Systems biology, post-genomic analysis and emerging technologies
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An agent-based model of prostate Cancer bone metastasis progression and response to Radium223
Bone metastasis is the most frequent complication in prostate cancer patients and associated outcome remains fatal. Radium223 (Rad223), a bone targeting radioisotope improves overall survival in patients (3.6 ...BMC Cancer 2020 20:605Integration of genomics, metagenomics, and metabolomics to identify interplay between susceptibility alleles and microbiota in adenoma initiation
Colorectal cancer (CRC) is a multifactorial disease resulting from both genetic predisposition and environmental factors including the gut microbiota (GM), but deciphering the influence of genetic variants, en...BMC Cancer 2020 20:600Ex vivo modelling of drug efficacy in a rare metastatic urachal carcinoma
Ex vivo drug screening refers to the out-of-body assessment of drug efficacy in patient derived vital tumor cells. The purpose of these methods is to enable functional testing of patient specific efficacy of a...BMC Cancer 2020 20:590Prognostic characterization of OAS1/OAS2/OAS3/OASL in breast cancer
Prognostic biomarkers remain a focus in breast cancer during last decades. More reliable predictors to adequately characterize the prognosis of breast cancer are essential. The 2′-5′-oligoadenylate synthetases...BMC Cancer 2020 20:575The initial engraftment of tumor cells is critical for the future growth pattern: a mathematical study based on simulations and animal experiments
Xenograft mouse tumor models are used to study mechanisms of tumor growth and metastasis formation and to investigate the efficacy of different therapeutic interventions. After injection the engrafted cells fo...BMC Cancer 2020 20:524Text mining in a literature review of urothelial cancer using topic model
Urothelial cancer (UC) includes carcinomas of the bladder, ureters, and renal pelvis. New treatments and biomarkers of UC emerged in this decade. To identify the key information in a vast amount of literature ...BMC Cancer 2020 20:462Right and left-sided colon cancers - specificity of molecular mechanisms in tumorigenesis and progression
Given the differences in embryonic origin, vascular and nervous supplies, microbiotic burden, and main physiological functions of left and right colons, tumor location is increasingly suggested to dictate tumo...BMC Cancer 2020 20:317Deconvolution of diffuse gastric cancer and the suppression of CD34 on the BALB/c nude mice model
Gastric cancer is a considerable burden for worldwide patients. And diffuse gastric cancer is the most insidious subgroup with poor survival. The phenotypic characterization of the diffuse gastric cancer cell ...BMC Cancer 2020 20:314Sepsis-associated pathways segregate cancer groups
Sepsis and cancer are both leading causes of death, and occurrence of any one, increases the likelihood of the other. While cancer patients are susceptible to sepsis, survivors of sepsis are also susceptible t...BMC Cancer 2020 20:309Computational models applied to metabolomics data hints at the relevance of glutamine metabolism in breast cancer
Metabolomics has a great potential in the development of new biomarkers in cancer and it has experiment recent technical advances.BMC Cancer 2020 20:307Relationship of lymphovascular invasion with lymph node metastasis and prognosis in superficial esophageal carcinoma: systematic review and meta-analysis
The development of tumor cells inside the lymphatics or blood vessels is known as lymphovascular invasion (LVI). The correlation between LVI, lymph node metastasis (LNM), and the diagnosis of superficial esoph...BMC Cancer 2020 20:176Temporal changes in gut microbiota profile in children with acute lymphoblastic leukemia prior to commencement-, during-, and post-cessation of chemotherapy
Alteration in gut microbiota has been recently linked with childhood leukemia and the use of chemotherapy. Whether the perturbed microbiota community is restored after disease remission and cessation of cancer...BMC Cancer 2020 20:151Systematical identifications of prognostic meaningful lung adenocarcinoma subtypes and the underlying mutational and expressional characters
Lung adenocarcinoma (LUAD) is one of the most common cancer types, threatening the human health around the world. However, the high heterogeneity and complexity of LUAD limit the benefits of targeted therapies...BMC Cancer 2020 20:56An in silico exploration of combining Interleukin-12 with Oxaliplatin to treat liver-metastatic colorectal cancer
Combining anti-cancer therapies with orthogonal modes of action, such as direct cytotoxicity and immunostimulatory, hold promise for expanding clinical benefit to patients with metastatic disease. For instance...BMC Cancer 2020 20:26The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues
Utilization of RNA sequencing methods to measure gene expression from archival formalin-fixed paraffin-embedded (FFPE) tumor samples in translational research and clinical trials requires reliable interpretati...BMC Cancer 2019 19:1189Comparing biological information contained in mRNA and non-coding RNAs for classification of lung cancer patients
Deciphering the meaning of the human DNA is an outstanding goal which would revolutionize medicine and our way for treating diseases. In recent years, non-coding RNAs have attracted much attention and shown to...BMC Cancer 2019 19:1176Methodology of predicting novel key regulators in ovarian cancer network: a network theoretical approach
Identification of key regulator/s in ovarian cancer (OC) network is important for potential drug target and prevention from this cancer. This study proposes a method to identify the key regulators of this netw...BMC Cancer 2019 19:1129Ovarian cancer circulating extracelluar vesicles promote coagulation and have a potential in diagnosis: an iTRAQ based proteomic analysis
Circulating extracelluar vesicles (EVs) in epithelial ovarian cancer (EOC) patients emanate from multiple cells. These EVs are emerging as a new type of biomarker as they can be obtained by non-invasive approa...BMC Cancer 2019 19:1095System-based approaches as prognostic tools for glioblastoma
The evasion of apoptosis is a hallmark of cancer. Understanding this process holistically and overcoming apoptosis resistance is a goal of many research teams in order to develop better treatment options for c...BMC Cancer 2019 19:1092Tumor cell sensitivity to vemurafenib can be predicted from protein expression in a BRAF-V600E basket trial setting
Genetics-based basket trials have emerged to test targeted therapeutics across multiple cancer types. However, while vemurafenib is FDA-approved for BRAF-V600E melanomas, the non-melanoma basket trial was unsucce...BMC Cancer 2019 19:1025lionessR: single sample network inference in R
In biomedical research, network inference algorithms are typically used to infer complex association patterns between biological entities, such as between genes or proteins, using data from a population. This ...BMC Cancer 2019 19:1003Validation of computational determination of microsatellite status using whole exome sequencing data from colorectal cancer patients
Microsatellite instability (MSI), resulting from a defective mismatch repair system, occurs in approximately 15% of sporadic colorectal cancers (CRC). Since MSI is associated with a poor response to 5-fluorour...BMC Cancer 2019 19:971Distinct signatures of lung cancer types: aberrant mucin O-glycosylation and compromised immune response
Genomic initiatives such as The Cancer Genome Atlas (TCGA) contain data from -omics profiling of thousands of tumor samples, which may be used to decipher cancer signaling, and related alterations. Managing an...BMC Cancer 2019 19:824The design, analysis and application of mouse clinical trials in oncology drug development
Mouse clinical trials (MCTs) are becoming wildly used in pre-clinical oncology drug development, but a statistical framework is yet to be developed. In this study, we establish such as framework and provide ge...BMC Cancer 2019 19:718Absence of an embryonic stem cell DNA methylation signature in human cancer
Differentiated cells that arise from stem cells in early development contain DNA methylation features that provide a memory trace of their fetal cell origin (FCO). The FCO signature was developed to estimate t...BMC Cancer 2019 19:711Best fitting tumor growth models of the von Bertalanffy-PütterType
Longitudinal studies of tumor volume have used certain named mathematical growth models. The Bertalanffy-Pütter differential equation unifies them: It uses five parameters, amongst them two exponents related t...BMC Cancer 2019 19:683Novel significant stage-specific differentially expressed genes in hepatocellular carcinoma
Liver cancer is among top deadly cancers worldwide with a very poor prognosis, and the liver is a vulnerable site for metastases of other cancers. Early diagnosis is crucial for treatment of the predominant li...BMC Cancer 2019 19:663Biological molecular layer classification of muscle-invasive bladder cancer opens new treatment opportunities
Muscle-invasive bladder tumors are associated with a high risk of relapse and metastasis even after neoadjuvant chemotherapy and radical cystectomy. Therefore, further therapeutic options are needed and molecu...BMC Cancer 2019 19:636A subtype of oral, laryngeal, esophageal, and lung, squamous cell carcinoma with high levels of TrkB-T1 neurotrophin receptor mRNA
The NTRK2 genetic locus encodes neurotrophin membrane receptors that play an important role in normal neural tissue plasticity, growth, and survival. One NTRK2-encoded protein is TrkB-FL, which can regulate mu...BMC Cancer 2019 19:607Circulating tumor cell and cell-free RNA capture and expression analysis identify platelet-associated genes in metastatic lung cancer
Circulating tumor cells (CTC) and plasma cell-free RNA (cfRNA) can serve as biomarkers for prognosis and treatment response in lung cancer. One barrier to the selected or routine use of CTCs and plasma cfRNA i...BMC Cancer 2019 19:603Computational analysis of receptor tyrosine kinase inhibitors and cancer metabolism: implications for treatment and discovery of potential therapeutic signatures
Receptor tyrosine kinase (RTK) inhibitors are frequently used to treat cancers and the results have been mixed, some of these small molecule drugs are highly successful while others show a more modest response...BMC Cancer 2019 19:600Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma
Cancer patients with advanced disease routinely exhaust available clinical regimens and lack actionable genomic medicine results, leaving a large patient population without effective treatments options when th...BMC Cancer 2019 19:593Exploring serum and immunoglobulin G N-glycome as diagnostic biomarkers for early detection of breast cancer in Ethiopian women
Alterations in protein glycosylation patterns have potentially been targeted for biomarker discovery in a wide range of diseases including cancer. Although there have been improvements in patient diagnosis and...BMC Cancer 2019 19:588
The value of 3D visualization operative planning system in ultrasound-guided percutaneous microwave ablation for large hepatic hemangiomas: a clinical comparative study
To evaluate the value of a three dimension (3D)visualization operative planning system in ultrasound-guided percutaneous microwave ablation (US-PMWA) for large hepatic hemangiomas (LHHs).BMC Cancer 2019 19:550Impact of body mass index and fat distribution on sex steroid levels in endometrial carcinoma: a retrospective study
Obesity is an important cause of multiple cancer types, amongst which endometrial cancer (EC). The relation between obesity and cancer is complicated and involves alterations in insulin metabolism, response to...BMC Cancer 2019 19:547Stochastic modelling of tyrosine kinase inhibitor rotation therapy in chronic myeloid leukaemia
Resistance towards targeted cancer treatments caused by single nucleotide variations is a major issue in many malignancies. Currently, there are a number of available drugs for chronic myeloid leukaemia (CML),...BMC Cancer 2019 19:508How many samples are needed to infer truly clonal mutations from heterogenous tumours?
Modern cancer treatment strategies aim to target tumour specific genetic (or epigenetic) alterations. Treatment response improves if these alterations are clonal, i.e. present in all cancer cells within tumour...BMC Cancer 2019 19:403Protein interaction disruption in cancer
Most methods that integrate network and mutation data to study cancer focus on the effects of genes/proteins, quantifying the effect of mutations or differential expression of a gene and its neighbors, or iden...BMC Cancer 2019 19:370Differential proteomic comparison of breast cancer secretome using a quantitative paired analysis workflow
Worldwide, breast cancer is the main cause of cancer mortality in women. Most cases originate in mammary ductal cells that produce the nipple aspirate fluid (NAF). In cancer patients, this secretome contains p...BMC Cancer 2019 19:365A novel microfluidic device capable of maintaining functional thyroid carcinoma specimens ex vivo provides a new drug screening platform
Though the management of malignancies has improved vastly in recent years, many treatment options lack the desired efficacy and fail to adequately augment patient morbidity and mortality. It is increasingly cl...BMC Cancer 2019 19:259Molecular tumor analysis and liquid biopsy: a feasibility investigation analyzing circulating tumor DNA in patients with central nervous system lymphomas
Central nervous system lymphomas (CNSL) is a devastating disease. Currently, a confirmatory biopsy is required prior to treatment.BMC Cancer 2019 19:192Different next-generation sequencing pipelines based detection of tumor DNA in cerebrospinal fluid of lung adenocarcinoma cancer patients with leptomeningeal metastases
The nucleic acid mutation status in intracranial metastasis is markedly significant clinically. The goal of the current study was to explore whether the tumor-associated mutations can be detected by different ...BMC Cancer 2019 19:143Development of a miRNA-seq based prognostic signature in lung adenocarcinoma
We utilized miRNAs expression and clinical data to develop a prognostic signature for patients with lung adenocarcinoma, with respect to their overall survival, to identify high-risk subjects based on their mi...BMC Cancer 2019 19:34OMCD: OncomiR Cancer Database
microRNAs (miRNAs) are crucially important in the development of cancer. Their dysregulation, commonly observed in various types of cancer, is largely cancer-dependent. Thus, to understand the tumor biology an...BMC Cancer 2018 18:1223Factors associated with high-risk HPV infection and cervical cancer screening methods among rural Uyghur women aged > 30 years in Xinjiang
Cervical cancer is the most common genital malignant tumor in women worldwide. However, the reliability of different detection methods may vary according to populations and epidemics. This study analyzed facto...BMC Cancer 2018 18:1162The predictive powers of plasma trefoil factor 3 or its related micro RNAs for patients with hepatocellular carcinoma
Earlier diagnosis is beneficial for the prognosis of hepatocellular carcinoma (HCC). Alpha fetoprotein (AFP) is the most widely used biomarker for HCC, but its sensitivity and specificity are only 60 and 90%, ...BMC Cancer 2018 18:1110Inflammation marker ESR is effective in predicting outcome of diffuse large B-cell lymphoma
Systemic inflammation has been implicated in cancer development and progression. This study examined the best cutoff value of erythrocyte sedimentation rate (ESR) in diffuse large B-cell lymphoma (DLBCL) patie...BMC Cancer 2018 18:997The plasma glutamate concentration as a complementary tool to differentiate benign PET-positive lung lesions from lung cancer
Pulmonary imaging often identifies suspicious abnormalities resulting in supplementary diagnostic procedures. This study aims to investigate whether the metabolic fingerprint of plasma allows to discriminate b...BMC Cancer 2018 18:868An in-silico study examining the induction of apoptosis by Cryptotanshinone in metastatic melanoma cell lines
Metastatic melanoma is an aggressive form of skin cancer that evades various anti-cancer treatments including surgery, radio-,immuno- and chemo-therapy. TRAIL-induced apoptosis is a desirable method to treat m...BMC Cancer 2018 18:855Early detection of colorectal adenocarcinoma: a clinical decision support tool based on plasma porphyrin accumulation and risk factors
An increase in naturally-occurring porphyrins has been described in the blood of subjects bearing different kinds of tumors, including colorectal, and this is probably related to a systemic alteration of heme ...BMC Cancer 2018 18:841
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