Patent Grant
10457938
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.
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.
Torque Teno Virus (TTV) is a viral species belonging to the family Anelloviridae, genus Alphatorquevirus. 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.
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 suppressor Adenomatous 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.
(A) TTV-HD14a. The numbers over the lines indicate the nucleotide number. NCR—Non-coding region. (B) Details of the non-coding region. The numbers indicate the nucleotide number. The hairpins over the line indicate the pre-miRNA encoded in sense orientation. The hairpins under the line indicate the pre-miRNA encoded in antisense orientation. The names over and under the hairpins are the names given to the pre-miRNA.
(A) Schematic representation of the plasmids containing the CMV promoter and the non coding region (NCR) in sense (+) or antisense (−) orientation. The constructs are named pCDNA3.1(+)-TTV-HD14a-NCR-Sense and pCDNA3.1(+)-TTV-HD14a-NCR-AntiSense, respectively. The numbers over and under the lines indicate the nucleotide number. The hairpins and the vertical lines indicate the pre-miRNA in sense or antisense orientation. The names of the pre-miRNA are written below the lines.
(B-E) Northern blots showing the results with the indicated probes and transfections (Sense—HEK293TT cells transfected with pCDNA3.1(+)-TTV-HD14a-NCR-Sense. Anti-sense—HEK293TT cells transfected with pCDNA3.1(+)-TTV-HD14a-NCR-AntiSense. Mock—HEK293TT cells transfected with pCDNA3.1(+)). Probe sequences are listed in Table 4.
(A) Complementarity between TTV-HD14a-mir-2, p (1 (SEQ ID NO:77), 2 (SEQ ID NO:82) and 3 (SEQ ID NO:84)) TTV-HD14a-mir-2-3p(4 (SEQ ID NO:86)) with respective APC mRNA (SEQ ID NOs: 76,81, 83 and 85). Positions relative to APC transcript variant 2 (NCBI accession number: NM_001127510.2; SEQ ID NO:82).
(B, C and D) Complementarity between TTV-HD14a-ASmir-2-3p (B1: (SEQ ID NO:88, B2: (SEQ ID NO:90), C: (SEQ ID NO: 92), D: (SEQ ID NO: 94) and respectively APC promoters 1 (B1: (SEQ ID NO:87), B2 (SEQ ID NO:89), 2 (C: (SEQ ID NO: 91) and 3 (D: (SEQ ID NO: 93), respectively, as stored in EPDNew Human. The shown positions relate to the transcription start site (TSS) in reference to EPD New Human (EPDNew Human names: APC_1, APC_2 and APC_3).
(E) Relative expression levels of APC as measured by qPCR (Mean for Sense=0.747 and for AntiSense=0.650). ΔCt was calculated respect to HPRT. ΔΔCt was calculated respect to mock transfected cells. Differential values were normalized to 1. Sense—Relative values for HER 293TT cells transfected with pCDNA3.1(+)-TTVHD14a-NCR-Sense. Antisense—Relative values for HEK293TT cells transfected with pCDNA3.1(+)-TTVHD14a-NCR-AntiSense. Mock—Relative values for HEK293TT cells transfected with pCDNA3.1(+). TTV-HD14a—Relative values for cells transfected with the full-length TV-HD14a virus. +−SD; N=6. Statistical significance calculated using unpaired two-tailed Student T-Test.
HEK293TT were transfected in a 24 well format with 300 ng of TTV-HD14a virus or pCDNA-3.1(−)-TTV-HD14a-NCR(2820-3516) Sense (referred in the graphic as “Sense”) or pCDNA-3.1(−)-TTV-HD14a-NCR(3516-2820)-AntiSense (referred in the graphic as “Antisense”) or pCDNA3.1(−) (referred in the graphic as “Vector”) or Silencer siAPC (Life technologies) plus 60 ng of TOPFLASH vector (provided by M. Boutros lab) and 5 ng of CMV-renilla. Luciferase activity was measured 72 h after transfection. (A) Firefly luciferase units normalized to Renilla luciferase (B) Fold change respect to vector.
Accordingly, the present invention relates to a TTV polynucleic acid comprising: (a) a nucleotide sequence depicted in Table 1, 2a or 2b; (b) a nucleotide sequence having at least 60% identity to the nucleotide sequence of (a) and containing the nucleotide sequence CATCCYY (with Y=C or T); (c) a fragment of the nucleotide sequence of (a) or (b) and containing the nucleotide sequence CATCCYY (with Y=C or T); or (d) a nucleotide sequence which is complementary to any of said nucleotide sequences.
A further embodiment of the present invention relates to a TTV polynucleic acid, wherein the TTV polynucleic acid is a mature TTV miRNA molecule consisting of 19 to 29 nt, preferably about 22 nt, and comprise the nucleotide sequence CATCCY (with Y=C or T) or CAUCCYY (with Y: C or U). In a preferred embodiment the mature TTV miRNA molecule according to the invention (a) is a nucleotide sequence underlined in Table 2a or 2b; (b) consists of a nucleotide sequence having at least 60%, preferably at least 80%, most preferably at least 90% identity to the nucleotide sequence of (a) underlined in Table 2A or 2B and comprises the nucleotide sequence CATCCYY (with Y=C or T) or CAUCCYY (with Y: C or U); (c) is a fragment of a nucleotide sequence of (a) underlined in Table 2A or 2B and comprises the nucleotide sequence CATCCYY (with Y=C or T) or CAUCCYY (with Y: C or U) or (d) is a nucleotide sequence being complementary to a nucleotide sequence of (a), (b) or (c). In the context of the present invention a “mature TTV miRNA” is a polynucleic acid of an miRNA derived from a TTV.
The term “polynucleic acid” refers to a single-stranded or double-stranded nucleic acid sequence. A polynucleic acid may consist of deoxyribonucleotides or ribonucleotides, nucleotide analogues or modified nucleotides or may have been adapted for diagnostic or therapeutic purposes. A polynucleic acid may also comprise a double stranded cDNA clone which can be used, for example, for cloning purposes. In the following statements and findings made on the DNA level apply to the RNA level accordingly and vice versa.
The TTV polynucleic acid and the mature TTV miRNA of the invention can be prepared according to well-known routine methods, for example, by (a) isolating the entire DNA or, preferably, RNA from a sample, (b) detecting the TTV sequence by hybridization or PCR and (c) cloning of the TTV sequence into a vector (d) by synthesis of the respective nucleotides of the miRNA sequence.
Also included within the present invention are sequence variants of the polynucleic acid and the mature TTV miRNA molecules of the invention containing either deletions and/or insertions of one or more nucleotides, especially insertions or deletions of one or more codons, mainly at the extremities of oligonucleotides (either 3′ or 5′) and which show at least 60%, 70%, 80%, 90%, 95% or 98% identity to said polynucleic acid sequence of the invention and contain the consensus sequence CATCCYY (with Y=C or T). Polynucleic acid sequences according to the present invention which are similar to the sequence as shown in Table 1, 2a or 2b can be characterized and isolated according to any of the techniques known in the art, such as amplification by means of sequence-specific primers, hybridization with sequence-specific probes under more or less stringent conditions, sequence determination of the genetic information of TTV etc. The variants and fragments of the TTV polynucleic acid sequences of the present invention are still able to interfere with or inhibit the expression of their target gene, for example APC.
In a particular preferred embodiment the TTV polynucleic acid sequence (if DNA) contains the consensus sequence CATCCYY (with Y=C or T), i.e. CATCCCC, CATCCCT, CATCCTC or CATCCTT. In another particular preferred embodiment the TTV polynucleic acid sequence (if RNA) contains the consensus sequence CAUCCYY (with Y=C or U), i.e. CAUCCCC, CAUCCCU, CAUCCUC or CAUCCUU. In this regard particular reference is made to Table 2b below.
In a particular preferred embodiment 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. In this regard particular reference is made to Table 8 below. Therefore, in a further embodiment the invention relates to variants of the polynucleic acid as described above which comprise the seed motif AUCCCUC and bind to at least one of the interaction sites within APC mRNA shown in Table 8 and, preferably, downregulate APC.
Also included in the present invention are analogous miRNAs in other human TT virus types and variants and in similarly structured single-stranded DNA viruses of the human or animal origin. Anelloviruses have been demonstrated in domestic animals in part with similar nucleotide sequences as human TT viruses [77].
Furthermore, the present invention relates to an oligonucleotide primer comprising part of the TTV polynucleic acid of the present invention, said primer being capable of acting as primer for specifically sequencing or specifically amplifying a certain TTV miRNA.
The term “primer” refers to a single stranded DNA oligonucleotide sequence capable of acting as a point of initiation for synthesis of a primer extension product which is complementary to the nucleic acid strand to be copied. The length and the sequence of the primer must be such that they allow to specifically prime the synthesis of the extension products. Preferably the primer is at least about 10, preferably at least 15 nucleotides. Specific length and sequence will depend on the complexity of the required DNA or RNA targets, as well as on the conditions of primer use such as temperature, ionic strength etc. The amplification primers do not have to match exactly with the corresponding template sequence to warrant proper amplification. The amplification method used can be either polymerase chain reaction (PCR), ligase chain reaction (LCR), nucleic acid sequence-based amplification (NASBA), transcription-based amplification system (TAS), strand displacement amplification (SDA) or amplification by means of Qß replicase or any other suitable method to amplify nucleic acid molecules using primer extension. During amplification or synthesis, the amplified products can be conveniently labelled either using labelled primers or by incorporating labelled nucleotides. Labels may be isotopic (32P, 35S, etc.) or non-isotopic (biotin, digoxigenin, etc.).
The present invention also relates to an oligonucleotide probe comprising part of the TTV polynucleic acid of the present invention, said probe being capable of acting as a hybridization probe for specific detection of a certain TTV miRNA in vitro and in vivo.
The term “probe” refers to single stranded sequence-specific oligonucleotides which have a sequence which is complementary to the target sequence of the TTV polynucleic acid to be detected. Preferably, these probes are about 5 to 50 nucleotides long, more preferably from about 10 to 25 nucleotides. The probe can be fixed to a solid support, i.e., any substrate to which an oligonucleotide probe can be coupled, provided that it retains its hybridization characteristics and provided that the background level of hybridization remains low. Usually the solid substrate will be a microtiter plate, a membrane (e.g. nylon or nitrocellulose) or a microsphere (bead). Prior to application to the membrane or fixation it may be convenient to modify the nucleic acid probe in order to facilitate fixation or improve the hybridization efficiency. Such modifications may encompass homopolymer tailing, coupling with different reactive groups such as aliphatic groups, NH, groups, SH groups, carboxylic groups, or coupling with biotin or haptens.
In an embodiment of the invention the probe is an anti-miR oligonucleotide. An anti-miR oligonucleotide is a single-stranded RNA complementary to the miRNA molecule according to the invention. It can be delivered in its RNA form or being expressed from a vector, using a polymerase III promoter. Such an anti-miR oligonucleotide can be used for inhibiting the miRNA of the present invention. Methods for inhibiting miRNA by anti-miRs are described by Stenvang et al. in [81], which publication is incorporated by reference.
A further embodiment of the invention are miRNA sponges. A miRNA sponge is a messenger RNA with several, preferably 6-8, perfect complementary binding sites to the polynucleotide acid, i.e. mature TTV miRNA, of the invention. The binding sites can also include mismatches in the nucleotides from 10 to 13 of the mature TTV miRNA, to avoid direct RNA slicing and degradation which makes them more effective.
A further embodiment of the invention are tough decoy inhibitors. A tough decoy inhibitor is a miRNA consisting of a hairpin comprising a large internal bulge exposing two of the miRNA interaction sites of APC shown in Table 8 with imperfect baise-pairing with the TTV miRNA of the invention. The design of such a tough decoy inhibitor and methods of suppressing miRNA by a tough decoy inhibitor are described in [82] and [83] which are incorporated by reference.
The anti-miR, miRNA spounge and tough decoy inhibitor according to the invention are inhibitors of the TTV polynucleic acid as described above, in a preferred embodiment of a mature TTV miRNA shown underlined in Table 2A and 2B, which prevent the interaction between the TTV polynucleic acid and APC such that APC is not downregulated.
The present invention also relates to a vector containing a TTV polynucleic acid, oligonucleotide primer, oligonucleotide probe, anti-miR, miRNA sponge or tough decoy inhibitor of the invention allowing, e.g., expression, mutagenesis or a modification of a sequence by recombination of DNA sequences. Preferably, the vectors are plasmids, cosmids, viruses, bacteriophages and other vectors usually used in the field of genetic engineering. Vectors suitable for use in the present invention include, but are not limited to the T7-based expression vector for expression in mammalian cells and baculovirus-derived vectors for expression in insect cells. Preferably, the polynucleic acid of the invention or part thereof is operatively linked to the regulatory elements in the recombinant vector of the invention that guarantee the transcription and synthesis of an mRNA in prokaryotic and/or eukaryotic cells that can be translated. The nucleotide sequence to be transcribed can be operably linked to a promoter like a T7, metallothionein I or polyhedrin promoter.
The present invention also relates to recombinant host cells transiently or stably containing the TTV polynucleic acid (or fragments thereof) or vectors of the invention. A host cell is understood to be an organism that is capable to take up in vitro recombinant DNA and, if the case may be, to synthesize the polypeptids encoded by the polynucleotides of the invention. Preferably, these cells are prokaryotic or eukaryotic cells, for example mammalian cells, bacterial cells, insect cells or yeast cells.
The present invention also relates to a diagnostic kit containing a TTV polynucleic acid, an oligonucleotide primer, an oligonucleotide probe, a polypeptide and/or an antibody of the present invention.
For hybridization based assays, according to the hybridization solution (SSC, SSPE, etc.), the probes should be stringently hybridized to the target (with or without prior amplification) at their appropriate temperature in order to attain sufficient specificity. However, by slightly modifying the polynucleotide, (DNA and/or RNA) probes, either by adding or deleting one or a few nucleotides at their extremities (either 3′ or 5′), or substituting some non-essential nucleotides (i.e. nucleotides not essential to discriminate between types) by others (including modified nucleotides or inosine) these probes or variants thereof can be caused to hybridize specifically at the same hybridization conditions (i.e. the same temperature and the same hybridization solution). Also changing the amount (concentration) of probe used may be beneficial to obtain more specific hybridization results.
Suitable assay methods for purposes of the present invention to detect hybrids formed between the oligonucleotide probes and a TTV polynucleic acid in a sample may comprise any of the assay formats known in the art, such as the conventional dot-blot format, sandwich hybridization or reverse hybridization. For example, the detection can be accomplished using a dot blot format, the unlabelled amplified sample being bound to a membrane, the membrane being incorporated with at least one labelled probe under suitable hybridization and wash conditions, and the presence of bound probe being monitored. An alternative and preferred method is a “reverse” dot-blot format, in which the amplified sequence contains a label. In this format, the unlabelled oligonucleotide probes are bound to a solid support and exposed to the labelled sample under appropriate stringent hybridization and subsequent washing conditions. It is to be understood that also any other assay method which relies on the formation of a hybrid between the nucleic acids of the sample and the oligonucleotide probes according to the present invention may be used.
The present invention also relates to the use of a TTV polynucleic acid, an oligonucleotide primer, or an oligonucleotide probe of the present invention as an early marker for the future development of cancer, preferably colorectal or colon cancer.
Accordingly, an embodiment of the present invention relates to a method of detecting or diagnosing of colon cancer, comprising the steps of:
(a) isolating miRNA from a patients sample;
(b) sequencing the miRNA isolated in step (a); and
(c) determining, if an miRNA selected from the miRNA shown in Table 2B is present in the sample, whereas the presence of an miRNA shown in Table 2B indicates colon cancer.
For determining miRNA labelled oligonucleotides may be used.
Optionally, the method may comprise a further step (d) of quantifying the miRNA level in sample to distinguish between patients with colon cancer from healthy controls.
Preferably, in step (a) the miRNA is isolated from plasma or serum and the miRNA is quantified by using TaqMan miRNA qRT-PCR-assays as described in [86] which is incorporated by reference.
Alternatively, the miRNA may be isolated directly from the tumor and a miRNA sequencing may be performed to detect the miRNA or sections of any kind (e.g. cryo-sections, sections from paraffin embedded tissue) may be made directly on the tumor and an hybridization for the miRNA as described above may be performed in-situ.
Finally, the present invention also relates to the use of a TTV polynucleic acid of the present invention as a lead component for the development of a medicament for prevention or treatment of cancer, preferably colorectal or colon cancer. These medicaments may be inhibitors of any interaction between miRNAs and tumour suppressor genes to avoid cancer development or recurrence and cancer treatment. Thus, the specific TT virus miRNA or of its derivatives or of related miRNAs are useful for diagnostic, prevention or therapeutic applications in the cancer field.
Such inhibitor of an interaction between miRNA and tumor suppressor genes, for example APC, can be an anti-miR, A miRNA sponge or a tough decoy inhibitor as described above.
The inhibitor can be delivered to the tumor site by using an adeno associated virus (AAV) in order to deliver the inhibitor to counter effect the TTV miRNA according to the invention. An AAV gene therapy suitable for delivering one of the above miRNA inhibitors to the tumor is described in [84] which is incorporated by reference.
A further example of a suitable method for delivering the above inhibitors against TTV miRNA to a tumor is known as low pH-induced transmembrane structure (pHILP) [85]. This phILP construct consists of a peptide that crosses the plasma membrane only under acidic conditions which are typical of the tumor microenvironment. A peptide nucleic acid of an TTV miRNA inhibitor can be attached to this pHILP in order to be delivered specifically to cells in the tumor microenvironment. Preferably, this peptide is an anti-miR, which will cause the inhibition of the TTV miRNA according to the invention. A suitable method for delivering a TTV miRNA inhibitor with a pHILP construct is described in [85] which is incorporated by reference.
A further embodiment of the invention is a method of delivering a lead component for the development of a medicament for prevention or treatment of cancer, preferably colorectal cancer comprising the step of administrating to a patient suffering from a cancer, in particular colorectal cancer (a) a pharmaceutical composition comprising an adeno-associated virus expressing an inhibitor of the miRNA of the invention selected from the group consisting of anti-miR, miRNA sponge and tough decoy inhibitor of a miRNA interacting with a tumor suppressor gene and a pharmaceutically acceptable carrier or (b) a pharmaceutical composition comprising an inhibitor of the miRNA of the invention attached to a pHILP construct and a pharmaceutically acceptable carrier.
A further embodiment of the invention is (a) an adeno-associated virus for the use of delivering an inhibitor of TTV miRNA to tumor cells or (b) a pHILP construct for the use of delivering an inhibitor of a miRNA of the invention to tumor cells.
Preferably, the inhibitor to be delivered is selected from the group consisting of anti-miR, miRNA sponge and tough decoy inhibitor and is an inhibitor of a mature TTV miRNA as shown underlined in Table 2B which interacts with APC.
The following examples illustrate the invention and are not construed as any limitation of the invention.
(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.
(B) Plasmid Construction
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).
(D) Probes Labeling
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.
(E) Northern Blot
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).
(F) RT-qPCR
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 for Homo sapiens. Mature Bayes is run on the web-based tool.
(H) miRNA Target Predictions
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.
Table 1
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.
GGCGGAAGCAACTCCACTTTCTCACAAAATGGCGGCGGAGCACTTCCGGCTTGCCCAAAATGGCCGCC (SEQ ID NO: 5)
GGCGGAAGCAGCTCCACTTTCTCACAAAATGGCGGCGGAGCACTTCCGGCTTGCCCAAAATGGCGG-- (SEQ ID NO: 6)
GGCGGAAGCAGCTCCACCCTCTCACATAATGGCGGCGGAGCACTCCCGGCTTGCCCAAAATGGCGG-- (SEQ ID NO: 7)
TCACGTGACCTGACGTCACGGC-- (SEQ ID NO: 12)
CCCACGTGGCCTGTCACGT------ (SEQ ID NO: 13)
CCACGTGACGT-TGACGTCACAGCC (SEQ ID NO: 16)
GTCACGTGACCGAAGAGGACTTCCGGGTTGTGACTCCTCCCCAGTCAGGTGACTTGTGACGT------- (SEQ ID NO: 19)
ACTTCAGTGTTTAAGTACCTCCCCAGTCACGTGACTTATGACGT------- (SEQ ID NO: 20)
GAAGTGCTCCGCCGCCATTTTGTGAGAAAGTGGAGTTGCTTCCGCCTTACTTAAAATGGC--- (SEQ ID NO: 21)
GAAGTGCTCCGCCGCCATTTTGTGAGAAAGTGGAGCTGCTTCCGCCTTACTTAAAATGGCGG- (SEQ ID NO: 22)
CCTCAAC--TACTTAAGATGG---- (SEQ ID NO: 25)
CGTCAGC--TACTTAAAATGG---- (SEQ ID NO: 26)
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 and
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.
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 (
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.
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 (
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 (
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.
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.
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).
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).
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 in
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.
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 for Firefly luciferase under the control of a minimum promoter and seven binding sites for the TCF4/beta catenin complex (TOPFLASH plasmid). Additionally, Renilla Luciferase under 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 (
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.
| Number | Date | Country | Kind |
|---|---|---|---|
| 13003062 | Jun 2013 | EP | regional |
This application is a continuation of PCT/EP2014/078346, filed on Dec. 17, 2014; which claims the priority of PCT/EP2014/062251, filed on Jun. 12, 2014. This application is also a continuation-in-part of PCT/EP2014/062251, filed on Jun. 12, 2014, which claims the priority of EP 13003062.0, filed on Jun. 14, 2013. The contents of the above-identified applications are incorporated herein by reference in their entireties.
| Number | Name | Date | Kind |
|---|---|---|---|
| 5702891 | Kolberg | Dec 1997 | A |
| 7655785 | Bentwich | Feb 2010 | B1 |
| 20030050470 | An | Mar 2003 | A1 |
| 20050181439 | Choi | Aug 2005 | A1 |
| 20070044171 | Kovalic | Feb 2007 | A1 |
| 20090062131 | Mounts | Mar 2009 | A1 |
| 20090081675 | Colston, Jr. | Mar 2009 | A1 |
| 20130267429 | Gardner | Oct 2013 | A1 |
| Number | Date | Country |
|---|---|---|
| 1992691 | Nov 2008 | EP |
| 2399928 | Dec 2011 | EP |
| WO 0177384 | Oct 2001 | WO |
| 2005005658 | Jan 2005 | WO |
| WO-2011160848 | Dec 2011 | WO |
| Entry |
|---|
| Kincaid et al., “Virus-Encoded microRNAs: An Overview and a Look to the Future”, PLOS Pathogens, Dec. 2012, vol. 8, No. 12, pp. 1-11. |
| De Villiers et al., “TTV Infection in Colorectal Cancer Tissues and Normal Mucosa”, Int. J. Cancer, 2007, vol. 121,pp. 2109-2112. |
| McLaughlin-Drubin et al., “Viruses Associated with Human Cancer”, Biochimica et Biophysica Acta, 2008, vol. 1782, pp. 127-150. |
| De Villiers et al., “The Diversity of Torque Teno Viruses: In Vitro Replication Leads to the Formation of Additional Replication-Competent Subviral Molecules”, Journal of Virology, 2011, vol. 85, No. 14, pp. 7284-7295. |
| Liang et al, “A human Herpesvirus miRNA Attenuates Interferon Signaling and Contributes to Maintenance of Viral Latency by Targeting IKK”, Cell Research, 2011, vol. 21, pp. 793-806. |
| Pfeffer et al, “Viruses, microRNAs and Cancer”, Oncogene, 2006, vol. 25, pp. 6211-6219. |
| Kincaid et al, “A Human Torque Teno Virus Encodes a MicroRNA That Inhibits Interferon Signaling”, PLOS Pathogens, 2013, vol. 9, No. 12, pp. 1-14. |
| Mitchell et al, “Circulating microRNAs as Stable Blood-Based Markers for Cancer Detection”, PNAS, 2008, vol. 105, No. 30, pp. 10513-10518. |
| Number | Date | Country | |
|---|---|---|---|
| 20160160216 A1 | Jun 2016 | US | |
| 20170283798 A9 | Oct 2017 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/EP2014/078346 | Dec 2014 | US |
| Child | 14966110 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/EP2014/062251 | Jun 2014 | US |
| Child | PCT/EP2014/078346 | US |
