Highlights in Pathology: Molecular Pathology (March 2019)

Dr. Brandon Sheffield, William Osler Health System

1. Updated IASCL, AMP, CAP guidelines for molecular testing in lung cancer

This publication, issued jointly by the International Association for the Study of Lung Cancer (IASLC), Association of Molecular Pathology (AMP) and College of American Pathologists (CAP) provides a comprehensive review of the literature with respect to molecular testing for the treatment of non-small cell lung cancer.  This updated guideline is intended to expand upon the previously issued 2013 guideline by the same organizations.

As expected, the recommendation to test all non-squamous non-small cell carcinomas for EGFR activating mutations and ALK rearrangements remains strong.  

Additionally, sufficient evidence is now available to support the strong recommendation that “ROS1 testing must be performed on all lung adenocarcinoma patients, regardless of clinical characteristics”.

Additional biomarkers, including BRAF, MET, HER2, RET, NTRK, and others are discussed. The evidence to support routine testing for these markers continues to grow, and testing for these is recommended; however, they are still not viewed as mandatory.  

PD-L1 and other biomarkers of immunotherapy are not discussed in this paper.

The publication of this new guideline places pressure on pathology laboratories to provide, at the bare minimum, ROS1 testing in addition to EGFR, ALK, and PD-L1.  

The majority of laboratories in Canada do not provide routine ROS1 testing and there is currently no funding provided by provincial health authorities.  

Possible testing modalities include immunohistochemistry, fluorescent  in situ hybridization, and next-generation sequencing-based approaches.  

Validation of ROS1 tests is particularly challenging given the low prevalence of ROS1-rearranged cancer (approximately 1% of all non-small cell lung carcinoma).

Pay attention to how Canadian laboratories respond to this challenge over the coming months. 

2. Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology

J Mol Diagn. 2018 Mar;20(2):129-159. doi: 10.1016/j.jmoldx.2017.11.004. Epub 2018 Jan 23. Lindeman NI1, Cagle PT2, Aisner DL3, Arcila ME4, Beasley MB5, Bernicker EH6, Colasacco C7, Dacic S8, Hirsch FR9, Kerr K10, Kwiatkowski DJ11, Ladanyi M12, Nowak JA13, Sholl L14, Temple-Smolkin R15, Solomon B16, Souter LH, Thunnissen E17, Tsao MS18, Ventura CB7, Wynes MW19, Yatabe Y20.

Simultaneously published: 

  • J Thorac Oncol. 2018 Mar;13(3):323-358
  • Arch Pathol Lab Med. 2018 Mar;142(3):321-346. 

Molecular classification of endometrial carcinoma.

The widespread availability of next-generation sequencing technologies has sparked a revolution in our understanding of malignancies at the genomic level.  

The Cancer Genome Atlas (TCGA) is an international research network assembled to pool omics-level data on various tumor types.  

TCGA projects include melanoma, gastric cancers, breast cancers, and many others.  One of the biggest surprises; however, has come from the comprehensive profiling of endometrial carcinomas.

These carcinomas have traditionally been classified morphologically as type 1 or type 2, endometrioid or serous, and graded by pathologists based on the amount of glandular differentiation.  This has all changed based on the new TCGA classification of endometrial carcinomas. 

Four distinct molecular subgroups were identified.  

  1. The copy number high group corresponds to the of high-grade serous type, features TP53 inactivating mutations and carries a poor prognosis.  
  2. Copy number low corresponds to the endomertrioid subtype.
  3. A hypermutated group was identified as being a distinct molecular subgroup, defined by mismatch-repair deficiency and a high mutational burden. This group can be readily identified by pathologists using immunohistochemistry.  
  4. And the biggest surprise, an ultramutated subgroup was identified. This group contains a mutational burden even higher than the hypermutated group. This group is characterized by mutations in the DNA polymerase epsilon (POLE) gene. Interestingly, this group carries an incredibly favourable prognosis, with near 100% overall survival. Endometrial cancers belonging to this subgroup can be identified by sequencing of the POLE gene. 

It will be interesting to see how this new molecular classification can be adapted into clinical practice, as it certainly has the potential to improve upon our treatment of this disease.

3. Integrated genomic characterization of endometrial carcinoma

Nature. 2013 May 2;497(7447):67-73. doi: 10.1038/nature12113. Cancer Genome Atlas Research Network, Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y, Shen H, Robertson AG, Pashtan I, Shen R, Benz CC, Yau C, Laird PW, Ding L, Zhang W, Mills GB, Kucherlapati R, Mardis ER, Levine DA.

Mismatch repair deficiency and immunotherapy

Immunotherapy, specifically PD1/PD-L1 checkpoint inhibitors, have revolutionized the treatment of advanced malignancy in the past decade.  This new class of drugs offers potentially curative therapy to patients who were viewed as palliative with dismal prognoses, not more than a few years ago.  While immunologists and drug developers have delivered this whopping success, and medical oncologists have embraced these new treatments with open arms, the pathology community has struggled to keep up and pair these new therapies with appropriate biomarkers.  We know that many, but not all, patients benefit from these treatments.  Immunohistochemistry for PD-L1, and genomic profiling for tumor mutational burden are currently utilized; however neither of these markers has provided the definitive predictive effect that we have previously seen with driver mutations and tyrosine kinase inhibitors.

This paper, published in The New England Journal of Medicine, highlights the utility of mismatch-repair deficiency as a biomarker for immunotherapy.   Mismatch repair deficient tumors typically feature very high tumor mutational burdens; however this distinct subgroup of hypermutated tumors comes with a definitive test that can be easily performed in any anatomic pathology lab, MMR immunohistochemistry.  While the technique may have been introduced for Lynch syndrome screening, it now certainly has a role as a predictive biomarker. 

Importantly, this work has led to the first tumor-agnostic indication of a drug by the United States Food and Drug Administration.  This is a critical milestone in the field of molecular pathology and personalized medicine, allowing for the treatment of a cancer based on its molecular underpinnings while de-emphasizing the site of origin.

Unfortunately, immunotherapy is still not available in Canada for patients with MMR-deficient tumors.  This is an area where we as pathologists will have to advocate for our patients, and help recognize the importance of MMR deficiency as a predictive biomarker for a new and highly effective class of anti-cancer drugs. 

N Engl J Med. 2015 Jun 25;372(26):2509-20. doi: 10.1056/NEJMoa1500596. Epub 2015 May 30.

Le DT1, Uram JN, Wang H, Bartlett BR, Kemberling H, Eyring AD, Skora AD, Luber BS, Azad NS, Laheru D, Biedrzycki B, Donehower RC, Zaheer A, Fisher GA, Crocenzi TS, Lee JJ, Duffy SM, Goldberg RM, de la Chapelle A, Koshiji M, Bhaijee F, Huebner T, Hruban RH, Wood LD, Cuka N, Pardoll DM, Papadopoulos N, Kinzler KW, Zhou S, Cornish TC, Taube JM, Anders RA, Eshleman JR, Vogelstein B, Diaz LA Jr.


Over the past decades, tremendous progress has been made in the treatment of breast cancer.  Widespread implementation of screening programs, improved surgical care, and hormonal therapy, to name a few, have helped transform this disease from a deadly cancer to a manageable illness for most patients. 

Currently, it is likely that we as a medical community are over-treating many breast cancer patients.  Nearly a decade ago, gene expression profiling changed the way we think about breast cancer by demonstrating reproducible subtypes under the overarching umbrella of ‘breast cancer’.  Gene expression profiling has since proven to be a useful prognostic and predictive marker for breast cancer treatment.    

The TAILORx study demonstrates that a gene expression profiling tool (Oncotype Dx) is able to differentiate distinct groups of ER-positive, localized breast cancer patients who will NOT benefit from adjuvant chemotherapy, and who can be treated adequately with hormonal therapy alone.  This finding will spare the side effects, costs, and societal burden of chemotherapy in this very large subset of patients.

There are many political and regulatory issues clouding the field of gene-expression profiling in breast cancer.  It will be of great interest how our governments, health authorities, and hospitals, navigate these issues as gene expression profiling is clearly now integral in breast cancer treatment. 

N Engl J Med. 2018 Jul 12;379(2):111-121. doi: 10.1056/NEJMoa1804710. Epub 2018 Jun 3.

Adjuvant Chemotherapy Guided by a 21-Gene Expression Assay in Breast Cancer.

Sparano JA1, Gray RJ1, Makower DF1, Pritchard KI1, Albain KS1, Hayes DF1, Geyer CE Jr1, Dees EC1, Goetz MP1, Olson JA Jr1, Lively T1, Badve SS1, Saphner TJ1, Wagner LI1, Whelan TJ1, Ellis MJ1, Paik S1, Wood WC1, Ravdin PM1, Keane MM1, Gomez Moreno HL1, Reddy PS1, Goggins TF1, Mayer IA1, Brufsky AM1, Toppmeyer DL1, Kaklamani VG1, Berenberg JL1, Abrams J1, Sledge GW Jr1.