X-ray cross-complementing family: the bridge linking DNA damage repair and cancer

Abstract Genomic instability is a common hallmark of human tumours. As a carrier of genetic information, DNA is constantly threatened by various damaging factors that, if not repaired in time, can affect the transmission of genetic information and lead to cellular carcinogenesis. In response to these threats, cells have evolved a range of DNA damage response mechanisms, including DNA damage repair, to maintain genomic stability. The X-ray repair cross-complementary gene family (XRCC) comprises an important class of DNA damage repair genes that encode proteins that play important roles in DNA single-strand breakage and DNA base damage repair. The dysfunction of the XRCC gene family is associated with the development of various tumours. In the context of tumours, mutations in XRCC and its aberrant expression, result in abnormal DNA damage repair, thus contributing to the malignant progression of tumour cells. In this review, we summarise the significant roles played by XRCC in diverse tumour types. In addition, we discuss the correlation between the XRCC family members and tumour therapeutic sensitivity

Exploring the efficacy and beneficial population of preimplantation genetic testing for aneuploidy start from the oocyte retrieval cycle: a real-world study

Abstract Background Preimplantation genetic testing for aneuploidy (PGT-A) is widely used as an embryo selection technique in in vitro fertilization (IVF), but its effectiveness and potential beneficiary populations are unclear. Methods This retrospective cohort study included patients who underwent their first oocyte retrieval cycles at CITIC-Xiangya between January 2016 and November 2019, and the associated fresh and thawed embryo transfer cycles up to November 30, 2020. PGT-A (PGT-A group) and intracytoplasmic sperm injection (ICSI)/IVF (non-PGT-A group) cycles were included. The numbers of oocytes and embryos obtained were unrestricted. In total, 60,580 patients were enrolled, and baseline data were matched between groups using 1:3 propensity score matching. Sensitivity analyses, including propensity score stratification and traditional multivariate logistic regression, were performed on the original unmatched cohort to check the robustness of the overall results. Analyses were stratified by age, body mass index, ovarian reserve/responsiveness, and potential indications to explore benefits in subgroups. The primary outcome was cumulative live birth rate (CLBR). The other outcomes included live birth rate (LBR), pregnancy loss rate, clinical pregnancy rate, pregnancy complications, low birth weight rate, and neonatal malformation rate. Results In total, 4195 PGT-A users were matched with 10,140 non-PGT-A users. A significant reduction in CLBR was observed in women using PGT-A (27.5% vs. 31.1%; odds ratio (OR) = 0.84, 95% confidence interval (CI) 0.78–0.91; P < 0.001). However, women using PGT-A had higher first-transfer pregnancy (63.9% vs. 46.9%; OR = 2.01, 95% CI 1.81–2.23; P < 0.001) and LBR (52.6% vs. 34.2%, OR = 2.13, 95% CI 1.92–2.36; P < 0.001) rates and lower rates of early miscarriage (12.8% vs. 20.2%; OR = 0.58, 95% CI 0.48–0.70; P < 0.001), preterm birth (8.6% vs 17.3%; P < 0.001), and low birth weight (4.9% vs. 19.3%; P < 0.001). Moreover, subgroup analyses revealed that women aged ≥ 38 years, diagnosed with recurrent pregnancy loss or intrauterine adhesions benefited from PGT-A, with a significant increase in first-transfer LBR without a decrease in CLBR. Conclusion PGT-A does not increase and decrease CLBR per oocyte retrieval cycle; nonetheless, it is effective in infertile populations with specific indications. PGT-A reduces complications associated with multiple gestations

The dynamic changes of X chromosome inactivation during early culture of human embryonic stem cells

X chromosome inactivation (XCI) is required for dosage compensation of X-linked genes in human female cells. Several previous reports have described the promiscuous XCI status in long-term cultured female human embryonic stem cells (hESCs), and the majority of them exhibit non-random XCI. However, when and how such female hESCs acquire the aberrant XCI states during culture is unknown. Herein, through comparing the XCI states in 18 paired hES cell lines throughout early culture, we revealed a uniform dynamic change during this culture period under a widely used culture condition. The female initial hESCs (ihESCs, P4-P9) expressed XIST RNA, H3K27me3 punctate enrichment and displayed random XCI pattern. By further culturing, the female early hESCs (ehESCs, P20–P30) lost the expression of XIST RNA, H3K27me3 punctate enrichment and exhibited a completely skewed XCI pattern. Importantly, a subset of X-linked genes was up-regulated in ehESCs, including some cancer-related genes. At last, we found 5% physiological oxygen was beneficial for the expression of XIST and H3K27me3 punctate enrichment, but not for the XCI pattern. We conclude that the XCI dynamic change is a frequent epigenetic instability event during early culture, which is accompanied by the up-regulation of some X-linked genes. Furthermore, we emphasize that physiological oxygen is beneficial for XCI fidelity

Identification of Proteins Related to Epigenetic Regulation in the Malignant Transformation of Aberrant Karyotypic Human Embryonic Stem Cells by Quantitative Proteomics

<div><p>Previous reports have demonstrated that human embryonic stem cells (hESCs) tend to develop genomic alterations and progress to a malignant state during long-term in vitro culture. This raises concerns of the clinical safety in using cultured hESCs. However, transformed hESCs might serve as an excellent model to determine the process of embryonic stem cell transition. In this study, ITRAQ-based tandem mass spectrometry was used to quantify normal and aberrant karyotypic hESCs proteins from simple to more complex karyotypic abnormalities. We identified and quantified 2583 proteins, and found that the expression levels of 316 proteins that represented at least 23 functional molecular groups were significantly different in both normal and abnormal hESCs. Dysregulated protein expression in epigenetic regulation was further verified in six pairs of hESC lines in early and late passage. In summary, this study is the first large-scale quantitative proteomic analysis of the malignant transformation of aberrant karyotypic hESCs. The data generated should serve as a useful reference of stem cell-derived tumor progression. Increased expression of both HDAC2 and CTNNB1 are detected as early as the pre-neoplastic stage, and might serve as prognostic markers in the malignant transformation of hESCs.</p></div

Copy number variation comparison of four differentially expressed genes.

<p>Quantification of <i>DNMT3B</i>, <i>VIM</i>, <i>CTNNB1</i> and <i>HDAC2</i> in abnormal and normal <i>ch</i>HES-3 cell lines, EC cells and six pairs of hESC lines at early and late passage (<i>ch</i>HES-8 P11/P34, <i>ch</i>HES-69 P13/P27, <i>ch</i>HES-20 P22/P107, <i>ch</i>HES-22 P35/P98, <i>ch</i>HES-32 P19/P27, <i>ch</i>HES-35 P32/P77). Gene copy number was compared with β-globin gene of nuclear as an endogenous reference gene. P represents for the hESCs culture passage in vitro. Data are represented as mean ± S.D. (n = 3). Copy number in the genes area of <i>DNMT3B</i>, <i>VIM</i>, <i>CTNNB1</i> and <i>HDAC2</i> were showed no significant difference in the same cell line at early and late passages or in abnormal and normal <i>ch</i>HES-3 cell lines by independent t-test.</p

Western blot analysis to validate differentially expressed proteins in early and late passage hESCs.

<p>Differentially-expressed proteins and proteomic analysis in the same cell line at early and late passages (<i>ch</i>HES-8 P11/P34, <i>ch</i>HES-69 P13/P27, <i>ch</i>HES-20 P22/P107, <i>ch</i>HES-22 P35/P98, <i>ch</i>HES-32 P19/P27, <i>ch</i>HES-35 P32/P77) were compared. <i>P</i> represents for the hESCs culture passage <i>in vitro</i>. The late-passage hESCs are over 15∼20 passages prolonged culture in optimal culture conditions after the early–passage hESCs. Data are represented as mean ± S.D. (n = 6). *<i>P</i><0.05, ** <i>P</i><0.01 with respect to the protein expression in six early passages of hESC lines by independent sample t tests.</p

Real-time quantitative RT-PCR analysis of <i>DNMT3B</i> and <i>VIM</i> expression levels in six pairs of hESCs.

<p>Real-time quantitative RT-PCR analysis of <i>DNMT3B</i> (A) and <i>VIM</i> (B) expression levels in six pairs of hESC lines at early and late passage (<i>ch</i>HES-8 P11/P34, <i>ch</i>HES-69 P13/P27, <i>ch</i>HES-20 P22/P107, <i>ch</i>HES-22 P35/P98, <i>ch</i>HES-32 P19/P27, <i>ch</i>HES-35 P32/P77). P represents for the hESCs culture passage in vitro. Data are represented as mean ± S.D. (n = 3). *<i>P</i><0.05, **<i>P</i><0.01 with respect to the mRNA expression in six early passages of hESC lines by independent sample t tests.</p

Comparative analysis of transcriptomic and proteomic data in normal and karyotypically aberrant <i>ch</i>HES-3 cells.

<p>(A) Showing the Venn diagrams of the number of differentially expressed protein (a) and gene probes (b) of 2583 expressed proteins in SIMP (red), COMP (green) <i>ch</i>HES-3 cells, and EC cells (blue) as compared with normal <i>ch</i>HES-3 cells. (B) Pairwise comparison of the protein (a–c) and mRNA (d–f) ratios between normal <i>ch</i>HES-3 cells with karyotypically aberrant <i>ch</i>HES-3 cells and EC cells. Microarray and iTRAQ data of 2583 proteins in SIMP as compared normal (a, d); or in COMP as compared normal (b, e) <i>ch</i>HES-3 cells; or between EC cells and normal (c, f) <i>ch</i>HES-3 cells. Comparative analyses were expressed as being up-regulated or down-regulated or unchanged.</p