Cancer genome landscape: a radiologist’s guide to cancer genome medicine with imaging correlates

To understand the complexity of the mutations involved in tumorigenesis, these have been classified into passenger mutations, occurring in the “preneoplastic” phase with no effect on neoplastic process, and driver mutations, responsible for invasiveness and metastatic potential [5, 20].

Mutations conferring selective growth advantage and ultimately responsible for tumorigenesis are termed driver mutations. On average, an adult cancer needs 1–8 driver gene mutations to occur. Given their critical role in the process of oncogenesis, it is not surprising that unique driver mutations have been associated with specific imaging characteristics and response patterns on diagnostic imaging. For example, research in the field of radiogenomics have sought to differentiate imaging features of different molecular subtypes of non-small cell lung cancer (NSCLC) based on specific driver mutations, including anaplastic lymphoma kinase (ALK) or epithelial growth factor receptor (EGFR). EGFR-mutated NSCLC, for instance, has been associated with specific CT features such as higher rates of pleural retraction, homogeneous enhancement, smaller size, oval shape, and fewer calcifications [21‐23].

Identifying which genes contain driver mutations is challenging, and current data are derived from studies analyzing the frequency of mutated genes in a given cancer type. Among the mutated genes in a cancer, the ones more commonly mutated are more likely to contain driver mutations, whereas the less frequently mutated genes, yet numerically more present in cancers, are less likely to contain driver mutations: from sequencing of 3284 tumors, only 125 driver genes for 294,881 mutations were identified [24, 25]. Of these, 54 were oncogenes and 71 were tumor suppressor genes. In addition, genes expressed aberrantly in tumors, yet not frequently mutated are involved in tumorigenesis, and are termed epi-genes. These are altered through changes in DNA methylation or chromatin modification [5].

Cancer development and progression cannot be explained only in terms of driver and passenger mutations: in many cancers, only one or two driver mutated genes are identified. This contradicts the somatic evolution model, in which multiple sequential mutations acquired over decades are needed for a cancer to arise [14]. This apparent contradiction can be only partially resolved considering the technical and conceptual limitations of whole genome sequencing: many driver mutations cannot be identified with current sequencing techniques, and the vast majority of cancer genome studies focused at identifying mutations at exon levels, ignoring intergenic or intronic mutations [5]. In addition, epi-genes are extremely difficult to sequence, yet are often responsible for carcinogenesis. Nonetheless, the “dark matter” responsible for cancer development has not been fully understood.

Pathways acting on cell fate alter the ratio between differentiating cells, which cannot undergo division, and dividing cells, shifting the ratio toward the latter, conferring selective growth advantage to the tumor [5, 50].

Pathways that function through this process include gene regulation by steroid hormones, which can be targeted by hormonal therapies, and chromatin modifications, which can be targeted by drugs inhibiting histone deacetylases [50‐52].

The first pathway is exemplified by estrogen and progesterone receptor-positive (ER/PR⁺) breast cancer. These types of breast cancer show later development and higher frequency of bone metastases on scintigraphy and lower frequency of brain metastases on brain MRI, compared to their hormone receptor negative (HR⁻) counterparts [29, 30]. In addition, ER⁺ breast cancers tend to be smaller with irregular borders and low ADC values on breast MRI and are associated with low accuracy of MRI in predicting residual tumor extent after neoadjuvant systemic therapy, when compared to triple-negative or HER⁺ breast cancers [31, 32].

This pathway is targeted by tamoxifen, selective estrogen receptor modulator, and anastrozole or letrozole, two FDA-approved aromatase inhibitors to treat HR⁺ breast cancer (Fig. 2) [53, 54].

The chromatin modification pathway is targeted by histone deacetylases inhibitors, which include vorinostat, approved by the FDA for cutaneous T cell lymphoma treatment. Histone deacetylase enzymes switch cells from quiescent to replicative status and in addition, increase cell death by apoptotic and non-apoptotic mechanisms [55]. Histone deacetylases inhibitors keep cells in quiescent status, avoiding initiation of cell replication [56].

Cancer cells which can proliferate in unfavorable conditions, such as hypoxia or low glucose levels, will have a selective growth advantage compared to healthy cells. Mutations in the various pathways encoding for receptors for growth factors or for proteins involved in downstream cell growth pathways allow survival in unfavorable conditions. Identified pathways targeting cell survival are the receptor tyrosine kinase (RTK)/RAS, PI3K/AKT/mechanistic target of rapamycin (mTor), pathways regulating cycle cell and apoptosis, and TGF-beta pathway (Figs. 3, 4, and 5).

The RAS/RAF/MEK pathway, the MAPK pathway, and the JAK/STAT pathways share common tyrosine kinase receptors and transcription factors and are currently thought to be part of the RTK-RAS pathway, which is one of the most well-studied signaling pathways with critical role in cell cycle progression and growth. In this pathway, activation of epidermal growth factor receptor (EGFR) by its associated growth factor EGF and other RTKs leads to downstream activation of RAS GTPases and RAF kinases such as BRAF. Subsequent activation of additional kinase proteins such as MEK and MAPK follows in this signal pathway. These pathways ultimately lead to translocation of ERK/MAPK to the nucleus with subsequent transcription factor phosphorylation that regulates cell growth (Figs. 3 and 4) [57].

Mutations in the genes along the RTK/RAS pathway can occur at different levels, from the growth factors receptors to the downstream effectors [5, 9, 26]. Imaging correlates of mutations along this pathway include the EGFR-mutant NSCLC. When compared to EGFR wild-type NSCLC, this is more commonly associated with air bronchograms, pleural retraction, small lesion size, and absence of fibrosis [37, 38]. In patients with exon 21 mutation, groundglass opacity morphology and volume are significantly higher than in patients with exon 19 mutation or EGFR wild-type NSCLC [39]. In addition, EGFR-mutated NSCLC shows more commonly spiculated morphology and more commonly present with bone and lung metastases compared to its ALK-mutated counterpart [40]. The clinically important RTK-RAS signaling pathway serves as the basis for modern EGFR inhibitors, now a critical pillar of modern oncologic therapeutic management across numerous malignancies. In normal cells, when EGFR binds to an extracellular growth factor, various signaling pathways are activated, including the PI3K/AKT/mTor, JAK/STAT, and the RAS/RAF/MAPK pathways. EGFR inhibitors such as erlotinib and gefitinib are commonly employed for the targeted treatment of NSCLC testing positive for EGFR mutations, which are associated with pulmonary toxicity (Fig. 3) [58].

EGFR-mutated or EGFR-overexpressing colorectal cancer is associated with higher rates of radiological tumor response to cetuximab, an anti-EGF antibody, and response to treatment may be predicted by early decrease in tumor size on follow-up imaging acquired by 8 weeks after cetuximab initiation has also been associated with improved long-term survival [41, 59]. Cetuximab has also been associated with development of interstitial pneumonitis with CT findings of new bilateral patchy areas of ground glass attenuation [60, 61].

HER2-mutated breast cancers tend to be multicentric and multifocal with nodal involvement, are more commonly associated with liver metastases than the HR⁺ breast cancer, and have increased risk of central nervous system relapses particularly if already treated with trastuzumab, a monoclonal antibody binding to the extracellular domain of HER2 [42]. HER2-mutated NSCLC frequently present with disseminated lung nodules and tumor excavation patterns [43].

Another RTK that has been extensively studied is KIT, a type III receptor kinase composed of an extracellular ligand, a transmembrane region, and an intracellular domain with a juxtamembrane region and tyrosine kinase domains [8]. After ligand binding, KIT causes phosphorylation and subsequent downstream activation of the RAS/RAF/MAPK, JAK/STAT, and PI3K/AKT/mTor signaling pathways [62]. Mutations in KIT gene are present in 85% of gastrointestinal stromal tumors (GISTs), commonly at exon 11, which confers increased sensitivity to imatinib, a KIT tyrosine kinase inhibitor, and at exon 9, which confers increased sensitivity to sunitinib, a vascular endothelial growth factor receptor inhibitor which also targets KIT [63]. Specific KIT mutational variants have been associated with different initial imaging presentations, response patterns, and recurrence patterns. For example, GIST patients with exon 11 mutations tend to experience better tumor response on follow-up imaging and lower rates of disease recurrence following treatment with imatinib compared to patients with exon 9 mutations, which portends a more aggressive course [24, 25, 44]. Despite the improved prognosis associated with exon 11 mutations, a sizeable proportion of these patients will develop resistance to treatment within 6 months due to secondary mutations in exon 13 or 17 [44]. For patients harboring these secondary mutations, radiologists should be aware that these patients are at high risk of developing recurrence and progressive disease on subsequent imaging while on treatment with imatinib.

Patients with mutations in BRAF (most commonly BRAFV600) and MEK, two effectors in the RTK/RAS pathway, can be treated with BRAF and MEK inhibitors [5]. Available BRAF inhibitors utilized for the treatment of advanced BRAF-mutant melanoma include vemurafenib and dabrafenib. Tumor response to BRAF inhibitors is often rapid (Fig. 4). Nonetheless, development of acquired resistance ultimately occurs in the majority of cases with evidence of progressive disease on follow-up imaging. Combination therapy with BRAF and MEK inhibitors has been shown to reduce the rate of acquired resistance and lead to improved response rates in BRAFV600-mutant advanced melanoma [64, 65]. Combination BRAF/MEK inhibitor therapy is thus now the standard targeted therapy treatment, with available BRAF/MEK inhibitor combinations including vemurafenib/cobimetinib, dabrafenib/trametinib, and encorafenib/binimetinib.

The JAK tyrosine kinase and the STAT transcriptor factors play a key role in regulating cellular proliferation of hematopoietic precursor cells. Mutations in JAK2 leading to constitutive activation of the JAK-STAT pathway are common in polycythemia vera [66]. Ruxolitinib is an FDA-approved JAK1/JAK2 inhibitor for treatment of myelofibrosis and polycythemia vera [67].

Constitutive activation of PI3K/AKT/mTor pathway by a mutated receptor tyrosine kinase leads to the chronic production of growth factor ligands, which send signals to normal cells to supply growth factors, increasing receptor proteins on the cancer cell surface to make them more sensitive to growth factor ligand [68]. In addition, mutations along the PI3K/AKT/mTor pathway increase migration, proliferation, and motility. Many types of cancer show mutations along the PI3K/AKT/mTor pathway including neuroendocrine tumors, renal cell carcinoma, breast cancer, perivascular epithelioid cell tumors, and gastrointestinal stromal tumors [68].

The PI3K/AKT/mTor pathway is targeted by mTor inhibitors including everolimus, currently approved by the FDA for various cancers, including locally advanced, unresectable, or metastatic neuroendocrine tumors of pancreatic origin, and advanced renal cell carcinoma after failure of treatment with sunitinib or sorafenib (Fig. 5) [69].

Other mechanisms which confer selective growth advantage to cancer cells involve mutations of genes regulating cycle cell and apoptosis.

When growth factors stimulate quiescent cells to enter the cell cycle, D-type cyclins associate with CDK4/6 to promote cell cycle progression through G1 phase [70]. Palbociclib and ribociclib inhibit CDK4/6-Cyclin D action in promoting cell cycle progression and are FDA approved for HR⁺ HER2 negative advanced and/or metastatic breast cancer in combination with an aromatase inhibitor in postmenopausal women.

Apoptosis, or programmed cell death, acts as a defense against cancer growth [71]. Various proteins, including BCL-2, inhibit apoptosis by binding to and suppressing proapoptotic proteins [71]. Resistance to apoptosis occurs in chronic lymphocytic leukemia, which is associated with elevated BCL-2 protein expression [8]. Venetoclax, a BH3-mimetic FDA-approved drug for 17p-deleted refractory chronic lymphocytic leukemia, antagonizes BCL-2 and induces apoptosis [72].

TGF-β promotes tumorigenesis via a variety of mechanisms, making this pathway an emerging pathway for potential targeting in anticancer treatments. Various drugs targeting this pathway are currently under investigation for treatment of different cancers, although none has been granted FDA approval [73].

Any cell is exposed to toxic substances present in the microenvironment in which they reside. Replicative checkpoints prevent damaged cells to progress into the cell cycle or force the damaged cell to undergo apoptosis. Cells with mutations in genes regulating these checkpoints will have selective growth advantage compared to nonmutated cells [5]. Genes whose mutations acts on these checkpoints include TP53, ATM, and BRCA which are observed in breast and hereditary pancreatic cancers [74].

BRCA1 and BRCA2 are tumor suppressor genes which activate specific DNA repair processes in cases of damaged DNA. BRCA1-mutated breast cancer show low prevalence of calcifications on mammogram, more common with BRCA2 mutation. In addition, BRCA1-mutated breast cancer shows predilection for posterior breast and prepectoral region and show fibroadenoma-like benign morphologic features such as oval/round shape and smooth margins, or non-mass-like enhancement on MRI [48]. BRCA-mutated high grade serous ovarian cancer commonly shows peritoneal disease, peritoneal spread of disease in the gastrohepatic ligament, supradiaphragmatic lymphadenopathy, and mesenteric involvement on CT [49].

Poly (ADP-ribose) polymerases (PARP) 1/2 inhibitors are two targeted agents particularly effective in patients with mutated BRCA. In patients with BRCA loss-of-function mutations, PARP1 and -2 repair DNA single- or double-DNA strand breaks (Fig. 6) [75, 76]. PARP inhibition can cause genetic errors with double-strand breaks that ultimately lead to cell death [8, 77].

Various PARP inhibitors are currently used in clinical practice, including olaparib, niraparib, and talazoparib which have been granted FDA approval for treatment of ovarian or BRCA-mutated breast cancer. Resistance to PARP inhibitors represent a major barrier to the survival of patients with BRCA1- and BRCA2-mutated cancers and is thought to be related to various mechanisms, including mutations in BRCA, restoring its DNA repair function (Fig. 6) [77, 78]. Patients with ovarian carcinoma who develop secondary mutations in BRCA1/2 are not only likely to develop resistance and progressive disease on follow-up imaging when treated with platinum chemotherapy but also may similarly develop resistance to PARP inhibitors. Radiologists should thus be aware that these secondary mutations increase the likelihood that subsequent follow-up imaging will demonstrate increased tumor burden [78, 79].