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Identification of SATB1 As a Specific Biomarker for Lymph Node

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ANTICANCER RESEARCH 36 : 4069-4076 (2016) Identification of SATB1 as a Specific Biomarker for Lymph Node Metastasis in Colorectal Cancer HIRONOBU BABA 1, TOSHIAKI ISHIKAWA 1, KAORU MOGUSHI 2, MEGUMI ISHIGURO 3, HIROYUKI UETAKE 3, HIROSHI TANAKA 2 and KENICHI SUGIHARA 1 1Department of Surgical Oncology, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan; 2Department of Systems Biology, Graduate School of Biochemical Science, Tokyo Medical and Dental University, Tokyo, Japan; 3Translational Oncology, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan Abstract. Background/Aim: The integration of gene role in LNM of CRC. SATB1 may be a biomarker of LNM expression analysis and genomic profiling represents an and of recurrence after surgery for CRC. efficient approach to the discovery of cancer-related genes. Lymph node metastasis (LNM) is a significant prognostic Colorectal cancer (CRC) is the third most common cancer factor in colorectal cancer (CRC). Detection and analysis of and the second most common cause of cancer-related factors related to LNM will help develop new diagnostic mortality in the world (1). In Japan, the incidence of CRC methods or therapies. In this study, we aimed to identify has doubled over the past 20 years and it is the second most genes that are significantly related to LNM in CRC through common cause of death among neoplastic diseases (2). The integrated copy number analysis (CNA) and gene expression tumor-node-metastasis (TNM) classification system of the analysis. Materials and Methods: Genes showing both up- International Union against Cancer (UICC) remains the most regulated expression and copy number gains in cases reliable indicator of prognosis for CRC patients and provides involving CRC with LNM were extracted as candidate the basis for therapeutic decision-making. Overall survival biomarkers. Expression of the mRNA of the final candidate (OS) in patients with lymph node metastasis (LNM) is was validated in 124 patients using quantitative reverse significantly shorter than in patients without LNM (3). LNM transcription polymerase chain reaction (qRT-PCR) assays. is a poor prognostic factor and precise diagnosis of LNM Expression of the protein encoded by this candidate gene contributes to more selective therapy for CRC. Thus, was assessed using immunohistochemical (IHC) staining of identification of genes that correlate with LNM should be tissue σ from 328 patients. The association between protein useful in the diagnosis and therapy of CRC. expression and clinicopathological features was also Microarray analysis is a useful tool for identifying examined. Results: Special AT-rich sequence-binding protein potential biomarker genes for use in cancer prognosis and 1 (SATB1) was extracted from integrated microarray investigating several thousand cancer-related or cancer- analysis. SATB1 mRNA expression in cancer tissue was specific genes at once (4, 5). significantly higher in patients with LNM than without LNM. Recently, single nucleotide polymorphism microarray SATB1 protein overexpression was significantly associated (SNP array) analysis has become a useful tool for examining with LNM. Moreover, overexpression of SATB1 was an copy number aberrations (CNAs). CNAs, including gains at independent poor prognostic factor in stage I-III, especially chromosomes 7, 8, 13 and 20, as well as losses at in stage II CRC. Conclusion: SATB1 may play an important chromosomes 1, 8, 17 and 18, are often observed in CRC and are related to the metastasis of CRC (6-9). Several studies have suggested the utility of integrating gene expression analysis with genomic profiling for the discovery Correspondence to: Toshiaki Ishikawa, Department of Surgical of cancer-related genes (10, 11). Genes that show a Oncology, Graduate School, Tokyo Medical and Dental University, significant positive association with expression and CNAs 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8519, Japan. Tel: +81 may play an important role in cancer progression. We, 358035261, Fax: +81 358030139, e-mail: [email protected] therefore, aimed to identify genes that are significantly Key Words: Colorectal cancer, biomarker, microarray analysis, related to LNM in CRC through integrated copy number and Special AT-rich sequence-binding protein 1 (SATB1), prognostic gene expression analysis. We considered that genes that are factor. overexpressed and have an amplified copy number in LNM 0250-7005/2016 $2.00+.40 4069 ANTICANCER RESEARCH 36 : 4069-4076 (2016) of CRC must have the potential to serve as useful therapeutic copy number gain were extracted using Fisher’s exact test ( p< 0.01). targets or clinical biomarkers. Among the genes that were common to both groups, those that were We identified several such genes through integrated analysis overexpressed (fold change >2.0, p< 0.05) in patients with LNM were selected as candidates for further analysis. and showed that one of those genes, Special AT-rich sequence- binding protein 1 ( SATB1 ), is up-regulated in tumors with Quantitative RT-PCR . Quantitative RT-PCR analyses were performed LNM. SATB1 has been found to be overexpressed in several using frozen tissues from 124 patients. Total RNA (10 μg) that was kinds of malignant tumors, which suggests a crucial role for extracted from bulk samples of cancer and adjacent non-neoplastic SATB1 in promoting tumor invasion and metastasis (12-20). tissues was reverse-transcribed into cDNA using a High Capacity This is the first study to demonstrate a significant correlation cDNA Reverse Transcription Kit (Applied Biosystems, Foster City, of SATB1 with LNM in CRC. CA, USA). TaqMan gene expression assays ( SATB1 , Hs00161515_m1; β- actin, Hs99999903_m1; Applied Biosystems) were used to determine the expression of SATB1. β- Actin was used Materials and Methods as an internal control. PCR was performed using the TaqMan Universal PCR Master Mix (Applied Biosystems). All calculated Patients. Primary tumors from 328 patients who underwent curative concentrations of target genes were normalized to the amount of the surgery for CRC between 2002 and 2011 at the Tokyo Medical and endogenous reference by the comparative Ct method for relative Dental University Hospital (Tokyo, Japan) were analyzed in this quantification ( ΔΔ Ct method) using Relative Quantification Study study. According to pathological examination, LNM were present Software (7300 Sequence Detection System version 1.2.1; Applied in 144 patients and absent in 184 patients (median follow-up Biosystems). Each assay was performed in duplicate. time=62 months). All patients provided written informed consent to participate in this study that was approved by the Institutional Immunohistochemistry. IHC studies of SATB1 expression were Review Board (approval number: 831). conducted using a FFPE tissue block from each 328 patients. Among the 328 patients enrolled, a total of 156 patients were After deparaffinization through a series of incubations in assigned to the integrated analyses for extraction of candidate genes. decreasing concentrations of ethanol, antigen was retrieved by The immunohistochemical (IHC) studies were performed using microwaving (Microwave-MI 77; Azumaya Corporation, Tokyo, formalin-fixed paraffin-embedded (FFPE) samples from 328 patients. Japan) for 25 min in pH 9 buffer (code 415211; Nichirei, Biosciences, Tokyo, Japan). Endogenous peroxidase activity was DNA extraction and copy number analysis. After resection, cancer quenched by 15 min of incubation in a mixture of 3% hydrogen tissues were immediately embedded in Tissue-Tek OCT compound peroxide solution in 100% methanol. After washing with phosphate- medium (Sakura Finetek Japan, Tokyo, Japan). Laser capture buffered saline (PBS), the specimens were incubated with a rabbit microdissection (LCM) was performed using an Application monoclonal anti-SATB1 antibody (EPR3895, ab92307; Abcam, Solutions LCM System (Leica Microsystems, Tokyo, Japan). Tumor Cambridge, UK) at a 1:100 dilution for 15 min at room temperature DNA was extracted and purified using a QIAamp DNA micro kit and, then, overnight at 4˚C. The sections were washed three times (Qiagen, Hilden, Germany). Copy number analysis (CNA) was with 0.1% Tween 20/PBS and incubated with peroxidase-labeled performed using a Gene Chip Human Mapping 250K Sty array polymer (Histofine Simple Stain Max PO (MULTI); Nichirei (Affymetrix, Santa Clara, CA, USA). Genomic DNA was digested Bioscience) for 30 min at room temperature. Peroxidase activity was using the enzyme Sty I and a Sty1 adaptor was used prior to the detected via incubation with 0.02% 3,3’-diaminobenzi-dine polymerase chain reaction (PCR) reaction. After hybridization, the tetrahydrochloride (Nichirei Bioscience) for 30 min. The sections microarrays were transferred to a totally automated Gene Chip were counterstained with 1% Mayer’s hematoxylin, dehydrated and Fluidics Station 450 (Affymetrix). After fluorescence staining, finally coverslipped. microarray images were scanned using the Gene Chip Scanner 3000 SATB1 expression was graded by two independent observers. The 7G (Affymetrix). The microarray data were analyzed using the staining patterns were evaluated using the immunoreactive score (IRS) Chromosome CNA Tool (Affymetrix). proposed by Remmele and Stegner (21) in which IRS=staining intensity (SI) × percentage of positive cells (PP). SI was determined RNA extraction and gene expression analysis. For quantitative 0, negative; 1, weak; 2, moderate; and 3, strong. PP was defined as 1, reverse transcription-polymerase
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