Title: Characterization of TGF#-associated molecular features and drug responses in
gastrointestinal adenocarcinoma
Version: 4 Date: 01 Feb 2021
Reviewer's report:
Comments to the Author
This bioinformatical research classified patients with GIAD into TGF-# high/low subtypes
using gene expression status of TGF-# signaling and analyzed the differences in multi-omics
between the two subtypes. Moreover, some anticancer drugs that target the genes with different
expression between the two subtypes were identified using the public database of cancer
cell lines. I agree that this study provides some essential information about the molecular
characteristics of TGF-# high/low subtypes in GIAD. However, in publishing this article in BMC
Gastroenterology, I have a few problems and questions as follows.
1. The abstract of this manuscript lacks the Methods section. This does not seem to fulfill the
criteria of BMC Gastroenterology.
2. Why does the trend of mRNA expression differences not match that of protein expression
differences in Figure 2?
3. I recommend describing why gene amplifications and deletions were more common in the
TGF-# low group, especially in STAD.
4. This research showed dabrafenib, a mutant BRAF-V600 specific inhibitor, can target multiple
oncogenes with different expression associated with TGF-#. You might want to describe your
ideas or to refer to previous reports on the relationship between BRAF-V600 inhibitor in the
article.
5. I suppose that “drug resistant drug” in the abstract and “Exprssion” in Figure 5e are typo. You
might also want to clarify which types of GIAD are shown in Figure S1, B to E.
Title: Characterization of TGF#-associated molecular features and drug responses in
gastrointestinal adenocarcinoma
Version: 4 Date: 01 Feb 2021
Reviewer's report:
Comments to the Author
This bioinformatical research classified patients with GIAD into TGF-# high/low subtypes
using gene expression status of TGF-# signaling and analyzed the differences in multi-omics
between the two subtypes. Moreover, some anticancer drugs that target the genes with different
expression between the two subtypes were identified using the public database of cancer
cell lines. I agree that this study provides some essential information about the molecular
characteristics of TGF-# high/low subtypes in GIAD. However, in publishing this article in BMC
Gastroenterology, I have a few problems and questions as follows.
1. The abstract of this manuscript lacks the Methods section. This does not seem to fulfill the
criteria of BMC Gastroenterology.
2. Why does the trend of mRNA expression differences not match that of protein expression
differences in Figure 2?
3. I recommend describing why gene amplifications and deletions were more common in the
TGF-# low group, especially in STAD.
4. This research showed dabrafenib, a mutant BRAF-V600 specific inhibitor, can target multiple
oncogenes with different expression associated with TGF-#. You might want to describe your
ideas or to refer to previous reports on the relationship between BRAF-V600 inhibitor in the
article.
5. I suppose that “drug resistant drug” in the abstract and “Exprssion” in Figure 5e are typo. You
might also want to clarify which types of GIAD are shown in Figure S1, B to E.
Please review this paper.
user
Title: Characterization of TGF#-associated molecular features and drug responses in
gastrointestinal adenocarcinoma
Version: 4 Date: 01 Feb 2021
Reviewer's report:
Comments to the Author
This bioinformatical research classified patients with GIAD into TGF-# high/low subtypes
using gene expression status of TGF-# signaling and analyzed the differences in multi-omics
between the two subtypes. Moreover, some anticancer drugs that target the genes with different
expression between the two subtypes were identified using the public database of cancer
cell lines. I agree that this study provides some essential information about the molecular
characteristics of TGF-# high/low subtypes in GIAD. However, in publishing this article in BMC
Gastroenterology, I have a few problems and questions as follows.
1. The abstract of this manuscript lacks the Methods section. This does not seem to fulfill the
criteria of BMC Gastroenterology.
2. Why does the trend of mRNA expression differences not match that of protein expression
differences in Figure 2?
3. I recommend describing why gene amplifications and deletions were more common in the
TGF-# low group, especially in STAD.
4. This research showed dabrafenib, a mutant BRAF-V600 specific inhibitor, can target multiple
oncogenes with different expression associated with TGF-#. You might want to describe your
ideas or to refer to previous reports on the relationship between BRAF-V600 inhibitor in the
article.
5. I suppose that “drug resistant drug” in the abstract and “Exprssion” in Figure 5e are typo. You
might also want to clarify which types of GIAD are shown in Figure S1, B to E.
assistant