# Genomic Analysis of Response to Neoadjuvant Chemotherapy in Esophageal Adenocarcinoma
## 4 Discussion
Abnormal activity of the CDK/cyclin complexes in esophageal adenocarcinoma has been shown to be a marker of acquired chemo-radio-resistance [65; 66]. _CDK4/6_ inhibitors could be promising therapeutics for non-responders to NAC with copy number changes in this axis. In particular, _CDK4/6_ inhibitors palbcoli-clib, ribociclib and abemaciclib have shown efficacy in vitro models of EAC [25; 67] andpromising results in breast cancer, non-small cell lung cancer and melanoma patients [68]. Similarly, the use of ABT-348, a multitarget Aurora kinase and _VEGFR_ inhibitor [69], is currently being explored in phase I and II clinical trials in patients with _CDKN2A_-deficient tumors [70; 71], suggesting additional targeted therapies to this axis are closer to clinical adoption. Previous genomic analyses suggest that copy number changes to RTKs are pervasive in EAC, with the potential for targeting with RTK inhibitors specific to the activated pathways, such as trastuzumab and ABT-806 for _ERBB2_ (amplified in responders) and _EGFR_ (amplified in non-responders), respectively [24; 72]. _ERBB2_ overexpressing tumors are already treated in the metastatic setting with trastuzumab [73] and recent phase II trials in the perioperative setting are encouraging [74; 75]. We found that _EGFR_ is uniquely amplified in non-responders, suggesting that anti-_EGFR_ antibodies cetuximab or ABT-806 may be useful therapies in these patients. _EGFR_-amplified EAC patients have been shown to particularly benefit from cetuximab [76]. It is well tolerated by EAC patients [77] and has gone through phase III trials as a neoadjuvant therapy in addition to chemotherapy or chemoradiation, showing a modest improvement in recurrence-free survival [78]. However, several other phase III trials have failed to show benefits of cetuximab use in unselected populations of esophageal cancer patients [79; 80]. _KRAS_ mutations are known to confer resistance to cetuximab in colorectal cancer [81; 82], and while this is unclear in EAC due to the rarity of _KRAS_ mutations and unselected patient populations [78; 83], _KRAS_-mutant tumors in our dataset bore the same mutations in codons 12 and 13 as the resistant colorectal tumors and were non-responders. Taken together these trials underscore the need for careful selection of patient populations to be treated with RTK inhibitors based on mutation status. Finally, we report that Neuron Navigator-3 (_NAV3_), a known tumor suppressor downstream of _EGFR_[84], is mutated exclusively in non-responders. _NAV3_ is a microtubule-binding protein whose expression is regulated by _TP73_ and induced by _EGF_ in breast cancer cells [84]. In our cohort we observed that _NAV3_ was co-mutated with _CDKN2A_, with most mutations being missense. Predictions of neoantigen recognition in lung adenocarcinoma suggest that _NAV3_ is one of the most commonly mutated genes with predicted neoantigen recognition in this disease as well [85]. The functional consequences of these mutations in EAC are unclear but we predict several to be functionally deleterious. _NAV3_ is primarily implicated as a metastasis suppressor in multiple cancer types. _NAV3_ is upregulated in response to DNA damage in colon carcinoma cells and is involved in the suppression of migration and invasion in vitro [86]. Loss of heterozygosity occurs in colorectal cancer and this associates with lymph node metastasis [87]. _NAV3_ expression is attenuated in metastatic colon cancer [86], breast cancer and lung cancer [84] and its knockdown promotes invasive behaviors [84; 86], platinum drug resistance [88] and epithelial mesenchymal transition in vitro [86] and enhances metastasis in vivo [84]. The inhibitory effect of _NAV3_ on invasion and metastasis may be due to its promotion of slower, directional cell migration as opposed to the random migration observed in _NAV3_ knockdown cells, which enhances their ability to explore their environment [84].