Dear editor
I would like to offer a comparative analysis of the recently published
study titled “A Novel Super-Enhancer-Related Gene Signature Predicts
Prognosis and Immune Microenvironment for Breast Cancer” by Qing Wu, Xuan
Tao, Yang Luo, Shiyao Zheng, Nan Lin, and Xianhe Xie (BMC Cancer volume 23, Article
number: 776, 2023). In light of the study’s findings, it is essential to
consider its contributions alongside related research to provide a comprehensive
perspective on the topic.
Wu et al. [
1] presents a
unique approach to prognosis prediction by utilizing a super-enhancer-related gene
signature (SERGs) in the context of breast cancer. The authors establish a
prognostic signature based on six genes: ZIC2, NFE2, FOXJ1, KLF15, POU3F2, and SPIB.
While this is a pioneering effort, there are notable comparisons and insights to be
drawn from previous research.
Firstly, the Wu et al. utilized RNA-sequencing data from The Cancer
Genome Atlas (TCGA) and established a prognostic signature using six SERGs. While
the approach is valid, it is essential to acknowledge the potential heterogeneity
within the TCGA dataset itself. To this end, we emphasize the necessity of
conducting subgroup analyses. Such analyses would provide more accurate insights
into the signature’s effectiveness across different breast cancer subtypes,
potentially revealing varied prognostic implications based on these subtypes. Breast
cancer is a highly heterogeneous disease with various molecular subtypes that can
impact prognosis. Without proper subtype-specific analysis, the applicability of the
proposed signature to diverse breast cancer subtypes may be limited.
Comparatively, it is worth noting that other prognostic gene expression
signatures have been developed and compared in the context of breast cancer
prognosis. However, to present something novel or more persuasive, it is crucial to
not only benchmark the SERGs signature against these established signatures but also
to integrate a more comprehensive immune panel study. This would enable a deeper
exploration into how the immune microenvironment affects breast cancer prognosis,
potentially leading to more impactful conclusions. In particular, the work by
Haibe-Kains et al. [
2] compared the
prognostic performance of three gene expression signatures, revealing agreement and
overlapping prediction rates. This comparative aspect highlights the importance of
benchmarking the proposed SERGs signature against other established signatures on
independent patient cohorts, shedding light on its relative predictive power.
Furthermore, the authors emphasize the immune microenvironment prediction capacity
of their SERGs signature. However, direct comparison with existing immune-related
gene signatures could offer a more comprehensive understanding of its strengths and
limitations. For example, the study by Liu et al. [
3] developed an immune checkpoint-related gene signature
specifically for triple-negative breast cancer (TNBC), showcasing both prognostic
and immune status prediction capabilities. Considering the evolving landscape of
immunotherapy, such comparisons would provide valuable insights into the unique
contributions of the SERGs signature in the context of immune-related
predictions.
Breast cancer is categorized into various types and subtypes, determined
by characteristics such as specific receptors, gene expression patterns, and
histological features. The focus is solely on patients with
Her2 + breast cancer, without specifying the different groups
involved [
4].
ZIC2, a gene, shows notably higher expression in the BT549 cell line
compared to the MCF7 cell line. The BT549 cell line belongs to the basal-like
subtype, while MCF7 represents the luminal A subtype. These subtypes are
characterized by unique molecular attributes and distinct gene expression patterns.
The variation in ZIC2 expression between these subtypes may stem from differences in
their regulatory mechanisms or the signaling pathways unique to each subtype.
Genetic variations commonly found in breast cancer cell lines, such as mutations,
amplifications, deletions, or epigenetic changes, could influence the expression of
ZIC2. These genetic differences between BT549 and MCF7 may affect the regulation of
ZIC2 expression, as observed by Makki 2015, leading to different expression levels
of the ZIC2 gene in the two cell lines.
Breast cancer, being a multifaceted and diverse illness, consists of
various subtypes and exhibits a wide range of molecular characteristics. The
super-enhancers and their corresponding genes can vary significantly among these
subtypes and from patient to patient. This variability poses a significant challenge
in pinpointing consistent and dependable biomarkers [
5]. The relationship between SERS and tumor characteristics such
as Tumor Mutational Burden (TMB), mutation counts, and copy number burdens remains
unexplored in both groups. In breast cancer cases with low TMB, fewer somatic
mutations are typically found in the coding regions of the tumor genome. Generally,
breast cancer has a lower TMB compared to other cancer types. However, in breast
cancer treatment, TMB might not be the key biomarker for selecting targeted
therapies, as other genetic alterations and biomarkers like hormone receptor or HER2
status could be more significant. TMB has become notable for its role in predicting
the response to immunotherapy, especially immune checkpoint inhibitors. It’s
observed that tumors with higher TMB are more likely to produce neoantigens, which
are new antigens capable of triggering a more robust immune response. This can make
immunotherapies more effective [
6,
7].
Super enhancers, heavily reliant on specific transcription co-factors
like BET and BRD4 in each cell and tissue, play a crucial role in defining and
maintaining cell and tissue identity. These super enhancers, especially those
containing cell-type-specific master transcription factors, are often associated
with genes that determine cell identity [
8]. They are vital in managing mammalian cell identity but can
also change dynamically in response to various stimuli, treatments, or during
disease progression. The persistence and uniformity of ZIC2-associated super
enhancers across different times and conditions is a subject of research, important
for confirming ZIC2’s reliability as a prognostic biomarker [
9]. However, the lack of detailed information
about patients’ treatment histories, including radiotherapy or drug
treatments, limits the effectiveness of ZIC2 as a prognosis predictor. Moreover,
super enhancers and their related genes can have varying effects depending on the
context. The significance of ZIC2, as a gene linked to super enhancers, may differ
based on cellular circumstances, genetic makeup, and environmental factors. Hence,
it’s essential to understand these context-dependent impacts to accurately
assess ZIC2’s prognostic value [
10]. In the environment of a tumor, the battle for nutrients
between immune cells and cancer cells plays a key role in determining the
tumor’s outcome. It’s important to link Surface Enhanced Raman
Scattering (SERS) with changes in metabolic pathways or network alterations. Such
metabolic exchanges can influence how immune cells operate, the advancement of the
tumor, and the effectiveness of treatments [
11].
In conclusion, while the study by Wu et al. presents an innovative
approach, we highlight the necessity of addressing potential dataset heterogeneity
through subgroup analysis and the importance of conducting a more comprehensive
immune panel study to enhance the understanding of the immune
microenvironment’s role in breast cancer. However, to ensure its clinical
applicability and robustness, it is crucial to address potential heterogeneity
within the dataset, benchmark its performance against other prognostic signatures,
and compare its immune-related prediction capacity with established immune gene
signatures. Such considerations would contribute to a more holistic interpretation
of the study’s findings and their potential implications.
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