A fully coupled space-time multiscale modeling framework for predicting tumor growth

Most biological systems encountered in living organisms involve highly complex heterogeneous multi-component structures that exhibit different physical, chemical, and biological behavior at different spatial and temporal scales. The development of predictive mathematical and computational models of multiscale events in such systems is a major challenge in contemporary computational biomechanics, particularly the development of models of growing tumors in humans. The aim of this study is to develop a general framework for tumor growth prediction by considering major biological events at tissue, cellular, and subcellular scales. The key to developing such multiscale models is how to bridge spatial and temporal scales that range from 10^-3 to 10³ mm in space and from 10^-6 to 10⁷ s in time. In this paper, a fully coupled space-time multiscale framework for modeling tumor growth is developed. The framework consists of a tissue scale model, a model of cellular activities, and a subcellular transduction signaling pathway model. The tissue, cellular, and subcellular models in this framework are solved using partial differential equations for tissue growth, agent-based model for cellular events, and ordinary differential equations for signaling transduction pathway as a network at subcellular scale. The model is calibrated using experimental observations. Moreover, this model is biologically-driven from a signaling pathway, volumetrically-consistent between cellular and tissue scale in terms of tumor volume evolution in time, and a biophysically-sound tissue model that satisfies all conservation laws. The results show that the model is capable of predicting major characteristics of tumor growth such as the morphological instability, growth patterns of different cell phenotypes, compact regions of the higher cell density at the tumor region, and the reduction of growth rate due to drug delivery. The predicted treatment outcomes show a reduction in proliferation at different rates in response to different drug dosages. Moreover, the results of several 3D applications to tumor growth and the evolution of cellular and subcellular events are presented.

Exploring the key genes and signaling transduction pathways related to the survival time of glioblastoma multiforme patients by a novel survival analysis model

BACKGROUND

This study is to explore the key genes and signaling transduction pathways related to the survival time of glioblastoma multiforme (GBM) patients.

RESULTS

Our results not only showed that mutually explored GBM survival time related genes and signaling transduction pathways are closely related to the GBM, but also demonstrated that our innovated constrained optimization algorithm (CoxSisLasso strategy) are better than the classical methods (CoxLasso and CoxSis strategy).

CONCLUSION

We analyzed why the CoxSisLasso strategy can outperform the existing classical methods and discuss how to extend this research in the distant future.

Comparison of Gene Expression Profile Between Tumor Tissue and Adjacent Non-tumor Tissue in Patients with Gastric Gastrointestinal Stromal Tumor (GIST)

Gastrointestinal stromal tumors (GISTs) are defined as spindle cell and/or epithelioid tumors originated from interstitial Cajal cells or precursors in the digestive tract. This study was conducted to identify genes differing in expression between the gastric tumors and the adjacent non-cancerous mucosas in patients with primary gastric GIST. The gene expression profile was determined by using oligonucleotide-based DNA microarrays and further validated by quantitative real-time PCR. The Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis was performed to predict signaling pathways involved in gastric GIST. Our data showed that the expression levels of 957 genes (RAB39B, member RAS oncogene family; VCAN, versican; etc.) were higher and that of 526 genes (CXCL14, chemokine C-X-C motif ligand 14; MTUS1, microtubule-associated tumor suppressor 1; etc.) were lower in the gastric tumor tissues as compared with normal gastric tissues. Results from KEGG pathway analysis revealed that the differentially expressed genes were enriched into 16 signaling transduction pathways, including Hedeghog and Wnt signaling pathways. Our study may provide basis for identification of novel biomarkers associated with primary gastric GIST pathogenesis and for exploration of underlying mechanisms involved in this gastric sarcoma.

Calcium-sensing receptor in the T lymphocyte enhanced the apoptosis and cytokine secretion in sepsis

Calcium-sensing receptor (CaSR) is a member of the G protein-coupled receptor superfamily that existed in lymphocytes and promoted cytokine secretion. Lymphocytes are also involved in sepsis. However, the role of CaSR in lymphocytes in sepsis is unclear. In this study, we want to examine whether the CaSR in lymphocytes in sepsis is involved in the cytokine secretions and apoptosis and make clear the relationship between NF-κB and MAPK signal transduction pathways. We investigated the issues mentioned earlier using Western blotting, ELISA, and Flow Cytometry. The sepsis was remodeled by cecal ligation and puncture (CLP). We found that CaSR protein expression increased in the peripheral blood T lymphocytes in CLP rats. The calcimimetic R568 (NPS R568) promoted, whereas the calcilytic NPS 2143 attenuated, signaling pathways proteins P65 (subunit of NF-κB), ERK1/2, and JNK (one subgroup of MAPKs) phosphorylation. However, P-P38 and P-JAKs exhibit no significant changes. Furthermore, the production TNF-α and IL-4 was greater in CLP rats than in normal rats, and NPS R568 promoted secretion of these cytokines. Simultaneously, the apoptotic ratio of T cells in CLP increased, and NPS R 568 exacerbated the apoptosis degree. However, these effects could also be inhibited by U0126 or SP600125 (MAPKs pathway inhibitor) or Bay-11-7082 or (NF-κB pathway inhibitor). From these results, we can conclude that, in the sepsis, CaSR activation promoted T-cell apoptosis and the secretion of pro-inflammatory cytokine TNF-α and anti-inflammatory cytokines IL-4 probably through NF-κB and partial MAPK signal transduction pathways.

Function of the CaMKII-ryanodine receptor signaling pathway in rabbits with left ventricular hypertrophy and triggered ventricular arrhythmia

BACKGROUND

Calcium calmodulin-dependent kinase II (CaMKII) can be more active in patients with left ventricular hypertrophy (LVH), which in turn causes phosphorylation of ryanodine receptors, resulting in inactivation and the instability of intracellular calcium homeostasis. The present study aimed to determine the effect of CaMKII-ryanodine receptor pathway signaling in rabbits with left ventricular hypertrophy and triggered ventricular arrhythmia.

METHODS

Forty New Zealand rabbits were randomized into four groups (10 per group): sham group, LVH group, KN-93 group (LVH+KN-93), and ryanodine group (LVH+ryanodine). Rabbits in the LVH, KN-93, and ryanodine groups were used to establish a left ventricular hypertrophy model by the coarctation of the abdominal aorta, while those in the sham group did not undergo the coarctation. After eight weeks, action potentials (APs) were recorded simultaneously in the endocardium and epicardium, and a transmural electrocardiogram (ECG) was also recorded in the rabbit left ventricular wedge model. Drugs were administered to the animals in the KN-93 and ryanodine groups, and the frequency of triggered APs and ventricular tachycardia was recorded after the rabbits were given isoprenaline (1 μmol/L) and high-frequency stimulation.

RESULTS

The frequency (animals/group) of triggered APs was 0/10 in the sham group, 10/10 in the LVH group, 4/10 in the KN-93 group, and 1/10 in the ryanodine group. The frequencies of ventricular tachycardia were 0/10, 9/10, 3/10, and 1/10, respectively. The frequencies of polymorphic ventricular tachycardia or ventricular fibrillation were 0/10, 7/10, 2/10, and 1/10, respectively. The frequencies of triggered ventricular arrhythmias in the KN-93 and ryanodine groups were much lower than those in the LVH group (P<0.05).

CONCLUSIONS

KN-93 and ryanodine can effectively reduce the occurrence of triggered ventricular arrhythmia in rabbits with LVH. The CaMKII-ryanodine signaling pathway can be used as a new means of treating ventricular arrhythmia.

Relationship between nuclear factor-kappa B and cell apoptosis

The roles of nuclear factor-kappa B (NF-κB) fa-mily and its signaling transduction pathway in apoptosis has been the focus of intense investigation all over the world. Researches show that NF-κB signaling pathway exerts anti-apoptotic function via many other proteins, including IAPs, Bcl-2, TRAF, JNK, FLIP, A20, Gadd45b, MnSOD and so on, but the exact mechanism remains unclear. Inhibition of NF-κB activation can promote the process of programmed cell death, and may become new avenues for therapeutic intervention in immune diseases, chronic inflammatory diseases and certain cancers. Furthermore, recent studies reveal that NF-κB can promote apoptosis, and the types and quantity of NF-κB subunits play a key role in apoptosis. In this review, we presented an overview of the progress in the relationship between NF-κB and apoptosis.