Laser capture microdissection for biomedical research: towards high-throughput, multi-omics, and single-cell resolution

Guo, Wenbo; Hu, Yining; Qian, Jingyang; Zhu, Linyang; Cheng, Jiajing; Liao, Jie; Fan, Xiaohui

doi:10.1016/j.jgg.2023.07.011

Cited by 14 publications

(3 citation statements)

References 98 publications

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“…In relation to studying the downstream effects of dystrophin deficiency, a holistic systems biological analysis of the complex pathogenesis of DMD would greatly enhance our insights into organ crosstalk and encompass an integrative multi-omics approach. This integromics strategy would ideally consist of genomics [ 440 , 441 , 442 ], transcriptomics [ 443 , 444 , 445 ], top-down proteomics [ 17 , 59 , 60 , 61 ], bottom-up proteomics [ 46 , 107 ], subproteomics [ 108 , 109 , 110 , 213 ], the proteomic evaluation of PTMs [ 117 , 291 , 446 , 447 ], metabolomics [ 448 , 449 ], lipidomics [ 450 , 451 , 452 ], glycomics [ 453 ], immunomics [ 454 ], secretomics [ 218 , 219 , 220 , 221 , 455 ] and high-throughput cytomics [ 158 , 172 , 456 , 457 ], as summarized in Figure 6 .…”

Section: The Pathoproteomic Profiling Of Duchenne Muscular Dystrophymentioning

confidence: 99%

“…In relation to studying the downstream effects of dystrophin deficiency, a holist systems biological analysis of the complex pathogenesis of DMD would greatly enhanc our insights into organ crosstalk and encompass an integrative multi-omics approac This integromics strategy would ideally consist of genomics [440][441][442], transcriptomi [443][444][445], top-down proteomics [17,[59][60][61], bottom-up proteomics [46,107], subprot omics [108][109][110]213], the proteomic evaluation of PTMs [117,291,446,447], metabolomi [448,449], lipidomics [450][451][452], glycomics [453], immunomics [454], secretomics [218 221,455] and high-throughput cytomics [158,172,456,457], as summarized in Figure 6. Importantly, the integration of proteomic data sets from both bottom-up and top down approaches would be extremely helpful in identifying and characterizing specifi proteoforms in highly complex tissue systems [458,459].…”

Section: Integromics: Systems Biological Multi-omics Analysis Of Dyst...mentioning

confidence: 99%

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How Can Proteomics Help to Elucidate the Pathophysiological Crosstalk in Muscular Dystrophy and Associated Multi-System Dysfunction?

Dowling,

Trollet,

Negroni

et al. 2024

Proteomes

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This perspective article is concerned with the question of how proteomics, which is a core technique of systems biology that is deeply embedded in the multi-omics field of modern bioresearch, can help us better understand the molecular pathogenesis of complex diseases. As an illustrative example of a monogenetic disorder that primarily affects the neuromuscular system but is characterized by a plethora of multi-system pathophysiological alterations, the muscle-wasting disease Duchenne muscular dystrophy was examined. Recent achievements in the field of dystrophinopathy research are described with special reference to the proteome-wide complexity of neuromuscular changes and body-wide alterations/adaptations. Based on a description of the current applications of top-down versus bottom-up proteomic approaches and their technical challenges, future systems biological approaches are outlined. The envisaged holistic and integromic bioanalysis would encompass the integration of diverse omics-type studies including inter- and intra-proteomics as the core disciplines for systematic protein evaluations, with sophisticated biomolecular analyses, including physiology, molecular biology, biochemistry and histochemistry. Integrated proteomic findings promise to be instrumental in improving our detailed knowledge of pathogenic mechanisms and multi-system dysfunction, widening the available biomarker signature of dystrophinopathy for improved diagnostic/prognostic procedures, and advancing the identification of novel therapeutic targets to treat Duchenne muscular dystrophy.

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Section: The Pathoproteomic Profiling Of Duchenne Muscular Dystrophymentioning

confidence: 99%

Section: Integromics: Systems Biological Multi-omics Analysis Of Dyst...mentioning

confidence: 99%

How Can Proteomics Help to Elucidate the Pathophysiological Crosstalk in Muscular Dystrophy and Associated Multi-System Dysfunction?

Dowling,

Trollet,

Negroni

et al. 2024

Proteomes

View full text Add to dashboard Cite

show abstract

“…A key technique of molecular cell biology, laser-assisted microdissection [228], can be conveniently adapted for microproteomic applications [229] and used to study protein populations in small cellular regions of interest [230,231]. In general, the highly focused isolation of cellular structures employing direct microscopical visualization of tissues can be used to generate detailed systems biological maps through the bioanalysis of pure histological specimens [232].…”

Section: Microproteomic Analysis Using Laser Capture Microdissectionmentioning

confidence: 99%

Mass Spectrometry-Based Proteomic Technology and Its Application to Study Skeletal Muscle Cell Biology

Dowling,

Swandulla,

Ohlendieck

2023

Cells

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Voluntary striated muscles are characterized by a highly complex and dynamic proteome that efficiently adapts to changed physiological demands or alters considerably during pathophysiological dysfunction. The skeletal muscle proteome has been extensively studied in relation to myogenesis, fiber type specification, muscle transitions, the effects of physical exercise, disuse atrophy, neuromuscular disorders, muscle co-morbidities and sarcopenia of old age. Since muscle tissue accounts for approximately 40% of body mass in humans, alterations in the skeletal muscle proteome have considerable influence on whole-body physiology. This review outlines the main bioanalytical avenues taken in the proteomic characterization of skeletal muscle tissues, including top-down proteomics focusing on the characterization of intact proteoforms and their post-translational modifications, bottom-up proteomics, which is a peptide-centric method concerned with the large-scale detection of proteins in complex mixtures, and subproteomics that examines the protein composition of distinct subcellular fractions. Mass spectrometric studies over the last two decades have decisively improved our general cell biological understanding of protein diversity and the heterogeneous composition of individual myofibers in skeletal muscles. This detailed proteomic knowledge can now be integrated with findings from other omics-type methodologies to establish a systems biological view of skeletal muscle function.

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Methods for Selective Gene Expression Profiling in Single Tertiary Lymphoid Structure Using Laser Capture Microdissection

Gutierrez-Chavez,

Knockaert,

Dieu-Nosjean

et al. 2024

Methods in Molecular Biology

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Laser capture microdissection for biomedical research: towards high-throughput, multi-omics, and single-cell resolution

Cited by 14 publications

References 98 publications

How Can Proteomics Help to Elucidate the Pathophysiological Crosstalk in Muscular Dystrophy and Associated Multi-System Dysfunction?

How Can Proteomics Help to Elucidate the Pathophysiological Crosstalk in Muscular Dystrophy and Associated Multi-System Dysfunction?

Mass Spectrometry-Based Proteomic Technology and Its Application to Study Skeletal Muscle Cell Biology

Methods for Selective Gene Expression Profiling in Single Tertiary Lymphoid Structure Using Laser Capture Microdissection

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