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The article positions omics-driven systems biology and high-throughput technologies to build systems-based phenotypic maps that reveal individual tumor functional plasticity. It spotlights PHENOSTAMP, a high-dimensional, visually intuitive reference map capturing transitional cancer states such as EMT and MET and enabling assessment of therapy response and resistance at single-cell resolution.",{"@graph":69,"@context":122},[70,84,105],{"@type":71,"itemListElement":72},"BreadcrumbList",[73,77,79,82],{"item":74,"name":75,"@type":76,"position":8},"https://docshare.wps.com","Home","ListItem",{"item":78,"name":9,"@type":76,"position":14},"https://docshare.wps.com/document/",{"item":80,"name":35,"@type":76,"position":81},"https://docshare.wps.com/document/healthcare/",3,{"item":83,"name":65,"@type":76,"position":19},"https://docshare.wps.com/document/phenotypic-maps-for-precision-medicine-a-promising-systems-biology-tool-for-assessing-therapy-response-and-resistance-at-a-personalized-level/406301/",{"url":83,"name":65,"@type":85,"image":86,"author":91,"headline":65,"publisher":94,"fileFormat":97,"inLanguage":63,"description":67,"dateModified":98,"datePublished":99,"encodingFormat":97,"isAccessibleForFree":100,"interactionStatistic":101},"DigitalDocument",{"url":87,"@type":88,"width":89,"height":90},"https://docshare.wps.com/thumbnails/phenotypic-maps-for-precision-medicine-a-promising-systems-biology-tool-for-assessing-therapy-response-and-resistance-at-a-personalized-level/406301.png","ImageObject",300,407,{"name":92,"@type":93},"4398046744996","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-11-04","2026-09-28",true,{"@type":102,"interactionType":103,"userInteractionCount":52},"InteractionCounter",{"@type":104},"ViewAction",{"@type":106,"mainEntity":107},"FAQPage",[108,114,118],{"name":109,"@type":110,"acceptedAnswer":111},"Why does therapy resistance require personalized approaches in precision medicine?","Question",{"text":112,"@type":113},"Therapy resistance is driven by tumor intra- and inter-heterogeneity plus the plasticity of resistant phenotypes that evolve during treatment. These factors make uniform strategies insufficient for durable responses.","Answer",{"name":115,"@type":110,"acceptedAnswer":116},"How does systems biology support the shift toward personalized medicine?",{"text":117,"@type":113},"Omics-driven systems biology uses high-throughput technologies and novel bioinformatics tools to construct systems-based maps. These maps provide a comprehensive view of individual tumors’ functional plasticity.",{"name":119,"@type":110,"acceptedAnswer":120},"What is PHENOSTAMP and what does its phenotypic map enable?",{"text":121,"@type":113},"PHENOSTAMP builds a visually intuitive, user-friendly reference map from high-dimensional data. It captures transitional states such as EMT and MET and helps researchers and clinicians assess a clinical specimen one at a time relative to phenotypic heterogeneity.","https://schema.org",{"og:url":83,"og:type":124,"og:title":65,"og:site_name":95,"og:description":67},"article",{"robots":126,"canonical":83},"index,follow",{"doc_id":128,"site_id":62},406301,1790865185,{"code":4,"msg":5,"data":131},{"doc_id":128,"user_id":132,"nickname":92,"user_avatar":66,"doc_module":4,"category_id":34,"category_name":35,"doc_title":65,"doc_description":67,"doc_content":133,"file_id":134,"file_url":135,"file_type":136,"file_size":137,"view_count":52,"is_deleted":4,"is_public":8,"is_downloadable":8,"audit_status":8,"page_count":44,"language":138,"language_code":63,"site_id":62,"html_lang":63,"table_of_contents":139,"faqs":140,"seo_title":141,"seo_description":67,"update_tm":142,"read_time":143,"preview_page_count":4},4398046744996,"TYPE Perspective  \nPUBLISHED 25 October 2023 DOI 10.3389/fnetp.2023.1256104  \nOPEN ACCESS  \nEDITED BY  \nMohit Kumar Jolly,  \nIndian Institute of Science (IISc), India  \nREVIEWED BY  \nSugandha Bhatia,  \nQueensland University of Technology, Australia  \nNandini Verma,  \nAdvanced Centre for Treatment, Research and Education in Cancer, India  \n*CORRESPONDENCE  \nLoukia G. Karacosta,  \n [lgkaracosta@mdanderson.org](lgkaracosta@mdanderson.org)  \n†These authors have contributed equally to this work and share first authorship  \nRECEIVED 10 July 2023  \nACCEPTED 28 September 2023  \nPUBLISHED 25 October 2023  \nCITATION  \nBhattacharyya S, Ehsan SF and Karacosta LG (2023), Phenotypic maps for precision medicine: a promising systems biology tool for assessing therapy response and resistance at a personalized level.  \nFront. Netw. Physiol. 3:1256104 .  \ndoi: 10.3389/fnetp.2023.1256104  \nCOPYRIGHT  \n© 2023 Bhattacharyya, Ehsan and Karacosta. This is an open-access article distributed under the terms of the  \nCreative Commons Attribution License (CC BY) . The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.  \nPhenotypic maps for precision medicine: a promising systems biology tool for assessing therapy response and resistance at a personalized level  \nSayantan Bhattacharyya 1†, Shafqat F. Ehsan 1,2† and Loukia G. Karacosta 1*  \n1Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, United States, 2Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States  \nIn this perspective we discuss how tumor heterogeneity and therapy resistance necessitate a focus on more personalized approaches, prompting a shift toward precision medicine. At the heart of the shift towards personalized medicine, omics-driven systems biology becomes a driving force as it leverages highthroughput technologies and novel bioinformatics tools. These enable the creation of systems-based maps, providing a comprehensive view of individual tumor’s functional plasticity. We highlight the innovative PHENOSTAMP program, which leverages high-dimensional data to construct a visually intuitive and userfriendly map. This map was created to encapsulate complex transitional states in cancer cells, such as Epithelial-Mesenchymal Transition (EMT) and MesenchymalEpithelial Transition (MET), offering a visually intuitive way to understand disease progression and therapeutic responses at single-cell resolution in relation to EMTrelated single-cell phenotypes. Most importantly, PHENOSTAMP functions as a reference map, which allows researchers and clinicians to assess one clinical specimen at a time in relation to their phenotypic heterogeneity, setting the foundation on constructing phenotypic maps for personalized medicine. This perspective argues that such dynamic predictive maps could also catalyze the development of personalized cancer treatment. They hold the potential to transform our understanding of cancer biology, providing a foundation for a future where therapy is tailored to each patient’s unique molecular and cellular tumor profile. As our knowledge of cancer expands, these maps can be continually refined, ensuring they remain a valuable tool in precision oncology.  \nKEYWORDS  \npersonalized medicine, phenotypic maps, therapy resistance, tumor heterogeneity, multi-omics, systems biology, computational biology  \nIntroduction  \nTherapy resistance remains the major culprit of cancer related mortality (Vasan et al., 2019). Overcoming resistance poses a significant challenge given the intra-and inter-heterogeneity of tumors and the plastic nature of therapy resistant phenotypes that develop over time during treatment (Zhu ","cbCaimnXATWWLzP8","https://ap.wps.com/l/cbCaimnXATWWLzP8","pdf",1474154,"English","# Introduction\n## Limits of marker-based personalization\n## Heterogeneity, TME interactions, and resistance\n# PHENOSTAMP and phenotypic maps\n## Single-cell EMT/MET state visualization\n## Reference mapping for clinical specimens\n# Outlook for precision oncology","[{\"question\":\"Why does therapy resistance require personalized approaches in precision medicine?\",\"answer\":\"Therapy resistance is driven by tumor intra- and inter-heterogeneity plus the plasticity of resistant phenotypes that evolve during treatment. These factors make uniform strategies insufficient for durable responses.\"},{\"question\":\"How does systems biology support the shift toward personalized medicine?\",\"answer\":\"Omics-driven systems biology uses high-throughput technologies and novel bioinformatics tools to construct systems-based maps. These maps provide a comprehensive view of individual tumors’ functional plasticity.\"},{\"question\":\"What is PHENOSTAMP and what does its phenotypic map enable?\",\"answer\":\"PHENOSTAMP builds a visually intuitive, user-friendly reference map from high-dimensional data. It captures transitional states such as EMT and MET and helps researchers and clinicians assess a clinical specimen one at a time relative to phenotypic heterogeneity.\"}]","Phenotypic maps for precision medicine: a promising systems biology tool for assessing therapy response and resistance at a personalized level | PDF",1790564716,23]