Association of Chromosome 19 to Lung Cancer Genotypes and Phenotypes

Cancer Metastasis Rev DOI 10.1007/s10555-015-9556-2

Association of chromosome 19 to lung cancer genotypes and phenotypes

Xiangdong Wang1 & Yong Zhang 1 & Carol L. Nilsson2 & Frode S. Berven3 & Per E. Andrén4 & Elisabet Carlsohn5 & Johan Malm7 & Manuel Fuentes7 & Ákos Végvári6,8 & Charlotte Welinder6,9 & Thomas E. Fehniger6,10 & Melinda Rezeli8 & Goutham Edula11 & Sophia Hober12 & Toshihide Nishimura13 & György Marko-Varga6,8,13

# Springer Science+Business Media New York 2015

Abstract The Chromosome 19 Consortium, a part of the aberrations include translocation t(15, 19) (q13, p13.1) fusion Chromosome-Centric Human Proteome Project (C-HPP, oncogene BRD4-NUT, DNA repair genes (ERCC1, ERCC2, http://www.C-HPP.org), is tasked with the understanding XRCC1), TGFβ1 pathway activation genes (TGFB1, LTBP4) chromosome 19 functions at the gene and protein levels, as , Dyrk1B, and potential oncogenesis protector genes such as well as their roles in lung oncogenesis. Comparative genomic NFkB pathway inhibition genes (NFKBIB, PPP1R13L) and hybridization (CGH) studies revealed chromosome aberration EGLN2. In conclusion, neXtProt is an effective resource for in lung cancer subtypes, including ADC, SCC, LCC, and the validation of gene aberrations identified in genomic SCLC. The most common abnormality is 19p loss and 19q studies. It promises to enhance our understanding of lung gain. Sixty-four aberrant genes identified in previous genomic cancer oncogenesis. studies and their encoded protein functions were further validated in the neXtProt database (http://www.nextprot.org/). Among those, the loss of tumor suppressor genes STK11, Keywords Proteins . Genes . Antibodies . mRNA . Mass MUM1, KISS1R (19p13.3), and BRG1 (19p13.13) is spectrometry . Bioinformatics . Protein microarray . Human associated with lung oncogenesis or remote metastasis. Gene disease

Xiangdong Wang and Yong Zhang contributed equally to this work.

* Xiangdong Wang 7 Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, [email protected] Unidad de Proteomica, Departamento de Medicina and Servicio General de Citometría-Nucleus, University of Salamanca, * György Marko-Varga 37007 Salamanca, Spain [email protected] 8 Clinical Protein Science & Imaging, Biomedical Center, Department 1 Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, of Measurement Technology and Industrial Electrical Engineering, Fudan University, Shanghai, China Lund University, BMC C13, 221 84 Lund, Sweden 2 Department of Pharmacology and Toxicology, UTMB Cancer 9 Department of Oncology and Pathology, Clinical Sciences, Lund Center, University of Texas Medical Branch, Galveston, TX 77555, University, 221 85 Lund, Sweden USA 3 Department of Biomedicine, University of Bergen, 10 Institute of Clinical Medicine, Tallinn University of Technology, 5009 Bergen, Norway 12618 Tallinn, Estonia 4 Department of Pharmaceutical Biosciences, Uppsala University, 751 11 24 Uppsala, Sweden Clinnovo Research Labs, Hyderabad, India 5 Proteomics Core Facility, Göteborg University, 413 12 School of Biotechnology, Department of Proteomics, Royal Institute 90 Göteborg, Sweden of Technology, 106 91 Stockholm, Sweden 6 Department of Laboratory Medicine, Section for Clinical Chemistry, Lund University, Skåne University Hospital in Malmö, 205 13 First Department of Surgery, Tokyo Medical University, 6-7-1 02 Malmö, Sweden Nishishinjiku Shinjiku-ku, Tokyo 160-0023, Japan Cancer Metastasis Rev

1 Introduction Lung cancer Lung cancer Lung cancer risk subtype prognosis Lung cancer is the leading diagnosed cancer as well as CGH study the leading cause of cancer death globally. It accounts for 13 % (1.82 million) of the total new cancer cases Gene aberraon in chromosome 19 and 18 % (1.59 million) of the deaths in cancer in 2012 around the world [1]. Lung cancer is also the leading Protein level validaon in cause of death accounting for 29 % and 26 % of total C-HPP based database cancer deaths in men and women, respectively. The five year survival for all stage lung cancer patients is only Gene and protein funcon annotaon about 15 %, and for stage IV patients, just 3–4%[2,

3]. Chromosome aberrations related to lung oncogenesis Potenal lung mechanisms have been revealed recently. About 50 % oncogenesis of the lung adenocarcinoma (ADC) tumors bear Bdriver mechanism mutations^. EGFR mutations are the most common Fig. 1 Workflow identifying molecular mechanism of lung oncogenesis. drive mutations in lung ADC, usually due to losses in To decipher the oncogenesis mechanism chromosome 19 gene exon 19, or point mutations of exon 21 in chromosome aberrations identified in GCH studies with lung cancer subtype, risk, 7[4]. About 4 % of lung ADCs are caused by EML4- and prognosis were enrolled. The indentified aberration genes were integrated and further inquired in chromosome centric neXProt to ALK fusion genes, usually intron 13 of EML4 in chro- explore potential lung oncogenesis mechanism mosome 1 fused to intron 20 of ALK in chromosome 2 [5]. Targeted treatments aimed at the driver mutation proteins remarkably increase the overall survival of lung Chromosome 19 has the highest gene density of all human ADC patients. With comparative genomic hybridization chromosomes, more than double the genome-wide average. (CGH) methods and high throughout genome-wide as- Furthermore, it has large clusters of gene families that corre- sociation studies (GWAS), more chromosomal variants spond to high G + C content and CpG islands which indicate associated with lung oncogenesis have been identified. its rich biological and evolutionary significance. Chromosome The importance of chromosome 19 gene aberrations was 19 is also unique in its density of repeat sequences (55 % vs clearly demonstrated by the previous studies. the genome average of 44.8 %) [14]. The Chromosome-Centric Human Proteome Project (C- The C-HPP project targets the identification of all HPP) is a global consortium dedicated to mapping the entire gene-coding proteins with a special emphasis on the human complement of proteins, with global membership missing proteins, which account for almost 30 % of (http://www.c-hpp.org)[6–10]. The Chromosome 19 the proteins in the human proteome. The ENCODE ini- Consortium has investigated gene expression using tiative has been linked to the C-HPP initiative and pro- complementary analysis platforms, to provide a genome- vides newly identified gene activity that may predict wide human protein resource database, and detailed maps of novel proteoforms [13]. The data resources of the HPP protein molecular pathways, interactions, and networks. The are comprised of Ensemble, which is linked to the Chromosome 19 project has already contributed to the anno- neXtProt, PeptideAtlas, and gpmDB databases. Recently, tations of severe diseases, especially glioblastoma [11–13]. the numbers of highly confident protein identifications The present article focuses on chromosome 19 gene aber- in these data resources that were announced recently by rations in different lung cancer subtypes, including non-small Marko-Varga et al [15]. The number of missing proteins cell lung cancer (NSCLC): ADC, squamous cell carcinoma during one year was decreased from 32.7 % in 2012 to (SCC), large cell carcinoma (LCC), and small cell lung cancer 26.2 % in 2013 (September, lecture by G. Omenn, at (SCLC), and their potential role in lung oncogenesis. We have HUPO World Congress, Yokohama, Japan). In the Sep- explored gene polymorphisms on chromosome 19 that are tember 19, 2014, release of neXtProt, the number of translated into protein variants, and offer potential mecha- protein-coding genes is about 20000. Roughly 18 % of nisms involved, as well as potential targeted therapeutics for the complete set of human protein coding genes is miss- the future (Fig. 1). ing at the protein level currently. As for chromosome 19, according to of neXtProt database released on Jan- uary 2015, there are estimated 1,432 protein-coding 2 Bioinformatic annotation of chromosome 19 genes, including 244 genes with transcript-based evidence (PE2) available. Of these 1,432 genes, 2,707 al- Chromosome 19 spans about 64 million base pairs, ternative splicing variants are listed, as well as 199N- representing more than 2 % of the human genome. acetylated and 407 phorphoproteins. Cancer Metastasis Rev

19P In SCC, the aberrations of chromosome 19 losses or gains DNA loss were both indentified. One CGH study in Eastern lung SCC DNA gain demonstrated DNA amplifications on 19p [21]. Gains of 19q13.13 were increased in Western lung SCC patients ADC 19p13.11 [22]. Furthermore, gene losses of chromosome 19 in adjacent bronchial mucosa were detected in SCC and LCC both in primary lung carcinomas. Chromosome 19 losses may be the early event in SCC oncogenesis [23]. Whole exon se- Asbstos 19p13.3 SCC quencing (n= 51) and copy number analysis (n=47) of induced ADC resected SCLC tumors was compared with matched non- cancer samples from Eastern SCLC patients. Genetic am- Smoker ADC 19p13.1 plifications in the PI3K/AKT/mTOR pathway were detected in 36 % of SCLC, including AKT2 (9 %), located in 19q13.2 [24]. Western people showed two amplified regions in chromosome 19q13.2-3 in 4 types of lung cancer (ADC, SCC, LCC, and SCLC). 265 lung cancer samples were compared with 272 non-malignant samples. Single 19q12 SCC nucleotide polymorphism (SNP) RT-PCR revealed a vari- Non-smoker ADC 19q13.1 Smoker SCC ant allele of DNA repair gene ERCC2 rs1052559a and rs1799793 in 19q13.2–3 were significantly over- 19q13.2-3 Smoker health represented in female lung cancer [25]. Similarly, a Chinese population study of 247 lung cancer cases and 253 non- 19q13.13 LCC cancer controls, matched by age, gender, and ethnicity, also ADC SCLC Smoker AEC found nine SNP in three DNA repair genes (XRCC1, ERCC1, ERCC2) in the region of chromosome 19q13.2–3 19q13.42 were over-represented in the cancer group [26].

Gene aberrations of lung cancer risk factor Smoking is the 19q main risk factor associated with lung cancer around the world. Chromosome 19q13 amplification induced by smoking has Fig. 2 Different gene aberration of lung cancer phenotypes: ADC (adenocarcinoma), SCC (squamous cell carcinoma), LCC (large cell been demonstrated to occur. A recent genome-wide associa- carcinoma), and SCLC (small cell lung cancer); smoker or non-smoker. tion study (GWAS) study in western people compared the The main chromosome gene aberrations are 19p.13 loss and 19q12-13 transcriptome of airway basal cells (BC) purified from the gain airway epithelium of healthy nonsmokers and healthy smokers. 166 (25 %) of the differentially expressed genes 3 Chromosome 19 gene abnormalities in lung cancer are located on chromosome 19, with 13 genes up-regulated on 19q13.2, including 4 genes (NFKBIB, LTBP4, EGLN2, Types of gene aberrations related to lung cancer pheno- and TGFB1) associated with risk for chronic obstructive pul- types (Fig. 2) CGH studies implicate chromosome 19p loss monary disease (COPD). Another QWAS study also revealed and 19q amplification/high level polysomy in lung ADC. A EGLN2 SNP rs3733829 variant and CYP2A6 is strongly as- study of 31 Eastern lung ADC cases showed the frequent sociated with cigarette history [27]. These gene aberrations deletions on 19p (41.9 %) [16]. The loss of ICAM1 may be associated with smoking-related lung cancer risk (19p13.2) was most frequent in Eastern lung ADC [17]. An- [28]. SNPs (rs1800469, rs1982072, and rs2241714) in the other study of 226 lung ADC samples from Eastern Asian (n= promoter region of the TGFB1 were reported to be associated 90) and Western (n= 136) patients, DNA aberrations, and with COPD and lung cancer in cigarette smokers [29]. A copy number variations were detected by use of a high- HapMap (http://www.hapmap.org/)-based study in Eastern resolution microarray platform. A multivariate model identi- ADC and SCC patients demonstrated 19q13.3 SNP fied a higher rate of genomic loss on 19p13.3 (29 related variations, including ERCC2, PPP1R13, ERCC1, and genes) and 19p13.11 (14 related genes) ethnicity-specific in CD3EAP, were related with smoking duration and lung lung cancer patients from Western [18]. Other studies demon- cancer risk [30]. A large study of SNPs previously strated frequent DNA amplifications at 19q13 in Eastern lung associated with smoking behavior in 894 lung cancer cases ADC [19] and frequently over-expressed regions on 19q12 and 1,805 controls revealed rs7937 of RAB4B and rs4105144 (50 %) [20]. of CYP2A6, were associated with increased circulating Cancer Metastasis Rev cotinine but decreased lung cancer risk, and may be protective alterations, including losses at 19p, were observed more fre- of lung cancer [31]. quently in metastatic tumors [40](Table1).

Chromosome 19 aberration in non-smokers of lung cancer cases have also been identified in 19p and 19q13, with 3.1 Chromosome 19-related protein variation validation some distinct from smokers. In an early study of Western lung cancer cases, gene losses at chromosomal 19p (58 %) The 64 aberration genes indentified on chromosome 19 geno- were presented significantly more often in ADC from mic positions above were further queried in neXtProt by The smokers [32]. Another study showed that 19q13.3 gene Proteomic Browser (TPB)[41]. TBP generate data integration imbalance was significantly more associated in ADC with and an analysis browser for the C-HPP database, collecting non-smokers, especially 19q13.1-q13.2 in non-smoker data of each protein from public proteomic databases. The eastern lung ADC [19]. Another study suggests that software is useful to define biological functions and study CD3EAP SNP rs967591 variant allele carriers are at in- human physiology in health and disease. Figure 3 shows that creased susceptibility of lung ADC among nonsmoking 95.31 % (61/64) of genes were also expressed as proteins and Chinese women [33]. Asbestos exposure is known to pre- 100 % of genes had corresponding transcript expression. The dispose to both lung ADC and pleural malignant mesothe- protein functions of these genes were further investigated in lioma. Asbestos exposure may result in damage of chromo- neXtProt database, as shown in supplement table. some 19, leading to chromosome 19 loss and asbestos- associated oncogenesis. An increased number of chromosome 19p losses in the tumors of asbestos-exposed patients 4 Chromosome 19 aberration-related lung in comparison with tumors from non-exposed subjects with oncogenesis mechanism (Fig. 4) similar distribution of tumor histology in both groups (39 versus 12 %) [34]. In BEAS2B immortalized human bron- Tumor suppressor genes losses Chromosome deletions as- chial epithelial cells, a 48-h exposure to crocidolite asbestos sociated with mutations in tumor suppressor genes are well- was found to induce chromosomal fragmentation. Further- known genetic abnormalities in tumors [42]. Chromosome more, an increased frequency of 19p fragmentation was 19p gene losses have been indentified in several studies. Some observed after the crocidolite treatment in comparison with of which were tumor suppressor genes and the inactivation of untreated controls. The damage was detected in 19p13.3- which may be the potential oncogenesis mechanism of lung p13.1. Furthermore, allelic imbalance of 19p13 was detect- cancer. Serine/threonine-protein kinase 11 (STK11, also ed in 79 % of the asbestos exposed and 45 % of the non- known as LKB1), a tumor suppressor gene located on exposed lung cancer patients [35, 36]. 19p13.3, is frequently deleted in lung cancer [43]. The deletion of LKB1 results in tumorigenesis and metastasis in a Gene aberrations implicated in drug resistance and prog- mouse model of NSCLC [44]. The LKB1 protein has serine- nosis in lung cancer The poor response of lung cancer to threonine kinase activity, phosphorylating the T-loop of AMP- standard of care treatments and high mortality are compelling activated protein kinase (AMPK) family proteins, thus pro- reasons elucidate the genetic alterations related drug resistance moting the inhibition activity of mTOR signaling [45]. and prognosis. A Chinese CGH study analyzed non-small cell STK11 phosphorylates non-AMPK family proteins, p53/ lung cancer (NSCLC) tissues from 88 patients with advanced TP53, to regulate p53/TP53-dependent apoptosis pathway. NSCLC (52 with chemo-sensitivity and 36 with chemo-resis- LKB1 inactivation frequently accompanies P53 inactivation tance). 19p gains were correlated with the sensitivity of the and KRAS mutations [46]. Also, the LKB1-dependent kinase NSCLC tumor and 19q gains were correlated with chemo- salt-inducible kinase 1 modulates induction of anoikis and resistance [37]. ERCC1 and ERCC2 genes are known to be tumor suppressor p53 activity to inhibit metastasis in lung associated with the resistance to platinum-based chemothera- cancer [47]. py [38]. Thus, it is not surprising that 19q13.2-3 damage resulting in ERCC1 and ERCC2 gene deletions detected in LKB1 alterations frequently occur simultaneously with the exhaled breath condensate-DNA, are predictors of poor sur- inactivation of another important tumor suppressor gene, vival in NSCLC patients [39]. Researches with cohort of pa- BRG1 (SMARCA4), located on chromosome 19p13.11. tients with lung SCC using array-based CGH identified that BRG1 encodes a core chromatin-remodeling factor in SWI/ gain of 19q12 increased localized lymph node metastases SNF complexes [48]. Approximately 10 % of primary human rather than remote metastases [22]. Another study of a cohort NSCLCs display deficiency in the BRG1 ATPase. BRG1 si- of 42 lung SCC patients compared non-metastatic (TxN0M0) lencing in NSCLC cells alters cell morphology and increases and metastatic (TxN1-2M0) tumors to define chromosomal tumorigenic potential [49]. Mutant melanoma-associated an- imbalances related to lymph node metastases. Genetic tigen 1, encoded by MUM1 (19p13.3), is involved in the Cancer Metastasis Rev

Table 1 Gene aberrations of chromosome 19 in lung cancer phenotypes

Author Phonotype Style Location Aberration Related genes

Broet, P. ADC Copy number 19p13.3 Loss PTBP1, PRG2(LPPR3), AZU1, PRTN3, ELA2(ELANE), CFD, MED16, C19orf22, KISS1R, ARID3A, WDR18, GRIN3B, C19orf6, CNN2, ABCA7, HMHA1, POLR2E, GPX4, SBNO2, STK11, C19orf26, ATP5D, MIDN, C19orf23, CIRBP, C19orf24, EFNA2, MUM1, NDUFS7 19p13.11 USE1, OCEL1, NR2F6, USHBP1, C19orf62, ANKLE1, ABHD8, MRPL34, DDA1, ANO8, GTPBP3, PLVAP, BST2, FAM125A(MVB12A) Yen, C.C. ADC Copy number 19p Loss N/A Shen, H. ADC Copy number 19q12 Gain N/A Choi, J.S. ADC Copy number 19q13.42 Gain N/A 19p13.2 Loss ICAM1 Wong, M.P. Non-smoker ADC Copy number 19q13.1-2 Gain N/A Choi, Y.W. SCC Copy number 19p Gain N/A Boelens, SCC Copy number 19q13.13 Gain N/A M. C. Kayser, K. SCC, LCC Copy number 19 Loss N/A Ryan, D.M. Smoker airway Copy number 19q13.2 Gain NFKBIB, PAK4, DYRK1B, MAP3K10, epithelium cells SERTAD1, LTBP4, NUMBL, EGLN2, TGFB1, B3GNT8, RABAC1, CIC, MEGF8 Li, Y. Smoker ADC, SNP 19q13.2 rs1800469, rs1982072 TGFB1 SCC rs2241714 Yin, J. ADC, SCC SNP 19q13.3 rs2298881 rs321 ERCC2, 2980, rs3212964 PPP1R13, rs3916874 rs238 ERCC1, 415 rs4803817 CD3EAP rs1046282, rs735482 Bloom, A.J. Smoker health SNP 19q13 rs3733829 EGLN2, CYP2A6 Timofeeva, M.N. ADC, SCC SNP 19q13 rs7937 rs4105144 RAB4B, CYP2A6 Sanchez-Cespedes, M. Non-smoker ADC Copy number 19p Loss N/A Wong, M.P. Non-smoker ADC Copy number 19q13.3 Gain/loss N/A Yin, J. Non-smoker ADC SNP 19q13.3 rs967591 CD3EAP Vogel, U. ADC, SCC, LCC, SNP 19q13.2-3 rs1052559ars1799793 XPD(ERCC2) SCLC Yin, J. N/A SNP 19q13.2-3 XRCC1, ERCC1, ERCC2 Vanhecke, E. ADC, SCC Copy number 19q13.3 Gain ERCC1 Hu, Y. ADC, SCC, LCC Copy number 19p13.1-3 Gain N/A 19q Gain Simon, G.R. ADC, SCC LCC Copy number 19q13 Gain ERCC1 Carpagnano, G.E. ADC, SCC LOH or MI 19q13.2-3 Loss ERCC1, ERCC2 Boelens, M.C. SCC Copy Number 19q12 Gain N/A Rydzanicz, M. SCC Copy number 19p Loss N/A

DNA damage response pathway by contributing to the main- result in DNA chromatin instability, contributing to lung tenance of chromatin architecture. It is recruited to the vicinity oncogenesis. of DNA breaks by TP53BP1 and plays an accessory role to The gene KISS1R (19p13.3) encoded the protein KiSS1 facilitate damage-induced chromatin changes and promoting Receptor for metastin (kisspeptin-54), is a metastasis suppres- chromatin relaxation [50]. The deficiency of both genes may sor that suppresses metastases in some cancers. KiSS1 Cancer Metastasis Rev

Fig. 3 The protein expression A Strong evidence (PE), post-translational Probable modification (PTE), and transcript expression (TE)level Dubious evidence validated of the genes indentified No evidence as part of lung oncogenesis. PE According to the proteomic PTM browser (TPB) on the neXtprot TE database a gene losses on 19p; b gene gains in 19q B

PE PTM TE

Receptor coupled to metastin, play a potential role in sup- cancer cell proliferation [55]. Notch3 is one of four known pressing cancer metastasis. In a study of 56 NSCLC cases, mammalian homologues of the Drosophila Notch receptor, the KISS1 or KISS1R low expression was significantly asso- essential for determining cell fate [56]. BRD4-NUT results ciated with poor overall survival. The product of the metastin, in highly over-expressed Notch3 gene, associated with karyo- was also lower in the serum of patients with stage IV NSCLC typic abnormalities of chromosome 19p in lung cancer cell compared to that in stage IIIB NSCLC [51]. The metastasis lines [57]. BRD4 also activates NF-kappa-B [58] and regu- suppressing properties may be mediated in part by cell cycle lates p53/TP53-mediated transcription, following phosphory- arrest and induction of apoptosis in lung cancer. lation by CK2 [59].

Translocation t(15;19) (q13, p13.1) fusion oncogens T(15, DNA repair gene functions Amplification of the DNA re- 19) (q13, p13.1) was identified as a acquired translocation pair genes ERCC1, ERCC2, and XRCC1 located on fusion transcript of the 3' end BRD4 on chromosome 19p is 19q13.31-32 were identified in lung cancer. The protein prod- fused to the 5' end of NUT on chromosome 15q, forming a ucts of these genes are essential for nucleotide excision repair 6.4-kb fusion oncogene, BRD4-NUT, though rare lung cancer of DNA lesions such as those induced by UV light or electro- [52, 53]. BRD4-NUT is the first fusion oncogene mechanism philic compounds, including cisplatin. The expression of presenting a poorly differentiated carcinoma with high aggres- ERCC1 and ERCC2 is a marker of intact DNA repair function sion [54]. Wild-type BRD4 was shown to inhibit G1 to S and genomic damage degree. High expression of ERCC may progression and fusion augments the inhibition of progression reduce the accumulation of genetic aberrations and predict to S phase compared with wild-type BRD4, leading to lung good survival. In a study of 51 surgically resected tumors from

MUM1 BRG1 KISS1R LKB1 AKT 2 BRD4-NUT PPP1R13L EGLN2 DYK1B ERCC1 LTBP4 ERCC2 NFKBIB XRCC1 SIK1 TGFB1

BRD4 Cycle arrest +p

DNA repair AMPK chroman stable STAT3 NFkB mTOR P53 EMT apoptosis

Cell survival Cell cycle progression Cell growth

Lung oncogenesis Fig. 4 Chromosome 19 aberration mechanism of lung cancer. The loss of tumor suppressor genes LKB1, BRG1, KISS1R, and MUM1 in 19p, together with the duplication of oncogenesis gene in 19q region leads to activation of mTOR, NFkB, and STAT3 pathways, resulting in lung cancer progression Cancer Metastasis Rev

NSCLC patients (ADC, SCC, and LCC), patients with high early-stage lung cancer in both the cytoplasm and nucleus. ERCC1 expression had better survival [60]. Unfortunately, Mirk knockdown by siRNA induced cell apoptosis, up- high expression of these DNA repair genes was also associat- regulation of Bak, a Bcl-2 family member, and activator of ed with cisplatin chemotherapy failure. For instance, NSCLC transcription 3 tyrosine phosphorylation. Mirk knockdown led cells with high ERCC1 copy number were 3-fold more resis- to decreased cell colony formation in vitro, delayed tumor tant to cisplatin and survival rate of patients with ERCC1 gene growth, and sensitization to cisplatin-induced apoptosis [70]. amplification was shorter after chemotherapy. [61]. Mirk also contributes to G0 arrest by destabilization of cyclin D1 and stabilization of p27kip1 to maintain the viability of AKT2 gene variation in lung cancer AKT2 (19q13.2) is quiescent lung cancer cells, and it could be negatively regu- one of three isoforms of AKT. AKT regulates metabolism, lated by mitogen-activated protein kinase/extracellular signal- proliferation, cell survival, growth, and angiogenesis, through regulated kinase signaling [71]. a PI3K-associated pathway. AKT2 amplification was observed in 6.5 % of total AKT-expressing tumors (3.5 % of EGLN2 EGLN2 (19q13.2), encodes protein also known as all tumors). Increased AKT2 gene copy numbers were more PHD1, is a cellular oxygen sensor that catalyzes the post- prevalent in SCLC [62]. AKT2 was also found to be recipro- translational formation of 4-hydroxyproline in hypoxia- cal to EGFR mutations in NSCLC patients. AKT inhibition, inducible factor (HIF) alpha proteins. PHD1 may affect cellu- most importantly AKT2 inhibition, shows synergy with lar response to hypoxic conditions. It is associated with EGFR TKI inhibition, to increase inhibition of EGFR- smoking-induced lung cancer susceptibility [72]. PHD1 in- mutated NSCLC cells [63]. The selective targeting of AKT2 hibits NF-kappaB activity and NFKB target genes in lung may provide a new treatment option in NSCLC. cancer cells. PHD1 induces cell cycle arrest in lung cancer cells, resulting in the suppression of cell proliferation. Xeno- TGFB pathway modulation TGFβ1 and its activator graft tumor growth assays indicate that PHD1 plays a critical LTBP4, located in 19q.13.2, were both up-regulated in lung role in suppressing lung cancer growth. These findings reveal cancer. LTBP4 May be involved in the assembly, secretion, a new protective role of PHD1 in lung cancer, and therefore is and targeting of TGFβ1 to sites at which it is stored, a potential target in lung cancer therapy [73]. performing critical roles in controlling and directing the activity of TGFβ1. TGFβ1 is a multifunctional protein that controls proliferation, differentiation, and other functions in many 5Conclusions cell types, especially in lung cancer epithelial mesenchymal transition (EMT). EMT is the process by which epithelial cells The research of the gene aberrations of lung cancer in the past depolarize and acquire a mesenchymal phenotype, and is a decades indicates that chromosome 19 aberration is quite common early step in the process of metastasis [64]. EMT common in lung cancer and definitely accounts for a part of induction is accompanied by the up-regulation of human lung cancer patients. Several genomic studies revealed that glioma-associated oncogene homolog 1 mRNA and protein chromosome 19 variation is a potential oncogenesis mecha- levels [65]. The extracellular signal-regulated kinase pathway nisms for a subset of lung malignancies, especially NSCLC. can mediate TGFβ1-induced EMT in NSCLC and may be a Genes identified in previous studies were validated at the pro- potential target for the treatment of NSCLC [66]. tein level by queries of the chromosome centric neXtProt database and further explored for potential oncogenesis mecha- NFkB pathway modulation Two NFkB pathway inhibition nisms. Tumor suppressor gene losses in 19p and gene ampli- genes, NFKBIB, and PPP1R13L, located in 19q13.2 and fications in 19q are most the frequent abnormalities. In con- 19q13.32, respectively, were amplified in lung cancer. clusion, the genomic and proteomic databases provided effec- NFKBIB, encodes the protein NFkB inhibitor β inhibits NF- tive methods to validate gene aberrations. The understanding kappa-B by trapping it in the cytoplasm [67]. PPP1R13L of chromosome 19 aberrations-related molecular mechanisms plays a central role in the regulation of apoptosis and transcrip- on lung oncogenesis, invasion, and migration, will help to tion, via inhibition of NF-kappa-B. PPP1R13L also inhibits explore new treatment strategies in future, even though the the action of SP1 and p53/TP53 function, perhaps by extensive investigation is further required. preventing association between p53/TP53 and ASPP1 or ASPP2, therefore suppressing the subsequent activation of Acknowledgements The work was supported by Zhongshan Distin- apoptosis [68, 69]. The overall chromosome 19 aberration in guished Professor Grant (XDW), The National Nature Science Founda- lung cancer oncogenesis is shown in Figs. 3 and 4. tion of China (91230204, 81270099, 81320108001, 81270131, 81300010), The Shanghai Committee of Science and Technology (12JC1402200, 12431900207, 11410708600, 14431905100), Operation Dyrk1B Over expression of Mirk, encoded by Dyrk1B funding of Shanghai Institute of Clinical Bioinformatics, and Ministry of (19q13.2), was found in nearly 90 % of tumor specimens of Education, Academic Special Science and Research Foundation for PhD Cancer Metastasis Rev

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