TTV miRNA sequences as an early marker for the future development of cancer and as a target for cancer treatment and prevention

Described are TTV miRNAs and probes and primers comprising part of said TTV miRNA polynucleic acid. The use of said compounds for diagnosis of cancer or predisposition of cancer is also described.

REFERENCE TO SEQUENCE LISTING, TABLE OR COMPUTER PROGRAM

The Sequence Listing is concurrently submitted herewith with the specification as an ASCII formatted text file via EFS-Web with a file name of Sequence Listing.txt with a creation date of Dec. 9, 2015, and a size of 32.9 kilobytes. The Sequence Listing filed via EFS-Web is part of the specification and is hereby incorporated in its entirety by reference herein.

TECHNICAL FIELD

The present invention relates to novel TTV miRNA as well as probes and primers comprising part of said novel TTV miRNA polynucleic acid. Finally, the present invention relates to the use of said compounds as an early marker for the future development of cancer.

BACKGROUND

Torque Teno Virus (TTV) is a viral species belonging to the family Anelloviridae, genusAlphatorquevirus. Viruses classified into this specie present a circular, single stranded DNA (ssDNA) genome of 3.7-3.8 Kb of length, and are non-enveloped [2,3]. They were first discovered in 1997 in a patient presenting post-transfusion non A to G hepatitis [1]. A high divergence in the nucleotide sequence among different TTV strains is observed, reaching to more than 70% in some cases. Although the genomic organization is also variable, all of them contain a non-coding region, spanning 1.2 Kb [22]. The non-coding region has been demonstrated to harbour a promoter in its 3′ end [4] and a highly conserved region of 70 bp within this 3′ end is hypothesized to be the origin of replication of the viruses. It is estimated that more than 90% of humans are infected with one or more TTV strains. The number of different isolates (more than 200), their ubiquity and the lack of reliable and simple techniques to differentiate between them, have made it difficult to obtain enough epidemiological evidence in support of a causative relationship between TTV infection and a specific disease [23-28]. TTV viruses are known to infect several human tissues [21]. Limited data are available on the replication cycle, and even less on the function of the proteins encoded by these viruses.

MicroRNAs (miRNA) are small RNA molecules ranging between 19 and 29 nt and usually of 22 nt in length. They mediate post-transcriptional gene silencing (PTGS) by inducing cleavage, destabilization or translational inhibition of a target messenger RNA (mRNA) [9,10,11,12]. They do that by guiding the RISC complex to a concrete mRNA, interacting with it by base pairing. This interaction is thought to be mediated mainly by a perfect match between the target mRNA 3′ untranslated region (UTR) and the miRNA “seed” (nucleotides from 2 to 7) [7,8,80], whereas a perfect match means that each of the “seed” nucleotides hybridizes by a Watson and Crick pairing with respective nucleotides of the target mRNA. In contrast, recent findings suggest that non-perfect matches (no Watson and Crick pairing or seeds containing one mismatch) in this region are more abundant than perfect matches [6]. The same study suggests that miRNA-mRNA pairings in coding sequences (CDS) are as abundant as those in 3″UTRs. Moreover, they demonstrate that some miRNAs tend to hybridize with mRNAs in a region totally different from the seed, and they are still able to exert PTGS. To increase even more the complexity of the miRNA-based gene expression regulation, in the last few years some examples of transcriptional gene silencing (TGS) and transcriptional gene activation (known as RNA activation (RNAa)) mediated by miRNA have appeared [29-33]. While the mechanisms mediating these two events are still poorly understood, it cannot be discarded that TGS and RNAa are general features of some miRNA. The number of known endogenous human miRNAs has increased very fast in the last few years. The number of mature miRNA annotated in miRBase is 2042 [13-16]. In addition, a large number of virally encoded miRNA has also been shown to use the cellular miRNA silencing machinery. Since the discovery of the first human viral encoded miRNA [5] its number has increased to 157 [13-16]. The majority of these miRNA are encoded by DNA viruses, especially those belonging to Herpesviridae and Polyomaviridae families. Recently, a bovine oncogenic RNA virus (Bovine Leukemia Virus) was reported to encode 8 mature miRNA, demonstrating that this type of viruses also can express them. Despite the large number of viral miRNA discovered, the function of most of them still remains elusive, although in the last years some reports have shed light over this issue. For instance, miRNAs encoded by both Polyoma and Herpes viruses have been demonstrated to help these viruses to escape the host immune response, by regulating viral [17] or host [18,19] protein expression. Another important finding was made some months ago when it was demonstrated that Epstein-Barr virus-encoded miRNAs are sufficient to transform cells by themselves [20], suggesting that viral miRNAs could be able to mediate an oncogenic process under the adequate conditions. Very recently, it was shown that TTV encode for miRNA's, and the role of one of this miRNA's in interferon signalling inhibition was demonstrated [78]

APC (Adenomatous Polyposis coli) is a very important tumour suppressor, especially in the context of colorectal cancer. Virtually all colorectal cancers carry inactivating APC mutations or epigenetic changes inactivating the transcription of this gene. Its tumour suppressor activity is thought to be mediated by its function in inhibition of wnt signalling, although it has also been implicated in migration and correct mitotic spindle assembly.

SUMMARY OF THE INVENTION

The technical problem underlying the present invention is to provide means (or markers) for diagnosis of cancer or diagnosis of a disposition to said disease. Another technical problem is to provide means for preventing cancer development and cancer recurrence by inhibiting a specific target.

The solution to said technical problem is achieved by providing the embodiments characterized in the claims.

Few aspects are known concerning the interaction between TTVs and their host. In the studies resulting in the present invention it was elucidated that TTV encode miRNAs, as well as their significance for the TTV infection and pathogenicity, mainly focusing on their possible role in cancer. Pre-miRNAs expressed by TTV strains are provided. The miRNA are transcribed from the non-coding region of the virus, in both sense and antisense orientations. Some miRNAs encoded in both orientations can, directly or indirectly, downregulate the tumor suppressorAdenomatous Polyposis Coli(APC) at the mRNA level. Surprisingly, the inventors identified a link between TTV and tumour suppressor regulation and this finding suggests a role of TTV in cancer development. This work represents the first molecular link between TTV and cancer.

Material and Methods

(A) Cell Culture and Transfections

HEK293TT cells [76] cultured in Dulbeco's Eagle Modified Medium (DMEM Sigma) supplemented with 10% FBS, 1% Glutamax and 1% NGAA. Cells are transfected when 50% confluent, 24 h after seeding (7 million for T-75 flask and 800.000 per well for a 6 well plate). Transfections are performed using Lipofectamine and Plus reagent (Life Technologies, catalog n. 11514 and 18324) according to the manufacturer's instructions.

The TTV NCR is PCR amplified using suitable primers. For example, the TTV-HD14a NCR is PCR amplified using primers TT-ON9 5′ gattatggtacctttccaactacgactgggtgt (SEQ ID NO:83) and TT-ON10 5′ gattatggtacctctaccattcgtcaccgctgtt (SEQ ID NO:84) using pCDNA3.1(+)-TTV-HD14a as template (a plasmid containing full-length TTV-HD14a linearized and cloned into XbaI site). PCR product is run on a 1% agarose gel and DNA stained using ethidium bromide. Bands corresponding to the expected size (˜1200 bp) are cut and subsequently extracted from agarose using QIAEXII gel extraction kit (QIAGEN). 4 μg of pCDNA3.1(+) (Life technologies) are cut using KpnI and dephosphorylated using FastAP (Thermo scientific). PCR product is cut using the same procedure, but not dephosphorylated. Cut plasmid and PCR products are cleaned up by using QIAEXII gel extraction kit.

Ligation of the plasmid and the amplified fragment corresponding to the TTV NCR, for example TTV-HD14a NCR, is performed using T4DNA ligase (Thermo Scientific) Ligation product is transformed into NovaBlue Singles competent cells (Merck Millipore) according to the manufacturer instructions, and seeded in LB agar plates supplemented with ampicillin as selection marker. Plates are incubated 20 hours at 37° C. Single colonies are picked and seeded in LB medium supplemented with ampicillin. These cultures are incubated 20 hours. Plasmid is extracted using PureLink Quick Plasmid Miniprep Kit (Life technologies). 1 μg of each plasmid are double cut with SacI and NheI (Thermo Scientific). Cut products are run in 1% agarose gels. The restriction strategy allows us to distinguish between inserts clones in the sense and antisense orientation. Two positive plasmids, one containing the sense and the other one the antisense insert, are chosen and sent for sequencing. After confirming the sequence, plasmids are prepared for transfection by using Plasmid Max Kit (Qiagen).

(C) RNA Extraction and DNAse Treatment

Cells are harvested 48-72 h post-transfection. Cells are homogenized using QiaShreder (Qiagen) according to manufacturer instructions. Lysates are then subjected to RNA extraction using miRNAeasy mini kit or RNAeasy mini kit (Qiagen) depending on the purpose of the RNA (for miRNA Northern blot or for RT-qPCR), according to manufacturer instructions.

After elution, RNA samples are treated with RQ1 Dnase (Promega) according to manufacturer instructions, with the addition of RNasin (Promega). Phenol-Chloroform extraction followed by ethanol precipitation is performed, and the resulting pellet is resuspended in DEPC water. RNA quality and concentration are tested using NanoDrop 2000c (Thermo Scientific).

Custom DNA oligos are ordered to Sigma (Table 4). Probes are 3′ biotin labeled. 10 pmoles of each probe are incubated with 4U of Terminal Deoxynucleotidyl transferase (TdT) and 2,5 nanomoles of Biotin-11-dUTP (Thermo Scientific) in 1×TdT buffer, overnight. Probes are subjected to Isoamyl alcohol-Chloroform extraction and the total volume is used for subsequent hybridization.

30-50 μg of total RNA per sample are separated by electrophoresis using 15% polyacrylamide (29:1) gels cast in 7M urea and buffered with 1×TBE using a MiniProtean cell (Bio-Rad). The electrophoresis buffer is 0.5×TBE. Gels are stained with EtBr.

For blotting, gels are placed over a sheet of nylon hybridization membrane (Hybond-NX®, Amersham/Pharmacia) pre-wetted in 0.5×TBE. This is then sandwiched between pieces of 3 MM Whatman filter paper (one layer under the membrane and three over the gel), also pre-wetted in 0.5×TBE and placed in a Trans-Blot SD semidry transfer cell (Bio-Rad). Excess liquid and air bubbles are squeezed from the sandwich by rolling the surface with a pipette. Electrophoretic transfer of RNA from the gel to the membrane is carried out at 400 W for 60-90″ min. After transfer, RNA is crosslinked to the membrane by ultraviolet exposure using Stratalinker (Stratagene).

Membranes are cut as needed and hybridized with the appropriated biotin labeled probe (Table 4) o/n in Ultrahyb Oligo buffer (Life technologies) at 42° C. After hybridization, 4 washes are performed; the first one with 2×SSC 30 min at 42° C., the second one with 2×SSC 0.5% SDS 30 min at 42° C. and the last two with 2×SSC 0.5% SDS 30 min at 55° C. Hybridization signals are detected using BrightStar BioDetect Kit (Life technologies) according to the manufacturer instructions. Film used: (Fiji).

1 μg of RNA is used to make cDNA with superscript III and RnaseOUT (Life technologies) according to manufacturer instructions. cDNA is diluted 1:10. qPCR is performed using Taqman fast master mix and Taqman expression assays, in a qPCR machine StepOne plus (Applied Biosystems).

(G) Pre-miRNA Prediction and Mature miRNA Prediction

V-mir is set to default configuration, changing the sequence type to circular. CID-miRNA is run on the web-based tool, using the default run configuration forHomo sapiens. Mature Bayes is run on the web-based tool.

DIANA microT 3.0 is run on the web-based tool (no options are given for this program). RNA hybrid is run using constraint nucleotide configuration, from nucleotide 2 to 8 of the miRNA. G:U pairs are allowed.

Predicted pre-miRNA from TTV-HD14a using CID-miRNA and V-mir that match three criteria: being predicted by both programs, score over 150 for V-mir and located in the non-coding region of the virus.

TABLE 2BTTV mature miRNA present in the TCGA small RNA sequencingdatasets of colon adenocarcinoma with similarity in thenucleotides from 1 to 7 (comprising the seed (nt 2 to 7)) toTTV-HD14a-mir-2-3p . The TTV miRNA are shown in the context ofthe pre-miRNA sequence. The identical conserved nucleotides from1 to 7 (comprising the seed (nt 2 to 7)) are boxed. Positionscontaining identical nucleotides are marked by a (*) andpositions containing nucleotides originated by a transition aremarked by (°). They are classified in groups according to theirpre-miRNA sequence. In all cases, the 3p mature miRNA isunderlined. The seed is written in italicized letters. The box 3contains the consensus sequence for the nucleotides from 1 to 7.A — adenine, T — thymine, C — cytosine, G — guanine, Y — C or T.Seed of a miRNA: nucleotides 2 to 7 of the mature form of the miRNA [80]TTV pre-miRNABoxrelated toTTV Sequence1TTV-HD14a2TTV-HD18a3Consensus sequence for the nucleotides from 1 to 7 (comprising the seed (nt 2-7))Common to all the TTV

TABLE 3Genes predicted to be down-regulated by the TTV-HD14a and atleast two other TTV strains miRNA. Notice that some strainshave more than one putative miRNA that is predicted to down-regulate some of the genes.Number of TTVNumber of TTVisolatesmiRNANCBIpredicted topredicted toaccessiondown-regulatedown-regulateGenenumberititAPC2NM_005883.24 (Out of 9)8SOX4NM_003107.23 (Out of 9)3TNRC6BNM_001162501.14 (Out of 9)7BNC2NM_017637.53 (Out of 9)4ONECUT2NM_004852.25 (Out of 9)7BCL11aNM_022893.33 (Out of 9)3SLIT1NM_003061.23 (Out of 9)3MLLNM_153827.45 (Out of 9)8MACF1NM_012090.58 (Out of 9)12DSTNM_001144769.29 (Out of 9)13CREB5NM_182898.23 (Out of 9)3CHD5NM_015557.23 (Out of 9)4SSRP1NM_003146.23 (Out of 9)3MINK1NM_001197104.15 (Out of 9)5

miRNA Prediction

To address the question about the possible function of the non-coding region (NCR) of TTVs beyond its promoter activity, the inventors had the idea that it also generates non-coding RNAs, such as miRNAs. Therefore, they used available miRNA prediction algorithms, with which they identified several candidate pre-miRNAs in the NCR of some TTVs. The inventors chose to use two of such algorithms: CID-miRNA [34] and Vmir [35-36]. The first one was chosen because of its high specificity and the second one because of its higher sensitivity. To consider a pre-miRNA structure as a candidate, they used the criterion that it should be predicted by both programs, with a cut-off value over 125 for the V-mir program and that it had to be located in the NCR of the virus. After filtering, only 4 pre-miRNA candidates (Table 1 andFIG. 1B), two in sense orientation and two in antisense orientation, were considered as putative pre-miRNA and were further evaluated.

In order to check the conservation of the pre-miRNA sequences among different TTV isolates, the inventors performed the same prediction in seven different strains: TTV-HD16a (FR751476, version FR751476.1 GI:339511352, 7 Jul. 2011), TTV-C3T0F (AB064597, version AB064597.1 GI:17827196, 25 Jun. 2008), TTV-HD23a (FR751500, version FR751500.1 GI:339511376, 7 Jul. 2011), TTV-YonKc197 (AB038624, version AB038624.1 GI:7415899, 20 Sep. 2000), TTV-SANBAN (AB025946, version AB025946.2 GI:5572683, 3 Nov. 2009), TTV-Sle2057 (AM712030, version AM712030.1 GI:156104055, 19 Feb. 2008) and TTV-tth8 (AJ620231, version AJ620231.1 GI:49203022, 3 Feb. 2009(GenBank accession numbers and versions in brackets) They then grouped the resulting pre-miRNA in different classes (Table 2A), according to their sequence similarity. As can be observed, the conservation of the sequences is rather poor, being strange the total identity between two pre-miRNA from different strains.

Mature- and pre-miRNAs similar to TTV-HD14a pre-miRNA that contain a mature miRNA with an equal or similar seed to that of TTV-HD14a-3p miRNA which also includes TTV-HD18a-like pre-miRNAs were found within patients by screening TGCA datasets. These miRNAs are shown in Table 2B. The similarity within the nucleotides 1 to 8 of these miRNAs with that of TTV-HD14a miRNAs indicates, that these miRNAs are downregulating APC as well.

TTV-HD14a can Transcribe Four Precursor miRNA Encoded in its NCR

To address the question whether the predicted pre-miRNAs could be processed, the NCR of TTV-HD14a was cloned downstream of the CMV promoter, in sense or antisense orientation, using the plasmid pCDNA3.1(+)-zeo as scaffold (FIG. 2A). The inventors then transfected HEK293TT cells with these plasmids and performed Northern Blot hybridization with specific probes against the 3′ or 5′arm of each putative pre-miRNA (Table 4) (FIG. 2B-E). The inventors could clearly detect bands that match the expected size for a pre-miRNA with the probes directed against the 3′ and 5′arm of TTV-HD14a-mir-2 and TTV-HD14a-ASmir-2. Moreover, the inventors were able to detect a transcript matching the expected size for a mature miRNA within the 5′arm of TTV-HD14a-mir-2. On the other hand, the inventors were able to detect transcripts matching the expected sizes with the probes directed against the 3′arm only of TTV-HD14a-mir-1 and TTV-HD14a-ASmir-1.

These results demonstrate that TTV-HD14a encodes for several precursor miRNA in both orientations; and at least one of them can be processed into a mature miRNA.

Target Prediction

It is well known that the major feature of miRNA is downregulating gene expression in a post-transcriptional manner. It is also known that this effect is caused by the mature form of the miRNAs, and not by their precursors. Although the inventors were not able to see any mature miRNA for three of the pre-miRNA, they think that low expression levels of these miRNAs rather than their absence might be the reason of this. In any case, it is necessary to identify the sequence of the mature miRNA to perform accurate predictions, and this is hard to determine by experimental methods different from miRNA-seq. To overcome this problem, the inventors decided to use an in-silico mature miRNA predictor, Mature Bayes [37]. This program predicts the mature miRNA from a pre-miRNA sequence. After doing that with all the predicted miRNA precursors (Table 2), they used DIANA-microT-3.0 [38-39] to predict possible targets. They reasoned that, despite the variability in their sequences, the putative TTV mature miRNAs should have some targets in common. So, after performing the predictions, the inventors compared the results among the different TTV strains and considered as good candidates the targets that were predicted for some miRNAs belonging to TTV-HD14a and, at least, two more TTV strains. Candidate targets are listed in Table 3.

In addition to this approach, the inventors performed a direct comparison of the predicted mature miRNA from TTV-HD14a with the CDS, 3′UTR and promoter regions of several tumor suppressor genes using RNA Hybrid [40]. This program allows to directly detecting the complementary sequence of a given miRNA within a gene, independently of the conservation or localization of complementary sequence. This is useful, as most of the other prediction programs do not take into account the CDS or promoter region of the genes, while it has been demonstrated that a seed pairing with the first one can mediate PTGS and with the second one can cause TGS or RNAa [11,12,29-33]. The inventors found seed complementarity between the APC gene and TTV-HD14a-mir-2-5p in three different points within the APC mRNA sequence, two in the CDS and one in the 3″UTR (FIG. 3A—1,2and3). In addition, a possible interaction site between TTV-HD14a-mir-2-3p and APC mRNA was present in the CDS (FIG. 3A-4). The inventors also found complementarity between the TTV-HD14a-ASmir-2-3p and three of the four promoters listed for APC in the Eukaryotic Promoter Database New Human (EPD New Human) [59] (accession names APC_1, APC_2 APC_3 and APC_4) (FIG. 3B-D).

APC is Down-Regulated after Transfection with pCDNA3.1(+)-TTVHD14a-NCR-Sense

To check the possible APC down-regulation mediated by the TTV-HD14a miRNA the inventors transiently transfected HEK293TT cells with the constructs encoding the miRNA, with the full length TTV-HD14a virus or mock transfected them, followed by RT-qPCR (FIG. 3E+F). APC down-regulation by the miRNA itself as well as by the full length genome (coding for the miRNA) is significant in comparison to the mock transfected.

After transfection with pCDNA3.1(+)-TTV-HD14a-NCZ-Sense, which is intended to produce 4 mature miRNAs (TTV-HD14a-mir-1-5p, TTV-HD14a-mir-1-3p, TTV-HD14a-mir-2-5p and TTV-HD14a-mir-2-3p), the inventors can observe a statistically significant increase of GAPDH transcript:

GAPDH (Glyceraldehyde-3-phosphate-dehydrogenase) is a gene usually used as internal control (housekeeping gene), at the mRNA and protein levels, because its levels of expression are very constant among very different conditions.

GAPDH is up-regulated in the majority of cancers and under hypoxic conditions [72, 73, 74]. The inventors suggest that the TTV miRNA dependent up-regulation of GAPDH is mediated indirectly by APC down-regulation.

Microarray Analysis Reveals the Landscape of TTV-HD14a miRNA's Induced Alterations

72 h after transfection of cells with the two different constructs, the full-length TTV HD14a genome or an empty plasmid RNA was isolated and microarray analysis was performed. Table 5 includes all the genes that were consistently deregulated between the transfection with the constructs and with the full-length virus.

With these genes also Gene ontology analyses were performed. The results are shown in Table 6. As can be seen, TTV miRNA might be deregulating several pathways important for cancer progression.

Screening the TCGA for TTV miRNA Associated with Cancer

The TCGA (The Cancer Genome Atlas) is an initiative of the NIH. The data stored within this repository consist of sequencing datasets from cancer and normal tissue extracted from patients. In this regard, the data extracted by this analysis can be considered as “in vivo”, since it comes directly from tumors of patients. In an effort to establish a relationship between TTV miRNA and cancer, the small-RNA sequencing data for colon adenocarcinoma, lung adenocarcinoma, breast carcinoma and hepatocellular carcinoma from the TCGA initiative was mapped against all the full-length TTV genomes included in the NCBI database plus several newly identified TTV from the inventors's laboratory. To exclude artifacts, miRNA taken into consideration complied to the following: mapping with 2 mismatches or less to TTV genomes and mapping in a region where the RNA is predicted to acquire the characteristic hairpin structure of a pre-miRNA (Table 7).

TABLE 7Small RNA sequencing datasets from patients with different malignancies were screened forthe presence of TTV miRNA. TTV positive patients were considered when having at leastone read mapping to a TTV miRNA. Patients positive for TTV encoding a mature miRNApresenting the “consensus sequence” where considered when having at least one readmapping to a TTV strain that encodes for a mature miRNA that contains the “consensussequence”. The “consensus sequence“, the TTV strains found in the TCGA containing theconsensus sequence and the mature miRNA form these TTV strains are listed in Table 2B.+Patients positive forTotalTTV encoding anumber of% of TTVmature miRNApatientsTTV positivepositivepresenting theCancer typescreenedpatientspatients“consensus sequence”%Colon carcinoma4217618,052256535312,5890736Hepatocellular1471912,9251700796,12244898carcinomaLung2132511,737089294,22535211adenocarcinoma(Ongoing)Breast141117,8014184410,70921986carcinoma(ongoing)

TTV-HD14a-2-3p analogous miRNA (meaning, with 80% homology or more in the nucleotides from 1 to 7 of the miRNA, comprising the seed) (Table 2B) were found at higher frequency in colon cancer patients than in the other three type of cancer being screened so far.

The slight differences in the seed of the miRNA shown in Table 2B in respect to TTV-HD14a-mir-2-3p do not alter the predicted binding sites in APC mRNA. Thus, the miRNA shown in Table 2Bare also able to down-regulate APC (Table 8).

It is shown how, despite the single nucleotide polymorphisms (SNP) found in the seed of diverse TTV miRNA's respect to the TTV-HD14a-mir-2-3p seed, the predicted interaction site with APC mRNA shown inFIG. 3(A.4) would be conserved. (B) Here the inventors show how the most conserved seed motif (AUCCUC) has three additional possible interaction sites within APC mRNA in addition to the previously described for TTV-HD14a-mir-2-3p.

Positions are shown in relation to the nucleotide number of APC transcript variant 2 mRNA (NCBI accession number: NM 001127510.2, SEQ ID NO:82)

Seed interaction sites are shown in black bold letters. Sequence corresponding to APC mRNA are shown in italicized letters.

This supports a causal role for this type of TTV miRNA of Table 2B in this disease or, at least, an association between them.

A significant increase in TTV load in cancer patients compared to normal controls has been demonstrated [44]. In the case of colon cancer, this increase in viral load would presumably be represented mainly by the TTV strains encoding for miRNA analogous to that of TTV-HD14a.

Wnt Activation by a TTV miRNA

APC exerts its tumor suppressor activity by downregulating canonical Wnt pathway, although other putative roles for this protein have been suggested. This effect is mediated by its participation in the “destruction complex”. The destruction complex is formed by APC, AXIN, and GSK3-beta, among others. This complex phosphorylates beta-catenin, allowing its ubiquitination and degradation by the proteasome. In the absence of any of the proteins of the destruction complex, its function is impaired. The final outcome is the cytoplasmic accumulation of beta-catenin, that can be then translocated into the nucleus, where it activates transcription of its target genes, together with the transcription factor TCF4 or LEF1. It is well documented that this pathway is upregulated in several malignancies, as well as in other diseases. Consequently, we thought that the APC down-regulation could lead to an activation of Wnt pathway. To check this, a gene reporter approach was used. HEK293TT cells were transfected with the plasmids encoding for TTV-HD14a miRNA, with the TTV-HD14a full genome, or mock transfected, together with a plasmid encoding forFirefly luciferaseunder the control of a minimum promoter and seven binding sites for the TCF4/beta catenin complex (TOPFLASH plasmid). Additionally,Renilla Luciferaseunder the control of CMV promoter was used for normalization purposes. An upregulation of wnt pathway resulted in cells with the plasmid encoding for the sense-miRNA or with the TTV-HD14a virus in comparison to mock transfected cells (FIG. 5).

CONCLUSIONS

The above results highlight the importance of the experimental findings as diagnostic method for TTV infection and identifies TTV miRNA as promising target for cancer prevention, treatment or recurrence.

It is known that TTV replicate in several tissues [21], but they only replicate in peripheral blood mononuclear cells when these cells are activated [42]. It was recently demonstrated that TTV replicate more efficiently when they are co-infecting cells with Epstein Barr virus [41].

Very few things are known about the molecular mechanisms mediating infection, replication and virus-host interaction of the TTVs. Here, the inventors provide evidence which supports that several TTVs encode miRNA and that some of them have a biologically relevant role, especially in relation to cancer development.

It has been shown in the present invention that the encoded miRNA of TTV-HD14a and Table 2B can down-regulate APC, an important tumor suppressor. Hence, being infected with any of the TTV's encoding for the miRNA's included in the present invention could represent a risk factor for the development of colon cancer, as well as many other cancer types.

To support these findings, the inventors detected TTV miRNA's that down-regulate APC in a higher frequency in colon adenocarcinoma patients in comparison to other three types of cancer (lung adenocarcinoma, hepatocellular carcinoma and breast invasive carcinoma). Consequently, TTV miRNA's presented here represent a target for the prevention of colon cancer, as well as a putative biomarker for the early detection of a subset of these cancers.

REFERENCES