Altered kinetics of nonhomologous end joining and class switch recombination in ligase IV–deficient B cells

Immunoglobulin heavy chain class switch recombination (CSR) is believed to occur through the generation and repair of DNA double-strand breaks (DSBs) in the long and repetitive switch regions. Although implied, the role of the major vertebrate DSB repair pathway, nonhomologous end joining (NHEJ), in CSR has been controversial. By somatic gene targeting of DNA ligase IV (Lig4; a key component of NHEJ) in a B cell line (CH12F3) capable of highly efficient CSR in vitro, we found that NHEJ is required for efficient CSR. Disruption of the Lig4 gene in CH12F3 cells severely inhibits the initial rate of CSR and causes a late cell proliferation defect under cytokine stimulation. However, unlike V(D)J recombination, which absolutely requires NHEJ, CSR accumulates to a substantial level in Lig4-null cells. The data revealed a fast-acting NHEJ and a slow-acting alterative end joining of switch region breaks during CSR

DNA Ligase I Is Not Essential for Mammalian Cell Viability

SummaryOf the three DNA ligases present in all vertebrates, DNA ligase I (Lig1) has been considered essential for ligating Okazaki fragments during DNA replication and thereby essential for cell viability. Here, we report the striking finding that a Lig1-null murine B cell line is viable. Surprisingly, the Lig1-null cells exhibit normal proliferation and normal immunoglobulin heavy chain class switch recombination and are not hypersensitive to a wide variety of DNA damaging agents. These findings demonstrate that Lig1 is not absolutely required for cellular DNA replication and repair and that either Lig3 or Lig4 can substitute for the role of Lig1 in joining Okazaki fragments. The establishment of a Lig1-null cell line will greatly facilitate the characterization of DNA ligase function in mammalian cells, but the finding alone profoundly reprioritizes the role of ligase I in DNA replication, repair, and recombination

Endonuclease and redox activities of human apurinic/apyrimidinic endonuclease 1 have distinctive and essential functions in IgA class switch recombination

The base excision repair (BER) pathway is an important DNA repair pathway and is essential for immune responses. In fact, it regulates both the antigen-stimulated somatic hypermutation (SHM) process and plays a central function in the process of class switch recombination (CSR). For both processes, a central role for apurinic/apyrimidinic endonuclease 1 (APE1) has been demonstrated. APE1 acts also as a master regulator of gene expression through its redox activity. APE1's redox activity stimulates the DNA-binding activity of several transcription factors, including NF-\u3baB and a few others involved in inflammation and in immune responses. Therefore, it is possible that APE1 has a role in regulating the CSR through its function as a redox coactivator. The present study was undertaken to address this question. Using the CSR-competent mouse B-cell line CH12F3 and a combination of specific inhibitors of APE1's redox (APX3330) and repair (compound 3) activities, APE1-deficient or -reconstituted cell lines expressing redox-deficient or endonuclease-deficient proteins, and APX3330-treated mice, we determined the contributions of both endonuclease and redox functions of APE1 in CSR. We found that APE1's endonuclease activity is essential for IgA-class switch recombination. We provide evidence that the redox function of APE1 appears to play a role in regulating CSR through the interleukin-6 signaling pathway and in proper IgA expression. Our results shed light on APE1's redox function in the control of cancer growth through modulation of the IgA CSR process

Joint Exploration and Mining of Memory-Relevant Brain Anatomic and Connectomic Patterns via a Three-Way Association Model

Early change in memory performance is a key symptom of many brain diseases, but its underlying mechanism remains largely unknown. While structural MRI has been playing an essential role in revealing potentially relevant brain regions, increasing availability of diffusion MRI data (e.g., Human Connectome Project (HCP)) provides excellent opportunities for exploration of their complex coordination. Given the complementary information held in these two imaging modalities, we hypothesize that studying them as a whole, rather than individually, and exploring their association will provide us valuable insights of the memory mechanism. However, many existing association methods, such as sparse canonical correlation analysis (SCCA), only manage to handle two-way association and thus cannot guarantee the selection of biomarkers and associations to be memory relevant. To overcome this limitation, we propose a new outcome-relevant SCCA model (OSCCA) together with a new algorithm to enable the three-way associations among brain connectivity, anatomic structure and episodic memory performance. In comparison with traditional SCCA, we demonstrate the effectiveness of our model with both synthetic and real data from the HCP cohort

Effect of the categorization method on the diagnostic performance of ultrasound risk stratification systems for thyroid nodules

ObjectiveTo evaluate whether the categorization methods of risk stratification systems (RSSs) is a decisive factor that influenced the diagnostic performances and unnecessary FNA rates in order to choose optimal RSS for the management of thyroid nodules.MethodsFrom July 2013 to January 2019, 2667 patients with 3944 thyroid nodules had undergone pathological diagnosis after thyroidectomy and/or US-guided FNA. US categories were assigned according to the six RSSs. The diagnostic performances and unnecessary FNA rates were calculated and compared according to the US-based final assessment categories and the unified size thresholds for biopsy proposed by ACR-TIRADS, respectively.ResultsA total of 1781 (45.2%) thyroid nodules were diagnosed as malignant after thyroidectomy or biopsy. Significantly lowest specificity and accuracy, along with the highest unnecessary FNA rates were seen in EU-TIRADS for both US categories (47.9%, 70.2%, and 39.4%, respectively, all P < 0.05) and indications for FNA (54.2%, 50.0%, and 55.4%, respectively, all P < 0.05). Diagnostic performances for US-based final assessment categories exhibited similar accuracy for AI-TIRADS, Kwak-TIRADS, C-TIRADS, and ATA guidelines (78.0%, 77.8%, 77.9%, and 76.3%, respectively, all P > 0.05), while the lowest unnecessary FNA rate was seen in C-TIRADS (30.9%) and without significant differences to that of AI-TIRADS, Kwak-TIRADS, and ATA guideline (31.5%, 31.7%, and 33.6%, respectively, all P > 0.05). Diagnostic performance for US-FNA indications showed similar accuracy for ACR-TIRADS, Kwak-TIRADS, C-TIRADS and ATA guidelines (58.0%, 59.7%, 58.7%, and 57.1%, respectively, all P > 0.05). The highest accuracy and lowest unnecessary FNA rate were seen in AI-TIRADS (61.9%, 38.6%) and without significant differences to that of Kwak-TIRADS(59.7%, 42.9%) and C-TIRADS 58.7%, 43.9%, all P > 0.05).ConclusionThe different US categorization methods used by each RSS were not determinant influential factors in diagnostic performance and unnecessary FNA rate. For daily clinical practice, the score-based counting RSS was an optimal choice

Asian financial integration: Global or regional? Evidence from money and bond markets

This paper investigates the degree of global versus regional financial integration in Southeast Asia during the period 2004–2012. We examine integration in the money and bond markets in Asia by employing a covered-interest-parity-based measure of financial integration. The impact of the 2008 financial crisis as well as the recent regional bond initiatives on the integration process of Asian money and bond markets respectively are specifically investigated. Empirically, we adopt the Phillips and Sul (2007) convergence methodology that has not been previously employed to examine the integration process in Asian money and bond markets. We find evidence of both global and regional integration in the money market pre 2008 but once the crisis hit, the process of global integration comes to an abrupt halt. However, regional integration, albeit at a slower pace, is still clearly evident in the post-crisis period. As for the Asian bond market, evidence of both global and regional integration is found but, in comparison, the latter is more convergent post 2008. Regional integration is stronger when interest rates with longer maturity are considered. In addition, we identify some convergent subgroups of countries and this suggests that a multi-tiered style of convergence is present