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Multi-Omics Model Applied to Cancer Genetics

Francesco Pettini, Anna Visibelli, Vittoria Cicaloni, Daniele Iovinelli, Ottavia Spiga
2021 International Journal of Molecular Sciences  
In fact, it is essential to providing general theoretical information on genomics, epigenomics, and transcriptomics to understand the phases of multi-omics approach.  ...  We consider how to create a multi-omics model. In the last section, we describe the new frontiers and future perspectives of this field.  ...  Hypermethylation of CpG islands in the promoter region of a tumor suppressor or otherwise cancer-related gene is often associated with transcriptional silencing of the related gene.  ... 
doi:10.3390/ijms22115751 pmid:34072237 fatcat:xo4fgxhu5faupcvs4oi3yvbywy

The current issues and future perspective of artificial intelligence for developing new treatment strategy in non-small cell lung cancer: harmonization of molecular cancer biology and artificial intelligence

Ichidai Tanaka, Taiki Furukawa, Masahiro Morise
2021 Cancer Cell International  
However, integrated analysis of multi-omics data is extremely labor intensive, making the development of new analysis technology indispensable.  ...  Recently, a variety of new findings have been reported based on multi-omics analysis in combination with various clinical information.  ...  Acknowledgements The authors would like to thank Enago (www. enago. jp) for the English language review.  ... 
doi:10.1186/s12935-021-02165-7 pmid:34446006 pmcid:PMC8393743 fatcat:ksvydxnfnnehfno2qbtdeagcgm

Molecular subtyping of colorectal cancer: Recent progress, new challenges and emerging opportunities

Wei Wang, Raju Kandimalla, Hao Huang, Lina Zhu, Ying Li, Feng Gao, Ajay Goel, Xin Wang
2018 Seminars in Cancer Biology  
Also prominent in CRC are mutations in the TP53 tumor suppressor gene, which play a crucial role in cell proliferation and apoptosis [45, 46] .  ...  A more precise understanding of the biological properties that distinguish patients with colorectal tumors, especially in terms of their clinical features, is a key requirement towards a more robust, targeted-drug  ...  A major difference is that most sporadic MSI tumors evolve via hypermethylation of the MLH1 gene promoter, while Lynch syndrome tumors primarily acquire MSI through germline mutations in one of the MMR  ... 
doi:10.1016/j.semcancer.2018.05.002 pmid:29775690 pmcid:PMC6240404 fatcat:jtfffdfoznenfmigdydgekqxby

Current Insights and Advancements in Head and Neck Cancer: Emerging Biomarkers and Therapeutics with Cues from Single Cell and 3D Model Omics Profiling

Yashika Jawa, Pooja Yadav, Shruti Gupta, Sivapar V Mathan, Jyoti Pandey, Ajay K Saxena, Suneel Kateriya, Ashu B Tiku, Neelima Mondal, Jaydeep Bhattacharya, Shandar Ahmad, Rupesh Chaturvedi (+3 others)
2021 Frontiers in Oncology  
Bioinformatic tools are used for study of differentially expressed genes and further omics data analysis.  ...  In the final analysis, this review suggests that the development of improved target-specific personalized therapies can combat HNC's global plight.  ...  ACKNOWLEDGMENTS We would like to thank Souvik Sur, Ritish Syanti, Titas Mondal and Ashwani for contribution to the ideas in the manuscript.  ... 
doi:10.3389/fonc.2021.676948 pmid:34490084 pmcid:PMC8418074 fatcat:vv54u3q4e5f4vlha35a4bk2ma4

The Role of Network Science in Glioblastoma

Marta B Lopes, Eduarda P Martins, Susana Vinga, Bruno M Costa
2021 Cancers  
In the particular case of cancer genomics, network discovery is challenged by the multitude of available high-dimensional heterogeneous views of data.  ...  Identifying the architecture of molecular GBM networks is essential to understanding the information flow and better informing drug development and pre-clinical studies.  ...  cancer subtype identification from multi-omics data, which are obtained by combining features' ranking in the network and their expression variation.  ... 
doi:10.3390/cancers13051045 pmid:33801334 pmcid:PMC7958335 fatcat:24qpogtftvekvekcvkx6luqie4

Omics analyses provide insights to CART cell therapy resistance

Michelle J. Cox, Saad S. Kenderian
2021 Journal of Translational Genetics and Genomics  
Resistance to CART cell therapy can be mediated by the cancer cells, the tumor microenvironment, or the patient's T cells.  ...  In this review, we will outline lessons learned from multi-omics studies (1) to identify biomarkers of response or toxicity to CART cell therapy or (2) to develop biomarker-guided therapeutic interventions  ...  It was not until the 1970s that we began to link these changes to specific genes.  ... 
doi:10.20517/jtgg.2021.06 fatcat:fwvsbiypfzawpf2rcozsv5qo2e

Epigenome dysregulation in cholangiocarcinoma

Colm J. O'Rourke, Patricia Munoz-Garrido, Esmeralda L. Aguayo, Jesper B. Andersen
2018 Biochimica et Biophysica Acta - Molecular Basis of Disease  
Epigenomics is a fast-evolving field of research that has lately attracted considerable interest, mainly due to the reversibility of epigenetic marks.  ...  Clinically, among solid tumors, the field is still limited.  ...  This region is commonly deleted in different cancers and contains many tumor suppressor genes.  ... 
doi:10.1016/j.bbadis.2017.06.014 pmid:28645654 fatcat:c7lcwcicjrh2tenwguo74kzk6m

Precision Medicine: An Optimal Approach to Patient Care in Renal Cell Carcinoma

Revati Sharma, George Kannourakis, Prashanth Prithviraj, Nuzhat Ahmed
2022 Frontiers in Medicine  
Renal cell cancer (RCC) is a heterogeneous tumor that shows both intra- and inter-heterogeneity.  ...  It is anticipated that combined efforts from all sectors involved will make PM accessible to RCC and other patients with cancer, making a tremendous positive leap on individualized treatment strategies  ...  TABLE 1 | 1 Description of multi-omics data repositories related to cancer.  ... 
doi:10.3389/fmed.2022.766869 pmid:35775004 pmcid:PMC9237320 fatcat:2qy6l5ujmneedbzzcnf4lkmceu

Tumor Profiling at the Service of Cancer Therapy

Ceres Fernandez-Rozadilla, Ana Rita Simões, Matilde E. Lleonart, Amancio Carnero, Ángel Carracedo
2021 Frontiers in Oncology  
Cancer treatment options have evolved significantly in the past few years.  ...  In this review, we will focus on how tumor profiling has evolved over the past decades to deliver more efficient and personalized treatment options, and how novel technologies can help us envisage the  ...  Research on oncogenes and tumor suppressor genes (the two main types of genes in which mutations drive cancer development) has been strongly active since the first description of a cancer-causing mutation  ... 
doi:10.3389/fonc.2020.595613 pmid:33505911 pmcid:PMC7832432 fatcat:vvklzjond5d6fcbcnl33er6jk4

Cancer cell metabolism as new targets for novel designed therapies

Igor Marín de Mas, Esther Aguilar, Anusha Jayaraman, Ibrahim H Polat, Alfonso Martín-Bernabé, Rohit Bharat, Carles Foguet, Enric Milà, Balázs Papp, Josep J Centelles, Marta Cascante
2014 Future Medicinal Chemistry  
process of tumor development: the capability to sustain proliferative signaling, resistance to cell death, evasion of growth suppression, ability of replicative immortality, tumor-promoting inflammation  ...  The advent of high-throughput technologies to amass an abundance of omic data, together with the development of new computational methods that allow the integration and analysis of omic data by using genome-scale  ...  process of tumor development: the capability to sustain proliferative signaling, resistance to cell death, evasion of growth suppression, ability of replicative immortality, tumor-promoting inflammation  ... 
doi:10.4155/fmc.14.119 fatcat:cn2xqoern5do5op3bb3t4g2xda

Precision Medicine and Melanoma: Multi-Omics Approaches to Monitoring the Immunotherapy Response

Fabio Valenti, Italia Falcone, Sara Ungania, Flora Desiderio, Patrizio Giacomini, Chiara Bazzichetto, Fabiana Conciatori, Enzo Gallo, Francesco Cognetti, Gennaro Ciliberto, Aldo Morrone, Antonino Guerrisi
2021 International Journal of Molecular Sciences  
processes underlying the biology of cancer; therefore, improving the tumor clinical management.  ...  The recent multi-omics analyses (genomics, transcriptomics, proteomics, metabolomics, radiomics, etc.) and the technological evolution of data interpretation have allowed to identify and understand several  ...  PTEN is an important tumor suppressor gene involved in cell growth, survival, and cell motility.  ... 
doi:10.3390/ijms22083837 pmid:33917181 pmcid:PMC8067863 fatcat:l273buhckbe3tkcitxmpcasfie

Knowledge-driven genomic interactions: an application in ovarian cancer

Dokyoon Kim, Ruowang Li, Scott M Dudek, Alex T Frase, Sarah A Pendergrass, Marylyn D Ritchie
2014 BioData Mining  
Further, single-gene expression outcome prediction is limited for cancer evaluation since genes do not act in isolation, but rather interact with other genes in complex signaling or regulatory networks  ...  Effective cancer clinical outcome prediction for understanding of the mechanism of various types of cancer has been pursued using molecular-based data such as gene expression profiles, an approach that  ...  The results published here are in whole or part based upon data generated by The Cancer Genome Atlas pilot project established by the NCI and NHGRI.  ... 
doi:10.1186/1756-0381-7-20 pmid:25214892 pmcid:PMC4161273 fatcat:mx32nzzcnjdfpe3fuz3rpbb764

Molecular Classification of Renal Cell Carcinoma and Its Implication in Future Clinical Practice

Jozefina Casuscelli, Yann-Alexandre Vano, Wolf Herve Fridman, James J. Hsieh
2017 Kidney Cancer  
Here, we attempt to classify ccRCC based on contemporary molecular features with emphasis on their respective potential significance in clinical practice.  ...  Metastatic RCC (mRCC) is lethal and refractory to conventional chemotherapeutic agents.  ...  The gene set used to classify RCC tumors in ccA/ccB was then optimized and simplified by Brooks and colleagues using a centroid-based classification algorithm (called prediction analysis of microarray  ... 
doi:10.3233/kca-170008 pmid:30334000 pmcid:PMC6179110 fatcat:rdvdb3ivffcbdmtti6zfsccfpe

Immune-Related Mutational Landscape and Gene Signatures: Prognostic Value and Therapeutic Impact for Head and Neck Cancer

Bohai Feng, Jochen Hess
2021 Cancers  
This review aims to provide a holistic view on how the immune landscape dictates the tumor fate and vice versa, and how integrative analysis of multi-omics data contribute to our current knowledge on the  ...  The availability of multi-omics data and emerging computational technologies facilitate not only a deeper understanding of the cellular composition in the tumor immune microenvironment but also enables  ...  Conclusions and Perspectives The integrative analysis of multi-omics data is a powerful tool to elucidate immunerelated cellular and molecular profiles with a strong impact on cancer immune escape and  ... 
doi:10.3390/cancers13051162 pmid:33800421 pmcid:PMC7962834 fatcat:yak7rpzm6rbljchqjpgqfquimi

Liquid Biopsy Based Circulating Biomarkers in Metastatic Prostate Cancer

Eshwari Dathathri, Khrystany T. Isebia, Fikri Abali, Martijn P. Lolkema, John W. M. Martens, Leon W. M. M. Terstappen, Ruchi Bansal
2022 Frontiers in Oncology  
castration sensitive prostate cancer (mCSPC) and castration resistant prostate cancer (mCRPC).  ...  secretome from (circulating) tumor cells and tumor microenvironment in metastatic prostate cancer.  ...  Job van Riet for his contribution to section 2.2 Genetic biomarkers.  ... 
doi:10.3389/fonc.2022.863472 pmid:35669415 pmcid:PMC9165750 fatcat:fxk6m5hvtnemlnw7zkdbsf3boy
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