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{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4385186","sourcedb":"PMC","sourceid":"4385186","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4385186","text":"Results\n\nMutational Signatures of ESCC\nTo extract the mutational signatures that cause somatic mutations in ESCC and identify driver genes or pathways contributing to ESCC in Chinese individuals, we sequenced the genome of 104 ESCC tumors and matched adjacent normal tissues from individuals recruited from the Taihang Mountains in north-central China (Table S1). WGS (median coverage of 65×) of 14 tumors and WES (median coverage of 132×) of 90 tumors were performed (Figure S1). The average mutation rate was 3.9 coding mutations/Mb in WGS samples and 2.4 non-silent mutations/Mb in WES samples (Table S2). This rate is consistent with recently published mutation rates in ESCC.6 A high frequency of C\u003eT transitions was identified in the overall dataset18 (Figure S2A), and C\u003eG transversions occurred more frequently in ESCC than in EAC19 (Figure S2B). We selected candidate non-silent mutations identified in 96 tumors for validation by using the deep target capture system (at least 365×). Validation rates were 97.8% for identified SNVs and 58% for indels. We also analyzed our previously published ESCC mutation dataset6 of 17 WGS and 71 WES samples recruited from the Chaoshan District of Gongdong Province, another area of high ESCC prevalence in China (Figure S1E).\nTo identify the mutational signatures within ESCC genomes, we applied the non-negative matrix-factorization method20 to a combined mutation set of 192 ESCC tumors (14 WGS and 90 WES samples from this study and 88 from Song et al.6) and uncovered three mutational signatures (Figure 1 and Figure S3). Signature A was characterized by C\u003eG, C\u003eT, and C\u003eA mutations at TpCpX trinucleotides (suggesting collateral damage following DNA-element retrotransposition or exogenous viruses) and was associated with mutations in the APOBEC family of cytidine deaminases.21–25 Moreover, hotspot mutations (c.1624G\u003eA [p.Glu542Lys] and c.1633G\u003eA [p.Glu545Lys]) on the SMG PIK3CA (MIM 171834) were significantly enriched in ESCC tumors that had an APOBEC signature (p = 0.0028, Fisher’s exact test, one-sided), implicating APOBEC activity as a key driver of PIK3CA mutagenesis in ESCC. Signature B was characterized by an enrichment of C\u003eT mutations at XpCpG trinucleotides as a result of an elevated rate of spontaneous 5-methyl-cytosine deamination.26 The elevated C\u003eT mutation rate at XpCpG trinucleotides is a well-recognized mutational mechanism probably due to deamination to thymine of methylated cytosines, which are usually at XpCpGs.26 Signature C was represented by types that, to our knowledge, are not yet known.\nTobacco smoking is consistently reported as an important risk factor for esophageal cancer, especially for squamous cell carcinoma27 and gastric cancer.28 The combined cohort of 192 ESCC individuals (104 from this study and 88 from Song et al.6) included 153 smoking and 39 non-smoking individuals (Table S1). Notably, we observed no smoking-associated signature characterized by C\u003eA mutations, which was defined by Alexandrov et al.,29 within ESCC genomes. Furthermore, we compared the proportion of C\u003eA transversions between smoking and non-smoking individuals and observed no statistically significant difference (p = 0.687, Figure 1C). Additionally, we found no smoking-associated signature in 149 EACs (at least 49 of 149 individuals with a history of smoking) from a pan-cancer study.19,29 These results indicate that the smoking-associated signature of C\u003eA mutations is limited in EC. Considering that epidemiological studies suggest that tobacco consumption might be associated with EC,30 we speculate that other smoking-associated signatures that have not been recognized might contribute to malignancy of ESCC.\n\nCNAs of ESCC\nTo investigate somatic CNAs in ESCC, we applied a modified GISTIC method to profile genome segments with CNAs in the 14 WGS tumors (Figure S4A). This analysis yielded 126 significantly altered regions (Table S4). One of the most significantly altered regions, 3q26.1–q29, contains SOX2 (MIM 184429), encoding a member of the SRY-related HMG-box family of transcription factors involved in embryonic development regulation and in cell-fate determination.31 This gene is overexpressed in ESCC and associated with chemoresistance. Downregulation of SOX2 might inhibit ESCC tumorigenesis and increase sensitivity to chemotherapy.32 Notably, of the nine tumors harboring SOX2 amplifications, we observed one focal (defined as \u003c100 kb) CNA containing only SOX2 (Figure S5), indicating that SOX2 is the most likely target of 3q26 amplification in ESCC.\nFocal CNAs are more likely to contain driver genes that confer clonal advantage, are causally implicated in oncogenesis, and have been positively selected during the evolution of the cancer.33 Therefore, to identify genes affected by recurrent CNAs, we used the Integrative Genomics Viewer to manually inspect the 126 significantly altered regions. This approach identified recurrent focal CNAs, including amplified chromosomal segments containing CBX4 and CBX834,35 (Figure S4B). Amplification of these genes was validated by FISH and qPCR copy-number assay (Figure 2A). Of the 104 ESCC specimens, 39% and 51% of tumors had an immunoreactivity score for CBX4 and CBX8 levels, respectively, which is at least double that of matched normal tissue (TIRS/NIRS \u003e 2; Figure 2B). Moreover, silencing CBX4 and CBX8 in KYSE2 and KYSE510 cells (which harbor high endogenous expression) significantly inhibited cell proliferation, colony formation, and cell invasion (Figures 2C–2E; Figure S6). These results suggest that CBX4 and CBX8 amplification and the resultant protein upregulation contribute to the development of ESCC and that they might thus serve as potential drug targets for ESCC treatment.\n\nSMGs\nWe next applied the MutSigCV method36 to identify SMGs in the combined 192 ESCC tumors (Figure S1E) and discovered nine such genes driven by point mutations (false discovery rate, q \u003c 0.1) and six further genes with p \u003c 0.01 (Figure 3A). Eleven of these 15 genes—including AJUBA, ZNF750, FAT1, FBXW7 (MIM 606278), and PTCH1 (MIM 601309) and the chromatin-remodeling genes CREBBP (MIM 600140) and BAP1 (MIM 603089)—harbored frequent inactivating mutations. Although AJUBA, ZNF750, FAT1, and FBXW7 were recently implicated as tumor suppressors in ESCC,7,37 their roles in mice models and the mechanisms by which they function as tumor suppressors are limited. As in other cancers,38,39 particularly EAC,19 this analysis also identified well-known cancer-associated genes, such as TP53 (MIM 191170), PIK3CA, and CDKN2A (MIM 600160), as SMGs in ESCC, thus providing evidence of common dysfunctions in cell-cycle control and apoptotic signaling.\nAJUBA, which encodes a LIM domain protein, inhibits the ATR-dependent DNA-damage response and is involved in several cellular processes, such as cell-fate determination, cytoskeletal organization, transcriptional repression, mitotic commitment, cell-cell adhesion, and migration.40 Along with LIMD1 (MIM 604543), AJUBA has been proposed to be a major component of the miRNA-mediated gene-silencing machinery and might have a tumor-suppressive function.41 However, the biological functions of AJUBA in ESCC tumorigenesis have never been reported. The following AJUBA mutations were identified and verified in four tumor samples: two stop-gain mutations (c.985G\u003eT [p.Glu329∗] and c.1057C\u003eT [p.Gln353∗]) and two frameshift indels (c.790_791insT [p.Val264fs∗] and c.152delG [p.Gly51fs∗]) in the 104-individual cohort and one frameshift insertion (c.1249_1250insA [p.Ala417fs∗]) and one splice-site mutation in two individuals from our previous cohort6 (Figure 3B; Figure S7A; Table S3). These mutational events result in truncated or disrupted protein products that lack proper LIM domains, indicating that they are loss-of-function mutations, and these mutations in AJUBA, encoding the truncated or disrupted protein, are expected to promote ESCC oncogenesis. In support of this possibility, immunoblot analysis showed the presence of truncated AJUBA in ESCC tumors (Figure 4A). AJUBA knockdown in KYSE140 and KYSE510 cells led to increased cell growth, colony formation, cell migration, and cell invasion (Figure S8). Moreover, exogenous levels of wild-type AJUBA in KYSE30 and KYSE150 cells with low endogenous AJUBA levels suppressed cell growth, cell migration, and cell invasion; these effects were abrogated by AJUBA alterations (p.Gln353∗ and p.Val264fs∗; Figures 4B–4F). Together with our genetic observations, these functional data indicate that AJUBA might act as a tumor suppressor in ESCC and that the AJUBA mutations observed in ESCC abrogate its tumor-suppressive function.\nMutations in ZNF750, a tumor-associated gene located at 17q25,7 were identified in 6% of ESCC tumors. We identified 11 somatic mutations, of which we verified (via Sanger sequencing) six, including two nonsense mutations (c.620G\u003eA [p.Trp207∗] and c.209C\u003eA [p.Ser70∗]), one indel (c.108_111del [p.Glu37Lysfs∗]), and three missense mutations (c.96T\u003eA [p.Phe32Leu], c.1520A\u003eC [p.Asp507Ala], and c.1508C\u003eG [p.Ser503Cys]) in ZNF750 in the 104-individual cohort. In addition, five (c.414C\u003eA [p.Cys138∗], c.770C\u003eA [p.Ser257∗], c.85C\u003eT [p.Gln29∗], c.625_626insAA [p.Ala209fs∗], and c.1621G\u003eA [p.Ala541Thr]) out of 11 somatic mutations were verified by Sanger sequencing in our previous cohort6 (n = 88; Figure 3B). Sixty-four percent of the mutations identified in ZNF750 are inactivating. Additionally, ZNF750 deletions, but no somatic mutations, were observed in 3 out of 14 tumor samples in the WGS set (21%, G-score \u003e 0.23) and validated with a qPCR copy-number assay. The qPCR copy-number assay also determined that four out of six tumor samples harboring ZNF750 mutations or indels in the 90-sample WES set were affected by deletions, indicating that inactivation of both alleles had occurred in these individuals (Figures S9A–S9C). Notably, frequent loss of heterozygosity at 17q25.3 has been previously reported in ESCC,42 but no gene at or near the 17q25.3 region was identified. Our genetic data strongly indicate that ZNF750 is the missing piece of this puzzle.\nWe next used the immunohistochemical method to determine whether a correlation exists between these genetic changes and the amount of ZNF750. As expected, ZNF750, a nuclear factor, was strongly stained in the nuclei of normal esophageal epithelial cells. Surprisingly, though, it was dramatically upregulated in the cytoplasm of ESCC tumor cells in comparison to that of normal tissue cells. Moreover, individuals with tumors harboring ZNF750 mutations had higher cytoplasmic expression levels than did those lacking ZNF750 mutations (Figure 5A). Mislocalization of a truncated (p.Ser70∗) ZNF750 (Figure 5B) indicated that cytoplasm translocation was partly caused by loss of the C-terminal nuclear localization sequence. ZNF750 regulates the gene program controlling terminal epidermal differentiation.43 For investigating a function for ZNF750 in tumorigenesis, shRNA-mediated stable ZNF750 depletion was followed by transfection with wild-type or altered (p.Ser70∗ or p.Trp207∗) ZNF750 in KYSE150 and KYSE140 cells. ZNF750 knockdown strongly promoted KYSE150 and KYSE140 cell proliferation, migration, and invasion. Moreover, functional studies demonstrated that wild-type ZNF750 inhibited cell growth, migration, and invasion, and this effect was abrogated by altered (p.Ser70∗ or p.Trp207∗) ZNF750 (Figure 5C; Figures S9D and S9E). Finally, ZNF750 depletion and p.Ser70∗ ZNF750 markedly increased tumor size in the xenograft system in mice, whereas wild-type ZNF750 significantly decreased it (Figure 5D). Our genetic observations and functional data therefore suggest that ZNF750 acts as a tumor suppressor in ESCC.\nFAT1, which encodes a cadherin-like protein commonly expressed in epithelial tissues,44 was mutated in 15% of ESCC tumors. Notably, 13 mutations (77%) were truncating (stop-gain and frameshift) (Table S3). FAT1 is reported to regulate cell-cell adhesion and other cell behavior by controlling actin polymerization.44 Recently, Morris et al. reported that FAT1 suppresses cancer cell growth by binding β-catenin and preventing nuclear localization.44 FAT1 inactivation, via mutations that affect the cytoplasmic domain, leads to aberrant Wnt/β-catenin signaling in multiple cancer types.45 In our cohort, we discovered mutations affecting cadherin repeats and laminin G domains but no mutations affecting the cytoplasmic domain. This observation indicates that mutations affecting FAT1 extracellular domains might disrupt cell-cell associations and increase invasiveness and thus potentially contribute to ESCC tumorigenesis. FBXW7 mutations were observed in eight ESCC tumors in our cohort: these included two nonsense mutations (c.1005T\u003eA [p.Cys335∗] and c.409G\u003eT [p.Glu137∗]), one frameshift deletion (c.736_739del [p.Gly247Profs∗] and inactivating mutations), and five missense mutations predicted to be deleterious by SIFT and PolyPhen-2 analyses (Table S3).46 FBXW7 mutations and copy-number loss and a subsequent decreased FBXW7 level have been observed in various cancer types.46,47 Decreased amounts of FBXW7 are reported to correlate with poor prognosis;47 however, we observed no correlation between FBXW7 mutations and prognosis in our cohort.\nInactivating mutations in several chromatin-remodeling genes, including CREBBP and BAP1, frequently occurred in our 104 ESCC samples. CREBBP and EP300 (MIM 602700) mutations occurred in 11/104 ESCC tumors (Table S3). Inactivating CREBBP and EP300 mutations have been reported in various human cancer types.6,48 We also identified mutations in BAP1, which encodes a nuclear deubiquitinase involved in chromatin remodeling.49 BAP1 mutations have been reported in renal carcinoma and uveal melanoma,49 but not in ESCC to date. Moreover, frequent truncating mutations were observed in the chromatin-remodeling genes KMT2D (MLL2 [MIM 602113]) and KMT2C (MLL3 [MIM 606833]) (14% together) and KDM6A (MIM 300128) (3%) (Table S3). At least one chromatin-remodeling gene was altered in 33/104 ESCC tumors.\n\nAltered Pathways in ESCC\nIn our screen, SMGs were enriched in four pathways known to be important in cancer, including the cell cycle, NOTCH signaling, PI3K signaling, and cell adhesion. In addition, analyses of the KEGG pathway revealed overrepresented mutations of hedgehog (Hh) signaling and MAPK signaling, and a high percentage of truncating mutations were observed in chromatin-remodeling genes (Figure 6A). Eleven recurrent mutated genes involving the cell-cycle regulatory pathway were identified, and TP53, CDKN2A, and RB1 (MIM 614041) accounted for 88%, 8%, and 2%, respectively (Table S3). Moreover, frequent truncating mutations were observed in KMT2D and KMT2C (14%), CREBBP and EP300 (13%), and KDM6A (3%). Genes involved in the PI3K-AKT-mTOR pathway were mutated in 29% of 104 tumors, and PIK3CA was the most significantly altered gene (17%). Immunohistochemical analysis confirmed the presence of PIK3CA, AKT1, and GLI1 in tumors (compared with matched normal tissue) in the 104-individual WGS and WES cohorts (Figure 6B). Hence, these data shed light on the essential role of dysregulation of these critical pathways in tumorigenesis of 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