US20120144511A1 - Muteins of the pyrroline-5-carboxylate reductase 1 - Google Patents

Muteins of the pyrroline-5-carboxylate reductase 1 Download PDF

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US20120144511A1
US20120144511A1 US13/322,750 US201013322750A US2012144511A1 US 20120144511 A1 US20120144511 A1 US 20120144511A1 US 201013322750 A US201013322750 A US 201013322750A US 2012144511 A1 US2012144511 A1 US 2012144511A1
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pycr1
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Bruno Reversade
Stefan Mundlos
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Agency for Science Technology and Research Singapore
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Definitions

  • the present invention relates to muteins of the pyrroline-5-carboxylate reductase 1 (PYCR1).
  • PYCR1 pyrroline-5-carboxylate reductase 1
  • the present invention also relates to a method of determining in a subject a predisposition of having an age related disorder associated with PYCR1, methods of identifying a compound capable of modifying the expression of PYCR1, and methods of treating a subject having an age-related disorder associated with PYCR1.
  • the present invention further relates to a genetically modified animal and a method of modifying the expression of the PYCR1 gene in an animal.
  • Wrinldy skin and bone loss are typical features associated with ageing. In some monogenetic diseases, these changes occur prematurely resulting in a progeroid appearance of affected individuals.
  • wrinkly skin or cutis laxa is used as a common denominator of several overlapping syndromal disorders including autosomal dominant cutis laxa (ADCL; MIM 123700), autosomal recessive cutis laxa type I (ARCL1; MIM 219100), autosomal recessive cutis laxa type II (ARCL2; MIM 219200, also called wrinkly skin syndrome (WSS; MIM 278250)), de Barsy syndrome (DBS; MIM 219150), and gerodermia osteodysplastica (GO, MIM 231070). Diagnosis is often difficult in these conditions due to a broad clinical overlap.
  • the invention provides a mutein of the PYCR1, wherein at least one of the amino acid residues at sequence positions 4 to 220 and 222 to 266 of the wild type amino acid sequence of PYCR1 as set forth in Swiss-Prot Accession No. P32322 is mutated.
  • the invention provides a mutein of PYCR1.
  • the mutein includes a mutation of at least one of the amino acid residues at sequence positions 4 to 266 of the wild type amino acid sequence of PYCR1 as set forth in Swiss-Prot Accession No. P32322, wherein the mutation leads to a reduced function or loss of function of the mutein compared to the wild-type protein.
  • the invention provides a nucleic acid molecule.
  • the nucleic acid molecule includes a nucleotide sequence encoding a mutein as described above.
  • the invention provides a method of determining in a subject a predisposition of having an age-related disorder associated with pyrroline-5-carboxylate reductase 1 (PYCR1).
  • the method includes analyzing a nucleic acid sample obtained from a subject for the presence of a nucleotide sequence encoding a mutein as describe above, wherein the presence of the nucleotide sequence indicates a predisposition of the subject having or being at risk for having the age-related disorder.
  • the invention provides use of a nucleic acid molecule comprising a nucleotide sequence encoding a mutein described above, for diagnosing or determining a predisposition of having an age-related disorder associated with PYCR1.
  • the invention provides a method for identifying a compound capable of modifying the expression of a PYCR1 gene.
  • the method includes: contacting a compound of interest with a nucleic acid molecule comprising a nucleotide sequence encoding pyrroline-5-carboxylate reductase 1 (PYCR1) or a functional fragment or mutant thereof, and measuring the expression of the nucleotide sequence encoding pyrroline-5-carboxylate reductase 1 (PYCR1) or a functional fragment or functional mutant thereof.
  • the invention provides a method of modifying the expression of a PYCR1 gene in a cell.
  • the method includes introducing a nucleic acid molecule comprising a nucleotide sequence encoding pyrroline-5-carboxylate reductase 1 (PYCR1) or a functional fragment or functional mutant thereof into the cell.
  • PYCR1 pyrroline-5-carboxylate reductase 1
  • the invention provides a method of treating a subject having an age-related disorder associated with PYCR1 or being at risk to develop an age-related disorder associated with PYCR1.
  • the method includes introducing a nucleic acid molecule comprising a nucleotide sequence encoding pyrroline-5-carboxylate reductase 1 (PYCR1) or a functional fragment or functional mutant thereof into the subject.
  • PYCR1 pyrroline-5-carboxylate reductase 1
  • the invention provides a method of treating a subject having an age-related disorder associated with PYCR1 or being at risk to develop an age-related disorder associated with PYCR1.
  • the method includes administering to the subject a compound capable of modifying the expression of a PYCR1 gene.
  • the invention provides a genetically modified animal.
  • the genetically modified animal includes a nucleic acid encoding pyrroline-5-carboxylate reductase 1 (PYCR1), wherein the nucleic acid is inactive.
  • PYCR1 pyrroline-5-carboxylate reductase 1
  • the invention provides a method of modifying the expression of the PYCR1 gene in an animal.
  • the method includes administering to the animal a compound capable of modifying the expression of the PYCR1 gene.
  • the invention provides a method of identifying a compound capable of modifying the expression of a PYCR1 gene.
  • the method includes administering the compound of interest to a genetically modified animal as described above; and determining whether the compound is capable of modifying the expression of the PYCR gene.
  • the invention provides a method of identifying a compound capable of modifying the expression of a PYCR1 gene.
  • the method includes providing an isolated skin flap comprising at least one layer of living animal skin, said flap being attached to a test animal; and applying the compound of interest in contact with the living animal skin.
  • Mutations in PYCR1 associated with a spectrum of disorders characterized by wrinldy skin, osteoporosis and progeroid appearance are described herein.
  • the inventors have detected disease-causing mutations in the PYCR1 gene.
  • Such mutations of the PYCR1 gene are muteins of PYCR1, wherein at least one of the amino acid residues at sequence positions 4 to 220 and 222 to 266 of the wild type amino acid sequence of PYCR1 as set forth in Swiss-Prot Accession No. P32322 is mutated (see FIG. 6 ).
  • the muteins can comprise a mutation of at least one of the amino acid residues at sequence positions 4 to 266 of the wild type amino acid sequence of PYCR1 as set forth in Swiss-Prot Accession No. P32322, wherein the mutation leads to a reduced function or loss of function of the mutein compared to the wild-type protein.
  • the muteins described according to the invention can be identified or determined by any standard methods for example by homozygosity mapping using pooled DNA samples obtained from members of large kindreds in order to identify a chromosomal locus of interest or a candidate region thereof. Once a candidate region of the chromosomal locus is identified, the region can be screened for disease-causing mutations using conventional sequencing and genomic locus capture followed by high-throughput sequencing methods.
  • a mutein described according to the present invention can also be derived from a single nucleotide polymorphism (SNP).
  • SNP refers to a single nucleotide polymorphism at a particular position in the human genome that varies among a population of individuals. This single nucleotide polymorphism can for example be a single base change in the DNA sequence, with a usual alternative of two possible nucleotides at a given position.
  • a SNP may be identified by its name or by location within a particular sequence. Various methods known to persons skilled in the art can be used to produce SNPs.
  • SNPs according to the present invention can for example be derived from comparison of sequence data from Expression Sequence Tag (EST) production projects, in particularl if the libraries used were constructed using tissues from different individuals (Picoult-Newberg L., et al, Mining SNPs from EST databases, Genome Res. 9 (1999) 167-174).
  • SNPs according to the present invention can also be derived using a reduced representation shotgun (RRS) approach as described in Altshuler D. et al., An SNP map of human genome generated by reduced representation shotgun sequencing, Nature 407 (2000) 513-516.
  • RTS reduced representation shotgun
  • mutations into the wild type amino acid sequence of PYCR1 as long as the desired purpose is achieved, for example to achieve a reduced or loss of function of a mutein of the invention compared to the respective wild-type protein.
  • mutations can for example include substitutions, deletions and insertions of the wild type amino acid sequence of PYCR1.
  • Examples of possible alterations include conservatively modified variations where the alteration is the substitution of an amino acid with a chemically similar amino acid. Tables providing functionally similar amino acids are well known in the art.
  • amino acid sequence of PYCR1 can also be modified by non-conservative alterations.
  • At least one of the amino acid residues at sequence positions 4, 119, 179, 189, 206, 251, 257 and 266 of the wild type amino acid sequence of PYCR1 is mutated.
  • the mutation of the amino acid residue at sequence position 4 of the wild type amino acid sequence of PYCR1 can be mutated by a frameshift mutation leading to a translation stop codon occurring at the codon that encodes for sequence position 50 of the wild type amino acid sequence of PYCR1.
  • amino acid residue at sequence position 119 of the wild type amino acid sequence of PYCR1 can be replaced by glycine or histidine.
  • the amino acid residue at sequence position 179 of the wild type amino acid sequence of PYCR1 can be replaced by a hydrophilic amino acid.
  • the hydrophilic amino acid can for example be a hydroxyl-containing amino acid. Examples of such hydroxyl-containing amino acids include serine or threonine.
  • the amino acid residue at sequence position 189 of the wild type amino acid sequence of PYCR1 can be replaced by a hydrophobic amino acid.
  • the hydrophobic amino acid can for example be an aliphatic amino acid. Examples of such an aliphatic amino acid can include isoleucine, leucine and valine.
  • the amino acid residue at sequence position 206 of the wild type amino acid sequence of PYCR1 can be replaced by an aromatic amino acid or a positively charged amino acid.
  • aromatic amino acid can include phenylalanine, tyrosine and tryptophan.
  • positively charged amino acid can include arginine or lysine.
  • the amino acid residue at sequence position 251 of the wild type amino acid sequence of PYCR1 can be replaced by histidine.
  • the amino acid residue at sequence position 257 of the wild type amino acid sequence of PYCR1 can be replaced by a hydrophilic amino acid.
  • This hydrophilic amino acid can for example be a hydroxyl-containing amino acid. Examples of such a hydroxyl-containing amino acid can be a serine or threonine.
  • amino acid residue at sequence position 266 of the wild type amino acid sequence of PYCR1 can be replaced by glutamine or asparagine.
  • sequence of a mutein according to the present invention can also be modified for the purpose of improved stability, production, purification or applicability.
  • peptide segments which are not crucial for folding into a functional three-dimensional structure can be removed for these purposes, if wanted.
  • Disulfide bonds can be eliminated by substitution of the cysteine residues or new disulfide bonds can be introduced at another site.
  • cysteine residues can also be newly introduced in order to prepare, for example, corresponding protein conjugates by chemical coupling with other components.
  • Binding sites for further ligands, such as for example metal ions, can also be built into the mutein.
  • amino acid residue refers to an amino acid either in the D or L form or to an amino acid mimetic that can be incorporated into a polypeptide by an amide bond.
  • the positively charged amino acid residue at position 89 can for example either be a naturally occurring amino acid residue that is positively charged under physiological conditions such as arginine or lysine or a non-natural mimetic such as a lysine residue the ⁇ -amino group of which is alkylated in order to yield a (quarternary) ammonium-salt having a permanent positive charge.
  • wild type in reference to an animal or an amino acid sequence as used herein, means a phenotype, genotype or a gene that predominates in a natural population of organisms or strain of organisms in contrast to the forms that were genetically altered in a natural or artificial environment.
  • the clinical features of 35 affected individuals from 22 families were studied and summarized in Table 1. Those features include congenital skin wrinkling, most pronounced on the dorsum of hands and feet, generalized connective tissue weakness, finger contractures, hernias, osteoporosis and a triangular face with a progeroid appearance which is due to lax skin and hypoplasia of the jaw often resulting in prognathism ( FIG. 1 a - d ). Ultrastructural investigation of the skin revealed rarefaction and fragmentation of elastic fibers similar to changes described in autosomal recessive cutis laxa (ARCL) ( FIG. 1 e - h ). No glycosylation abnormalities were detected by standard diagnostics.
  • ARCL autosomal recessive cutis laxa
  • nucleic acid molecule comprising a nucleotide sequence encoding a mutein according to the present invention.
  • nucleic acid refers to any nucleic acid molecule in any possible configuration, such as a linearized single stranded, a double stranded or a combination thereof.
  • nucleic acids may include, but are not limited to DNA molecules (e.g., cDNA or genomic DNA), RNA molecules (e.g., mRNA), antisense RNA, short interfering (siRNA), micro RNA (miRNA), analogues of the DNA or RNA generated using nucleotide analogues or using nucleic acid chemistry, cDNA synthetic DNA, a copolymer of DNA and RNA, oligonucleotides, PNA (protein nucleic acids), or combinations thereof.
  • DNA or RNA may be of genomic or synthetic origin and may be single or double stranded.
  • a respective nucleic acid may furthermore contain non-natural nucleotide analogues and/or be linked to an affinity tag or a label.
  • nucleotide includes native (naturally occurring) nucleotides, which include a nitrogenous base selected from the group consisting of adenine, thymidine, cytosine, guanine and uracil, a sugar selected from the group of ribose, arabinose, xylose, and pyranose, and deoxyribose (the combination of the base and sugar generally referred to as a “nucleoside”), and one to three phosphate groups, and which can form phosphodiester internucleosidyl linkages.
  • the “nucleotide” also refers to nucleotide analogs.
  • Such analogs can have a sugar analog, a base analog and/or an internucleosidyl linkage analog. Additionally, analogs exhibiting non-standard base pairing are also included (see for example U.S. Pat. No. 5,432,272).
  • Such nucleotide analogs include nucleotides that are chemically modified in the natural base (“base analogs”), chemically modified in the natural sugar (“sugar analogs”), and/or chemically modified in the natural phosphodiester or any other internucleosidyl linkage (“internucleosidyl linkage analogs”).
  • the aromatic ring or rings contain at least one nitrogen atom.
  • the nucleotide base is capable of forming Watson-Crick and/or Hoogsteen hydrogen bonds with an appropriately complementary nucleotide base.
  • Exemplary nucleotide bases and analogs thereof include, but are not limited to, naturally occurring nucleotide bases, e.g., adenine, guanine, cytosine, uracil, and thymine, and analogs of the naturally occurring nucleotide bases, e.g., 7-deazaadenine, 7-deazaguanine, 7-deaza-8-azaguanine, 7-deaza-8-azaadenine, N6 ⁇ 2-isopentenyladenine, N2-dimethylguanine (dmG), 7-methylguanine (7mG), inosine, nebularine, 2-aminopurine, 2-amino-6-chloropurine, 2,6-diaminopurine, hypoxanthine, pseudouridine, pseudocytosine, pseudoiso
  • RNA uracil
  • a nucleic acid molecule used according to the invention can comprise a nucleotide sequence encoding a mutein of the present invention.
  • the nucleic acid used according to the invention can comprise a nucleotide sequence pyrroline-5-carboxylate reductase 1 (PYCR1) or a functional fragment or mutant thereof.
  • PYCR1 pyrroline-5-carboxylate reductase 1
  • the term “functional mutant” of PYCR1 used herein refers to a variant protein other than the muteins of the present invention, in which the function is essentially retained. For example, one or more amino acids that is not relevant for said function may have been exchanged.
  • the term “functional fragment” as used herein refers to a fragment of PYCR1, having sufficient length to provide its desired function.
  • a nucleic acid molecule as used herein such as DNA can for example be regarded to be “capable of expressing a nucleic acid molecule or a coding nucleotide sequence” or capable “to allow expression of a nucleotide sequence” if it contains regulatory nucleotide sequences which contain transcriptional and translational information and such sequences are “operably linked” to nucleotide sequences which encode a mutein of the present invention.
  • An operable linkage is a linkage in which the regulatory DNA sequences and the DNA sequences sought to be expressed are connected in such a way as to permit gene sequence expression.
  • regulatory regions needed for gene sequence expression may vary from organism to organism, but shall, in general include a promoter region which, in prokaryotes, contains only the promoter or both the promoter which directs the initiation of RNA transcription as well as the DNA sequences which, when transcribed into RNA will signal the initiation of the synthesis.
  • Such regions will normally include non-coding regions which are located 5′ and 3′ to the nucleotide sequence to be expressed and which are involved with initiation of transcription and translation such as the TATA box, capping sequence, CAAT sequences.
  • the nucleic acid molecule of or used in according to the invention can in some embodiments be altered by inserting or deleting at least one nucleotide from the nucleotide sequence. In other embodiments, at least one of the splice sites of the nucleotide sequence of the nucleic acid molecule can be mutated.
  • the term “splice site” refers to specific nucleic acid sequences that are capable of being recognized by the splicing machinery of a eukaryotic cell as suitable for being cut and/or ligated to a corresponding splice site. Splice sites allow for the excision of introns present in a pre-mRNA transcript.
  • the donor splice site typically the 5′ portion of the intron is referred to as the donor splice site and the 3′ corresponding splice site is referred to as the acceptor splice site.
  • the term splice site includes, for example, naturally occurring splice sites, engineered splice sites. Engineered splice sites may be mutated sites for example. The mutation of the splice sites enables the control of the ratio between the polypeptides translated from the different populations of transcripts. Splice sites are well known in the art and any may be utilized in the present invention.
  • the nucleic acid molecule may be comprised in a vector, for example an expression vector.
  • a vector is capable of integrating the nucleic acid as described above and can comprise a sequence coding for restriction cleavage site which adjoins the nucleic acid encoding the mutein of the present invention or PYCR1 or a functional fragment or mutant thereof in 5′ or/and 3′ direction.
  • the vector can also contain replication sites and control sequence derived from a species compatible with the host that is used for expression.
  • the term “vector” relates to a single or double-stranded circular nucleic acid molecule that can be introduced, e.g. transfected into cells and replicated within or independently of a cell genome.
  • a circular double-stranded nucleic acid molecule can be cut and thereby linearised upon treatment with restriction enzymes.
  • restriction enzymes An assortment of nucleic acid vectors, restriction enzymes, and the knowledge of the nucleotide sequences cut by restriction enzymes are readily available to those skilled in the art.
  • a nucleic acid molecule encoding a mutein of the present invention or PYCR1 or a functional fragment or mutant thereof can be inserted into a vector by cutting the vector with restriction enzymes and ligating the two pieces together.
  • Any vectors suitable for genetic cloning that are known to the person skilled in art can be used in the present invention. Examples of these vectors may include but are not limited to pUC18, pUC19, BR322, pBR325, pBR327 and pBR328.
  • the nucleic acid encoding the mutein of the invention or PYCR1 or a functional fragment or mutant thereof and/or the respective vector may be contained within a host cell capable of expressing the nucleic acid.
  • the host cell disclosed herein can also contain a nucleic acid as defined above.
  • the host cell as used herein includes any host cells that can be used as expression systems to produce recombinant proteins in particular the mutein as described above or PYCR or a functional fragment or mutant thereof.
  • Exemplary host cells are prokaryotic host cells, such as, but are not limited to, Escherichia coli ( E. coli ), Bacillus subtilis, and Salmonella typhimurium; and eukaroyotic host cells including mammalian, avian, fungal, and insect cells.
  • Various methods of introducing the vector into the host cell are known to persons skilled in the art, such as transformation, transfection, electroporation and biolistics.
  • the invention also provides a nucleic acid molecule comprising a nucleotide sequence encoding a mutein of the invention for use in diagnosing or determining a predisposition of having an age-related disorder associated with PYCR1.
  • the age-related disorder can be but is not limited to cutis laxa (wrinkly skin syndrome), de Barsy syndrome and gerodermia osteodysplasia.
  • the invention provides a method of determining in a subject a predisposition of having an age-related disorder associated with pyrroline-5-carboxylate reductase 1 (PYCR1).
  • the method includes analyzing a nucleic acid sample obtained from the subject for the presence of a nucleotide sequence encoding a mutein of the invention, wherein the presence of the nucleotide sequence indicates a predisposition of the subject having or being at risk for having the age-related disorder.
  • the invention also provides a method of identifying a compound capable of modifying the expression of a PYCR1 gene.
  • the method includes contacting a compound of interest with a nucleic acid molecule comprising a nucleotide sequence encoding PYCR1 or a functional fragment or mutant thereof.
  • the method further includes measuring the expression of the nucleotide sequence encoding PYCR1 or a functional fragment or functional mutant thereof. Subsequently, the result of the measurement can be compared with that of a control measurement in which the compound of interest is not added.
  • the invention also provides a genetically modified animal.
  • the genetically modified animal includes a nucleic acid encoding PYCR1 gene in which the nucleic acid is inactive.
  • the nucleic acid leads to a loss of function of the PYCR1 gene.
  • the nucleic acid that encodes the PYCR1 gene can be inactivated by genetic methods that are well known in the art.
  • the nucleic acid can for example be inactivated by using gene knockout or knockdown methods, morpholino antisense oligomers, or other known methods that can lead to a loss of function of the PYCR1 gene.
  • the term “animal” can include all vertebrate, including humans. It can also include an individual animal in all stages of development, including embryonic and foetal stages.
  • the genetic material of the animal can be modified using genetic engineering techniques such as recombinant DNA technology.
  • Recombinant DNA can for example be produced through the addition of a relevant DNA into an existing organismal genome, such as a plasmid, to code for or alter different traits for a specific purpose. Examples of such an animal can include but are not limited to a xenopus, a fish, an amphibian, a reptile and a bird.
  • the genetically modified animal used in the present invention may also be a mammal. In some embodiments, the mammal may include a human, a rodent, Canis, Ungulate, Felidae, Leporidae, and Macaque.
  • Examples of a rodent include, but are not limited to, a mouse, rat, squirrel, chipmunk, gopher, porcupine, beaver, hamster, gerbil, guinea pig, chinchilla, prairie dog, and groundhog.
  • Examples of Canis include, but are not limited to a dog, wolf, coyote and jackal.
  • Examples of Ungulate include, but are not limited to a horse, donkey, zebra, sheep, pig, goat, camel, giraffe and moose.
  • Examples of Felidae include, but are not limited to a cat, caracal, cougar, cheetah and leopard.
  • Examples of Leporidae include, but are not limited to a rabbit, hare and jackrabbit.
  • An example of a Macaque includes a rhesus monkey.
  • the invention provides a method of identifying a compound capable of modifying the expression of a PYCR1 gene.
  • the method includes administering the compound of interest to an animal or a genetically modified animal as described herein.
  • the method further includes determining whether the compound is capable of modifying the expression of the PYCR1 gene.
  • a compound of interest used in according to the present invention can be formulated into any form as long as the compound is capable of modifying the expression of the PYCR1 gene.
  • the compound can for example be formulated in a form of a pharmaceutical or cosmetic composition.
  • a cosmetic composition includes gels, ointment, cream, lotion, serum, pastes, soaps, aerosols, soluble tablets, powder, sticks, water-based or oil-based suspensions and emulsions.
  • the expression of the PYCR1 can be modified either at the gene or protein level.
  • a gene expression level or an amount of a protein level is deemed to be “modified” or “modulated” when the gene expression/activity/amount of the respective protein is increased or decreased by for example about 10%, about 25%, about 50%, about 75%, about 100%, or higher, as compared to the control level.
  • an expression level or an activity level or a protein level/amount is deemed “increased” or “decreased” when gene expression /or an activity /protein level is increased or decreased by for example at least about 0.1, at least about 0.2, at least about 1, at least about 2, at least about 5, or at least about 10 or more fold as compared to a control level.
  • the compound of interest used in the methods of the invention can for example increase or decrease the expression of the PYCR1 gene.
  • the method includes introducing a nucleic acid molecule comprising a nucleotide sequence encoding pyrroline-5-carboxylate reductase 1 (PYCR1) or a functional fragment or functional mutant thereof into the cell.
  • PYCR1 pyrroline-5-carboxylate reductase 1
  • Any cell may be used in the present method of the invention.
  • the cell is obtained or derived from a host organism, which may be any organism.
  • the cell may be directly taken, e.g. isolated, from a respective host organism in form of a sample such as e.g. a biopsy or a blood sample. It may also have been obtained, e.g.
  • the cell used according to the invention may be comprised in a host organism. It may for instance be present in the blood or in tissue, including in an organ, of the host organism.
  • the host organism from which the cell is derived or obtained, including isolated, purified or enriched, or in which it is included, may be any organism such as a microorganism, an animal, such as a fish, an amphibian, a reptile, a bird, a mammal, including a rodent species, an invertebrate species, e.g. of the subclass Lissamphibia that includes e.g.
  • mammals include, but are not limited to, a rat, a mouse, a rabbit, a squirrel, a vole, a platypus, a chicken, a cow, a goat, a sheep, a pig, a dog, a mouflon, a guinea pig, a hamster, a chimpanzee, a rhesus monkey a macque or a human.
  • the invention also provides a method of modifying the expression of the PYCR1 gene in an animal including the animals described above.
  • the method includes administering to the animal a compound capable of modifying the expression of the PYCR1 gene.
  • the compound can in some embodiments include a nucleic acid molecule that is capable of modifying the expression of the PYCR1 gene. Examples of such a nucleic acid molecule are described above and include an antisense RNA, short interfering (siRNA), micro RNA (miRNA), peptide nucleic acid (PNA) and combinations thereof.
  • the method includes introducing a nucleic acid molecule comprising a nucleotide sequence encoding PYCR1 or a functional fragment or functional mutant thereof into the subject.
  • the method can also include administering a compound capable of modifying the expression of the PYCR1 gene.
  • a respective use may for example be the manufacture of a medicament or a pharmaceutical composition for this purpose.
  • the method of the invention includes the use of a nucleic acid or a compound as defined above, including the use in the manufacture of a medicament.
  • the compound that is capable of modifying the expression of PYCR1 can be identified using the methods of the invention described herein. In this context, the methods of or used according to the invention can be performed in vivo or in vitro.
  • administer relates to a method of incorporating a compound of interest, a nucleic acid according to the invention or a respective pharmaceutical composition thereof, into one or more cells or tissues of an organism.
  • routes of administration of a respective compound, nucleic acid or pharmaceutical composition thereof include oral, transdermal, and parenteral delivery. Suitable routes of administration may for example include depot, oral, rectal, transmucosal, intravenous, intramedullary injections, as well as intrathecal, direct intraventricular, intraperitoneal, intranasal or intraocular injections.
  • missense mutations eight missense mutations, one frameshift mutation, five splice site mutation and one 22 bp deletion comprising the exon-intron boundary of exon 5 were identified (Table 1, FIG. 6 ). Five of these mutations were recurrent, even though the affected individuals did not have a common ethnic background.
  • skin fibroblasts were isolated from probands and their unaffected siblings ( FIG. 2 ). Strongly reduced PYCR1 protein levels were detected in fibroblasts from patient (SJ) with a homozygous splice site mutation and a compound heterozygous patient (DI) with a missense and a frame shift mutation ( FIG. 2 a ).
  • the missense mutations p.Gly206Trp and p.Arg251His resulted in a reduction of protein levels relative to control cells ( FIG. 2 a ).
  • the PYCR1 protein which has been often described as cytosolic, co-localized with the mitochondrial matrix protein ⁇ 1 -Pyrroline-5-carboxylate synthase (P5CS), which also belongs to the proline metabolic pathway ( FIG. 2 b - f ). It can therefore be concluded that PYCR1 is a mitochondrial protein and that the mutations described herein lead to a loss-of-function.
  • the mitochondrial network was examined in more detail, based on mitochondrial localization of PYCR1.
  • Ultrastructural analysis revealed abnormal morphology of mitochondria and their cristae ( FIG. 3 a,b ). These differences were exacerbated upon oxidative stress ( FIG. 3 c - e ).
  • Addition of H 2 O 2 to the cell culture media induced the collapse of the filamentous mitochondrial network in cells from affected individuals, while almost no changes were observed in mitochondria of control cells ( FIG. 3 f ).
  • patient and control fibroblasts showed no differences in their levels of apoptosis.
  • a 5-fold increase in cell death in patients' fibroblasts when compared to control was detected after a short exposure to H 2 O 2 ( FIG. 3 f ). This suggests that PYCR1 is involved in the cell's response to oxidative stress.
  • PYCR1 the function of PYCR1 during embryogenesis was investigated, since patients with mutations in PYCR1 are affected at birth. conserveed throughout evolution, PYCR1 orthologues are found across bacteria, plants, insects and vertebrates ( FIG. 4 a ). To model the disease in Xenopus embryos, a morpholino (MO) against Pycr1 according to the invention was designed ( FIG. 4 b ). Pycr1-depleted embryos showed no obvious developmental defects until early tadpole stage. By stage 30, Pycr 1 morphant embryos failed to develop eyes and a tail bud ( FIG. 4 c,d ).
  • MO morpholino
  • FIG. 11 a,b morpholino-mediated knockdown of Pycr1 and Pycr2 in zebrafish led to a similar skin phenotype ( FIG. 11 a,b ) which was rescued by injection of human wild-type PYCR1 mRNA ( FIG. 11 d,e ).
  • Pycr1 morphants had no visible circulating red blood cells ( FIG. 10 a,b ). This anemia was traced back to the loss of Scl expression, a marker for primitive hematopoiesis, at stage 25 ( FIG. 5 e,f ).
  • the anemia observed in frogs may reflect the dual roles played by Pycr1 in this species, which lacks the Pycr2 gene.
  • Pycr1 In humans, PYCR2's role in erythrocytes has been well documented 24-25 . Taken together the above results suggest that loss-of-function mutations in PYCR1 compromise mitochondrial function which leads to apoptosis during embryogenesis and to a general inability to thrive during adult life.
  • PYCR1 belongs to the NAD(P)-binding Rossmann-fold domains superfamily that catalyzes the conversion of 1-pyrroline-5-carboxylate (P5C) to L-proline.
  • P5C 1-pyrroline-5-carboxylate
  • OMIM 612652 skin laxity
  • ARCL2 often includes mild or moderate mental retardation and brain anomalies 16 .
  • the phenotypic similarities suggest a common, yet to be determined, pathogenetic mechanism in these conditions.
  • increased apoptosis is also seen in fibroblasts from ARCL2 patients with ATP6V0A2 defects 17 .
  • ROS reactive oxygen species
  • PYCR1 may provide adaptive protection against stress by maintaining a reservoir of rapidly mobilizable proline and reducing equivalents into mitochondria 25 .
  • mutations in PYCR1 leading to a loss of PYCR1 function are a major cause of autosomal recessive cutis laxa evoking a phenotype that overlaps with gerodermia osteodysplastica, ARCL type 2 and ARCL type 3.
  • the pathophysiological basis is an impaired mitochondrial function leading to developmental defects through increased apoptosis.
  • the importance of mitochondrial function in the process of ageing highlighted by the inventors can help to develop novel treatment strategies for common age-related disorders 27 .
  • Such treatment strategies may include new pharmaceutical or cosmetic applications to treat age-related disorders or prevent the effects of ageing, such as skin wrinkling.
  • screening assays using an experimental animal can be generated to screen for new cosmetic compounds or pharmaceutical compositions.
  • An example of the experimental animal may include a nude mouse in which a living human skin graft carrying a mutation of the PYCR1 gene is grafted onto the nude mouse.
  • the invention also provides a method of identifying a compound capable of modifying the expression of a PYCR1 gene.
  • the method includes providing an isolated skin flap comprising at least one layer of living animal skin, said flap being attached to a test animal, as for example described in U.S. Pat. No. 4,677,968.
  • the method further includes applying the compound of interest to the living animal skin.
  • the compound of interest can be directly applied onto the living human skin which is grafted onto the nude mouse.
  • the compounds that are used according to this method can be of any form including a pharmaceutical or cosmetic composition as described above.
  • the skin flap can include cells that express the mutein of the invention.
  • the cells can for example include fibroblast cells.
  • the skin flap can include a layer of living human skin on one surface and a living animal skin on the other surface.
  • the skin flap can be served by an isolated vasculature which can be attached to the test animal.
  • the living animal skin can be of the same or different species than the test animal.
  • the animal can be a human or a rodent, including an athymic rodent for example.
  • the above screening assay may provide a method for identifying and analyzing the effect of cosmetic or pharmaceutical compositions in contact with the living human skin.
  • the compound of interest can be tested on the skin by direct surface application. The behaviour and effect of the living human skin in response to different compounds can be studied.
  • Genotyping and linkage analysis DNA samples were obtained from 22 families after participants gave their informed consent and after approval by the local ethic commission (Ethikkommission der Charotti). We performed genome-wide linkage analysis in eight families using the Affymetrix GeneChip® Human Mapping 250K Arrays (Affymetrix, Santa Clara, Calif.). Genotypes were called by the GeneChip® DNA Analysis Software (GDAS v2.0, Affymetrix). We verified sample genders by counting heterozygous SNPs on the X chromosome. Relationship errors were evaluated with the help of the program Graphical Relationship Representation. The program PedCheck was applied to detect Mendelian errors and data for SNPs with such errors were removed from the data set.
  • Non-Mendelian errors were identified by using the program MERLIN and unlikely genotypes for related samples were deleted 28 .
  • Nonparametric linkage analysis using all genotypes of a chromosome simultaneously was carried out with MERLIN.
  • Parametric linkage analysis was performed by a modified version of the program GENEHUNTER 2.1 through stepwise use of a sliding window with sets of 110 or 200 SNPs. Haplotypes were reconstructed with GENEHUNTER 2.1 and presented graphically with HaploPainter 29 .
  • Positional candidate genes were obtained from the GenB ank (http://www.ncbi.nlm.nih.gov/mapview/) and Ensembl (http://www.ensembl.org) databases. Genes were analyzed by direct sequencing of DNA with primers flanking each exon. Primer sequences were based on the reference sequences of each gene. The primer sequences for PYCR1 mutation screening are given in supplementary Table 1. Sequence analysis was done with the BigDye Terminator cycle sequencing kit (Applied Biosystems, Foster City, Calif.), and products were run on a 3730 DNA Analyzer (Applied Biosystems, Foster City, Calif.).
  • Genomic loci capture Briefly, custom arrays (Agilent 244K) were designed to target every exonic sequence of the genes present in the locus 17q25 between 72,048,357 and 78,774,742 excluding the highly repeated regions. DNA libraries were prepared following the Illumina library generation protocol version 2.3 and were hybridized to the custom arrays according to the Agilent CGH 244K array protocol, then washed, eluted and amplified. Each sample was submitted to one channel of Illumina flowcell and sequenced by Illumina Genome Analyzer (GA) using standard manufacturer's protocol.
  • GA Illumina Genome Analyzer
  • the image data was processed by the provided GA Pipeline version 1.0 and all sequences were aligned to the human reference genome (UCSC build 18, http://genome.ucsc.edu) by Blat-like Fast Accurate Search Tool (BFAST, https://secure.genome.ucla.edu/index.php/BFAST, N. Homer et al., in preparation). Mismatches were filtered for those seen 2 or more times, where the mutation was seen 100% of the time (homozygous), and did not overlap with a known dbSNP129 entry mismatch.
  • the open source SeqWare project which provides a LIMS tool for tracking samples (SeqWare LIMS) and a pipeline for sequence analysis (SeqWare Pipeline), (http://seqware.sourceforge.net) was used throughout this work.
  • Immunofluorescence analysis For immunofluorescence, cells were washed in phosphate-buffered saline (PBS) three times. Cells were fixed in 4% (wt/vol) paraformaldehyde in 1 ⁇ PBS for 10 min and permeabilized with 0.4% (vol/vol) Triton-X100 in 3% BSA in 1 ⁇ PBS for 10min at 4° C. Specific antibodies against PYCR1 (rabbit anti-PYCR1 (Proteintech) 1:500 and P5CS (mouse anti P5CS (Abnova) 1:300 were incubated over night in 3% BSA at 4° C.
  • PYCR1 rabbit anti-PYCR1 (Proteintech) 1:500
  • P5CS mouse anti P5CS (Abnova) 1:300 were incubated over night in 3% BSA at 4° C.
  • Mitochondrial morphology Morphology of the mitochondial network was investigated after treatment with hydrogene peroxide (neoLab). Cells were cultivated up to 50% confluence. Treatment with every substance was performed in normal medium. Cells were loaded with 100 nM Mito Tracker Red CM-H2XRos (Invitrogen). Cells were incubated with 500 ⁇ M H 2 O 2 for 5 min. Cells were fixed in 4% (wt/vol) paraformaldehyde in 1 ⁇ PBS for 10 min at 4° C. DNA was stained by DAPI and cells were mounted in Fluoromount (Scientific Services). Pictures of every sample were collected randomly using a BX60 Olympus microscope and the mitochondrial morphology was determined.
  • Apoptosis assay For apoptosis measurement after hydrogene peroxide (neoLab) treatment cells were incubated with 200 ⁇ M H 2 O 2 for one hour without FCS. After stress periode medium was changed to normal medium with 0.4% FCS and cells were incubated at normal conditions for additionally 24 hours. The same experiment was performed with medium supplemented with 5 mM L-Proline (Sigma-Adrich). Cells were fixed in 4% (wt/vol) paraformaldehyde in 1 ⁇ PBS for 10 min and permeabilized with 0.1% (vol/vol) Triton-X100 in 3% BSA in lx PBS for 2 min on ice.
  • TUNEL assay (Roche) was performed according to manufacturer specifications. Cells were fixed in 4% (wt/vol) paraformaldehyde in lx PBS for 10min at 4° C. DNA was stained by DAPI and cells were mounted in Fluoromount (Scientific Services). Pictures were collected randomly. Each experiment was performed three times. More than 2000 cells were analysed per assay.
  • Proliferation assay For the assessment of the proliferation rate 2.5 ⁇ 10 4 cells were seeded on glass coverslips. The cells were incubated for 8 hours in medium containing 10 ⁇ M Bromodesoxyuridine (BrdU) (Roche). Cells were fixed in 4% (wt/vol) paraformaldehyde in 1 ⁇ PBS for 10 min after 24, 48 and 72 hours and then incubated in 3 N HCL for 10 min at room temperature. They were permeabilized with 0.1% (vol/vol) Triton-X100 in 3% BSA in 1 ⁇ PBS for 30 min at 4° C. Specific antibody against BrdU (G3G4) 1:500 were incubated for 1 hour at room temperature.
  • PrdU Bromodesoxyuridine
  • Morpholino Oligos and RNA injections The 25-bp Morpholino (MO) antisense oligomers for Xenopus Pycr1 was obtained from Gene Tools and consisted of the following sequence: 5′-AGCTCCTATGAAGCCCACACTCATG-3′. The MO was resuspended in sterile water to a concentration of 1 mM according to manufacturer's instructions. Embryos were injected four times radially at the two- to four-cell stage with 4 nl (33 ng MO/injection). Synthetic capped mRNAs of human PYCR1 cDNA was used for rescue experiments at 200 pg in each blastomere at the 4-cell stage.
  • Protocols for fertilization, injections, whole-mount in situ hybridization and TUNEL can be found at http://www.reversade.com-a.googlepages.com/protocols 30 .
  • Analysis of cell death on live embryos was performed by incubating tadpoles in the dark for 30 min with acridine orange (2 ug/ml) in Barth 0.1 ⁇ . After extensive washes in Barth 0.1 ⁇ , images of embryos were captured under fluorescence (480 nm) with a Leica DFC 300 FX camera. Parabiosis was performed at stage 22, on dechorionated embryos joined by ventral ectoderm after small incisions were performed.
  • Parabiotic embryos were cultured in Barth 1 ⁇ until healed and transferred into Steinberg 1 ⁇ solution.
  • a stereomicroscope M205 FA equipped with an ICD camera from Leica was used to capture images of embryos in successive focal planes. Images were then merged into one picture with Photoshop CS3®.
  • a test animal for skin grafting To obtain an isolated skin flap on a test animal, incisions were made along the three sides of a subject area of a nude mouse. Prior to the incision, the nude mouse was anesthetized by intraperitoneal ketamine. Human skin was obtained from the patients of the families referred to in Table 1 for grafting onto the nude mouse. The human skin graft was approximately the same size and configuration as the skin flap created on the nude mouse. The human skin graft were either used immediately or stored in RPMI-1640 with 10% bovine serum at 4° C. for up to approximately 72 hours or until used for grafting.
  • the human skin graft was surgically attached to the subcutaneous surface of the isolated flap area of the nude mouse.
  • the skin flap and the human skin graft was sutured in place, creating a sandwich having a vasculature sandwiched between the skin layers, such that substantially all blood leaving the flap flow through the isolated vasculature.
  • the vascularised flap was then moved through a subcutaneous tunnel to the dorsal side of the mouse, where it was sutured in place for testing.
  • the mouse was provided with an injection of cyclosporine subcutaneously at a dosage of 25mg/kg/day.
  • Genbank Refseq DNA Homo sapiens PYCR1 isoformA NM — 006907.2, Homo sapiens PYCR1 isoform B NM — 153824.1, Xenopus laevis PYCR1 NM — 001091619, Danio rerio PYCR1 BC095354; Danio rerio PYCR2 BC060905.
  • FIG. 1 Phenotypic characteristics of patients with PYCR1-related autosomal recessive progeroid syndrome of de Barsy.
  • e-h Findings in skin biopsy from affected individual from family DI.
  • FIG. 2 Effect of PYCR1 mutations.
  • (b) In control fibroblasts PYCR1 and the mitochondrial matrix protein P5CS co-localize. In fibroblasts from patients DI (e) and SJ (d) immunostaining for PYCR 1 signals is undetectable. In contrast, in fibroblasts from TP (c) and EU (d) PYCR1-staining in mitochondria is reduced in intensity relative to control. Note abnormal mitochondrial network in DI, SJ and TP. Scale bar 20 ⁇ m.
  • FIG. 3 Loss of PYCR1 causes increased sensitivity to oxidative stress.
  • (a,b) Ultrastructural analysis of mitochondrial morphology. While mitochondria (a) in control fibroblasts have regularly arranged cristae, (b) fibroblasts from affected individual DI show strongly altered cristae and a reduced diameter, Scale bar: (c,d) Changes in mitochondrial morphology upon oxidative stress. Addition of 500 ⁇ m. H 2 O 2 to cell culture media for 10 min leads to mitochondrial network collapse in fibroblasts from affected individual from family SJ (d), tubular mitochondrial network remains largely intact in control cells (c), scale bar: 20 ⁇ m. (e) Quantification of the mitochondrial morphology changes upon oxidative stress.
  • FIG. 4 Phenotype of Pycr1 Xenopus morphants.
  • Pycr1 is evolutionary conserved from bacteria, plants, insects to vertebrates.
  • Dorsal MO-injections impaired eye but not tail development.
  • Ventral MO-injections impaired tail but not eye development, suggesting that Pycr1 is required cell-autonomously.
  • White arrowheads point to skin wrinkles which develop into ectodermal edemas by stage 40.
  • FIG. 5 Skin hypoplasia in Pycr1 morphants is accompanied by spontaneous apoptosis and is independent of anemia.
  • FIG. 9 Partial rescue of the Pycr1 morphant phenotype by overexpression of human wild-type Pycr1 mRNA but not mutant Pycr1 K215-D319del mRNA.
  • FIG. 10 Blood defects in Pycr1 morphants are alleviated by parabiosis.
  • FIG. 11 Knockdown of Pycr1 and Pycr2 in zebrafish leads to malformation, epidermal atrophy and increased apoptosis.
  • (a-h) Control, Pycr1 morphant, Pycr2 morphant, Pycr1+2 morphant and Pycr1+2 morphant zebrafish injected with 20 pg human PYCR1 mRNA at stage 24 h.
  • (f-h) Control, Pycr 1+2 morphant and Pycr1+2 morphant zebrafish injected with 20 pg human PYCR1 mRNA at stage 48 hours. Note reduced length of morphant fishes, abnormally bowed tail and loosening of the epidermis around the yolk sac.
  • FIG. 12 shows the amino acid sequence of PYCR1 gene (Swiss Prot Accession No. P32322).

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