RAD50 regulates mitotic progression independent of DNA repair functions

Gene co-expression network analysis reveals key regulatory and responsive genes regulating the intensity of carotenoid coloration in scallop muscle

Carotenoids are biologically active pigments widely distributed in nature, playing crucial roles in the growth, development, immunity, and coloration of animals. As important nutrients, carotenoids are also considered important parameters for evaluating the economic value of farmed animals, including aquatic organisms. However, for marine animals that accumulate a large amount of specific carotenoids, the molecular mechanism underlying the bioavailability of carotenoids remains insufficiently explored, particularly with regard to the regulation of carotenoid pigmentation intensity. This study investigated the carotenoid coloration mechanism in the adductor muscle of "Haida golden scallop", a variety of Yesso scallop (Patinopecten yessoensis), with high carotenoid content and varying coloration intensity in adductor muscle. Through transcriptomic analysis and weighted gene co-expression network analysis (WGCNA), three carotenoid accumulation-associated modules (MEgreenyellow module, MEgreen, and MEsalmon) were identified. Two PARP9/14/15 genes, previously identified as crucial regulators of carotenoid accumulation at the genomic level, were identified as the hub genes of MEgreenyellow module, which exhibited a significant positive correlation with the concentrations of both pectenolone and pectenoxanthin. Specifically, PARP9/14/15-1 showed strong connectivity with genes involved in carotenoid absorption and transport, such as LRP1, SRB-like 1, ABCA3, and StARD; while PARP9/14/15-2 was associated with NPC1L1, a gene critical for carotenoid absorption. It is proposed that PARP9/14/15s may modulate the accumulation of pectenolone and pectenoxanthin in the adductor muscle of "Haida golden scallop" by regulating the expression of these carotenoid-related genes. Furthermore, genes within the other two carotenoid accumulation-associated modules were significantly enriched in pathways related to immune response (MEgreen) and DNA damage repair (MEsalmon), suggesting that these pathways may be in response to carotenoid accumulation levels. This study provides valuable insights into the molecular mechanisms underlying carotenoid accumulation and pigmentation intensity in bivalves, offering theoretical guidance for the breeding of carotenoid-rich aquaculture strains.

Characterizing the Ovarian Cytogenetic Dynamics of Sichuan Bream (Sinibrama taeniatus) During Vitellogenesis at a Single-Cell Resolution

Vitellogenesis in fish represents a critical phase of oogenesis, significantly influencing the nutritional provisioning for oocyte maturation and subsequent offspring development. However, research on the physiological mechanisms governing vitellogenesis at the single-cell level remains limited. In this study, we performed single-nucleus RNA sequencing (snRNA-seq) on the ovaries of Sichuan bream (Sinibrama taeniatus). We first identified six distinct cell types (germ cells, follicular cells, immune cells, stromal cells, endothelial cells, and epithelial cells) in the ovaries based on typical functional marker genes. Subsequently, we reconstructed the developmental trajectory of germ cells using pseudotime analysis, which describes the transcriptional dynamics of germ cells at various developmental stages. Additionally, we identified transcription factors (TFs) specific to germ cells that exhibit high activity at each developmental stage. Furthermore, we analyzed the genetic functional heterogeneity of germ cells and follicular cells at different developmental stages to elucidate their contributions to vitellogenesis. Finally, cell interaction analysis revealed that germ cells communicate with somatic cells or with each other via multiple receptors and ligands to regulate growth, development, and yolk acquisition. These findings enhance our understanding of the physiological mechanisms underlying vitellogenesis in fish, providing a theoretical foundation for regulating ovarian development in farmed fish.

A deep intronic mutation causes RAD50 deficiency through an unusual mechanism of distant exon activation

This study identifies and characterizes a novel type of splicing mutation in RAD50 deficiency, a rare genetic disorder.

Bone Marrow Failure and Immunodeficiency Associated with Human RAD50 Variants

PURPOSE

The MRE11-RAD50-NBN (MRN) complex plays a key role in recognizing and signaling DNA double-strand breaks. Pathogenic variants in NBN and MRE11 give rise to the autosomal-recessive diseases, Nijmegen breakage syndrome (NBS) and ataxia telangiectasia-like disorder, respectively. The clinical consequences of pathogenic variants in RAD50 are incompletely understood. We aimed to characterize a newly identified RAD50 deficiency/NBS-like disorder (NBSLD) patient with bone marrow failure and immunodeficiency.

METHODS

We report on a girl with microcephaly, mental retardation, bird-like face, short stature, bone marrow failure and B-cell immunodeficiency. We searched for candidate gene by whole-exome sequencing and analyzed the cellular phenotype of patient-derived fibroblasts using immunoblotting, radiation sensitivity assays and lentiviral complementation experiments.

RESULTS

Compound heterozygosity for two variants in the RAD50 gene (p.Arg83His and p.Glu485Ter) was identified in this patient. The expression of RAD50 protein and MRN complex formation was maintained in the cells derived from this patient. DNA damage-induced activation of the ATM kinase was markedly decreased, which was restored by the expression of wild-type (WT) RAD50. Radiosensitivity appeared inconspicuous in the patient-derived cell line as assessed by colony formation assay. The RAD50R83H missense substitution did not rescue the mitotic defect in complementation experiments using RAD50-deficient fibroblasts, whereas RAD50WT did. The RAD50E485X nonsense variant was associated with in-frame skipping of exon 10 (p.Glu485_545del).

CONCLUSION

These findings indicate important roles of RAD50 in human bone marrow and immune cells. RAD50 deficiency/NBSLD can manifest as a distinct inborn error of immunity characterized by bone marrow failure and B-cell immunodeficiency.

Double-strand DNA break repair: molecular mechanisms and therapeutic targets

Double-strand break (DSB), a significant DNA damage brought on by ionizing radiation, acts as an initiating signal in tumor radiotherapy, causing cancer cells death. The two primary pathways for DNA DSB repair in mammalian cells are nonhomologous end joining (NHEJ) and homologous recombination (HR), which cooperate and compete with one another to achieve effective repair. The DSB repair mechanism depends on numerous regulatory variables. DSB recognition and the recruitment of DNA repair components, for instance, depend on the MRE11-RAD50-NBS1 (MRN) complex and the Ku70/80 heterodimer/DNA-PKcs (DNA-PK) complex, whose control is crucial in determining the DSB repair pathway choice and efficiency of HR and NHEJ. In-depth elucidation on the DSB repair pathway's molecular mechanisms has greatly facilitated for creation of repair proteins or pathways-specific inhibitors to advance precise cancer therapy and boost the effectiveness of cancer radiotherapy. The architectures, roles, molecular processes, and inhibitors of significant target proteins in the DSB repair pathways are reviewed in this article. The strategy and application in cancer therapy are also discussed based on the advancement of inhibitors targeted DSB damage response and repair proteins.

Large-Scale Proteomics Data Reveal Integrated Prognosis-Related Protein Signatures and Role of SMAD4 and RAD50 in Prognosis and Immune Infiltrations of Prostate Cancer Microenvironment

As prostate cancer (PCa) is one of the most commonly diagnosed cancer worldwide, identifying potential prognostic biomarkers is crucial. In this study, the survival information, gene expression, and protein expression data of 344 PCa cases were collected from the Cancer Proteome Atlas (TCPA) and the Cancer Genome Atlas (TCGA) to investigate the potential prognostic biomarkers. The integrated prognosis-related proteins (IPRPs) model was constructed based on the risk score of each patients using machine-learning algorithm. IPRPs model suggested that Elevated RAD50 expression (p = 0.016) and down-regulated SMAD4 expression (p = 0.017) were significantly correlated with unfavorable outcomes for PCa patients. Immunohistochemical (IHC) staining and western blot (WB) analysis revealed significant differential expression of SMAD4 and RAD50 protein between tumor and normal tissues in validation cohort. According to the overall IHC score, patients with low SMAD4 (p < 0.0001) expression and high RAD50 expression (p = 0.0001) were significantly correlated with poor outcomes. Besides, expression of SMAD4 showed significantly negative correlation with most immune checkpoint molecules, and the low SMAD4 expression group exhibited significantly high levels of LAG3 (p < 0.05), TGFβ (p < 0.001), and PD-L1 (p < 0.05) compared with the high SMAD4 expression group in the validation cohort. Patients with low SMAD4 expression had significantly higher infiltration of memory B cells (p = 0.002), CD8 + T cells (p < 0.001), regulatory T cells (p = 0.006), M2-type macrophages (p < 0.001), and significantly lower infiltration of naïve B cells (p = 0.002), plasma cells (p < 0.001), resting memory CD4 + T cells (p < 0.001) and eosinophils (p = 0.045). Candidate proteins were mainly involved in antigen processing and presentation, stem cell differentiation, and type I interferon pathways.

Supplementary Information

The online version contains supplementary material available at 10.1007/s43657-022-00070-1.

Targeting the splicing isoforms of spleen tyrosine kinase affects the viability of colorectal cancer cells

Spleen tyrosine kinase (Syk) expression have been both positively and negatively associated with tumorigenesis. Our goal was to evaluate the contribution of Syk and its two splice variants, full length Syk (L) and short isoform Syk (S), in the tumor biology of colorectal cancer cells (CRC). The analysis of Syk expression in primary human colorectal tumors, as well as the analysis of TCGA database, revealed a high Syk mRNA expression score in colorectal cancer tumors, suggesting a tumor promotor role of Syk in CRC. Our analysis showed that Syk (L) isoform is highly expressed in the majority of the tumor tissues and that it remains expressed in tumors in which global Syk expression is downregulated, suggesting the dependence of tumors to Syk (L) isoform. We also identified a small cluster of tumor tissues, which express a high proportion of Syk (S) isoform. This specific cluster is associated with overexpressed genes related to translation and mitochondria, and down regulated genes implicated in the progression of mitosis. For our functional studies, we used short hairpin RNA tools to target the expression of Syk in CRC cells bearing the activating K-Ras (G13D) mutation. Our results showed that while global Syk knock down increases cell proliferation and cell motility, Syk (L) expression silencing affects the viability and induces the apoptosis of the cells, confirming the dependence of cells on Syk (L) isoform for their survival. Finally, we report the promising potential of compound C-13, an original non-enzymatic inhibitor of Syk isolated in our group. In vitro studies showed that C-13 exerts cytotoxic effects on Syk-positive CRC cells by inhibiting their proliferation and their motility, and by inducing their apoptosis, while Syk-negative cell lines viability was not affected. Moreover, the oral and intraperitoneal administration of C-13 reduced the tumor growth of CRC DLD-1 cells xenografts in Nude mice in vivo.

The circular RNA circNlgnmediates doxorubicin-inducedcardiac remodeling and fibrosis

Doxorubicin is a chemotherapeutic medication commonly used to treat many types of cancers, but it has side effects including vomiting, rash, hair loss, and bone marrow suppression. The most dangerous side effects are cardiomyopathy, cardiofibrosis, and heart failure, as doxorubicin generates cytotoxicity and stops DNA replication. There is no treatment to block these side effects. We have developed a transgenic mouse line overexpressing the circular RNA circNlgn and shown that circNlgn is a mediator of doxorubicin-induced cardiofibrosis. Increased expression of circNlgn decreased cardiac function and induced cardiofibrosis by upregulating Gadd45b, Sema4C, and RAD50 and activating p38 and pJNK in circNlgn transgenic heart. Silencing circNlgn decreased the effects of doxorubicin on cardiac cell activities and prevented doxorubicin-induced expression of fibrosis-associated molecules. The protein (Nlgn173) translated by circNlgn could bind and activate H2AX, producing γH2AX, resulting in upregulation of IL-1b, IL-2Rb, IL-6, EGR1, and EGR3. We showed that silencing these molecules in the signaling pathway prevented doxorubicin-induced cardiomyocyte apoptosis, increased cardiomyocyte viability, decreased cardiac fibroblast proliferation, and inhibited collagen production. This mechanism may hold therapeutic implications for mitigating the side effects of doxorubicin therapy in cancer patients.

Single-Cell Atlas of the Chinese Tongue Sole (Cynoglossus semilaevis) Ovary Reveals Transcriptional Programs of Oogenesis in Fish

Oogenesis is a highly orchestrated process that depends on regulation by autocrine/paracrine hormones and growth factors. However, many details of the molecular mechanisms that regulate fish oogenesis remain elusive. Here, we performed a single-cell RNA sequencing (scRNA-seq) analysis of the molecular signatures of distinct ovarian cell categories in adult Chinese tongue sole (Cynoglossus semilaevis). We characterized the successive stepwise development of three germ cell subtypes. Notably, we identified the cellular composition of fish follicle walls, including four granulosa cell types and one theca cell type, and we proposed important transcription factors (TFs) showing high activity in the regulation of cell identity. Moreover, we found that the extensive niche–germline bidirectional communications regulate fish oogenesis, whereas ovulation in fish is accompanied by the coordination of simultaneous and tightly sequential processes across different granulosa cells. Additionally, a systems biology analysis of the homologous genes shared by Chinese tongue sole and macaques revealed remarkably conserved biological processes in germ cells and granulosa cells across vertebrates. Our results provide key insights into the cell-type-specific mechanisms underlying fish oogenesis at a single-cell resolution, which offers important clues for exploring fish breeding mechanisms and the evolution of vertebrate reproductive systems.

Mechanisms of Genome Maintenance in Plants: Playing It Safe With Breaks and Bumps

Maintenance of genomic integrity is critical for the perpetuation of all forms of life including humans. Living organisms are constantly exposed to stress from internal metabolic processes and external environmental sources causing damage to the DNA, thereby promoting genomic instability. To counter the deleterious effects of genomic instability, organisms have evolved general and specific DNA damage repair (DDR) pathways that act either independently or mutually to repair the DNA damage. The mechanisms by which various DNA repair pathways are activated have been fairly investigated in model organisms including bacteria, fungi, and mammals; however, very little is known regarding how plants sense and repair DNA damage. Plants being sessile are innately exposed to a wide range of DNA-damaging agents both from biotic and abiotic sources such as ultraviolet rays or metabolic by-products. To escape their harmful effects, plants also harbor highly conserved DDR pathways that share several components with the DDR machinery of other organisms. Maintenance of genomic integrity is key for plant survival due to lack of reserve germline as the derivation of the new plant occurs from the meristem. Untowardly, the accumulation of mutations in the meristem will result in a wide range of genetic abnormalities in new plants affecting plant growth development and crop yield. In this review, we will discuss various DNA repair pathways in plants and describe how the deficiency of each repair pathway affects plant growth and development.

The deacetylation-phosphorylation regulation of SIRT2-SMC1A axis as a mechanism of antimitotic catastrophe in early tumorigenesis

Improper distribution of chromosomes during mitosis can contribute to malignant transformation. Higher eukaryotes have evolved a mitotic catastrophe mechanism for eliminating mitosis-incompetent cells; however, the signaling cascade and its epigenetic regulation are poorly understood. Our analyses of human cancerous tissue revealed that the NAD-dependent deacetylase SIRT2 is up-regulated in early-stage carcinomas of various organs. Mass spectrometry analysis revealed that SIRT2 interacts with and deacetylates the structural maintenance of chromosomes protein 1 (SMC1A), which then promotes SMC1A phosphorylation to properly drive mitosis. We have further demonstrated that inhibition of SIRT2 activity or continuously increasing SMC1A-K579 acetylation causes abnormal chromosome segregation, which, in turn, induces mitotic catastrophe in cancer cells and enhances their vulnerability to chemotherapeutic agents. These findings suggest that regulation of the SIRT2-SMC1A axis through deacetylation-phosphorylation permits escape from mitotic catastrophe, thus allowing early precursor lesions to overcome oncogenic stress.

Mutation Spectra of the MRN (MRE11, RAD50, NBS1/NBN) Break Sensor in Cancer Cells

Simple Summary

A DNA double strand break cuts a chromosome in two and is one of the most dangerous forms of DNA damage. Improper repair can lead to various chromosomal re-arrangements that have been detected in almost all cancer cells. A complex of three proteins (MRE11, RAD50, NBS1 or NBN) detects chromosome breaks and orchestrates repair processes. Mutations in these “break sensor” genes have been described in a multitude of cancers. Here, we provide a comprehensive analysis of reported mutations from data deposited on the Catalogue of Somatic Mutations in Cancer (COSMIC) archive. We also undertake an evolutionary analysis of these genes with the aim to understand whether these mutations preferentially accumulate in conserved residues. Interestingly, we find that mutations are overrepresented in evolutionarily conserved residues of RAD50 and NBS1/NBN but not MRE11.

Abstract

The MRN complex (MRE11, RAD50, NBS1/NBN) is a DNA double strand break sensor in eukaryotes. The complex directly participates in, or coordinates, several activities at the break such as DNA resection, activation of the DNA damage checkpoint, chromatin remodeling and recruitment of the repair machinery. Mutations in components of the MRN complex have been described in cancer cells for several decades. Using the Catalogue of Somatic Mutations in Cancer (COSMIC) database, we characterized all the reported MRN mutations. This analysis revealed several hotspot frameshift mutations in all three genes that introduce premature stop codons and truncate large regions of the C-termini. We also found through evolutionary analyses that COSMIC mutations are enriched in conserved residues of NBS1/NBN and RAD50 but not in MRE11. Given that all three genes are important to carcinogenesis, we propose these differential enrichment patterns may reflect a more severe pleiotropic role for MRE11.