Terms Of Biological Mechanisms Research Articles

LAMC1-mediated preadipocytes differentiation promoted peritoneum pre-metastatic niche formation and gastric cancer metastasis.

Gastric cancer is anatomically proximal to peritoneum. Gastric cancer peritoneal metastasis is a complex biological process which is corresponded with disharmony within dysfunctional adipose tissue and metabolism reprogramming. Laminin gamma 1 (LAMC1) is highly expressed in cancer cells of peritoneal metastatic sites, however, the mechanism of LAMC1-metiated gastric cancer metastases to adipose tissue-rich peritoneum remains unclear. In our study, immunohistochemical staining, single cell sequencing, a co-culture model, luciferase reporter, RNA immunoprecipitation (RIP), Chromatin immunoprecipitation (CHIP) and single-molecular magnetic tweezers assays were conducted, and our results showed that LAMC1 related to Perilipin-1 content was highly expressed in peritoneal metastatic sites and mainly secreted by tumor cells. Gastric cancer cells secreted LAMC1 in an autocrine manner to detached from the primary site and promoted preadipocytes mature, rupture and release of free fatty acids (FFAs) in the peritoneal microenvironment to form pre-metastatic niche by the paracrine pathway. Reversely, differentiated preadipocyte-derived conditioned medium inhibited glycolysis and enhanced fatty acid oxidation (FAO) rate to promote cell proliferation, mesenchymal-epithelial transformation which led to tumor peritoneal colonization. In terms of biological mechanisms, one of differentiated preadipocyte-derived FFAs, palmitic acid-activated STAT3 inhibited miR-193a-3p by binding to its promoter directly; Using single-molecular magnetic tweezers, this binding manner was proved to be stable, reversable and ATP-dependent. Moreover, miR-193a-3p regulated LAMC1 in a post-translational manner. Furthermore, high LAMC1 expression in serum predicted a higher risk of peritoneal metastasis. In conclusion, our results illustrated that palmitic acid/p-STAT3/miR-193a-3p/LAMC1 pathway promotes preadipocyte differentiation, pre-metastatic niche formation and gastric cancer cell colonization to peritoneum.

Major depressive disorder with childhood trauma:Clinical characteristics, biological mechanism, and therapeutic implications.

Major depressive disorder (MDD) is a main type of mood disorder, characterized by significant and lasting depressed mood. Until now, the pathogenesis of MDD is not clear, but it is certain that biological, psychological, and social factors are involved. Childhood trauma is considered to be an important factor in the development of this disease. Previous studies have found that nearly half of the patients with MDD have experienced childhood trauma, and different types of childhood trauma, gender, and age show different effects on this disease. In addition, the clinical characteristics of MDD patients with childhood trauma are also different, which often have more severe depressive symptoms, higher risk of suicide, and more severe cognitive impairment. The response to antidepressants is also worse. In terms of biological mechanisms and marker characteristics, the serotonin transporter gene and the FKBP prolyl isomerase 5 have been shown to play an important role in MDD and childhood trauma. Moreover, some brain imaging and biomarkers showed specific features, such as changes in gray matter in the dorsal lateral prefrontal cortex, and abnormal changes in hypothalamic-pituitary-adrenal axis function.

The singular patient in patient-centred care: physiotherapists’ accounts of treatment of patients with chronic muscle pain

A patient-centred approach has gained increasing interest in medicine and other health sciences. Whereas there are discussions about the meaning of a patient-centred approach and what the concept entails, little...

Age Effects and Temporal Trends in HPV-Related and HPV-Unrelated Oral Cancer in the United States: A Multistage Carcinogenesis Modeling Analysis.

Differences in prognosis in HPV-positive and HPV-negative oral (oropharyngeal and oral cavity) squamous cell carcinomas (OSCCs) and increasing incidence of HPV-related cancers have spurred interest in demographic and temporal trends in OSCC incidence. We leverage multistage clonal expansion (MSCE) models coupled with age—period—cohort (APC) epidemiological models to analyze OSCC data in the SEER cancer registry (1973–2012). MSCE models are based on the initiation—promotion—malignant conversion paradigm in carcinogenesis and allow for interpretation of trends in terms of biological mechanisms. APC models seek to differentiate between the temporal effects of age, period, and birth cohort on cancer risk. Previous studies have looked at the effect of period and cohort on tumor initiation, and we extend this to compare model fits of period and cohort effects on each of tumor initiation, promotion, and malignant conversion rates. HPV-related, HPV-unrelated except oral tongue, and HPV-unrelated oral tongue sites are best described by placing period and cohort effects on the initiation rate. HPV-related and non-oral-tongue HPV-unrelated cancers have similar promotion rates, suggesting similar tumorigenesis dynamics once initiated. Estimates of promotion rates at oral tongue sites are lower, corresponding to a longer sojourn time; this finding is consistent with the hypothesis of an etiology distinct from HPV or alcohol and tobacco use. Finally, for the three subsite groups, men have higher initiation rates than women of the same race, and black people have higher promotion than white people of the same sex. These differences explain part of the racial and sex differences in OSCC incidence.

A structure-based protocol for learning the family-specific mechanisms of membrane-binding domains

Motivation: Peripheral membrane-targeting domain (MTD) families, such as C1-, C2- and PH domains, play a key role in signal transduction and membrane trafficking by dynamically translocating their parent proteins to specific plasma membranes when changes in lipid composition occur. It is, however, difficult to determine the subset of domains within families displaying this property, as sequence motifs signifying the membrane binding properties are not well defined. For this reason, procedures based on sequence similarity alone are often insufficient in computational identification of MTDs within families (yielding less than 65% accuracy even with a sequence identity of 70%).Results: We present a machine learning protocol for determining membrane-targeting properties achieving 85–90% accuracy in separating binding and non-binding domains within families. Our model is based on features from both sequence and structure, thereby incorporation statistics obtained from the entire domain family and domain-specific physical quantities such as surface electrostatics. In addition, by using the enriched rules in alternating decision tree classifiers, we are able to determine the meaning of the assigned function labels in terms of biological mechanisms.Conclusions: The high accuracy of the learned models and good agreement between the rules discovered using the ADtree classifier and mechanisms reported in the literature reflect the value of machine learning protocols in both prediction and biological knowledge discovery. Our protocol can thus potentially be used as a general function annotation and knowledge mining tool for other protein domains.Availability: metador.bioengr.uic.eduContact: huilu@uic.edu

Performance Comparison of Two Gene Set Analysis Methods for Genome-wide Association Study Results: GSA-SNP vs i-GSEA4GWAS

Gene set analysis (GSA) is useful in interpreting a genome-wide association study (GWAS) result in terms of biological mechanism. We compared the performance of two different GSA implementations that accept GWAS p-values of single nucleotide polymorphisms (SNPs) or gene-by-gene summaries thereof, GSA-SNP and i-GSEA4GWAS, under the same settings of inputs and parameters. GSA runs were made with two sets of p-values from a Korean type 2 diabetes mellitus GWAS study: 259,188 and 1,152,947 SNPs of the original and imputed genotype datasets, respectively. When Gene Ontology terms were used as gene sets, i-GSEA4GWAS produced 283 and 1,070 hits for the unimputed and imputed datasets, respectively. On the other hand, GSA-SNP reported 94 and 38 hits, respectively, for both datasets. Similar, but to a lesser degree, trends were observed with Kyoto Encyclopedia of Genes and Genomes (KEGG) gene sets as well. The huge number of hits by i-GSEA4GWAS for the imputed dataset was probably an artifact due to the scaling step in the algorithm. The decrease in hits by GSA-SNP for the imputed dataset may be due to the fact that it relies on Z-statistics, which is sensitive to variations in the background level of associations. Judicious evaluation of the GSA outcomes, perhaps based on multiple programs, is recommended.

Statins discontinuation in compliant chronic users induces atherothrombotic profile despite baseline clinical setting and treatments

Statins offer important benefits for the large populations of individuals at high risk for cardiovascular and cerebrovascular events in both primary and secondary preventions [1]. Due to the positive clinical impact, the concern of statins withdrawal on putative rebound vascular events has been suggested and evaluated both in terms of biological mechanisms or clinical settings as extensively reviewed [2–3]. Furthermore, although from retrospective analysis, several observations have confirmed an increased events rate especially when statins were withdrawn during acute phase of acute vascular stress like coronary syndromes [4–5], major vascular surgery [6–7] and ischemic stroke [8], also in a randomized study [9].

Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus

Silencers and enhancer-blockers (EBs) are cis-acting, negative regulatory elements (NREs) that control interactions between promoters and enhancers. Although relatively uncharacterized in terms of biological mechanisms, these elements are likely to be abundant in the genome. We developed an experimental strategy to identify silencers and EBs using transient transfection assays. A known insulator and EB from the chicken beta-globin locus, cHS4, served as a control element for these assays. We examined 47 sequences from a 1.8-Mb region of human chromosome 7 for silencer and EB activities. The majority of functional elements displayed directional and promoter-specific activities. A limited number of sequences acted in a dual manner, as both silencers and EBs. We examined genomic data, epigenetic modifications, and sequence motifs within these regions. Strong silencer elements contained a novel CT-rich motif, often in multiple copies. Deletion of the motif from three regions caused a measurable loss of silencing ability in these sequences. Moreover, five duplicate occurrences of this motif were identified in the cHS4 insulator. These motifs provided an explanation for an uncharacterized silencing activity we measured in the insulator element. Overall, we identified 15 novel NREs, which contribute new insights into the prevalence and composition of sequences that negatively regulate gene expression.

Oral contraceptives and ovarian cancer.

The protection conveyed by oral contraceptives against ovarian cancer risk is one of the best established and most important features of epithelial ovarian cancer on a public health scale. Ovarian cancer incidence and mortality rates have been declining in most developed countries for women born after 1920, and the decline was greater in countries where oral contraceptive use has been more widespread. Thus, data from descriptive epidemiology are consistent with a favourable effect of oral contraceptives on ovarian cancer risks. The overall estimated protection from cohort and case-control studies is approximately 40% in ever oral contraceptive users, and increases with duration of use to more than 50% for users of 5 years or longer. The favourable effect of oral contraceptives against ovarian cancer risk persists for at least 10-15 years after use has ceased, and it is not confined to any particular type of oral contraceptive formulation. However, available data do not provide definite evidence for more recent low-dose formulations and for longer periods of latency or recency of use. The protection is also observed on borderline malignancy ovarian neoplasms, and probably on benign epithelial cysts as well. There is suggestive evidence of some protection for sex-cord-stromal cancers, but not for germ cell neoplasms. In terms of biological mechanisms, oral contraceptives are thought to act on ovarian cancer risk by affecting the lifetime number of ovulations. The protection attributable to oral contraceptives on ovarian cancer risk is one of the major issues on any individual risk/benefit assessment and public health evaluation of this type of contraceptive use.

The "Synergistic" Action of Mixed Irradiation with High-LET and Low-LET Radiation

The combined modalities of various agents such as radiation, chemicals and physical agents are often used, and exposure to mixture of agents sometimes occurs in nature. However, it is not clear whether these combined effects are synergistic, partly because definition of the term {open_quotes}synergism{close_quotes} is confusing, as pointed out by Streffer and Mueller. It is, of course, desirable that the definition should be simple and widely applicable to all agents. Yet the underlying mechanisms of the effects of different agents are probably different, and the mechanisms of combined effects are different and more complicated than those of a single agent. It is therefore important to define synergism taking each underlying mechanism into consideration. From this viewpoint, the definitions of synergism which have been used to date are examined with respect to the effect of a mixture of different types of radiation on cells, and they are shown to be inappropriate and misleading. This is probably attributable to simply treating the resulting phenomena (cell survival in most cases) without adequately taking into consideration the knowledge of underlying biological mechanisms in defining the synergism that may occur with irradiation. This commentary discusses the inappropriateness of current definitions and proposes a new definitionmore » in terms of biological mechanisms as a counterproposal. 16 refs., 6 figs.« less