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Investigation of Global Gene Expression of Human Blastocysts Diagnosed as Mosaic using Next-generation Sequencing

  • Reproductive Biology: Original Article
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Abstract

Embryos are diagnosed as mosaic if their chromosomal copy number falls between euploid and aneuploid. The purpose of this study was to investigate the impact of mosaicism on global gene expression. This study included 42 blastocysts that underwent preimplantation genetic testing for aneuploidy (PGT-A) and were donated for IRB approved research. Fourteen blastocysts were diagnosed as mosaic with Next-generation Sequencing (NGS). Three NGS diagnosed euploid embryos, and 25 aneuploid embryos (9 NGS, 14 array Comparative Genomic Hybridization, 2 Single Nucleotide Polymorphism array) were used as comparisons. RNA-sequencing was performed on all of the blastocysts. Differentially expressed genes (DEGs) were calculated using DESeq2/3.5 (R Bioconductor Package) with p < 0.05 considered significantly differentially expressed. Pathway analysis was performed on mosaic embryos using EnrichR with p < 0.05 considered significant. With euploid embryo gene expression used as a control, 12 of 14 mosaic embryos had fewer DEGs compared to aneuploid embryos involving the same chromosome. On principal component analysis (PCA), mosaic embryos mapped separately from aneuploid embryos. Pathways involving cell proliferation, differentiation, and apoptosis were the most disrupted within mosaic embryos. Mosaic embryos have decreased disruption of global gene expression compared to aneuploid embryos. This study was limited by the small sample size, lack of replicate samples for each mosaic abnormality, and use of multiple different PGT-A platforms for the diagnosis of aneuploid embryos.

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Data Availability

Raw data, sample descriptions, and processed data (gene normalized counts) for all samples are publically available on GEO (Gene Expression Omnibus), accession number GSE151219.

Code Availability

Bioinformatics was performed using the following software: STAR/2.5 aligner (to align sequence reads to the hg19 ensemble reference transcriptome), featureCounts/1.5.3 (gene counting), DESeq2/3.5 using the R Bioconductor Package (Differential Gene Expression), EnrichR (pathway enrichment analysis).

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Acknowledgements

We would like to thank Bevin Kaplan for supporting this research as well as the Genome Technology Center and the Applied Bioinformatics Laboratories departments for their collaboration.

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Author notes

  1. Susan M. Maxwell

    Present address: Northwell Health Fertility of New York City, 210A East 64th St., Floor 1, New York, NY, 10065, USA

Authors and Affiliations

  1. New York University Langone Fertility Center, 660 First Ave., Floor 5, New York, NY, 10016, USA

    Susan M. Maxwell, Fang Wang, James A. Grifo & Frederick Licciardi

  2. Applied Bioinformatics Laboratories, New York University Langone Health, 227 East 30th St., 7th Floor, New York, NY, USA

    Tenzin C. Lhakhang, Ziyan Lin & Aristotelis Tsirigos

  3. Hackensack Meridian Health, 40 Prospect Ave, Hackensack, NJ, 07601, USA

    Yael G. Kramer

  4. Genome Technology Center, New York University Langone Health, 550 First Ave., MSB 308, New York, NY, 10016, USA

    Yutong Zhang & Adriana Heguy

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  1. Susan M. Maxwell
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Contributions

All authors contributed to study concept and design. Sample preparation and acquisition of data was performed by Susan M. Maxwell, Yael G. Kramer, Yutong Zhang, and Fang Wang. Analysis and interpretation of data was performed by all authors. The manuscript was drafted by Susan M. Maxwell, and all authors participated in manuscript revision and approval of the final manuscript.

Corresponding author

Correspondence to Susan M. Maxwell.

Ethics declarations

Ethics Approval and Consent to Participate

This study was non-human subject research utilizing de-identified human embryos donated for research. Patients signed a consent for the disposal of their embryos for research purposes. The collection and use of discarded embryos for research was approved by the IRB at the New York University School of Medicine, study number i16-00154.

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The authors declare no competing interests.

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Susan M. Maxwell and Tenzin C. Lhakhang should be regarded as joint First Authors.

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Maxwell, S.M., Lhakhang, T.C., Lin, Z. et al. Investigation of Global Gene Expression of Human Blastocysts Diagnosed as Mosaic using Next-generation Sequencing. Reprod. Sci. 29, 1597–1607 (2022). https://doi.org/10.1007/s43032-022-00899-x

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  • DOI: https://doi.org/10.1007/s43032-022-00899-x

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