{"title":"Novel omics technology driving translational research in precision oncology.","authors":"Anubhav Basu, Anshul Budhraja, Juwayria, Dasari Abhilash, Ishaan Gupta","doi":"10.1016/bs.adgen.2021.08.003","DOIUrl":"https://doi.org/10.1016/bs.adgen.2021.08.003","url":null,"abstract":"<p><p>In this review, we summarize the current challenges faced by cancer researchers and motivate the use of novel genomics solutions. We follow this up with a comprehensive overview of three recent genomics technologies: liquid biopsy, single-cell RNA sequencing and spatial transcriptomics. We discuss a few representative protocols/assays for each technology along with their strengths, weaknesses, optimal use-cases, and their current stage of clinical deployment by summarizing trial data. We focus on how these technologies help us develop a better understanding of cancer as a rapidly evolving heterogeneous genetic disease that modulates its immediate microenvironment leading to systemic macro-level changes in the patient body. We summarize the review with a flowchart that integrates these three technologies in the existing workflows of clinicians and researchers toward robust detection, accurate diagnosis, and precision oncology.</p>","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":" ","pages":"81-145"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39789673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Advances in GeneticsPub Date : 2021-01-01Epub Date: 2021-10-23DOI: 10.1016/bs.adgen.2021.08.002
Prashant Mehta, Sneha J Bothra
{"title":"PARP inhibitors in hereditary breast and ovarian cancer and other cancers: A review.","authors":"Prashant Mehta, Sneha J Bothra","doi":"10.1016/bs.adgen.2021.08.002","DOIUrl":"https://doi.org/10.1016/bs.adgen.2021.08.002","url":null,"abstract":"<p><p>There has been a paradigm shift in the management of cancer, with the immense progress in cancer genomics. More and more targeted therapies are becoming available by the day and personalized medicine is becoming popular with specific drugs being designed for selected subgroups of patients. One such new class of targeted drugs in the armamentarium is Poly ADP Ribose Polymerase (PARP) inhibitors (PARPi), which inhibit the enzyme PARP, thus interfering with DNA repair. This strategy utilizes a pre-existing genomic lesion in tumors with homologous recombination repair defects (including BRCA mutations), weakening tumor cells further by blocking the alternate pathway of DNA repair. In this review, we discuss in detail, the evolution, genetics, mechanism of action, mechanism of resistance, indications of use of PARP inhibitors, as well as combination with other agents and future directions.</p>","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":" ","pages":"35-80"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39944455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Advances in GeneticsPub Date : 2021-01-01Epub Date: 2020-12-08DOI: 10.1016/bs.adgen.2020.11.002
Alejandro Mata-Cabana, Carmen Pérez-Nieto, María Olmedo
{"title":"Nutritional control of postembryonic development progression and arrest in Caenorhabditis elegans.","authors":"Alejandro Mata-Cabana, Carmen Pérez-Nieto, María Olmedo","doi":"10.1016/bs.adgen.2020.11.002","DOIUrl":"https://doi.org/10.1016/bs.adgen.2020.11.002","url":null,"abstract":"<p><p>Developmental programs are under strict genetic control that favors robustness of the process. In order to guarantee the same outcome in different environmental situations, development is modulated by input pathways, which inform about external conditions. In the nematode Caenorhabditis elegans, the process of postembryonic development involves a series of stereotypic cell divisions, the progression of which is controlled by the nutritional status of the animal. C. elegans can arrest development at different larval stages, leading to cell arrest of the relevant divisions of the stage. This means that studying the nutritional control of development in C. elegans we can learn about the mechanisms controlling cell division in an in vivo model. In this work, we reviewed the current knowledge about the nutrient sensing pathways that control the progression or arrest of development in response to nutrient availability, with a special focus on the arrest at the L1 stage.</p>","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":"107 ","pages":"33-87"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.adgen.2020.11.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25412367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Advances in GeneticsPub Date : 2021-01-01Epub Date: 2021-10-28DOI: 10.1016/bs.adgen.2021.08.005
Maninder Kaur Ahluwalia
{"title":"Nutrigenetics and nutrigenomics-A personalized approach to nutrition.","authors":"Maninder Kaur Ahluwalia","doi":"10.1016/bs.adgen.2021.08.005","DOIUrl":"https://doi.org/10.1016/bs.adgen.2021.08.005","url":null,"abstract":"<p><p>The prevalence of non-communicable diseases has been on an upward trajectory for some time and this puts an enormous burden on the healthcare expenditure. Lifestyle modifications including dietary interventions hold an immense promise to manage and prevent these diseases. Recent advances in genomic research provide evidence that focussing these efforts on individual variations in abilities to metabolize nutrients (nutrigenetics) and exploring the role of dietary compounds on gene expression (nutrigenomics and nutri-epigenomics) can lead to more meaningful personalized dietary strategies to promote optimal health. This chapter aims to provide examples on these gene-diet interactions at multiple levels to support the need of embedding targeted dietary interventions as a way forward to prevent, avoid and manage diseases.</p>","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":" ","pages":"277-340"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39944453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Advances in GeneticsPub Date : 2021-01-01Epub Date: 2020-12-17DOI: 10.1016/bs.adgen.2020.11.003
J Lydia Pramitha, Sumi Rana, Pooja Rani Aggarwal, Rajasekaran Ravikesavan, A John Joel, Mehanathan Muthamilarasan
{"title":"Diverse role of phytic acid in plants and approaches to develop low-phytate grains to enhance bioavailability of micronutrients.","authors":"J Lydia Pramitha, Sumi Rana, Pooja Rani Aggarwal, Rajasekaran Ravikesavan, A John Joel, Mehanathan Muthamilarasan","doi":"10.1016/bs.adgen.2020.11.003","DOIUrl":"https://doi.org/10.1016/bs.adgen.2020.11.003","url":null,"abstract":"<p><p>Natural or synthetic compounds that interfere with the bioavailability of nutrients are called antinutrients. Phytic acid (PA) is one of the major antinutrients present in the grains and acts as a chelator of micronutrients. The presence of six reactive phosphate groups in PA hinders the absorption of micronutrients in the gut of non-ruminants. Consumption of PA-rich diet leads to deficiency of minerals such as iron and zinc among human population. On the contrary, PA is a natural antioxidant, and PA-derived molecules function in various signal transduction pathways. Therefore, optimal concentration of PA needs to be maintained in plants to avoid adverse pleiotropic effects, as well as to ensure micronutrient bioavailability in the diets. Given this, the chapter enumerates the structure, biosynthesis, and accumulation of PA in food grains followed by their roles in growth, development, and stress responses. Further, the chapter elaborates on the antinutritional properties of PA and explains the conventional breeding and transgene-based approaches deployed to develop low-PA varieties. Studies have shown that conventional breeding methods could develop low-PA lines; however, the pleiotropic effects of these methods viz. reduced yield, embryo abnormalities, and poor seed quality hinder the use of breeding strategies. Overexpression of phytase in the endosperm and RNAi-mediated silencing of genes involved in myo-inositol biosynthesis overcome these constraints. Next-generation genome editing approaches, including CRISPR-Cas9 enable the manipulation of more than one gene involved in PA biosynthesis pathway through multiplex editing, and scope exists to deploy such tools in developing varieties with optimal PA levels.</p>","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":"107 ","pages":"89-120"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25412284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Advances in GeneticsPub Date : 2021-01-01Epub Date: 2021-08-26DOI: 10.1016/bs.adgen.2021.08.001
Dan Reisel, Chawan Baran, Ranjit Manchanda
{"title":"Preventive population genomics: The model of BRCA related cancers.","authors":"Dan Reisel, Chawan Baran, Ranjit Manchanda","doi":"10.1016/bs.adgen.2021.08.001","DOIUrl":"https://doi.org/10.1016/bs.adgen.2021.08.001","url":null,"abstract":"<p><p>Preventive population genomics offers the prospect of population stratification for targeting screening and prevention and tailoring care to those at greatest risk. Within cancer, this approach is now within reach, given our expanding knowledge of its heritable components, improved ability to predict risk, and increasing availability of effective preventive strategies. Advances in technology and bioinformatics has made population-testing technically feasible. The BRCA model provides 30 years of insight and experience of how to conceive of and construct care and serves as an initial model for preventive population genomics. Population-based BRCA-testing in the Jewish population is feasible, acceptable, reduces anxiety, does not detrimentally affect psychological well-being or quality of life, is cost-effective and is now beginning to be implemented. Population-based BRCA-testing and multigene panel testing in the wider general population is cost-effective for numerous health systems and can save thousands more lives than the current clinical strategy. There is huge potential for using both genetic and non-genetic information in complex risk prediction algorithms to stratify populations for risk adapted screening and prevention. While numerous strides have been made in the last decade several issues need resolving for population genomics to fulfil its promise and potential for maximizing precision prevention. Healthcare systems need to overcome significant challenges associated with developing delivery pathways, infrastructure expansion including laboratory services, clinical workforce training, scaling of management pathways for screening and prevention. Large-scale real world population studies are needed to evaluate context specific population-testing implementation models for cancer risk prediction, screening and prevention.</p>","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":" ","pages":"1-33"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39944450","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Advances in GeneticsPub Date : 2021-01-01Epub Date: 2021-09-08DOI: 10.1016/bs.adgen.2021.08.007
Keshab Bhattarai, Keshab Bhattarai, Bikash Baral
{"title":"Next-generation microbial drugs developed from microbiome's natural products.","authors":"Keshab Bhattarai, Keshab Bhattarai, Bikash Baral","doi":"10.1016/bs.adgen.2021.08.007","DOIUrl":"https://doi.org/10.1016/bs.adgen.2021.08.007","url":null,"abstract":"<p><p>Scientists working in natural products chemistry have been enticed by the current advancements being made in the discovery of novel \"magic bullets\" from microbes homed to all conceivable environments. Even though researchers continue to face challenges funneling the novel bioactive compounds in the global therapeutic industries, it seems most likely that the discovery of some \"hit molecules\" with significant biomedical applications is not that far. We applaud novel natural products for their ability to combat the spread of superbugs and aid in the prevention of currently observed antibiotic resistance. This in-depth investigation covers a wide range of microbiomes with a proclivity for synthesizing novel compounds to combat the spread of superbugs. Furthermore, we use this opportunity to explore various groups of secondary metabolites and their biosynthetic pathways in various microbiota found in mammals, insects, and humans. This systematic study, when taken as a whole, offers detail understanding on the biomedical fate of various groups of compounds originated from diverse microbiomes. For gathering all information that has been uncovered and released so far, we have also presented the huge diversity of microbes that are associated with humans and their metabolic products. To conclude, this concrete review suggests novel ideas that will prove immensely helpful in reducing the danger posed by superbugs while also improving the efficacy of antibiotics.</p>","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":" ","pages":"341-382"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39944454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Advances in GeneticsPub Date : 2021-01-01Epub Date: 2021-02-02DOI: 10.1016/bs.adgen.2020.11.001
Mayank Bansal, Mayank Garg, Anurag Agrawal
{"title":"Advances in asthma genetics.","authors":"Mayank Bansal, Mayank Garg, Anurag Agrawal","doi":"10.1016/bs.adgen.2020.11.001","DOIUrl":"https://doi.org/10.1016/bs.adgen.2020.11.001","url":null,"abstract":"<p><p>While asthma has a strong genetic component, our current ability to systematically understand and predict asthma risk remains low, despite over a hundred genetic associations. The reasons for this unfilled gap range from technical limitations of current approaches to fundamental deficiencies in the way we understand asthma. These are discussed in the context of genomic advances.</p>","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":"107 ","pages":"1-32"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/bs.adgen.2020.11.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25412363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Advances in GeneticsPub Date : 2021-01-01Epub Date: 2021-09-21DOI: 10.1016/bs.adgen.2021.08.004
Neha Pathak, Sindhura Chitikela, Prabhat Singh Malik
{"title":"Recent advances in lung cancer genomics: Application in targeted therapy.","authors":"Neha Pathak, Sindhura Chitikela, Prabhat Singh Malik","doi":"10.1016/bs.adgen.2021.08.004","DOIUrl":"https://doi.org/10.1016/bs.adgen.2021.08.004","url":null,"abstract":"<p><p>Genomic characterization of lung cancer has not only improved our understanding of disease biology and carcinogenesis but also revealed several therapeutic opportunities. Targeting tumor dependencies on specific genomic alterations (oncogene addiction) has accelerated the therapeutic developments and significantly improved the outcomes even in advanced stage of disease. Identification of genomic alterations predicting response to specific targeted treatment is the key to success for this \"personalized treatment\" approach. Availability of multiple choices of therapeutic options for specific genomic alterations highlight the importance of optimum sequencing of drugs. Multiplex gene testing has become mandatory in view of constantly increasing number of therapeutic targets and effective treatment options. Influence of genomic characteristics on response to immunotherapy further makes comprehensive genomic profiling necessary before therapeutic decision making. A comprehensive elucidation of resistance mechanisms and directed treatments have made the continuum of care possible and transformed this deadly disease into a chronic condition. Liquid biopsy-based approach has made the dynamic monitoring of disease possible and enabled treatment optimizations accordingly. Current lung cancer management is the perfect example of \"precision-medicine\" in clinical oncology.</p>","PeriodicalId":50949,"journal":{"name":"Advances in Genetics","volume":" ","pages":"201-275"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39944452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}