PDL1 (CD274), or programmed cell death-ligand 1, is an immune checkpoint receptor involved in immune escape in cancer, and it is upregulated in many cancers including NSCLC (Zhang, 2016). High levels of expression of PDL1 are associated with poor prognosis in NSCLC and pulmonary lymphoepithelioma-like carcinoma (Zhang 2016). Expression is also associated with EGFR mutations, the onset of which may directly lead to upregulation of PDL1 (Chen, 2015; Tang, 2015). Levels of expression of PDL1 detected through immunohistochemistry can predict response to PD1 therapy (Sorensen, 2016). Current clinical trials involving PDL1 inhibitors have shown impressive results in treating advanced stage cancers, particularly melanoma. Placental trophoblasts and macrophages are the best positive controls for this target.

PD1 (Programmed Death Receptor 1) is an immune checkpoint protein active in T cells that is a target alongside its ligand PDL1 and also CTLA-4 for immunotherapy in lung and other cancers (Alsaab, 2017). PD1 is involved in negatively regulating T cell inflammatory activity and, when bound to receptors on tumor cells, can work to subdue tumor suppression by inhibiting the immune response. Targeted inhibition of PD1 itself can therefore function as an anti-cancer therapy by reactivating this response (Jin, 2011; Francisco, 2010; Fife, 2011).

Aryl hydrocarbon receptor (AHR) is a transcription factor involved in xenobiotic metabolism and autophagy and it is expressed in many tissues including lung. In cancer, AHR is involved in migration and proliferation, and is upregulated in pancreatic, liver, head and neck, lung, thyroid and gastrointestinal tumors. AHR appears to function in both tumor suppression and tumorigenesis depending on the cell type and tissue (Tsai, 2017; Safe, 2013). In the lung, AHR expression is correlated with smoking-induced tumors, where carcinogens such as BaP directly bind to AHR and induce xenobiotic metabolism. Activation of AHR leads to upregulation of CYP1A1 and other cytochrome P450 enzymes, which are responsible for metabolizing carcinogens but can sometimes create a more damaging substance in error (Tsay, 2013). Higher expression of AHR in lung carcinomas is associated with a worse prognosis, particularly in tumors with mutant EGFR. In these tumors, the activation of AHR induces oncogenic Src expression and functional proliferative signaling (PI3K/Akt), resulting in resistance to tyrosine kinase inhibitors that target EGFR (Ye, 2017).

Surfactant protein A (SFTPA1) is involved in host defense in the lung and its expression is necessary for tubular myelin formation and in reducing surface tension within alveoli (Lopez-Rodriguez, 2016). Germline mutations in SFTPA1 that result in impaired surfactant secretion and respiratory insufficiency have been implicated in a hereditary predisposition for lung fibrosis and cancer (Nathan, 2016). The specific nature of surfactant A to lung tissue has made it a useful marker in lung diseases including adenocarcinoma (Takahashi, 2006). It has comparable sensitivity to marker NKX2-1 /TTF-1 and is particularly useful in distinguishing NKX2-1-positive lung from thyroid tumors (Tan, 2008).

SOX2 is a Yamanaka factor and master regulator involved in embryogenesis and transdifferentiation (Takahashi, 2006; Whyte, 2013). In squamous cell carcinoma of the lung, SOX2 frequently has amplified copy number (~20% of cases) and overexpression of the gene is found in roughly 90% of cases (Fukazawa, 2015; Rudin, 2012). Upregulation of SOX2 is likely a primary determinant of the transformation of basal cells into carcinomas of various subtypes, and the variable upstream inactivation of different tumor suppressors seems to decide which subtype. Specifically, in the lung SOX2 overexpression results in squamous cell carcinoma following loss of PTEN, CDKN2A/CDKN2B and/or STK11, while upregulation subsequent to TP53 inactivation results in adenocarcinoma (Murray, 2016; Ferone, 2016).

APOBEC3B is a cytidine deaminase involved in DNA repair and also somatic hypermutation. The deregulation of APOBEC family members including APOBEC3B has been implicated as a frequent driving source of mutagenesis in breast cancer and in other tissues (Nik-Zainal, 2012; McBride, 2008; Hwang, 2015). Campbell et al have also identified APOBEC mutation signatures in lung cancer, and further studies have found evidence of APOBEC3B upregulation in lung cancer and a correlation between increased expression and worse prognosis in NSCLC , making it an interesting and potentially important target for immunohistochemistry (Campbell 2016; Sasaki, 2014; Shumei, 2016).

MET (hepatocyte growth factor receptor / HGFR) is a receptor tyrosine kinase that is normally active in embryonic stem cells and progenitor cells. During embryogenesis, MET expression allows cells to burrow into adjacent areas in order to generate new embryonic structures, and in adult tissues, this invasive potential is a normal and essential component of wound repair. MET also promotes cell growth and inhibits apoptosis. In cancers, Met activation is associated with an aggressive, invasive phenotype and confers a poor prognosis, triggering tumor growth and ingrowth of new blood vessels. MET deregulation is common in human cancers, and contributes to therapeutic resistance, as it can be induced by chemotherapeutic agents and radiation. Hence Met inhibition, either targeting the receptor or HGFR ligand, is an area of interest, both as a primary and adjuvant means of treating cancer.

CK5 (KRT5) is positive in mesothelioma and in squamous carcinoma and rare in adenocarcinoma. It is a useful marker when used alongside CK6 and TP63 and in comparison with NKX2-1 staining for subtyping squamous cell versus adenocarcinomas of the lung (Carney, 2015; Rekhtman, 2011)

CK6 (KRT6) stains positively in mesothelioma and squamous carcinoma and is rare in adenocarcinoma. KRT6 is useful as a marker when used together with TP63 and KRT5 for subtyping squamous cell versus adenocarcinomas of the lung (Carney, 2015; Rekhtman, 2011).

CHGA (Chromogranin A) encodes a protein involved in the production of secretory vesicles in endocrine and neuroendocrine cells. Levels of this protein correlate with the number of secretory vesicles present, and staining of this protein is useful for subtyping neuroendocrine tumors in multiple tissues including the lung (Gut, 2016; Syversen, 2004). Serum of patients with small cell lung cancer can be checked for circulating CHGA, and in this context it has been shown to have more sensitivity than neuroendocrine marker NSE (Taneja, 2004). Sensitivity of CHGA is expected to increase with clinical stage (Seregni, 2001).

NKX2-1 (also known as TTF-1) is a transcription factor with a necessary function in the differentiation of lung, thyroid and forebrain cells, and it regulates the expression of surfactant proteins in the lung that are required for host defense and stability (Boggaram, 2009) . NKX2-1 is a useful cancer marker for distinguishing a primary adenocarcinoma from other metastases, particularly when combined with Napsin A in a marker panel (Anagnostou, 2008; Ye, 2011). It is often expressed in adenocarcinoma, where expression is correlated with EGFR mutation and also higher rates of survival in some patients (Wan, 2014; Anagnostou, 2008).

CD56 (NCAM1 / neural cell adhesion molecule 1) is a cell adhesion protein expressed in natural killer cells where its expression acts as a reliable marker of activation (Pruitt, 2011; Van Acker, 2017). It is often considered the most specific and sensitive of small cell neuroendocrine markers in the lung (Rekhtman, 2010), and is particularly useful in diagnosing small cell cancers with intense crush artefact (Kontogianni, 2005).

DSG3 (Desmoglein-3) identifies squamous differentiaton and is a highly specific and sensitive marker for pulmonary squamous cell carcinomas, particularly in subtyping from other classes of lung cancer (Savci-Heijink, 2009). Desmosomal protein is expressed in squamous epithelium where it forms part of the desmosomal structures that comprise cell junctions. Upregulation of DSG3 has been correlated with metastasis in a number of cancers including lung, potentially due to DSG3’s role in cell-adhesion and migration mechanics via regulation of the WNT/B-Catenin/TCF signaling pathway (Weed, 2015).

SYP (Synaptophysin) is a protein associated with neuronal synaptic vesical membranes that regulates endocytosis. In immunohistochemistry, Synaptophysin acts as a small cell neuroendocrine marker, and it is a very sensitive marker of neuroendocrine differentiation (Wiedenmann, 1986; Fisseler-Eckhoff, 2012).

Napsin A (NAPSA) is a secreted pepsidase produced in type II pneumocytes and renal tubular epithelium. It is involved in processing surfactant B in the lung and acts as a useful cytoplasmic marker for primary lung adenocarcinomas (Brasch, 2003; Ueno, 2004; Siddiqui, 2012). When paired with transcription factor TTF-1 and squamous markers TP63 and KRT5 in a marker panel, Napsin A is useful for distinguishing primary lung adenocarcinomas from other metastases (Ye, 2011; Turner, 2012; Siddiqui, 2012 ).

EGFR (Epidermal growth factor receptor) is an ERBB family receptor tyrosine kinase involved in regulating proliferation, apoptosis and other aspects of the cell cycle through the MAPK and PI3K/AKT signaling pathways. Mutations or overexpression of EGFR, often coinciding with increased copy number of the gene, occur in 40-90% of NSCLC tumors and mutations are recurrent in adenocarcinomas and in never-smokers (Bethune, 2010; Oronsky, 2017). As a biomarker, EGFR expression predicts response to tyrosine kinase inhibitor chemotherapy (TKI's) alongside testing for common activating mutations in EGFR (such as the L858R substitution) (Ladanyi, 2008). Individuals with inactivating mutations or with wild-type EGFR expression do not tend to see benefits from TKI treatment, and it is necessary to test for levels of wild type EGFR and mutation status to determine the appropriate therapy (Oronsky, 2017).

KRAS is a RAS/MAPK signaling pathway kinase with driving hotspot mutations in many tissues. KRAS is mutated in roughly 30% of lung adenocarcinomas and is less frequent in in squamous NSCLC (~5%), and it does not have detectable mutations in small cell lung cancer (Bhattacharya, 2015; Westcott, 2013). The most common KRAS mutation in lung cancer is the substitution G12C, but G12V and G12D also frequently occur (Bhattacharya, 2015).