Vanhie, A. | bioRxiv Science

bioRxiv2024

Long-read whole-genome sequencing-based concurrent haplotyping and aneuploidy profiling of single cells

Long-read whole-genome sequencing (lrWGS) enhances haplotyping by providing more phasing information per read compared to short-read sequencing. However, its use for single-cell haplotype phasing remains underexplored. This proof-of-concept study examines lrWGS data from single cells for small variant (SNV and indel) calling and haplotyping using the Genome in a Bottle (GIAB) Ashkenazi trio. lrWGS was performed on single-cell (1 cell) and multi-cell (10 cells) samples from the offspring. Chromosome-length haplotypes were obtained by leveraging both long reads and pedigree information. These haplotypes were further refined by replacing them with matched parental haplotypes. In single-cell and multi-cell samples, 92% and 98% of heterozygous SNVs, and 74% and 78% of heterozygous indels were accurately haplotyped. Applied to human embryos for preimplantation genetic testing (PGT), lrWGS demonstrated 100% consistency with array-based methods for detecting monogenic disorders, without requiring phasing references. Aneuploidies were accurately detected, with insights into the mechanistic origins of chromosomal abnormalities inferred from the parental unique allele fractions. We show that lrWGS-based concurrent haplotyping and aneuploidy profiling of single cells provides an alternative to current PGT methods, with applications potential in areas such as cell-based prenatal diagnosis and animal and plant breeding.

genomics↗

bioRxiv2024

Investigating endometriosis development and endometriosis-related pain over time and in relation to estrogen in a laparoscopic mouse model

BackgroundEndometriosis is a complex disease, and its pathophysiology is still unclear. Therefore, endometriosis animal models need to be carefully selected and examined to be useful for identification of novel therapies for women with endometriosis. In this study, we evaluated endometriosis-associated pain, and time- and estrogen-related development of endometriotic lesions after laparoscopic implantation of menstrual endometrium in a homologous mouse model for endometriosis. MethodsEndometriosis was induced by laparoscopic introduction of 10 menstrual endometrial tissue pieces into the peritoneum of ovariectomized recipient mice (59 estrogen-substituted; 59 estrogen-depleted). Sham animals (57 estrogen-substituted; 60 estrogen-depleted) received 10 pieces of perigonadal adipose tissue. The animals were sacrificed at 1, 2, 3, 4, 6 or 8 weeks after induction, the attached peritoneal implants localized and excised and immunohistochemically analyzed. Additionally, endometriosis-related pain was evaluated by measuring mechanical allodynia, thermal hyperalgesia, locomotor activity and anxiety-like behavior before and after tissue implantation. ResultsAt least one implant per mouse could be retrieved in 94% (111/118) of the endometrial tissue animals and in 78% (91/117) of the adipose tissue animals (p<0.001). Peritoneal implant take rate was significantly higher in endometrial tissue animals (2.5{+/-}1.4) compared to adipose tissue animals (1.6{+/-}1.5) (p<0.0001), regardless of estrogen supplementation and time of sacrifice. Hemosiderin could be observed more often (p<0.0001) in attached peritoneal implants of the endometrial tissue animals (67%, 68/101), compared to the adipose tissue animals (37%, 31/83). Ki67 staining showed a higher proliferation index in the attached peritoneal implants retrieved after one week, compared to the other time points of both endometrial tissue and adipose tissue animals. The behavioral test showed no significant difference in mechanical and thermal sensitivity, locomotor activity and anxiety-behavior between the menstrual endometrial tissue and adipose tissue implanted animals. Nevertheless, the estrogen-substituted animals showed decreased activity in the tests featuring thermal nociception and anxiety-like behavior, compared to the estrogen-depleted animals. Additionally, time after implantation showed to have a positive effect on thermal sensitivity, locomotor activity and anxiety-related behavior in all animals, as the mice became less sensitive to thermal stimuli, more active in the open field test and buried less marbles in the marble burying test. ConclusionThis study showed an increased attachment of menstrual endometrium compared to adipose tissue in the peritoneum when using laparoscopic induction. There was no apparent influence of estrogen on tissue attachment, proliferation or appearance. A decrease in cell proliferation in peritoneal implants occurred over time. Locomotor activity, anxiety-like behavior, and mechanical and thermal sensitivity of the animals was not affected after induction of endometriosis, regardless of the type of implanted tissue. Altogether, we showed that the current methodology used to induce endometriosis was not sufficient to develop endometriotic lesions that contained both stromal and epithelial cells. Moreover, the current methodology was not able to detect specific endometriosis-related pain. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/583957v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@119ad34org.highwire.dtl.DTLVardef@ba5b8borg.highwire.dtl.DTLVardef@d020ccorg.highwire.dtl.DTLVardef@1941e8_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗