Nature Structural & Molecular Biology, Год журнала: 2022, Номер 29(10), С. 978 - 989
Опубликована: Окт. 1, 2022
Язык: Английский
Frontiers in Immunology, Год журнала: 2019, Номер 10
Опубликована: Окт. 29, 2019
Multiplex immunophenotyping technologies are indispensable for a deeper understanding of biological systems. Until recently, high-dimensional cellular analyses implied the loss tissue context as they were mostly performed in single-cell suspensions. The advent imaging mass cytometry introduced possibility to simultaneously detect multitude markers sections. This technique can be applied various sources including snap-frozen and formalin-fixed, paraffin-embedded (FFPE) tissues. However, number methodological challenges must overcome when developing large antibody panels order preserve signal intensity specificity antigen detection. We report development 40-marker panel on FFPE tissues with particular focus study cancer immune microenvironments. It comprises variety cell lineage activation well surrogates states tissue-specific (e.g., stroma, epithelium, vessels) contextualization within tissue. Importantly, we developed an optimized workflow maximum performance by separating antibodies into two distinct incubation steps, at different temperatures times, shown significantly improve immunodetection. Furthermore, provide insight validation process discuss why some and/or not compatible technique. work is aimed supporting implementation other laboratories describing procedures detail. described here excellent monitoring tool that readily research.
Язык: Английский
Процитировано
134
Molecular & Cellular Proteomics, Год журнала: 2021, Номер 20, С. 100165 - 100165
Опубликована: Янв. 1, 2021
Targeted proteomics via selected reaction monitoring (SRM) or parallel (PRM) enables fast and sensitive detection of a preselected set target peptides. However, the number peptides that can be monitored in conventional targeting methods is usually rather small. Recently, series has been described employ intelligent acquisition strategies to increase efficiency mass spectrometers detect These are based on one two strategies. First, retention time adjustment-based enable scheduling peptide times. include Picky, iRT, as well spike-in free real-time adjustment such MaxQuant.Live. Second, triggered SureQuant, Pseudo-PRM, TOMAHAQ, Scout-MRM, targeted scans initiated by abundant labeled synthetic added samples before run. Both spectrometer better focus data This either more higher targets per Here, we provide an overview available advanced highlight their intrinsic strengths weaknesses compatibility with specific experimental setups. Our goal basic introduction for people starting work this field.
Язык: Английский
Процитировано
90
Seminars in Cancer Biology, Год журнала: 2021, Номер 84, С. 199 - 213
Опубликована: Апрель 13, 2021
Язык: Английский
Процитировано
74
FEBS Journal, Год журнала: 2021, Номер 288(21), С. 6142 - 6158
Опубликована: Фев. 24, 2021
The past decades have seen tremendous developments with respect to "specific" therapeutics that target key signaling molecules conquer cancer. advancements multiomics technologies, especially genomics, allowed physicians and molecular oncologists design "tailor-made" solutions the specific oncogenes are deregulated in individual patients, a strategy which has turned out be successful though patients quickly develop resistance. swift integration of multidisciplinary approaches led development "next generation" and, synergistic therapeutic regimes combined immune checkpoint inhibitors reactivate dampened response, provided much-needed promise for cancer patients. Despite these advances, large portion druggable genome remains understudied, role system needs further attention. Establishment patient-derived organoid models fastened preclinical validation novel clinical translation. We summarized current advances challenges also stress importance biobanking collection longitudinal data sets structured information, as well critical "high content sets" will play designing new tailor-made fashion.
Язык: Английский
Процитировано
69
Genes & Diseases, Год журнала: 2022, Номер 10(3), С. 960 - 989
Опубликована: Авг. 23, 2022
Continuous revision of the histologic and stage-wise classification lung cancer by World Health Organization (WHO) provides foundation for therapeutic advances promoting molecular targeted immunotherapies ensuring accurate diagnosis. Cancer epidemiologic data provide helpful information prevention, diagnosis, management, supporting health-care interventions. Global mortality projections from 2016 to 2060 show that will overtake ischemic heart diseases (IHD) as leading cause death (18.9 million) immediately after 2030, surpassing non-small cell (NSCLC), which accounts 85 percent cancers. The clinical stage at diagnosis is main prognostic factor in NSCLC therapies. Advanced early diagnostic methods are essential initial stages reduced compared advanced stages. Sophisticated approaches proper histological management have improved efficiency. Although immune checkpoint inhibitors (ICIs) therapies refined late-stage NSCLC, specificity sensitivity biomarkers should be focusing on prospective studies, followed their use tools. liquid biopsy candidates such circulating tumor cells (CTCs), cell-free DNA (cfDNA), educated platelets (TEP), extracellular vesicles (EVs) possess cancer-derived biomolecules aid tracing: driver mutations cancer, acquired resistance caused various generations agents, refractory disease, prognosis, surveillance.
Язык: Английский
Процитировано
66
Mass Spectrometry Reviews, Год журнала: 2021, Номер 41(5), С. 842 - 860
Опубликована: Март 24, 2021
Abstract The lacrimal film has attracted increasing interest in the last decades as a potential source of biomarkers physiopathological states, due to its accessibility, moderate complexity, and responsiveness ocular systemic diseases. High‐performance liquid chromatography‐mass spectrometry (LC‐MS) led effective approaches tear proteomics, despite intrinsic limitations sample amounts. This review focuses on recent progress strategy technology, with an emphasis for personalized medicine. After introduction lacrimal‐film composition, examples applications biomarker discovery are discussed, comparing based pooled‐sample single‐tear analysis. Then, most critical steps experimental pipeline, that is, collection, fractionation, LC‐MS implementation, discussed reference proteome‐coverage optimization. Advantages challenges alternative procedures highlighted. Despite still limited number studies, quantitative including investigation, could offer unique contributions identification low‐invasiveness, sustained‐accessibility biomarkers, development therapy diagnosis.
Язык: Английский
Процитировано
57
Current Opinion in Chemical Biology, Год журнала: 2022, Номер 70, С. 102180 - 102180
Опубликована: Июнь 29, 2022
Язык: Английский
Процитировано
38
PROTEOMICS, Год журнала: 2022, Номер 23(7-8)
Опубликована: Авг. 15, 2022
Tumor tissue processing methodologies in combination with data-independent acquisition mass spectrometry (DIA-MS) have emerged that can comprehensively analyze the proteome of multiple tumor samples accurately and reproducibly. Increasing recognition adoption these technologies has resulted a tranche studies providing novel insights into cancer classification systems, functional biology, biomarkers, treatment response drug targets. Despite this, some limited exceptions, MS-based proteomics not yet been implemented routine clinical practice. Here, we summarize use DIA-MS may pave way for future applications, highlight role alternative MS multi-omic strategies. We discuss limitations challenges this field to date propose steps integrating proteomic data clinic.
Язык: Английский
Процитировано
38
Molecules, Год журнала: 2023, Номер 28(12), С. 4768 - 4768
Опубликована: Июнь 14, 2023
Breast cancer (BC) is characterized by an extensive genotypic and phenotypic heterogeneity. In-depth investigations into the molecular bases of BC phenotypes, carcinogenesis, progression, metastasis are necessary for accurate diagnoses, prognoses, therapy assessments in predictive, precision, personalized oncology. This review discusses both classic as well several novel omics fields that involved or should be used modern investigations, which may integrated a holistic term, onco-breastomics. Rapid recent advances profiling strategies analytical techniques based on high-throughput sequencing mass spectrometry (MS) development have generated large-scale multi-omics datasets, mainly emerging from three ”big omics”, central dogma biology: genomics, transcriptomics, proteomics. Metabolomics-based approaches also reflect dynamic response cells to genetic modifications. Interactomics promotes view research constructing characterizing protein–protein interaction (PPI) networks provide hypothesis pathophysiological processes progression subtyping. The emergence new omics- epiomics-based multidimensional opportunities gain insights heterogeneity its underlying mechanisms. main epiomics (epigenomics, epitranscriptomics, epiproteomics) focused epigenetic DNA changes, RNAs modifications, posttranslational modifications (PTMs) affecting protein functions in-depth understanding cell proliferation, migration, invasion. Novel fields, such epichaperomics epimetabolomics, could investigate interactome induced stressors PPI metabolites, drivers BC-causing phenotypes. Over last years, proteomics-derived omics, matrisomics, exosomics, secretomics, kinomics, phosphoproteomics, immunomics, provided valuable data deep dysregulated pathways their tumor microenvironment (TME) immune (TIMW). Most these datasets still assessed individually using distinct approches do not generate desired expected global-integrative knowledge with applications clinical diagnostics. However, hyphenated approaches, proteo-genomics, proteo-transcriptomics, phosphoproteomics-exosomics useful identification putative biomarkers therapeutic targets. To develop non-invasive diagnostic tests discover BC, omics-based allow significant blood/plasma-based omics. Salivaomics, urinomics, milkomics appear integrative high potential early diagnoses BC. Thus, analysis circulome considered frontier liquid biopsy. Omics-based modeling, classification subtype characterization. future single-cell analyses.
Язык: Английский
Процитировано
33
Chemical Science, Год журнала: 2023, Номер 14(11), С. 2887 - 2900
Опубликована: Янв. 1, 2023
Highly sensitive and reproducible analysis of samples containing low amounts protein is restricted by sample loss the introduction contaminants during processing. Here, we report an All-in-One digital microfluidic (DMF) pipeline for proteomic reduction, alkylation, digestion, isotopic labeling analysis. The system features end-to-end automation, with integrated thermal control optimized droplet additives manipulation analysis, automated interface to liquid chromatography tandem mass spectrometry (HPLC-MS/MS). Dimethyl was into allow relative quantification trace at nanogram level, new applied evaluating cancer cell lines tissue samples. Several known proteins (including HSP90AB1, HSPB1, LDHA, ENO1, PGK1, KRT18, AKR1C2) pathways were observed between model breast related hormone response, metabolism, morphology. Furthermore, differentially quantified (such as PGS2, UGDH, ASPN, LUM, COEA1, PRELP) found in comparisons healthy tissues, suggesting potential utility emerging application sub-typing. In sum, represents a powerful tool proteome processing be useful mass-limited wide range applications.
Язык: Английский
Процитировано
27