ADAR1 Editing and its Role in Cancer
Round 1
Reviewer 1 Report
The review “ ADAR1 editing and its role in cancer” by Xu and Öhman is an excellent and timely review about the this emerging filed. It is fun to read and give a very good view of the “big picture” and the fine details of the current status of this exciting field and where its heading.
Minor suggestion:
Line 32: “and ADAR2 is mainly expressed in the brain” - Recent work has shown that ADAR2 expression is highest the artery (PMID: 30087110).
Line 64: “ADAR1 protects the organism from several diseases associated with IFN activation such as.. systemic lupus erythematosus [28]” this reference is less relevant as in this paper – an elevation of RNA editing was found. More appropriate reference can be PMID: 29592874 (psoriasis).
Line 78:” However, in a few cases … silencing or deletion of ADAR1 reduces the malignant…” I believe that instead of “reduces” it should be “increase”.
Line 151: Consider to mention a recent work that screen for editing sites in miRNAs and their alterations in cancer, where several additional reliable and significant sites were found. (PMID: 29165639)
Consider to add a short discussion about the potential role of RNA editing in creating antigens (PMID: 30254248 )
Author Response
Answers to reviewer 1
The review “ ADAR1 editing and its role in cancer” by Xu and Öhman is an excellent and timely review about the this emerging filed. It is fun to read and give a very good view of the “big picture” and the fine details of the current status of this exciting field and where its heading.
Minor suggestion:
Line 32: “and ADAR2 is mainly expressed in the brain” - Recent work has shown that ADAR2 expression is highest the artery (PMID: 30087110).
Answer: Thank you, this has been added to the text and changed.
Line 64: “ADAR1 protects the organism from several diseases associated with IFN activation such as.. systemic lupus erythematosus [28]” this reference is less relevant as in this paper – an elevation of RNA editing was found. More appropriate reference can be PMID: 29592874 (psoriasis).
Answer: Thank you, this reference has been changed.
Line 78:” However, in a few cases … silencing or deletion of ADAR1 reduces the malignant…” I believe that instead of “reduces” it should be “increase”.
Answer: We apologize for this mistake and thank the reviewer for pointing it out.
Line 151: Consider to mention a recent work that screen for editing sites in miRNAs and their alterations in cancer, where several additional reliable and significant sites were found. (PMID: 29165639)
Answer: This reference has been added to the text in the second paragraph, line 273 on page 5.
Consider to add a short discussion about the potential role of RNA editing in creating antigens (PMID: 30254248 )
Answer: This reference has been added to the text on page 2, line 132, discussed in the fifth paragraph on page 5 and added to table 1.
Reviewer 2 Report
This review describes a list of reported ADAR1 mediated editing events in coding regions, non-coding region of coding genes, non-coding RNAs, and microRNAs and their role in cancer. They also reviewed the repressive function of ADAR1 in innate immunity via inhibiting MDA5-MAVS and OAS-mediated IFN activation and PKR activation. In the last part, authors suggest potential clinical application by using ADAR1 expression as well as editing levels of specific genes as biomarkers and targeting them for therapy. Overall, this review provides valuable insights into role of ADAR1 editing in cancer and well summarizes the current findings in the area.
On page 5, line 179-180, the authors mentioned about the role of ADAR1 in melanoma independent of its RNA editing function. Although this review paper is being focused on the role of ADAR1 editing in cancer, the authors may consider including one or two paragraphs to briefly discuss about the editing-independent role of ADAR1 in cancer.
Minor comments:
Line 79, “silencing or deletion of ADAR1 reduces the malignant properties.” it should be “promotes the malignant properties”.
Line 110, “activation of the Akt/mTOR signaling pathway or activate STAT3” should be “activation of the Akt/mTOR signaling pathway or STAT3”
Line 168, “Editing of Gabra3 reduce its own….thereby inhibit AKT activation” should be “Editing of Gabra3 reduces its own….thereby inhibits AKT activation”
Line 205, “IFNα and IFNβ then trigger… and transactivates” should be IFNα and IFNβ then trigger… and transactivate”
Line 235, “candidates of depeleated genes” should be “depleted”
Line 252, “The immunoregulatory effect and ….of IFN makes it” should be “The immunoregulatory effect and ….of IFN make it”
Author Response
Answers to reviewer 2
This review describes a list of reported ADAR1 mediated editing events in coding regions, non-coding region of coding genes, non-coding RNAs, and microRNAs and their role in cancer. They also reviewed the repressive function of ADAR1 in innate immunity via inhibiting MDA5-MAVS and OAS-mediated IFN activation and PKR activation. In the last part, authors suggest potential clinical application by using ADAR1 expression as well as editing levels of specific genes as biomarkers and targeting them for therapy. Overall, this review provides valuable insights into role of ADAR1 editing in cancer and well summarizes the current findings in the area.
On page 5, line 179-180, the authors mentioned about the role of ADAR1 in melanoma independent of its RNA editing function. Although this review paper is being focused on the role of ADAR1 editing in cancer, the authors may consider including one or two paragraphs to briefly discuss about the editing-independent role of ADAR1 in cancer.
Answer: To clarify, we have divided section 2 into section 2.1 and 2.2 to clearly show the editing dependent and independent roles of ADAR1. The section about the editing independent role of ADAR1 has also been extended.
Minor comments:
Line 79, “silencing or deletion of ADAR1 reduces the malignant properties.” it should be “promotesthe malignant properties”.
Answer: We apologize for this mistake and thank the reviewer for pointing it out.
Line 110, “activation of the Akt/mTOR signaling pathway or activate STAT3” should be “activation of the Akt/mTOR signaling pathway or STAT3”
Answer: Thank you, this has been changed.
Line 168, “Editing of Gabra3 reduce its own….thereby inhibit AKT activation” should be “Editing of Gabra3 reduces its own….thereby inhibits AKT activation”
Answer: Thank you, this has been changed.
Line 205, “IFNα and IFNβ then trigger… and transactivates” should be IFNα and IFNβ then trigger… and transactivate”
Answer: Thank you, this has been changed.
Line 235, “candidates of depeleated genes” should be “depleted”
Line 252, “The immunoregulatory effect and ….of IFN makes it” should be “The immunoregulatory effect and ….of IFN make it”
Answer: Thank you, these things have been changed.
Reviewer 3 Report
This is a timely review, coinciding with important advances in our understanding of the role of A-I editing in cancers. The authors have encompassed these very recent publications comprehensively in this manuscript.
In general the review is excellent quality and I believe the manuscript could be accepted in its current form. However, some comments follow, that may further improve the review.
The quality of writing is in general excellent, but could be improved in certain areas. Particularly, the use of semi-colons is not always correct. Semi colons should be used to join independent clauses. Please particularly check the abstract for use of semi colons, and page 6 for general editing.
The authors discuss the functions of ADAR in the context of 'RNA mutations'. However, I believe they could further acknowledge that editing independent functions also occur. In fact, a number of the references they use refer to editing independent effects. (eg. Markel lab reference referring to ADAR involvement in cancer immune escape (see also Nemlich 2018 ITGB3 in melanoma invasion)).
Further, in line 81 the authors imply that editing in non-exonic regions do not have any effect. However this is not supported by research. eg see complimentary data from Sagredo 2018 and Peng 2018 in breast cancer lines. Less than 3% of alternatively edited sites are in exons in BC, yet it can account for as many differences in final protein a.a. sequence as genomic mutations. However, the majority of editing sites in intronic and 3' UTR regions still appear to have functional consequences. ie in protein expression levels. For potentially relevant mechanisms see for eg differential binding of proteins mediating RNA localisation and stability. (eg Wang et al 2013).
The authors raise some intriguing points regarding inflammation and the immune system that may warrant further attention/highlighting. Particularly, further discussion of how many cancers exist in inflammatory microenvironments, and how ADAR1 isoforms would typically be regulated under these conditions, as well as the role of IFN signalling in immune detection vs immune evasion by cancers may be of interest. Eg Further discussion of ADAR regulation of PD-1 responses, as well as the role of mir-222 as a biomarker for ipilimumab response (Galore Haskel 2015) would be very topical . The authors address this in the paragraph beginning line 224, but the potential implications could be discussed in more detail.
Further discussion of the causes of abberant ADAR regulation may also be welcome. It is briefly discussed on line 74, but other mechanisms could be acknowledged eg post-translational modification, (bTrCP, stress response) and ADAR3 (eg Zhang 2018), Localisation Eg. higher expression in cytoplasm is also correlated with protection in some models (Caponio et al 2018).
Additional minor comments are in the manuscript attached
Comments for author File: 
Comments.pdf
Author Response
Answers to reviewer 3
This is a timely review, coinciding with important advances in our understanding of the role of A-I editing in cancers. The authors have encompassed these very recent publications comprehensively in this manuscript.
In general the review is excellent quality and I believe the manuscript could be accepted in its current form. However, some comments follow, that may further improve the review.
The quality of writing is in general excellent, but could be improved in certain areas. Particularly, the use of semi-colons is not always correct. Semi colons should be used to join independent clauses. Please particularly check the abstract for use of semi colons, and page 6 for general editing.
Answer: The sentences with the semi colons has been added by the editor and was not in our original final version of the manuscript. They have now been changed back to the original version.
The authors discuss the functions of ADAR in the context of 'RNA mutations'. However, I believe they could further acknowledge that editing independent functions also occur. In fact, a number of the references they use refer to editing independent effects. (eg. Markel lab reference referring to ADAR involvement in cancer immune escape (see also Nemlich 2018 ITGB3 in melanoma invasion)).
Answer: Thank you. We have divided section 2 into section 2.1 and 2.2 to clearly show the editing dependent and independent roles of ADAR1. The section about the editing independent role of ADAR1 has also been extended.
Further, in line 81 the authors imply that editing in non-exonic regions do not have any effect. However this is not supported by research. eg see complimentary data from Sagredo 2018 and Peng 2018 in breast cancer lines. Less than 3% of alternatively edited sites are in exons in BC, yet it can account for as many differences in final protein a.a. sequence as genomic mutations. However, the majority of editing sites in intronic and 3' UTR regions still appear to have functional consequences. ie in protein expression levels. For potentially relevant mechanisms see for eg differential binding of proteins mediating RNA localisation and stability. (eg Wang et al 2013).
Answer: Thank you. These things have been changed.
The authors raise some intriguing points regarding inflammation and the immune system that may warrant further attention/highlighting. Particularly, further discussion of how many cancers exist in inflammatory microenvironments, and how ADAR1 isoforms would typically be regulated under these conditions, as well as the role of IFN signalling in immune detection vs immune evasion by cancers may be of interest.
Eg Further discussion of ADAR regulation of PD-1 responses, as well as the role of mir-222 as a biomarker for ipilimumab response (Galore Haskel 2015) would be very topical . The authors address this in the paragraph beginning line 224, but the potential implications could be discussed in more detail.
Answer: Thank you. These things have been added to the text.
Further discussion of the causes of abberant ADAR regulation may also be welcome. It is briefly discussed on line 74, but other mechanisms could be acknowledged eg post-translational modification, (bTrCP, stress response) and ADAR3 (eg Zhang 2018), Localisation Eg. higher expression in cytoplasm is also correlated with protection in some models (Caponio et al 2018).
Answer: We are aware of other causes of aberrant ADAR regulation that may cause cancer, particularly regulation by ADAR3 but have chosen to exclude these discussions and focus on the role of ADAR1.
Additional minor comments are in the manuscript attached
Answer: Thank you. These things have been changed according to the referee’s requests.
