CN111304333B

CN111304333B - Novel application of SERINC4 gene

Info

Publication number: CN111304333B
Application number: CN202010177510.1A
Authority: CN
Inventors: 钱海利; 张颖; 王婷; 马飞; 林晨; 李春晓; 赵振国; 郭建宾
Original assignee: Cancer Hospital and Institute of CAMS and PUMC
Current assignee: Cancer Hospital and Institute of CAMS and PUMC
Priority date: 2020-03-13
Filing date: 2020-03-13
Publication date: 2021-03-02
Anticipated expiration: 2040-03-13
Also published as: CN111304333A

Abstract

The invention relates to a novel application of a SERINC4 gene, in particular to a novel application of a SERINC4 gene in predicting prognosis of an endometrial cancer patient. The invention discovers that the molecular marker SERINC4 is related to endometrial cancer prognosis for the first time, and can be used for endometrial cancer prognosis prediction by detecting the change of SERINC4 of a subject. The invention provides a theoretical basis for the mechanism research of endometrial cancer and provides an auxiliary means for prognosis prediction of endometrial cancer.

Description

Novel application of SERINC4 gene

Technical Field

The invention belongs to the field of biomedicine, and relates to a new application of a SERINC4 gene, in particular to a new application of a SERINC4 gene in predicting prognosis of an endometrial cancer patient.

Background

Endometrial Cancer is one of the most common malignancies of the female reproductive tract, with increasing incidence in recent years (Jemal A, Bray F, Melissa M, et al. Global Cancer statistics [ J ]. CA Cancer Clin J Clin,2011,61(2):69-90), and second-most in developing countries, second to cervical Cancer, has surpassed cervical Cancer in developed countries, becoming the most common malignancy of the female reproductive tract. Approximately 75% of patients are diagnosed early with a 5-year survival rate of 90%, but there is still a 10-15% recurrence rate in early patients (Odagiri T, Watari H, Hosaka M, et al. multivariate Survival analysis of the patient with a recurrent endermic Cancer. J. Gynecol Oncol,2011,22(1): 3-8; Del Carmen MG, Boruta DM 2nd, Schorge JO, et al. Currenten Endometric Cancer,2011,54(2): 266-) 277). The 5-year overall survival of endometrial cancer in developing and developed countries is 67% and 82% (Tangjitgamol S, Anderson BO, See HT, et al. management of end clinical cancer in Asia: related from the ovarian Oncology Summit 2009[ J ]. Lancet Oncol,2009,10(11): 1119-containing 1127), respectively, and the mortality of endometrial cancer patients has doubled over the past 20 years in the United states (Sorosky JI. Endometric cancer. Obstet Gynecol,2008,111(2): 436-containing 447), severely harming women' S health. Therefore, the study on high risk factors of prognosis and the early establishment of individual treatment schemes become hot spots of clinical research. The high-risk factors proved to be late pathological stage, low differentiation, deep muscular layer infiltration, special pathological type and the like. However, the biological behavior and prognosis of tumors cannot be fully judged only by pathological features, and the research of specific molecular markers provides a new platform for the diagnosis. The oncogenes, cancer suppressor genes, steroid hormone receptors and the like related to the intimal cancer are found at present, but highly specific factors are not found, the relationship between part of the found factors and the intimal cancer prognosis is still controversial, and a large amount of clinical data prove that the factors cannot be used for guiding clinical treatment.

Disclosure of Invention

In order to overcome the defects in the prior art, the invention aims to provide a gene marker for predicting the prognosis of an endometrial cancer patient.

In order to test the purpose, the invention adopts the following technical scheme:

the invention provides application of SERINC4 gene in preparation of a product for predicting prognosis of endometrial cancer patients.

Further, the product predicts prognosis of an endometrial cancer patient by determining the expression level of SERINC4 in a sample.

Further, SERINC4 is highly expressed in endometrial cancer patients with good prognosis and is lowly expressed in endometrial cancer patients with poor prognosis.

Further, the product comprises detecting changes in SERINC4 gene expression by sequencing techniques, nucleic acid hybridization techniques, nucleic acid amplification techniques, or immunoassays.

Further, the nucleic acid amplification technique is selected from the group consisting of polymerase chain reaction, reverse transcription polymerase chain reaction, transcription mediated amplification, ligase chain reaction, strand displacement amplification and nucleic acid sequence based amplification.

The invention provides a product for predicting prognosis of an endometrial cancer patient, wherein the product can predict the prognosis of the endometrial cancer patient by detecting SERINC4 gene expression in a sample.

Further, the product comprises a chip, a kit or a formulation.

Wherein, the chip comprises a gene chip and a protein chip; the gene chip comprises a solid phase carrier and oligonucleotide probes fixed on the solid phase carrier, wherein the oligonucleotide probes comprise oligonucleotide probes aiming at SERINC4 gene for detecting the transcription level of SERINC4 gene; the protein chip comprises a solid phase carrier and a specific antibody or ligand of SERINC4 protein fixed on the solid phase carrier; the kit comprises a gene detection kit and a protein immunodetection kit; the gene detection kit comprises a reagent for detecting the transcription level of SERINC4 gene; the protein immunodetection kit comprises a specific antibody or ligand of SERINC4 protein.

The gene chip or the gene detection kit can be used for detecting the expression levels of a plurality of genes including SERINC4 genes. The protein chip or the protein immunodetection kit can be used for detecting the expression level of a plurality of proteins including SERINC4 protein. The molecular markers of the endometrial cancer are detected simultaneously, so that the accuracy of prognosis prediction of the endometrial cancer can be greatly improved.

Further, the ligand comprises an interacting molecule of a protein encoded by SERINC 4.

In a particular embodiment of the invention, the sample source is tissue.

The invention has the advantages and beneficial effects that:

the invention discovers that the molecular marker SERINC4 is related to endometrial cancer prognosis for the first time, and can be used for endometrial cancer prognosis prediction by detecting the change of SERINC4 of a subject.

The invention provides a theoretical basis for the mechanism research of endometrial cancer and provides an auxiliary means for prognosis prediction of endometrial cancer.

Drawings

FIG. 1 shows a graph of survival of endometrial cancer patients;

figure 2 shows a ROC plot for predicting prognosis of endometrial cancer patients using the SERINC4 gene.

Detailed Description

The invention is widely and deeply researched, and through a large amount of screening, the SERINC4 is found to be specifically and highly expressed in endometrial cancer patients with good prognosis for the first time.

SERINC4

The protein encoded by SERINC4 gene can phosphorylate carbohydrates such as ribulose, ribitol, L-arabitol, etc.

SERINC4 polynucleotide or protein (polypeptide) sequences useful in the present invention include SERINC4 of various origins and species, and include wild type, mutant SERINC4, or active fragments thereof. In some embodiments of the invention, the SERINC4 is derived from a human.

The polynucleotide of the present invention may be in the form of DNA or RNA. The form of DNA includes cDNA, genomic DNA or artificially synthesized DNA. The DNA may be single-stranded or double-stranded. The DNA may be the coding strand or the non-coding strand.

The polypeptide of the present invention may be a recombinant polypeptide, a natural polypeptide, a synthetic polypeptide, preferably a recombinant polypeptide. The polypeptides of the invention may or may not also include an initial methionine residue.

Polynucleotides encoding the mature polypeptide of SERINC4 include: a coding sequence encoding only the mature polypeptide; the coding sequence for the mature polypeptide and various additional coding sequences; the coding sequence (and optionally additional coding sequences) as well as non-coding sequences for the mature polypeptide. The term "polynucleotide encoding a polypeptide" may include a polynucleotide encoding the polypeptide, and may also include additional coding and/or non-coding sequences.

The present invention also relates to variants of the above polynucleotides which encode polypeptides having the same amino acid sequence as the present invention or fragments, analogs and derivatives of the polypeptides. The variant of the polynucleotide may be a naturally occurring allelic variant or a non-naturally occurring variant. These nucleotide variants include substitution variants, deletion variants and insertion variants. As is known in the art, an allelic variant is a substitution of a polynucleotide, which may be a substitution, deletion, or insertion of one or more nucleotides, without substantially altering the function of the encoded polypeptide.

The invention also relates to nucleic acid fragments, including sense and antisense nucleic acid fragments, which hybridize to the sequences described above. As used herein, a "nucleic acid fragment" is at least 15 nucleotides, preferably at least 30 nucleotides, more preferably at least 50 nucleotides, and most preferably at least 100 nucleotides in length. The nucleic acid fragments may be used in amplification techniques of nucleic acids, such as PCR, to determine and/or isolate a polynucleotide encoding SERINC4 protein.

The full-length nucleotide sequence or fragment of human SERINC4 of the invention can be obtained by PCR amplification method, recombination method or artificial synthesis method. For the PCR amplification method, primers can be designed based on the disclosed nucleotide sequences, particularly open reading frame sequences, and the sequences can be amplified using a commercially available cDNA library or a cDNA library prepared by a conventional method known to those skilled in the art as a template. When the sequence is long, two or more PCR amplifications are often required, and then the amplified fragments are spliced together in the correct order. Once the sequence of interest has been obtained, it can be obtained in large quantities by recombinant methods. This is usually done by cloning it into a vector, transferring it into a cell, and isolating the relevant sequence from the propagated host cell by conventional methods.

Host cells and vectors

The gene-carrying vector of the present invention is a variety of vectors known in the art, such as commercially available vectors, including plasmids, cosmids, phages, viruses, and the like. The host cell may be a prokaryotic cell, such as a bacterial cell; or lower eukaryotic cells, such as yeast cells; or higher eukaryotic cells, such as mammalian cells. Representative examples are: coli, bacterial cells of the genus streptomyces; fungal cells such as yeast; a plant cell; insect cells of Drosophila S2 or Sf 9; CHO, COS, or 293 cell.

Transformation of a host cell with recombinant DNA can be carried out using conventional techniques well known to those skilled in the art. When the host is prokaryotic, e.g., E.coli, competent cells capable of DNA uptake can be harvested after exponential growth phase using CaCl₂Methods, the steps used are well known in the art. Another method is to use MgCl₂. If desired, transformation can also be carried out by electroporation. When the host is a eukaryote, the following DNA transfection methods may be used: calcium phosphate coprecipitation, conventional mechanical methods such as microinjection, electroporation, liposome encapsulation, etc.

The recombinant polypeptide in the above method may be expressed intracellularly or on the cell membrane, or secreted extracellularly. If necessary, the recombinant protein can be isolated and purified by various separation methods using its physical, chemical and other properties. These methods are well known to those skilled in the art. Examples of such methods include, but are not limited to: conventional renaturation treatment, treatment with a protein precipitant (such as salt precipitation), centrifugation, cell lysis by osmosis, sonication, ultracentrifugation, molecular sieve chromatography (gel filtration), adsorption chromatography, ion exchange chromatography, High Performance Liquid Chromatography (HPLC), and other various liquid chromatography techniques, and combinations thereof.

Reagent kit

The kit of the invention can be used for detecting the expression of SERINC4, and preferably, the kit comprises an effective detection amount of a reagent for detecting SERINC4 gene, and one or more substances selected from the following group: container, instructions for use, positive control, negative control, buffer, adjuvant or solvent. For example, a solution for suspending or immobilizing cells, a detectable label or label, a solution for facilitating hybridization of nucleic acids, a solution for lysing cells, or a solution for nucleic acid purification.

The kit of the present invention may further comprise instructions for use of the kit, which describe how to use the kit for detection and how to use the detection result for prognosis of cancer.

With the kit of the present invention, SERINC4 can be detected by various methods selected from the group consisting of (including but not limited to): real-time quantitative reverse transcription PCR, biochip detection method, southern blotting, northern blotting or in situ hybridization. The detection mode can be adjusted and changed by those skilled in the art according to actual conditions and needs.

Detection techniques (methods)

The genes of the invention are detected using a variety of detection techniques known to those of ordinary skill in the art, including, but not limited to: nucleic acid sequencing, nucleic acid hybridization, nucleic acid amplification technology and immunodetection technology.

Illustrative, non-limiting examples of nucleic acid sequencing techniques include, but are not limited to, chain terminator (Sanger) sequencing and dye terminator sequencing. One of ordinary skill in the art will recognize that RNA is typically reverse transcribed into DNA prior to sequencing because it is less stable in cells and more susceptible to nuclease attack in experiments.

Another illustrative, non-limiting example of a nucleic acid sequencing technique includes next generation sequencing (deep sequencing/high throughput sequencing), which is a unimolecular cluster-based sequencing-by-synthesis technique based on proprietary reversible termination chemical reaction principles. Random fragments of genome DNA are attached to an optically transparent glass surface during sequencing, hundreds of millions of clusters are formed on the glass surface after the DNA fragments are extended and subjected to bridge amplification, each cluster is a monomolecular cluster with thousands of identical templates, and then four kinds of special deoxyribonucleotides with fluorescent groups are utilized to sequence the template DNA to be detected by a reversible edge-to-edge synthesis sequencing technology.

Illustrative, non-limiting examples of nucleic acid hybridization techniques include, but are not limited to, In Situ Hybridization (ISH), microarrays, and Southern or Northern blots. In Situ Hybridization (ISH) is a hybridization of specific DNA or RNA sequences in a tissue section or section using a labeled complementary DNA or RNA strand as a probe (in situ) or in the entire tissue if the tissue is small enough (whole tissue embedded ISH). DNA ISH can be used to determine the structure of chromosomes. RNA ISH is used to measure and locate mRNA and other transcripts (e.g., ncRNA) within tissue sections or whole tissue embedding. Sample cells and tissues are typically treated to fix the target transcript in situ and to increase probe access. The probe is hybridized to the target sequence at high temperature, and then excess probe is washed away. The localization and quantification of base-labeled probes in tissues labeled with radiation, fluorescence or antigens is performed using autoradiography, fluorescence microscopy or immunohistochemistry, respectively. ISH can also use two or more probes labeled with radioactive or other non-radioactive labels to detect two or more transcripts simultaneously.

The present invention can amplify nucleic acids (e.g., ncRNA) prior to or simultaneously with detection. Illustrative non-limiting examples of nucleic acid amplification techniques include, but are not limited to: polymerase Chain Reaction (PCR), reverse transcription polymerase chain reaction (RT-PCR), Transcription Mediated Amplification (TMA), Ligase Chain Reaction (LCR), Strand Displacement Amplification (SDA), and Nucleic Acid Sequence Based Amplification (NASBA). One of ordinary skill in the art will recognize that certain amplification techniques (e.g., PCR) require reverse transcription of RNA into DNA prior to amplification (e.g., RT-PCR), while other amplification techniques directly amplify RNA (e.g., TMA and NASBA).

The polymerase chain reaction, commonly referred to as PCR, uses multiple cycles of denaturation, annealing of primer pairs to opposite strands, and primer extension to exponentially increase the copy number of a target nucleic acid sequence; transcription-mediated amplification of TMA (autocatalytically synthesizing multiple copies of a target nucleic acid sequence under conditions of substantially constant temperature, ionic strength and pH, wherein multiple RNA copies of the target sequence autocatalytically generate additional copies; ligase chain reaction of LCR uses two sets of complementary DNA oligonucleotides that hybridize to adjacent regions of the target nucleic acid; other amplification methods include, for example, nucleic acid sequence-based amplification commonly known as NASBA; amplification of the probe molecule itself using RNA replicase (commonly known as Q.beta.replicase), transcription-based amplification methods, and self-sustained sequence amplification.

Chip and method for manufacturing the same

The term "chip", also referred to as an "array", refers to a solid support comprising attached nucleic acid or peptide probes. Arrays typically comprise a plurality of different nucleic acid or peptide probes attached to the surface of a substrate at different known locations. These arrays, also known as "microarrays," can generally be produced using either mechanosynthesis methods or light-guided synthesis methods that incorporate a combination of photolithography and solid-phase synthesis methods. The array may comprise a flat surface, or may be nucleic acids or peptides on beads, gels, polymer surfaces, fibers such as optical fibers, glass, or any other suitable substrate. The array may be packaged in a manner that allows for diagnostic or other manipulation of the fully functional device.

The term "gene chip" is a collection of microscopic DNA spots attached to a solid surface (e.g., glass, plastic, or silicon chips) to form an array for simultaneous expression profiling or expression level monitoring of thousands of genes. The immobilized DNA fragments, called probes, thousands of which can be used in a single DNA microarray. Microarrays can be used to identify disease genes or transcripts (e.g., ncrnas) by comparing gene expression in disease and normal cells. Microarrays can be fabricated using a variety of techniques, including but not limited to: printing onto a glass slide with a fine-pointed needle, photolithography using a pre-fabricated mask, photolithography using a dynamic micro-mirror device, ink-jet printing, or electrochemical methods on a micro-electrode array.

The term "protein chip" refers to an array of capture reagents capable of binding protein markers. Typically, the capture reagent is a polyclonal or monoclonal antibody that binds to a specific protein. In other words, any protein, polypeptide, nucleic acid, or other molecule or surface that can specifically bind to a protein can be used in a protein array. These arrays typically include hundreds or thousands of different capture reagents located at addressable regions. When the markers are labeled with detectable molecules, the binding of the capture reagent to the markers on the protein array is typically quantified.

The protein chip is provided with protein detection points which can be randomly distributed, or distributed in different detection areas of the chip, or relatively intensively distributed in one or more specific detection areas of the chip.

As used herein, the term "spots" refers to spots on a protein chip for detecting a protein, such as SERINC4 protein, typically by spotting a monoclonal antibody against SERINC4 protein on the chip substrate.

The protein chip suitable for use in the present invention is not particularly limited, and blank protein chips of various structures known in the art may be used. Typically, these protein chip carriers include: immunomicrospheres, glass sheets, plastic sheets, Nitrocellulose (NC) membranes, PVDF membranes, and the like, among which immunomicrospheres and various substrates are particularly preferable. The method comprises the steps of sequentially fixing polypeptide, protein or antibody on various carriers by adopting an in-situ synthesis method, a mechanical spotting method or a covalent bonding method to form a chip for detection, enabling the fluorescence-labeled antibody or other components to interact with the chip, washing out components which are not complementarily combined with the protein on the chip by rinsing, and measuring the fluorescence intensity of each point on the chip or other carriers and the marker intensity by utilizing a scanner such as fluorescence or a laser confocal scanning technology to analyze the content of each protein, thereby achieving the purpose of measuring various proteins.

Antibodies

In the present invention, the term "antibody" refers to a natural or synthetic antibody that selectively binds to an antigen of interest. The term includes polyclonal and monoclonal antibodies. In addition to intact immunoglobulin molecules, fragments or polymers of those immunoglobulin molecules, as well as human or humanized forms of immunoglobulin molecules that selectively bind an antigen of interest, are also included within the scope of the term "antibody" so long as they exhibit the desired biological activity. "monoclonal antibody" refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical and/or bind the same epitope, with such variants generally being present in minor amounts, except for possible variants that may arise during the course of production of the monoclonal antibody. Such monoclonal antibodies typically include an antibody comprising a polypeptide sequence that binds to a target, wherein the target-binding polypeptide sequence is obtained by a process that includes selecting a single target-binding polypeptide sequence from a plurality of polypeptide sequences.

Monoclonal antibodies also include "chimeric" antibodies in which a portion of the heavy and/or light chain is identical to or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain is identical to or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity.

Polyclonal antibodies include antibodies raised against SERINC4 protein immunized against an animal (e.g., a mouse) producing human antibodies. When a chimeric antibody or a humanized antibody is prepared, amino acids in the variable region (e.g., FR) and/or constant region may be replaced with other amino acids, or the like.

The term "sample" as used herein includes any cellular, tissue or bodily fluid sample, including, but not limited to, a tissue or a source of a cellular sample may be derived from solid tissue of a fresh, frozen and/or preserved organ or tissue sample, or biopsy or aspirate, blood or any blood component; body fluids such as cerebrospinal fluid, amniotic fluid, peritoneal fluid or interstitial fluid. The tissue sample may be primary or in vitro cultured cells or cell lines. Alternatively, the tissue or cell sample is taken from a diseased tissue/organ. Tissue samples may contain compounds that the tissue naturally mixes with, such as preservatives, anticoagulants, buffers, fixatives, nutrients, antibiotics, or similar compounds.

The present invention will be described in further detail with reference to the accompanying drawings and examples. The following examples are intended to illustrate the invention only and are not intended to limit the scope of the invention. Experimental procedures without specific conditions noted in the examples, generally following conventional conditions, such as Sambrook et al, molecular cloning: the conditions described in the laboratory Manual (New York: Cold Spring harbor laboratory Press,1989), or according to the manufacturer's recommendations.

Example 1 screening for differentially expressed genes associated with survival in endometrial cancer patients

1. Data set

Sequencing data of 333 example Endometrial cancer patients published in Nature in the TCGA database were used as an analytical dataset (Urerine Corpus Endometric Carcinoma (TCGA, Nature 2013)).

2. Analytical method

There were 52 cases of advanced (stageIII, IV) endometrial adenocarcinoma with mRNA expression level data in the TCGA database, and the grouping strategy considered high survival cases for more than 5 years, 11 cases, and low survival cases for less than 2 years and patients who died, 4 cases. Differentially expressed genes present between endometrial adenocarcinoma long-term and short-term patients were obtained using the relevant R language package (edgeR) (absolute Pearson correlation coefficient to overall patient survival > 0.3). In 273 cases, the first 20 differentially expressed genes were analyzed for patient survival and ROC curve in the endometrial cancer transcriptome sequencing dataset, based on the ROC curve model, i.e., the area under the curve (AUC value) is greater than or equal to 0.7, which is considered as a model for predicting the length of patient survival.

3. Analysis results

By using mapping software, the survival time (OS) of the patient obtained by follow-up visits of a group with low SERINC4 gene expression level and a group with high SERINC4 gene expression level is used as an abscissa, the survival rate is used as an ordinate to map, the result of the patient survival analysis is shown in figure 1, the survival time of the endometrial cancer patient with high SERINC4 gene expression level is long, the survival time of the endometrial cancer patient with low SERINC4 gene expression level is short, the difference has statistical significance (P <0.05), the prognosis of the patient with high SERINC4 gene expression level is obviously better than that of the patient with low SERINC4 gene expression level, namely, the higher SERINC4 gene expression level is closely related to the better prognosis of the patient. Results of ROC curve analysis shown in FIG. 2 and Table 1, the AUC value of the SERINC4 gene for predicting the survival time of endometrial cancer patients is 0.787, which indicates that the SERINC4 gene can be used as a molecular marker for predicting the survival time of endometrial cancer patients.

TABLE 1ROC Curve analysis results

a. Under the assumption of nonparametric formula; b. setting a null value: true area 0.5

The above description of the embodiments is only intended to illustrate the method of the invention and its core idea. It should be noted that, for those skilled in the art, without departing from the principle of the present invention, several improvements and modifications can be made to the present invention, and these improvements and modifications will also fall into the protection scope of the claims of the present invention.

Claims

Use of the SERINC4 gene for the preparation of a product for predicting the prognosis of a patient with endometrial cancer.
2. The use of claim 1, wherein the product is for predicting prognosis of an endometrial cancer patient by determining the level of SERINC4 expression in the sample.
3. The use of claim 2, wherein SERINC4 is highly expressed in endometrial cancer patients with a good prognosis and is lowly expressed in endometrial cancer patients with a poor prognosis.
4. The use according to any one of claims 1 to 3, wherein the product comprises a product for detecting changes in SERINC4 gene expression by sequencing techniques, nucleic acid hybridization techniques, nucleic acid amplification techniques or immunoassays.
5. The use according to claim 4, wherein the nucleic acid amplification technique is selected from the group consisting of polymerase chain reaction, reverse transcription polymerase chain reaction, transcription mediated amplification, ligase chain reaction, strand displacement amplification and nucleic acid sequence based amplification.
6. The use of claim 1, wherein the product comprises a chip, a kit or a formulation.
7. The use of claim 6, wherein said chip, kit or formulation comprises specific primers, probes for the SERINC4 gene or antibodies or ligands for the protein encoded by SERINC 4.
8. Use according to claim 7, wherein said ligand comprises an interacting molecule of a protein encoded by SERINC 4.
9. The use of claim 2, wherein the sample source is tissue.