scholarly journals Onco-Multi-OMICS Approach: A New Frontier in Cancer Research

2018 ◽  
Vol 2018 ◽  
pp. 1-14 ◽  
Author(s):  
Sajib Chakraborty ◽  
Md. Ismail Hosen ◽  
Musaddeque Ahmed ◽  
Hossain Uddin Shekhar
Keyword(s):  
Cancer Research ◽  
Systems Biology ◽  
Cancer Cells ◽  
Cellular Response ◽  
Molecular Mechanisms ◽  
The Cancer Genome Atlas ◽  
Resolving Power ◽  
Cancer Hallmarks ◽  
Molecular Alterations ◽  
Integrated Omics

The acquisition of cancer hallmarks requires molecular alterations at multiple levels including genome, epigenome, transcriptome, proteome, and metabolome. In the past decade, numerous attempts have been made to untangle the molecular mechanisms of carcinogenesis involving single OMICS approaches such as scanning the genome for cancer-specific mutations and identifying altered epigenetic-landscapes within cancer cells or by exploring the differential expression of mRNA and protein through transcriptomics and proteomics techniques, respectively. While these single-level OMICS approaches have contributed towards the identification of cancer-specific mutations, epigenetic alterations, and molecular subtyping of tumors based on gene/protein-expression, they lack the resolving-power to establish the casual relationship between molecular signatures and the phenotypic manifestation of cancer hallmarks. In contrast, the multi-OMICS approaches involving the interrogation of the cancer cells/tissues in multiple dimensions have the potential to uncover the intricate molecular mechanism underlying different phenotypic manifestations of cancer hallmarks such as metastasis and angiogenesis. Moreover, multi-OMICS approaches can be used to dissect the cellular response to chemo- or immunotherapy as well as discover molecular candidates with diagnostic/prognostic value. In this review, we focused on the applications of different multi-OMICS approaches in the field of cancer research and discussed how these approaches are shaping the field of personalized oncomedicine. We have highlighted pioneering studies from “The Cancer Genome Atlas (TCGA)” consortium encompassing integrated OMICS analysis of over 11,000 tumors from 33 most prevalent forms of cancer. Accumulation of huge cancer-specific multi-OMICS data in repositories like TCGA provides a unique opportunity for the systems biology approach to tackle the complexity of cancer cells through the unification of experimental data and computational/mathematical models. In future, systems biology based approach is likely to predict the phenotypic changes of cancer cells upon chemo-/immunotherapy treatment. This review is sought to encourage investigators to bring these different approaches together for interrogating cancer at molecular, cellular, and systems levels.

scholarly journals The Impact of Age and Sex in DLBCL: Systems Biology Analyses Identify Distinct Molecular Changes and Signaling Networks

2015 ◽  
Vol 14 ◽  
pp. CIN.S34144 ◽  
Author(s):  
Afshin Beheshti ◽  
Donna Neuberg ◽  
J. Tyson Mcdonald ◽  
Charles R. Vanderburg ◽  
Andrew M. Evens
Keyword(s):  
Systems Biology ◽  
Tumor Progression ◽  
B Cell Lymphoma ◽  
The Cancer Genome Atlas ◽  
Young Females ◽  
Molecular Alterations ◽  
Cancer Genome Atlas ◽  
Male Patients ◽  
The Impact ◽  
Age And Sex

Potential molecular alterations based on age and sex are not well defined in diffuse large B-cell lymphoma (DLBCL). We examined global transcriptome DLBCL data from The Cancer Genome Atlas (TCGA) via a systems biology approach to determine the molecular differences associated with age and sex. Collectively, sex and age revealed striking transcriptional differences with older age associated with decreased metabolism and telomere functions and female sex was associated with decreased interferon signaling, transcription, cell cycle, and PD-1 signaling. We discovered that the key genes for most groups strongly regulated immune function activity. Furthermore, older females were predicted to have less DLBCL progression versus older males and young females. Finally, analyses in systems biology revealed that JUN and CYCS signaling were the most critical factors associated with tumor progression in older and male patients. We identified important molecular perturbations in DLBCL that were strongly associated with age and sex and were predicted to strongly influence tumor progression.

scholarly journals Role of acidic tumor microenvironment in tumor pathogenesis and targeting

2020 ◽  
pp. 34-40
Author(s):  
Vishal Sharma ◽  
Chhaya Bawa ◽  
Kuldeep Chand Vatsyan
Keyword(s):  
Cell Growth ◽  
Tumor Microenvironment ◽  
Cancer Cells ◽  
Molecular Mechanisms ◽  
Physiological State ◽  
Therapeutic Interventions ◽  
Cancer Cell Growth ◽  
Molecular Alterations ◽  
Cancer Pathogenesis

Extensive efforts are going on to understand the molecular mechanisms behind tumor initiation, progression, and invasion and find novel targets for cancer treatment. The physiological state of the tumor microenvironment (TME) is crucial to every step of tumor cell growth and angiogenesis. Cancer cells are rarely in contact with each other. The intervening medium between the cancer cells, immune cells, and other cells become acidic, which significantly affects cancer pathogenesis. It could be a novel targeting marker and may help treat tumors. Even after extensive research in this area, the nature of molecular alterations and the basic mechanisms in the tumor microenvironment remains unclear. Based on recent studies of TME, this mini-review bids a more inclusive overview of the role of TME in cancer cell growth. Also, it helps to understand the potential of TME for therapeutic interventions.

scholarly journals The Circadian Protein PER1 Modulates the Cellular Response to Anticancer Treatments

2021 ◽  
Vol 22 (6) ◽  
pp. 2974
Author(s):  
Marina Maria Bellet ◽  
Claudia Stincardini ◽  
Claudio Costantini ◽  
Marco Gargaro ◽  
Stefania Pieroni ◽  
...  
Keyword(s):  
Circadian Rhythms ◽  
Circadian Clock ◽  
Cancer Cells ◽  
Cellular Response ◽  
Molecular Mechanisms ◽  
Antitumor Agents ◽  
Pharmacological Therapy ◽  
Drug Induced

The circadian clock driven by the daily light–dark and temperature cycles of the environment regulates fundamental physiological processes and perturbations of these sophisticated mechanisms may result in pathological conditions, including cancer. While experimental evidence is building up to unravel the link between circadian rhythms and tumorigenesis, it is becoming increasingly apparent that the response to antitumor agents is similarly dependent on the circadian clock, given the dependence of each drug on the circadian regulation of cell cycle, DNA repair and apoptosis. However, the molecular mechanisms that link the circadian machinery to the action of anticancer treatments is still poorly understood, thus limiting the application of circadian rhythms-driven pharmacological therapy, or chronotherapy, in the clinical practice. Herein, we demonstrate the circadian protein period 1 (PER1) and the tumor suppressor p53 negatively cross-regulate each other’s expression and activity to modulate the sensitivity of cancer cells to anticancer treatments. Specifically, PER1 physically interacts with p53 to reduce its stability and impair its transcriptional activity, while p53 represses the transcription of PER1. Functionally, we could show that PER1 reduced the sensitivity of cancer cells to drug-induced apoptosis, both in vitro and in vivo in NOD scid gamma (NSG) mice xenotransplanted with a lung cancer cell line. Therefore, our results emphasize the importance of understanding the relationship between the circadian clock and tumor regulatory proteins as the basis for the future development of cancer chronotherapy.

scholarly journals Macrophages induce inflammation by efferocytosis of apoptotic prostate cancer cells via HIF-1α stabilization

2021 ◽  
Author(s):  
Veronica Mendoza-Reinoso ◽  
Patricia M Schnepp ◽  
Dah Youn Baek ◽  
John R Rubin ◽  
Ernestina Schipani ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Cancer Cells ◽  
Cellular Response ◽  
Molecular Mechanisms ◽  
Cytokine Gene Expression ◽  
Prostate Cancer Cells ◽  
Significant Enrichment ◽  
Hif Prolyl Hydroxylase ◽  
Phosphorylated Stat3 ◽  
Pro Inflammatory Cytokines

Clearance of apoptotic cancer cells by macrophages, known as efferocytosis, fuels the bone-metastatic growth of prostate cancer cells via pro-inflammatory and immunosuppressive processes. However, the exact molecular mechanisms remain unclear. In this study, single-cell transcriptomics of bone marrow macrophages undergoing efferocytosis of apoptotic prostate cancer cells revealed a significant enrichment of a cellular response to hypoxia. Here we show that efferocytic macrophages promote HIF-1α stabilization under normoxic conditions through interaction with phosphorylated STAT3. Inflammatory cytokine gene expression analysis of efferocytic HIF-1α-mutant macrophages revealed a reduced expression of the pro-tumorigenic Mif. Furthermore, stabilization of HIF-1α using the HIF-prolyl-hydroxylase inhibitor, Roxadustat, enhanced MIF expression in macrophages. Finally, macrophages treated with recombinant MIF protein activated NF-κB (p65) signaling and increased the expression of pro-inflammatory cytokines. Altogether, these findings suggest that the clearance of apoptotic cancer cells by tumor-associated macrophages triggers p-STAT3/HIF-1α/MIF signaling to enhance tumor-promoting inflammation in bone, suggesting this axis as a target for metastatic prostate cancer.

scholarly journals Pan-Cancer Analysis of Molecular Characteristics and Oncogenic Role of PRMT5 in Human Cancers

2021 ◽  
Author(s):  
He Liu ◽  
Lexi Huang ◽  
Kunpeng Jia ◽  
Xiaohua Pan
Keyword(s):  
Breast Cancer ◽  
Cancer Cells ◽  
Breast Cancer Cells ◽  
Molecular Mechanisms ◽  
The Cancer Genome Atlas ◽  
Cancer Development ◽  
Nuclear Antigen ◽  
Molecular Characteristics ◽  
Importance Value ◽  
Pan Cancer

Abstract Background Accumulating evidence supports the correlation of protein arginine methyltransferase 5 (PRMT5) and cancers development. However, the expression and prognostic values of PRMT5 in various cancers have not been clarified. Methods Here, based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets, we performed a pan-cancer analysis to explore the expression profile , prognostic value landscape, relationship with tumor-infiltrating immune cells, and potential molecular mechanisms of PRMT5 in cancer development. Moreover, CCK8, wound healing and transwell assays, and western blotting analysis were conducted to evaluate how PRMT5 affects the proliferation and migration, and expression of related hallmarks in breast cancer cells. Results We found that PRMT5 was upregulated in most cancers and PRMT5 harbored distinct prognostic values across different cancer types. In addition, PRMT5 expression was negatively correlated with CD8 + T cells in tumors of cervical squamous cell carcinoma and endocervical adenocarcinoma (CSEC) and Skin Cutaneous Melanoma (SKCM), and positively correlated with the cancer-associated fibroblasts in tumors of adrenocortical carcinoma, CESC, cholangio carcinoma, liver hepatocellular carcinoma, pancreatic adenocarcinoma, and SKCM-Primary. Moreover, the enrichment analysis identified that PRMT5 mechanistically regulated cancers development by acting on DNA and RNA metabolism, and stress response related pathways. By further gene silencing experiment, we confirmed tha t PRMT5 knockdown reduced the proliferative and migrative capacities, as well as the expression of PCNA (proliferating cell nuclear antigen), p21 and HMGB1 (high mobility group box 1 protein) in breast cancer cells. Conclusion Collectively, our pan-cancer study highlighted the importance value of PRMT5 in cancer development and prognosis, and pharmacologic targeting at PRMT5 may provide a novel approach for the treatment of cancers.

scholarly journals Microbial Systems Ecology to Understand Cross-Feeding in Microbiomes

2021 ◽  
Vol 12 ◽  
Author(s):  
Victor Mataigne ◽  
Nathan Vannier ◽  
Philippe Vandenkoornhuyse ◽  
Stéphane Hacquard
Keyword(s):  
Microbial Community ◽  
Systems Biology ◽  
Microbial Communities ◽  
Molecular Mechanisms ◽  
Microbial Community Composition ◽  
Systems Ecology ◽  
New Concepts ◽  
Integrated Omics ◽  
Genome Scale ◽  
Microbial Systems

Understanding how microorganism-microorganism interactions shape microbial assemblages is a key to deciphering the evolution of dependencies and co-existence in complex microbiomes. Metabolic dependencies in cross-feeding exist in microbial communities and can at least partially determine microbial community composition. To parry the complexity and experimental limitations caused by the large number of possible interactions, new concepts from systems biology aim to decipher how the components of a system interact with each other. The idea that cross-feeding does impact microbiome assemblages has developed both theoretically and empirically, following a systems biology framework applied to microbial communities, formalized as microbial systems ecology (MSE) and relying on integrated-omics data. This framework merges cellular and community scales and offers new avenues to untangle microbial coexistence primarily by metabolic modeling, one of the main approaches used for mechanistic studies. In this mini-review, we first give a concise explanation of microbial cross-feeding. We then discuss how MSE can enable progress in microbial research. Finally, we provide an overview of a MSE framework mostly based on genome-scale metabolic-network reconstruction that combines top-down and bottom-up approaches to assess the molecular mechanisms of deterministic processes of microbial community assembly that is particularly suitable for use in synthetic biology and microbiome engineering.

Molecular Mechanisms Involved in the Antitumor Activity of Isolated Lectins from Marine Organisms: A Systematic Review

2020 ◽  
Vol 21 (6) ◽  
pp. 616-625
Author(s):  
Hugo Jefferson Ferreira ◽  
Evandro Moreira de Almeida ◽  
Wildson Max Barbosa da Silva ◽  
Edson Holanda Teixeira ◽  
Luiz Gonzaga do Nascimento Neto
Keyword(s):  
Systematic Review ◽  
Antitumor Activity ◽  
Cancer Cells ◽  
Molecular Mechanisms ◽  
Marine Organisms ◽  
Mitogen Activated Protein Kinase ◽  
Sialyl Lewis X ◽  
Molecular Alterations ◽  
Mitogen Activated Protein ◽  
Complex Glycans

Introduction: Tumor cells may present several molecular alterations that favor their malignancy, among which there is the expression of tumor-related antigens, such as truncated T-glycans, Thomsen-nouvelle, sialyl-Lewis X and sialyl Tn, which may help in the diagnosis and treatment using specific target molecules. Lectins are ubiquitous proteins capable of interacting with specific carbohydrates. Lectins isolated from marine organisms have important characteristics such as low immunogenicity and can bind to complex glycans compared to plant lectins. Objective: This work evaluated, through a systematic review, the molecular mechanisms of antitumor activity of lectins isolated from marine organisms. Methodology: The Pubmed, Lilacs, Science Direct, Wiley and Scopus databases were reviewed using the descriptors: marine lectin and cancer. Articles in English, published between January 2008 and December 2018, which proposed the molecular mechanisms of anticancer activity of lectins from marine organisms were eligible for the study. Results: 17 articles were eligible. The lectins showed promising performance against cancer cells, presenting specific cytotoxicity for some types of malignant cells. The articles presented several lectins specific to different carbohydrates, modulating: pro and anti-apoptotic proteins, transcription factor E2F-1, via mitogen-activated protein kinase. In addition, exogenous lectin expression in cancer cells has been shown to be a promising way to treat cancer. Conclusion: This review showed the various studies that described the molecular mechanisms caused by marine lectins with antineoplastic potential. This knowledge is relevant for the development and use of the next generations of lectins isolated from marine organisms, supporting their potential in cancer treatment.

scholarly journals Long non-coding RNA ZFAS1 promotes pancreatic cancer proliferation and metastasis by sponging miR-497-5p to regulate HMGA2 expression

2021 ◽  
Vol 12 (10) ◽  
Author(s):  
Min Rao ◽  
Song Xu ◽  
Yong Zhang ◽  
Yifan Liu ◽  
Wenkang Luan ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Cancer Cells ◽  
Molecular Mechanisms ◽  
Biological Effects ◽  
The Cancer Genome Atlas ◽  
Luciferase Reporter ◽  
Cancer Data ◽  
Pancreatic Cancer Cells ◽  
Cancer Tissues

AbstractThe lncRNA ZFAS1 plays a carcinogenic regulatory role in many human tumours, but it is rarely reported in pancreatic cancer. We identify the role and molecular mechanisms of ZFAS1 in pancreatic cancer. The expression of ZFAS1, miR-497-5p and HMGA2 in pancreatic cancer tissues was detected by qRT-PCR. Pancreatic cancer data in The Cancer Genome Atlas were also included in this study. CCK8, EdU, transwell and scratch wound assays were used to investigate the biological effects of ZFAS1 in pancreatic cancer cells. MS2-RIP, RNA pull-down, RNA-ChIP and luciferase reporter assays were used to clarify the molecular biological mechanisms of ZFAS1 in pancreatic cancer. The role of ZFAS1 in vivo was also confirmed via xenograft experiments. ZFAS1 was overexpressed in pancreatic cancer tissues. ZFAS1 promoted the growth and metastasis of pancreatic cancer cells, and miR-497-5p acted as a tumour suppressor gene in pancreatic cancer by targeting HMGA2. We also demonstrated that ZFAS1 exerts its effects by promoting HMGA2 expression through decoying miR-497-5p. We also found that ZFAS1 promoted the progression of pancreatic cancer in vivo by modulating the miR-497-5p/HMGA2 axis. In conclusion, this study revealed a new role for and the molecular mechanisms of ZFAS1 in pancreatic cancer, identifying ZFAS1 as a novel target for the diagnosis and treatment of pancreatic cancer.

Effects and Mechanisms of Anlotinib and Dihydroartemisinin Combination Therapy in Ameliorating Malignant Biological Behavior of Gastric Cancer Cells

2020 ◽  
Vol 21 ◽  
Author(s):  
Qiong Luo ◽  
Suyun Zhang ◽  
Donghuan Zhang ◽  
Rui Feng ◽  
Nan Li ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Cancer Cells ◽  
Molecular Mechanisms ◽  
Chorioallantoic Membrane ◽  
Cell Counting ◽  
Biological Behavior ◽  
Gastric Cancer Cells ◽  
Invasion And Migration ◽  
Apoptosis Related Protein ◽  
And Migration

Background: Gastric cancer(GC) is currently one of the major malignancies that threatens human lives and health. Anlotinib is a novel small-molecule that inhibits angiogenesis to exert anti-tumor effects. However, the function in gastric cancer is incompletely understood. Objective: The aim of the present study was to investigate the anti-tumor effects and molecular mechanisms of anlotinib combined with dihydroartemisinin (DHA) in SGC7901 gastric cancer cells. Method: Different concentrations of anlotinib and DHA were used to treat SGC7901 gastric cancer cells, after which cell proliferation was measured. Drug interactions of anlotinib and DHA were analyzed by the Chou-Talalay method with CompuSyn software. proliferation, apoptosis, invasion, migration, and angiogenesis were measured using the cell counting kit-8 (CCK8) assay, flow cytometry, Transwell invasion assays, scratch assays, and chicken chorioallantoic membrane (CAM) assays. proliferation-associated protein (Ki67), apoptosis-related protein (Bcl-2), and vascular endothelial growth factor A (VEGF-A) were quantified by Western bloting. Results: The combination of 2.5 μmol/L of anlotinib and 5 of μmol/L DHA was highly synergistic in inhibiting cell growth, significantly increased the apoptosis rate and suppressed obviously the invasion and migration capability and angiogenesis of gastric cancer cells. In addition, the expression levels of Ki67, Bcl-2, and VEGF-A, as well as angiogenesis, were significantly decreased in the Combination of drugs compared with in control and either drug alone. Conclusion: The combination of anlotinib and DHA showed synergistic antitumor activity, suggesting their potential in treating patients with gastric cancer.

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