Mutational and Expression Profile of ZNF217, ZNF750, ZNF703 Zinc Finger Genes in Kenyan Women Diagnosed with Breast Cancer
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eLife Assessment
This study presents a valuable finding on the mutational landscape and expression profile of ZNF molecules in 23 Kenyan women with breast cancer. The evidence supporting the claims of the authors is solid, although inclusion of a larger number of patient samples, more statistical details and sufficient comparison with existing large-scale datasets would have strengthened the study. The work will be of interest to medical biologists working in the field of breast cancer.
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Abstract
Objectives
To characterize the somatic mutational spectrum and transcriptomic expression of the zinc-finger genes ZNF217, ZNF703, and ZNF750 in Kenyan women with breast cancer, and to explore their associations with clinicopathologic features.
Methods
Whole-exome sequencing and RNA-sequencing were performed on paired tumor and adjacent normal tissues from 23 consented patients treated at two Kenyan referral hospitals. Variants were called with Mutect2 using a study-specific panel of normal; functional consequences were annotated with VEP. After featureCounts quantification, differential expression was analyzed in DESeq2 (fold-change ≥ 1.5, p < 0.05). Two-sample t-tests (mutations) and ANOVA (expression) evaluated relationships with HER2 status and clinical stage.
Results
A total of 358 somatic mutations were detected: 170 in ZNF217, 24 in ZNF703 and 164 in ZNF750. Single-nucleotide substitutions (319 SNPs) dominated, with C→T and A→G changes most common; 27 deletions and 2 insertions were also observed. Frameshift events in ZNF217 and ZNF703 introduced premature stop codons predicted to truncate protein function. All three genes were significantly up-regulated in tumors versus normal (ZNF217 p = 0.0004), with the greatest expression in HER2-positive tumors and in stages 2–3 disease. Mutation burden for each gene did not differ by HER2 status (p > 0.56) or by stage (p > 0.32).
Conclusions
Kenyan breast tumors harbor frequent, functionally relevant mutations and marked over-expression of ZNF217, ZNF703, and ZNF750. These alterations, especially the pronounced up-regulation of ZNF217, highlight the trio’s potential as diagnostic or prognostic biomarkers and warrant larger studies to validate their clinical utility and suitability as therapeutic targets in sub-Saharan African populations.
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eLife Assessment
This study presents a valuable finding on the mutational landscape and expression profile of ZNF molecules in 23 Kenyan women with breast cancer. The evidence supporting the claims of the authors is solid, although inclusion of a larger number of patient samples, more statistical details and sufficient comparison with existing large-scale datasets would have strengthened the study. The work will be of interest to medical biologists working in the field of breast cancer.
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Reviewer #1 (Public review):
Summary:
This manuscript investigates mutations and expression patterns of zinc finger proteins in Kenyan breast cancer patients. Whole-exome sequencing and RNA-seq were performed on 23 breast cancer samples alongside matched normal tissues.
Strengths:
Whole-exome sequencing and RNA-seq were performed on 23 breast cancer samples alongside matched normal tissues in Kenyan breast cancer patients. The authors identified mutations in ZNF217, ZNF703, and ZNF750.
Weaknesses:
(1) Research scope:
The results primarily focus on mutations in ZNF217, ZNF703, and ZNF750, with limited correlation analyses between mutations and gene expression. The rationale for focusing only on these genes is unclear. Given the availability of large breast cancer cohorts such as TCGA and METABRIC, the authors should compare their …
Reviewer #1 (Public review):
Summary:
This manuscript investigates mutations and expression patterns of zinc finger proteins in Kenyan breast cancer patients. Whole-exome sequencing and RNA-seq were performed on 23 breast cancer samples alongside matched normal tissues.
Strengths:
Whole-exome sequencing and RNA-seq were performed on 23 breast cancer samples alongside matched normal tissues in Kenyan breast cancer patients. The authors identified mutations in ZNF217, ZNF703, and ZNF750.
Weaknesses:
(1) Research scope:
The results primarily focus on mutations in ZNF217, ZNF703, and ZNF750, with limited correlation analyses between mutations and gene expression. The rationale for focusing only on these genes is unclear. Given the availability of large breast cancer cohorts such as TCGA and METABRIC, the authors should compare their mutation profiles with these datasets. Beyond European and U.S. cohorts, sequencing data from multiple countries, including a recent Nigerian breast cancer study (doi: 10.1038/s41467-021-27079-w), should also be considered. Since whole-exome sequencing was performed, it is unclear why only four genes were highlighted, and why comparisons to previous literature were not included.
(2) Language and Style Issues
There are many typos and clear errors in the main text (e.g. (ref)).
Additionally, several statements read unnaturally. For example:
"Investigators uncovered 170 mutations ..." should instead be phrased as "We identified 170 mutations ...."
"The research team ..." should be rephrased as "Our team ...."
(3) Methods and Data Analysis Details
The methods section is vague, with general descriptions rather than specific details of data processing and analysis. The authors should provide:
(a) Parameters used for trimming, mapping, and variant calling (rather than referencing another paper such as Tang et al. 2023).
(b) Statistical methods for somatic mutation/SNP detection.
(c) Details of RNA purification and RNA-seq library preparation.
Without these details, the reproducibility of the study is limited.
(4) Data Reporting
This study has the potential to provide a valuable resource for the field. However, data-sharing plans are unclear. The authors should:
a) Deposit sequencing data in a public repository.
b) Provide supplementary tables listing all detected mutations and all differentially expressed genes (DEGs).
c) Clarify whether raw or adjusted p-values were used for DEG analysis.
d) Perform DEG analyses stratified by breast cancer subtypes, since differential expression was observed by HER2 status, and some zinc finger proteins are known to be enriched in luminal subtypes.
(5) Mutation Analysis
Visualizations of mutation distribution across protein domains would greatly strengthen interpretation. Comparing mutation distribution and frequency with published datasets would also contextualize the findings.
Comments on revisions:
The revised manuscript hasn't addressed any of these concerns. Careful proofreading is recommended, even if the authors do not intend to make further modifications to the manuscript.
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Reviewer #2 (Public review):
Summary:
This work integrated the mutational landscape and expression profile of ZNF molecules in 23 Kenyan women with breast cancer.
Strengths:
The mutation landscape of ZNF217, ZNF703, and ZNF750 were comprehensively studied and correlate with tumor stage and HER2 status to highlight the clinical significance.
Weaknesses:
The current cohort size is relatively small to reach significant findings, and targeted exploration on ZNF family without emphasizing the reason or clinical significance hinders the overall significance of the entire work.
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Reviewer #3 (Public review):
Summary:
This revised study analyzes the somatic mutational profiles and transcriptomic expression of three zinc-finger genes (ZNF217, ZNF703, ZNF750) in 23 Kenyan women with breast cancer, using whole-exome sequencing and RNA-sequencing of paired tumor-normal tissues. A total of 358 somatic mutations were detected, and all three genes were significantly upregulated in tumors compared to normal tissues (ZNF217 showing the most prominent difference). Higher expression was observed in HER2-positive tumors, though mutation burden for each gene did not correlate significantly with HER2 status or cancer stage. The findings provide preliminary evidence for the idenfication of diagnostic/prognostic biomarkers or therapeutic targets in sub-Saharan African populations.
Strengths:
The study's key strengths lie in its …
Reviewer #3 (Public review):
Summary:
This revised study analyzes the somatic mutational profiles and transcriptomic expression of three zinc-finger genes (ZNF217, ZNF703, ZNF750) in 23 Kenyan women with breast cancer, using whole-exome sequencing and RNA-sequencing of paired tumor-normal tissues. A total of 358 somatic mutations were detected, and all three genes were significantly upregulated in tumors compared to normal tissues (ZNF217 showing the most prominent difference). Higher expression was observed in HER2-positive tumors, though mutation burden for each gene did not correlate significantly with HER2 status or cancer stage. The findings provide preliminary evidence for the idenfication of diagnostic/prognostic biomarkers or therapeutic targets in sub-Saharan African populations.
Strengths:
The study's key strengths lie in its focus on an underrepresented Kenyan cohort, addressing a critical gap in sub-Saharan African breast cancer genomic research. It integrates DNA-level mutation analysis with RNA-level expression data, leveraging standardized bioinformatics pipelines (e.g., Mutect2 for variant calling, DESeq2 for differential expression) and rigorous quality control to deliver detailed insights into mutation types, functional impacts, and amino acid changes. Additionally, it explores gene expression patterns across different cancer stages and HER2 status subgroups, generating targeted hypotheses for future validation and enhancing the reliability of its findings.
Weaknesses:
The author has enhanced the descriptive depth of the study by adding details on mutations, expression subgroup analyses, and functional annotations but has not addressed the core weaknesses of small cohort size and lack of functional validation. While the revised version is more comprehensive in cataloging molecular alterations, it remains confined to descriptive analysis, with no substantial improvement in the reliability or generalizability of its conclusions.
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Author response:
I have updated the manuscript by correcting errors.
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eLife Assessment
This study presents a valuable finding on mutations in ZNF217, ZNF703, and ZNF750 through 23 breast cancer samples alongside matched normal tissues in Kenyan breast cancer patients. The evidence supporting the claims of the authors is solid, yet the analysis of the manuscript lacks methodological transparency, statistical detail, and sufficient comparison with existing large-scale datasets. The work will be of interest to medical biologists and scientists working in the field of breast cancer.
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Reviewer #1 (Public review):
Summary:
This manuscript investigates mutations and expression patterns of zinc finger proteins in Kenyan breast cancer patients.
Strengths:
Whole-exome sequencing and RNA-seq were performed on 23 breast cancer samples alongside matched normal tissues in Kenyan breast cancer patients. The authors identified mutations in ZNF217, ZNF703, and ZNF750.
Weaknesses:
(1) Research scope:
The results primarily focus on mutations in ZNF217, ZNF703, and ZNF750, with limited correlation analyses between mutations and gene expression. The rationale for focusing only on these genes is unclear. Given the availability of large breast cancer cohorts such as TCGA and METABRIC, the authors should compare their mutation profiles with these datasets. Beyond European and U.S. cohorts, sequencing data from multiple countries, …
Reviewer #1 (Public review):
Summary:
This manuscript investigates mutations and expression patterns of zinc finger proteins in Kenyan breast cancer patients.
Strengths:
Whole-exome sequencing and RNA-seq were performed on 23 breast cancer samples alongside matched normal tissues in Kenyan breast cancer patients. The authors identified mutations in ZNF217, ZNF703, and ZNF750.
Weaknesses:
(1) Research scope:
The results primarily focus on mutations in ZNF217, ZNF703, and ZNF750, with limited correlation analyses between mutations and gene expression. The rationale for focusing only on these genes is unclear. Given the availability of large breast cancer cohorts such as TCGA and METABRIC, the authors should compare their mutation profiles with these datasets. Beyond European and U.S. cohorts, sequencing data from multiple countries, including a recent Nigerian breast cancer study (doi: 10.1038/s41467-021-27079-w), should also be considered. Since whole-exome sequencing was performed, it is unclear why only four genes were highlighted and why comparisons to previous literature were not included.
(2) Language and Style Issues:
Several statements read somewhat 'unnaturally', and I strongly recommend proofreading.
(3) Methods and Data Analysis Details:
The methods section is vague, with general descriptions rather than specific details of data processing and analysis. The authors should provide:
(a) Parameters used for trimming, mapping, and variant calling (rather than referencing another paper such as Tang et al. 2023).
(b) Statistical methods for somatic mutation/SNP detection.
(c) Details of RNA purification and RNA-seq library preparation.
Without these details, the reproducibility of the study is limited.
(4) Data Reporting:
This study has the potential to provide a valuable resource for the field. However, data-sharing plans are unclear. The authors should:
(a) deposit sequencing data in a public repository.
(b) provide supplementary tables listing all detected mutations and all differentially expressed genes (DEGs).
(c) clarify whether raw or adjusted p-values were used for DEG analysis.
(d) perform DEG analyses stratified by breast cancer subtypes, since differential expression was observed by HER2 status, and some zinc finger proteins are known to be enriched in luminal subtypes.
(5) Mutation Analysis:
Visualizations of mutation distribution across protein domains would greatly strengthen interpretation. Comparing mutation distribution and frequency with published datasets would also contextualize the findings.
-
Reviewer #2 (Public review):
Summary:
This work integrated the mutational landscape and expression profile of ZNF molecules in 23 Kenyan women with breast cancer.
Strengths:
The mutation landscape of ZNF217, ZNF703, and ZNF750 was comprehensively studied and correlated with tumor stage and HER2 status to highlight the clinical significance.
Weaknesses:
The current study design is relatively simple, and there is a limited cohort size, which is relatively small to reach significant findings. Thus, sample size enrichment, along with more analytic work, is needed.
Targeted exploration of the ZNF family without emphasizing the reason or clinical significance hinders the overall significance of the entire work.
-
Reviewer #3 (Public review):
Summary:
The authors aimed to define the somatic mutational landscape and transcriptomic expression of the ZNF217, ZNF703, and ZNF750 genes in breast cancers from Kenyan women and to investigate associations with clinicopathological features like HER2 status and cancer stage. They employed whole-exome and RNA-sequencing on 23 paired tumor-normal samples to achieve this.
Strengths:
(1) A major strength is the focus on a Kenyan cohort, addressing a critical gap in genomic studies of breast cancer, which are predominantly based on European or Asian populations.
(2) The integration of DNA- and RNA-level data from the same patients provides a comprehensive view, linking genetic alterations to expression changes.
Weaknesses:
(1) The small cohort size (n=23) significantly limits the statistical power to detect …
Reviewer #3 (Public review):
Summary:
The authors aimed to define the somatic mutational landscape and transcriptomic expression of the ZNF217, ZNF703, and ZNF750 genes in breast cancers from Kenyan women and to investigate associations with clinicopathological features like HER2 status and cancer stage. They employed whole-exome and RNA-sequencing on 23 paired tumor-normal samples to achieve this.
Strengths:
(1) A major strength is the focus on a Kenyan cohort, addressing a critical gap in genomic studies of breast cancer, which are predominantly based on European or Asian populations.
(2) The integration of DNA- and RNA-level data from the same patients provides a comprehensive view, linking genetic alterations to expression changes.
Weaknesses:
(1) The small cohort size (n=23) significantly limits the statistical power to detect associations between genetic features and clinical subgroups (e.g., HER2 status, stage), rendering the negative findings inconclusive.
(2) The study is primarily descriptive. While it effectively catalogs mutations and expression changes, it does not include functional experiments to validate the biological impact of the identified alterations.
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