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May 16, 2015 - Abstract The Chromosome 19 Consortium, a part of the. Chromosome-Centric Human Proteome Project (C-HPP, http:// · www.C-HPP.org), is ...
Cancer Metastasis Rev (2015) 34:217–226 DOI 10.1007/s10555-015-9556-2

Association of chromosome 19 to lung cancer genotypes and phenotypes Xiangdong Wang 1 & Yong Zhang 1 & Carol L. Nilsson 2,15 & Frode S. Berven 3 & Per E. Andrén 4 & Elisabet Carlsohn 5 & Peter Horvatovich 6 & Johan Malm 7 & Manuel Fuentes 8 & Ákos Végvári 9 & Charlotte Welinder 10 & Thomas E. Fehniger 9,16 & Melinda Rezeli 11 & Goutham Edula 12 & Sophia Hober 13 & Toshihide Nishimura 14 & György Marko-Varga 9,14

Published online: 16 May 2015 # Springer Science+Business Media New York 2015

Abstract The Chromosome 19 Consortium, a part of the Chromosome-Centric Human Proteome Project (C-HPP, http:// www.C-HPP.org), is tasked with the understanding chromosome 19 functions at the gene and protein levels, as well as their roles in lung oncogenesis. Comparative genomic hybridization (CGH) studies revealed chromosome aberration in lung cancer subtypes, including ADC, SCC, LCC, and SCLC. The most common abnormality is 19p loss and 19q gain. Sixty-four aberrant genes identified in previous genomic 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, MUM1, KISS1R (19p13.3), and BRG1 (19p13.13) is associated with lung oncogenesis or remote metastasis. Gene aberrations include translocation t(15, 19) (q13, p13.1) fusion oncogene BRD4NUT, DNA repair genes (ERCC1, ERCC2, XRCC1), TGFβ1 pathway activation genes (TGFB1, LTBP4), Dyrk1B, and potential oncogenesis protector genes such as NFkB pathway inhibition genes (NFKBIB, PPP1R13L) and EGLN2. In conclusion, neXtProt is an effective resource for the validation of gene aberrations identified in genomic studies. It promises to enhance our understanding of lung cancer oncogenesis.

Xiangdong Wang and Yong Zhang contributed equally to this work. * Xiangdong Wang [email protected]

8

Centro de Investigación del Cáncer/IBMCC (USAL/CSIC)-IBSAL, Unidad de Proteomica, Departamento de Medicina and Servicio General de Citometría-Nucleus, University of Salamanca, 37007 Salamanca, Spain

9

Department of Biomedical Engineering, Clinical Protein Science and Imaging, Biomedical Center, Lund University, BMC D13, 221 00 Lund, Sweden

10

Department of Oncology and Pathology, Clinical Sciences, Lund University, 221 85 Lund, Sweden

11

Department of Biomedical Engineering, Clinical Protein Science & Imaging, Lund University, BMC D13, 221 84 Lund, Sweden

12

Clinnovo Research Labs, Hyderabad, India

13

Department of Proteomics, School of Biotechnology, Royal Institute of Technology, 106 91 Stockholm, Sweden

Proteomics Core Facility, Göteborg University, 413 90 Göteborg, Sweden

14

First Department of Surgery, Tokyo Medical University, 6-7-1 Nishishinjiku Shinjiku-ku, Tokyo 160-0023, Japan

Department of Pharmacy, Analytical Biochemistry, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands

15

Department of Clinical Sciences, CEBMMS, Lund University, 22100 Lund, Sweden

16

Center of Excellence in Biological and Medical Mass Spectrometry, CEBMMS, Lund University, BMC D13, 221 00 Lund, Sweden

* György Marko-Varga [email protected] 1

Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University, Shanghai, China

2

Department of Pharmacology and Toxicology, UTMB Cancer Center, University of Texas Medical Branch, Galveston, TX 77555, USA

3

4

5

6

7

Department of Biomedicine, University of Bergen, 5009 Bergen, Norway Department of Pharmaceutical Biosciences, Biomolecular Imaging and Proteomics, Uppsala University, 751 24 Uppsala, Sweden

Department of Translational Medicine, Section for Clinical Chemistry, Lund University, Skåne University Hospital Malmö, SE-205 02 Malmö, Sweden

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Keywords Proteins . Genes . Antibodies . mRNA . Mass spectrometry . Bioinformatics . Protein microarray . Human disease

Cancer Metastasis Rev (2015) 34:217–226 Lung cancer risk

Lung cancer subtype

Lung cancer prognosis

CGH study Gene aberraon in chromosome 19

1 Introduction Lung cancer is the leading diagnosed cancer as well as the leading cause of cancer death globally. It accounts for 13 % (1.82 million) of the total new cancer cases and 18 % (1.59 million) of the deaths in cancer in 2012 around the world [1]. Lung cancer is also the leading cause of death accounting for 29 % and 26 % of total cancer deaths in men and women, respectively. The five year survival for all stage lung cancer patients is only about 15 %, and for stage IV patients, just 3–4 % [2, 3]. Chromosome aberrations related to lung oncogenesis mechanisms have been revealed recently. About 50 % of the lung adenocarcinoma (ADC) tumors bear Bdriver mutations^. EGFR mutations are the most common drive mutations in lung ADC, usually due to losses in exon 19, or point mutations of exon 21 in chromosome 7 [4]. About 4 % of lung ADCs are caused by EML4ALK fusion genes, usually intron 13 of EML4 in chromosome 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 ADC patients. With comparative genomic hybridization (CGH) methods and high throughout genome-wide association studies (GWAS), more chromosomal variants associated with lung oncogenesis have been identified. The importance of chromosome 19 gene aberrations was clearly demonstrated by the previous studies. The Chromosome-Centric Human Proteome Project (CHPP) is a global consortium dedicated to mapping the entire human complement of proteins, with global membership (http://www.c-hpp.org) [6–10]. The Chromosome 19 Consortium has investigated gene expression using complementary analysis platforms, to provide a genomewide human protein resource database, and detailed maps of protein molecular pathways, interactions, and networks. The Chromosome 19 project has already contributed to the annotations of severe diseases, especially glioblastoma [11–13]. The present article focuses on chromosome 19 gene aberrations in different lung cancer subtypes, including non-small cell lung cancer (NSCLC): ADC, squamous cell carcinoma (SCC), large cell carcinoma (LCC), and small cell lung cancer (SCLC), and their potential role in lung oncogenesis. We have explored gene polymorphisms on chromosome 19 that are translated into protein variants, and offer potential mechanisms involved, as well as potential targeted therapeutics for the future (Fig. 1).

Protein level validaon in C-HPP based database Gene and protein funcon annotaon Potenal lung oncogenesis mechanism

Fig. 1 Workflow identifying molecular mechanism of lung oncogenesis. To decipher the oncogenesis mechanism chromosome 19 gene aberrations identified in GCH studies with lung cancer subtype, risk, and prognosis were enrolled. The indentified aberration genes were integrated and further inquired in chromosome centric neXProt to explore potential lung oncogenesis mechanism

2 Bioinformatic annotation of chromosome 19 Chromosome 19 spans about 64 million base pairs, representing more than 2 % of the human genome. Chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average. Furthermore, it has large clusters of gene families that correspond to high G + C content and CpG islands which indicate its rich biological and evolutionary significance. Chromosome 19 is also unique in its density of repeat sequences (55 % vs the genome average of 44.8 %) [14]. The C-HPP project targets the identification of all genecoding proteins with a special emphasis on the missing proteins, which account for almost 30 % of the proteins in the human proteome. The ENCODE initiative has been linked to the C-HPP initiative and provides newly identified gene activity that may predict novel proteoforms [13]. The data resources of the HPP are comprised of Ensemble, which is linked to the neXtProt, PeptideAtlas, and gpmDB databases. Recently, the numbers of highly confident protein identifications in these data resources that were announced recently by Marko-Varga et al [15]. The number of missing proteins during one year was decreased from 32.7 % in 2012 to 26.2 % in 2013 (September, lecture by G. Omenn, at HUPO World Congress, Yokohama, Japan). In the September 19, 2014, release of neXtProt, the number of protein-coding genes is about 20000. Roughly 18 % of the complete set of human protein coding genes is missing at the protein level currently. As for chromosome 19, according to of neXtProt database released on January 2015, there are estimated 1,432 protein-coding genes, including 244 genes with transcript-based evidence (PE2) available. Of these 1,432 genes, 2,707 alternative splicing variants are listed, as well as 199N-acetylated and 407 phorphoproteins.

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19P DNA loss DNA gain ADC

19p13.11

Asbstos induced ADC

19p13.3

Smoker ADC

19p13.1

SCC

SCC

19q12 Non-smoker ADC

ADC

Smoker SCC

19q13.1 19q13.2-3

Smoker health

19q13.13

LCC SCLC Smoker AEC

19q13.42

19q Fig. 2 Different gene aberration of lung cancer phenotypes: ADC (adenocarcinoma), SCC (squamous cell carcinoma), LCC (large cell carcinoma), and SCLC (small cell lung cancer); smoker or non-smoker. The main chromosome gene aberrations are 19p.13 loss and 19q12-13 gain

3 Chromosome 19 gene abnormalities in lung cancer Types of gene aberrations related to lung cancer phenotypes (Fig. 2) CGH studies implicate chromosome 19p loss and 19q amplification/high level polysomy in lung ADC. A study of 31 Eastern lung ADC cases showed the frequent deletions on 19p (41.9 %) [16]. The loss of ICAM1 (19p13.2) was most frequent in Eastern lung ADC [17]. Another study of 226 lung ADC samples from Eastern Asian (n= 90) and Western (n= 136) patients, DNA aberrations, and copy number variations were detected by use of a highresolution microarray platform. A multivariate model identified a higher rate of genomic loss on 19p13.3 (29 related genes) and 19p13.11 (14 related genes) ethnicity-specific in lung cancer patients from Western [18]. Other studies demonstrated frequent DNA amplifications at 19q13 in Eastern lung ADC [19] and frequently over-expressed regions on 19q12 (50 %) [20].

In SCC, the aberrations of chromosome 19 losses or gains were both indentified. One CGH study in Eastern lung SCC demonstrated DNA amplifications on 19p [21]. Gains of 19q13.13 were increased in Western lung SCC patients [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 sequencing (n = 51) and copy number analysis (n = 47) of resected SCLC tumors was compared with matched noncancer samples from Eastern SCLC patients. Genetic amplifications 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 nucleotide polymorphism (SNP) RT-PCR revealed a variant allele of DNA repair gene ERCC2 rs1052559a and rs1799793 in 19q13.2–3 were significantly overrepresented in female lung cancer [25]. Similarly, a Chinese population study of 247 lung cancer cases and 253 noncancer controls, matched by age, gender, and ethnicity, also found nine SNP in three DNA repair genes (XRCC1, ERCC1, ERCC2) in the region of chromosome 19q13.2–3 were over-represented in the cancer group [26]. Gene aberrations of lung cancer risk factor Smoking is the main risk factor associated with lung cancer around the world. Chromosome 19q13 amplification induced by smoking has been demonstrated to occur. A recent genome-wide association study (GWAS) study in western people compared the transcriptome of airway basal cells (BC) purified from the airway epithelium of healthy nonsmokers and healthy smokers. 166 (25 %) of the differentially expressed genes are located on chromosome 19, with 13 genes up-regulated on 19q13.2, including 4 genes (NFKBIB, LTBP4, EGLN2, and TGFB1) associated with risk for chronic obstructive pulmonary disease (COPD). Another QWAS study also revealed EGLN2 SNP rs3733829 variant and CYP2A6 is strongly associated with cigarette history [27]. These gene aberrations may be associated with smoking-related lung cancer risk [28]. SNPs (rs1800469, rs1982072, and rs2241714) in the promoter region of the TGFB1 were reported to be associated with COPD and lung cancer in cigarette smokers [29]. A HapMap (http://www.hapmap.org/)-based study in Eastern ADC and SCC patients demonstrated 19q13.3 SNP variations, including ERCC2, PPP1R13, ERCC1, and CD3EAP, were related with smoking duration and lung cancer risk [30]. A large study of SNPs previously associated with smoking behavior in 894 lung cancer cases and 1,805 controls revealed rs7937 of RAB4B and rs4105144 of CYP2A6, were associated with increased circulating

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cotinine but decreased lung cancer risk, and may be protective of lung cancer [31]. Chromosome 19 aberration in non-smokers of lung cancer cases have also been identified in 19p and 19q13, with some distinct from smokers. In an early study of Western lung cancer cases, gene losses at chromosomal 19p (58 %) were presented significantly more often in ADC from smokers [32]. Another study showed that 19q13.3 gene imbalance was significantly more associated in ADC with non-smokers, especially 19q13.1-q13.2 in non-smoker eastern lung ADC [19]. Another study suggests that CD3EAP SNP rs967591 variant allele carriers are at increased susceptibility of lung ADC among nonsmoking Chinese women [33]. Asbestos exposure is known to predispose to both lung ADC and pleural malignant mesothelioma. Asbestos exposure may result in damage of chromosome 19, leading to chromosome 19 loss and asbestosassociated oncogenesis. An increased number of chromosome 19p losses in the tumors of asbestos-exposed patients in comparison with tumors from non-exposed subjects with similar distribution of tumor histology in both groups (39 versus 12 %) [34]. In BEAS2B immortalized human bronchial epithelial cells, a 48-h exposure to crocidolite asbestos was found to induce chromosomal fragmentation. Furthermore, an increased frequency of 19p fragmentation was observed after the crocidolite treatment in comparison with untreated controls. The damage was detected in 19p13.3p13.1. Furthermore, allelic imbalance of 19p13 was detected in 79 % of the asbestos exposed and 45 % of the nonexposed lung cancer patients [35, 36]. Gene aberrations implicated in drug resistance and prognosis in lung cancer The poor response of lung cancer to standard of care treatments and high mortality are compelling reasons elucidate the genetic alterations related drug resistance and prognosis. A Chinese CGH study analyzed non-small cell lung cancer (NSCLC) tissues from 88 patients with advanced NSCLC (52 with chemo-sensitivity and 36 with chemo-resistance). 19p gains were correlated with the sensitivity of the NSCLC tumor and 19q gains were correlated with chemoresistance [37]. ERCC1 and ERCC2 genes are known to be associated with the resistance to platinum-based chemotherapy [38]. Thus, it is not surprising that 19q13.2-3 damage resulting in ERCC1 and ERCC2 gene deletions detected in exhaled breath condensate-DNA, are predictors of poor survival in NSCLC patients [39]. Researches with cohort of patients with lung SCC using array-based CGH identified that gain of 19q12 increased localized lymph node metastases rather than remote metastases [22]. Another study of a cohort of 42 lung SCC patients compared non-metastatic (TxN0M0) and metastatic (TxN1-2M0) tumors to define chromosomal imbalances related to lymph node metastases. Genetic

Cancer Metastasis Rev (2015) 34:217–226

alterations, including losses at 19p, were observed more frequently in metastatic tumors [40] (Table 1).

3.1 Chromosome 19-related protein variation validation The 64 aberration genes indentified on chromosome 19 genomic positions above were further queried in neXtProt by The Proteomic Browser (TPB)[41]. TBP generate data integration and an analysis browser for the C-HPP database, collecting data of each protein from public proteomic databases. The software is useful to define biological functions and study human physiology in health and disease. Figure 3 shows that 95.31 % (61/64) of genes were also expressed as proteins and 100 % of genes had corresponding transcript expression. The protein functions of these genes were further investigated in neXtProt database, as shown in supplement table.

4 Chromosome 19 aberration-related lung oncogenesis mechanism (Fig. 4) Tumor suppressor genes losses Chromosome deletions associated with mutations in tumor suppressor genes are wellknown genetic abnormalities in tumors [42]. Chromosome 19p gene losses have been indentified in several studies. Some of which were tumor suppressor genes and the inactivation of which may be the potential oncogenesis mechanism of lung cancer. Serine/threonine-protein kinase 11 (STK11, also known as LKB1), a tumor suppressor gene located on 19p13.3, is frequently deleted in lung cancer [43]. The deletion of LKB1 results in tumorigenesis and metastasis in a mouse model of NSCLC [44]. The LKB1 protein has serinethreonine kinase activity, phosphorylating the T-loop of AMPactivated protein kinase (AMPK) family proteins, thus promoting the inhibition activity of mTOR signaling [45]. STK11 phosphorylates non-AMPK family proteins, p53/ TP53, to regulate p53/TP53-dependent apoptosis pathway. LKB1 inactivation frequently accompanies P53 inactivation and KRAS mutations [46]. Also, the LKB1-dependent kinase salt-inducible kinase 1 modulates induction of anoikis and tumor suppressor p53 activity to inhibit metastasis in lung cancer [47]. LKB1 alterations frequently occur simultaneously with the inactivation of another important tumor suppressor gene, BRG1 (SMARCA4), located on chromosome 19p13.11. BRG1 encodes a core chromatin-remodeling factor in SWI/ SNF complexes [48]. Approximately 10 % of primary human NSCLCs display deficiency in the BRG1 ATPase. BRG1 silencing in NSCLC cells alters cell morphology and increases tumorigenic potential [49]. Mutant melanoma-associated antigen 1, encoded by MUM1 (19p13.3), is involved in the

Cancer Metastasis Rev (2015) 34:217–226 Table 1

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Gene aberrations of chromosome 19 in lung cancer phenotypes

Author

Phonotype

Style

Location

Aberration

Related genes

Broet, P.

ADC

Copy number

19p13.3

Loss

Loss Gain Gain Loss Gain Gain Gain

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 USE1, OCEL1, NR2F6, USHBP1, C19orf62, ANKLE1, ABHD8, MRPL34, DDA1, ANO8, GTPBP3, PLVAP, BST2, FAM125A(MVB12A) N/A N/A N/A ICAM1 N/A N/A N/A

19p13.11

Yen, C.C. Shen, H. Choi, J.S.

ADC ADC ADC

Copy number Copy number Copy number

Wong, M.P. Choi, Y.W. Boelens, M. C. Kayser, K.

Non-smoker ADC SCC SCC

Copy number Copy number Copy number

19p 19q12 19q13.42 19p13.2 19q13.1-2 19p 19q13.13

SCC, LCC

Copy number

19

Loss

N/A

Ryan, D.M.

Smoker airway epithelium cells

Copy number

19q13.2

Gain

Li, Y.

Smoker ADC, SCC ADC, SCC

SNP

19q13.2

SNP

19q13.3

SNP SNP Copy number Copy number SNP SNP

19q13 19q13 19p 19q13.3 19q13.3 19q13.2-3

Yin, J. Vanhecke, E. Hu, Y.

Smoker health ADC, SCC Non-smoker ADC Non-smoker ADC Non-smoker ADC ADC, SCC, LCC, SCLC N/A ADC, SCC ADC, SCC, LCC

rs1800469, rs1982072 rs2241714 rs2298881 rs321 2980, rs3212964 rs3916874 rs238 415 rs4803817 rs1046282, rs735482 rs3733829 rs7937 rs4105144 Loss Gain/loss rs967591 rs1052559ars1799793

NFKBIB, PAK4, DYRK1B, MAP3K10, SERTAD1, LTBP4, NUMBL, EGLN2, TGFB1, B3GNT8, RABAC1, CIC, MEGF8 TGFB1

SNP Copy number Copy number

19q13.2-3 19q13.3 19p13.1-3 19q

Gain Gain Gain

Simon, G.R. Carpagnano, G.E. Boelens, M.C. Rydzanicz, M.

ADC, SCC LCC ADC, SCC SCC SCC

Copy number LOH or MI Copy Number Copy number

19q13 19q13.2-3 19q12 19p

Gain Loss Gain Loss

Yin, J.

Bloom, A.J. Timofeeva, M.N. Sanchez-Cespedes, M. Wong, M.P. Yin, J. Vogel, U.

DNA damage response pathway by contributing to the maintenance of chromatin architecture. It is recruited to the vicinity of DNA breaks by TP53BP1 and plays an accessory role to facilitate damage-induced chromatin changes and promoting chromatin relaxation [50]. The deficiency of both genes may

ERCC2, PPP1R13, ERCC1, CD3EAP EGLN2, CYP2A6 RAB4B, CYP2A6 N/A N/A CD3EAP XPD(ERCC2) XRCC1, ERCC1, ERCC2 ERCC1 N/A ERCC1 ERCC1, ERCC2 N/A N/A

result in DNA chromatin instability, contributing to lung oncogenesis. The gene KISS1R (19p13.3) encoded the protein KiSS1 Receptor for metastin (kisspeptin-54), is a metastasis suppressor that suppresses metastases in some cancers. KiSS1

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Fig. 3 The protein expression (PE), post-translational modification (PTE), and transcript expression (TE) level validated of the genes indentified as part of lung oncogenesis. According to the proteomic browser (TPB) on the neXtprot database a gene losses on 19p; b gene gains in 19q

A

Strong evidence Probable Dubious evidence No evidence

PE PTM TE

B

PE PTM TE

Receptor coupled to metastin, play a potential role in suppressing cancer metastasis. In a study of 56 NSCLC cases, the KISS1 or KISS1R low expression was significantly associated with poor overall survival. The product of the metastin, was also lower in the serum of patients with stage IV NSCLC compared to that in stage IIIB NSCLC [51]. The metastasis suppressing properties may be mediated in part by cell cycle arrest and induction of apoptosis in lung cancer.

cancer cell proliferation [55]. Notch3 is one of four known mammalian homologues of the Drosophila Notch receptor, essential for determining cell fate [56]. BRD4-NUT results in highly over-expressed Notch3 gene, associated with karyotypic abnormalities of chromosome 19p in lung cancer cell lines [57]. BRD4 also activates NF-kappa-B [58] and regulates p53/TP53-mediated transcription, following phosphorylation by CK2 [59].

Translocation t(15;19) (q13, p13.1) fusion oncogens T(15, 19) (q13, p13.1) was identified as a acquired translocation fusion transcript of the 3' end BRD4 on chromosome 19p is fused to the 5' end of NUT on chromosome 15q, forming a 6.4-kb fusion oncogene, BRD4-NUT, though rare lung cancer [52, 53]. BRD4-NUT is the first fusion oncogene mechanism presenting a poorly differentiated carcinoma with high aggression [54]. Wild-type BRD4 was shown to inhibit G1 to S progression and fusion augments the inhibition of progression to S phase compared with wild-type BRD4, leading to lung

DNA repair gene functions Amplification of the DNA repair genes ERCC1, ERCC2, and XRCC1 located on 19q13.31-32 were identified in lung cancer. The protein products of these genes are essential for nucleotide excision repair of DNA lesions such as those induced by UV light or electrophilic compounds, including cisplatin. The expression of ERCC1 and ERCC2 is a marker of intact DNA repair function and genomic damage degree. High expression of ERCC may reduce the accumulation of genetic aberrations and predict good survival. In a study of 51 surgically resected tumors from

MUM1

BRG1

KISS1R

LKB1

AKT 2

BRD4-NUT

PPP1R13L

EGLN2

DYK1B

NFKBIB

LTBP4

ERCC1 ERCC2 XRCC1

TGFB1

SIK1 Cycle arrest

BRD4

+p

DNA repair

AMPK chroman stable mTOR

P53

STAT3

NFkB

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 (2015) 34:217–226

NSCLC patients (ADC, SCC, and LCC), patients with high ERCC1 expression had better survival [60]. Unfortunately, high expression of these DNA repair genes was also associated with cisplatin chemotherapy failure. For instance, NSCLC cells with high ERCC1 copy number were 3-fold more resistant to cisplatin and survival rate of patients with ERCC1 gene amplification was shorter after chemotherapy. [61]. AKT2 gene variation in lung cancer AKT2 (19q13.2) is one of three isoforms of AKT. AKT regulates metabolism, proliferation, cell survival, growth, and angiogenesis, through a PI3K-associated pathway. AKT2 amplification was observed in 6.5 % of total AKT-expressing tumors (3.5 % of all tumors). Increased AKT2 gene copy numbers were more prevalent in SCLC [62]. AKT2 was also found to be reciprocal to EGFR mutations in NSCLC patients. AKT inhibition, most importantly AKT2 inhibition, shows synergy with EGFR TKI inhibition, to increase inhibition of EGFRmutated NSCLC cells [63]. The selective targeting of AKT2 may provide a new treatment option in NSCLC. TGFB pathway modulation TGFβ1 and its activator LTBP4, located in 19q.13.2, were both up-regulated in lung cancer. LTBP4 May be involved in the assembly, secretion, and targeting of TGFβ1 to sites at which it is stored, 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 cell types, especially in lung cancer epithelial mesenchymal transition (EMT). EMT is the process by which epithelial cells depolarize and acquire a mesenchymal phenotype, and is a common early step in the process of metastasis [64]. EMT induction is accompanied by the up-regulation of human glioma-associated oncogene homolog 1 mRNA and protein levels [65]. The extracellular signal-regulated kinase pathway can mediate TGFβ1-induced EMT in NSCLC and may be a potential target for the treatment of NSCLC [66]. NFkB pathway modulation Two NFkB pathway inhibition genes, NFKBIB, and PPP1R13L, located in 19q13.2 and 19q13.32, respectively, were amplified in lung cancer. NFKBIB, encodes the protein NFkB inhibitor β inhibits NFkappa-B by trapping it in the cytoplasm [67]. PPP1R13L plays a central role in the regulation of apoptosis and transcription, via inhibition of NF-kappa-B. PPP1R13L also inhibits the action of SP1 and p53/TP53 function, perhaps by preventing association between p53/TP53 and ASPP1 or ASPP2, therefore suppressing the subsequent activation of apoptosis [68, 69]. The overall chromosome 19 aberration in lung cancer oncogenesis is shown in Figs. 3 and 4. Dyrk1B Over expression of Mirk, encoded by Dyrk1B (19q13.2), was found in nearly 90 % of tumor specimens of

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early-stage lung cancer in both the cytoplasm and nucleus. Mirk knockdown by siRNA induced cell apoptosis, upregulation of Bak, a Bcl-2 family member, and activator of transcription 3 tyrosine phosphorylation. Mirk knockdown led to decreased cell colony formation in vitro, delayed tumor growth, and sensitization to cisplatin-induced apoptosis [70]. Mirk also contributes to G0 arrest by destabilization of cyclin D1 and stabilization of p27kip1 to maintain the viability of quiescent lung cancer cells, and it could be negatively regulated by mitogen-activated protein kinase/extracellular signalregulated kinase signaling [71]. EGLN2 EGLN2 (19q13.2), encodes protein also known as PHD1, is a cellular oxygen sensor that catalyzes the posttranslational formation of 4-hydroxyproline in hypoxiainducible factor (HIF) alpha proteins. PHD1 may affect cellular response to hypoxic conditions. It is associated with smoking-induced lung cancer susceptibility [72]. PHD1 inhibits NF-kappaB activity and NFKB target genes in lung cancer cells. PHD1 induces cell cycle arrest in lung cancer cells, resulting in the suppression of cell proliferation. Xenograft tumor growth assays indicate that PHD1 plays a critical role in suppressing lung cancer growth. These findings reveal a new protective role of PHD1 in lung cancer, and therefore is a potential target in lung cancer therapy [73].

5 Conclusions The research of the gene aberrations of lung cancer in the past decades indicates that chromosome 19 aberration is quite common in lung cancer and definitely accounts for a part of lung cancer patients. Several genomic studies revealed that chromosome 19 variation is a potential oncogenesis mechanisms for a subset of lung malignancies, especially NSCLC. Genes identified in previous studies were validated at the protein level by queries of the chromosome centric neXtProt database and further explored for potential oncogenesis mechanisms. Tumor suppressor gene losses in 19p and gene amplifications in 19q are most the frequent abnormalities. In conclusion, the genomic and proteomic databases provided effective methods to validate gene aberrations. The understanding of chromosome 19 aberrations-related molecular mechanisms on lung oncogenesis, invasion, and migration, will help to explore new treatment strategies in future, even though the extensive investigation is further required. Acknowledgements The work was supported by Zhongshan Distinguished Professor Grant (XDW), The National Nature Science Foundation of China (91230204, 81270099, 81320108001, 81270131, 81300010), The Shanghai Committee of Science and Technology (12JC1402200, 12431900207, 11410708600, 14431905100), Operation funding of Shanghai Institute of Clinical Bioinformatics, and Ministry of Education, Academic Special Science and Research Foundation for PhD

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Education (20130071110043). MF is supported by grant FIS14/01538 (ISCIII- Fondos FEDER EU) and Proteomics Units at CIC belongs to ProteoRed-PRB2 (PT13-001, ISCIII, Fondos FEDER-EU)

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