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Variations of chromosome 2 gene expressions among patients with lung cancer or non-cancer

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Abstract

Lung cancer is one of the most common malignancies worldwide. The present study aimed to investigate specific genotypes of different subtypes or stages of lung cancer through gene expression variations of chromosome 2 genes, trying to identify predictors for diagnosis or prognosis of lung cancer. About 537 patients with lung adenocarcinoma (ADC), 140 patients with lung squamous carcinoma (SQC), 9 patients with lung large cell carcinoma (LCC), 56 patients with small cell lung cancer (SCLC), and 590 patients without cancer were analyzed in present study. Co-expressed, subtype-specific, and stage-specific chromosome 2 genes were identified and further analyzed by bioinformatic methods. As a result, 15 or 10 genes were significantly up- or down-regulated in all four subtypes of lung cancer. GKN1, LOC100131510, prominin-2 (PROM2), IL37, and SNORA41 were identified as ADC-specific up-regulated genes; SQC-specific up-regulated genes included HOXD family (HOXD1, HOXD3, HOXD4, HOXD8, and HOXD9) and UGT1A family (UGT1A1, UGT1A3, UGT1A4, UGT1A5, UGT1A7, UGT1A8, UGT1A9, and UGT1A10); and LCC- or SCLC-specific genes were also identified. Nine genes were significantly up-expressed at all four stages of ADC while 230 genes at all three stages of SQC. MFSD2B, CCL20 and STAT1, or STARD7 and ZNF512 genes may be risk or protect factors in prognosis of ADC, while HTR2B, DPP4, and TGFBRAP1 genes may be risk factors in prognosis of SQC. Our results suggested that a number of altered chromosome 2 genes have the subtype or stage specificities of lung cancer and may be considered as diagnostic and prognostic biomarkers.

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Acknowledgments

This 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), the Zhejiang Provincial Natural Science Foundation (Z2080988), the Zhejiang Provincial Science Technology Department Foundation (2010C14011), and the Ministry of Education, Academic Special Science and Research Foundation for PhD Education (20130071110043).

Authors’ contributions

LMB contributed the data analyses and writing of the manuscript. YZ contributed the study design, collection of information, and data mining. HYW contributed the prognosis prediction analyses. XDW contributed the study design and preparation of the manuscript.

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Authors and Affiliations

  1. Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University Medical School, Shanghai, China

    Lianmin Bao, Yong Zhang, Jian Wang, Nian Dong, Xiaoqiong Su, Menglin Xu & Xiangdong Wang

  2. Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, China

    Haiyun Wang

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  1. Lianmin Bao
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Correspondence to Xiangdong Wang.

Electronic supplementary material

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Supplement Fig. 1

The pathways of targeted co-expressed genes in lung cancer. (GIF 45 kb)

High resolution image (TIF 348 kb)

Supplement Fig. 2

(GIF 148 kb)

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Supplement Fig. 3

(GIF 96 kb)

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Supplement Fig. 4

(GIF 92 kb)

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Supplement Table 1

Genes up-regulated in four subtypes of lung cancer compared with non-cancer. (XLSX 87 kb)

Supplement Table 2

Co-expressed genes in four subtypes of lung cancer. (XLSX 13 kb)

Supplement Table 3

Subtype-specific up or down genes in ADC, SQC, LCC, and SCLC. (XLSX 46 kb)

Supplement Table 4

Stage-specific up or down genes in ADC and SQC. (XLSX 22 kb)

Supplement Table 5

Identified genes of ADC or SQC predicted poor overall survival through TCGA survival model. (XLSX 11 kb)

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Bao, L., Zhang, Y., Wang, J. et al. Variations of chromosome 2 gene expressions among patients with lung cancer or non-cancer. Cell Biol Toxicol 32, 419–435 (2016). https://doi.org/10.1007/s10565-016-9343-z

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