Label‐Free Quantitative Proteomic Screening of Candidate Plasma Biomarkers for the Prognosis of Breast Cancer with Different Lymph Node Statuses

Chen, Ling; Zhao, Weibo; He, Jing; Li, Liqi; Meng, Di; Cai, Dongyan; Yu, Jinjin; Chen, Daozhen; Wu, Yibo; Zhou, Tao

doi:10.1002/prca.201700117

Cited by 6 publications

(4 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…SERPIND1, which was significantly up-regulated in the reactive perfusate samples, was also upregulated in node-negative Her2-positive BC patients 17 . KRT9 was significantly up-regulated in the metastatic perfusate samples; this was found to be up-regulated in node-positive Her2-positive patients previously 17 . Lobo et al found APOC3 to be up-regulated in patients with stage I/II BC (i.e.…”

Section: Resultsmentioning

confidence: 86%

“…With regard to proteomics, there is little concordance between the few studies that have tried to identify biomarkers of axillary disease in human serum/plasma samples [12][13][14][15][16][17] . Similarly, human tissue studies comparing the proteomes of primary BC to matched ALN metastases have yielded disparate data [18][19][20][21][22][23] .…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Proteomics of REPLICANT perfusate detects changes in the metastatic lymph node microenvironment

Stevenson

Barrow-McGee

et al. 2021

npj Breast Cancer

View full text Add to dashboard Cite

In breast cancer (BC), detecting low volumes of axillary lymph node (ALN) metastasis pre-operatively is difficult and novel biomarkers are needed. We recently showed that patient-derived ALNs can be sustained ex-vivo using normothermic perfusion. We now compare reactive (tumour-free; n = 5) and macrometastatic (containing tumour deposits >2 mm; n = 4) ALNs by combining whole section multiplex immunofluorescence with TMT-labelled LC-MS/MS of the circulating perfusate. Macrometastases contained significantly fewer B cells and T cells (CD4+/CD8+/regulatory) than reactive nodes (p = 0.02). Similarly, pathway analysis of the perfusate proteome (119/1453 proteins significantly differentially expressed) showed that immune function was diminished in macrometastases in favour of ‘extracellular matrix degradation’; only ‘neutrophil degranulation’ was preserved. Qualitative comparison of the perfusate proteome to that of node-positive pancreatic and prostatic adenocarcinoma also highlighted ‘neutrophil degranulation’ as a contributing factor to nodal metastasis. Thus, metastasis-induced changes in the REPLICANT perfusate proteome are detectable, and could facilitate biomarker discovery.

show abstract

Section: Resultsmentioning

confidence: 86%

Section: Introductionmentioning

confidence: 99%

Proteomics of REPLICANT perfusate detects changes in the metastatic lymph node microenvironment

Stevenson

Barrow-McGee

et al. 2021

npj Breast Cancer

View full text Add to dashboard Cite

show abstract

“…The fact that we identified such a high number of bound proteins is mainly due to the extensive fractionation strategies we applied post low-abundance protein enrichment. Most proteomics studies that have employed the ProteoMiner kit with no additional fractionation report identification of ∼500–1000 proteins. ,,, …”

Section: Discussionmentioning

confidence: 99%

“…Most proteomics studies that have employed the ProteoMiner kit with no additional fractionation report identification of ∼500−1000 proteins. 16,19,20,54 While analyzing the ProteoMiner unbound fractions (flowthrough), we identified 3682 total proteins in the flowthrough, indicating that the fractionation facilitated identification of increased numbers of proteins but also demonstrated bead saturation of a very large number of proteins, which would be problematic for subsequent quantitative work. To overcome this quantification issue, it is possible that the proteins uniquely expressed in the bound fraction, but not present in the unbound fraction, could be compared in a relative quantification approach since these are not saturated.…”

Section: ■ Discussionmentioning

confidence: 99%

Extending the Depth of Human Plasma Proteome Coverage Using Simple Fractionation Techniques

et al. 2021

View full text Add to dashboard Cite

Human plasma is one of the most widely used tissues in clinical analysis, and plasma-based biomarkers are used for monitoring patient health status and/or response to medical treatment to avoid unnecessary invasive biopsy. Data-driven plasma proteomics has suffered from a lack of throughput and detection sensitivity, largely due to the complexity of the plasma proteome and in particular the enormous quantitative dynamic range, estimated to be between 9 and 13 orders of magnitude between the lowest and the highest abundance protein. A major challenge is to identify workflows that can achieve depth of plasma proteome coverage while minimizing the complexity of the sample workup and maximizing the sample throughput. In this study, we have performed intensive depletion of high-abundant plasma proteins or enrichment of lowabundant proteins using the Agilent multiple affinity removal liquid chromatography (LC) columnHuman 6 (Hu6), the Agilent multiple affinity removal LC columnHuman 14 (Hu14), and ProteoMiner followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS PAGE) and C18 prefractionation techniques. We compared the performance of each of these fractionation approaches to identify the method that satisfies requirements for analysis of clinical samples and to include good plasma proteome coverage in combination with reasonable sample output. In this study, we report that one-dimensional (1D) gel-based prefractionation allows parallel sample processing and no loss of proteome coverage, compared with serial chromatographic separation, and significantly accelerates analysis time, particularly important for large clinical projects. Furthermore, we show that a variety of methodologies can achieve similarly high plasma proteome coverage, allowing flexibility in method selection based on project-specific needs. These considerations are important in the effort to accelerate plasma proteomics research so as to provide efficient, reliable, and accurate diagnoses, population-based health screening, clinical research studies, and other clinical work.

show abstract

Proteomic Interrogation in Cancer Biomarker

Kang

2021

Advances in Experimental Medicine and Biology

View full text Add to dashboard Cite

Label‐Free Quantitative Proteomic Screening of Candidate Plasma Biomarkers for the Prognosis of Breast Cancer with Different Lymph Node Statuses

Abstract: The present dataset provides a list of candidate biomarkers that could be used for early differentiation diagnosis and prognosis of breast cancer with lymph node metastasis.

Cited by 6 publications

References 26 publications

Proteomics of REPLICANT perfusate detects changes in the metastatic lymph node microenvironment

Proteomics of REPLICANT perfusate detects changes in the metastatic lymph node microenvironment

Extending the Depth of Human Plasma Proteome Coverage Using Simple Fractionation Techniques

Proteomic Interrogation in Cancer Biomarker

Contact Info

Product

Resources

About