Novel Mutations in a Lethal Case of Lymphomatous Adult T Cell Lymphoma with Cryptic Myocardial Involvement

Round 1

Reviewer 1 Report

Current Oncology - Manuscript curroncol-1061239 – Hashemi Zonouz et al.

Comments to the Authors:

The authors present interesting data which may represent a useful contribution to the field. However, the manuscript would benefit from some minor revisions so that the readers would be able to fully appreciate the case report.

Specific Points of Criticism and Suggestions for Improvement:

(1)  Abstract, line 3:  It would be useful to write out the meanings of the acronyms „FDG“ and „PET/CT“.

(2)  Introduction, 1st paragraph, line 2:  The word "caused" implies a direct line between infection and development of the tumor. However, only about 1 in 1,500 infected persons develop ATLL and mostly after an extremely long latent period between HTLV-1 infection and the start of ATLL. So, maybe use a more cautious wording like "is thought to be initiated" or similar. In this context, the last part of this sentence is useful "... which is necessary but not sufficient for its pathogenesis".

(3)  Introduction, 2nd paragraph, line 5:  Could the expression „casual role“ be a typing error? „causal role“?

(4)  Results, 1st paragraph, line 4:  For readers outside of USA and the Commonwealth it might be of advantage to use here the unit system of kilogramm (kg).

(5)  Results, 3rd paragraph, lines 9-13:  The list of mutations may be better appreciated in a small table.

(6)  Results, 4th paragraph, line 1:  The components of this chemotherapy regimen ESHAP should be written out.

(7a)  Figure 1, legend:  There seem to be some typing errors in the first line: „… shows and area of focal.thickening …“.

(7b)  Figure 1, legend:  It would be useful to explain what the arrows are supposed to show.

(8)  Discussion:  There are various longer listings of genes in the Discussion. Is there any order in these listings? One idea would be to arrange them alphabetically within the same listing. For example: 3rd paragraph, lines 8-9; 4th paragraph, lines 1-2; and elsewhere.

(9)  Discussion:  Many gene alterations are mentioned in the text. I wonder whether these aspects could be presented more „reader-friendly“ in some sort of table, maybe listing the genes, their alterations, their functions and the literature references.

Author Response

(1)  Abstract, line 3:  It would be useful to write out the meanings of the acronyms „FDG“ and „PET/CT“.

This has been done.

(2)  Introduction, 1st paragraph, line 2:  The word "caused" implies a direct line between infection and development of the tumor. However, only about 1 in 1,500 infected persons develop ATLL and mostly after an extremely long latent period between HTLV-1 infection and the start of ATLL. So, maybe use a more cautious wording like "is thought to be initiated" or similar. In this context, the last part of this sentence is useful "... which is necessary but not sufficient for its pathogenesis".

 

This has been done.

 

(3)  Introduction, 2nd paragraph, line 5:  Could the expression „casual role“ be a typing error? „causal role“?

Typo corrected.

(4)  Results, 1st paragraph, line 4:  For readers outside of USA and the Commonwealth it might be of advantage to use here the unit system of kilogramm (kg).

This has been done.

(5)  Results, 3rd paragraph, lines 9-13:  The list of mutations may be better appreciated in a small table.

This has been done.

 

(6)  Results, 4th paragraph, line 1:  The components of this chemotherapy regimen ESHAP should be written out.

This has been done.

(7a)  Figure 1, legend:  There seem to be some typing errors in the first line: „… shows and area of focal.thickening …“.

This has been done.

(7b)  Figure 1, legend:  It would be useful to explain what the arrows are supposed to show.

This has been done.

(8)  Discussion:  There are various longer listings of genes in the Discussion. Is there any order in these listings? One idea would be to arrange them alphabetically within the same listing. For example: 3rd paragraph, lines 8-9; 4th paragraph, lines 1-2; and elsewhere.

This has been done.

(9)  Discussion:  Many gene alterations are mentioned in the text. I wonder whether these aspects could be presented more „reader-friendly“ in some sort of table, maybe listing the genes, their alterations, their functions and the literature references.

The genes were ordered alphabetically for ease of reading.

Reviewer 2 Report

The authors describe an interesting case of ATLL with myocardial involvement and report novel gene mutations by NGS analysis of nodal tumor sample. The results appear relevant. I suggest to add more informations about NGS method used. 

Author Response

The authors describe an interesting case of ATLL with myocardial involvement and report novel gene mutations by NGS analysis of nodal tumor sample. The results appear relevant. I suggest to add more informations about NGS method used. 

 

This has been done.

Reviewer 3 Report

In the present draft the authors investigated histological features of a lethal lymphomatous case of North American ATLL with extensive cardiac involvement, and performed DNA seq looking for mutational landscape. Data are associated with a certain degree of novelty, and the topic discussed is compatible with the area of interest of the journal. However, the current manuscript presents some significative problems (listed below) and looks incomplete.

Here my suggestions:

Point 1: How did the authors called the mutations? What did they sequence? I suppose DNA. How did they call the mutation? Did they sequence matched normal? 

Point 2: the authors should  describe the general mutation burden (number of mut per Kb, percentages of different kinds of mutations, how many mutation are SNP-deletions-insertions.....)

Point 3: there is any correlation of the identified mutation? Do the identified mutations belong to the same/convergent pathways? Are the identified mutations predicted to be pathogenetic?

Point 4: Did the author analyze CNV (copy number variation?)

Point 5: what is the allelic frequency of the identified mutations? 

Point 6: could be nice to confirm the identified mutations (at least the more important/predicted to be pathogenetic) with PCR followed by Sanger sequence

Point 7: the authors should comment if the same mutations they identified have been already described in ATLL related literature.

Therefore, major revision is suggested for the current proposal.

Author Response

Point 1: How did the authors called the mutations? What did they sequence? I suppose DNA. How did they call the mutation? Did they sequence matched normal? 

- NGS performed at Foundation Medicine on DNA and RNA and interpreted following the guidelines of the American College of Medical Genetics

Point 2: the authors should  describe the general mutation burden (number of mut per Kb, percentages of different kinds of mutations, how many mutation are SNP-deletions-insertions.....)

= The analysis revealed and intermediate tumor mutational burden (9 mutations per megabase)

Point 3: there is any correlation of the identified mutation? Do the identified mutations belong to the same/convergent pathways? Are the identified mutations predicted to be pathogenetic?

The relevant paragraphs in the discussion have been updated.

Point 4: Did the author analyze CNV (copy number variation?)

Yes as stated in the paper amplification and loss of various genes were found.

Point 5: what is the allelic frequency of the identified mutations? 

The allelic frequency has been added in the text.

Point 6: could be nice to confirm the identified mutations (at least the more important/predicted to be pathogenetic) with PCR followed by Sanger sequence

The Foundation Medicine report is CLIA licensed and highly reliable.  The median exon coverage of this

was 846X (high quality). The reported predicted positive value is >99%.

Point 7: the authors should comment if the same mutations they identified have been already described in ATLL related literature.

The discussion has been expanded to clarify the molecular pathogenesis of ATLL in the context of our findings.

Round 2

Reviewer 3 Report

The authors provided sufficient material/data to answer relevant questions. To me, the manuscript is now improved and acceptable for publication.