Whole-genome sequencing of paired prostate cancer cell cultures from 10 African American men reveals recurrent DNA-repair alterations

Whole-genome sequencing of matched tumor and adjacent non-malignant primary cell cultures from 10 African American men with prostate cancer revealed a heterogeneous genomic landscape marked by chromosomal instability and recurrent alterations in genes involved in chromatin remodeling and DNA-damage response. The laboratory study was part of a prospective, institutional-review-board-approved clinical trial that obtained annotated prostate specimens from patients undergoing prostatectomy.

Researchers analyzed 10 matched pairs of primary cultures, with each pair derived from a prostate tumor and non-tumor tissue collected from the same patient. The patients had Gleason grades of 7, preoperative prostate-specific antigen levels ranging from 3.4 to 13 nanograms per milliliter, and pathologic stages from T2 to T3. Six tumors were classified as organ-confined, while four showed extraprostatic extension.

The paired design allowed investigators to identify somatic alterations using each patient’s non-malignant cells as a reference for subtracting germline variation and sequencing artifacts. The epithelial cultures were expanded through conditional reprogramming before sequencing. To limit interference from the mouse fibroblast feeder layer used during culture, investigators separately aligned reads to human and mouse reference genomes, removed reads with stronger or similar mouse alignment scores, and used additional checks to identify residual mouse sequence among candidate variants.

Whole-genome sequencing was performed with Illumina paired-end reads, and sequencing outputs passed quality-control thresholds of at least 110 gigabases, approximately 30-fold mean coverage and at least 95% coverage at 10-fold depth. Somatic variants were called with GATK MuTect2 using each matched non-tumor sample as the germline control, then annotated and evaluated for predicted functional impact. Tumor mutational burden was defined as nonsynonymous somatic mutations per megabase of the coding genome.

Mutations were distributed unevenly across the cohort, with clusters on chromosomes 1, 2, 3, 11, 17 and X. After counts were normalized by chromosome length, chromosome 17 had the highest mutation density, followed by chromosome 19. Tumor mutational burden ranged from 0.73 mutations per megabase in sample AP44 to 46.37 mutations per megabase in AP9, demonstrating substantial variation among the 10 patient models.

The analysis also identified evidence of genomic instability. Chromothripsis was defined through patterns including mutation clusters within individual chromosomes, complex rearrangements and oscillating copy-number states, while kataegis was identified from localized hypermutation near rearrangement breakpoints, including C-to-T or C-to-G substitutions in cytosine-rich motifs. Copy-number alterations were prominent on chromosomes 1 and 2 among the four samples represented in the copy-number heatmap. These findings characterize the analyzed cultures and do not establish clinical effects.

Alterations affecting chromatin remodeling and epigenetic regulation were among the most frequent findings. Reported mutation frequencies were 31.6% for KDM6A, 21.1% for ATRX, 7.9% for ARID1A and 5.3% for CHD1. DNA-damage-response genes also showed recurrent alterations: ATM occurred in 10.5% of samples, BRCA2 in 7.9%, BRCA1 in 5.3% and RAD51 in 2.6%. Pathway mapping placed the prioritized alterations on axes including PI3K/AKT/mTOR, Wnt signaling and androgen receptor pathways.

Functional-impact scoring and pathway analysis prioritized shared variants in genes including ATM and CDK12, while also identifying sample-specific candidates. One example was a candidate FOXA1-SSTR1 event comprising a missense variant in FOXA1 and an adjacent structural rearrangement involving SSTR1. The investigators also compared the cohort with predominantly European-ancestry genomic datasets and reported candidate mutations not represented in those references. Because the sample was small, the distinctness and therapeutic relevance of these candidates remain exploratory.

Genotype-phenotype analyses did not find statistically significant associations between tumor mutational burden and preoperative prostate-specific antigen, Gleason grade group or pathologic stage. The copy-number analysis included only four patients, and its associations with prostate-specific antigen and grade group were also non-significant. The investigators therefore described the findings as hypothesis-generating and called for validation in larger independent cohorts. The study did not report patient treatment, clinical outcomes, response to targeted drugs or evidence that any identified alteration produced a clinical benefit.

The principal limitations were the small, exclusively African American cohort of 10 patients, which was not designed to establish population-level mutation frequencies, and the use of conditionally reprogrammed cultures as experimental models rather than a direct survey of every cell in each tumor. Within those bounds, the paired cell models provide a renewable resource for functional testing of candidate variants and preclinical studies. The results support further investigation of ancestry-informed genomic profiling in larger, independent cohorts rather than treatment conclusions based on this discovery cohort.

Subject of Research: Whole-genome characterization of prostate cancer genomic alterations in paired primary cultures from African American men

Article Title: Personalized genomic landscape of prostate cancer in African American men reveals novel drivers and therapeutic opportunities

Article References: Murthy, S., Fago, K., Knight, J., Kowalczyk, K., Hankins, R., Bandi, G., Dritschilo, A., & Jung, M. (2026). Personalized genomic landscape of prostate cancer in African American men reveals novel drivers and therapeutic opportunities. PLOS One, 21(10), e0360389. https://doi.org/10.1371/journal.pone.0360389

Image Credits: AI Generated

DOI: 10.1371/journal.pone.0360389

Keywords: prostate cancer, African American men, whole-genome sequencing, paired primary cultures, somatic mutations, genomic instability, DNA damage response, chromatin remodeling, precision oncology, tumor mutational burden, Personalized, genomic