Standardized RNA extraction protocol for Entamoeba species: advancing molecular diagnostics and amebiasis control

Amebiasis, caused by Entamoeba histolytica, remains a major public health challenge in endemic regions and is often misdiagnosed due to its morphological similarity to the non-pathogenic species E. dispar. The limitations of light microscopy and the high cost of immunological assays. This study aimed to standardize RNA extraction methods in Entamoeba to support high-quality transcriptomic analyses and molecular investigations Six RNA extraction protocols were compared using E. histolytica and E. dispar trophozoites, and RNA yield, purity, and integrity were assessed by spectrophotometry (NanoDrop), fluorometry (Qubit), and automated electrophoresis (TapeStation). The TRIzol + RNeasy protocol provided the highest purity ratios (260/280 and 260/230) and was selected as the standard method. Extracted RNA showed good integrity (RINe 7.2 for E. histolytica and 6.6 for E. dispar), supporting RNA-Seq library construction. Two library preparation strategies were evaluated: poly(A) selection and ribosomal RNA (rRNA) depletion. Both generated libraries with appropriate profiles; however, poly(A) selection was more efficient, yielding higher RNA concentrations and low residual rRNA (<3.5%), whereas rRNA depletion remained inefficient (~87% rRNA). This standardized RNA extraction workflow combined with poly(A) selection represents an effective strategy for transcriptomic analyses in Entamoeba, providing a robust methodological foundation to advance transcriptomic studies, biomarker discovery, and a deeper understanding of Entamoeba biology.