A computational model elucidating mechanisms and variability in theta burst stimulation responses.

Theta burst stimulation (TBS) is a form of repetitive transcranial magnetic stimulation (rTMS) with unknown underlying mechanisms and highly variable responses across subjects. To investigate these issues, we developed a simple computational model. Our model consisted of two neurons linked by an excitatory synapse that incorporates two mechanisms: short-term plasticity (STP) and spike-timing-dependent plasticity (STDP). We applied a variable-amplitude current through I-clamp with a TBS time pattern to the pre- and post-synaptic neurons, simulating synaptic plasticity. We analyzed the results and provided an explanation for the effects of TBS, as well as the variability of responses to it. Our findings suggest that the interplay of STP and STDP mechanisms determines the direction of plasticity, which selectively affects synapses in extended neurons and underlies functional effects. Our model describes how the timing, number, and intensity of pulses delivered to neurons during rTMS contribute to induced plasticity. This not only successfully explains the different effects of intermittent TBS (iTBS) and continuous TBS (cTBS), but also predicts the results of other protocols such as 10 Hz rTMS. We propose that the variability in responses to TBS can be attributed to the variable span of neuronal thresholds across individuals and sessions. Our model suggests a biologically plausible mechanism for the diverse responses to TBS protocols and aligns with experimental data on iTBS and cTBS outcomes. This model could potentially aid in improving TBS and rTMS protocols and customizing treatments for patients, brain areas, and brain disorders.

Effects of exposure to alternating low-intensity, intermediate-frequency electric fields on the differentiation of human leukemic cell line U937.

Studying the bioeffects of electric fields have been the subject of ongoing research which led to promising therapeutic effect, particularly in cancer treatment. Here, we investigated the impact of low-intensity, intermediate-frequency alternating electric fields on the differentiation of human myeloid leukemia cell line U937. The results showed a near twofold increase in differentiation of U937 cells treated for 24 h by alternating 600 kHz, 150 V/m electric fields, in comparison to their control groups. This measure was evaluated by latex bead phagocytosis assay, nitro blue tetrazolium test, and cell cycle analysis which revealed a significant shift in the number of cells from G2 +M to G0 +G1 phases. The simulation result for the intracellular field intensity showed around 50% attenuation with respect to the applied external field for our setup which ruled out masking of the applied field by the internal electric noise of the cell. Based on previous studies we postulate a possible calcium-related effect for the observed differentiation, yet the exact underlying mechanism requires further investigation. Finally, our results may offer a potential therapeutic method for leukemia in the future.

Frequency dependence of ultrasonic effects on the kinetics of hen egg white lysozyme fibrillation.

Our study aimed to investigate the effects of ultrasound on the fibrillation kinetics of HEWL (hen egg white lysozyme) and its physicochemical properties. Ultrasound, a mechanical wave, can induce conformational changes in proteins. To achieve this, we developed an ultrasound exposure system and used various biophysical techniques, including ThT fluorescence spectroscopy, ATR-FTIR, Far-UV CD spectrophotometry, Fluorescence microscopy, UV-spectroscopy, and seeding experiments. Our results revealed that higher frequencies significantly accelerated the fibrillation of lysozyme by unfolding the native protein and promoting the fibrillation process, thereby reducing the lag time. We observed a change in the secondary structure of the sonicated protein change to the ß-structure, but there was no difference in the Tm of native and sonicated proteins. Furthermore, we found that higher ultrasound frequencies had a greater seeding effect. We propose that the effect of frequency can be explained by the impact of the Reynolds number, and for the Megahertz frequency range, we are almost at the transition regime of turbulence. Our results suggest that laminar flows may not induce any significant change in the fibrillation kinetics, while turbulent flows may affect the process.

Indirect effects of interference of two emerging environmental contaminants on cell health: Radiofrequency radiation and gold nanoparticles.

BACKGROUND: The global need for wireless technologies is growing rapidly. So, we have been exposed to a new type of environmental pollution: radiofrequency radiation (RFR). Recent studies have shown that RFR can cause not only direct effects but also indirect or non-targeted effects such as the bystander effect (BE). In this study, we investigated the BE induced by RFR in the present of gold nanoparticles (GNP). Moreover, we studied the expression of cyclooxygenase-2 (COX-2). METHODS: Non-toxic dose of 15-nm GNP was used to treat the Chinese Hamster Ovary (CHO) cells. After 48 h of incubation, cells were exposed to 900 MHz GSM RFR for 24 h. Then we collected the cell culture medium of these cells (conditioned culture medium, CCM) and transferred it to new cells (bystander cells). Cell deaths, DNA breaks, oxidative stress and COX-2 expression were analyzed in all groups. RESULTS: The results showed that RFR increased metabolic death in cells treated with GNP. Inversely, the colony formation ability was reduced in bystander cells and RFR exposed cells either in the presence or absence of GNP. Also, the level of reactive oxygen species (ROS) in GNP treated cells showed a significant reduction compared to those of untreated cells. However, RFR-induced DNA breaks and the frequencies of micronuclei (MN) were not significantly affected by GNP. The expression of COX-2 mRNA increased in RFR GNP treated cells, but the difference was not significant. CONCLUSION: Our results for the first time indicated that RFR induce indirect effects in the presence of GNP. However, the molecular mediators of these effects differ from those in the absence of GNP. Also, to our knowledge, this is the first study to show that COX-2 is not involved in the bystander effect induced by 900 MHz RFR.

Alternating electric fields can improve chemotherapy treatment efficacy in blood cancer cell U937 (non-adherent cells).

BACKGROUND: Recent achievements in cancer therapy are the use of alternating electrical fields at intermediate frequencies (100-300 kHz) and low intensities (1-3 V/cm), which specifically target cell proliferation while affecting different cellular activities depending on the frequency used. METHODS: In this article, we examine the effect of electric fields on spherical suspended cells and propose the combination of Daunorubicin, a chemotherapy agent widely used in the treatment of acute myeloid leukemia, with electric field exposure. U937 cells were subjected to an electric field with a frequency of 200 kHz and an intensity of 0.75 V/cm, or to a combination of Daunorubicin and electric field exposure, resulting in a significant reduction in cell proliferation. Furthermore, the application of an electric field to U937 cells increased Daunorubicin uptake. RESULTS: Apoptosis and DNA damage were induced by the electric field or in conjunction with Daunorubicin. Notably, normal cells exposed to an electric field did not show significant damage, indicating a selective effect on dividing cancer cells (U937). Moreover, the electric field affects the U937 cell line either alone or in combination with Daunorubicin. This effect may be due to increased membrane permeability. CONCLUSIONS: Our findings suggest that the use of electric fields at intermediate frequencies and low intensities, either alone or in combination with Daunorubicin, has potential as a selective anti-cancer therapy for dividing cancer cells, particularly in the treatment of acute myeloid leukemia. Further research is needed to fully understand the underlying mechanisms and to optimize the use of this therapy.

Chemical Modification of the Amino Groups of Human Insulin: Investigating Structural Properties and Amorphous Aggregation of Acetylated Species.

The efficacy of human recombinant insulin can be affected by its aggregation. Effects of acetylation were observed on insulin structure, stability, and aggregation at 37 and 50 °C and pH of 5.0 and 7.4 with the use of spectroscopy, circular dichroism (CD), dynamic light scattering (DLS), and atomic force microscopy (AFM). Raman and FTIR results were indicative of structural changes in AC-INS, and CD analyses showed a slight increase in ß-sheet content in AC-INS. Melting temperature (Tm) measurements indicated an overall more stable structure and spectroscopic assessment showed a more compact one. Formation of amorphous aggregates was followed over time and kinetics parameters showed a longer nucleation phase (higher t* amount) and lower aggregates amount (lower Alim) for acetylated insulin (AC-INS) compared to native (N-INS) in all tested conditions. The results of amyloid-specific probes approved the formation of amorphous aggregates. Size particle and microscopic analysis suggested that AC-INS was less prone to form aggregates, which were smaller if formed. In conclusion, this study has demonstrated that controlled acetylation of insulin may lead to its higher stability and lower propensity toward amorphous aggregation and has provided insight into the result of this type of post-translational protein modification.

Design, optimization and characterization of a novel antibacterial chitosan-based hydrogel dressing for promoting blood coagulation and full-thickness wound healing: A biochemical and biophysical study.

The use of hydrogel dressings has become increasingly popular as a scaffold for skin tissue engineering. Herein, we have developed an innovative wound dressing using chitosan, fibrinogen, nisin, and EDTA as an effective antibacterial scaffold for wound treatment. The structural and functional characteristics of the hydrogel, including morphology, mechanical strength, drug encapsulation and release, swelling behaviors, blood coagulation, cytotoxicity, and antibacterial activity, were studied. Spectroscopic studies indicated that the attachment of chitosan to fibrinogen is associated with minimal change in its secondary structure; subsequently, at higher temperatures, it is expected to preserve fibrinogen's conformational stability. Mechanical and blood coagulation analyses indicated that the incorporation of fibrinogen into the hydrogel resulted in accelerated clotting and enhanced mechanical properties. Our cell studies showed biocompatibility and non-toxicity of the hydrogel along with the promotion of cell migration. In addition, the prepared hydrogel indicated an antibacterial behavior against both Gram-positive and Gram-negative bacteria. Interestingly, the in vivo data revealed enhanced tissue regeneration and recovery within 17 days in the studied animals. Taken together, the results obtained from in vitro and histological assessments indicate that this innovatively designed hydrogel shows good potential as a candidate for wound healing.

Targeting myeloid-derived suppressor cells in combination with tumor cell vaccination predicts anti-tumor immunity and breast cancer dormancy: an in silico experiment.

Among the different breast cancer subsets, triple-negative breast cancer (TNBC) has the worst prognosis and limited options for targeted therapies. Immunotherapies are emerging as novel treatment opportunities for TNBC. However, the surging immune response elicited by immunotherapies to eradicate cancer cells can select resistant cancer cells, which may result in immune escape and tumor evolution and progression. Alternatively, maintaining the equilibrium phase of the immune response may be advantageous for keeping a long-term immune response in the presence of a small-size residual tumor. Myeloid-derived suppressor cells (MDSCs) are activated, expanded, and recruited to the tumor microenvironment by tumor-derived signals and can shape a pro-tumorigenic micro-environment by suppressing the innate and adaptive anti-tumor immune responses. We recently proposed a model describing immune-mediated breast cancer dormancy instigated by a vaccine consisting of dormant, immunogenic breast cancer cells derived from the murine 4T1 TNBC-like cell line. Strikingly, these 4T1-derived dormant cells recruited fewer MDSCs compared to aggressive 4T1 cells. Recent experimental studies demonstrated that inactivating MDSCs has a profound impact on reconstituting immune surveillance against the tumor. Here, we developed a deterministic mathematical model for simulating MDSCs depletion from mice bearing aggressive 4T1 tumors resulting in immunomodulation. Our computational simulations indicate that a vaccination strategy with a small number of tumor cells in combination with MDSC depletion can elicit an effective immune response suppressing the growth of a subsequent challenge with aggressive tumor cells, resulting in sustained tumor dormancy. The results predict a novel therapeutic opportunity based on the induction of effective anti-tumor immunity and tumor dormancy.

Neuroprotective Effect of Propolis Polyphenol-Based Nanosheets in Cellular and Animal Models of Rotenone-Induced Parkinson's Disease.

Considering the central role of oxidative stress in the onset and progress of Parkinson's diseases (PD), search for compounds with antioxidant properties has attracted a growing body of attention. Here, we compare the neuroprotective effect of bulk and nano forms of the polyphenolic fraction of propolis (PFP) against rotenone-induced cellular and animal models of PD. Mass spectrometric analysis of PFP confirmed the presence of multiple polyphenols including kaempferol, naringenin, coumaric acid, vanillic acid, and ferulic acid. In vitro cellular experiments indicate the improved efficiency of the nano form, compared to the bulk form, of PFP in attenuating rotenone-induced cytotoxicity characterized by a decrease in cell viability, release of lactate dehydrogenase, increased ROS generation, depolarization of the mitochondrial membrane, decreased antioxidant enzyme activity, and apoptosis induction. In vivo experiments revealed that while no significant neuroprotection was observed relating to the bulk form, PFP nanosheets were very effective in protecting animals, as evidenced by the improved behavioral and neurochemical parameters, including decreased lipid peroxidation, increased GSH content, and antioxidant enzyme activity enhancement. We suggest that improved neuroprotective effects of PFP nanosheets may be attributed to their increased water solubility and enrichment with oxygen-containing functional groups (such as OH and COOH), leading to increased antioxidant activity of these compounds.

Distinct Dynamics of Migratory Response to PD-1 and CTLA-4 Blockade Reveals New Mechanistic Insights for Potential T-Cell Reinvigoration following Immune Checkpoint Blockade.

Cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and programmed cell death protein 1 (PD-1), two clinically relevant targets for the immunotherapy of cancer, are negative regulators of T-cell activation and migration. Optimizing the therapeutic response to CTLA-4 and PD-1 blockade calls for a more comprehensive insight into the coordinated function of these immune regulators. Mathematical modeling can be used to elucidate nonlinear tumor-immune interactions and highlight the underlying mechanisms to tackle the problem. Here, we investigated and statistically characterized the dynamics of T-cell migration as a measure of the functional response to these pathways. We used a previously developed three-dimensional organotypic culture of patient-derived tumor spheroids treated with anti-CTLA-4 and anti-PD-1 antibodies for this purpose. Experiment-based dynamical modeling revealed the delayed kinetics of PD-1 activation, which originates from the distinct characteristics of PD-1 and CTLA-4 regulation, and followed through with the modification of their contributions to immune modulation. The simulation results show good agreement with the tumor cell reduction and active immune cell count in each experiment. Our findings demonstrate that while PD-1 activation provokes a more exhaustive intracellular cascade within a mature tumor environment, the time-delayed kinetics of PD-1 activation outweighs its preeminence at the individual cell level and consequently confers a functional dominance to the CTLA-4 checkpoint. The proposed model explains the distinct immunostimulatory pattern of PD-1 and CTLA-4 blockade based on mechanisms involved in the regulation of their expression and may be useful for planning effective treatment schemes targeting PD-1 and CTLA-4 functions.

Differential biological responses of adherent and non-adherent (cancer and non-cancerous) cells to variable extremely low frequency magnetic fields.

Extremely low-frequency electromagnetic field (ELF-EMF) induces biological effects on different cells through various signaling pathways. To study the impact of the ELF-EMF on living cells under an optimal physiological condition, we have designed and constructed a novel system that eliminates several limitations of other ELF-EMF systems. Apoptosis and cell number were assessed by flow cytometry and the Trypan Blue dye exclusion method, respectively. In vitro cell survival was evaluated by colony formation assay. The distribution of cells in the cell cycle, intracellular ROS level, and autophagy were analyzed by flow cytometer. Suspended cells differentiation was assessed by phagocytosis of latex particles and NBT reduction assay. Our results showed that response to the exposure to ELF-EMF is specific and depends on the biological state of the cell. For DU145, HUVEC, and K562 cell lines the optimum results were obtained at the frequency of 0.01 Hz, while for MDA-MB-231, the optimum response was obtained at 1 Hz. Long-term exposure to ELF-EMF in adherent cells effectively inhibited proliferation by arresting the cell population at the cell cycle G2/M phase and increased intracellular ROS level, leading to morphological changes and cell death. The K562 cells exposed to the ELF-EMF differentiate via induction of autophagy and decreasing the cell number. Our novel ELF-EMF instrument could change morphological and cell behaviors, including proliferation, differentiation, and cell death.

Designing a new alginate-fibrinogen biomaterial composite hydrogel for wound healing.

Wound healing is a complex process and rapid healing necessitates a proper micro-environment. Therefore, design and fabrication of an efficacious wound dressing is an impressive innovation in the field of wound healing. The fabricated wound dressing in this scenario was designed using a combination of the appropriate coagulating and anti-bacterial materials like fibrinogen (as coagulating agent), nisin (as anti-bacterial agent), ethylenediaminetetraacetic acid (as anti-bacterial agent), and alginate (as wound healing agent). Biophysical characterization showed that the interaction of fibrinogen and alginate was associated with minor changes in the secondary structure of the protein. Conformational studies showed that the protein was structurally stable at 42 °C, is the maximum temperature of the infected wound. The properties of the hydrogel such as swelling, mechanical resistance, nisin release, antibacterial activity, cytotoxicity, gel porosity, and blood coagulation were assessed. The results showed a slow release for the nisin during 48 h. Antibacterial studies showed an inhibitory effect on the growth of Gram-negative and Gram-positive bacteria. The hydrogel was also capable to absorb a considerable amount of water and provide oxygenation as well as incorporation of the drug into its structure due to its sufficient porosity. Scanning electron microscopy showed pore sizes of about 14-198 µm in the hydrogel. Cell viability studies indicated high biocompatibility of the hydrogel. Blood coagulation test also confirmed the effectiveness of the synthesized hydrogel in accelerating the process of blood clot formation. In vivo studies showed higher rates of wound healing, re-epithelialization, and collagen deposition. According to the findings from in vitro as well as in vivo studies, the designed hydrogel can be considered as a novel attractive wound dressing after further prerequisite assessments.

An overview of the biological effects of extremely low frequency electromagnetic fields combined with ionizing radiation.

By growing the electrical power networks and electronic devices, electromagnetic fields (EMF) have become an inseparable part of the modern world. Considering the inevitable exposure to a various range of EMFs, especially at extremely low frequencies (ELF-EMF), investigating the biological effects of ELF-EMFs on biological systems became a global issue. The possible adverse consequences of these exposures were studied, along with their potential therapeutic capabilities. Also, their biological impacts in combination with other chemical and physical agents, specifically ionizing radiation (IR), as a co-carcinogen or as adjuvant therapy in combination with radiotherapy were explored. Here, we review the results of several in-vitro and in-vivo studies and discuss some proposed possible mechanisms of ELF-EMFs' actions in combination with IR. The results of these experiments could be fruitful to develop more precise safety standards for environmental ELF-EMFs exposures. Furthermore, it could evaluate the therapeutic capacities of ELF-EMFs alone or as an improver of radiotherapy.

Analyzing large scale gene expression data in colorectal cancer reveals important clues; CLCA1 and SELENBP1 downregulated in CRC not in normal and not in adenoma.

Early detection of colorectal cancer (CRC) increases the chances of survival and reduces the therapeutic problems and costs of treatment. Since molecular biomarkers can help us diagnose colorectal cancer early, we need to identify novel gene for predicting the early stages of tumorigenesis. Here, we integrated five independent CRC gene expression datasets derived from expression profiling by array comparing CRC with normal samples in: GSE21510, GSE4107, GSE25071, GSE15781 dataset, and GSE8671 dataset, including 64 samples from 32 patients comparing 32 colonic normal mucosa with 32 colorectal adenoma. To detect genes that expressed differentially in experimental circumstances of these datasets, we used web tool of GEO2R to compare groups of samples in the GEO data series. Furthermore, we constructed the protein-protein interactions network by STRING database for mostly downregulated genes and the expression of their members in PPI network were studied into five datasets separately. Also, the level of expression of selected biomarker genes in different stages of CRC compared to normal was studied. Our data revealed 17 common downregulated genes (average fold change (FC) in five tests ≥6) in CRC in comparison with normal (Test 1 to Test 4) and in adenoma compared with normal (Test 5). Studying of gene expression of PPI network members of these downregulated genes led to identifying of CLCA1, SELENBP1, CWC25, ACOT11, GUCY2C and ALDH1A1 as suppressor genes and PTGS2, PROCR, MOCS3 and NFS1 as oncogenes which respectively downregulated and upregulated in CRC. Since decreasing of gene expression was seen in CRC comparing with normal and due to no different expression seen for these 10 genes in adenoma, they, especially CLCA1 and SELENBP1, could be considered as biomarkers for early detection of CRC. Before using these signature genes in the clinic; however, further validations are required.

The state of the art of biomedical applications of optogenetics.

BACKGROUND AND OBJECTIVE: Optogenetics has opened new insights into biomedical research with the ability to manipulate and control cellular activity using light in combination with genetically engineered photosensitive proteins. By stimulating with light, this method provides high spatiotemporal and high specificity resolution, which is in contrast to conventional pharmacological or electrical stimulation. Optogenetics was initially introduced to control neural activities but was gradually extended to other biomedical fields. STUDY DESIGN: In this paper, firstly, we summarize the current optogenetic tools stimulated by different light sources, including lasers, light-emitting diodes, and laser diodes. Second, we outline the variety of biomedical applications of optogenetics not only for neuronal circuits but also for various kinds of cells and tissues from cardiomyocytes to ganglion cells. Furthermore, we highlight the potential of this technique for treating neurological disorders, cardiac arrhythmia, visual impairment, hearing loss, and urinary bladder diseases as well as clarify the mechanisms underlying cancer progression and control of stem cell differentiation. CONCLUSION: We sought to summarize the various types of promising applications of optogenetics to treat a broad spectrum of disorders. It is conceivable to expect that optogenetics profits a growing number of patients suffering from a range of different diseases in the near future.

Optogenetic Stimulation of Primary Cardiomyocytes Expressing ChR2.

Introduction: Non-clinical cardiovascular drug safety assessment is the main step in the progress of new pharmaceutical products. Cardiac drug safety testing focuses on a delayed rectifier potassium channel block and QT interval prolongation, whereas optogenetics is a powerful technology for modulating the electrophysiological properties of excitable cells. Methods: For this purpose, the blue light-gated ion channel, channelrhodopsin-2 (ChR2), has been introduced into isolated primary neonatal cardiomyocytes via a lentiviral vector. After being subjected to optical stimulation, transmembrane potential and intracellular calcium were assessed. Results: Here, we generated cardiomyocytes expressing ChR2 (light-sensitive protein), that upon optical stimulation, the cardiomyocytes depolarized result from alterations of membrane voltage and intracellular calcium. Conclusion: This cell model was easily adapted to a cell culture system in a laboratory, making this method very attractive for therapeutic research on cardiac optogenetics.

Conifer: clonal tree inference for tumor heterogeneity with single-cell and bulk sequencing data.

BACKGROUND: Genetic heterogeneity of a cancer tumor that develops during clonal evolution is one of the reasons for cancer treatment failure, by increasing the chance of drug resistance. Clones are cell populations with different genotypes, resulting from differences in somatic mutations that occur and accumulate during cancer development. An appropriate approach for identifying clones is determining the variant allele frequency of mutations that occurred in the tumor. Although bulk sequencing data can be used to provide that information, the frequencies are not informative enough for identifying different clones with the same prevalence and their evolutionary relationships. On the other hand, single-cell sequencing data provides valuable information about branching events in the evolution of a cancerous tumor. However, the temporal order of mutations may be determined with ambiguities using only single-cell data, while variant allele frequencies from bulk sequencing data can provide beneficial information for inferring the temporal order of mutations with fewer ambiguities. RESULT: In this study, a new method called Conifer (ClONal tree Inference For hEterogeneity of tumoR) is proposed which combines aggregated variant allele frequency from bulk sequencing data with branching event information from single-cell sequencing data to more accurately identify clones and their evolutionary relationships. It is proven that the accuracy of clone identification and clonal tree inference is increased by using Conifer compared to other existing methods on various sets of simulated data. In addition, it is discussed that the evolutionary tree provided by Conifer on real cancer data sets is highly consistent with information in both bulk and single-cell data. CONCLUSIONS: In this study, we have provided an accurate and robust method to identify clones of tumor heterogeneity and their evolutionary history by combining single-cell and bulk sequencing data.

Butein combined with radiotherapy enhances radioresponse of gastric cancer cell by impairing DNA damage repair.

Radiation therapy is common in the current procedures of cancer treatment, but in many cases, radiation resistance of cancerous tissue limits efficacy in clinical applications. Therefore, the use of radiosensitizers has been introduced as an effective strategy to increase the efficiency of radiotherapy. Butein (2', 3, 4, 4'-Tetrahydroxychalcone), a polyphenolic compound of flavonoids family, presents anti-cancer properties and inhibits the signaling pathways associated with radiation resistance. Therefore, we hypothesized that butein in combination with radiation may increase radiosensitivity. To evaluate the radiosensitizing effect of butein, we used MKN-45 cell line and performed several assays such as MTT, soft-agar colony formation, apoptosis, cell cycle, and comet assays. Based on obtained results, butein significantly enhanced radiosensitivity of MKN-45 cells. Butein treatment abrogated the radiation-induced G2/M cell cycle arrest, increased DNA damage, enhanced apoptosis, and reduced colony-forming ability of irradiated cells. This study on MKN-45 cells demonstrates that combination of butein with radiotherapy increases its radiosensitivity by abrogating the radiation-induced G2/M blockage, impairing DNA repair, and enhancing apoptotic and reproductive cell death. Therefore, we suggest butein as a candidate for combination with radiation therapy to decrease dose of radiation delivered to the patients and its corresponding side effects.

Dormant Tumor Cell Vaccination: A Mathematical Model of Immunological Dormancy in Triple-Negative Breast Cancer.

Triple-negative breast cancer (TNBC) is a molecular subtype of breast malignancy with a poor clinical prognosis. There is growing evidence that some chemotherapeutic agents induce an adaptive anti-tumor immune response. This reaction has been proposed to maintain the equilibrium phase of the immunoediting process and to control tumor growth by immunological cancer dormancy. We recently reported a model of immunological breast cancer dormancy based on the murine 4T1 TNBC model. Treatment of 4T1 cells in vitro with high-dose chemotherapy activated the type I interferon (type I IFN) signaling pathway, causing a switch from immunosuppressive to cytotoxic T lymphocyte-dependent immune response in vivo, resulting in sustained dormancy. Here, we developed a deterministic mathematical model based on the assumption that two cell subpopulations exist within the treated tumor: one population with high type I IFN signaling and immunogenicity and lower growth rate; the other population with low type I IFN signaling and immunogenicity and higher growth rate. The model reproduced cancer dormancy, elimination, and immune-escape in agreement with our previously reported experimental data. It predicted that the injection of dormant tumor cells with active type I IFN signaling results in complete growth control of the aggressive parental cancer cells injected at a later time point, but also of an already established aggressive tumor. Taken together, our results indicate that a dormant cell population can suppress the growth of an aggressive counterpart by eliciting a cytotoxic T lymphocyte-dependent immune response.

A novel pattern matching algorithm for genomic patterns related to protein motifs.

Background: Patterns on proteins and genomic sequences are vastly analyzed, extracted and collected in databases. Although protein patterns originate from genomic coding regions, very few works have directly or indirectly dealt with coding region patterns induced from protein patterns. Results: In this paper, we have defined a new genomic pattern structure suitable for representing induced patterns from proteins. The provided pattern structure, which is called "Consecutive Positions Scoring Matrix (CPSSM)", is a replacement for protein patterns and profiles in the genomic context. CPSSMs can be identified, discovered, and searched in genomes. Then, we have presented a novel pattern matching algorithm between the defined genomic pattern and genomic sequences based on dynamic programming. In addition, we have modified the provided algorithm to support intronic gaps and huge sequences. We have implemented and tested the provided algorithm on real data. The results on Saccharomyces cerevisiae's genome show 132% more true positives and no false negatives and the results on human genome show no false negatives and 10 times as many true positives as those in previous works. Conclusion: CPSSM and provided methods could be used for open reading frame detection and gene finding. The application is available with source codes to run and download at http://app.foroughmand.ir/cpssm/.