Novel transcriptomic alterations in poorly differentiated endometrial carcinomas: evidence from South African women

Poorly differentiated endometrial carcinoma in Black African women is under-characterized at the transcriptomic level, although it is known for aggressive subtypes. We conducted the first RNA-seq analysis of formalin-fixed, paraffin-embedded (FFPE) tumors from Black South African women to explore population-specific gene expression, alternative splicing, and novel isoforms.

Seventy-six FFPE tumor samples passed RNA quality thresholds (DV200 ≥ 30%) and were sequenced on the PacBio Onso™ short-read platform. StringTie assembled transcripts and estimated transcripts per million (TPMs); differential expression was quantified by mean log₂ fold-change (|log₂FC| ≥ 0.5). SUPPA2 computed percent spliced-in (PSI) values for five splicing event classes. Reactome over-representation analysis identified enriched pathways, and novel isoforms were validated by read coverage and expression support.

Cohort-level analysis (n = 76) revealed the coordinated activation of signaling and broad repression of transcriptional programs. We detected 17,990 dysregulated transcripts (4,483 upregulated and 13,507 downregulated; range -4.81 to +2.99). Prominent upregulated transcripts included GJA1 (+2.99), GRN (+2.60), ZC3H3 (+2.58), PCSK4 (+2.55), HSPB7 (+2.55), BICRA (+2.49), LINC02692 (+2.23), MKNK2 (+2.03), and RARA (+0.76). Strong downregulation was observed for MRPL15 (-4.81), ZSCAN23 (-4.46), NUF2 (-4.37), RTN1 (-4.33), EIF3I (-4.31), CDC73 (-3.36), MYC (-2.96), FRS2 (-2.90), and zinc-finger factors including ZNF569 (-3.36), ZNF573 (-2.92), ZNF793 (-2.33), and ZNF382 (-1.87). Reactome enrichment linked the upregulated set to MAPK family/GPCR signaling, while the downregulated categories were associated with gene expression (transcription), RNA polymerase II transcription, cell cycle, and metabolism. Alternative splicing was pervasive, with recurrent high-magnitude events at cancer-relevant loci including GJA1 (SE), NF2 (A3/A5), LIN37 (A5), ECT2 (A3/A5), BCL2L11 (A3), UQCRH (A5), CSE1L (A3), BROX (A3), and multiple ZNFs. StringTie identified previously unannotated isoforms at LINC02692 (+2.23), LINC01605 (-0.62), ZNF793 (-2.33), ZNF382 (-1.87), and retained-intron transcripts at RAD51 (+1.30), RPS24 (-0.97), and RPS3A (-0.62).

Poorly differentiated endometrial carcinomas in Black South African women show a distinct MAPK-linked activation pattern, along with transcriptional repression and extensive splicing changes. Aligning with findings in African Americans, this cohort highlights the unique aspects of isoform-resolved splicing and zinc-finger repression, suggesting that translational control, retinoid signaling, and RNA processing may be targets for biomarkers and therapy.