Feasibility of Phosphoproteomics on Leftover Samples After RNA Extraction With Guanidinium Thiocyanate

Rolfs, Frank; Piersma, Sander R.; Dias, Mariana Paes; Jonkers, Jos; Jiménez, Connie R.

doi:10.1016/j.mcpro.2021.100078

Cited by 10 publications

(24 citation statements)

References 46 publications

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“…Plasma (100 µl) was directly lysed with 1 ml TRIzol ® reagent. Total RNA was extracted using the phenol chloroform method ( 18 ). The concentration and quality of RNA was measured using ultraviolet spectrophotometry (Nanodrop ND2000; Thermo Fisher Scientific, Inc.).…”

Section: Methodsmentioning

confidence: 99%

Relationship between miRNA‑433 and SPP1 in the presence of fracture and traumatic brain injury

et al. 2021

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Limb fracture combined with traumatic brain injury (TBI) is one of the most common multiple injuries and patients often suffer from severe craniocerebral injury combined with long bone fracture of the limbs. The present study examined the expression of osteopontin (SPP1) in the tibial fracture callus and heterotopic ossification tissues in craniocerebral injury and investigated its relationship with miR-433. A total of 26 patients with tibial fracture combined with brain injury were included in the TBI group, and 26 patients with simple tibial fracture were included in the control group. The patients received immobilization treatment and callus was collected during the operation. At the time of steel plate removal tissue ossification samples from patients with heterotopic ossification were collected. Peripheral blood was collected from all patients on the morning of the operation day. Expression of miR-433 and SPP1 mRNA was determined by reverse transcription-quantitative PCR and SPP1 protein expression was measured by western blotting. Dual luciferase reporter assay was used to identify the direct interaction between miR-433 and SPP1 mRNA. The human osteoblast line hFOB1.19 was transfected with agomiR-433 to overexpress miR-433 and expression of SPP1 was also examined. TBI enhanced the incidence of callus formation and heterotopic ossification in patients with fracture but did not alter fracture healing time. SPP1 mRNA and protein expression was elevated in patients who had tibial fracture in combination with craniocerebral injury in comparison with controls By contrast, expression of miR-433 was decreased in patients who had tibial fracture in combination with craniocerebral injury in comparison with controls. miR-433 regulated the expression of SPP1 mRNA and protein by directly binding to the 3'-untranslated region of SPP1 mRNA. The present study suggests that SPP1 mRNA and protein levels are increased in the callus, heterotopic ossification tissues and plasma from patients with tibial fracture combined with brain injury in comparison with controls. This elevation may be due to the reduced expression of miR-433.

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Section: Methodsmentioning

confidence: 99%

Relationship between miRNA‑433 and SPP1 in the presence of fracture and traumatic brain injury

et al. 2021

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“…33 Jimenez published a phosphoproteomics study of AML focused on response to Flt3 inhibitors 34 and bench-marked a protocol that enabled (phospho)proteomics on the same sample. 35 Further analyses were performed on the DIA-MS-based pan-cancer atlas of 1200+ cancers representing 22 cancer types (The Cancer Proteome Atlas, www.cancerproteome.org) led by the Jimenez and Guo laboratories. They plan to expand to a larger Cancer HPP community effort.…”

Section: Cancersmentioning

confidence: 99%

“…Guo published a review on high-throughput proteomics and AI for cancer biomarker discovery . Jimenez published a phosphoproteomics study of AML focused on response to Flt3 inhibitors and bench-marked a protocol that enabled (phospho)proteomics on the same sample . Further analyses were performed on the DIA-MS-based pan-cancer atlas of 1200+ cancers representing 22 cancer types (The Cancer Proteome Atlas, ) led by the Jimenez and Guo laboratories.…”

Section: Highlights From the B/d-hppmentioning

confidence: 99%

“…The first HGI large community study, which compared glycoinformatics solutions for intact glycopeptide analysis from LC-MS/ MS data, a recognized bottleneck in the field, 36 was completed in 2021 with 55 participants (many HUPO members) across 22 teams from 11 different countries. The work was published in Nature Methods 35 and presented at international meetings by Thaysen-Andersen (HUPO 2021, Australian Glycoscience Symposium), Kolarich (Queensland MS Symposium, Lorne Proteomics), and Packer (Microscale Separations and Bioanalysis, B/D HPP Webinar), and at the Dagstuhl Seminar on Computational Proteomics in order to directly help the community create the toolboxes required to address unexplored glycobiology-focused fundamental and applied research questions in human health and disease.…”

Section: Glycoproteomicsmentioning

confidence: 99%

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The 2022 Report on the Human Proteome from the HUPO Human Proteome Project

et al. 2022

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The 2022 Metrics of the Human Proteome from the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 407 (93.2%) of the 19 750 predicted proteins coded in the human genome, a net gain of 50 since 2021 from data sets generated around the world and reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 78 from 1421 to 1343. This represents continuing experimental progress on the human proteome parts list across all the chromosomes, as well as significant reclassifications. Meanwhile, applying proteomics in a vast array of biological and clinical studies continues to yield significant findings and growing integration with other omics platforms. We present highlights from the Chromosome-Centric HPP, Biology and Disease-driven HPP, and HPP Resource Pillars, compare features of mass spectrometry and Olink and Somalogic platforms, note the emergence of translation products from ribosome profiling of small open reading frames, and discuss the launch of the initial HPP Grand Challenge Project, "A Function for Each Protein".

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“…The sequential phosphopeptide capture strategy as used here allows pTyr-phosphoproteomics to be performed together with global phosphoproteomics and proteomics on the same samples. Recent developments enable phosphoproteomics and proteomics in conjunction with other omics analyses on the same samples with further streamlining of protocols ( 16 , 17 , 39 ). Together, these integrative approaches will further motivate the development of phosphoproteomics-based companion diagnostics for more informed patient stratification and treatment decisions, further contributing to the realization of personalized anticancer medicine.…”

Section: Discussionmentioning

confidence: 99%

Phosphoproteomics of patient-derived xenografts identifies targets and markers associated with sensitivity and resistance to EGFR blockade in colorectal cancer

et al. 2023

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Epidermal growth factor receptor (EGFR) is a well-exploited therapeutic target in metastatic colorectal cancer (mCRC). Unfortunately, not all patients benefit from current EGFR inhibitors. Mass spectrometry–based proteomics and phosphoproteomics were performed on 30 genomically and pharmacologically characterized mCRC patient–derived xenografts (PDXs) to investigate the molecular basis of response to EGFR blockade and identify alternative drug targets to overcome resistance. Both the tyrosine and global phosphoproteome as well as the proteome harbored distinctive response signatures. We found that increased pathway activity related to mitogen-activated protein kinase (MAPK) inhibition and abundant tyrosine phosphorylation of cell junction proteins, such as CXADR and CLDN1/3, in sensitive tumors, whereas epithelial-mesenchymal transition and increased MAPK and AKT signaling were more prevalent in resistant tumors. Furthermore, the ranking of kinase activities in single samples confirmed the driver activity of ERBB2, EGFR, and MET in cetuximab-resistant tumors. This analysis also revealed high kinase activity of several members of the Src and ephrin kinase family in 2 CRC PDX models with genomically unexplained resistance. Inhibition of these hyperactive kinases, alone or in combination with cetuximab, resulted in growth inhibition of ex vivo PDX-derived organoids and in vivo PDXs. Together, these findings highlight the potential value of phosphoproteomics to improve our understanding of anti-EGFR treatment and response prediction in mCRC and bring to the forefront alternative drug targets in cetuximab-resistant tumors.

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Feasibility of Phosphoproteomics on Leftover Samples After RNA Extraction With Guanidinium Thiocyanate

Abstract: RNA-Bee UreaTiO 2 MS/MS Urea RNA-Bee high similarity phosphosites cells tissue + IR PTM-SEA

Cited by 10 publications

References 46 publications

Relationship between miRNA‑433 and SPP1 in the presence of fracture and traumatic brain injury

Relationship between miRNA‑433 and SPP1 in the presence of fracture and traumatic brain injury

The 2022 Report on the Human Proteome from the HUPO Human Proteome Project

Phosphoproteomics of patient-derived xenografts identifies targets and markers associated with sensitivity and resistance to EGFR blockade in colorectal cancer

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