Download cover letter - Annals of Gastroenterology

Subhankar Chakraborty, M.D., Ph.D.
NEBRASKA’S HEALTH SCIENCE CENTER
A partner with Nebraska Health System
May 8, 2017
Editor-in-Chief
Annals of Gastroenterology
Dear Editor
Thank you for considering our manuscript entitled “In Silico Analysis Identifies Genes
Common between Five Primary Gastrointestinal Cancer Sites with Potential Therapeutic
Implications” for review. We thank the reviewers for their insightful comments and suggestions. We
have revised the manuscript and hope the changes made will be acceptable to the reviewers. We
have included a point by point answer to the comments from the reviewers. I look forward to hearing
from you soon.
Reviewer comments with rebuttal
Reviewer A:
This is a very interesting and detailed manuscript that merits publication in your journal. The only
thing that according to my opinion needs to be greatly elaborated is the clinical relevance of this
manuscripts findings. This is something that should be added in the manuscript before its publication.
Response: We thank the reviewer for his positive comments. We have added a discussion
about the clinical implications of the study in the revised manuscript.
Reviewer B:
The current study is an interesting investigation in public databases with microarrays data regarding
the genetic profile of the most common GI cancer. Despite the high numbers of samples and genes
analyzed the studies presented several weaknesses which should be addressed before the
manuscript is
considering suitable for publication
• The main point is that the study is looking like fishing expedition, No rational is providing for the
selection of specific tumors, tools, database, genes.
Response: We thank the reviewer for his comments. We beg to differ from the reviewer and we
provide specific examples to hopefully answer his/her concern. These are directly derived
from the manuscript.
Rationale: "While there are numerous studies that have investigated the global gene
expression in various GI cancers compared to normal GI tissue, there are differences in the
results from study to study. Thus, analysis of results from multiple studies provides the
opportunity to get a more accurate picture of differential gene expression in cancer tissues.
The gastrointestinal tract is embryologically derived from the endoderm with the esophagus
and stomach derived from the foregut, duodenum from the foregut and midgut, liver from the
ventral mesentery, pancreas from the septum transversum, transverse and ascending colon
from the midgut and the transverse colon and rectum from the hindgut. If we could identify a
Department of Internal Medicine, 982055 Nebraska Medical Center, University of Nebraska Medical Center. Omaha, NE 68198-2055. Phone:
(978)-810-5992, E-mail: [email protected]
set of genes that are common between cancers arising from multiple GI sites, this would help
identify pathways and in turn targets for therapy of GI malignancies"
Why we chose Oncomine: "The Oncomine database allows us to compare gene expression
across multiple studies to identify the genes that are differentially over or under expressed in
majority of the studies."
• Related with this there is no data regarding the biological function of the genes up-or downregulated in each cancer type, not even for a general description of them (i.e. transcription factor,
oncogene, growth factor,
invasion etc).
Response: We thank the reviewer for his suggestion. We agree that we have not provided a
description of the function of every up or downregulated gene. There are 5,000 genes that
were included in initial analysis and it would be difficult with space constraints to describe the
function of each gene. There are several online tools that are available to look up the function
of a particular gene.
• The tile includes the ambitious term “potential therapeutic implications” but in the body of the
manuscript no data provided. The author should delete this from the title or discuss in details this
issue in the discussion section
Response: We appreciate the reviewer's comments. We have added further discussion about
the clinical applications of this article in the revised manuscript. We have also revised the title
to read "In Silico Analysis Identifies Genes Common between Five Primary Gastrointestinal
Cancer Sites with Potential Clinical Applications". We feel the study has wide applications
including diagnosis, therapy and prognosis of GI cancers.
If you have any questions, please contact me at (978) 810 5992. Thank you for your
consideration.
Looking forward to hearing from you soon.
Sincerely,
Subhankar Chakraborty, M.D., Ph.D.
Dept. of Internal Medicine,
University of Nebraska Medical
Omaha. Nebraska
Center.
Department of Internal Medicine, 982055 Nebraska Medical Center, University of Nebraska Medical Center. Omaha, NE 68198-2055. Phone:
(978)-810-5992, E-mail: [email protected]