Integrating multi-omics to unravel host-microbiome interactions in inflammatory bowel disease

Cell Reports Medicine, Journal Year: 2024, Volume and Issue: 5(9), P. 101738 - 101738

Published: Sept. 1, 2024

Language: Английский

---

Worldwide Innovative Network (WIN) Consortium in Personalized Cancer Medicine: Bringing next-generation precision oncology to patients

Oncotarget, Journal Year: 2025, Volume and Issue: 16(1), P. 140 - 162

Published: March 12, 2025

// Wafik S. El-Deiry 1 , 2 Catherine Bresson Fanny Wunder Benedito A. Carneiro Don Dizon Jeremy L. Warner Stephanie Graff Christopher G. Azzoli Eric T. Wong Liang Cheng Sendurai Mani Howard P. Safran Casey Williams 3 Tobias Meissner Benjamin Solomon Eitan Rubin 4 Angel Porgador Guy Berchem 5 6 7 Pierre Saintigny 8 9 Amir Onn 10 Jair Bar 11 Raanan Berger Manon Gantenbein Zhen Chen 12 Cristiano de Pádua Souza 13 Rui Manuel Vieira Reis 14 Marina Sekacheva 15 Andrés Cervantes 16 William Dahut 17 Christina M. Annunziata Kerri Gober Khaled Musallam 18 Humaid O. Al-Shamsi Ibrahim Abu-Gheida Ramon Salazar 19 Sewanti Limaye 20 Adel Aref 21 Roger R. Reddel Mohammed Ussama Al Homsi 22 Abdul Rouf Said Dermime Jassim Suwaidi Catalin Vlad 23 Rares Buiga Amal Omari 24 Hikmat Abdel-Razeq Luis F. Oñate-Ocaña 25 Finn Cilius Nielsen 26 Leah Graham 27 Jens Rueter Anthony Joshua 28 29 Eugenia Girda 30 Steven Libutti Gregory Riedlinger E. Salem 31 Carol J. Farhangfar Ruben Mesa Bishoy Faltas 32 Olivier Elemento C.S. Pramesh 33 Manju Sengar Satoru Aoyama 34 Sadakatsu Ikeda Ioana Berindan-Neagoe 35 36 Himabindu Gaddipati 37 Mandar Kulkarni Elisabeth Auzias 38 Maria Gerogianni Nicolas Wolikow Simon Istolainen Pessie Schlafrig 39 Naftali Z. Frankel Amanda Ferraro 40 Jim Palma 41 Alejandro Piris Gimenez 42 Alberto Hernando-Calvo Enriqueta Felip Apostolia Tsimberidou 43 Roy Herbst 44 Josep Tabernero Richard Schilsky 45 Jia Liu Yves Lussier 46 Jacques Raynaud Gerald Batist 47 Shai Magidi and Razelle Kurzrock 48 Worldwide Innovative Network (WIN) Association – WIN Consortium, Chevilly-Larue, France Legorreta Cancer Center at Brown University, Providence, RI 02912, USA Avera Institute, Sioux Falls, SD 57105, Ben-Gurion University of the Negev, Be'er Sheva, Israel Centre Hospitalier du Luxembourg, Luxembourg Esch-sur-Alzette, Institute Health, Department Medical Oncology, Léon Bérard, Lyon, Claude Bernard Lyon INSERM 1052, CNRS 5286, Research Jusidman Center, Sheba Ramat Gan, Faculty Health Sciences, Tel Aviv Aviv, Fudan Shanghai Shanghai, China Molecular Oncology Barretos Hospital, Barretos, Brazil Life Sciences (ICVS), School Minho, Braga, Portugal I.M Sechenov First State Moscow, Russian Federation INCLIVA Instituto Investigación Sanitaria, Valencia, Spain American Society, Atlanta, Georgia, MD 21742, Burjeel City (BMC), Mohamed Bin Zayed City, Abu Dhabi, UAE Deparment. Institut Català d'Oncologia. Oncobell Program (IDIBELL), Universitat Barcelona (Campus Bellvitge), CIBERONC, Barcelona, Sir H.N. Reliance Foundation Hospital Centre, Mumbai, India ProCan, Children's The Sydney, Australia National for Care Hamad Corporation, Doha, Qatar Ion Chiricuta, Cluj, Romania King Hussein Amman, Jordan Nacional Cancerología (INCan), Mexico Rigshospitalet, Copenhagen, Denmark Jackson Laboratory, Maine Genomics Initiative, Harbor, ME 04609, Kinghorn St Vincent's Darlinghurst, Clinical Medicine, Medicine New South Wales, Rutgers Brunswick, NJ 08901, Wake Forest Sciences/Atrium (WFUHS), Winston-Salem, NC 27157, Weill Cornell College, NY 10065, Tata Memorial Affiliated to Homi Bhabha Science Tokyo Tokyo, Japan Pharmacy Iuliu Hatieganu, Academy Bucharest, Vyas (VCR Park), Maharanipeta, Visakhpatnam, Andhra Pradesh, Cure51, Paris, CHAIM Resource Organization, 10950, is an A*, LLC, Manalapan Township, 07726, TargetCancer Foundation, Cambridge, MA 02139, Vall d'Hebron Campus (VHIO), Texas, M.D. Anderson Houston, TX 77030, Yale Haven, CT 06510, Chicago, IL 60637, Utah, Salt Lake UT 84112, Segal Jewish McGill Montreal, Quebec, Canada College Wisconsin, Milwaukee, WI 53226, Correspondence to: El-Deiry, email: [email protected] Keywords: precision oncology; N-of-1 basket trials; AI algorithms; digital pathology; drug access Received: December 30, 2024 Accepted: February 27, 2025 Published: March 12, Copyright: © et al. This open article distributed under terms Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, reproduction in any medium, provided original author source are credited. ABSTRACT human genome project ushered a genomic medicine era that was largely unimaginable three decades ago. Discoveries druggable cancer drivers enabled biomarker-driven gene- immune-targeted therapy transformed treatment. Minimizing treatment not expected benefit, toxicity—including financial time—are important goals modern oncology. Consortium Personalized founded by Drs. John Mendelsohn Thomas Tursz vision innovation, collaboration global impact Through pursuit transcriptomic signatures, artificial intelligence (AI) algorithms, clinical trials input from international Tumor Board (MTB), has led way demonstrating patient benefit precision-therapeutics through molecularly-driven studies. Next-Generation Precision (WINGPO) being developed neoadjuvant, adjuvant or metastatic settings, incorporate real-world data, pathology, advanced algorithms guide MTB prioritization combinations diverse population. pursued target multiple drivers/hallmarks individual patients. continues be impactful with industry, government, sponsors, funders, academic community centers, advocates, other stakeholders tackle challenges including access, costs, regulatory barriers, support. WIN's collaborative next generation oncology will selection patients cancers based on serial liquid tissue biopsies exploratory omics transcriptomics, proteomics, metabolomics functional medicine. Our accelerate future care.

Language: Английский

---

From data chaos to precision medicine

Nature Machine Intelligence, Journal Year: 2025, Volume and Issue: unknown

Published: March 13, 2025

---

Computational tools in genomics and proteomics

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 489 - 518

Published: Jan. 1, 2025

Language: Английский

---

Next-Generation Sequencing: a powerful multi-purpose tool in cell line development for biologics production

Computational and Structural Biotechnology Journal, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Within the biopharmaceutical industry, cell line development (CLD) process generates recombinant mammalian lines for expression of therapeutic proteins. Analytical methods extensive characterisation protein product are well established; however, over recent years, next-generation sequencing (NGS) technologies have rapidly become an integral part CLD workflow. NGS can be used different applications to characterise genome, epigenome and transcriptome lines. The resulting datasets, especially when integrated with systems biology models, give comprehensive insights that applied optimize lines, media, fermentation processes. also provides monitor genetic variability during CLD. High coverage experiments indeed ensure integrity plasmids, identify integration sites, verify monoclonality This review summarises role in advancing production safety efficacy

Language: Английский

---

Polymerase Chain Reaction Chips for Biomarker Discovery and Validation in Drug Development

Micromachines, Journal Year: 2025, Volume and Issue: 16(3), P. 243 - 243

Published: Feb. 20, 2025

Polymerase chain reaction (PCR) chips are advanced, microfluidic platforms that have revolutionized biomarker discovery and validation because of their high sensitivity, specificity, throughput levels. These miniaturize traditional PCR processes for the speed precision nucleic acid detection relevant to advancing drug development. Biomarkers, which useful in helping explain disease mechanisms, patient stratification, therapeutic monitoring, hard identify validate due complexity biological systems limitations techniques. The challenges respond include high-throughput capabilities coupled with real-time quantitative analysis, enabling researchers novel biomarkers greater accuracy reproducibility. More recent design improvements further expanded functionality also digital multiplex technologies. Digital ideal quantifying rare biomarkers, is essential oncology infectious research. In contrast, enable simultaneous analysis multiple targets, therefore simplifying validation. Furthermore, single-cell made it possible detect at unprecedented resolution, hence revealing heterogeneity within cell populations. transforming development, target identification, efficacy assessment. They play a major role development companion diagnostics and, therefore, pave way personalized medicine, ensuring right receives treatment. While this tremendously promising technology has exhibited many regarding its scalability, integration other omics technologies, conformity regulatory requirements, still prevail. Future breakthroughs chip manufacturing, artificial intelligence, multi-omics applications will expand capabilities. not only be important acceleration but raising bar improving outcomes hence, global health care as these technologies continue mature.

Language: Английский

---

Multi-omics data for machine learning algorithms

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 197 - 221

Published: Jan. 1, 2025

Language: Английский

---

Multi-omics and drug development

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 147 - 171

Published: Jan. 1, 2025

---

Multi-omics approaches for biomarker discovery and precision diagnosis of prediabetes

Frontiers in Endocrinology, Journal Year: 2025, Volume and Issue: 16

Published: March 14, 2025

Recent advancements in multi-omics technologies have provided unprecedented opportunities to identify biomarkers associated with prediabetes, offering novel insights into its diagnosis and management. This review synthesizes the latest findings on prediabetes from multiple omics domains, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiomics, radiomics. We explore how these elucidate molecular cellular mechanisms underlying analyze potential predictive value disease progression. Integrating data helps address limitations of traditional diagnostic methods, enabling early detection, personalized interventions, improved patient outcomes. However, challenges such as integration, standardization, clinical validation translation remain be resolved. Future research leveraging artificial intelligence machine learning is expected further enhance power technologies, contributing precision tailored management prediabetes.

Language: Английский

---

Translational Advances in Oncogene and Tumor-Suppressor Gene Research

Cancers, Journal Year: 2025, Volume and Issue: 17(6), P. 1008 - 1008

Published: March 17, 2025

Cancer, characterized by the uncontrolled proliferation of cells, is one leading causes death globally, with approximately in five people developing disease their lifetime. While many driver genes were identified decades ago, and most cancers can be classified based on morphology progression, there still a significant gap knowledge about genetic aberrations nuclear DNA damage. The study two critical groups genes—tumor suppressors, which inhibit promote apoptosis, oncogenes, regulate survival—can help to understand genomic behind tumorigenesis, more personalized approaches diagnosis treatment. Aberration tumor undergo two-hit loss-of-function mutations, activated forms proto-oncogenes that experience one-hit gain-of-function are responsible for dysregulation key signaling pathways cell division, such as p53, Rb, Ras/Raf/ERK/MAPK, PI3K/AKT, Wnt/β-catenin. Modern breakthroughs genomics research, like next-generation sequencing, have provided efficient strategies mapping unique changes contribute heterogeneity. Novel therapeutic enabled medicine, helping address variability suppressors oncogenes. This comprehensive review examines molecular mechanisms tumor-suppressor they regulate, epigenetic modifications, heterogeneity, drug resistance drive carcinogenesis. Moreover, explores clinical application sequencing techniques, multiomics, diagnostic procedures, pharmacogenomics, treatment prevention options, discussing future directions emerging technologies.

Language: Английский

---