KR20160141218A

KR20160141218A - Biomarker composition for diagnosing cancer with mitochondrial dysfunction and method for diagnosing cancer using the same marker

Info

Publication number: KR20160141218A
Application number: KR1020150075944A
Authority: KR
Inventors: 윤계순; 우현구; 이영경; 임종진
Original assignee: 아주대학교산학협력단
Priority date: 2015-05-29
Filing date: 2015-05-29
Publication date: 2016-12-08
Also published as: KR101816345B1

Abstract

The present invention relates to a biomarker composition for diagnosing malignancy of cancer and a method for diagnosing cancer using the same. More particularly, the present invention relates to a biomarker composition for diagnosing cancer, A gene or a protein encoded by the gene, and a method of diagnosing cancer using the composition. The present invention can be utilized as a useful biomarker for diagnosing malignant cancer by using the main gene mutated in cancer cells due to a decrease in mitochondrial function.

Description

TECHNICAL FIELD The present invention relates to a biomarker composition for diagnosing malignant cancer and a method of diagnosing cancer using the same,

TECHNICAL FIELD The present invention relates to a biomarker composition for diagnosing malignancy-deficient cancer and a method of diagnosing cancer using the same.

Mitochondria are intracellular organelles that regulate the energy production required by cells. Normal cells produce energy through oxidative phosphorylation of mitochondria in the presence of oxygen, and produce energy using only the corresponding process when oxygen is not present. However, in many cancer cells, it has been observed that mitochondrial ATP production is degraded, and ATP is synthesized depending on the process regardless of the presence or absence of oxygen. Thus, there is insufficient study on how the degradation of mitochondrial function observed in cancer cells is due to what mechanism, and how it is related to the proliferative capacity and invasion of cancer cells. Several recent studies have reported that mitochondrial dysfunction promotes cancer metastasis in several cancer types, including breast, stomach, or liver cancer. In other words, it has been shown that mitochondrial deficiency plays an important role in cancer progression. Therefore, it is important to identify the major mechanisms by which mitochondrial deficiency plays a role in cancer progression.

PCT Publication No. WO2010-064702 (Jun. 10, 2010)

It is an object of the present invention to provide a biomarker composition for diagnosing cancer whose function is deteriorated by mitochondria and a method of diagnosing cancer using the same.

The present invention provides a biomarker composition for diagnosing malignancy of malfunctioning cancer, comprising at least one gene selected from the group consisting of NFIX, SEL1L3, NFE2L1, PABPC1L, HINT3, PSPH, TGFB1, PPP1R15A and TMEM49 or a protein encoded by the gene do.

The present invention also relates to a primer or a probe specifically binding to at least one gene selected from the group consisting of NFIX, SEL1L3, NFE2L1, PABPC1L, HINT3, PSPH, TGFB1, PPP1R15A and TMEM49, Or a peptide having a binding domain specific to the protein. The present invention also provides a kit for diagnosing malfunction of a mitochondrial cancer.

The present invention also provides a method for detecting mRNA expression levels of at least one gene selected from the group consisting of NFIX, SEL1L3, NFE2L1, PABPC1L, HINT3, PSPH, TGFB1, PPP1R15A and TMEM49 from cancer patient samples or the expression level of the protein encoded by the gene A method for providing information necessary for diagnosis of a malfunctioning cancer of the mitochondria.

Fig. 1 shows the results of gene expression changes in mitochondria-deficient invasive hepatic cancer cells. Three different SNU liver cancer cell lines (SNU354, SNU387 and SNU423) and Ch-L clones were cultured for 2 hours to maintain exponential growth period. (a) The oxygen consumption rate (OCR) was measured using an XF analyzer. (b) Western blot analysis of mitochondrial respiratory subunits. (c) Cell invasion activity was performed using Matrigel ^TM -coated Transwell ^TM . The number of invaded cells was measured. Representative photographs of invaded cells are shown in the panel below. **, p < Ch-L by student t-test. (d) Heatmap of genes that are differentially expressed between mitochondrial respiratory active and mitochondrial respiratory deficient hepatocarcinoma cells (mitochondrial 'tumoral defect' characteristics). As a result of gene expression profiling, a total of 2,774 genes showing a difference in expression showed a difference of more than 2 times in expression. Of these, 1301 genes were commonly up-regulated and 1473 genes were down-regulated in mitochondrial deficient cells compared to mitochondrial activated cells. (e) Functional enrichment analysis results for commonly up-regulated genes (1301 genes) and down-regulated genes (1473 genes). The concentration score represents the -log 10 converted p-values calculated from the gene cluster enrichment assay.
Fig. 2 shows the results of analysis of CMD gene characteristics. (a) Ch-L clones were analyzed by treating four different respiratory inhibitors for 12 hours: 5 μM Rotenone (Ro), 200 μM TTFA, 5 μM antimycin A (AA) or 5 μM oligomycin (Oli). Comparing the gene expression profiles of the cells, we obtained 131 genes that were commonly up-regulated (mitochondrial 'functional defect' characteristics). (b) Gene expression profiles of MDA-MB435 and its ρ0 cells were compared, resulting in up-regulated 1760 genes (mitochondrial 'genetic defect' characteristics). (c) Ten genes were obtained from CMD characteristics from three independent mitochondrial deficiency conditions (tumor, genetic and functional deficiency). (d) and (e) Kaplan-Meier plot analysis of overall survival (left panel) and recurrence free survival (right panel) from independent open data (GSE4024 and GSE14520), respectively. Patients were stratified based on the expression status of CMD characteristics (CMD_UP vs CMD_DOWN).

Thus, the present inventors sought to clarify the main regulatory mechanism of mitochondrial deficiency in cancer progression. We identified mitochondrial depletion in hepatocarcinoma cells and identified three independently designed mitochondrial depletion models (liver cancer cells with low respiratory activity, ie, tumor deficiency; pharmacologically respiratory depressed cells, ie, deficient function; And genetic expression profiling of cancer cells deficient in mitochondrial DNA, i. E. Genetic deficiency) to identify 10 common mitochondrial defect (CMD) genes and completed the present invention.

The present invention provides a biomarker composition for diagnosing malignancy of malfunctioning cancer, comprising at least one gene selected from the group consisting of NFIX, SEL1L3, NFE2L1, PABPC1L, HINT3, PSPH, TGFB1, PPP1R15A and TMEM49 or a protein encoded by the gene do. The composition may further comprise a NUPR1 gene or a protein encoded by the gene. Preferably, the cancer may be liver cancer, but is not limited thereto.

The "NFIX" of the present invention is a Nuclear factor 1 X-type (CCAAT-binding transcription factor), NCBI accession no. NC_000019.10, but is not limited thereto.

"SEL1L3" of the present invention is a sel-1 suppressor of lin-12-like 3, and is NCBI accession no. NC_000004.12, but is not limited thereto.

"NFE2L1" of the present invention is a nuclear factor, erythroid 2-like 1, NCBI accession no. NC_000017.11, but is not limited thereto.

"PABPC1L" of the present invention is a poly (A) binding protein, cytoplasmic 1-like, as described in NCBI accession no. NC_000020.11, but is not limited thereto.

"HINT3" of the present invention is histidine triad nucleotide binding protein 3, NCBI accession no. NC_000006.12, but is not limited thereto.

"PSPH" of the present invention is a phosphoserine phosphatase, which is represented by NCBI accession no. NC_000007.14, but is not limited thereto.

"TGFB1" of the present invention is a transforming growth factor, beta 1, NCBI accession no. NC_000019.10, but is not limited thereto.

"PPP1R15A" of the present invention includes protein phosphatase 1, regulatory subunit 15A, NCBI accession no. NC_000019.10, but is not limited thereto.

The "TMEM49" of the present invention is a transmembrane protein 49, as described in NCBI accession no. NC_000017.11, but is not limited thereto.

The term "NUPR1" of the present invention is expressed as a nuclear protein transcriptional regulator 1 or nuclear protein 1, as NCBI accession no. NC_000016.10, but is not limited thereto.

The term " diagnosing " herein is used to determine the susceptibility of an object to a particular disease or disorder, to determine whether an object currently has a particular disease or disorder, Determining the prognosis of the object, or therametrics (e.g., monitoring the status of the object to provide information about the therapeutic efficacy).

In addition, a primer or a probe specifically binding to at least one gene selected from the group consisting of NFIX, SEL1L3, NFE2L1, PABPC1L, HINT3, PSPH, TGFB1, PPP1R15A and TMEM49 of the present invention, Or a peptide having a binding domain specific to the protein. The present invention also provides a kit for diagnosing malfunction of a mitochondrial cancer. The kit may further comprise a primer or a probe specifically binding to the NUPR1 gene, an antibody that specifically binds to the protein encoded by the gene, or a peptide having a binding domain specific to the protein. Preferably, the cancer may be liver cancer, but is not limited thereto.

The term "primer" refers to a short nucleic acid sequence capable of forming a base pair with a template complementary to a nucleic acid sequence having a short free 3 'hydroxyl group and acting as a starting point for template strand replication . Primers can initiate DNA synthesis in the presence of reagents for polymerization (i. E., DNA polymerase or reverse transcriptase) and four different nucleoside triphosphates at appropriate buffer solutions and temperatures. The PCR conditions, the lengths of the sense and antisense primers can be appropriately selected according to techniques known in the art.

The term "probe" means a nucleic acid fragment such as RNA or DNA corresponding to a few nucleotides or several hundreds of nucleotides that can specifically bind to an mRNA, and is labeled to confirm the presence or expression level of a specific mRNA . The probe may be prepared in the form of an oligonucleotide probe, a single strand DNA probe, a double strand DNA probe, or an RNA probe. Selection of suitable probes and hybridization conditions can be appropriately selected according to techniques known in the art.

As used herein, the term "antibody" means a specific immunoglobulin as indicated in the art and directed against an antigenic site. Any of those prepared through the above-mentioned one or more protein injections or commercially available can be used. In addition, the antibody includes a polyclonal antibody, a monoclonal antibody, and a fragment capable of binding to an epitope. The forms of the antibodies include polyclonal or monoclonal antibodies, including all immunoglobulin antibodies. The antibody refers to a complete form having two full-length light chains and two full-length heavy chains. The antibody also includes a special antibody such as a humanized antibody.

The term "peptide" refers to a polypeptide that does not have the structure of the intact antibody, but has a specific antigen binding site (binding domain) directed against the antigenic site. The peptide comprises a functional fragment of an antibody molecule that is not a complete form of the antibody having two light and two heavy chains. A functional fragment of an antibody molecule means a fragment having at least an antigen-binding function.

(1) the mRNA expression level of one or more genes selected from the group consisting of NFIX, SEL1L3, NFE2L1, PABPC1L, HINT3, PSPH, TGFB1, PPP1R15A and TMEM49 from a cancer patient sample, Measuring an expression level; And (2) comparing the mRNA expression level of the gene or the expression level of the protein encoded by the gene with a control sample. The present invention also provides a method for providing information necessary for diagnosis of a mitochondrial deficient cancer. In step (1) of the method, the mRNA expression level of the NUPR1 gene or the expression level of the protein encoded by the gene can be further measured. Preferably, the cancer may be liver cancer, but is not limited thereto.

In detail, the method for measuring the mRNA expression level may be RT-PCR, competitive RT-PCR, real-time RT-PCR, RNase protection assay (RPA) ), Northern blotting and DNA chips, but are not limited thereto.

In detail, the method for measuring the protein expression level may be Western blotting, enzyme linked immunosorbent assay (ELISA), radioimmunoassay (RIA), radioimmunodiffusion, Ouchterlony immunodiffusion, But are not limited to, rocket immunoelectrophoresis, tissue immunostaining, immunoprecipitation assays, Complement Fixation Assays, FACS and protein chips.

As used herein, the term " patient sample " refers to a tissue, cell, whole blood, serum, plasma, saliva, sputum, cerebrospinal fluid, or urine that differs from the control in the level of expression of the genes as mitochondrial defective cancer diagnostic biomarkers But are not limited to, samples.

As used herein, the term " cancer deficient in mitochondria "," cancer deficient in mitochondria ", or " mitochondrial deficient cancer " means that the ability of the mitochondrial to produce ATP is decreased in cancer cells. On the other hand, it has been reported that mitochondrial dysfunction promotes cancer metastasis in various cancer types including breast cancer, gastric cancer or liver cancer (PLoS One 2013; 8: e61677, Biochim Biophys Acta 2012; 1820: 1102-1110, PLoS One 2013; : e69485).

Hereinafter, the present invention will be described in detail with reference to embodiments which do not limit the present invention. It should be understood that the following embodiments of the present invention are only for embodying the present invention and do not limit or limit the scope of the present invention. It is therefore to be understood that within the scope of the appended claims, the invention may be practiced otherwise than as specifically described herein.

< Experimental Example >

The following experimental examples are intended to provide experimental examples that are commonly applied to the respective embodiments according to the present invention.

1. Establishment of cell culture and mitochondrial deficiency conditions

Human liver cancer cells (SNU-354, SNU-387 and SNU-423) were purchased from Korean Cell Line Bank (Seoul, Korea) and 10% GIBCO ^™ fetal bovine serum (FBS; Invitrogen) and GIBCO ^™ antibiotics Were incubated at 37 [deg.] C in a 5% CO ₂ humidified incubator in an added GIBCO ^TM RPMI1640 medium (Invitrogen, Carlsbad, CA). Chang cell clones were isolated by single cell dilution and Chang cell expansion (ATCC, Rockville, Md.). Chang clones with strong hepatic characteristics (Ch-L), which were verified by confirming liver-specific expression of albumin and carbamoyl-phosphate synthase-1, were used in the present invention. Ch-L clone was GIBCO ^TM Dulbecco's modified Eagle's medium with a 10% FBS was added GIBCO ^TM; cultured at (DMEM Invitrogen).

Three other mitochondrial deficiency conditions were established. For 'tumoral defect', mitochondrial deficient hepatocytes (SNU-354 and SNU-423) were used. The 'functional defect' condition is a condition in which the Ch-L clone is treated with a positive inhibitor of rotenone (complex I inhibitor), TTFA (complex II inhibitor), antimycin A (complex III inhibitor) and oligomycin complex V inhibitor) for 12 hours. The Rho0 clone of MDA-MB435 deficient in mitochondrial DNA (mtDNA) was obtained from Singh KK and used as a 'genetic defect' condition.

2. Human HCC Specimen

HCC tumors and surrounding tissues were obtained from 23 HCC patients (aged 34-70 years) who visited Ajou University Hospital from August 2008 to January 2010, and received consent from the Ajou University Bioethics Committee. None of the patients participating in the present invention received preoperative chemotherapy or radiotherapy.

3. Gene expression profiling and data analysis

To obtain the biotinylated cDNA, the total RNA was amplified and separated according to the manufacturer's instructions using the Ambion Illumina RNA amplification kit (Ambion, Austin, Tex.). Specifically, 550 ng of total RNA was reverse transcribed into cDNA using oligo-dT primers. Double strand cDNA was synthesized, and in vitro vitro ) and labeled with biotinylated dNTPs. The labeled cDNA samples (750 ng) were each hybridized with a human HT-12 expression v.4 bead array and detection of the analytical signal was performed according to the manufacturer's instructions (Illumina, Inc., San Diego, Calif.). The raw data was filtered with a detection value of p-value <0.05 and further processed by log2 conversion and quartile normalization. Gene ontology analysis and signal path analysis were performed using DAIVD software. The enrichment scores (ES) were calculated by applying the non-parametric Kolmogorov-Smirnov test analysis in gene set enrichment analysis to identify identified gene characteristics for each patient. -log10 Converted p-values were used as ES and significance of ES was measured by p <0.05. For clinical validation, a set of two independent cohort 1 (GSE4024, GSE1898, n = 139) and cohort 2 (GSE14520, n = 247) HCC gene expression profile data were obtained in the Gene Expression Omnibus (GEO) And gene and array centering. All data processing and survival analyzes were performed using R / Bioconductor packages.

4. Cell Oxygen Consumption Rate ( cellular oxygen consumption rate ; OCR ) Measure

To observe mitochondrial respiratory activity, OCR was measured using a Seahorse XF24 analyzer (Seahorse Bioscience Inc., MA).

5. Cellular invasion analysis

Cellular invasion assays were performed using Transwell ^TM Permeable Supports (8-μm pore size; Corning, Acton, MA) with pre-coated 7% Growth Factor Reduced BD Matrigel ^™ Matrix (Becton Dickinson Labware, Franklin Lakes, NJ) Respectively.

< Example 1> Mitochondrial respiratory deficiency in liver cancer cells - Reprogramming Character analysis

First, the present inventors examined the mitochondrial respiratory status and cytopathic activity of three different liver cancer cell lines (SNU387, SNU354, and SNU423). Ch-L clones were isolated and found to have liver-specific genes. The clone was used as a control for active mitochondria. SNU387 cells have OCR activity similar to Ch-L, whereas SNU354 and SNU423 cells have decreased OCRs, indicating mitochondrial respiratory deficiency (FIG. 1A). Mitochondrial In order to confirm breathing deficiency, the levels of expression of several mitochondrial complex proteins (I, II, III and IV) were observed. SNU354 and SNU423 expressed mitochondrial complex proteins at levels lower than Ch-L and SNU387 (Fig. 1B). To confirm the association of mitochondrial deficiency with malignant liver cancer, invasiveness was observed. As expected, mitochondrial deficient cells (i.e., SNU354 and SNU423 cells) were more invasive than SNU387 and Ch-L cells (Fig. 1c). Taken together, these results show that SNU354 and SNU423 cells have cancer cell invasion associated with mitochondrial respiratory impairment, which may be a suitable model for studying the role of mitochondrial deficiency in cancer progression.

Gene expression profiling was performed on SNU354 and SNU423 cells to study transcriptional volume regulation associated with mitochondrial damage in hepatoma cells. Differential expression of the levels of Ch-L and SNU387 cells at cut-off levels 1.4 fold Were identified. A total of 1,301 genes were up-regulated and 1,473 genes were down-regulated (Fig. 1d), which was named the 'tumoral defect' gene. Functional gene set enrichment analysis revealed that genes related to cell migration and cytoskeleton organization were clearly up-regulated in SNU354 and SNU423 cells (Fig. 1e) , Indicating that up-regulated genes are involved in the acquisition of aggressive phenotypes and are regulated by mitochondrial deficiency.

< Example 2> CMD Analysis of genes

To select genes directly regulated by mitochondrial respiration deficiency from 1,301 up-regulated genes, we established two additional mitochondrial deficient cell conditions: (1) exposure to several pharmacological mitochondrial respiratory inhibitors (2) a 'genetic defect' using ρ0 cells deficient in mtDNA. As a result of gene expression profiling of direct functional deficiency conditions, 131 up-regulated genes and 118 down-regulated genes were common for direct respiratory depression (Figure 2a). Comparison of gene expression between Rho0 cells and the parental MDA-MB435 cell line revealed 1,760 up-regulated genes and 1,604 down-regulated genes in Rho0 (Fig. 2b). Three independent mitochondrial deficiency model (tumor deficiency, deficient function and genetic deficiency) was, after ten CMD gene (NFIX, SEL1L3, NFE2L1, PABPC1L, NUPR1, HINT3, PSPH, TGFB1, PPP1R15A comparison And TMEM49 ) (Fig. 2C). By independent stimulation in liver cancer cells, these 10 genes appear to be directly inducible for mitochondrial damage.

To confirm the clinical significance of the CMD genes, we used two independent liver cancer cohorts (cohort 1 (GSE4024, n = 139) and cohort 2 (GSE14520, n = 247) We analyzed the association between clinical outcomes such as overall survival (OS) and recurrence-free survival (RFS). Patients who were stratified based on enrichment scores (ES) of CMD genes (ES> 1.3, p <0.05) showed that patients with increased expression of CMD genes had lower OS (cohorts 1 and 2 p = 0.025 and p = 0.0005) and RFS ( p = 0.008 and p = 0.0002 for cohorts 1 and 2, respectively) (Fig. 2d and Fig. 2e). These results show significant prognostic value of CMD characteristics that can play a central role in HCC progression.

Claims

NFIX, SEL1L3, NFE2L1, PABPC1L, HINT3, PSPH, TGFB1, PPP1R15A and TMEM49 or a protein encoded by said gene.

The biomarker composition according to claim 1, wherein the composition further comprises a NUPR1 gene or a protein encoded by the gene.

The biomarker composition according to any one of claims 1 to 3, wherein the cancer is liver cancer.

A primer or a probe specifically binding to at least one gene selected from the group consisting of NFIX, SEL1L3, NFE2L1, PABPC1L, HINT3, PSPH, TGFB1, PPP1R15A and TMEM49, an antibody specifically binding to the protein encoded by the gene, And a peptide having a binding domain specific to said protein.

5. The kit according to claim 4, wherein the kit further comprises a primer or a probe specifically binding to the NUPR1 gene, an antibody specifically binding to the protein encoded by the gene, or a peptide having a binding domain specific to the protein A kit for diagnosing malignant cancer with reduced function.

[Claim 5] The kit for diagnosing malignancy of malfunctioning cancer according to claim 4 or 5, wherein the cancer is liver cancer.

(1) measuring the mRNA expression level of one or more genes selected from the group consisting of NFIX, SEL1L3, NFE2L1, PABPC1L, HINT3, PSPH, TGFB1, PPP1R15A and TMEM49 from the cancer patient sample or the expression level of the protein encoded by the gene step; And
(2) comparing the mRNA expression level of the gene or the expression level of the protein encoded by the gene with a control sample.

[8] The method according to claim 7, wherein the step (1) further measures the mRNA expression level of the NUPR1 gene or the expression level of the protein encoded by the gene.

9. The method according to claim 7 or 8, wherein the cancer is liver cancer.

The method according to claim 7 or 8, wherein the mRNA expression level is measured by RT-PCR, competitive RT-PCR, real-time RT-PCR, Wherein the measurement is performed using any one selected from the group consisting of RPA (RNase protection assay), Northern blotting and DNA chip.

9. The method according to claim 7 or 8, wherein the protein expression level is measured by Western blotting, enzyme linked immunosorbent assay (ELISA), radioimmunoassay (RIA), radioimmunodiffusion, Using one selected from the group consisting of Ouchterlony immunodiffusion, rocket immunoelectrophoresis, tissue immuno staining, immunoprecipitation assay, Complement Fixation Assay, FACS and protein chip The method comprising the steps of: