Title: Single-cell transcriptomic analysis reveals prognosis-related stromal signatures that
potentiate stratification of patients with extrahepatic cholangiocarcinoma
Version: 1 Date: 05 Feb 2025
Reviewer's report:
Single-cell transcriptomic data remains exceedingly sparse for extrahepatic
cholangiocarcinoma, which is thought to be quite molecularly distinct from intrahepatic
cholangiocarcinoma, where there is slightly more (but still very little) data. Samples from 5
patients for this particular cancer type is actually quite substantial. I find their conclusions about
stratifying survival by tumor signature quite interesting.
The identification of a proliferative group enriched in MKI67 + HPLCs is consistent with the
idea that tumors with a higher fraction of actively dividing cells tend to be more aggressive, and
MKI67 expression has been consistently associated with aggressive tumor behavior and poorer
prognosis in many cancers (e.g., breast, colorectal, and lung cancers). This group, along with
the immune-suppressive Treg-enriched group correlating with poorer prognosis is also expected
given findings from other cancer types.
While neuronal markers (e.g., Schwann cell markers) are not as widely reported in the prognostic
stratification of many cancers, recent studies have begun to recognize that neural components
and perineural interactions can influence tumor behavior. In some contexts, the presence of
nerve-associated cells or signaling (e.g., SLIT2, known for its tumor-suppressive functions) has
been linked to better outcomes. I agree with the authors that finding Schwann-like markers in
eCCA is quite exciting and the association with a better prognosis is likely to open up some
exciting new research avenues. The HPLC finding will also probably drive further research.
Overall I believe this is an impressive, robust, and informative paper for the field.
Things to consider:
- In the Discussion, given the observation that SLIT2# Schwann cells are linked to a better
prognosis, contrasting several reports in other tumor types where Schwann cells have been
implicated in promoting perineural invasion and metastasis, I think adding potential reasons for
these discrepancies could be valuable.
- The use of Monocle v2 for trajectory analysis is acceptable, yet newer tools (e.g., Monocle 3
or other trajectory inference methods) might offer advantages.
- The identification of hematopoietic progenitor-like cells (HPLCs) based solely on marker
expression (e.g., CD34, CD38, PTPRC) and trajectory analysis, though interesting, may require
orthogonal validation. Without independent functional or protein-level confirmation, it remains
possible that these cells could represent an activated or transdifferentiated state rather than bona
fide extramedullary progenitors, especially given how much they apparently proliferate.
- The inferred developmental paths (e.g., fibroblast differentiation from uCAF to iCAF to mCAF
or the progression of CD8 + T cells from progenitor exhausted to exhausted states) are based
on computational pseudotime algorithms. These analyses are sensitive to parameter choices and
noise in the data. Further experimental validation (for example, using lineage-tracing or time-
course studies) would strengthen these interpretations.
Title: Single-cell transcriptomic analysis reveals prognosis-related stromal signatures that
potentiate stratification of patients with extrahepatic cholangiocarcinoma
Version: 1 Date: 05 Feb 2025
Reviewer's report:
Single-cell transcriptomic data remains exceedingly sparse for extrahepatic
cholangiocarcinoma, which is thought to be quite molecularly distinct from intrahepatic
cholangiocarcinoma, where there is slightly more (but still very little) data. Samples from 5
patients for this particular cancer type is actually quite substantial. I find their conclusions about
stratifying survival by tumor signature quite interesting.
The identification of a proliferative group enriched in MKI67 + HPLCs is consistent with the
idea that tumors with a higher fraction of actively dividing cells tend to be more aggressive, and
MKI67 expression has been consistently associated with aggressive tumor behavior and poorer
prognosis in many cancers (e.g., breast, colorectal, and lung cancers). This group, along with
the immune-suppressive Treg-enriched group correlating with poorer prognosis is also expected
given findings from other cancer types.
While neuronal markers (e.g., Schwann cell markers) are not as widely reported in the prognostic
stratification of many cancers, recent studies have begun to recognize that neural components
and perineural interactions can influence tumor behavior. In some contexts, the presence of
nerve-associated cells or signaling (e.g., SLIT2, known for its tumor-suppressive functions) has
been linked to better outcomes. I agree with the authors that finding Schwann-like markers in
eCCA is quite exciting and the association with a better prognosis is likely to open up some
exciting new research avenues. The HPLC finding will also probably drive further research.
Overall I believe this is an impressive, robust, and informative paper for the field.
Things to consider:
- In the Discussion, given the observation that SLIT2# Schwann cells are linked to a better
prognosis, contrasting several reports in other tumor types where Schwann cells have been
implicated in promoting perineural invasion and metastasis, I think adding potential reasons for
these discrepancies could be valuable.
- The use of Monocle v2 for trajectory analysis is acceptable, yet newer tools (e.g., Monocle 3
or other trajectory inference methods) might offer advantages.
- The identification of hematopoietic progenitor-like cells (HPLCs) based solely on marker
expression (e.g., CD34, CD38, PTPRC) and trajectory analysis, though interesting, may require
orthogonal validation. Without independent functional or protein-level confirmation, it remains
possible that these cells could represent an activated or transdifferentiated state rather than bona
fide extramedullary progenitors, especially given how much they apparently proliferate.
- The inferred developmental paths (e.g., fibroblast differentiation from uCAF to iCAF to mCAF
or the progression of CD8 + T cells from progenitor exhausted to exhausted states) are based
on computational pseudotime algorithms. These analyses are sensitive to parameter choices and
noise in the data. Further experimental validation (for example, using lineage-tracing or time-
course studies) would strengthen these interpretations.
Please review this paper.
user
Title: Single-cell transcriptomic analysis reveals prognosis-related stromal signatures that
potentiate stratification of patients with extrahepatic cholangiocarcinoma
Version: 1 Date: 05 Feb 2025
Reviewer's report:
Single-cell transcriptomic data remains exceedingly sparse for extrahepatic
cholangiocarcinoma, which is thought to be quite molecularly distinct from intrahepatic
cholangiocarcinoma, where there is slightly more (but still very little) data. Samples from 5
patients for this particular cancer type is actually quite substantial. I find their conclusions about
stratifying survival by tumor signature quite interesting.
The identification of a proliferative group enriched in MKI67 + HPLCs is consistent with the
idea that tumors with a higher fraction of actively dividing cells tend to be more aggressive, and
MKI67 expression has been consistently associated with aggressive tumor behavior and poorer
prognosis in many cancers (e.g., breast, colorectal, and lung cancers). This group, along with
the immune-suppressive Treg-enriched group correlating with poorer prognosis is also expected
given findings from other cancer types.
While neuronal markers (e.g., Schwann cell markers) are not as widely reported in the prognostic
stratification of many cancers, recent studies have begun to recognize that neural components
and perineural interactions can influence tumor behavior. In some contexts, the presence of
nerve-associated cells or signaling (e.g., SLIT2, known for its tumor-suppressive functions) has
been linked to better outcomes. I agree with the authors that finding Schwann-like markers in
eCCA is quite exciting and the association with a better prognosis is likely to open up some
exciting new research avenues. The HPLC finding will also probably drive further research.
Overall I believe this is an impressive, robust, and informative paper for the field.
Things to consider:
- In the Discussion, given the observation that SLIT2# Schwann cells are linked to a better
prognosis, contrasting several reports in other tumor types where Schwann cells have been
implicated in promoting perineural invasion and metastasis, I think adding potential reasons for
these discrepancies could be valuable.
- The use of Monocle v2 for trajectory analysis is acceptable, yet newer tools (e.g., Monocle 3
or other trajectory inference methods) might offer advantages.
- The identification of hematopoietic progenitor-like cells (HPLCs) based solely on marker
expression (e.g., CD34, CD38, PTPRC) and trajectory analysis, though interesting, may require
orthogonal validation. Without independent functional or protein-level confirmation, it remains
possible that these cells could represent an activated or transdifferentiated state rather than bona
fide extramedullary progenitors, especially given how much they apparently proliferate.
- The inferred developmental paths (e.g., fibroblast differentiation from uCAF to iCAF to mCAF
or the progression of CD8 + T cells from progenitor exhausted to exhausted states) are based
on computational pseudotime algorithms. These analyses are sensitive to parameter choices and
noise in the data. Further experimental validation (for example, using lineage-tracing or time-
course studies) would strengthen these interpretations.
assistant