Nature ProtocolsPub Date : 2026-09-04DOI: 10.1038/s41596-026-01422-1
Lu Wang, Jinyao Liu
{"title":"Dopamine polymerization-mediated surface functionalization of living cells for advanced therapeutic applications.","authors":"Lu Wang, Jinyao Liu","doi":"10.1038/s41596-026-01422-1","DOIUrl":"https://doi.org/10.1038/s41596-026-01422-1","url":null,"abstract":"<p><p>The engineering of living cells represents a promising biomedical frontier that enables the design of cells with tailored functionalities for advanced therapeutic applications. Genetic manipulation serves as a primary approach in cell engineering, yet it faces inherent limitations, including the complexity of multigene editing and poor cross-species applicability, which restrict the development of cells with sophisticated functionalities. Therefore, flexible and versatile engineering strategies capable of functionalizing living cells to address diverse therapeutic requirements are highly desirable. Given its pivotal role in mediating cellular interactions, the cell surface is an attractive target for directing cell engineering. The diverse functional groups present in surface biomolecules offer abundant chemical modification sites, making them highly amenable to functionalization. Leveraging this inherent chemical accessibility, we have recently developed a flexible and versatile platform for surface functionalization of living cells through in situ dopamine polymerization that allows us to design personalized living cells with customizable functions by tuning the surface components. Here we provide a detailed protocol describing two distinct methods for bacterial functionalization. The first method uses dopamine polymerization-mediated mono-functionalization to construct mucus-penetrating bacteria that can reinforce intestinal mucosal barrier to prevent colitis. The second method uses dopamine polymerization-mediated dual-functionalization to generate synergy-immunoactivation bacteria that can simultaneously induce anticancer and antiviral immunity to treat cancer and prevent infection. Excluding bacterial culture, preparation of mucus-penetrating bacteria and synergy-immunoactivation bacteria takes ~3 h and 1 h, respectively. We anticipate that this protocol can offer valuable guidance for the engineering of living cells with designable and tailorable functionalities for innovative cell-based therapy.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148891960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature ProtocolsPub Date : 2026-09-03DOI: 10.1038/s41596-026-01434-x
Jane Oberhauser, Bella Ding, Madigan M Reid, William H Xie, Andrew C Yang
{"title":"VINE-seq and MultiVINE-seq for single-nucleus and multiome profiling of the brain vasculature.","authors":"Jane Oberhauser, Bella Ding, Madigan M Reid, William H Xie, Andrew C Yang","doi":"10.1038/s41596-026-01434-x","DOIUrl":"https://doi.org/10.1038/s41596-026-01434-x","url":null,"abstract":"<p><p>The human cerebrovasculature is a critical yet historically understudied component of neurological health. Dysfunction of the diverse endothelial, mural, and perivascular cells that comprise cerebral vessels is central to diseases ranging from stroke to Alzheimer's disease. However, characterizing these cell populations at a molecular level has proven exceptionally challenging. Encased within a robust basement membrane, vascular cells resist standard dissociation methods, leading to their systematic depletion and underrepresentation in existing single-nucleus genomic atlases. This has created a major blind spot in neuroscience. To overcome this barrier, we developed vessel isolation and nucleus extraction for sequencing (VINE-seq) and its advanced iteration, MultiVINE-seq. The protocol provides a robust, reproducible workflow for the enrichment and high-resolution profiling of vascular, perivascular, and immune cells from fresh or frozen human and mouse brain tissue. First, intact vessels (predominantly capillaries and small arterioles/venules, 100 µm in diameter) are isolated from homogenized brain tissue via dextran-based density-gradient centrifugation, separating the vascular pellet from myelin and the parenchymal fraction. Second, the collected vessels are rigorously washed over a cell strainer to remove trapped contaminants. A critical innovation lies in the third stage: the optimized extraction of nuclei from purified vessels using enzymatic digestion. After extraction, the protocol uses fluorescence-activated cell sorting (FACS) to ensure collection of high-purity nuclei suitable for widely used droplet-based sequencing platforms (e.g., 10x Genomics single cell 3' or multiome). This protocol requires 4-5 h to complete and can be carried out by researchers with single-cell and flow cytometry training.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148888055","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature ProtocolsPub Date : 2026-09-01DOI: 10.1038/s41596-026-01429-8
Wei Zhai, Zhenyu Shi, Rui Tao, Zijian Li, Dan Dong, Jiabei Tang, Wenbin Wang, Lixin Wang, Hua Yang, Li Zhai, Xinyang Ruan, Yuxuan Wu, Jie Wang, Yao Yao, Chen Zhao, Qiyuan He, Zhuangchai Lai, Hua Zhang
{"title":"Salt-assisted synthesis of high phase-purity metastable 1T'-phase group VIB transition metal dichalcogenides.","authors":"Wei Zhai, Zhenyu Shi, Rui Tao, Zijian Li, Dan Dong, Jiabei Tang, Wenbin Wang, Lixin Wang, Hua Yang, Li Zhai, Xinyang Ruan, Yuxuan Wu, Jie Wang, Yao Yao, Chen Zhao, Qiyuan He, Zhuangchai Lai, Hua Zhang","doi":"10.1038/s41596-026-01429-8","DOIUrl":"https://doi.org/10.1038/s41596-026-01429-8","url":null,"abstract":"<p><p>With the increasing progress in the emerging field of phase engineering of nanomaterials, transition metal dichalcogenides (TMDs) with metastable phases have attracted extensive research interest owing to their unique physicochemical properties and promising potential for various applications. Unlike their semiconducting counterparts, metastable 1T'-phase group VIB TMDs exhibit distinctive metallic behavior, making them highly promising for clean energy electrocatalysis (for example, hydrogen evolution), high-performance electronics and superconducting devices. However, conventional synthetic strategies usually suffer from low yields, poor phase purity, small crystal size and harsh experimental conditions, hindering their fundamental research and practical applications. Here we describe a salt-assisted method for the controlled preparation of various metastable 1T'-phase group VIB TMDs with high crystalline quality and high phase purity. In this context, 'salt-assisted' refers to the co-annealing of commercially available 2H-phase TMDs, chalcogen powders (for example, S or Se) and alkali metal salts (for example, K<sub>2</sub>C<sub>2</sub>O<sub>4</sub>·H<sub>2</sub>O or K<sub>2</sub>CO<sub>3</sub>). When heated in a tube furnace under an H<sub>2</sub>/Ar atmosphere, these alkali metal salts trigger a phase transformation of TMDs from the thermodynamically stable 2H phase to the metastable 1T' phase. This Protocol describes the details of experimental procedures to prepare a series of 1T'-TMDs, that is, MoS<sub>2</sub>, MoSe<sub>2</sub>, WS<sub>2</sub>, WSe<sub>2</sub>, MoS<sub>2x</sub>Se<sub>2(1-x)</sub> and WS<sub>2x</sub>Se<sub>2(1-x)</sub>. It takes ~37 h 20 min and yields robust 1T'-TMD crystals with their size of up to hundreds of micrometers at a gram scale (up to ~2 g per batch), overcoming the longstanding synthetic bottlenecks and paving the way for advanced fundamental studies and the exploration of practical applications.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148874812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature ProtocolsPub Date : 2026-08-28DOI: 10.1038/s41596-026-01442-x
Chaojun Zhang, Zhewei Yan, Jing Li, Mingjie Liu
{"title":"Shear-flow-induced assembly of 2D nanosheets for the fabrication of composite films with high tensile strength.","authors":"Chaojun Zhang, Zhewei Yan, Jing Li, Mingjie Liu","doi":"10.1038/s41596-026-01442-x","DOIUrl":"https://doi.org/10.1038/s41596-026-01442-x","url":null,"abstract":"<p><p>High-performance bioinspired composite materials require the precise alignment of synthetic nanosheets to mimic the mechanical properties of highly ordered laminated microstructures found in nature. Here, we detail a nanosheet superspreading alignment strategy for fabricating nanocomposite films that uses shear-flow forces at the interface between two immiscible phases to induce long-range, high-order alignment of the 2D nanosheets that enhances the films' mechanical properties. In situ interface crystallization or cross-linking follows the alignment and effectively locks the oriented configuration (the resulting orientation order parameter is >0.85). Subsequent solvent dewetting enables continuous film formation over large areas while maintaining well-defined microstructural integrity. This process overcomes the misorientation and aggregation typical of conventional alignment methods and can be scaled using a multi-nozzle extrusion setup compatible with commercial heating and film-collection components. The step-by-step procedures cover the nanosheet precursor preparation, the continuous-film fabrication and their microstructural characterization and require ≤23 days to complete. The procedures are applicable to a broad range of nanosheet materials, including graphene oxide, MXenes, transition-metal dichalcogenides and layered clays, and the resulting composite films exhibit enhanced mechanical strength, toughness and multifunctionality. Nanocomposites based on graphene oxide and clay nanosheets exhibit a tensile strength of up to 1,215 ± 80 MPa (mean ± s.d) and a Young's modulus of 198.8 ± 6.5 GPa, while clay-based nanocomposite films reach a toughness of 36.7 ± 3.0 MJ m<sup>-3</sup>. Superspreading alignment is a versatile and robust approach for the scalable fabrication of high-performance composites for materials science.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148851041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature ProtocolsPub Date : 2026-08-25DOI: 10.1038/s41596-026-01428-9
Tianlai Xia, Laihui Xiao, Neha Yadav, Andrew P Dove, Rachel K O'Reilly
{"title":"Preparation of polycaprolactone-based 2D platelets via living crystallization-driven self-assembly.","authors":"Tianlai Xia, Laihui Xiao, Neha Yadav, Andrew P Dove, Rachel K O'Reilly","doi":"10.1038/s41596-026-01428-9","DOIUrl":"https://doi.org/10.1038/s41596-026-01428-9","url":null,"abstract":"<p><p>Here we describe the preparation of two-dimensional (2D) polymer platelets based on poly(ε-caprolactone) (PCL) using living crystallization-driven self-assembly (CDSA), a seeded growth strategy that uses crystallization as a directional driving force to achieve epitaxial growth with controlled size and shape. The method integrates ring-opening polymerization for preparation of PCL segments, reversible addition-fragmentation chain-transfer polymerization for corona-forming blocks, sonication fragmentation or the flash-freezing method to generate seed particles and living CDSA to produce uniform and monodisperse 2D nanostructures. These 2D platelets are prepared from mixtures of PCL-based homopolymers and PCL-b-PDMA block copolymers, where PDMA refers to poly(N,N-dimethylacrylamide); similar solvophilic blocks with comparable properties could also be employed in place of PDMA. In this system, the semicrystalline PCL block provides the driving force for self-assembly, while the amorphous solvophilic corona block imparts colloidal stability and tunes interfacial properties. Owing to the living nature of CDSA, the platelet dimensions scale linearly with the unimer-to-seed ratio, enabling reproducible control over platelet area, layered structures and overall morphology. The Protocol is compatible with a broad range of PCL-based polymers bearing diverse functional groups and corona chemistries, and it can be readily adapted to incorporate responsive, supramolecular or fluorescent components. The resulting 2D platelets serve as versatile model systems for probing CDSA mechanisms and as platforms for optical and stimuli-responsive materials. The complete workflow-from polymer synthesis to structural characterization-can be completed within ~2 weeks and can be performed by researchers with basic experience in polymer synthesis and self-assembly.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148819102","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature ProtocolsPub Date : 2026-08-24DOI: 10.1038/s41596-026-01421-2
Shuaige Bai, Youshi Lin, Cheng Xu, Kanyi Pu, Yan Zhang
{"title":"Synthesis of radioafterglow nanoprobes for deep-tissue imaging of hydrogen peroxide.","authors":"Shuaige Bai, Youshi Lin, Cheng Xu, Kanyi Pu, Yan Zhang","doi":"10.1038/s41596-026-01421-2","DOIUrl":"https://doi.org/10.1038/s41596-026-01421-2","url":null,"abstract":"<p><p>Afterglow imaging eliminates the need for real-time excitation light, thereby greatly reducing tissue autofluorescence to achieve highly sensitive bioimaging. However, the clinical translation of existing photoafterglow and sonoafterglow probes developed so far is hampered by their limited tissue penetration. To address this, we recently developed radioafterglow nanoprobes (RANPs) on the basis of a cascade X-ray energy-converting mechanism for cancer-specific imaging and image-guided surgery. RANPs are constructed by co-assembling radioabsorbers, radiosensitizers and radioafterglow substrates into the amphiphilic polymers using the film rehydration method. This approach is rapid (<10 min), offers precise control over the concentration of encapsulated compounds and is highly scalable. Upon X-ray irradiation, RANPs exhibit near-infrared radioafterglow emission (peaked at 788 nm), with long half-life (~4.8 min) and high brightness. These properties enable an excitation depth of the RANPs up to 15 cm, three times deeper than that of photoafterglow. Here we further develop a tumor-specific RANP for precision molecular imaging that activates its radioafterglow signal specifically in the presence of hydrogen peroxide, a key biomarker of the tumor microenvironment. This design enables the ultrasensitive detection (signal-to-background ratio of 169) and surgical resection of small tumors (1 mm<sup>3</sup>) under an X-ray dosage 20 times lower than that required for inorganic materials. This protocol is suitable for users with expertise in chemistry, biology and materials science. The typical timeline is 1-2 weeks for nanoprobe construction and characterization, 1-2 weeks for cell assays and 3-4 weeks for animal experiments.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148813517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Selective heavy-metal sequestration and rare-earth element recovery using metal-organic frameworks.","authors":"Dhruv Menon, Prathmesh Bhadane, Priya Mahato, Prateek Goyal, Iseult Lynch, Swaroop Chakraborty, Superb K Misra","doi":"10.1038/s41596-026-01425-y","DOIUrl":"https://doi.org/10.1038/s41596-026-01425-y","url":null,"abstract":"<p><p>Modern water treatment and resource recovery demand materials that combine high performance with real-world durability. Traditional remediation approaches (e.g., precipitation and coagulation) have drawbacks (e.g., poor selectivity) that can be overcome using adsorption-based strategies. Metal-organic frameworks (MOFs) offer high tunability, high uptake capacities and the potential for regeneration. Translating MOF adsorbents into scalable, reliable technologies requires consistent method reporting and improved mechanistic insight, toward improving long-term stability in realistic water matrices. In this protocol, we describe how to deploy and assess the performance of MOF-based adsorbents for simultaneous heavy-metal sequestration (e.g., Pb(II), Cd(II), Ni(II) and Mn(II)) and rare-earth element recovery (e.g., Nd(III), Y(III) and Dy(III)) from complex water matrices. The workflow is broadly applicable across MOF chemistries and is illustrated using Cu(II)-based frameworks as representative model systems, synthesized at gram scale using commercially available precursors. We stabilize these frameworks through controlled defect engineering (e.g., partial metal substitution) to mitigate hydrolytic degradation and prolong operation time. We further tune morphology (e.g., nanosheets) to enhance surface accessibility and enable recyclability. For industrial applicability, we shape the MOFs into macrobeads via a green process. The procedure comprises: (i) MOF synthesis; (ii) comprehensive pre-adsorption characterization to assess crystallinity, porosity, morphology and composition using powder X-ray diffraction, nitrogen adsorption-desorption, scanning electron microscopy and inductively coupled plasma optical emission spectrometry; (iii) mechanistic adsorption assessment with kinetic, isotherm, thermodynamic, pH and selectivity analyses; (iv) regeneration and recovery workflows; and (v) deployment considerations in complex aqueous matrices, including industrial effluents, saline waters and e-waste leachates. The protocol provides a reproducible framework for implementing MOF-based adsorption technologies in water remediation and circular resource applications.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148813528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature ProtocolsPub Date : 2026-08-17DOI: 10.1038/s41596-026-01415-0
Zhiqiang Pang, Yao Lu, Guangyan Zhou, Huiting Ou, Charles Viau, Fumihiko Matsuda, Niladri Basu, Jianguo Xia
{"title":"Using MetaboAnalyst 6.0 for exposomics data analysis-from LC-MS2 spectra processing to dose-response modeling and causal inference.","authors":"Zhiqiang Pang, Yao Lu, Guangyan Zhou, Huiting Ou, Charles Viau, Fumihiko Matsuda, Niladri Basu, Jianguo Xia","doi":"10.1038/s41596-026-01415-0","DOIUrl":"https://doi.org/10.1038/s41596-026-01415-0","url":null,"abstract":"<p><p>Exposomics is an emerging field of research that aims to comprehensively investigate individuals' environmental exposures and how these exposures relate to health outcomes. Liquid chromatography-tandem mass spectrometry is widely used in exposomics studies. MetaboAnalyst ( https://www.metaboanalyst.ca/ ) is a widely used platform for statistical and functional analysis of metabolomics data. The current MetaboAnalyst 6.0 release incorporates updates to meet the needs of exposomics studies, including improved support for tandem mass spectrometry compound identification, exposome annotation, dose-response analysis and linking to genetics and functions. Here we extend our 2022 Nature Protocol by providing step-by-step instructions on how to use MetaboAnalyst 6.0 for exposomics data analysis, including: liquid chromatography-tandem mass spectrometry spectra processing and compound identification (Stage 1), exposomics data processing and exploratory analysis (Stage 2), dose-response modeling to study metabolic responses to exposure levels (Stage 3) and leveraging known genetic associations for causal inference (Stage 4). We demonstrate Stages 1-3 using data from a recent blood exposomics study concerning electronic waste exposure. Stage 4 is illustrated through an investigation of the potential causal link between ʟ-isoleucine and type 2 diabetes. Stage 1 may take ~2 h to complete depending on server load, and the remaining stages may be executed in a total of ~90 min.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148795787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature ProtocolsPub Date : 2026-08-17DOI: 10.1038/s41596-026-01426-x
Behnoush Abedi-Ardekani, Arash Nikmanesh, Masoud Sotoudeh, Valerie Gaborieau, Farid Azmoudeh-Ardalan, Hiva Saffar, Stefano Serra, Christine Carreira, Priscilia Chopard, Sophie Ferlicot, Jean-Yves Scoazec, Christophe Lallemand, Elodie Colney, Sophie Guillot, Fatemeh Ghasemi-Kebria, Ana Carolina de Carvalho, Aida Ferreiro-Iglesias, Sandra Perdomo, Paul Brennan, Manuel Salto-Tellez, Gholamreaz Roshandel
{"title":"Centralized processing of frozen tumor tissues for global cancer genomics.","authors":"Behnoush Abedi-Ardekani, Arash Nikmanesh, Masoud Sotoudeh, Valerie Gaborieau, Farid Azmoudeh-Ardalan, Hiva Saffar, Stefano Serra, Christine Carreira, Priscilia Chopard, Sophie Ferlicot, Jean-Yves Scoazec, Christophe Lallemand, Elodie Colney, Sophie Guillot, Fatemeh Ghasemi-Kebria, Ana Carolina de Carvalho, Aida Ferreiro-Iglesias, Sandra Perdomo, Paul Brennan, Manuel Salto-Tellez, Gholamreaz Roshandel","doi":"10.1038/s41596-026-01426-x","DOIUrl":"https://doi.org/10.1038/s41596-026-01426-x","url":null,"abstract":"<p><p>Here we present the pathology workflow of the Mutographs project, a 7-year, multicancer genomics initiative led by the Sanger Institute and funded by Cancer Research UK. Mutographs aims to elucidate global differences in cancer incidence through whole-genome sequencing and mutational signature analysis of selected cancers with unexplained variation of incidence rate worldwide. The Protocol was developed by the International Agency for Research on Cancer, where pathology assessment and paired tumor-blood DNA extraction were performed. We provide details for handling frozen cancer tissues for multistep pathology evaluation and quality control, tumor-enrichment methods (such as macrodissecion and laser-capture microdissection) for certain tumor types, and manual and automated DNA extraction. This Protocol has achieved an overall success rate of 88% in providing high-quality DNA for whole-genome sequencing, aiding in the decision to exclude low-quality or noneligible tissues. This Protocol provides a reproducible, fully integrated pathology-molecular pipeline in challenging conditions to ensure high-quality DNA and reliable data interpretation at an unprecedented multinational scale and could be considered a model for high-quality tissue processing in international genomics initiatives. It is based on routine practice of pathology and requires practical experience of processing frozen tissues and morphological assessment of frozen tissues by digital pathology.</p>","PeriodicalId":18901,"journal":{"name":"Nature Protocols","volume":" ","pages":""},"PeriodicalIF":18.4,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148795766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}