N-acetylcysteine effectively alleviates systemic lupus erythematosus in mice via regulation of oxidative stress

Purpose: To study the influence of N-acetylcysteine (NAC) on systemic lupus  erythematosus (SLE) mice, and the mechanism(s) involved. Methods: Fourteen MRL/lpr SLE mice aged 5 weeks (mean weight = 20.35 ± 2.12 g) were divided into two 7-mouse groups: SLE (control) and treatment groups. The control group comprised healthy female SPF-grade C57BL/6 mice (n = 7). The treatment group mice received intraperitoneal injection of NAC at a dose of 250 mg/kg daily for 8 weeks. The serum levels of malondialdehyde (MDA) and nitric oxide (NO), and activities of glutathione peroxidase (GPx) and superoxide dismutase (SOD), were assayed using standard methods. The level of urine protein and activity of anti-double stranded (ds) DNA antibody were determined using their respective enzyme-linked assay (ELISA) kits. Results: The spleens of mice in SLE mice were significantly enlarged, relative to control mice, but they were reduced significantly by NAC (p < 0.05). N-Acetylcysteine (NAC) also significantly reduced the serum levels of MDA and NO in SLE mice, but significantly  increased the serum activities of superoxide dismutase and GPx. Moreover, urine protein concentration and activity of anti-dsDNA antibody in SLE mice significantly increased, but reduced significantly by NAC treatment (p < 0.05). Conclusion: These results suggest that NAC effectively alleviates SLE in mice via regulation of oxidative stress. Thus, NAC has the potentials for development into a therapy for the management of SLE. Keywords: Anti-dsDNA antibodies, Antioxidant enzymes, N-acetylcysteine, Oxidative stress, Systemic lupus erythematosu

CNETML: Maximum likelihood inference of phylogeny from copy number profiles of spatio-temporal samples

Phylogenetic trees based on copy number alterations (CNAs) for multi-region samples of a single cancer patient are helpful to understand the spatio-temporal evolution of cancers, especially in tumours driven by chromosomal instability. Due to the high cost of deep sequencing data, low-coverage data are more accessible in practice, which only allow the calling of (relative) total copy numbers due to the lower resolution. However, methods to reconstruct sample phylogenies from CNAs often use allele-specific copy numbers and those using total copy number are mostly distance matrix or maximum parsimony methods which do not handle temporal data or estimate mutation rates. In this work, we developed a new maximum likelihood method based on a novel evolutionary model of CNAs, CNETML, to infer phylogenies from spatio-temporal samples taken within a single patient. CNETML is the first program to jointly infer the tree topology, node ages, and mutation rates from total copy numbers when samples were taken at different time points. Our extensive simulations suggest CNETML performed well even on relative copy numbers with subclonal whole genome doubling events and under slight violation of model assumptions. The application of CNETML to real data from Barrett’s esophagus patients also generated consistent results with previous discoveries and novel early CNAs for further investigations

CNETML: maximum likelihood inference of phylogeny from copy number profiles of multiple samples

Phylogenetic trees based on copy number profiles from multiple samples of a patient are helpful to understand cancer evolution. Here, we develop a new maximum likelihood method, CNETML, to infer phylogenies from such data. CNETML is the first program to jointly infer the tree topology, node ages, and mutation rates from total copy numbers of longitudinal samples. Our extensive simulations suggest CNETML performs well on copy numbers relative to ploidy and under slight violation of model assumptions. The application of CNETML to real data generates results consistent with previous discoveries and provides novel early copy number events for further investigation

The efficacy of acupuncture and decompression splints in the treatment of temporomandibular joint pain-dysfunction syndrome

Objectives: The goal of the present study was to evaluate the results of applying acupuncture or occlusal decompression splints in the treatment of patients diagnosed with the temporomandibular joint pain-dysfunction syndrome. Design of the study: We conducted a randomized clinical trial including 20 patients to whom the mentioned treatments were applied. Results were evaluated through an analogue pain scale, measurements of mouth opening and jaw lateral deviation in millimetres, and assessment of sensitivity to pressure on different points: preauricular, masseter muscle, temporal muscle and trapezius. Parameters were evaluated before and 30 days after the treatment. For standardized pressure, we used a pressure algometer. Results: Patients treated with decompression splints showed reductions in subjective pain and pain upon pressure on temporal, masseter and trapezius muscles, as well as increased mouth opening after the treatment. Patients treated with acupuncture showed pain reduction in the short term and improvements in all of the evaluated para- meters (stronger pressure was required to produce pain; mouth opening was improved). Conclusion: Acupuncture was an effective complement and/or an acceptable alternative to decompression splints in the treatment of myofascial pain and temporomandibular joint pain-dysfunction syndrome

Deterministic evolution and stringent selection during preneoplasia

The earliest events during human tumour initiation, although poorly characterized, may hold clues to malignancy detection and prevention1. Here we model occult preneoplasia by biallelic inactivation of TP53, a common early event in gastric cancer, in human gastric organoids. Causal relationships between this initiating genetic lesion and resulting phenotypes were established using experimental evolution in multiple clonally derived cultures over 2 years. TP53 loss elicited progressive aneuploidy, including copy number alterations and structural variants prevalent in gastric cancers, with evident preferred orders. Longitudinal single-cell sequencing of TP53-deficient gastric organoids similarly indicates progression towards malignant transcriptional programmes. Moreover, high-throughput lineage tracing with expressed cellular barcodes demonstrates reproducible dynamics whereby initially rare subclones with shared transcriptional programmes repeatedly attain clonal dominance. This powerful platform for experimental evolution exposes stringent selection, clonal interference and a marked degree of phenotypic convergence in premalignant epithelial organoids. These data imply predictability in the earliest stages of tumorigenesis and show evolutionary constraints and barriers to malignant transformation, with implications for earlier detection and interception of aggressive, genome-instable tumours

Reconstructing single-cell karyotype alterations in colorectal cancer identifies punctuated and gradual diversification patterns

Central to tumor evolution is the generation of genetic diversity. However, the extent and patterns by which de novo karyotype alterations emerge and propagate within human tumors are not well understood, especially at single-cell resolution. Here, we present 3D Live-Seq—a protocol that integrates live-cell imaging of tumor organoid outgrowth and whole-genome sequencing of each imaged cell to reconstruct evolving tumor cell karyotypes across consecutive cell generations. Using patient-derived colorectal cancer organoids and fresh tumor biopsies, we demonstrate that karyotype alterations of varying complexity are prevalent and can arise within a few cell generations. Sub-chromosomal acentric fragments were prone to replication and collective missegregation across consecutive cell divisions. In contrast, gross genome-wide karyotype alterations were generated in a single erroneous cell division, providing support that aneuploid tumor genomes can evolve via punctuated evolution. Mapping the temporal dynamics and patterns of karyotype diversification in cancer enables reconstructions of evolutionary paths to malignant fitness

ANALYZING LATERAL GENE TRANSFER WITH MACHINE LEARNING AND PHYLOGENETIC METHODS

Ph.DDOCTOR OF PHILOSOPH