Patent Application
20070065389
More and more people are becoming preoccupied with holding back or reversing the effects of ageing. In this context, causing white hair, which is deemed to be unsightly, to disappear by using a coloring treatment shampoo is now widely practised. However, while that technique can effectively remove the effects of the phenomenon, it has no effect whatsoever on the causes. For this reason, that solution is temporary and has to be repeated frequently.
In that context, the inventors have elected to explore the appearance of white hair or canities from a completely fresh angle, namely genetics.
Exploring canities from its genetic aspect brings to light the deep mechanisms of depigmentation. This means that genes which are involved in canities can be identified. This identification opens the door to a wide variety of applications, both cosmetic and therapeutic or diagnostic, in the field of hair care.
Investigating the genomic regions responsible for canities by genetic linkage analysis is entirely novel; past studies have attempted to decode the biochemistry of canities.
The inventors have elected to subscribe to the long-held hypothesis that premature canities (PC) or the appearance of white hairs early in life is hereditary. The familial nature of premature whitening of the hair in some people is clearly observable.
The second obstacle to carrying out reverse genetics methods concerns the exact definition of phenotype. It is vital to have a complete definition of the phenotype being studied. To guarantee the best chances of success for this type of gene identification, selection and composition of the sample used in the present invention were made using a rigorous protocol for attributing phenotype and selecting families. The “premature canities” phenotype was attributed only to individuals who had some white hair before the age of 25 and for whom half of the hairs of the head were gray at 30 years of age.
Further, it is highly probable that firstly, premature canities is of a multigenic rather than a monogenic origin and secondly, that environmental factors have an influence on phenotype. In fact, a set of causes which give rise to a predisposition to premature canities has to be defined rather than a single mutation which is responsible for the phenotype. In that context, reverse genetics is not usually the technique of choice used by geneticists. Thus, the use of this method by the inventors is novel.
The results of these studies have allowed the inventors to define chromosomal and/or genomic zones comprising the genes most probably involved in canities. In the present application, chromosomal regions or sub-regions identified by the inventors as comprising genes which are statistically involved in canities, will indiscriminately be termed “chromosomal regions of the invention” or “genomic regions of the invention” or “chromosomal zones of the invention” or “genomic zones of the invention”. The genes identified in the context of the present invention within said regions will be termed the “genes of the invention”.
In a first aspect, the present invention concerns the genes of the chromosomal regions which have been identified and in a second aspect, the invention concerns the use of derived products such as transcription or translation products, in the fields of cosmetics, therapeutics and diagnostics.
Regarding the fields of therapy and cosmetics, the present invention successively concerns the use of polynucleotides deriving from a gene included in a chromosomal region of the invention, the use of agents which are capable of modifying the function attaching to that gene, the use of gene expression products and the use of agents that can modify the function of said expression products. The joint or combined use of at least two of the preceding products may prove to be judicious, particularly in the therapeutic field.
The present invention also concerns a method for diagnosing premature canities based on allelic variations in genes comprised in the chromosomal regions of the invention. Regarding diagnosis, it may also be particularly pertinent to combine the information deriving from the different genes of the chromosomal zones of the invention.
Glossary
The terms used in the context of the present invention have the following meanings:
The term “polynucleotide fragment” means any molecule resulting from a linear concatenation of at least two nucleotides, said molecule possibly being monocatenary, bicatenary or tricatenary. It may thus be a double-stranded DNA molecule, a single-stranded DNA molecule, an RNA molecule, a single strand DNA-RNA duplex, a DNA-RNA triplex or any other combination. The polynucleotide fragment may be a natural isolate, a recombinant or a synthetic molecule. When the polynucleotide fragment comprises complementary strands, the complementarity is not necessarily perfect, but the affinity between the different strands is sufficient to allow a stable Watson-Crick type bond to be established between the two strands.
Although the base pairing is preferably of the Watson-Crick type, other types such as Hoogsteen or reverse Hoogsteen type pairings are also possible.
The sequence S of a molecule is considered to “correspond” to the sequence of a given DNA molecule if the concatenation of the bases of S can be deduced from that of the given DNA molecule using one of the following methods:
Furthermore, two sequences are considered to remain “corresponding” if globally they introduce less than one error in 10 in one of the preceding methods (complementarity or identity, with or without T/U exchange), preferably less than one error in 100. As a result, the two molecules also necessarily have similar lengths, the maximum variation in length being 10% according to the accepted error margin; preferably, the difference in length is less than 1%.
This definition does not assume that the two molecules are of the same nature, in particular as regards their backbone; it only concerns a correspondence in their sequences.
As an example, two identical DNA sequences “correspond” with each other. Similarly, if those two sequences are substantially identical, i.e. more than 90% identical, they correspond. An RNA sequence derived from translation of any DNA molecule “corresponds” to the sequence of that DNA molecule. Similarly, a synthetic sequence, for example a DNA-RNA hybrid, could correspond to a DNA sequence. The same is true between a DNA sequence and the anti-sense RNA sequence having that sequence as target.
On the same tack, the sequence S of a DNA molecule “corresponds” to the sequence of a given DNA molecule if the sequence S thereof can be deduced from that of the given DNA molecule using method 1 or 3 alone. The same latitude is permitted regarding the possibility of introducing errors into these processes, i.e. two DNA sequences remain “corresponding” if globally they introduce less than one error in 10 into the complementarity or identity processes, preferably less than one error in 100.
The term “expression products” of a DNA fragment encompasses all molecules that translate the genetic information carried by said fragment. RNA corresponding to transcription of the DNA fragment at all maturation stages is thus an expression product; this is the same for polypeptides at all stages of maturation resulting from the translation of RNA. If cleavages occur within the polypeptide, such as cleavage of addressing signals, all of the resulting polypeptides are also considered to be expression products of the initial DNA fragment.
Within the context of the invention, the primary “function” of a DNA fragment is preferably to be transcribed then translated into protein. The secondary function of the DNA can be assimilated to the function of the protein resulting from translation of said DNA. The function of a DNA fragment also has other meanings in the present invention. In particular, a DNA fragment may belong to a regulating region of a gene, and thus its function is to be the binding site for enhancers or inhibitors, or to be the binding site for RNA polymerase, or to be a recognition site for positioning RNA polymerase or any other function that can generally be assimilated with a regulating sequence.
Other functions can be envisaged for DNA fragments. In particular, their simple presence in a gene can facilitate recombination. Similarly, one function in accordance with the invention may be that of telomers and may be of significance in degeneracy. Other particular functions attributed to said DNA functions are well known to biologists.
A “genetic marker” is a detectable DNA sequence. In human genetics, markers are particular DNA sequences which can take different forms in different individuals. This marker polymorphism allows their transmission along genealogical branches to be followed.
Two major categories of conventional markers can be identified, namely microsatellite markers and SNPs (single nucleotide polymorphisms).
A microsatellite is a repeated DNA sequence constituted by a relatively simple motif, usually a di-, a tri- or a tetra-nucleotide. The number of repetitions changes for a given motif depending on the individual and can vary by several units (a minimum of a dozen for a di-nucleotide), up to over a hundred. Those sequences are dispersed throughout the genome, in an almost random manner, but at identical locations from one individual to another. They are highly abundant (about one every 10000 nucleotides=10 kb) and are highly polymorphic. The variation in the length of the tandem repeat constitutes the marker. Said microsatellite sequences are thus widely used as genetic markers.
Normally there is no explicit link between a microsatellite marker and a gene other than co-localization. According to current knowledge and apart from some rare cases of intragenic markers associated with certain diseases, the length of a tandem repeat is not linked to the role of the gene. In the context of the present invention, microsatellite makers are tools for localizing the genes involved in premature canities. As there is much less polymorphism in genes than in markers, a gene allele will be represented by several alleles of a single microsatellite marker.
Different methods exist for defining the localization of particular DNA sequences along chromosomes. The physical unit of measurement is the number of base pairs. However, the centimorgan is often used, and is a recombination unit and thus a genetic rather than a physical measurement. Two particular sequences of the same chromosome are separated by a centimorgan if they recombine once in a hundred times during meiosis. A centimorgan is approximately equivalent to 106 base pairs.
Another method for localizing particular DNA sequences along chromosomes consists of defining their position relative to markers which are evenly spaced along the chromosomes for which the position has been completely determined and is known. Markers which are widely used are microsatellite markers for which very complete maps exist. In particular, the GDB (genome database) is a database which is known worldwide for recording, inter alia, STSs (sequence tagged sites), which are specific unique limits of the DNA forming part of the microsatellites. A code DxSxxxx (for example D6S257) acts to identify said markers and is used as the accession number within the GDB. Said codes are a universal and unambiguous means of identification as only the GDB uses that type of code. As such microsatellite markers can be found about every 10 kb, it is thus possible to define the position of every sequence to about 10 kb, by indicating the microsatellite markers framing it.
An SNP (single nucleotide polymorphism) is a polymorphism which affects a single base in the DNA. This is the most widespread form of polymorphism in the human genome and is also characterized by high stability during transmission. The majority of said polymorphisms do not have functional implications. About 1 SNP is counted per 100 base pairs. Knowing those SNPs allows a map of the human genome to be established; SNPs thus serve as real genome markers; moreover, they are slow to mutate and have little chance of reappearing recurrently.
The term between two markers for a chromosomal region means the whole sequence between those two markers, limits included, and thus the sequence for the markers is included.
In reverse genetics, indices can localize a gene deriving from comparing transmission of a phenotype, which is assumed to be induced by a mutated gene or a given allele, with transmission of known markers, in the same family. Data regarding co-segregation of a phenotype and a marker allow genetic linkage analysis to be carried out.
Co-transmission of a phenotype and a marker suggests that the gene responsible for the phenotype and the marker are physically close to each other on the chromosome. The linkage is determined by analyzing the transmission model for a gene and a marker in the families carrying them.
Linkage analysis relies on the co-transmission of certain forms of markers with the defective or modified form of the gene. However, it is an indirect analysis in the sense that firstly, during a first step, a phenotype is associated with the defective or modified form of the gene. An error in assigning certain phenotypes vitiates the study. Secondly, that study is based on statistics, and those statistics rely on an analysis of a sample of the population and is thus a sampling method. Finally, it should be noted that when it is possible to associate a particular allele of the marker with an allele of a gene (in fact a phenotype), that association is only valid, a priori, for inter-familial samples.
The results of linkage analyses clearly depend on the degree of linkage between the marker and the locus of the disorder. Five centimorgans (5 cM) is considered to be a minimum linkage for a diagnosis. A 5 cM linkage means that there is a 95% chance of arriving at the correct conclusion and only a 1 in 20 chance of recombination occurring between the marker and the locus of the disorder.
The term gene as used in the present invention means not only the strictly encoding portion but also non-coding portions, such as the associated introns and the regulatory portions at the 5′ and 3′ ends, UTRs (untranslated regions), in particular the promoter or promoters, “enhancers” etc.
The inventors have identified 3 distinct chromosomal regions belonging to chromosomes 3, 5 and 11 which are involved in premature canities. These 3 regions are each chromosomal regions or zones of the invention. More particularly, the inventors have determined the implication of certain genes belonging to these chromosomal regions, termed the genes of the invention.
In a first aspect, the invention concerns the genes KIAA1042, CCK, CACNA1D, ARHGEF3 and AL133097 on human chromosome 3, identified by the inventors as being involved in premature canities and the uses of products derived from said genes, such as transcription or expression products. These genes form part of the first chromosomal zone of the invention which is delimited on chromosome 3 by the microsatellite markers D3S1277 and D3S1285. More particularly, this zone is termed the “first chromosomal zone of the invention”. More particularly still, the 5 genes mentioned will be termed the 5 genes of the invention on chromosome 3.
In a second aspect, the invention concerns the genes KLHL3, HNRPA0, CDC25C, EGR1, C5orf6, C5orf7, LOC51308, ETF1, HSPA9B, PCDHA1 to PCDHA13, CSF1R, RPL7, PDGFRB, TCOF1, AL133039, CD74, RPS14, NDST1, G3BP, GLRA1, C5orf3, MFAP3, GALNT10 and FLJ117151 on human chromosome 5 identified by the inventors as being involved in premature canities, and uses of products derived from said genes, such as transcription or expression products. These genes belong to the second chromosomal zone of the invention which is delimited on chromosome 5 by the microsatellite marker D5S2115 and D5S422. More particularly, this zone will be termed the “second chromosomal zone of the invention”. More particularly still, the genes mentioned will be termed the genes of the invention on chromosome 5.
In a third aspect, the invention concerns the genes GUCY1A2, CUL5, ACAT1, NPAT, ATM, AF035326, AF035327, AF035328, BC029536, FLJ20535, DRD2, ENS303941, IGSF4, LOC51092, BC010946, TAGLN, PCSK7 and ENS300650 on human chromosome 11 identified by the inventors as being involved in premature canities, and uses of products derived from said genes, such as transcription or expression products. These genes belong to the third chromosomal zone of the invention which is delimited on chromosome 11 by the microsatellite marker D11S898 and D11S925. More particularly, this zone will be termed the “third chromosomal zone of the invention”. More particularly still, the 18 genes mentioned will be termed the 28 genes of the invention on chromosome 11.
The genes KIAA1042, CCK, CACNA1D, ARHGEF3, AL133097, KLHL3, HNRPA0, CDC25C, EGR1, C5orf6, C5orf7, LOC51308, ETF1, HSPA9B, PCDHA1 to PCDHA13, CSF1R, RPL7, PDGFRB, TCOF1, AL133039, CD74, RPS14, NDST1, G3BP, GLRA1, C5orf3, MFAP3, GALNT10, FLJ117151, GUCY1A2, CUL5, ACAT1, NPAT, ATM, AF035326, AF035327, AF035328, BC029536, FLJ20535, DRD2, ENS303941, IGSF4, LOC51092, BC010946, TAGLN, PCSK7 and ENS300650 will be termed the genes of the invention.
For the three chromosomal zones identified above, the present invention encompasses polynucleotide fragments with a minimum length of 18 nucleotides, corresponding at least in part to one of the genes of the invention, said DNA fragments having the functional characteristic of being involved in canities or in premature canities, and possibly in both phenomena. The genes involved in premature canities are very probably also involved in age-related canities.
In accordance with one possibility envisaged by the present invention, a fragment involved in canities or premature canities and having a sequence satisfying the requirements mentioned above can be used in therapy.
More particularly, in a first aspect, the invention concerns genes on human chromosome 3 identified by the inventors as being involved in premature canities. In accordance with this aspect, a fragment encompassed by the invention has a sequence corresponding to all or part of a gene on human chromosome 3 selected from the KIAA1042, CCK, CACNA1D, ARHGEF3 and AL133097 genes. These genes are included in the first chromosomal zone of the invention delimited on chromosome 3 by the microsatellite markers D3S1277 and D3S1285.
The second aspect of the invention concerns genes on human chromosome 5 identified by the inventors as being involved in premature canities. In accordance with this aspect of the invention, a fragment encompassed by the invention has a sequence corresponding to all or part of a gene on human chromosome 5 selected from the KLHL3, HNRPA0, CDC25C, EGR1, C5orf6, C5orf7, LOC51308, ETF1, HSPA9B, PCDHA1 to PCDHA13, CSF1R, RPL7, PDGFRB, TCOF1, AL133039, CD74, RPS14, NDST1, G3BP, GLRA1, C5orf3, MFAP3, GALNT10 and FLJ117151 genes. Said genes are included in the second chromosomal zone of the invention delimited on chromosome 5 by the microsatellite markers D5S2115 and D5S422.
The third aspect of the invention concerns genes on human chromosome 11 identified by the inventors as being involved in premature canities. In accordance with this aspect of the invention, a fragment encompassed by the invention has a sequence corresponding to all or part of a gene on human chromosome 11 selected from the GUCY1A2, CUL5, ACAT1, NPAT, ATM, AF035326, AF035327, AF035328, BC029536, FLJ20535, DRD2, ENS303941, IGSF4, LOC51092, BC010946, TAGLN, PCSK7 and ENS300650 genes. Said genes are included in the second chromosomal zone of the invention delimited on chromosome 11 by the microsatellite markers D11S898 and D11S925.
The polynucleotide fragment referred to in the invention corresponds to a fragment of a chromosome. This fragment has a minimum length of 18 nucleotides, and a maximum length which can be up to the total length of the gene in question, or several genes of the invention. Preferably, the fragment has more than 18 nucleotides. A particularly preferred length is in the range 18 to 10000 nucleotides, more preferably in the range 30 to 8000 nucleotides.
In accordance with preferred variations of the invention, reference is made to fragments the length of which is in the range 30 to 5000 nucleotides, preferably in the range 50 to 3000 nucleotides, for example in the range 100 to 2000 nucleotides, or in the range 200 to 1000 nucleotides.
The invention also concerns the use in cosmetics or therapy of a polynucleotide fragment or the expression product of a fragment or an agent modulating the function of a fragment, or of an agent modulating the function of the expression product of a fragment, where the fragment in question corresponds to all or part of a gene of human chromosome 11 selected from the GUCY1A2, CUL5, ACAT1, NPAT, ATM, AF035326, AF035327, AF035328, BC029536, FLJ20535, DRD2, ENS303941, IGSF4, LOC51092, BC010946, TAGLN, PCSK7 and ENS300650 genes or to all or part of a gene on human chromosome 5 selected from the KLHL3, HNRPA0, CDC25C, EGR1, C5orf6, C5orf7, LOC51308, ETF1, HSPA9B, PCDHA1 to PCDHA13, CSF1R, RPL7, PDGFRB, TCOF1, AL133039, CD74, RPS14, NDST1, G3BP, GLRA1, C5orf3, MFAP3, GALNT10 and FLJ117151 genes or to all or part of a gene on chromosome 3 selected from the KIAA1042, CCK, CACNA1D, ARHGEF3 and AL133097 genes. In a preferred case, the fragment more particularly corresponds to a portion of an exon of one of said genes.
In the following text, the term “products of the invention” will be used to designate the fragment, the expression product of a fragment, the agent modulating the function of a fragment, and the agent modulating the function of the expression product of a polynucleotide fragment corresponding to all or part of one of the genes of the invention.
For the genes identified by the inventors, the present invention firstly concerns uses in the cosmetics field. The term “cosmetics” means any application which modifies only esthetics and is not therapeutic in nature.
Regarding all of the uses of the invention in the cosmetics field, the product of the invention can be packaged in various appropriate forms, alone or in combination with other agents. In particular, preferred forms are intended for local application and are in the form of creams, lotions, gels, emulsions, pomades and shampoos. Other forms can also be envisaged for the uses of the invention, in particular in the form of pills for oral administration.
Of the different cosmetic aims in the context of the invention, a particularly preferred area is that of pigmentation. The pigmentation may be that of the skin or of the phanera, and may concern the color of the pigmentation or the absence of pigmentation; problems affecting the quality and intensity of pigmentation are also affected by the present invention.
In particular, the invention is aimed at using at least one product of the invention to prevent and/or limit and/or arrest the development of canities.
The invention also encompasses the use of at least one product of the invention to encourage natural pigmentation of gray hair of the head and/or body.
The present invention also pertains to a cosmetic method for treating canities, characterized in that a composition comprising at least one product of the invention is applied to the zone to be treated.
The invention also pertains to a cosmetic treatment method to encourage the natural pigmentation of gray or white hair of the head and/or body, characterized in that a composition comprising at least one product of the invention is applied to the zone to be treated
Non-limiting examples of the zones to be treated are the scalp, eyebrows, mustache and/or beard.
More particularly, the methods for treating canities and the natural pigmentation of gray or white head and/or body hair consist of applying a composition comprising at least one product of the invention.
Treatment methods for combating canities and/or stimulating the natural pigmentation of gray or white head and/or body hair can, for example, consist of applying the composition to the hair and scalp at night, leaving the composition in contact overnight and then optionally shampooing in the morning or washing the hair with said composition and leaving it in contact for a few minutes before rinsing. The composition of the invention has been shown to be particularly advantageous when applied in the form of a hair lotion, which may be rinsed out, or even in the form of a shampoo.
Regarding the genes identified by the inventors, the present invention then concerns therapeutic uses in the field of pigmentation.
Disorders affecting the pigmentation system, whether of the skin or phanera, can have severe consequences on the health of affected persons. Skin pigmentation acts as a barrier to attack by light; in particular, persons suffering from albinism are deprived of protection against sunlight, which constitutes a major danger to them. Other disorders involving pigmentation are also encompassed by the present invention.
In the context of therapeutic and cosmetic uses that can modify a characteristic of pigmentation, we preferably refer to skin pigmentation. In other cases envisaged by the present invention, the type of pigmentation which is to be modified concerns the pigmentation of phanera, in particular the nails or body hair.
In a particularly preferred case of the present invention, the pigmentation the characteristics of which are to be modified is that of the hair system in general and the hair of the head, mustache and eyebrows in particular. The present invention can modify the phenomenon whereby pigmentation of the hair of the head is halted, namely canities, in particular when it occurs prematurely in a person, whereupon we speak of premature canities.
For all therapeutic uses, the active products in the composition of a medicament are preferably associated with pharmaceutically acceptable excipients. Any administrative route which is considered acceptable can be used in the context of the invention, in particular intradermal, intravenous, muscular, oral, otic, nasal or optical. The formulation is preferably adapted to the selected administrative route.
Uses for manufacturing a medicament of the invention may involve other active principles in their formulations. Similarly, administration of a medicament as defined in the invention can be combined with administering another medicament, whether said administration is simultaneous, sequential or separate.
The various products used in the context of therapeutic uses can be combined and form part of the composition of a single medicament, or they may be employed in the manufacture of various medicaments. In particular, if they form part of the composition of distinct medicaments, they may be administered at different frequencies.
The preferred features and variations of the products employed in the uses of the invention may be identical in the context of their uses in cosmetology and for the uses of the same product in the manufacture of a medicament.
In both cases, the use of the products of the invention may require the product to be introduced into a body fluid or into the body tissues or into the cells. For introduction into cells, it may be necessary for the product to be active in the cell cytoplasm or in the cell nucleus.
The first use in cosmetics or therapeutics envisaged in the context of the invention is the use of a polynucleotide fragment the sequence of which at least partially corresponds to one of the genes of the invention. For therapeutic uses, the polynucleotide fragment is used in manufacturing a medicament.
Regarding the chemical nature of this polynucleotide fragment, it may be a single or double strand, circular or linear DNA molecule, an RNA molecule or any other molecule envisaged in the definition of the polynucleotide fragment given above.
Regarding its environment, said fragment may be or may form part of a plasmid, a viral genome or another type of vector. In other cases, it may form part of the genome of a cell, or of a cell which has been genetically modified to include that fragment in its genome. It may also be an isolated molecule.
Regarding regions surrounding said fragment, it is preferably under the control of regulating sequences. If the fragment is inserted in a vector, said vector preferably includes all of the sequences necessary for transcription and possibly translation of the fragment. Said fragment can also be surrounded by flanking regions which allow a step for homologous recombination with a further polynucleotide fragment, possibly resulting in insertion of the fragment of the invention into the genomic DNA of a target cell.
The polynucleotide fragment as described may be in its natural form or it may be synthetic in nature, or it may be partly one and partly the other, in particular if it is a “duplex” molecule constituted by two strands of different origins. In the different cases envisaged by the present invention, the polynucleotide fragment can be isolated; it may have undergone a purification step. It may also be a recombinant fragment, for example one synthesized in another organism. In a preferred example, it is a DNA fragment which has been amplified by PCR (polymerase chain reaction) then purified.
In other constructions envisaged by the present invention, the first use employs a polynucleotide fragment associated with a probe. This characteristic can, inter alia, allow the localization of the fragment to be followed from the extracellular medium to the cell, or from the cytoplasm to the nucleus, or it can allow its interaction with DNA or RNA or proteins to be determined. The probe can also enable degradation of the fragment to be monitored. The probe is preferably fluorescent, radioactive or enzymatic in nature. The skilled person will know which type of probe is best adapted to the characteristic which is to be monitored.
The polynucleotide fragment employed in the context of this first use of the invention can be used in a hybridization test, in a sequencing test, in a microsequencing test or in a mis-pairing detection test.
Said fragment of the invention contains at least 18 successive nucleotides, said 18 nucleotides constituting a sequence which corresponds to all or part of one of the 5 genes of the invention on human chromosome 3 or to all or part of one of the genes of the invention on chromosome 5 or to all or part of one of the 18 genes of the invention on human chromosome 11. In particular, a fragment of the invention may contain only 18 complementary bases of 18 successive bases of one of the genes of the invention.
In a further particular case, the fragment described may be cDNA or RNA of one of the genes described above. It may correspond to one or more exons of one of the genes, and may correspond to a regulating sequence for one of the genes identified on chromosomes 3, 5 and 11.
In the context of said first use, the number of polynucleotide fragments as defined above is not limited and is not necessarily restricted to a single fragment.
In particular, it may employ a plurality of polynucleotide fragments the sequence of which at least partially corresponds to one of the genes of the invention within the chromosomal regions of the invention. Preferably, the sequences of the different fragments correspond to distinct genes or to distinct exons.
This first use of the invention is preferably in the cosmetics field.
Said use can also enable the manufacture of a medicament for a therapeutic action in the pigmentation field.
In a particular case, the first use described involves a genetic modification whether or not it is induced by a nucleotide fragment as described.
In the case in which a gene responsible for pigmentation is defective as it has mutated, said first use of the invention can restore the function of that gene by introducing a polynucleotide fragment which represents a new wild-type copy of the defective endogenic gene.
When gene activation is responsible for depigmentation, said first use of the invention can abolish the function of the gene by introducing an antisense RNA which will block translation of the gene.
In a second use envisaged by the present invention, in the field of therapy and cosmetics, an agent modulating the function of a DNA fragment corresponding at least in part to one of the genes identified in the context of the present invention is used. For therapeutic uses, this defined agent is involved in the manufacture of a medicament. Preferably, the DNA fragment has at least 18 nucleotides.
Said agent of the invention may be capable of modulating the function of an exogenic DNA fragment a portion of the sequence of which corresponds to one of the genes identified by the inventors, or it may be capable of modulating the function of an endogenic sequence included in one of the genes identified by the invention. Preferably, an agent acting in this second use in accordance with the invention not only modulates the function of an exogenic DNA fragment as defined, but also of the corresponding endogenic DNA fragment.
The DNA fragment the function of which is modulated may partially correspond to one of the 5 genes of the invention on chromosome 3. Alternatively, the DNA fragment the function of which is modulated may correspond in part to one of the genes of chromosome 5, or to one of the 18 genes of the invention on chromosome 11. In particular, it may be a plasmid having just one short sequence corresponding to one of the chromosomal regions mentioned. Preferably, the sequence correspondence is established over at least 18 successive nucleotides.
The above statements in the definition section regarding the meaning of the “function of a DNA fragment” are applicable regarding envisaging all of the uses corresponding to a second use of the invention.
Given the plurality of functions of DNA fragments, modulation of said fragments encompasses very different aspects. In the particular case in which the function of said fragment is to be transcribed, modulating said function consists of encouraging or inhibiting the capacity of said fragment to be transcribed. It may also consist of modifying the transcription initiation and termination sites, or modifying the degree of transcription initiation. In another case, modulating the function may also consist of modifying RNA splicing, for example by modifying DNA recognition sequences responsible for distribution between introns and exons.
When the DNA fragment is part of a regulating sequence, modifying its function may consist of inhibiting binding of enhancers or inhibitors. In contrast, it may consist of encouraging binding, or encouraging binding of other transcription factors. This is also the case with sequences used by RNA polymerase.
In the context of said use in accordance with the invention, as is the case with all other uses in accordance with the invention, the number of products, in this case agents modulating the function of a DNA fragment corresponding at least in part to one of the genes of the present invention, is not limited and may be greater than one.
However, in the context of this second use, the different agents used have in common that they all modulate the function of DNA fragments the sequence of which belongs to or corresponds at least in part to the same chromosomal region of the invention. In accordance with the first aspect of the invention, said region is that on human chromosome 3 identified by the inventors. In accordance with the second and third aspects of the invention, the chromosomal region in question is that identified by the inventors on chromosomes 5 and 11 respectively. The various agents may modulate the same gene in one of the regions, or different genes in the same region of the invention.
Examples of agents of the invention are single strand DNA molecules which can bind to defined sub-regions in one of the genes of the invention, to form triple helices. Under said conditions, agents of the invention destroy the function of the sub-region to which they hybridize.
Other preferred agents of the invention are polypeptides capable of interacting with defined sub-regions of one of the genes of the invention. Preferably, the agents of the invention are enhancers or inhibitors which bind to regulating regions of one of the genes of the invention on human chromosome 3 or to one of those on human chromosome 5 or to one of those on chromosome 11.
A further category of the agents of the invention concerns molecules capable of interacting with precise regions along the DNA to change its conformation. A further category concerns molecules interacting with inhibitors or enhancers to modify their function, the inhibitors or enhancers having the initial function of modifying the expression of DNA fragments belonging to one of the genes identified in the context of the present invention.
An agent used in accordance with said second use of the invention can in particular modulate the function of a DNA fragment corresponding to 18 successive bases of one of the genes described above.
This second use of the invention is preferably in the cosmetics field. Said use can also allow a medicament to be manufactured for a therapeutic action in the pigmentation field.
In a particular case, this second use involves genetic modification whether or not induced by an agent modulating the function of a DNA fragment as described.
When gene activation is responsible for depigmentation, said second use of the invention can abolish the function of said gene by introducing an agent which will block translation of said gene by binding to its promoter region, for example.
When inactivation of a gene is responsible for depigmentation, said second use of the invention can restore the function of said gene by introducing an agent which will activate gene transcription, for example by binding to its promoter region, or by binding to an inhibitor which will thus stop inactivating that gene.
A third use envisaged by the present invention in the field of therapeutics and cosmetics is the use of an agent modulating the function of an expression product of a DNA fragment corresponding at least in part to one of the genes of the invention. For therapeutic uses, the agent defined is involved in the manufacture of a medicament. Preferably, the DNA fragment has at least 18 nucleotides.
In particular, such an agent of the invention modulates the function of a transcript from a DNA fragment which corresponds at least in part to one of the 5 genes of the invention on chromosome 3. In another case, an agent of the invention modulates the function of a polypeptide derived from translation of one of the transcripts mentioned. Alternatively, the DNA fragment the function of the expression product of which is modulated may correspond at least in part to one of the genes of the invention on chromosome 5 or to a gene of the invention on chromosome 11.
Said agent of the invention may be capable of modulating the function of the expression product of an exogenic DNA fragment a portion of the sequence for which corresponds to one of the genes of the invention identified by the inventors, or it may be capable of modulating the function of the expression product of an endogenic sequence included in the genes of the invention. Preferably, an agent acting in this third use of the invention not only modulates the function of an expression product of an exogenic DNA fragment as defined above, but also of the corresponding endogenic DNA fragment.
The polypeptide's function can be modulated in different manners. In particular, its activity, yield, specificity, avidity for an antibody can be increased or decreased, its substrate can be modified for an enzyme, and its degree of conversion can be modified.
Preferred agents of the invention are RNA molecules, termed antisense RNA, which hybridize with at least one transcript from a DNA fragment corresponding at least in part to one of the genes of the invention. Other agents fulfilling the same roles may be single strand DNA molecules or hybrid DNA-RNA molecules. The role of said agents of the invention is preferably to encourage, prevent, retard, accelerate or introduce errors into translation of said transcript.
Other preferred agents of the invention belong to the polypeptide class. In particular, the invention concerns proteins that can bind to said transcript and thus modulate its translation. Such agents from the polypeptide class may be of natural or synthetic origin (synthesized chemically or biotechnologically). In particular, it may be an antibody. As mentioned above, said modulation can result in encouraging, preventing, retarding, accelerating or introducing errors into translation of said transcript. In particular, the interaction between the polypeptides and said transcript may constitute an obstacle to normal ribosome binding.
Agents as defined in the present invention may modulate the function of the protein encoded by a DNA fragment corresponding at least in part to one of the 5 genes of the invention on human chromosome 3 or to one of the genes of the invention on chromosome 5 or to one of the 18 genes of the invention on chromosome 11. Said agents may or may not be proteic in nature. An agent of the invention may intervene at an early stage, preventing correct folding of the protein. An agent of the invention may also modify the function of said protein by modifying the three-dimensional structure after folding. It is also possible for said agent to be a protein inhibitor, in particular a competitive inhibitor.
Agents that may be suitable in the context of the present invention are not limited to those cited above.
In the context of said third use, the number of agents modifying the function of an expression product as defined above is not limited and is not necessarily restricted to a single agent.
However, in the context of said third use, the different agents employed therein may have in common the fact that they all modulate the function of expression products of DNA fragments the sequence for which belongs to or corresponds at least in part to a gene from the same chromosomal region of the invention. In accordance with the first aspect of the invention, said region is that identified by the inventors on human chromosome 3. In accordance with the second and third aspects of the present invention, the chromosomal region in question is that identified by the inventors on chromosomes 5 and 11 respectively.
This third use of the invention is preferably in the cosmetics field.
This use can also allow the manufacture of a medicament for therapeutic use, in the pigmentation field.
In a particular case, the third described use involves a genetic modification, whether or not introduced by an agent modulating the function of an expression product of a DNA fragment as described herein.
In the case in which activation of the gene is responsible for depigmentation, said third use of the invention can destroy the function of that gene by introducing an antisense DNA which will block translation of said gene by preventing RNA-protein passage. A further preferred situation consists of selecting as the agent an antibody that is capable of binding to the protein resulting from translation of said gene.
A fourth use envisaged by the present invention in the therapeutic field and in the cosmetics field is the use of an expression product of a DNA fragment corresponding at least in part to one of the genes identified in the context of the present invention. For therapeutic uses, the agent defined above is used in the manufacture of a medicament. Preferably, the DNA fragment has at least 18 nucleotides.
In particular, said expression product is the RNA transcript derived from a DNA fragment corresponding at least in part to one of the 5 genes of the invention on chromosome 3, or to one of the genes of the invention on chromosome 5, or to one of the 18 genes of the invention on chromosome 11, whatever the maturation stage of said transcript. In the case of splicing, the transcript can thus be smaller than the DNA fragment from which it is derived. Preferably, if the expression product is a RNA molecule, it comprises at least 18 nucleotides.
In a further preferred case, an expression product of the invention is derived from translation of one of the transcripts mentioned above. Said expression product can thus comprise less than 6 amino acids if the transcript from which it is derived has undergone splicing steps. Preferably, a peptide expression product contains at least 6 amino acids.
The expression product of the invention does not necessarily derive from the steps of transcription or translation of genomic DNA. In particular, an expression product used in accordance with the invention can be an expression product from exogenic DNA at least a portion of the sequence of which corresponds to part of one of the genes of the invention.
The present invention also envisages the use of a completely synthetic agent which is similar to the expression product of an exogenic or endogenic DNA fragment corresponding at least in part to one of the genes of the invention.
Preferred expression products for use in the present invention are RNA molecules, termed antisense RNA, which hybridize with at least one transcript from a DNA fragment corresponding at least in part to one of the genes of the invention. In particular, to form antisense RNAs having a specific RNA as the target, it is possible to use RNA from transcription of the same sequence of DNA as the target but not of the leader strand, but of its complementary sequence carried by the other strand. This produces RNA fragments that are complementary to target fragments normally synthesized by the cell. The expected role of said expression products of the invention is preferably to encourage, prevent, retard, accelerate or introduce errors in the translation of transcripts normally synthesized by the cell.
Other preferred expression products belong to the polypeptide class. In particular, the invention concerns proteins that are capable of introducing a change into the function of the cell in which they are active.
In the context of this use of the invention, the number of expression products of a DNA fragment the sequence of which belongs to or corresponds at least in part to one of the genes of the invention is not limited and may be greater than one.
However, in the context of this fourth use, the different products employed have in common the fact that they are all expression products of DNA fragments the sequence of which belongs to or corresponds at least in part to a gene from the same chromosomal region of the invention. In the first aspect of the invention, said region is that on human chromosome 3 identified by the inventors. In accordance with the second and third aspects of the invention, the chromosomal region in question is that identified by the inventors on chromosomes 5 and 11 respectively.
This fourth use of the invention is preferably in the cosmetics field.
This use can also allow the manufacture of a medicament for therapeutic action in the pigmentation field.
In a particular envisaged case, the fourth use described involves a genetic modification whether or not it is induced by an expression product of a DNA fragment as described.
In the case in which gene activation is responsible for the depigmentation, said fourth use of the invention can abolish the function of said gene by introducing an antisense RNA which will block translation of said gene by binding itself to the transcript synthesized by the cell.
In the case in which inactivation of a gene is responsible for depigmentation, said fourth use of the invention can restore the function of said gene by introducing RNA allowing synthesis of the protein encoded by the gene, or the protein encoded by the gene, into the cell or a molecule.
For the four types of uses described above in the context of the invention, the cosmetic uses are preferably in the pigmentation field.
For the four types of uses described above, the product of the invention could be incorporated into a cosmetic or pharmaceutical composition.
Said composition comprises, in a pharmaceutically or cosmetically acceptable medium, a quantity of products of the invention in the range 0.001% to 10% by weight per volume.
The composition can be administered orally or applied to the skin (onto any skin zone of the body) and/or onto the scalp or hair.
For oral administration, the composition may contain the product(s) of the invention in solution in a food quality liquid such as an aqueous or hydroalcoholic solution, which may be flavored. They may also be incorporated into a solid ingestable excipient and, for example, be in the form of granules, pills, tablets or dragees. They can also be taken up into solution in a food quality liquid which may then be packaged into ingestable capsules.
Depending on the manner of administration, the composition can be presented in any of the normal galenical forms, particular those in cosmetology.
A preferred composition of the invention is a cosmetic composition adapted for topical application to the scalp and/or the skin.
For topical application, the composition which can be used can in particular be in the form of an aqueous, hydroalcoholic or oily solution or a lotion or serum type dispersion, or as a milk type emulsion with a liquid or semi-liquid consistency obtained by dispersing an oily phase in an aqueous phase (O/W) or vice versa (W/O), or suspensions or emulsions of a soft cream-like consistency or an aqueous or anhydrous gel, or microcapsules or micro particles, or vesicular ionic and/or non ionic dispersions. They can be in the form of an unguent, tincture, cream, pomade, powder, patch, impregnated pad, solution, emulsion or vesicular dispersion, lotion, gel, spray, suspension, shampoo, aerosol or foam. They may be anhydrous or aqueous. They may also consist of solid preparations constituting soaps or cleansing bars.
These compositions are prepared using the usual methods.
In particular, the composition can be a hair care composition, especially a shampoo, a setting lotion, a treatment lotion, a styling cream or gel, a coloring composition (in particular oxidizing dyes) which may be in the form of coloring shampoo, hair restructuring lotions or masks.
When the invention consists in a use for cosmetic applications, the composition is preferably a cream, a hair lotion, shampoo or conditioner.
The quantities of different constituents of the compositions are those conventionally used in the fields under consideration.
When the composition is an emulsion, the proportion of the oily phase can be from 5% to 80% by weight, preferably 5% to 50% by weight with respect to the total composition weight. The oils, waxes, emulsifiers and co-emulsifiers used in the composition in the form of an emulsion are selected from those conventionally used in the cosmetics field. The emulsifier and co-emulsifier are present in the composition in a proportion of 0.3% to 30% by weight, preferably 0.5% to 20% by weight with respect to the total composition weight. The emulsion may also contain lipid vesicles.
When the composition is an oily solution or gel, the oily phase can represent more than
In a variation, the composition will be such that the products of the invention are encapsulated in an envelope such as microspheres, nanospheres, oleosomes or nanocapsules, the envelope being selected depending on the chemical nature of the product of the invention.
As an example, the microspheres may be prepared using the method described in European patent application EP-A-0 375 520.
The nanospheres may be in the form of an aqueous suspension and may be prepared using the methods described in French patent applications FR-A-0015686 and FR-A-0101438.
Oleosomes consist of an oil-in-water emulsion formed by oil globules provided with a lamellar liquid crystal envelope dispersed in an aqueous phase (see European patent applications EP-A-0 641 557 and EP-A-0 705 593).
The products of the invention can also be encapsulated into nanocapsules consisting of a lamellar envelope obtained from a silicone surfactant (see EP-A-0 780 115); the nanocapsules can also be prepared from hydrodispersible sulfonic polyesters (see FR-A-0113337).
The products of the invention may also be complexed onto the surface of oily cationic globules regardless of their size (see EP-A-1 010 413, EP-A-1 010 414, EP-A-1 010 415, EP-A-1 010 416, EP-A-1 013 338, EP-A-1 016 453, EP-A-1 018 363, EP-A-1 020 219, EP-A-1 025 898, EP-A-1 020 101, EP-A-1 120 102, EP-A-1 129 684, EP-A-1 160 005 and EP-A-1 172 077).
Finally, the products of the invention can be complexed onto the surface of nanocapsules or nanoparticles provided with a lamellar envelope (see EP-A-0 447 318 and EP-A-0 557 489) and containing a cationic surfactant on the surface (see the references cited above for cationic surfactants).
In particular, a composition in which the products of the invention have an envelope with a diameter of 10 μm or less is preferred.
In known manner, the composition can also contain the usual adjuvants in the cosmetics field, such as hydrophilic or lipophilic gelling agents, hydrophilic or lipophilic additives, preservatives, antioxidants, solvents, fragrances, fillers, filters, odor absorbers and coloring materials. The quantities of the various adjuvants are those which are conventionally used in the cosmetics field, for example 0.01% to 10% of the total composition weight. Depending on their nature, said adjuvants can be introduced into the oily phase, into the aqueous phase and/or into the lipid spherules.
Oils or waxes that can be cited are mineral oils (Vaseline oil), vegetable oils (the liquid fraction of shea butter, sunflower seed oil), animal oils (perhydrosqualene), synthesis oils (purcellin oil), silicone oils or waxes (cyclomethicone) and fluorinated oils (perfluoropolyethers), beeswax, carnauba wax or paraffin. Fatty alcohols and fatty acids (stearic acid) can be added to said oils.
Suitable emulsifying agents which can be cited are glycerol stearate, polysorbate 60 and the PEG-6/PEG-32/glycol stearate mixture sold by Gattefosse under the trade name Tefose® 63.
Suitable solvents which can be used which can be cited are lower alcohols, in particular ethanol and isopropanol and propylene glycol.
Hydrophilic gelling agents which can be used which may be cited are carboxyvinyl polymers (carbomers), acrylic copolymers such as acrylate/alkylacrylate copolymers, polyacrylamides, polysaccharides such as hydroxypropylcellulose, natural gums and clays, and, as lipophilic gelling agents, modified clays such as bentonites, metallic salts of fatty acids such as aluminum stearates and hydrophobic silica, ethylcellulose and polyethylene.
The compositions can have other active agents associated with the product of the invention. Examples of such active agents which can be cited by way of example are:
In particular, they may be active agents that can stimulate regrowth and/or inhibit hair loss; particular non limiting examples thereof are as follows:
In another implementational possibility, the present invention concerns methods for diagnosing a predisposition to premature canities in an individual.
Premature canities is a phenotype which has been defined by the inventors as, inter alia, being characterized by the appearance of the first white hairs early in life, and preferably at about 18 years of age. Since this phenotype is transmitted to the next generation, it may prove important for individuals for whom one parent or relative is affected, to determine, before the appearance of symptoms, whether or not they will be affected. The diagnostic method of the invention is perfectly suited to individuals under 18 years of age.
Since it is probable that environmental factors play a role in the “canities” phenotype as in “premature canities”, thanks to the methods of the invention, we can determine the risks of developing such a phenotype, i.e. a predisposition to premature canities.
A method of the invention for determining a predisposition to premature canities comprises a first step for selecting one or more markers which will be used in the subsequent steps. The term “marker” means a DNA sequence the various allelic variations of which carry information. Such a marker may be a short sequence of a gene the mutation of which is the source of the phenotype. It may also be a marker which is physically located on the chromosome in a region very close to a gene involved in premature canities. Preferably, the marker is a SNP (single nucleotide polymorphism).
In accordance with a first aspect of a method of the invention, the selected marker or markers belong to the region on human chromosome 3 comprising the KIAA1042, CCK, CACNA1D, ARHGEF3 and AL133097 genes. Preferably, the selected markers belong to the sequence for one of said genes.
In accordance with a second aspect of a method of the invention, the selected marker or markers belong to the region on human chromosome 5 comprising the KLHL3, HNRPA0, CDC25C, EGR1, C5orf6, C5orf7, LOC51308, ETF1, HSPA9B, PCDHA1 to PCDHA13, CSF1R, RPL7, PDGFRB, TCOF1, AL133039, CD74, RPS14, NDST1, G3BP, GLRA1, C5orf3, MFAP3, GALNT10 and FLJ117151 genes. Preferably, the selected markers belong to the sequence for one of said genes.
In accordance with a third aspect of a method of the invention, the selected marker or markers belong to the region on human chromosome 11 comprising the GUCY1A2, CUL5, ACAT1, NPAT, ATM, AF035326, AF035327, AF035328, BC029536, FLJ20535, DRD2, ENS303941, IGSF4, LOC51092, BC010946, TAGLN, PCSK7 and ENS300650 genes. Preferably, the selected markers belong to the sequence for one of said genes.
The next step in carrying out the method of the invention consists, for the selected marker or markers, in determining the alleles present in a sample of genetic material from the individual undergoing the diagnostic test. Two different alleles carried by the two versions of the chromosome can be identified.
The sample containing the genetic material may be blood, a single drop being sufficient to carry out the method of the invention. Other body fluid samples may be used in the context of the invention. It is also possible to use a few cells from the individual. The skilled person will known how to determine which sample could be used in the context of this test, while minimizing discomfort for the individual concerned. This diagnostic test could optionally be coupled with other genetic tests.
Routine techniques which are well known to the molecular biologists could be used to determine alleles for the selected marker or markers; in particular, hybridization tests are particularly appropriate in this type of step.
Various markers are potentially preferred in the context of carrying out the method of the invention. In particular, bi-allelic markers may prove particularly suitable if one allelic form translates as a predisposition to premature canities while the other allelic form, in contrast, reflects the absence of said predisposition. Other more routine markers are polymorphic and can be found in at least two allelic forms, and generally more than two.
Markers which can be selected for the first step of the method of the invention include SNPs which are particularly well known. When selecting the marker, it is very important to base it on the informative value of the marker polymorphism. One particularly advantageous situation consists of selecting a marker certain allelic variations of which translate into a predisposition to premature canities while all of the other variations reflect the absence of said predisposition. In many situations, the marker does not entirely satisfy said condition, i.e. certain alleles are preferentially present but not exclusively present in individuals predisposed to canities. In these situations, it may be judicious to select several markers to establish a diagnostic test which is as reliable as possible.
When the selected markers are SNPs, the various allelic variations correspond to modification of a base. A particularly advantageous situation to be investigated when selecting a marker corresponds to the situation in which certain alleles (modification of a base) are characteristic of a predisposition to premature canities.
In accordance with the first aspect of a method of the invention, the marker or markers selected for the first step could be selected from the SNPs on chromosome 3 mentioned in the summarizing table in Example 2.
In accordance with the second aspect of a method of the invention, the marker or markers selected for the first step could be selected from the SNPs on chromosome 5 mentioned in the summarizing table in Example 2.
In accordance with the third aspect of a method of the invention, the marker or markers selected for the first step could be selected from the SNPs on chromosome 11 mentioned in the summarizing table in Example 2.
The methods of the invention are not limited to the two steps described and may contain other steps anterior or posterior to the two steps mentioned.
In particular, a method of the invention may comprise the supplemental step of comparing the allelic form of the selected marker or markers with the allelic form of the marker or markers in other individuals. This supplemental comparison step may prove necessary in order to establish a diagnosis. In this case, it may be useful to make a comparison with the form of the marker or markers in individuals manifestly affected with premature canities and optionally also with the form of the marker or markers in individuals who are manifestly free of said predisposition.
Given that premature canities is probably a multigenic disorder, the causes of predisposition are many and it may be difficult for all of them to be envisaged exhaustively. In contrast, within one family some members of which are prematurely affected with canities, it is highly probable that the cause of the susceptibility is unique. For this reason, during the comparison step, mentioned as an optional third step in the methods of the invention, a particularly information-rich comparison is comparison of alleles of the marker for the individual undergoing the test with alleles of the same marker for persons in his family where the phenotype is known. If several markers have been selected, this operation should preferably be repeated for all markers.
The present invention also concerns methods for screening molecules having a particular effect. In particular, the invention concerns a method for identifying molecules that can modulate the function of a polynucleotide fragment. In accordance with the first aspect of the invention, the polynucleotide fragment the function of which is to be modulated comprises at least 18 consecutive nucleotides the sequence for which corresponds to all or part of a gene on human chromosome 3 selected from the KIAA1042, CCK, CACNA1D, ARHGEF3 and AL133097 genes. In accordance with the second aspect of the invention, the polynucleotide fragment the function of which is to be modulated comprises at least 18 consecutive nucleotides the sequence for which corresponds to all or part of a gene on human chromosome 5 selected from the KLHL3, HNRPA0, CDC25C, EGR1, C5orf6, C5orf7, LOC51308, ETF1, HSPA9B, PCDHA1 to PCDHA13, CSF1R, RPL7, PDGFRB, TCOF1, AL133039, CD74, RPS14, NDST1, G3BP, GLRA1, CSorf3, MFAP3, GALNT10 and FJ117151 genes. Finally, in accordance with the third aspect of the invention, the polynucleotide fragment the function of which is to be modulated comprises at least 18 consecutive nucleotides the sequence for which corresponds to all or part of a gene on human chromosome 11 selected from the GUCY A2, CUL5, ACAT1, NPAT, ATM, AF035326, AF035327, AF035328, BC029536, FLJ20535, DRD2, ENS303941, IGSF4, LOC51092, BC010946, TAGLN, PCSK7 and ENS300650 genes.
The method for identifying molecules that are capable of modulating the function of one or other of said fragments comprises a step for bringing the molecule to be tested into the presence of the polynucleotide fragment. Another step in the method is detecting a variation in a parameter linked to the function of said fragment, for example detecting any binding of said molecule to the polynucleotide fragment demonstrated by a ligand detection technique.
The “second use of the invention” is the use of an agent modulating the function of a DNA fragment corresponding at least in part to one of the genes of the invention. The screening method allows such agents to be identified.
The various functions which a polynucleotide fragment can carry out have already been explained in the present application. In particular, these functions depend on the nature of the polynucleotide fragment, for example whether it is DNA or RNA. Modulation of the function may correspond to a reduction in the capacity to be transcribed or translated or to a change in the capacity to interact with other factors. Depending on the properties of said fragment, the skilled person can determine the parameter the variation of which is easy to monitor.
The identification method of the invention is not limited to the steps described above; other anterior or posterior steps can be applied.
The present invention also encompasses molecules identified by the method described above. In particular, the present invention encompasses inhibitors for the functions of the polynucleotide fragments of the invention.
The present invention also concerns methods for screening molecules that are capable of modulating the function of the expression product of a polynucleotide fragment of the invention. In accordance with the first aspect of the invention, the expression product the function of which is to be modulated is that of a DNA fragment that belongs to and/or corresponds to all or part of one of the 5 genes of the invention on human chromosome 3. In accordance with the second aspect of the invention, the expression product the function of which is to be modulated is that of a DNA fragment belonging to and/or corresponding to all or part of one of the genes of the invention on human chromosome 5. In accordance with the third aspect of the invention, the expression product the function of which is to be modulated is that of a DNA fragment belonging to and/or corresponding to all or part of one of the 18 genes of the invention on human chromosome 11. Preferably, the DNA fragment comprises at least 18 nucleotides.
The method for identifying molecules that can modulate the function of the expression product of a DNA fragment as described comprises a step for bringing the test molecule into the presence of the expression product. A further step in the method is detecting a variation in a parameter linked to the function of said expression product, for example detecting any binding of said molecule to the expression product, demonstrated by a ligand detection method.
As mentioned above in the application, the term “expression product of a DNA fragment” means both RNA molecules derived from transcription of the fragment at any maturation stage, and polypeptides from translation, at any maturation stage. For a molecule of RNA, different maturation stages are represented for example by the presence or absence of a cap, a polyadenylated tail. The term “various maturation stages of a polypeptide” includes, inter alia, polypeptides before and after folding, before and after cleavage of the various addressing signals, with or without glycosylation, and with or without disulfide bridges.
The functions fulfilled by the expression products of DNA fragments are very numerous and depend on the nature of the expression product in question. Examples have already been given above in the present application.
The “third use of the invention” is the use of an agent modulating the function of the expression product of a DNA fragment. The screening method allows such agents to be identified. Regarding what should be understood by the term “modulate the function of the expression product of a DNA fragment”, examples have already been given to define the third use of the invention.
Depending on the properties of said expression product, the skilled person is capable of determining the parameter the variation of which is easy to monitor.
The identification method of the invention is not limited to the steps described above; other anterior or posterior steps can be applied.
The present invention also encompasses the molecules identified by the method described above. In particular, the present invention encompasses inhibitors of the functions of the expression products of the polynucleotide fragments of the invention.
The present invention also allows to bring to light the genes involved in skin, hair and phanera pigmentation, within the three chromosomal zones of the invention. One particular use envisaged by the present invention thus consists of using SNP markers in each of the chromosomal regions of interest with the aim of localizing the genes involved in pigmentation more accurately, and more particularly those involved in the progressive or sudden interruption in the pigmentation of the skin or of the phanera.
The present invention resides in the identification by the inventors of genes on human chromosomes 3, 5 and 11 involved in the pigmentation or depigmentation phenomenon. This genetic basis has allowed them to envisage the uses in therapy and cosmetics described above, as well as the diagnostic methods illustrated above.
However, as mentioned above, the inventors suspect that many genes are involved in pigmentation phenomena and in those linked to regulation and cessation of that pigmentation.
For this reason, particularly preferred uses are those which are drawn from a combination of the results obtained for the three chromosomal zones of the invention.
In particular, a first combinational use in the cosmetics and therapeutic fields preferably employs at least two polynucleotide fragments the sequence of each of which corresponds at least in part to that of one of the 5 genes of the invention on human chromosome 3 or to that of one of the genes of the invention on human chromosome 5, or to that of one of the 18 genes of the invention on human chromosome 11.
Furthermore, in another patent application filed on the same day by the same Applicant, the inventors used a similar method to identify other genes which are also involved in the pigmentation or depigmentation phenomenon, on chromosomes 6 (between markers D6S1629 and D6S257) and 9 (between the D9S290 marker and the telomeric region). This genetic basis has allowed them to envisage therapeutic and cosmetic uses that are similar to those described above, as well as diagnostic methods that are similar to those illustrated above.
Preferably, two or more fragments are used, the sequence of at least one of which corresponds at least in part to those mentioned above on chromosomes 3, 5 and 11, the sequence of the other or others corresponding at least in part or to those mentioned above on chromosomes 3, 5 and 11, or to that of a gene on human chromosome 6 selected from the HLAG, NT—007592.445, NT—007592.446, NT—007592.506, NT—007592.507, NT—007592.508, HSPA1B, G8, NEU1, NG22, BAT8, HLA-DMB, HLA-DMA, BRD2, HLA-DQA1, HLA-DQA2, NT—007592.588, GRM4, RNF23, FLJ22638, NT—007592.459 and NT—007592.457 genes, or to that of a gene on human chromosome 9 selected from the FREQ, NT—030046.18, NT—030046.17, GTF3C5, CEL, CELL, FS, ABO, BARHL1, DDX31, GTF3C4 and Q96MA6 genes. Preferred genes are DDX31 and GTF3C4.
Preferably, of the different polynucleotide fragments employed, at least two have sequences corresponding to two distinct chromosomes or to two distinct genes. It is also envisageable that for the same gene, the various fragments employed have different chemical natures, for example DNA for the first fragment and RNA for the second fragment. It can also be envisaged that the different fragments could have a sequence corresponding to the same gene, but with small variations permitted by the definition of “corresponding sequences”, i.e. at most one different nucleotide in 10, preferably 1 in 100.
The fragments contain at least 18 consecutive nucleotides, said 18 nucleotides forming the sequence which must at least partially correspond to one of the genes of the invention. One of the fragments contains at least 18 successive nucleotides corresponding at least in part to one of the genes of the invention.
All of the preferred uses, the chemical nature of the fragments, their environment, have already been explained in detail in the section describing the first use of the invention.
When at least two polynucleotide fragments are used, said two fragments are preferably carried by distinct molecules. It can also be envisaged that said two fragments could, for example, form part of the same vector. In a preferred case, the different fragments are of the same chemical nature, for example DNA for all fragments.
For therapeutic uses, the polynucleotide fragments are used in the manufacture of a medicament.
A second combinational use envisaged by the present invention in the cosmetics and therapeutic fields is the use of a combination of at least two agents each modulating the function of a DNA fragment selected from fragments belonging and/or corresponding to all or part of one of the 5 genes of the invention on human chromosome 3, or to one of the genes of the invention on human chromosome 5 or to one of the 18 genes of the invention on human chromosome 11.
A preferred use is drawn from the results obtained on chromosomes 6 and 9. Thus, it is advantageous to use two or more agents, at least one modulating the function of a DNA fragment selected from fragments belonging and/or corresponding to all or part of the genes mentioned above on chromosomes 3, 5 and 11, the other agent or agents each modulating the function of a DNA fragment selected from fragments belonging and/or corresponding to all or part of a gene of the invention or to a gene selected from the HLAG, NT—007592.445, NT—007592.446, NT—007592.506, NT—007592.507, NT—007592.508, HSPA1B, G8, NEU1, NG22, BAT8, HLA-DMB, HLA-DMA, BRD2, HLA-DQA1, HLA-DQA2, NT—007592.588, GRM4, RNF23, FLJ22638, NT—007592.459, NT—007592.457, FREQ, NT—030046.18, NT—030046.17, GTF3C5, CEL, CELL, FS, ABO, BARHL1, DDX31, GTF3C4 and Q96MA6 genes. Preferred genes are the DDX31 and GTF3C4 genes.
Preferably, of the different agents employed, at least two modulate the function of DNA fragments corresponding to two distinct chromosomes or to two genes. It is also envisageable that for the same chromosomal zone, the different agents employed modulate different functions of the same DNA fragment.
The fragments of DNA the function of which is modulated in accordance with the invention preferably contain at least 18 consecutive nucleotides, said 18 nucleotides forming the sequence which must at least partially correspond to one of the genes mentioned. One of the fragments contains at least 18 successive nucleotides corresponding at least in part to one of the genes of the invention.
All of the preferred uses for said agents have already been explained in detail in the section describing the second use of the invention.
For therapeutic uses, the agents are used in the manufacture of a medicament.
A third combinational use envisaged by the present invention in the cosmetics and therapeutic fields is the use of a combination of at least two agents each modulating the function of an expression product of a DNA fragment selected from fragments belonging and/or corresponding to all or part of one of the 5 genes of the invention on human chromosome 3, or to one of the genes of the invention on human chromosome 5, or to one of the 18 genes of the invention on human chromosome 11.
A preferred use is drawn from the results obtained on chromosomes 6 and 9. Thus, it is advantageous to use two or more agents, at least one modulating the function of an expression product of a DNA fragment selected from fragments belonging and/or corresponding to all or part of the genes of the invention on chromosomes 3, 5 and 11, the other agent or agents each modulating the function of an expression product of a DNA fragment selected from fragments belonging and/or corresponding to all or part of the genes mentioned above, or to all or part of a gene selected from the HLAG, NT—007592.445, NT—007592.446, NT—007592.506, NT—007592.507, NT—007592.508, HSPA1B, G8, NEU1, NG22, BAT8, HLA-DMB, HLA-DMA, BRD2, HLA-DQA1, HLA-DQA2, NT—007592.588, GRM4, RNF23, FLJ22638, NT—007592.459, NT—007592.457, FREQ, NT—030046.18, NT—030046.17, GTF3C5, CEL, CELL, FS, ABO, BARHL1, DDX31, GTF3C4 and Q96MA6 genes. Preferred genes are the DDX31 and GTF3C4 genes.
Preferably, of the different agents employed, at least two modulate the function of the expression product of DNA fragments corresponding to two distinct genes. It is also envisageable that for the same gene of the invention, the different agents employed could modulate different functions of the same expression product of a DNA fragment, for example RNA at different maturation stages, or RNA from different splices.
The fragments of DNA the function of the expression product of which is modulated in accordance with the invention preferably contain at least 18 consecutive nucleotides, said 18 nucleotides forming the sequence which must at least partially correspond to one of the genes mentioned. One of the fragments contains at least 18 successive nucleotides corresponding at least in part to one of the genes of the invention.
All of the preferred uses of said agents have already been explained in detail in the section describing the first use of the invention.
For therapeutic uses, the polynucleotide fragments are used in the manufacture of a medicament.
A fourth combinational use envisaged by the present invention in the cosmetics and therapeutic fields is the use of a combination of at least two expression products of DNA fragments selected from fragments belonging and/or corresponding to all or part of one of the 5 genes of the invention on human chromosome 3, or to one of the genes of the invention on human chromosome 5, or to one of the 18 genes of the invention on human chromosome 11.
A preferred use is drawn from the results obtained on chromosomes 6 and 9. Thus, it is advantageous to use two or more expression products, at least one being the expression product of a DNA fragment selected from fragments belonging and/or corresponding to all or part of one of the genes of the invention, the other or others each being the expression product of a DNA fragment selected from fragments belonging and/or corresponding to all or part of a gene of the invention or to a gene selected from the HLAG, NT—007592.445, NT—007592.446, NT 007592.506, NT 007592.507, NT—007592.508, HSPA1B, G8, NEU1, NG22, BAT8, HLA-DMB, HLA-DMA, BRD2, HLA-DQA1, HLA-DQA2, NT—007592.588, GRM4, RNF23, FLJ22638, NT—007592.459, NT—007592.457, FREQ, NT—030046.18, NT—030046.17, GTF3C5, CEL, CELL, FS, ABO, BARHL1, DDX31, GTF3C4 and Q96MA6 genes. Preferred genes are the DDX31 and GTF3C4 genes.
Preferably, of the different expression products employed, at least two are derived from DNA fragments corresponding to two distinct chromosomes or to two distinct genes. It is also envisageable that for the same gene of the invention, the different expression products employed could derive from the same DNA fragment, for example from RNA at different maturation stages, or RNA from different splices. The same possibilities apply to polypeptides derived from RNA translation.
The fragments of DNA the function of the expression product of which is modulated in accordance with the invention preferably contain at least 18 consecutive nucleotides, said 18 nucleotides forming the sequence which must at least partially correspond to one of the genes mentioned. One of the fragments contains at least 18 successive nucleotides corresponding at least in part to one of the genes of the invention.
All of the preferred uses of said agents have already been explained in detail in the section describing the fourth use of the invention.
For therapeutic uses, the polynucleotide fragments are used in the manufacture of a medicament.
For the four types of combinational uses described above in the context of the invention, the cosmetic uses preferably apply to the pigmentation field.
Of the many combinations envisaged by the present invention, a highly advantageous combination comprises at least one polynucleotide fragment or an expression product of a sequence corresponding to all or part of the DDX31 or GTF3C4 gene on human chromosome 9.
In order to profit from the combination of these chromosomal zones, the present invention also concerns combinational methods. Said methods are employed to determine any predisposition to premature canities.
A combinational method of the invention for determining a predisposition to premature canities comprises a first step for selecting at least two markers which will be employed in subsequent steps. The selected markers are selected from markers belonging to the region of human chromosome 3 comprising the KIAA1042, CCK, CACNA1D, ARHGEF3 and AL133097 genes, the markers belonging to the region of human chromosome 5 comprising the KLHL3, HNRPA0, CDC25C, EGR1, C5orf6, C5orf7, LOC51308, ETF1, HSPA9B, PCDHA1 to PCDHA13, CSF1R, RPL7, PDGFRB, TCOF1, AL133039, CD74, RPS14, NDST1, G3BP, GLRA1, C5orf3, MFAP3, GALNT10 and FLJ117151 genes and the markers belonging to the region of human chromosome 11 comprising the GUCY1A2, CUL5, ACAT1, NPAT, ATM, AF035326, AF035327, AF035328, BC029536, FLJ20535, DRD2, ENS303941, IGSF4, LOC51092, BC010946, TAGLN, PCSK7 and ENS300650 genes. Preferred markers belong to one of these genes.
In a variation of the method, at least one of the selected markers is selected from markers belonging to one of the regions mentioned above on chromosomes 3, 5 and 11, the other selected marker or markers belonging to the chromosomal regions mentioned above, or to that on human chromosome 6 comprised by markers D6S1629 and D6S257 or to that of human chromosome 9 comprised between the marker D9S290 and the telomeric region (long arm telomere). On chromosomes 6 and 9, the markers are preferably within a gene selected from the HLAG, NT—007592.445, NT—007592.446, NT—007592.506, NT—007592.507, NT—007592.508, HSPA1B, G8, NEU1, NG22, BAT8, HLA-DMB, HLA-DMA, BRD2, HLA-DQA1, HLA-DQA2, NT—007592.588, GRM4, RNF23, FLJ22638, NT—007592.459, NT—007592.457, FREQ, NT—030046.18, NT—030046.17, GTF3C5, CEL, CELL, FS, ABO, BARHL1, DDX31, GTF3C4 and Q96MA6 genes. Preferred genes are the DDX31 and GTF3C4 genes.
Preferably, of the selected markers, at least two do not belong to the same chromosomal region of the invention, and to the same gene of the invention.
The subsequent step in carrying out the method of the invention consists, for the selected markers, in determining the alleles present in a sample of genetic material from the individual undergoing the diagnostic test. Two different alleles carried by the two versions of the chromosome can be identified.
The conditions for carrying out said methods have already been explained in the part concerning diagnostic methods.
For the four types of combinational use described above, the combinations of the invention can be incorporated into a cosmetic or pharmaceutical composition as described above.
The combinational methods of the invention are not limited to the use of two markers, nor are they limited to the two steps described; they may contain other steps which are anterior or posterior to the two steps already mentioned.
In particular, a combinational method of the invention may comprise the supplementary step of comparing the allelic form of the selected markers with the allelic form of the same markers in other individuals. This supplementary comparison step may prove necessary in order to establish a diagnosis. In this case, it may be useful to make the comparison with the form of the markers in individuals who are manifestly affected by premature canities and optionally also with the form of the markers in individuals who are manifestly free from such a predisposition.
Regarding the diagnostic methods already mentioned in the present invention, one particularly advantageous situation consists in comparing the alleles of selected markers with the same markers in other individuals of the same family as the individual to be diagnosed.
Finally, the present invention can identify the genes involved in the pigmentation of the skin, hair and superficial body growth, in the five chromosomal zones mentioned. One particular use envisaged by the present invention thus consists of using a combination of SNP markers in each of the chromosomal regions of interest with the aim of localizing the genes involved in pigmentation more accurately, and more particularly those involved in the progressive or sudden interruption of the pigmentation of the skin or superficial body growth.
Finally, the present invention concerns a kit comprising a combination of at least two polynucleotide fragments selected from those comprising at least 18 consecutive nucleotides the sequence of which corresponds to all or part of one of the 5 genes of the invention on human chromosome 3, or to one of the genes of the invention on human chromosome 5, or to one of the 18 genes of the invention on human chromosome 11.
In a variation of the kit, it comprises two or more fragments, the sequence of at least one of which corresponds at least in part to those mentioned above on chromosomes 3, 5 and 11, the sequence of the other or of each of the others corresponding at least in part or to those mentioned above, or to that of a gene selected from the HLAG, NT—007592.445, NT—007592.446, NT—007592.506, NT—007592.507, NT—007592.508, HSPA1B, G8, NEU1, NG22, BAT8, HLA-DMB, HLA-DMA, BRD2, HLA-DQA1, HLA-DQA2, NT—007592.588, GRM4, RNF23, FLJ22638, NT—007592.459, NT—007592.457, FREQ, NT—030046.18, NT—030046.17, GTF3C5, CEL, CELL, FS, ABO, BARHL1, DDX31, GTF3C4 and Q96MA6 genes. Preferred genes are the DDX31 and GTF3C4 genes.
abscissa=position on genetic map (0=pter) ordinate=NPL score
The distance between markers is indicated in cM.
The columns show the mean Lod score, standard deviation, the minimum Lod score, the maximum Lod score and the group (A-E) in which the family is placed according to the score.
Potential Lod scores as a function of the degree of heterogeneity.
Results expressed by family
Results expressed by family.
Results expressed by family.
Results expressed by family.
Summary of Studies
In order to localize the gene or genes for premature canities (PC), a segregation analysis (genetic linkage) program was carried out in families for whom this trait is transmitted across the generations. At the end of a series of pre-selections on the basis of the statistical power of the sample and phenotype confirmation, twelve families were retained to participate in a linkage study and DNA was prepared from a sample of peripheral blood from each of the informative individuals (with and without the trait). The study was carried out using two principal approaches, analysis is targeted on a candidate region and a global genome study on the twenty-two autosomal chromosomes and the X chromosome.
From the set of analyses carried out, fixing or not fixing the parameters for transmitting the PC trait, 3 potential loci were discerned on chromosomes 11, 5 and 3 in addition to those identified on chromosomes 6 and 9. The three loci (chromosomes 11q14-q22, 5q31-q32, 3p14.1-p12.3) showed signs suggesting a link to PC.
This study, and in particular the discordance between the scores obtained for the parametric/non-parametric analyses, suggests that premature canities is not caused by a small number of genes with major effect, but rather it is governed by a multifactorial system involving the action of several predisposition genes.
Introduction
The hereditary nature of premature canities (PC) or the appearance of white hairs early in life is a long-held hypothesis because of the familial nature of premature whitening of the hair in some people.
To explore canities from a genetic viewpoint, a DNA segregation study was carried out in families in which canities appeared very early in life. To guarantee the best chances of success for this gene hunt, the composition of the sample for the study was determined using a rigorous protocol for attributing phenotype and for selecting families. The PC phenotype was only attributed to individuals of less than 25 years of age who had white hairs and for whom half of the hair of the head was gray at 30 years old. The families were retained for study on the basis of their statistical performance in the segregation analysis.
This part of the study is described using four principal periods:
The results obtained for each period are shown in the form of tables and Figures in a summary manner in the summarizing tables or in more detail in the detailed tables.
Results
A-Period 1: Choice of Families with the Aid of Binding Analysis Simulation
At the end of an attempt to select families with premature canities using informativity criteria for gene localization, 29 families underwent a genetic linkage analysis simulation. On the basis of the availability of all individuals, this project appeared to have very encouraging potential for success as nineteen pedigrees (i.e. 255 individuals) were then retained. This conclusion was only valid if the phenotypes were confirmed and if the majority of subjects agreed to participate in the study. In this selection there were seven highly informative families who individually could achieve or exceed a Lod score of Z=4.00 (i.e. greater than the lower limit of significance for a Lod score, which is Z=3.00). To stand the greatest chance of success, it was very important that the PC diagnosis was attributed rigorously.
The results of this study allowed the families which were then collected for the genetic study to be determined because of the robust nature of the clinical evaluation.
1. Criteria for Attributing a PC Phenotype
Twenty-nine families out of 65 were retained using structural criteria (total number of individuals, those affected, available) for the simulation analysis.
During the simulation process:
Clearly, these estimates only remain valid in the case in which each individual was viewed as having been attributed with the correct phenotype. In the event of uncertainty, the phenotype had to be indicated as unknown; it was then not taken into account in the study and thus did not have to be sampled. The Lod score reduced (in varying proportions) each time an individual was removed for an uncertain phenotype.
Genealogical trees were re-drawn using pedigree editing software which also constructed coded files (preplink files) for the genetic linkage analysis. In addition to codes indicating for each individual the parentage, sex, phenotype and genotype which was supplemented by the SLINK simulation software, an availability code (cd) (table 1) was attributed. It also weighted the informative character of each individual in the study using a code from 0 to 3.
The phenotype for each individual was assigned using the information in the pedigrees and descriptive tables of the Genormax report. However, for some individuals, the phenotype was modified using the criteria indicated in Table 2. The individuals not present in the initial pedigrees (identified by a number only) were phenotypically unknown, and were considered to be unavailable (cd=3).
a. Availability Codes
During the simulation, the only individuals taken into account were those for whom (Table 1):
the phenotype for premature canities had been clearly defined (Table 2).
b. Assignment of Phenotype According to Age
In order to avoid the risk of errors, the following criteria were defined for assigning phenotype as a function of age in individuals below 30 years of age. However, during the final clinical examination, it was desirable for the definition of the phenotype to be more quantitative.
c. Other Parameters
After examining the variation in the maximum Lod score in the Can65 family (test 100, 200, 300, 500 replications), the number of replications (generations of allelic combinations) was finally fixed at 200.
The frequency of the trait was fixed at 1%. The number of possible alleles for the genotype was fixed at 6 with an equivalent frequency for each one.
2. Results
a—Classification of Families According to Scores
Table 3 gives an indication of the GENORMAX family potential as a function of the maximum Lod score (Zmax) achieved (group A-E).
The maximum Lod score could only be achieved when a DNA marker was 100% informative in a family. Usually, even with the type of markers used (the most informative markers in the chromosomal regions to be examined), the Lod score will not reach its maximum value.
On genetic linkage analysis, to be significant, the Lod score has to reach or exceed a value of 3 (result to 1000/1).
b—Effect of Incorrect Diagnosis on Linkage Analysis Results
The effect of attributing an incorrect diagnosis was tested on the results of the analysis (in the case of linkage to a locus) by a simulation on family Can 46 by varying the phenotype of 1, 2 or 3 individuals (Table 4).
3. Discussion, Conclusion and Decisions
This simulation study allowed the 29 pre-selected families to be placed into 5 groups according to the maximum potential Lod score. While a linkage was significant as soon as a Lod score value of Z=3.00 was achieved, the inventors preferred to distinguish 2 groups when this criterion was verified, as the maximum simulated Lod score was very rarely reached. Thus, the probability for the real Lod score for families in group B (3≦Zmax<4) was quite low.
The families from group A were informative for genetic linkage analysis for localization of the gene/genes for premature canities. To this end, there could be no uncertainty as regards phenotype. In the case of doubt, it was recommended that the individual or even the family be excluded from the study.
However, in some of these families, the high proportion of affected/unaffected individuals (sometimes all children affected) must constitute a strong defence of the 100% genetic nature of the trait. Clearly, it cannot be excluded that in certain families the PC gene has been transmitted simultaneously by the paternal and maternal branches of the first generation. In this case, the young children were all affected (Can28, 43, 53 . . . ). In order to be able to consider these few families positively, it was highly desirable that this hypothesis be verified.
Families from group B were themselves very interesting as they allowed the sample to be expanded even if individually they could not reach a significant Lod score in the majority of cases. As a group, however, they could consolidate the Lod score, especially if it turned out that the trait was also genetically heterogeneous (slightly).
The families from group C could also be used in studies for replication of the genetic linkage results.
The families from groups D and E (Zmax<2) were not very informative for genetic linkage analysis.
Subject to a robust clinical characterization, it appears that the families of groups A, B and C were suitable for a genetic linkage analysis and they had to be included (individuals with cd=2). Genetic linkage analyses carried out on insufficiently characterized samples were destined for failure or to produce a “soft” result (inaccurate locus). Given that in such analyses, certain parameters can not be totally under control (in particular the informativity of the genotypes) and that genetic heterogeneity, which is still possible, renders the job more difficult (as it reduces the power of the analysis over the set of families), it thus appears vital to hold all the possible advantages right from the start. In this first step, the inventors thus strongly recommended that the phenotype for each individual with an appropriate availability code (cd=2) be carefully verified before inclusion (phenotype confirmed, or exclusion from sample/family).
B—Period 2: Capture of Samples, Confirmation of Phenotypes and New Estimates of Study Potential
On the basis of the results from period 1, the 19 families (groups A, B and C) retained to form a base in which the pedigrees will be sampled for genetic linkage analysis were contacted to confirm the PC diagnosis and capture a series of affected and unaffected individuals.
This medical phenotype verification campaign allowed a large number of PC diagnoses to be confirmed, but not all as planned. The refusal of a few key individuals (with PC) to participate in the project, the death of some others and a readjustment of part of the phenotypes meant that a certain number of families could not be retained and that the informativity potential of some other families was reduced.
1—Re-Estimation of Study Potential after Phenotype Confirmation
To re-estimate the potential of the study after phenotype verification, the inventors simulated a linkage analysis for the 8 families who could still be informative. Table 5 shows the results obtained for this set of 8 families in 3 situations of genetic heterogeneity (0%, i.e. all families linked to the same locus, 50% or only half the families linked to the same locus, 70% or only about a third of the families being linked).
2—Conclusion
Continuing in our efforts to optimize the sample for the linkage analyses, 4 supplementary families were identified (Table 6; 2 families—can65B and can46B —were collateral branches of families can65 and can46) and the phenotypes were verified again.
Following a new simulation (Table 7), it appeared that the maximum general linkage Lod score was slightly higher (Z=8.91) if the 12 retained families (strictly defined phenotypes) were linked to the same locus. The expected increase in the Lod score by adding the new families was, however, reduced by the correction and hardening of the phenotypes.
The power of the sample could also be observed from the viewpoint of the number of replications which reached or exceeded the Lod scores Z=1.0, Z=2.0, Z=3.0 respectively and which gave an approximation of the chance of finding a significant link (Table 8).
C—Period 3: Genetic Linkage Analysis of PC with Candidate Region
1—Hypothesis
The region 3 p14.1-p12.3 was termed a “candidate region” (CR) as it is associated with premature canities in (Klein) Waardenburg's syndrome (Type IIA) disease with which the trait is associated.
2—Final Composition of Families
With the aim of optimizing the technique, a sample of 92 affected and unaffected individuals out of the 12 families was retained (see
3—Microsatellite Markers Used
The distribution of markers over the candidate region on chromosome 3 is shown in
4—Linkage Analyses
Several types of linkage analysis were carried out to increase the probability of observing an existing linkage between the chromosomal region and PC.
For this analysis, the following two approaches were made:
The results are shown in Table 11.
6—Discussion and Conclusion
This study also highlights a locus strongly suggesting a predisposition to premature canities on chromosome 3 p14-p12 (towards markers D3S2409 and D3S1766; multipoints NPL=2.58 at position 12 and HLod:=1.55 at position 24).
This result positively documents the association assumptions relating to the chromosomal region 3p14-p12 as regards premature canities.
It should be noted that one family (CAN35) showed a relatively high linkage for this chromosomal region.
D—Period 4: Global Genetic Linkage Analysis of PC with the Genome
Global genome analysis allowed all of the chromosomes to be visited (global probe) to find regions which are involved and possibly a major locus which would govern premature canities. This major analysis also allowed the degree of genetic heterogeneity of PC to be estimated.
1—Content of Families
These were the same families as those studied in the candidate region phase (period 3), however with certain adjustments as regards their content (see Table 12). Some less informative members were replaced by others who had been recruited more recently, or for whom a diagnosis had been made later on.
In order to confirm the benefit of the change in the sample, a new linkage analysis simulation was carried out for the different genetic heterogeneity situations (Table 13 and the tables in
The power of the sample can also be observed from the viewpoint of the number of replications (genotypes) which achieve or exceed the Lod scores Z=1.0, Z=2.0, Z=3.0 respectively. The probability of finding a significant linkage (Table 14 and
Thus, the analyses could indicate significant linkages if the heterogeneity of the sample did not exceed 20% (i.e. only 1/5 of families not linking to a single major locus), but it is still possible to identify a linkage in the case in which half of the families are not linked to this locus.
2—DNA Markers
DNA from 96 individuals belonging to the selected 12 families was genotyped for 400 polymorphous markers distributed over 22 autosomes and the X chromosome (Table 15) using a mean inter-marker interval of 9.2 cM (density). These are DNA microsatellites which are composed of dinucleotide (CA)n type tandem repeats from the Genethon collection (Evry, France).
The observed mean degree of heterozygosity was 0.70, and the mean size of the inter-marker interval was 9.2 cM.
3—Linkage Analyses
For this global approach, the inventors carried out several types of analyses to optimize their performance in finding a linkage between a region of the genome and PC. Parametric analysis, which was more powerful, takes into account the mode of transmission of the trait and is the most suitable in the case of monogenic traits. Non-parametric analysis can identify a linkage even if the assumed mode of transmission is erroneous, and is also more robust in the case of multigenic traits.
For each of these analyses, the inventors used the methods mentioned above, the 2-point method (iterative analysis between the trait and each marker) and the multipoint method (global analysis on each chromosome using a marker map).
a—Analyses with Defined Parameters, Parametric (PL)
This is a deviation analysis of the proportion of alleles shared by pairs of affected individuals compared with random transmission of alleles (identity by descent). The inventors considered all pairs of affected individuals for the multipoint analysis, and pairs of siblings for the 2-point analysis.
The linkage probability scores were expressed as:
a—Detailed Results
Tables 16 (best 2-point analysis results) and 17 (best multipoint analysis results) report the best results obtained for the retained chromosomes.
b—Retained Results
Table 18 reports the best results retained for each type of analysis (PL, NPL) discussed below:
i) At end of PL:
a—A Lod score (2P) ZH=2.007 was obtained on the long arm on chromosome 5 (position 164.2 cM from the upper telomere), i.e. in a position 3/4 on the 5q31-q32 band.
b—Intermediate Lod scores (1.5<ZH<2.0)
We distinguished log10 scores for the allelic sharing deviation study, identity by descent (IBD), for all affected pairs (multipoint Z-all study scores) as well as p values for pairs of affected siblings (affected sib-pairs, 2-point study scores, p-values).
The best scores are shown as their rank compared with the limit of significance:
Z-all>3, 2.5<Z-all<3, 2.0<Z-all<2.5
On chromosome 6p21-p12, the score reached using the global genome markers had a Z-all=3.52 in position 71 (between markers D6S1610 and D6S257). However, the accuracy of the locus was probably affected by the large distance between these 2 markers of the global genome collection which was much larger than the observed mean interval (26.11 cM).
The second best score was achieved for chromosome 9q31-q32, position 151 (Z-all=3.37).
b—2.5<Z-all<3.0 scores
iii) Loci simultaneously identified by PL and NPL:
5—Discussion and Conclusion
Two scores which were significant or on the border of significance depending on whether the trait was considered to be monogenic or multifactorial (Lander and Kruglyak, 1995) were observed for chromosomes 6p21-p12 (NPL MP Z-all=3.59) and 9q31-q32 (NPL MP Z-all=3.37).
For these 2 loci, the most robust was that of 6p21-p12 which was reinforced by a MP-PL Lod score, which although average, maximized at ZH=1.42).
A further locus also appeared to be fairly interesting, and was located on the chromosome 11q14-q22 as the PL and NPL scores maximized at the same position 106 (Z-all 2.61, PL 1.52). The NPL score was in the suggestivity range in a case of monogenism or in a case of multigenism (suggestivity: monogenism 2<Z-all<3; multigenism 2.2<Z-all<3.6).
Finally, the locus 5q31-q32 with the best PL Lod score (2P) (ZH=2.00) was also located within suggestivity values (in monogenism).
A p value series had to be added for the sib affected analyses which were also within the suggestivity range (chromosomes 6q31.3-q33). These loci are also to be considered.
D—Discussion and General Conclusions
At the end of the various analysis periods, several chromosomal regions had been identified or suggested.
Validity of loci 11q14-q22, Sq31-q32, 3p14.1-p12.3
a—Chromosome 11g14-g22
The inventors identified a region between positions 100 and 115 (between D11S898 and D11S925) (
b—Chromosome 5q31-q32
This region had the same PL and two-point result for these analyses which was located at recombination fraction (theta) 0.14 (about 14 cM) from the D5S422 marker. By placing itself at this distance from D5S422 towards the top of the map (position 149), we arrive in the vicinity of the locus which has the best NPL multipoint score for chromosome 5 (Z-all=1.70, towards marker D5S436). A certain consensus also appeared for this locus (
c—Chromosome 3p14.1-p12.3
This is a region of almost 30 cM between positions 60 and 87 (between D3s1277 and D3s 1285 (
Subsequent to the work presented in Example 1, the inventors continued the analysis of the regions of chromosomes 3, 5 and 11 using techniques based on SNPs, to highlight the genes involved in premature canities.
Analysis of the whole of the genome of families for which the premature canities trait segregates highlighted 5 chromosomal regions which were linked with the phenotype. Beyond the loci 6p21-p12 (A) and 9q31-q32 (B) distinguished by significant Lod scores (nonparametric Lod score NPL=3.59 and NPL=3.36 respectively), other regions were of interest because of suggestive linkage scores in more than one analysis.
The region on chromosome 3 (3 p14.1-p12.3) showed results of equivalent amplitude obtained simultaneously in the study of candidate genes and global genome genes (candidate regions, multipoint non-parametric Lod score, CR-MP-NPL=2.58, candidate regions, 2-point parametric Lod score, CR-2P-PL=1.55, global genome, multipoint non-parametric Lod score, GG-MP-NPL=2.62).
The region on chromosome 5 (5q31-q32) was retained because of a single locus in PL-2 point analysis which achieved a significant Lod score (GG-2P-PL=2.00).
The region on chromosome 11 (11q14-q22) was retained because its score was among the five highest in NPL and in PL (GG-MP-NPL=2.61, and GG-2P-PL=1.52).
SNPs (single nucleotide polymorphisms) represent a form of polymorphism which is particularly widespread through the human genome and is very stable. The number of SNPs is estimated to be about 0.8 SNPs per 1000 nucleotides (coding and non coding sequences together) which allows a true map of the human genome to be established using SNPs. SNPs are often classified into different categories, in particular depending on whether or not they are in a coding region, in a regulating region or in another non coding region of the genome, whether the polymorphism modifies the coded amino acid or not, etc.
Following the “Human Genome Project”, SNPs are better known and recorded, including as their position in the genome (GDB).
Different methods have been developed to highlight these polymorphisms between different individuals, often based on methods used to detect point mutations (RFLP-PCR, hybridization with specific allele oligomers, mini-sequencing, direct sequencing, etc).
In the context of the present application, the inventors have used MALDI-TOF techniques (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry) to detect the different alleles of candidate SNPs. The skilled person will have more details of this technique, and they have been described in many publications (Stoerker J et al, Nat Biotechnol 2000, November; 18(11): 1213-6 and Tang K et al, Proc Natl Acad Sci USA 1999 August, 96, 10016-20).
In a first stage, the inventors defined the regions of chromosomes 3, 5 and 11 to be analyzed very accurately using SNPs. In a second step, 3848 SNPs belonging to the above regions were pre-selected on the basis of certain criteria (candidate SNPs in silico) and 3227 were retained following an experimental validation step. In a subsequent step, the inventors collected DNA from different individuals with premature canities and “control” individuals into different groups, then genotyped these different groups using 1264 SNPs selected out of the 3227.
The different steps are described in more detail in the following sections.
1—Definition of Regions to be Analyzed by SNPs
In a first stage, the inventors more precisely defined the regions of interest on chromosomes 3, 5 and 11, from results obtained from an analysis with microsatellite markers (see Example 1) for the 12 selected families (see Table 6).
The region of chromosome 3 denoted region C was defined by its chromosomal position and by three other types of coordinates for optimum precision and security in defining this region for the subsequent steps. The same was true for the region on chromosome 5 denoted region D, and for the region on chromosome 11, denoted region E.
The table below records the various cartographic characteristics of regions C, D and E (code and size of region in Mb and Kb, number of microsatellite markers bordering these regions, position on genome sequence, number of SNP). The two columns for the positions on the genome differ depending on the version of the database used (NCBI UCSC freeze April 2002 and June 2002).
The cumulative size of the three regions C+D+E was 77351 Kb, i.e. 77.106 bp.
*The position of the sequence (in terms of base pairs bp) is expressed as a function of the UCSC update number for the human genome database (http://genome.cse.ucsc.edu/) and/or a number for the assembled human genome sequence, in April 2002 (i.e. NCBI Build 29) or June 2002 (i.e. NCBI Build30).
UCSC Freeze (Correspondence with NCBI Assembled Genome Sequence, Build)
2—Investigation of SNP Candidates (In Silico) and Validation (Experimental)
Starting from regions C, D and E as defined above, a second step consisted of determining a collection of SNPs belonging to these regions to obtain a marker map for the three regions. These markers were also defined so that they covered the 77 Mbp (total length of the three regions) homogeneously and equidistantly. The distance between the different SNPs was fixed to an average of 50 kb. This operation was carried out by selecting 3848 SNPs satisfying these criteria (in silico SNP candidates).
Of the 3848 envisaged during the first step, 3332 SNPs were pre-selected, by removing SNPs separated by less than 14 kb. The selected 3332 SNPs were analyzed over the 92 control individuals (individuals from the Centre d'Etude du Polymorphisme Humain—Center for the study of human polymorphism) to validate the presence of at least two alleles for each SNP (polylmorphism validation).
3—DNA Pooling
In order to increase the genotyping capacity, a pooling strategy was carried out on the different DNAs. The power of this method has been recorded in various publications (in particular Werner et al, Hum Mutat 2002 July; 20(1):57-64, Bansal et al, Proc Natl Acad Sci USA 2002, Dec. 24;99(26): 16871-4).
To carry out pooling, DNA was assembled from different individuals with the “premature canities” trait (PC) and from control individuals. Pooling was carried out so that each of the DNA samples was represented in an equimolar manner, to guarantee that no individual would have a preponderant influence on the results. To this end, the exact concentration of each DNA sample was measured using the “picogreen” method in the various samples from individuals.
Groups were constituted taking into account a “phenotype score of canities intensity” which was attributed to each individual as follows.
Firstly, two sorts of criteria were defined, primary criteria to which score values of 2 were assigned, and secondary criteria to which score values of 1 were assigned.
There were 2 primary criteria (score value=2 for each), namely: (i) first white hairs below 18 years; (ii) fair pepper and salt hair at 30.
There were 3 secondary criteria (score value=1 for each), namely: (i) first white hairs below 25 years; (ii) dark pepper and salt hair at 30 years; (iii) family notion of premature canities.
Adding the scores for each individual with each of the diagnostic criteria meant that an intensity score for the premature canities phenotype could be assigned to each individual.
It was also possible to define several different groups depending on the phenotype score. Of the affected individuals, 72 individuals had a score of 4 or 5 or more and 132 individuals had a phenotype score of 2 or more.
Group AI: this group was constituted by DNA from 72 PC individuals with a phenotype score of 4 or 5.
Group AII: this group was constituted by DNA from 132 PC individuals with a phenotype score of 2, 3, 4 or 5.
Groups BI and BII: these groups were constituted by DNA from control individuals with a geographical origin close to that of the PC individuals. For these control individuals, the criteria for selection were: (i) age over 40 years; (ii) no signs of canities in the control individual; (iii) absence of family notion of canities. The criteria for pairing with an individual from group A1 or AII were identical geographical origin, same sex and identical hair color at 18 years of age.
In this manner, in addition to affected versus unaffected pairing by the PC phenotype, each PC individual from group AI was represented by a control individual in group BI with a close or identical geographical origin. This was the same for each individual in group AII.
The constitution of the different groups is shown diagrammatically in
The use of these rigorous methods for clinical diagnosis of affected and control subjects guaranteed the reliability of the quality of the phenotype data.
Further, the rigor of pairing using the rules fixed by the inventors was a guarantee of the pertinence of the statistical analyses comparing the genomic data from these individuals whether grouped into pools or compared individually.
4—Selection of Validated SNPs for Genotyping on Grouped DNA
Different groups of SNPs were constituted as follows:
Definition of groups 1, 2, 3 and 4:
A collection of 2142 SNPs from groups 1 and 2 was then validated for a minimum frequency of the rarest allele of 10%. Several SNPs from groups 3 and 4 (frequency of rare allele <10%) were also retained to be able to complete certain zones in which there were not enough SNPs from groups 1 and 2.
Using this method, 3227 SNPs were then validated.
Of the 3227 validated SNPs, 1264 were selected during a new selection step.
This new selection was based on the following criteria:
The vast majority of SNPs was selected from group 1 which represented the greatest reliabity.
In order to provide better cover of the regions to be analyzed the global size of which was 77 Mb, the analysis was concentrated on the genic regions and regions close to genes which were susceptible of containing regulating sequences, abandoning the regions with no genes. This could increase the coverage density (reduce inter-SNP intervals) in the coding regions and thus increase the probability of having several positive SNPs in zones associated with the PC trait (premature canities). The term “gene regions” means both regions containing known genes and those which are susceptible of containing them (predicted genes).
5—Allotyping Pooled DNA
For the 1264 SNPs retained during step 4, the subsequent step was to determine their allelotype, i.e. the frequency of each of the alleles, for the 4 groups of pooled DNA depending on the severity and premature nature of the phenotype (see the definition of the 4 groups in step 3 and
The allelic frequency of the two alleles was determined for each of the SNPs in the 4 groups.
However, because the experiment was carried out on pools rather than on individual DNA, only the allelotype was determined using this method rather than the genotype.
The statistical significance of the differences in allelic frequencies between groups AI and BI or AII and BII was estimated by the “p” value representing the significance. The lower the p value, the more statistically significant was the distance.
The experiments were repeated 3 times (3 PCR), each of the three PCRs then being tested 5 times using MALDI-TOF to obtain a reliable mean value.
Only results for the groups of 72 PC and their controls were considered, these appearing to be more homogeneous (comparisons of groups AII-BII only furnished a few positive results, and suspicion regarding the presence of false negatives arose).
The frequency of the two alleles for each of the SNPs was calculated for the different grouped DNAs. However, the genotypes were not determined in this type by this study and as a result, their frequencies among the different groups will not be available.
The statistical significance of the allelic frequency distances between the groups is estimated by a value “p”. Only SNPs with a p value of less than 0.0.05 (%) were retained.
a—Table of Allelotype Comparisons Between the Groups
The following tables illustrate the results obtained in the form of tables.
Definition of columns:
Only SNPs having a p-value of less than 5% are shown in the table, with the exception of negative SNPs located between two positive SNPs, which determines a double spot and those framing a cluster of interest.
The table below summarizes the number of positive SNPs in each region depending on whether they are:
linkage disequilibrium/frequencies
*LD: linkage disequilibrium
Results
i—Region C
Region C is characterized by a relatively large number of isolated positive SNPs. In contrast, the number of double spots or clusters was relatively low. LD (linkage disequilibrium) analysis and combined allelic frequencies revealed only 3 zones of interest. Of these 3 zones, 2 loci (positions 41527287-41677819 and 55638663-56042041) were characterized by a p-value of <1%.
The genetic content of these 3 zones (C1, C2, C3) is developed below:
C1(41527287-41677819):
Region D is characterized by a relative cluster density, and LD and freq analysis also showed several regions of interest. Seven zones (D1, D2, D3, D4, D5, D6, D7) were revealed for their cluster arrangement, their LD potential and the arrangement of allele frequencies. Of these 7 zones, 5 (in bold; D2, D3, D5, D6, D7) appeared to be more promising because of the significance of the comparison with at least one SNP.
The genetic content of these 7 zones is developed as follows:
DI(136479801-137007868):
Region E is also characterized by a relative cluster density and LD analysis and freq analysis shows 6 region zones of interest (E1, E2, E3, E4, E5, E6). Three zones, in bold, E2, E5, E6) were more promising because of the significance of the comparison between the samples.
The genetic content of these 6 zones is developed below:
EI(108893187-108944206)
Examples of Compositions
This lotion was applied daily to the zones to be treated, preferably to the whole scalp, for at least 10 days and preferably 1 to 2 months.
A reduction in the appearance of white or gray hairs and re-pigmentation of gray hair was observed.
This shampoo was used at each wash, leaving it on the hair for about one minute. Long term use, of the order of two months, resulted in progressive re-pigmentation of gray hair. This shampoo could also be used preventatively to retard whitening of the hair.
This gel was applied to the zones to be treated twice daily (morning and evening) with a finishing massage. After three months application, repigmentation of hair was observed in the treated zone.
| Number | Date | Country | Kind |
|---|---|---|---|
| 0208697 | Jul 2002 | FR | national |
| PCT/FR03/02153 | Jul 2003 | WO | international |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 11031033 | Jan 2005 | US |
| Child | 11583512 | Oct 2006 | US |
