Patent Abstract:
an isolated nucleic acid sequence encoding the yeast ndi1 protein of seq id no : 542 or a functional variant thereof is described . the nucleic acid sequence comprises at least 50 codons which are codon optimised compared with the sequence of yeast ndi1 gene of seq id no : 1 .

Detailed Description:
in the present invention delivery of ndi1 constructs ( fig1 ) has been used to protect cells in the presence of a complex i inhibitor , rotenone , ( fig2 - 8 and 12 ), hela cells and retinal ganglion cells ( rgcs ) were protected in the presence of ndi1 delivered as a wild type construct or as codon - optimised and immuno - optimised constructs ( fig2 - 4 ). for example , rgcs , the cells primarily affected in lhon , were protected in a rotenone - induced murine model of lhon . recombinant aav serotype 2 ( aav2 / 2 ) expressing wild type ndi1 from a cmv promoter ( aav - ndi1 , fig1 a ) was administered to mice using a single intravitreal injection . aav2 / 2 administered through this route has been shown to infect rgcs efficiently . moreover , intravitreal injection typically results in a broad area of retinal transduction as the vitreous contacts the entire underlying retinal surface 32 . intravitreal injection of aav provides a route of administration for the gene therapy which is directly applicable to human patients and is routinely used to administer drugs such as avastin and lucentis for treatment of wet amd . in this study , intravitreal injection of aav - ndi1 was utilised for the first time and was shown significantly to reduce rgc death and optic nerve atrophy seen in untreated eyes in response to rotenone administration and moreover , led to a preservation of retinal function as assessed by manganese enhanced magnetic resonance imaging ( memri ) and optokinetic responses ( okr ; fig5 - 8 ). in the present application , intravitreal injection of aav - ndi1 provided substantial protection against rotenone - induced insult , as assessed by a variety of assays ( fig5 - 8 ). notably , histological analyses demonstrated significant protection of both rgcs and the optic nerve ( fig5 and 6 ). furthermore , memri indicated that aav - ndi1 treatment preserved optic nerve function by enabling active transport of manganese ions through the optic nerve using voltage - gated calcium channels and hence provided evidence of the improved functional integrity of the optic nerve tissue in aav - ndi1 treated eyes compared to control eyes ( fig7 ). evaluation of visual function by optokinetics showed that the protection of rgcs and optic nerve integrity afforded by aav - ndi1 led to preservation of mouse vision in the presence of the complex i inhibitor rotenone ( fig8 ). the results highlight the potential therapeutic value of ndi1 - based therapies for lhon when intravitreally delivered using aav2 / 2 . following the successful delivery of aav - ndi1 to rgcs using intravitreal injection , ndi1 was codon optimised so that codons which are used more frequently in mammalian cells were introduced to the ndi1 yeast gene . codon modifications from 1 - 329 codons can be implemented to optimize expression of ndi1 in mammals while maintaining wild type amino acids . the maximal number of codons that can be altered in ndi1 to align codons with those most frequently used in mammals is 329 codons and these alterations were employed to generate a construct termed ophndi1 and also known as humanized ndi1 ( hndi1 ). plasmids containing ophndi1 ( hndi1 ) or wild type ndi1 , both expressed from a cytomegalovirus ( cmv ) promoter and containing a minimal polyadenylation ( polya ) signal , a modified rabbit beta - globin polyadenylation signal , were transiently transfected into hela cells using lipofectamine . levels of ndi1 protein expression from ndi1 and hndi1 constructs were compared using western blot analysis . hndi1 ( ophndi1 ) was determined to express more highly than wild type ndi1 indicating that codon optimising the ndi1 gene has indeed enhanced expression in mammalian cells ( fig9 a , 9 b and 10 ). a statistically significant difference in levels of expression was obtained between wild type and optimized ndi1 constructs ( fig9 a and 9 b ). the results obtained for ndi1 protein ( fig9 a and 9 b ) are mirrored by those obtained at the rna level in mice intravitreally injected with aav wild type and optimized ndi1 constructs using real - time rt pcr as the assay ( fig1 ). in addition both the wild type and the codon - optimised ndi1 constructs have been immuno - optimised by introducing one or more amino acid changes to modulate the immune response ( s ) ( table 1a & amp ; 1b and sequence listing ). amino acid modifications were undertaken subsequent to in silico analyses for potential immunogenic sites within ndi1 ( see fig1 a and 11 b , material and methods ). immuno - optimised constructs were generated for both the wild type ndi1 construct and for the codon - optimised hndi1 construct . modified codon - optimised and immuno - optimised ndi1 constructs were generated as high titre aav2 / 2 vectors ( 1 - 5 × 10 11 vg / ml ) using triple plasmid transfection methods in 293 cells followed by cesium chloride gradient purification of virus . representative immuno - optimised ndi1 and immuno - optimised hndi1 constructs inter alia v45i , i82v , l89i , i90y , v266i , l481i , l483m were generated as plasmids and or aav vectors . all nucleated mammalian cells present peptide fragments bound to mhc - i molecules on their cell surface . these fragments are derived from the degradation of proteins in the cytoplasm . as such , mhc - i presentation offers a snapshot of the pool of proteins being produced within each cell . cytotoxic t - cells inspect the peptide fragments presented by cells and can induce apoptosis in cells presenting non - self proteins , which is usually an indicator of viral infection . hela cells were transfected with ndi1 , hndi1 and immuno - optimised constructs and levels of rotenone insensitive respiration evaluated ( fig2 - 4 , 12 ). significant retention of oxygen consumption was observed in cells transfected with ndi1 , codon - optimised and immuno - optimised constructs ( fig2 - 4 , 12 ), when compared to untransfected control cells . in addition , to codon - optimized and immuno - optimized ndi1 constructs , a dual component construct was generated containing the cmv promoter driven ndi1 gene together with a ubiquitin promoter driven glial derived neurotrophic factor ( gdnf ) gene ( nsg ), the latter employing a neurturin polya signal ( fig1 ) and generated as an aav2 / 2 vector ( aav - nsg ). significantly higher levels of expression of ndi1 were achieved from this vector in vivo in mice after intravitreal injection compared to aav - ndi1 as evaluated by real time rt - pcr assays ( fig1 a and 10 c ). gdnf expression from aav - nsg was confirmed in mouse retinas by real time rt - pcr . furthermore , intravitreally delivery of aav - nsg resulted in preservation of cell function as evaluated by oxygen consumption measurements in rotenone treated hela cells ( fig1 ) and functional preservation in vivo using mri analyses of wild type mice intravitreally injected with aav - nsg vector ( fig7 ). mean mri signal intensity for dmso was 2 . 38 ± 0 . 04 , for rotenone alone was 2 . 30 ± 0 . 06 , for aav - ndi1 plus rotenone was 2 . 35 ± 0 . 07 and for aav - nsg plus rotenone was 2 . 37 ± 0 . 07 , significant differences were found between the rotenone alone treated mice and those treated with rotenone and either aav - ndi1 or aav - nsg ; for both rotenone versus aav - ndi1 and rotenone versus aav - nsg comparisons , p & lt ; 0 . 01 (**). indeed aav - ndi1 ( plus rotenone ) or aav - nsg ( plus rotenone ) treated mice did not differ significantly from wild type control mice treated with dmso alone . notably these mri results were established using a 4 - fold lower titre of aav - nsg than aav - ndi1 ( 5 . 99 × 10 11 vp / ml versus 2 . 5 × 10 11 vp / ml ) suggesting that less aav - nsg is required to mediate an equivalent beneficial effect . cohorts of adult wild type mice were intravitreally injected with 3 ul of aav2 / 2 vectors expressing either ndi1 , hndi1 , immuno - optimised hndi1 i82v , immuno - optimised ndi1 v266i or aav - nsg . two weeks post - injection retinas were harvested from treated mouse eyes and total rna extracted . levels of expression from aav vectors in mouse retinas were evaluated by real time rt - pcr ( fig1 ). levels of expression from different vectors could be directly compared as expression was evaluated by absolute copy number per unit of β - actin ( the housekeeping control ) for each vector . the standard curves were generated using plasmid dna standards with known copy number . expression levels achieved after aav intravitreal injection of vectors were greater in mouse eyes treated with aav - hndi1 or aav - nsg treated eyes compared to aav - ndi1 injected eyes ( fig1 ). all gene therapies which deliver non - human proteins risk activation of cytotoxic t - cell responses following presentation of peptide fragments derived from the transgenic protein . it is therefore important to the success of the treatment that immunogenicity of the transgenic protein is modulated . one of the most effective ways this can be done is by searching the sequence of the protein for fragments which are likely to strongly bind mhc - i , increasing the likelihood that they will be presented on the cell surface and so induce an immune reaction . this approach is complicated somewhat by the presence of many different mhc - i alleles in the human population , each of which may have slightly different binding affinities for different peptides . there are established bioinformatics methods for predicting the mhc - i binding affinity of a particular peptide , several of which are available as downloadable tools . for our purposes , the consensus prediction method of nielsen et al ( protein sci . 2003 may ; 12 ( 5 ): 1007 - 17 ) was most suitable , in addition to having excellent experimentally - validated accuracy . these tools were adapted and supporting software generated to enable prediction of affinity for a wide variety of mhc - i alleles . the computational tool thus generated may be applied and modified to predict other types of immune responses . all potential peptide fragments that could be derived from the ndi1 protein were assayed by the consensus prediction method for binding affinity to all well - characterised human mhc - i proteins . yeast ndi1 ( accession no : nm — 001182483 . 1 ) was cloned as described 53 . briefly , ndi1 was pcr amplified from total yeast dna extracted from s288c using the following primers f : ttctcgaggtagggtgtcagtttc ( seq id no : 543 ) and r : aaagcggccgcagtgatcaaccaatcttg ( seq id no : 544 ) and cloned into xhoi and noti sites of pcdna3 . 1 - ( invitrogen , paisley , uk ). a minimal poly - adenylation signals 4 was cloned downstream of ndi1 using noti and ecorv . the cmv immediate early promoter ( present in pcdna3 . 1 -), the ndi1 gene and poly - adenylation signal were isolated on a mlui and ecorv fragment , end filled and cloned into the noti sites of paav - mcs ( agilent technologies , la jolla , calif ., usa ) to create paav - ndi ; fig1 . paav - egfp was cloned as previously described 19 . the entire human gdnf coding sequence from the atg start codon ( nucleotides 201 - 836 of accession number nm — 000514 ) was cloned 3 - prime of a 347 bp human ubiquitin promoter ( nucleotides 3557 - 3904 of accession number d63791 ) and a human neurturin polya consisting of nucleotides 1057 - 1160 of accession number al161995 was cloned down - stream of the gdnf gene . this entire ubiquitin - driven gdnf cassette , including neurturin polya was cloned downstream of the cmv - driven ndi1 ( including the rabbit b - globulin polya ). codon optimized ndi1 sequences and / or with amino acid changes to reduce immunogenicity profiles were synthesized by geneart inc . these were isolated on a xbai and xhoi fragment and cloned into paav - mcs ( agilent technologies , la jolla , calif ., usa ) and pcdna3 . 1 - ( invitrogen , paisley , uk ) plasmids with a cmv immediate early promoter and minimal polya and verified by dna sequencing . recombinant aav2 / 2 viruses , aav - nd1 , aav - nsg , paav - ndi1 v266i , aav - hundi1 , paav - hundi1 182v and aav - egfp were prepared as described 20 , with a modified cesium chloride gradient as described 19 additional aav - nd1 , aav - nsg recombinant aav2 / 2 viruses were generated by the gene vector production center of nantes . genomic titres ( dnase - resistant viral particles per milliliter ; vp / ml ) were determined by quantitative real - time - polymerase chain reaction ( qrt - pcr ) according to the method of rohr et al . 21 human cervical carcinoma cells ( hela , atcc accession no . ccl - 2 ) were transfected with paav - ndi1 or paav - egfp using lipofectamine 2000 reagent , according to the manufacturer &# 39 ; s instructions ( invitrogen , carlsbad , calif ., usa ). 5 × 10 5 cells per well were seeded onto 6 - well plates containing 1 ml dulbecco &# 39 ; s modified eagle medium supplemented with 10 % calf serum , 2 mm glutamine and 1 mm sodium pyruvate and incubated overnight at 37 ° c . media was then aspirated and the cells were washed twice with phosphate - buffered saline ( pbs ). each well was transfected with 1 μg paav - ndi1 or 1 μg paav - egfp in triplicate . cells were harvested 48 hrs later and the cells from each triplicate pooled for an individual experiment , each experiment was repeated in triplicate . mitochondria were isolated from hela cells using anti - tom22 microbeads ( mitochondria isolation kit , miltenyi biotec gmbh , germany ). isolated mitochondria were washed twice in pbs and homogenised in 100 μl radioimmunoprecipitation assay ( ripa ) buffer ( 150 mm nacl , 1 % triton x - 100 , 0 . 5 % sodium deoxycholate , 0 . 1 % sds , 50 mm triscl ph 8 . 0 and 1 protease inhibitor cocktail tablet / 10 mls ( roche , mannheim , germany )). the homogenate was centrifuged at 10 , 000 g for 20 min at 4 ° c . and the supernatant removed for analysis . normalised protein samples were separated on 12 % polyacrylamide gels and electrophoretically transferred to pvdf membranes ( bio - rad , berkley , calif ., usa ). the pvdf membrane was blocked with 5 % non - fat milk in tris buffered saline ( tbs , 0 . 05m tris , 150 mm nacl , ph 7 . 5 ) and 0 . 05 % ( vol / vol ) tween 20 for 1 hr at room temperature . rabbit polyclonal antibodies to ndi1 ( 1 : 500 , cambridge research biochemicals , cleveland , uk ) and vdac1 ( 1 : 1000 , abcam , cambridge , uk ) were diluted in 5 % milk and incubated overnight at 4 ° c . membranes were washed twice with tbs and incubated with a secondary anti - rabbit ( igg ) horseradish peroxidise - conjugated antibody ( 1 : 2500 , sigma - aldrich , st . louis mo ., usa ) for 2 hr at room temperature , exposed to super - signal chemiluminescent substrate and enhancer ( pierce biotechnology , rochford , ill ., usa ) and signal detected using x - ray film ( kodak , rochester , n . y ., usa ). all western blots were repeated three times . respiratory measurements were performed in dmem at 37 ° c . on an oxygraph - 2k ( oroboros ® instruments gmbh , innsbruck , austria ) according to the manufacturer &# 39 ; s instructions . briefly , each chamber was calibrated with 2 mls dmem and stirred ( 200 rpm ) for 1 hr to saturate the media with oxygen . parallel experiments were run in the two chambers of the oxygraph - 2k using 1 × 10 6 paav - ndi1 or 1 × 10 6 paav - egfp transfected hela cells . following the addition of cells to the oxygen saturated media the chamber size was reduced to 2 ml to remove air . continuous readings were taken to establish the fully oxygenated baseline . 2 ul 5 mm rotenone ( 5 μm in 100 % ethanol ) was added to 1 × 10 6 paav - ndi1 or 1 × 10 6 paav - egfp transfected hela cells prior to transfer to the requisite chambers and continuous post - rotenone readings taken . continuous readings were taken both with and without rotenone until oxygen consumption stabilised . readings were taken from three independent transfections for each construct . wild type 129 s2 / svhsd ( harlan uk ltd , oxfordshire , uk ) mice were maintained under specific pathogen free ( spf ) housing conditions . intravitreal injections were carried out in strict compliance with the european communities regulations 2002 and 2005 ( cruelty to animals act ) and the association for research in vision and ophthalmology ( arvo ) statement for the use of animals . briefly , adult mice were anaesthetised and pupils dilated as described 57 . using topical anaesthesia ( amethocaine ), a small puncture was made in the sclera . a 34 - gauge blunt - ended microneedle attached to a 10 μl hamilton syringe was inserted through the puncture , and 0 . 6 μl 2 . 5 mm rotenone ( 1 . 5 nmol ) in dimethyl sulfoxide ( dmso , vehicle ), 0 . 6 μl dmso alone or 3 μl 1 × 10 12 vp / ml aav2 / 2 was slowly , over a two minute period , administered into the vitreous . following intravitreal injection , an anesthetic reversing agent ( 100 mg / 10 g body weight ; atipamezole hydrochloride ) was delivered by intraperitoneal injection . body temperature was maintained using a homeothermic heating device . all animal studies have been approved by the authors &# 39 ; institutional review board . adult wild type mice ( n = 6 ) were intravitrally injected with 3 × 10 9 vp aav - ndi1 while fellow eyes received 3 × 10 9 vp aav - egfp . retinas were harvested two weeks post - injection and total rna extracted using the qiagen rneasy kit according to the manufacturers specification . in vivo expression of ndi1 from aav - ndi1 was confirmed by reverse transcription pcr ( rt - pcr ) on a 7300 real time pcr system ( applied biosystems , foster city , calif ., usa ) using a quantitect sybr green rt - pcr kit ( qiagen ltd ., crawley , uk ) and resulting amplification products separated and sized on 2 . 5 % agarose gels . the following primers were used : ndi1 forward primer 5 ′ caccagttgggacagtagac 3 ′ ( seq id no : 545 ) and ndi1 reverse primer : 5 ′ cctcatagtaggtaacgttc 3 ′ ( seq id no : 546 ). humanised forms of ndi1 transcript were rt - pcr amplified with hndi1 forward primer 5 ′ gaacaccgtgaccatcaaga 3 ′ and hndi1 reverse primer 5 ′ gctgatcaggtagtcgtact 3 ′ β - actin was used as an internal control as described ( ref ). rt - pcrs were performed twice in triplicate or quadruplicate . levels of ndi1 or humanised ndi1 expression were determined by real time rt pcr using the quantitect sybr green rt pcr kit ( qiagen ). briefly , the copy number of two plasmid dna preparations containing either ndi1 or humanized ndi1 was determined by spectraphotometry on a nanodrop and serial dilutions of these plasmid dna preparations were prepared containing between 10e2 - 10e7 copies / μl . these standard curves were included in 96 - well plates that also included rna samples to be analysed . hence expression levels from all constructs , whether humanized or not , could be compared using absolute copy number , even though the primer pairs used for non humanized and humanized pcr amplification were not the same . expression levels were normalized using the internal housekeeping gene β - actin . eyes and optic nerves were fixed in 4 % paraformaldehyde in pbs ( ph 7 . 4 ) overnight at room 4 ° c . washed three times with pbs and cryoprotected using a sucrose gradient ( 10 %, 20 %, 30 %). 10 μm sections were cut on a cryostat ( hm 500 microm , leica , solms , germany ) at − 20 ° c . nuclei were counterstained with 4 ′, 6 - diamidino - 2 - phenylindole ( dapi ). specimens were analysed with a zeiss axiophot fluorescence microscope ( carl zeiss , oberkochen , germany ). corresponding microscope images taken with different filters were overlaid using photoshop v . 10 ( adobe systems europe , glasgow , uk ). for ganglion cell ( gcl ) counts the ganglion cells were labelled using neun ( abcam , cambridge , uk ) immunohistochemistry as previously described . the primary antibody was diluted 1 : 100 and visualised using cy3 - conjugated anti - mouse - igg secondary antibody ( jackson immunoresearch europe , suffolk , uk ). four retinal sections per eye from four mice per group were analysed ( n = 4 ). the sections were taken approximately 150 μm apart in the central retina ( 600 μm span in total ); 2 counts per section i . e . 8 counts per eye in total , were made using the count tool in photoshop ( adobe systems ). the diameter of the optic nerves was determined at approximately 5 mm from the optic nerve head from 3 animals per group ( n = 3 ). three measurements per nerve were made approximately 150 μm apart using the ruler tool in photoshop ( adobe systems ). procedures for tem were as previously described . briefly , three weeks post - rotenone injection optic nerves were fixed in 4 % paraformaldehyde in phosphate - buffered solution and fixed in 2 . 5 % glutaraldehyde in 0 . 1m cacodylate buffer ( ph 7 . 3 ) for 2 hr at room temperature . washed specimens were post - fixed in buffered 2 % osmium tetroxide , dehydrated and embedded in araldite . ultrathin cross - sections were cut on a vibratome ( leica vt 1000 s ), analysed using a tecnai 12 biotwin transmission electron microscope ( fei , eindhoven , holland ) and imaged with a sis megaview iii surface channel charge - coupled device ( sccd ) camera ( olympus soft imaging solutions , münster , germany ). the total number of membrane debris particles in the images was counted in 5 cross sections per optic nerve from 3 animals per group ( n = 3 ). optic nerve integrity in experimental and control mice was assessed by manganese ( mn 2 + ) enhanced magnetic resonance imaging ( memri ) technique using a 7 t bruker biospec 70 / 30 magnet ( bruker biospin , etlingen , germany ). memri demarcates active regions of the brain due to the ability of mn 2 + ions to enter excitable cells through voltage - gated calcium channels , thus analysis of mn 2 + transport through the optic nerve provides a good measure of its integrity . two hours prior to scanning , mice were anaesthetised and intravitreally injected , as described above , with 2 μl of 20 mg / ml manganese chloride solution . for image acquisition , mice were maintained under sedation with ketamine ( 375 μg / 10 g body weight ) and placed on an mri - compatible cradle which maintains the animal &# 39 ; s body temperature at 37 ° c . ( respiration and temperature were monitored for the duration of experiment ). the cradle was positioned within the mri scanner and an initial rapid pilot image acquired to ensure accurate positioning of the mouse . oblique coronal t 1 - weighted 2d images were acquired using flash sequence ( tr / te : 150 / 2 . 5 ms ; matrix : 128 × 128 ; field of view : 20 × 20 mm 2 ; flip angle 50 °; number of averages : 40 , the pixel resolution was 0 . 156 mm / pixel ). in the oblique coronal orientation ( 36 °), 20 slices , each measuring 0 . 35 mm in thickness with 0 . 45 mm inter slice gap , were recorded for an acquisition time of 9 min 36 sec . mri scans corresponding to the area immediately superior to the optic chiasm provided more consistent images compared to the optic nerve itself due to the variations in physically positioning each animal . log signal intensities in this region were quantified using image j © software ( http :// imagej . nih . gov / ij /). optokinetic response ( okr ) spatial frequency thresholds were measured blind by two independent researchers using a virtual optokinetic system ( vos , optomotry , cerebralmechanics , lethbridge , ab , canada ). optomotry 36 measures the threshold of the mouse &# 39 ; s optokinetic tracking response to moving gratings . briefly , a virtual - reality chamber is created with four 17 inch computer monitors facing into a square and the unrestrained mouse was placed on a platform in the centre . a video camera , situated above the animal , provided real - time video feedback . the experimenter centred the virtual drum on the mouse &# 39 ; s head and judged whether the mouse made slow tracking movements with its head and neck . the spatial frequency threshold , the point at which the mouse no longer tracked , was obtained by incrementally increasing the spatial frequency of the grating at 100 % contrast . a staircase procedure was used in which the step size was halved after each reversal , and terminated when the step size became smaller than the hardware resolution (˜ 0 . 003 c / d , 0 . 2 % contrast ). one staircase was presented for each direction of rotation to measure each eye separately , with the two staircases being interspersed . data sets of treated and untreated samples were pooled , averaged and standard deviation ( sd ) values calculated . statistical significance of differences between data sets was determined by either student &# 39 ; s two - tailed t - test or anova used with tukey &# 39 ; s multiple comparison post hoc test . in addition , the kruskall - wallis one - way analysis of variance was applied to the mri data set and mann whitney u - tests were undertaken on all other data sets to establish that statistical significance was maintained using nonparametric statistical models . analysis was performed using prism v . 5 . 0 c ( graphpad software , la jolla , calif ., usa ); differences with p & lt ; 0 . 05 were considered statistically significant all potential peptide fragments that could be derived from the ndi1 protein were assayed by the consensus prediction method for binding affinity to all well - characterised human mhc - i proteins . all epitopes displaying a high affinity for mhc - i ( defined as a predicted ic50 & lt ; 500 nm ) were noted , along with the corresponding mhc - i allele to which they had displayed high binding affinity . each potential peptide fragment was then assigned an ‘ immunogenicity score ’, defined as the sum of the frequencies of all mhc - i alleles in the global human population for which it had a high binding affinity . the highest - scoring fragments were then selected for potential modification to reduce immunogenicity . all possible single amino acid mutations for each of these immunogenic fragment sequences were generated , and each was assayed for immunogenicity by the above methods . in addition , the blosum62 matrix was used to calculate the sequence similarity between the original and mutated sequences . for each fragment , an optimal immunogenicity - reducing mutation was chosen . this was done by taking the set of all potential mutations for that fragment and eliminating all fragments which had an immunogenicity score greater than half of the immunogenicity score of the original fragment . the sequence with the highest sequence similarity to the original fragment ( as defined by the blosum62 matrix ) was selected as the optimal substitution for that position . in addition to the analyses described above using information regarding mhc - 1 alone , immunogenicity estimation and reduction in ndi1 was achieved via in silico modelling of antigen presentation via the mhc - i pathway using the iedb proteasomal cleavage / tap transport / mhc class i combined predictor . as fragments of 9 amino acids in length are the most commonly presented fragments by mhc - i , all possible sequences of 9 consecutive amino acids that could be derived from ndi1 were listed and passed to the iedb predictor for analysis . for every 9 - mer peptide p and mhc - i allele i , an immunogenicity value g p , i was generated which is proportional to the amount of that fragment that would be displayed on the cell surface by a given mhc - i allele , taking into account proteasomal degradation , transport and binding by mhc - i . an overall immunogenicity factor f p for the 9 - mer peptide was then calculated as where n i is the estimated prevalence of each allele in the global human population as a fraction of the total pool of alleles , calculated using population frequency data from the allele frequency net database ( gonzalez - galarza et al , 2011 ). in other words , f p represents the mean amount of that fragment that would be displayed on the surface of a cell for all mhc - i alleles , weighted by how frequently each allele occurs in the human population . each amino acid position a in the ndi1 peptide was then assigned an immunogenicity score s a defined as the sum of the immunogenicity factors for all 9 - mer peptides containing that amino acid . all positions whose immunogenicity score was less than one - fifth of the highest score were not considered further , as mutations at these positions would not be able to significantly affect the overall immunogenicity of the protein . for each of the remaining positions , a blosum matrix ( henikoff and henikoff , 1992 ) was used to identify potential mutations that would not be overly disruptive to the structure or function of ndi1 . a blosum matrix is calculated by aligning homologous protein sequences from many species against each other , and comparing the frequency with which each amino acid is replaced by every other amino acid . for two amino acids x and y , the blosum score b x , y is defined as the log - likelihood of the amino acid x replacing y or vice - versa in a given position in homologous peptides . as a direct consequence of this definition , b x , y = b y , x for all x and y ( in other words , all blosum matrices are symmetric ). a high blosum score for an amino - acid pair indicates that mutations changing one of those amino acids to the other are more likely to be observed in homologous proteins , indicating that such changes are less likely to severely disrupt protein structure . a blosum score can also be calculated between each amino acid and itself ( b x , x ), indicating the likelihood that that amino acid will remain constant between homologous proteins . for all possible mutations at a given position , δb was defined as the change in the blosum score for that mutation . more formally , given an initial amino acid x and a candidate replacement amino acid y , δb = b x , x − b x , y . all mutations for which δb was greater than 4 were considered too disruptive to protein function and not analysed further . for all remaining candidate mutations , immunogenicity factors f and scores s were recalculated for the post - mutation peptide using the iedb predictor . the reduction in immunogenicity δs was then determined , defined as the difference between the score s for that position in the original peptide versus the new score s after mutation . represent mutations which are likely to cause a large reduction in immunogenicity with a relatively small predicted impact on protein function . outputs with predicted amino acids and scores are provided in table x . the invention is not limited to the embodiments hereinbefore described which may be varied in construction and detail without departing from the spirit of the invention . 1 . yu - wai - man p , griffiths p g , chinnery p f . mitrochondrial optic neuropathies — disease mechanisms and therapeutic strategies . prog retin eye res . 30 : 81 - 114 ( 2011 ). 2 . chalmers r m and schapira a h . clinical , biochemical and molecular genetic features of leber &# 39 ; s hereditary optic neuropathy . biochim biophys acta . 1410 ( 2 ): 147 - 158 ( 1999 ). 3 . mackey d a , oostra r j , rosenberg t , nikoskelainen e , bronte - stewart j , poulton j , harding a e , govan g , bolhuis p a , norby s . primary pathogenic mtdna mutations in multigeneration pedigrees with leber hereditary optic neuropathy . am j hum genet . 59 ( 2 ): 481 - 485 ( 1996 ). 4 . jarrett s g , lin h , godley b f , boulton m e . mitrochondrial dna damage and its potential role in retinal degeneration . prog retin eye res . 27 ( 6 ): 596 - 607 ( 2008 ). 5 . ames a 3 rd . cns energy metabolism as related to function . brain res brain res rev . 34 : 42 - 68 ( 2000 ). 6 . yen m y , wang a g , wei y h . leber &# 39 ; s hereditary optic neuropathy : a multifactorial disease . prog retin eye res . 25 ( 4 ): 381 - 396 ( 2006 ). 7 . porter r k , joyce o j , farmer m k , heneghan r , tipton k f , andrews j f , mcbennett s m , lund m d , jensen c h , melia h p . indirect measurement of mitochondrial proton leak and its application . int j obes relat metab disord . 23 ( suppl 6 ): 512 - 18 ( 1999 ). 8 . yamada k , mashima y , kigasawa k , miyashita k , wakakura m , oguchi y . high incidence of visual recovery among four japanese patients with leber &# 39 ; s hereditary optic neuropathy with the 14484 mutation . j . neuroophthalmol . 17 ( 2 ): 103 - 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