Ref.: Ms. No. IMMU-D-09-00074
KIR3D genotypes and KIR2DS4 allelic variants in the AB KIR genotypes are
associated with Plasmodium positive individuals in malaria infection
Immunogenetics
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Below are the changes I made based on the points I received for revision.
General points
The authors must include a section in the results where they compare the distribution of KIR genes and A/B haplotypes in the Solomon Islanders with those reported for other populations, in particular other Pacific Island populations: Immunogenetics. 2006 58:523-532.
Such a comparison is hinted at in the section entitled 'KIR A/B genotypes' where it is stated "The frequencies of KIR AB genotypes were predominantly higher (51.9%) in the Melanesian subjects (Fig.2)." but neither the text nor the figure tells the reader who the Melanesians are being compared to.
I apologize for my writing that obviously misled the readers. In this sentence, I wanted to point out the predominanceof AB genotypes over AB and BB genotypes in the Melanesian study subjects.Therefore, I re-wrote the sentence: The KIR AB genotypes (51.9%) predominated over AA (18.2%) and BB (29.9%) genotypes in the Melanesian subjects.
In the results, I added the new section (with Fig.4) of KIR gene comparison with other populations under the title as Comparison of KIR gene frequencies of the Solomon Islands population (Melanesians) withother Pacific Island populations.
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The Discussion, which is too long and speculative, detracts from the results presented by Taniguchi and Kawabata. Although I would not insist that the Discussion be shortened and less speculative, the authors run the risk of having their paper cited by future papers on this subject for its erroneous speculation rather for it being the pioneering paper on KIR and endemic malaria.
If possible, I would like to submit my discussion as the current content to share my suggestions to encourage further investigations in association of KIR and malaria infection.
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Specific Points
In the abstract, the sentence "A tendency of an inheritable gene combination was observed by an increased frequency of a pair of KIR3DL1 and KIR2DS4 in the positive individuals" could be stated more clearly. It is confusing. And similar confusion exists in the Results section where
this observation is discussed. The authors do not adequately differentiate between alleles and genes.
I re-wrote the sentence as follows:
The higher frequency of a pair of KIR3DL1 and KIR2DS4 was observed in the positive individuals.
I apologize if I misunderstood the points you made, but regarding inadequate allele and gene differentiation in this paper, I was wondering if the confusion was caused because the investigation was made on:KIR3DS1/DL1 genes at genotypic level; and KIR2DS4 at allelic level (non-deleted vs. deleted). In this study, I was unable to have the opportunity to perform allelic level typing for KIR3DL1/DS1.
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Figure 1 would be more effective if the haplotypes in the AB and the BB groups were ordered according to their relative frequencies in the population (highest at the top, lowest at the bottom). At present there seems to be no logic to the order.
My original KIR genotype table was actually in the order of genotype frequencies (from the highest to the lowest). However, I decided to classify them into AA/AB/BB genotype groups so that more emphasize can be put on the distribution of the dominant AB genotypes over AA and BB, which were in this study found to be significantly linked to KIR3DS1/DL1 heterozygosity and KIR2DS4 non-deleted variants. Also, as noted in the result section (second paragraph), no particular genotypes with predominantly high frequencies were observed in this study population, therefore, I wanted to focus more on presenting the difference in A/B genotypes.
Also, I got this classification idea from Dr. Rajalingham (UCLA)’s recent paper, which I found his genotype table easy to follow: Distinct diversity of KIR genes in three southern Indian populations: comparison with world populations revealed a link between KIR gene content and pre-historic human migrations.
Rajalingam R, Du Z, Meenagh A, Luo L, Kavitha VJ, Pavithra-Arulvani R, Vidhyalakshmi A, Sharma SK, Balazs I, Reed EF, Pitchappan RM, Middleton D.
Immunogenetics. 2008 May;60(5):207-17. Epub 2008 Mar 28.
Therefore, if possible, I would like to keep the current genotype classification in this table.
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In the discussion it is stated: "Furthermore, inhibitory KIR3DL1 which is the most polymorphic of the KIR genes (Colonna and Samiridis 1995)." This reference was published long before anything tangible was known of KIR polymorphism. Norman 2008 Nature Genetics would be more appropriate.
Likewise, does the French 2001 reference report on KIR associations with AIDS?
Thank you. I removed the reference.
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In the Discussion the sub-section on 'KIR A/B genotypes and malaria' is confusing and appears contradictory. At different points heterozygosity seems both good and bad, or is it different heterozygous combinations.
I apologize that I confused my interpretation by myself, and had not noticed this contradiction until I had your comment on this paragraph. I rewrote the sentences as follows:
(previous sentences)
KIR A/B genotypes and malaria
The KIR A/B genotype frequencies alone did not reveal any difference between the two study subjects, which was the same conclusion obtained from the mere comparison of activating and inhibitory KIR gene numbers. However, when the A/B genotypic category was used in conjunction with KIR3D genotypes and KIR2DS4 allelic variants, statistically significant trend was observed in the positive group toward the higher frequency of AB genotype individuals with KIR3Dheterozygosity and KIR2DS4 non-deleted variants. It appears that in order to constitute beneficial genetic compositions against malaria, the KIR genes in the A haplotype group as the ‘core’ genes, need to team with KIR genes from the B haplotype group. And those KIR gene candidates could be restricted to particular alleles such as a KIR2DS4 non-deleted allele (KIR2DS4*001), and to zygosity levels such as KIR3D genotypes (KIR3DS1/3DL1heterozygosity) as shown in this study. It may suggest that a particular KIR genotype can be beneficial in protecting from malaria by the culminated effects of activating KIR genes generated by membrane-expressed KIR2DS4 non-deleted variants (in contrary to secreted KIR2DS4 by deleted variants), and KIR3DS1/3DL1heterozygosity as the most active KIR3Dzygosity in the AB genotypes.
(Corrected sentences)
It appears that deleterious effect of malaria infection was incremented by the tendency of the KIR genes in the A haplotype group as the ‘core’ genes to interact with the ones from the B haplotype group. In addition, those KIR gene candidates could be restricted to particular alleles such as a KIR2DS4 non-deleted allele (KIR2DS4*001), and to zygosity levels such as KIR3DL1/S1 genotypes (KIR3DL1/3DS1heterozygosity) as shown in this study to tip the balance of activating and inhibitory KIR effects toward being less protective against Malaria .
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Please have a native English speaker review the manuscript before resubmission.
I had the manuscript reviewed by a native English speaker as you recommended after all correction as above, and added her name in the acknowledgment section.
However, the new section I added for the comparison among Pacific Islands populations, has not yet reviewed by anybody because I thought some new corrections may be needed after your re-review.
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The other modification I made:
The nomenclature‘KIR3D’ used in the previous manuscript (including the title) was replaced with ‘KIR3DL1/S1’ to avoid the confusion with 3DL2 and 3DL3.