Background Huntington’s disease (HD) is a neurodegenerative disorder transmitted by the huntingtin (Htt) gene expansion. To date, there is no information about the effect of mutant Htt on the ultrastructure of undifferentiated human embryonic stem cells (hESCs), and cells differentiated from them.

Aims The aim of this study was to characterise ultrastructural changes in mHtt-hESCs at progressive stages of differentiation, using transmission electron microscopy (TEM).

Methods The mutant HD stem cell line, mHtt-hESCs line, (SIVF020-HD, CAG numbers 48, 17), and a normal gender-matched wild-type sibling control wtHtt-hESCs line, (SIVF019 CAG numbers 15, 18), were propagated in feeder-free mTeSR1 media and induced to form embryoid bodies (EBs). Differences were quantified from TEM images using ImageJ.

Results TEM shows glycogen-like aggregates and degenerative mitochondria in lysosomes of mHtt-hESCs. Lysosomes with membrane remnants inside and unidentified white patches were more frequently observed in mHtt-hESCs compared with wtHtt-hESCs. The lysosomal area was significantly increased by 64% (p < 0.05) in mHtt-hESCs compared with wtHtt-hESCs. At the EB stage, in the mHtt-EBs, enlarged lysosomes with degrading cellular remnants were frequently observed in the cytoplasm. A number of mHtt cells contained entire cells in huge lysosomes. These engulfed cells clearly displayed signs of apoptosis. There is 80% (p < 0.05) and 39% (p < 0.05) significant increase in lysosomal area and number in mHtt-hEBs compared with wtHtt-EBs.

Conclusions Our findings provide evidence of significant lysosomal and other cell structure abnormalities, beginning with undifferentiated mHtt-hESCs, and continuing during differentiation. These abnormalities may be markers of HD cytopathology that begin with the earliest, single-cell stages of embryonic development.