Comprehensive micro-scaled proteome and phosphoproteome characterization of archived retrospective cancer repositories
2021
Formalin-fixed paraffin-embedded (FFPE) tissues are a valuable resource for retrospective clinical studies. Here, we evaluate the feasibility of (phospho-)proteomics on FFPE lung tissue regarding protein extraction, quantification, pre-analytics, and sample size. After comparing protein extraction protocols, we use the best-performing protocol for the acquisition of deep (phospho-)proteomes from lung squamous cell and adenocarcinoma with >8,000 quantified proteins and >14,000 phosphosites with a tandem mass tag (TMT) approach. With a microscaled approach, we quantify 7,000 phosphosites, enabling the analysis of FFPE biopsies with limited tissue amounts. We also investigate the influence of pre-analytical variables including fixation time and heat-assisted de-crosslinking on protein extraction efficiency and proteome coverage. Our improved workflows provide quantitative information on protein abundance and phosphosite regulation for the most relevant oncogenes, tumor suppressors, and signaling pathways in lung cancer. Finally, we present general guidelines to which methods are best suited for different applications, highlighting TMT methods for comprehensive (phospho-)proteome profiling for focused clinical studies and label-free methods for large cohorts. Formalin-fixed, paraffin-embedded (FFPE) specimens are an attractive resource for retrospective clinical proteomics studies. Here, the authors benchmark and optimize proteomics workflows for FFPE sample analysis and provide guidelines on which methods to use for different samples and applications.
1
Citations in 🌏 GeoScience
[
{
"id": "3972776",
"title": "DNA methylation-based classification of sinonasal tumors",
"abstract": "The diagnosis of sinonasal tumors is challenging due to a heterogeneous spectrum of various differential diagnoses as well as poorly defined, disputed entities such as sinonasal undifferentiated carcinomas (SNUCs). In this study, we apply a machine learning algorithm based on DNA methylation patterns to classify sinonasal tumors with clinical-grade reliability. We further show that sinonasal tumors with SNUC morphology are not as undifferentiated as their current terminology suggests but rather reassigned to four distinct molecular classes defined by epigenetic, mutational and proteomic profiles. This includes two classes with neuroendocrine differentiation, characterized by IDH2 or SMARCA4/ARID1A mutations with an overall favorable clinical course, one class composed of highly aggressive SMARCB1-deficient carcinomas and another class with tumors that represent potentially previously misclassified adenoid cystic carcinomas. Our findings can aid in improving the diagnostic classification of sinonasal tumors and could help to change the current perception of SNUCs. Sinonasal tumour diagnosis can be complicated by the heterogeneity of disease and classification systems. Here, the authors use machine learning to classify sinonasal undifferentiated carcinomas into 4 molecular classe with differences in differentiation state and clinical outcome.",
"source_url": "https://www.nature.com/articles/s41467-022-34815-3",
"doc_type": 4,
"year": 2022,
"issue": 1,
"volume": 13,
"first_page": 1,
"last_page": 14,
"citation_count": 0,
"reference_count": 2,
"venue": {
"id": 2110000199,
"name": "NATURE COMMUNICATIONS",
"abbr": ""
},
"author": [
{
"id": 1004249733,
"name": "Jurmeister, Philipp"
},
{
"id": 1004249734,
"name": "Glöß, Stefanie"
},
{
"id": 1004249735,
"name": "Roller, Renée"
},
{
"id": 1004249736,
"name": "Leitheiser, Maximilian"
},
{
"id": 1000719005,
"name": "Simone Schmid"
},
{
"id": 1003920762,
"name": "Liliana H. Mochmann"
},
{
"id": 1004249737,
"name": "Payá Capilla, Emma"
},
{
"id": 1004249738,
"name": "Fritz, Rebecca"
},
{
"id": 1001441745,
"name": "Carsten Dittmayer"
},
{
"id": 1001612766,
"name": "Corinna Friedrich"
},
{
"id": 1004249739,
"name": "Thieme, Anne"
},
{
"id": 1004249740,
"name": "Keyl, Philipp"
},
{
"id": 1004249741,
"name": "Jarosch, Armin"
},
{
"id": 1001612767,
"name": "Simon Schallenberg"
},
{
"id": 1001169273,
"name": "Hendrik Bläker"
},
{
"id": 1004249742,
"name": "Hoffmann, Inga"
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{
"id": 1002375875,
"name": "Claudia Vollbrecht"
},
{
"id": 1003838227,
"name": "Annika Lehmann"
},
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"id": 1001312195,
"name": "Michael Hummel"
},
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"id": 1001411772,
"name": "Daniel Heim"
},
{
"id": 1001612769,
"name": "Mohamed Haji"
},
{
"id": 1004249743,
"name": "Harter, Patrick"
},
{
"id": 1001257620,
"name": "Benjamin Englert"
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{
"id": 1001209630,
"name": "Stephan Frank"
},
{
"id": 1001209628,
"name": "Jürgen Hench"
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"id": 1001209683,
"name": "Werner Paulus"
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{
"id": 1001209699,
"name": "Martin Hasselblatt"
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{
"id": 1001249030,
"name": "Wolfgang Hartmann"
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{
"id": 1001209596,
"name": "Hildegard Dohmen"
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{
"id": 1004249744,
"name": "Keber, Ursula"
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"id": 1001707545,
"name": "Paul Jank"
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{
"id": 1001223555,
"name": "Carsten Denkert"
},
{
"id": 1001231319,
"name": "Christine Stadelmann"
},
{
"id": 1003605003,
"name": "Felix Bremmer"
},
{
"id": 1004249745,
"name": "Richter, Annika"
},
{
"id": 1004249746,
"name": "Wefers, Annika"
},
{
"id": 1001812259,
"name": "Julika Ribbat-Idel"
},
{
"id": 1001206681,
"name": "Sven Perner"
},
{
"id": 1001816780,
"name": "Christian Idel"
},
{
"id": 1001229979,
"name": "Lorenzo Chiariotti"
},
{
"id": 1001552265,
"name": "Rosa Della Monica"
},
{
"id": 1004249747,
"name": "Marinelli, Alfredo"
},
{
"id": 1001209694,
"name": "Ulrich Schüller"
},
{
"id": 1001713595,
"name": "Michael Bockmayr"
},
{
"id": 1001632590,
"name": "Jacklyn Liu"
},
{
"id": 1001632619,
"name": "Valerie J. Lund"
},
{
"id": 1001509371,
"name": "Martin Forster"
},
{
"id": 1001209644,
"name": "Matt Lechner"
},
{
"id": 1004249748,
"name": "Lorenzo-Guerra, Sara L."
},
{
"id": 1002073398,
"name": "Mario Hermsen"
},
{
"id": 1001370186,
"name": "Pascal D. Johann"
},
{
"id": 1001284350,
"name": "Abbas Agaimy"
},
{
"id": 1001713593,
"name": "Philipp Seegerer"
},
{
"id": 1001209651,
"name": "Arend Koch"
},
{
"id": 1001209650,
"name": "Frank Heppner"
},
{
"id": 1001190494,
"name": "Stefan M. Pfister"
},
{
"id": 1001190487,
"name": "David T. W. Jones"
},
{
"id": 1001209579,
"name": "Martin Sill"
},
{
"id": 1001209701,
"name": "Andreas von Deimling"
},
{
"id": 1001209700,
"name": "Matija Snuderl"
},
{
"id": 1000289774,
"name": "Klaus-Robert Müller"
},
{
"id": 1004249749,
"name": "Forgó, Erna"
},
{
"id": 1001422750,
"name": "Brooke E. Howitt"
},
{
"id": 1001249224,
"name": "Philipp Mertins"
},
{
"id": 1001313326,
"name": "Frederick Klauschen"
},
{
"id": 1001209578,
"name": "David Capper"
}
],
"field": [
{
"id": 2015533717,
"name": "Glomus tumour"
},
{
"id": 2008621301,
"name": "Glomangioma"
},
{
"id": 2004556151,
"name": "Appendix cancer"
},
{
"id": 2009549671,
"name": "Pseudomyxoma peritonei"
}
],
"cite": [
{
"name": "GB/T 7714",
"text": "Philipp Jurmeister,, Stefanie Glöß,, Renée Roller,, et al. DNA methylation-based classification of sinonasal tumors[J]. NATURE COMMUNICATIONS, 2022, 13(1): 1-14."
},
{
"name": "MLA",
"text": "Philipp, Jurmeister,, et al. \"DNA methylation-based classification of sinonasal tumors\" NATURE COMMUNICATIONS., vol. 13, no. 1, 2022, pp. 1-14."
},
{
"name": "APA",
"text": "Philipp Jurmeister,, Stefanie Glöß,, Renée Roller,, Maximilian Leitheiser,, Schmid Simone, Mochmann Liliana H., ... & Friedrich Corinna (2022). DNA methylation-based classification of sinonasal tumors. NATURE COMMUNICATIONS, 13(1), 1-14."
},
{
"name": "BibTeX",
"text": "@inproceedings{Acemap3972776,\n title=\"DNA methylation-based classification of sinonasal tumors\",\n author=\"{Jurmeister, Philipp} and {Glöß, Stefanie} and {Roller, Renée} and {Leitheiser, Maximilian} and Simone {Schmid} and {Liliana H. Mochmann} and {Payá Capilla, Emma} and {Fritz, Rebecca} and Carsten {Dittmayer} and Corinna {Friedrich} and {Thieme, Anne} and {Keyl, Philipp} and {Jarosch, Armin} and Simon {Schallenberg} and {Hendrik Bläker} and {Hoffmann, Inga} and Claudia {Vollbrecht} and Annika {Lehmann} and Michael {Hummel} and Daniel {Heim} and Mohamed {Haji} and {Harter, Patrick} and Benjamin {Englert} and Stephan {Frank} and {Jürgen Hench} and Werner {Paulus} and Martin {Hasselblatt} and Wolfgang {Hartmann} and Hildegard {Dohmen} and {Keber, Ursula} and Paul {Jank} and Carsten {Denkert} and Christine {Stadelmann} and Felix {Bremmer} and {Richter, Annika} and {Wefers, Annika} and {Julika Ribbat-Idel} and Sven {Perner} and Christian {Idel} and Lorenzo {Chiariotti} and Rosa Della {Monica} and {Marinelli, Alfredo} and {Ulrich Schüller} and Michael {Bockmayr} and Jacklyn {Liu} and {Valerie J. Lund} and Martin {Forster} and Matt {Lechner} and {Lorenzo-Guerra, Sara L.} and Mario {Hermsen} and {Pascal D. Johann} and Abbas {Agaimy} and Philipp {Seegerer} and Arend {Koch} and Frank {Heppner} and {Stefan M. Pfister} and {David T. W. Jones} and Martin {Sill} and Andreas von {Deimling} and Matija {Snuderl} and {Klaus-Robert Müller} and {Forgó, Erna} and {Brooke E. Howitt} and Philipp {Mertins} and Frederick {Klauschen} and David {Capper}\",\n journal=\"NATURE COMMUNICATIONS\",\n volume=\"13\",\n number=\"1\",\n pages=\"1--14\",\n url=\"https://www.acemap.info/paper/3972776\",\n year=\"2022\"\n}"
}
]
}
]
