DIPARTIMENTO di SCIENZE BIOMEDICHE e BIOTECNOLOGICHE

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1 July 15, 2015 Science editor of World Journal of Gastroenterology Jing Yu Dear Prof. Jing Yu, please find enclosed a revised version of our paper Non-coding landscapes of Colorectal Cancer. We have modified the paper according to the Reviewers suggestions: enclosed you will also find a point-by-point reply (typed in red) to his/her comments. We changed the title, adding a hyphen between Non and coding The manuscript has been submitted to a commercial antiplagiarism tool (Plagtracker) and the title to Google Scholar. Finally, the manuscript has been edited for English by a mother tongue scientific expert of our University who provided a language editing certificate. You will find in attachment the pdf report of PlagTracker, the screenshot of Google Scholar, the language editing certificate and the copyright assignment. In its actual version, the paper comprises 5 tables and 1 figure. We thank you for your kind attention and the Reviewer for his helpful comments, which helped us to improve our paper. We hope that now our paper is found suitable for publication on World Journal of Gastroenterology. Sincerely Marco Ragusa, PhD Department of Biomedical and Biotechnological Sciences Via Santa Sofia 87, Catania Block 10, Building C, mragusa@unict.it

2 Reviewed by This is a quite comprehensive review about the involvement of non coding RNAs in the colorectal cancer disease. The study of non-coding RNAs as possible early diagnostic marker of cancer disease or as predictive/ prognostic markers of therapeutic outcome is of high interest. I would recommend some changes to possibly improve the manuscript: 1. A general comment: if from the abstract it appears that the review will summarize major finding on the translational applications of ncrnas on CRC diagnosis, prognosis, and therapy, this aspect is not so apparent in the following paragraphs. Specifically the terms prognostic and predictive should be used in a more specific manner and clearly discriminate between the predictive drug-related and the prognostic effect of a marker (i.e. The title of the chapter at page 19 is NON-CODING RNAS AS DIAGNOSTIC AND PREDICTIVE TOOLS but then the following paragraph is mirnas as diagnostic and prognostic CRC biomarkers and a mix of the prognostic or predictive value of mirnas is discussed). a. Several papers have been published on the predictive role of some mirnas expression (both in tumor or in plasma) on the response to pharmaco (5-FU-oxaliplatin-cetuximab-..)/radiotherapy in colorectal cancer (some references published before 2012 are reported below). These data could be collected on a paragraph about the predictive role of mirnas. We added now a new paragraph Non Coding RNAs with predictive power in CRC therapy response focused on predictive mirnas and lncrnas in therapy; while both paragraphs mirnas as diagnostic and prognostic CRC biomarkers and Pathological and clinical roles of lncrnas in CRC explain prognostic value of mirnas and lncrna, respectively. 2. Some paragraph (as the ones at page 6 and 14) are quite long, it could be useful to divide them in sub-paragraphs or add some additional figures. mirnas perform key roles in CRC initiation and evolution and The impact of lncrnas on CRC pathobiology paragraphs are quite long but difficult to divide in sub-paragraphs, because the most of ncrnas (especially mirnas) are involved in multiple molecular functions and biological processes. Indeed, the subdivision of paragraphs in groups of ncrnas involved in the same

3 pathway would be unfeasible: the same ncrna would be discussed and repeated in many subparagraphs, increasing the size of the whole manuscript. For easing the reading of these paragraphs, we bold typed the names of ncrnas in order to easily identify them inside the manuscript. However, the most relevant information about ncrna function are depicted in Figure 1. Furthermore, we schematically reported functions and clinical significances of all ncrnas (listed in alphanumeric order) cited in the manuscript, in order to quickly retrieve the most important information about their role and targets. 3. In the future perspectives, the potentiality of ncrnas based markers as predictive markers of tumor response to treatment could be also highlighted. Svoboda M, Izakovicova HL, Sefr R et al. micro-rnas mir125b and mir137 are frequently upregulated in response to capecitabine chemoradiotherapy of rectal cancer. Int. J. Oncol. 33(3), (2008). Hansen TF, Sorensen FB, Lindebjerg J, Jakobsen A. The predictive value of microrna 126 in relation to first line treatment with capecitabine and oxaliplatin in patients with metastatic colorectal cancer. BMC Cancer 12, 83 (2012). Pichler M, Winter E, Stotz M et al. Down-regulation of KRAS-interacting mirna 143 predicts poor prognosis but not response to EGFR-targeted agents in colorectal cancer. Br. J. Cancer 106(11), (2012). Drebber U, Lay M, Wedemeyer I et al. Altered levels of the onco-microrna 21 and the tumor-supressor micrornas 143 and 145 in advanced rectal cancer indicate successful neoadjuvant chemoradiotherapy. Int. J. Oncol. 39(2), (2011). Della Vittoria SG, Falcetta F, Carlomagno C et al. A specific mirna signature correlates with complete pathological response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer. Int. J. Radiat. Oncol. Biol. Phys. 83(4), (2012). These papers and others are cited in a new dedicated paragraph Non Coding RNAs with predictive power in CRC therapy response. Reviewed by The presented review is very poorly written and sometimes not easy to understand. There is a poor job for analysis and synthesis the findings of the authors. The authors offer a lot of information that

4 are not well-organized. I think the paper in this form is not publishable. I feel that the authors need to provide further information on the quality of the data. Moreover, this review has flaws with respect to English style, typos and grammar." (3) Definitely,I suggest to make copyediting of the paper by a proficient English speaker and recommend the author to rewrite the manuscript in more logical flow. For example, organize mirna according to the upregulation or downregulation relate to CRC, or relate to stage in CRC development. The microrna related polymorphisms should be mentioned in a subchapter relate to their risk and prognosis of CRC. You could say more about the application areas of the microrna relate to CRC. The paper has been now copyedited by mother tongue English. CRC associated single nucleotide polymorphisms in non coding RNAs paragraph has been added to report mirna and lncrna related polymorphisms in CRC. We choose to not divide ncrnas according to upregulation / downregulation in CRC or to their involvement in a specific CRC stage because in papers reporting expression profiles are shown both over- and under-expressed ncrnas; otherwise, several ncrnas are involved in multiple functions and processes, as well as, in different CRC stages. The strict sub-division of our treatise in up- and down- regulated molecules or by pathological functions would lead to a multiple repetition of the same papers, increasing the size of whole manuscript and make it tedious. Needless to say, that we tried to group ncrnas for type of expression where feasible, but it has not been always possible. For easing the reading of the manuscript, we bold typed the names of ncrnas in order to easily identify them inside the manuscript. Furthermore, we schematically reported functions and clinical significances of all ncrnas (listed in alphanumeric order) cited in the manuscript, in order to quickly retrieve the most important information about their role.

5 Reviewed by The present review summarizes the involvement of ncrnas in CRC pathobiology and their application to its diagnosis, prognosis and therapy. The review is rather long, but on the other hand is very well written and in detail. The following comments should be considered to improve the manuscript. Recently, it is suggested that stool samples have big potential for CRC screening. Few studies have already evaluated the feasibility of detecting mirnas in stool samples of patients with CRC. This should be addressed in this review. Similarly, there are several studies focused on expression of mirna-210 in CRC patients. This particular mir is not mentioned in this review. Recent review of Tokarz and Blasiak (2012) summarizing similar conclusions should be at least cited. Following the reviewer s suggestion, we added information about stool mirnas in CRC screening in paragraph mirnas as diagnostic and prognostic CRC biomarkers and also data on mir-210 in mirnas perform key roles in CRC initiation and evolution. Furthermore, we read and cited in Conclusions Tokarz and Blasiak (2012). Minor points: It is not clear why some of abbreviations of the gene/proteins are in brackets in italics and some not. This should be consistent. Examples: mir-143 targets KRAS (Kirsten rat sarcoma viral oncogene homolog) and MACC1 (Metastasis-Associated in Colon Cancer-1), thus playing an important role in regulation of EGFR and HGFR signalling. MiR-21 targets various tumour suppressor genes, as PDCD4 (programmed cell death 4), CCL20 [chemokine (C-C motif) ligand 20], CDC25A (cell division cycle 25 homolog A), PTEN (phosphatase and tensin homolog), thus promoting cell proliferation, invasion / intravasation / metastasis in CRC. Together with other let-7 family members, let-7c modulates cell cycle by targeting KRAS, and also is involved in suppressing metastasis via its targets MMP1(Matrix Metallopeptidase 1) and PBX3 (Pre-B-cell leukemia homeobox 3). Some of the abbreviations are not explained at all. Example: thus playing an important role in regulation of EGFR and HGFR signalling. When starting the new sentence with

6 word mir, always use the capitol letter. This is not consistent through all the manuscript. Typing errors: Page 9: CRCsamples Page 9: rate rate Page 11: in vitro is not in italic Page 21, 28: The Authors Page 35: applied o clinical We fixed abbreviation format and explained the missing ones. Moreover, we used capitol letter for mir at the beginning of new sentences and fixed typing errors suggested and other misprints. Reviewed by As a review paper, this manuscript comprehensively summarized non coding RNA in colorectal cancer. The manuscript is well written, the structure is well organized. Some typos and format issues are here and there. Please fix them. In addition, the reference list is a little bit long, please keep only necessary references. Typos and format issues were fixed. Some references have been deleted, but others have been added since reviewers asked extra paragraphs.