Title: Single-cell transcriptomic analysis reveals prognosis-related stromal signatures that
potentiate stratification of patients with extrahepatic cholangiocarcinoma
Version: 2 Date: 15 Feb 2025
Reviewer's report:
This reviewer reviewed the first manuscript (Reviewer 1), however, was skipped the R1, and
re-invited for R2. While they revised the manuscript appropriately, this reviewer still has some
concerns.
Authors' response to Point 6: Association between gene expression profile/subtype in tumors
and stromal subgroups:
Unfortunately, they did not answer this reviewer's question. While the authors mention existing
classifications, they do not actually analyze the relationship between their stromal subgroups
and tumor subtypes. If data is available, such an analysis would strengthen the study. If not, this
limitation should be acknowledged.
Authors' response to Point 1: Figure Legends: This reviewer finds that the figure legends still
lack sufficient detail. Simply listing the title of each result is not enough to help readers and
reviewers understand the data. A more detailed explanation of what each figure shows, including
key findings and their relevance to the study, is necessary. Please ensure that the legends clearly
describe the data presented in each figure to improve clarity and readability.
Authors' response to Point 4: Identification of epithelial cells and tumor cells: Unfortunately
they did not answer the question. This reviewer still finds the classification of epithelial and
tumor cells unclear. While distinguishing these populations may not be the main focus of this
study, epithelial and tumor cells have distinct biological properties and contributions to the tumor
microenvironment.
Since both cell types express epithelial markers, it remains unclear how the authors ensure that
the observed stromal features are not influenced by the presence of tumor cells. The response
mentions that InferCNV could be used to differentiate tumor cells from normal epithelial cells
but does not clarify whether this method was applied or why it was not used. If differentiation
between tumor and non-tumor epithelial cells is not possible, this limitation should be explicitly
stated in the manuscript.
Title: Single-cell transcriptomic analysis reveals prognosis-related stromal signatures that
potentiate stratification of patients with extrahepatic cholangiocarcinoma
Version: 2 Date: 15 Feb 2025
Reviewer's report:
This reviewer reviewed the first manuscript (Reviewer 1), however, was skipped the R1, and
re-invited for R2. While they revised the manuscript appropriately, this reviewer still has some
concerns.
Authors' response to Point 6: Association between gene expression profile/subtype in tumors
and stromal subgroups:
Unfortunately, they did not answer this reviewer's question. While the authors mention existing
classifications, they do not actually analyze the relationship between their stromal subgroups
and tumor subtypes. If data is available, such an analysis would strengthen the study. If not, this
limitation should be acknowledged.
Authors' response to Point 1: Figure Legends: This reviewer finds that the figure legends still
lack sufficient detail. Simply listing the title of each result is not enough to help readers and
reviewers understand the data. A more detailed explanation of what each figure shows, including
key findings and their relevance to the study, is necessary. Please ensure that the legends clearly
describe the data presented in each figure to improve clarity and readability.
Authors' response to Point 4: Identification of epithelial cells and tumor cells: Unfortunately
they did not answer the question. This reviewer still finds the classification of epithelial and
tumor cells unclear. While distinguishing these populations may not be the main focus of this
study, epithelial and tumor cells have distinct biological properties and contributions to the tumor
microenvironment.
Since both cell types express epithelial markers, it remains unclear how the authors ensure that
the observed stromal features are not influenced by the presence of tumor cells. The response
mentions that InferCNV could be used to differentiate tumor cells from normal epithelial cells
but does not clarify whether this method was applied or why it was not used. If differentiation
between tumor and non-tumor epithelial cells is not possible, this limitation should be explicitly
stated in the manuscript.
Please review this paper.
user
Title: Single-cell transcriptomic analysis reveals prognosis-related stromal signatures that
potentiate stratification of patients with extrahepatic cholangiocarcinoma
Version: 2 Date: 15 Feb 2025
Reviewer's report:
This reviewer reviewed the first manuscript (Reviewer 1), however, was skipped the R1, and
re-invited for R2. While they revised the manuscript appropriately, this reviewer still has some
concerns.
Authors' response to Point 6: Association between gene expression profile/subtype in tumors
and stromal subgroups:
Unfortunately, they did not answer this reviewer's question. While the authors mention existing
classifications, they do not actually analyze the relationship between their stromal subgroups
and tumor subtypes. If data is available, such an analysis would strengthen the study. If not, this
limitation should be acknowledged.
Authors' response to Point 1: Figure Legends: This reviewer finds that the figure legends still
lack sufficient detail. Simply listing the title of each result is not enough to help readers and
reviewers understand the data. A more detailed explanation of what each figure shows, including
key findings and their relevance to the study, is necessary. Please ensure that the legends clearly
describe the data presented in each figure to improve clarity and readability.
Authors' response to Point 4: Identification of epithelial cells and tumor cells: Unfortunately
they did not answer the question. This reviewer still finds the classification of epithelial and
tumor cells unclear. While distinguishing these populations may not be the main focus of this
study, epithelial and tumor cells have distinct biological properties and contributions to the tumor
microenvironment.
Since both cell types express epithelial markers, it remains unclear how the authors ensure that
the observed stromal features are not influenced by the presence of tumor cells. The response
mentions that InferCNV could be used to differentiate tumor cells from normal epithelial cells
but does not clarify whether this method was applied or why it was not used. If differentiation
between tumor and non-tumor epithelial cells is not possible, this limitation should be explicitly
stated in the manuscript.
assistant