Testing Alpha-1 Antitrypsin Deficiency in Black Populations
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsManuscript title: Alpha 1 Antitrypsin Testing in Black Populations
Type: review
Journal: Advances in Respiratory Medicine
Comments and Suggestions for Authors
Would you please find enclosed several comments/minor observations for improving the manuscript
a) In this review, Dr. Pascale Lafortune and colleagues provided a succinct but clear overview on the currently known variants, including allele frequencies other than mutations, of SERPINA1 gene and their impact on the Alpha 1 antitrypsin (AAT) deficiency in the black population.
b) The review is in general well written and well organized. However, as a main comment I suggest including more information on AAD and its impact in human physiology as the main causative factor for COPD. Authors can read these detailed reviews in the field PMID: 32800189, https://www.ncbi.nlm.nih.gov/books/NBK482180/ , PMID: 31258312, PMID: 33659933 PMID: 34408831
c) Tables are well designed and clear
d) The rationale of this review manuscript should be detailed in the introduction. Several notions from the first paragraph of section 4 can be used for the introduction.
e) The regulation of serpina1 gene should be detailed. The regulation of this gene is quite complex, as it presents several tissue-specific promoters, e.g., liver and neutrophil specific promoters. In addition, the promoter region of the serpina1 gene has also been reported to be under epigenetic regulation trough DNA methylation, authors can check PMID: 33015055 and PMID: 22161163. This information and supporting references should be included in the section describing the serpina1 gene.
f) Moreover, minor and less frequent mutations causing AAD have also been identified across serpina1 promoter PMID: 27296815
g) I suggest including a figure summarizing the main aspects of the manuscript. A summarizing figure might improve the interest from readers and the quality of the manuscript
Author Response
- a) In this review, Dr. Pascale Lafortune and colleagues provided a succinct but clear overview on the currently known variants, including allele frequencies other than mutations, of SERPINA1 gene and their impact on the Alpha 1 antitrypsin (AAT) deficiency in the black population.
Response: We thank the reviewer for their important feedback
- b) The review is in general well written and well organized. However, as a main comment I suggest including more information on AAD and its impact in human physiology as the main causative factor for COPD. Authors can read these detailed reviews in the field PMID: 32800189, https://www.ncbi.nlm.nih.gov/books/NBK482180/ , PMID: 31258312, PMID: 33659933 PMID: 34408831
Response: We have now added more information on the impact of AAT deficiency on human physiology. We have added the following:
“COPD development is common in AATD, especially in combination with cigarette smoke exposure. AATD patients with a smoking history typically present with emphysema on a chest computed tomography (CT) and confirmed with obstruction determined by spirometry. Chronic bronchitis or asthma are also observed but less frequently [3]. However, AATD subjects that do not smoke tend to get radiographic emphysema after 60 years old [4]. Asthma may be more prevalent in AATD individuals, as wheezing and dyspnea are some of the first pulmonary symptoms in AATD [5]. Bronchiectasis is also increased in AATD [6] and this is associated with atypical mycobacterial infection [7]. Therefore, AAT testing is recommended for subjects with subjects with emphysema, COPD, bronchiectasis, chronic bronchitis, and asthma subjects whose spirometry fails to return to normal upon the treatment of asthma [1].”
- c) Tables are well designed and clear
Response: We thank the reviewer for their important feedback
- d) The rationale of this review manuscript should be detailed in the introduction. Several notions from the first paragraph of section 4 can be used for the introduction.
Response: We have made these modifications. Please see the changes to the introduction (with track changes)
- e) The regulation of serpina1 gene should be detailed. The regulation of this gene is quite complex, as it presents several tissue-specific promoters, e.g., liver and neutrophil specific promoters. In addition, the promoter region of the serpina1 gene has also been reported to be under epigenetic regulation trough DNA methylation, authors can check PMID: 33015055 and PMID: 22161163. This information and supporting references should be included in the section describing the serpina1 gene.
Response: We have added a regulation of the SERPINA1 gene section. Please see section 3.1.
- f) Moreover, minor and less frequent mutations causing AAD have also been identified across serpina1 promoter PMID: 27296815
Response: We have outlined that there are other mutations that cause AAT deficiency across the SERPINA promotor and reference this manuscript. We added this line:
“There are many rare SERPINA1 variants that could be population specific [28] but require further investigation.”
- g) I suggest including a figure summarizing the main aspects of the manuscript. A summarizing figure might improve the interest from readers and the quality of the manuscript
Response: We have included a summarizing figure. Please see Figure #1
Reviewer 2 Report
Comments and Suggestions for Authors
The provided review manuscript nicely outlines the harmful AAT variants, the current epidemiology knowledge of AATD, health inequity and AATD prevalence in Black populations.
Author Response
The provided review manuscript nicely outlines the harmful AAT variants, the current epidemiology knowledge of AATD, health inequity and AATD prevalence in Black populations.
Response: We thank the reviewer for their feedback
Reviewer 3 Report
Comments and Suggestions for AuthorsPage 1 introduction half way:…. Chronic liver disease, or panniculitis. Irrespective of age or ethnicity, should be tested for AATD. In my opinion it would be helpful if the authors spend a few words on how they should be tested for AATD. In the joint statement of the American and European societies, genetic testing is suggested, although they do not necessarily mean costly DNA testing, cheaper iso-electric focusing, that is very well suited to identify the most common deficiency alleles in Caucasian populations, would probably be the method of choice. This is relevant as just testing for alpha-1 antitrypsin levels is quite useless, as it is an acute phase protein, that may be within normal limits in quite deficient patients.
Page2 heading 3 AATD mutations: typo in line 4 lss should read less.
Sentence : Few studies performing AAT testing… population: I am not sure, I understand wat is meant, due to difficult wording and lack of interpunction. I take it you mean that there are few unbiased studies that address the allele frequencies in the general population? Please rephrase.
In a recent study from the Canary Isles.. reported. I do not understand why you do not at all refer to the widely used, and freely accessible genetic sequencing control data repositories like GnomAD v2.1.1? I would believe this self reported healthy control database is not very much biased in favor nor against AATD. For the Z allele they find it 451 times in 25112 alleles from European non-Finisch extraction amounting to an allele frequency of 0.01796. for African American controls this was 62/24966 alleles, allele frequency 0.002483, and for the Latino- admixed American ones 134/35410 = 0.00378. The same exercise could be performed for the S allele.
Page 4 heading 4: last sentence: Further, a recent…. In African Americans. I do not understand what point you are trying to make, please explain.
Page 4 paragraph 4.1 With respect to the estimates stemming from clinical epidemiological studies from the 70ties and 80ties it would be quite informative to compare those again to the GnomAD data, although I do realize that African and Asian (sub) populations are underrepresented in these control databases, relative to Caucasian western populations.
Page 6 paragraph 5.0 somewhere in the middle: Next-generation sequencing genotyping….DNA[41]: Next generation sequencing genotyping refers to the sequencing technique used, and not to what part of the genome is targeted. This is relevant, as in clinical DNA testing currently whole exome sequencing is the gold standard using next generation sequencing genotyping, and this does not address deep intronic variants or variants in UTR’s, promotors, enhancers and such. Currently we mostly look into the protein coding regions even with next genetation sequencing genotyping for opportunistic reasons; it is much more difficult to separate pathogenetic variation from neutral genetic variation in these non-coding areas, and moreover there is much more variation present in these noncoding areas. So please change to whole genome next generation sequencing or state that noncoding regions could be potentially assessed.
Page 6: end of paragraph 5.0: you seem to advocate the use of sometimes rather costly commercially available direct-to-consumer tests as a possible way to achieve pre-symptomatic genetic screening for AATD. Personally I find that rather cynical. I would argue that costly direct-to-consumer genetic tests, that are not yet regulated by any quality control system, can hardly be the way to go to improve exsisting health inequities. Besides, there could also be potential danger in providing over the counter genetic information to people that have no genetic education/did not receive any genetic counseling.
The question we should ask in this respect is: would we as a population benefit from presymptomatic screening for AATD? If so we should ensure that proper screening facilities are set up with guarantied access for all eligible people. And not leave this to commercially available over the counter direct-to-consumer tests, of unmonitored reliability. But as long as the most important treatment for AATD amounts to maintaining a healthy life style (refrain from smoking and drinking too much alcohol), that would be advisable to anybody; it could be argued that the money spent on AATD screening for presymptomatic diagnosis would be better spent on campaigns promoting a healthier life style for everybody. Moreover the American thoracic Society/European respiratory statement on AATD ( your ref 1) is not in favor of such population screening, they explicitly advise against it. So probably leave out interestingly… to stage.
Author Response
Page 1 introduction half way:…. Chronic liver disease, or panniculitis. Irrespective of age or ethnicity, should be tested for AATD. In my opinion it would be helpful if the authors spend a few words on how they should be tested for AATD. In the joint statement of the American and European societies, genetic testing is suggested, although they do not necessarily mean costly DNA testing, cheaper iso-electric focusing, that is very well suited to identify the most common deficiency alleles in Caucasian populations, would probably be the method of choice. This is relevant as just testing for alpha-1 antitrypsin levels is quite useless, as it is an acute phase protein, that may be within normal limits in quite deficient patients.
Response: We agree with the reviewer and have added several sentences to outline this. Please see track changes in the introduction
Page2 heading 3 AATD mutations: typo in line 4 lss should read less.
Response: We have corrected this typo
Sentence : Few studies performing AAT testing… population: I am not sure, I understand wat is meant, due to difficult wording and lack of interpunction. I take it you mean that there are few unbiased studies that address the allele frequencies in the general population? Please rephrase.
Response: We have reworded this sentence.
In a recent study from the Canary Isles.. reported. I do not understand why you do not at all refer to the widely used, and freely accessible genetic sequencing control data repositories like GnomAD v2.1.1? I would believe this self reported healthy control database is not very much biased in favor nor against AATD. For the Z allele they find it 451 times in 25112 alleles from European non-Finisch extraction amounting to an allele frequency of 0.01796. for African American controls this was 62/24966 alleles, allele frequency 0.002483, and for the Latino- admixed American ones 134/35410 = 0.00378. The same exercise could be performed for the S allele.
Response: We thank the reviewer for their recommendation to reference gnomAD within the manuscript. We have added the following sentence:
“Finally, the Genome Aggregation Database (gnomAD) which is a shared aggregate exome and genome sequencing database from a variety of large-scale sequencing projects [17] is a usefully tool to look at SERPINA1 variants in multiple ethnic populations. These datasets may represent a better overall frequency for SERPINA1 variants in multiple populations.”
Page 4 heading 4: last sentence: Further, a recent…. In African Americans. I do not understand what point you are trying to make, please explain.
Response: There is likely heterogeneity in genetic effects when investigating race/ethnicity in lung function. Therefore, we cannot presume genetic variants associated with lung function identified by GWAS may be applicable to all populations (race, gender, etc)
Page 4 paragraph 4.1 With respect to the estimates stemming from clinical epidemiological studies from the 70ties and 80ties it would be quite informative to compare those again to the GnomAD data, although I do realize that African and Asian (sub) populations are underrepresented in these control databases, relative to Caucasian western populations.
Response: We agree with the reviewer. Due to the 5-day deadline for the resubmission of this manuscript, we have not performed this comparison here but we agree with the reviewer’s excellent recommendation. We have included this suggested in the conclusion section for important future approaches
Page 6 paragraph 5.0 somewhere in the middle: Next-generation sequencing genotyping….DNA[41]: Next generation sequencing genotyping refers to the sequencing technique used, and not to what part of the genome is targeted. This is relevant, as in clinical DNA testing currently whole exome sequencing is the gold standard using next generation sequencing genotyping, and this does not address deep intronic variants or variants in UTR’s, promotors, enhancers and such. Currently we mostly look into the protein coding regions even with next genetation sequencing genotyping for opportunistic reasons; it is much more difficult to separate pathogenetic variation from neutral genetic variation in these non-coding areas, and moreover there is much more variation present in these noncoding areas. So please change to whole genome next generation sequencing or state that noncoding regions could be potentially assessed.
Response: We have reworded these sentences to better reflect these techniques
Page 6: end of paragraph 5.0: you seem to advocate the use of sometimes rather costly commercially available direct-to-consumer tests as a possible way to achieve pre-symptomatic genetic screening for AATD. Personally I find that rather cynical. I would argue that costly direct-to-consumer genetic tests, that are not yet regulated by any quality control system, can hardly be the way to go to improve exsisting health inequities. Besides, there could also be potential danger in providing over the counter genetic information to people that have no genetic education/did not receive any genetic counseling.
Response: Our apologies, we were not advocating for the use of over-the-counter tests but providing information on current approaches to increase screening. We have added the following sentence:
“Commercially available direct-to-consumer genetic tests have also allowed people to explore the possibilities of genetic screening. However, one needs to be cautious with over-the-counter genetic testing as this results in the customer paying for the service, and these tests are not federally regulated in regards to quality controls, and provide no counseling service upon identification of possible genetic diseases.”
The question we should ask in this respect is: would we as a population benefit from presymptomatic screening for AATD? If so we should ensure that proper screening facilities are set up with guarantied access for all eligible people. And not leave this to commercially available over the counter direct-to-consumer tests, of unmonitored reliability. But as long as the most important treatment for AATD amounts to maintaining a healthy life style (refrain from smoking and drinking too much alcohol), that would be advisable to anybody; it could be argued that the money spent on AATD screening for presymptomatic diagnosis would be better spent on campaigns promoting a healthier life style for everybody. Moreover the American thoracic Society/European respiratory statement on AATD ( your ref 1) is not in favor of such population screening, they explicitly advise against it. So probably leave out interestingly… to stage.
Response: Please see the previous answer
Reviewer 4 Report
Comments and Suggestions for AuthorsThis is a very well written and informative manuscript. It is easy to read and understand. It can be published just as it is, however, I was hoping that the conclusions would have a bit more substance. The rest of the manuscript is very informative and all is very well written.
Author Response
This is a very well written and informative manuscript. It is easy to read and understand. It can be published just as it is, however, I was hoping that the conclusions would have a bit more substance. The rest of the manuscript is very informative and all is very well written.
Response: We thank the reviewer for their feedback. We have expanded on the conclusions and included a figure/Flowchart for the testing of AATD and possible management/treatment options
