Single-Cell Transcriptome Profiling Revealed That Vitrification of Somatic Cloned Porcine Blastocysts Causes Substantial Perturbations in Gene Expression

Zhang, Ling; Qi, Xin; Wei, Ning; Shentu, Luyan; Guo, Tao; Zhang, Xiangdong; Li, Yunsheng; Ma, Yangyang; Yu, Tong; Knott, Jack H.; Cao, Zubing; Zhang, Yunhai

doi:10.3389/fgene.2020.00640

Cited by 4 publications

(7 citation statements)

References 36 publications

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“…It seems they found 540 DEG (FDR 5%) between the VIT and the control group, but only showed 178 DEG in their supplemental material. However, when results of Zhang et al [ 40 ], Cuello et al [ 39 ], and our study were compared, no overlap was found between all the three studies. Seven DEG were in common for Cuello et al [ 39 ] and Zhang et al [ 40 ] ( ART3 , CELA2A , DUSP6 , NQO1 , NTRK3 , PGM5 , PHLDA3 ) and 8 genes between ours and Zhang et al ( ACTA1 , BHLHE40 , CYP1A1 , EMP1 , F2R , PIP4K2B , SLC10A1 , UCHL1 ) (the complete list of comparisons among studies can be found in Additional file 6 : Table S11).…”

Section: Discussioncontrasting

confidence: 45%

“…Further comparisons of our study with other studies in the literature performing extensive embryonic gene expression analysis by RNA-seq to find common alterations of the VIT procedure was complicated since in some cases vitrification was performed using other protocols or devices [ 40 ], embryos were subjected to other biotechnologies before the vitrification step [ 40 ] or VIT was performed in other species and at different developmental stages [ 58 ]. For example, a higher number of upregulated genes (782) was also found in bovine elongating conceptuses (d 14), with only 145 downregulated in VIT compared to CO embryos (of 927 total DEG identified) [ 58 ].…”

Section: Discussionmentioning

confidence: 97%

“…These embryos were vitrified on d 7, transferred to heifers and collected on d 14 of development, and further analyzed by RNA–seq [ 58 ]. Zhang et al [ 40 ] analyzed gene expression of embryos obtained after somatic cell nuclear transfer (SCNT), vitrified and used for gene expression analysis after a short IVC of 6 h (Additional file 6 : Table S11). The paper of Zhang et al [ 40 ] contains different statements about significant differences in expression levels between SCNT–VIT (vitrification group) vs. SCNT–CNT (control group).…”

Section: Discussionmentioning

confidence: 99%

“…Zhang et al [ 40 ] analyzed gene expression of embryos obtained after somatic cell nuclear transfer (SCNT), vitrified and used for gene expression analysis after a short IVC of 6 h (Additional file 6 : Table S11). The paper of Zhang et al [ 40 ] contains different statements about significant differences in expression levels between SCNT–VIT (vitrification group) vs. SCNT–CNT (control group). It seems they found 540 DEG (FDR 5%) between the VIT and the control group, but only showed 178 DEG in their supplemental material.…”

Section: Discussionmentioning

confidence: 99%

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Unveiling how vitrification affects the porcine blastocyst: clues from a transcriptomic study

Almiñana

Dubuisson

Bauersachs

et al. 2022

J Animal Sci Biotechnol

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Background Currently, there is a high demand for efficient pig embryo cryopreservation procedures in the porcine industry as well as for genetic diversity preservation and research purposes. To date, vitrification (VIT) is the most efficient method for pig embryo cryopreservation. Despite a high number of embryos survives in vitro after vitrification/warming procedures, the in vivo embryo survival rates after embryo transfer are variable among laboratories. So far, most studies have focused on cryoprotective agents and devices, while the VIT effects on porcine embryonic gene expression remained unclear. The few studies performed were based on vitrified/warmed embryos that were cultured in vitro (IVC) to allow them to re–expand. Thus, the specific alterations of VIT, IVC, and the cumulative effect of both remained unknown. To unveil the VIT-specific embryonic alterations, gene expression in VIT versus (vs.) IVC embryos was analyzed. Additionally, changes derived from both VIT and IVC vs. control embryos (CO) were analyzed to confirm the VIT embryonic alterations. Three groups of in vivo embryos at the blastocyst stage were analyzed by RNA–sequencing: (1) VIT embryos (vitrified/warmed and cultured in vitro), (2) IVC embryos and (3) CO embryos. Results RNA–sequencing revealed three clearly different mRNA profiles for VIT, IVC and CO embryos. Comparative analysis of mRNA profiles between VIT and IVC identified 321, differentially expressed genes (DEG) (FDR < 0.006). In VIT vs. CO and IVC vs. CO, 1901 and 1519 DEG were found, respectively, with an overlap of 1045 genes. VIT-specific functional alterations were associated to response to osmotic stress, response to hormones, and developmental growth. While alterations in response to hypoxia and mitophagy were related to the sum of VIT and IVC effects. Conclusions Our findings revealed new insights into the VIT procedure-specific alterations of embryonic gene expression by first comparing differences in VIT vs. IVC embryos and second by an integrative transcriptome analysis including in vivo control embryos. The identified VIT alterations might reflect the transcriptional signature of the embryo cryodamage but also the embryo healing process overcoming the VIT impacts. Selected validated genes were pointed as potential biomarkers that may help to improve vitrification.

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Section: Discussioncontrasting

confidence: 45%

Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Unveiling how vitrification affects the porcine blastocyst: clues from a transcriptomic study

Almiñana

Dubuisson

Bauersachs

et al. 2022

J Animal Sci Biotechnol

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“…On the other hand, the Smart-seq2 protocol has evolved into widely used tools for comprehensive analysis of the differential transcriptomes for vitrified oocytes in several mammalian species such as mice (Gao et al, 2017), pigs (Jia et al, 2019) and cattle (Wang et al, 2017;Huang et al, 2018;Zhang F. et al, 2020), which allows amplification to be performed for a small sample prior to the RNA sequencing (RNA-seq) (Picelli et al, 2014). More recently, the transcriptome features and differences of vitrified porcine cloned blastocysts have been investigated using RNA-seq (Zhang L. et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis of mRNAs and Long Non-Coding RNAs During Subsequent Embryo Development of Porcine Cloned Zygotes After Vitrification

et al. 2021

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Cryopreservation of porcine cloned zygotes has important implications for biotechnology and biomedicine research; however, lower embryo developmental potential remains an urgent problem to be resolved. For exploring the sublethal cryodamages during embryo development, this study was designed to acquire the mRNA and long non-coding RNA (lncRNA) profiles of 2-cells, 4-cells and blastocysts derived from vitrified porcine cloned zygotes using transcriptome sequencing. We identified 167 differentially expressed (DE) mRNAs and 516 DE lncRNAs in 2-cell stage, 469 DE mRNAs and 565 lncRNAs in 4-cell stage, and 389 DE mRNAs and 816 DE lncRNAs in blastocyst stage. Functional enrichment analysis revealed that the DE mRNAs during embryo development were involved in many regulatory mechanisms related to cell cycle, cell proliferation, apoptosis, metabolism and others. Moreover, the target genes of DE lncRNAs in the three embryonic stages were also enriched in many key GO terms or pathways such as “defense response”, “linoleic acid metabolic process”, “embryonic axis specification”, “negative regulation of protein neddylation”, etc., In conclusion, the present study provided comprehensive transcriptomic data about mRNAs and lncRNAs for the vitrified porcine cloned zygotes during different developmental stages, which contributed to further understand the potential cryodamage mechanisms responsible for impaired embryo development.

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Effect of vitrification on the expression of genes in porcine blastocysts derived from in vitro matured oocytes

Więsak

Goryszewska-Szczurek

2022

Systems Biology in Reproductive Medicine

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Single-Cell Transcriptome Profiling Revealed That Vitrification of Somatic Cloned Porcine Blastocysts Causes Substantial Perturbations in Gene Expression

Cited by 4 publications

References 36 publications

Unveiling how vitrification affects the porcine blastocyst: clues from a transcriptomic study

Unveiling how vitrification affects the porcine blastocyst: clues from a transcriptomic study

Transcriptome Analysis of mRNAs and Long Non-Coding RNAs During Subsequent Embryo Development of Porcine Cloned Zygotes After Vitrification

Effect of vitrification on the expression of genes in porcine blastocysts derived from in vitro matured oocytes

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