there is some controversial literature.8,20–22 Certainly, the current selection criteria for EGF-R TKI therapy results in a number of treatment failures, suggesting that refinements in the selection are necessary.23

Since ours was a feasibility study, the MDT did not act upon our additional test results. Nevertheless, we retrospectively evaluated their effect on eligibility for EGF-R targeted therapy. According to current guidelines, 66% of our patients would be eligible for these drugs. The addition of BRAF mutation status would bring this down to 45%. The inclusion of PTEN and HER-2 would reduce this cohort to 31% and, using all our data, we would predict that only 15 patients (14%) would respond optimally. These tests therefore may have huge implications on treatment decisions. Although we used published scoring systems for PTEN, c-MET, and HER-2 (Table 1), there are consensus issues,22–27 so it is crucial that suitable scoring systems are devised and validated against clinical response for these markers, and an external quality assurance process is established. We found disparities between scores for resection and biopsy tissue, which may be because of fixation/preanalytical processing or a reflection of disease process.

Other potential targeted therapies may be beneficial to CRC patients. For example, HER-2 overexpression may indicate good response to trastuzumab and lapatinib (Heracles trial28), loss of PTEN may indicate good response to mTOR inhibitors, which target the AKT pathway downstream of PTEN29 and over expression of c-MET may indicate response to MET and MEK inhibitors (MErCuRIC1 trial30). The FOCUS4 trial is currently stratifying CRC using biomarkers such as BRAF, PIK3/PTEN, and RAS to inform treatment.31 Our study complements this trial by demonstrating the feasibility of using these tests for routine stratification in a small DGH.

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Development of the Algorithm

Many of the authors (C.D., T.T., I.M.F., K.M., and A.C.) have had long associations with MDT/TB and understand the challenges of presenting ever-increasing molecular pathology data with complex ramifications for treatment decisions. The MDT/TB has only a few minutes allocated to each patient so requires a system of communication that summarizes all findings, is easily and quickly interpretable and can guide clinical decisions. We therefore constructed a graphic representation, structured to follow the then current clinical decision-making. Since then, rapid progress in CRC biomarker research has impacted further on treatment decisions. For instance, immunoscore,32 TILs (tumor infiltrating lymphocytes) and PD-L1 assessment were not widely used at the time of the study and immunomodulation with checkpoint inhibitors was unavailable as a treatment option in 2013.

We have therefore expanded and revised the algorithm to reflect what would be a working classification in 2017 and included test results with prognostic and therapeutic implications as well as traditional anatomical data (Fig. 4). This new algorithm is easy to update as new biomarkers emerge and guidelines change and can be customized to reflect local oncological practice.

FIGURE 4

FIGURE 4

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Financial Implications

NICE concluded that testing using IHC for MMR plus BRAF and MLH1 promoter methylation is a cost-effective use of NHS resources.6,33,34 Our approach to CRC testing could easily be adopted by all hospitals in response to NICE guidelines. In its most succinct form, this can be done with 5 IHC tests (MLH1, PMS2, MSH2, MSH6, and BRAF), with a relatively low burden on resources, although the health-economic case is predicated on central funding given the benefits to the NHS lie outside of pathology budgets.33 Additional tests could provide more accurate prediction and prognosis, thus reducing costs and delay caused by ineffective treatment.35

In the UK there is a large gap between the provision of cancer testing and demand.36 The estimated gap in CRC is the largest and in 2014 affected 10,704 patients (49%) who did not receive testing, potentially missing out on optimal treatment. The UK commissioning system funds tests for systemic anticancer treatment centrally whereas traditional IHC tests are commissioned locally. Funding of some IHC tests has therefore become separated from the funding of the associated targeted treatment. Furthermore, NHS departmental budgets are compartmentalized, so that savings made in Oncology and Surgery through the improvement of outcomes by personalized medicine are unavailable to Pathology. This is serious, as the health-economic case is predicated on central funding, given the benefits to the NHS lie outside of Pathology.33 Such current structures do not therefore fit current requirements and threaten the implementation of improved care pathways with a proven health-economic basis.

The use of IHC for drug selection for breast and lung cancer is well established.37,38 When other modalities of testing have been available, IHC is the most efficient and cost-effective platform.38 Our study demonstrates that IHC has a significant role to play in personalized medicine for CRC. The recent introduction of PD-L1 testing (the biomarker for checkpoint inhibitor therapy that can only be done by IHC in Histopathology services) reinforces its importance.

It is clear that we need a unified strategy to fund all companion diagnostics, irrespective of whether they are test tube-based or slide-based. If we fail to finance appropriately and adequately all tests that allow patients to receive the most appropriate medicine, we fail both patients and all who pay into the health system, as well as making a mockery of health-economic studies.

We hope this work will enable pathologists to take up the challenges of supporting personalized cancer treatment whether they work in large centers or in small hospitals. We acknowledge that the future is moving toward screening large panels of biomarkers and this may even involve liquid biopsies as opposed to tissue biopsies. Once such systems are established, running in sufficient quantities and can demonstrate concordance and quality, they may well be the most effective way of determining choice of targeted therapy. We are not there yet. We have to fill the gap for the patients of today. This requires education, an understanding of the current limitations as well as the future possibilities and the development of funding streams which are not divisive.

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ACKNOWLEDGMENTS

The authors acknowledge the support of Roche Tissue Diagnostics for funding this work and the Technology Strategy Board for funding the NGS panel. We are indebted to the following for advice, discussion and help with manuscript preparation: Anne Waydelich, Gilles Erb, Uwe Schalles, Paula Toro, Joakim Jagorstrand and Chris Hudson.

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Keywords:

colorectal cancer; Lynch syndrome; mismatch repair proteins; personalized medicine; targeted therapy

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