Highly accurate identification of cystic precursor lesions of pancreatic cancer through targeted mass spec Ometry: A phase II touch diagnostic study.

molecular screening based on high-throughput technology has greatly facilitated human research on genetic changes and accelerated our exploration of physiological and pathological mechanisms. However, the accuracy of high-throughput technology cannot reach 100%, so the real changes of differential genes analyzed by high-throughput screening still need to be verified. For example, DNA and mRNA can be verified by qPRC, and the most common protein verification method is WB or ELISA. These low-throughput technologies are highly targeted and highly accurate, but their throughput is small and inefficient, which is a burden for researchers who have more differential molecules to be verified, especially using WB or ELISA to verify differential proteins. As a mass spectrometry-based targeted protein detection technology,

PRM (Parallel Reaction Monitoring) can perform quantitative detection of dozens of target proteins at one time, greatly improving the verification efficiency of target proteins. Whether it is used to reveal protein characteristics under physiological and pathological conditions or to mine key molecules, proteomics +PRM verification is a very efficient technical means.

Jikai Gene provides PRM and PRM detection based on 4D mass spectrometer to help scientific researchers better conduct protein-related research. In this article, we will take you to understand the application of proteomics + PRM ideas in the literature and the application of PRM alone, hoping to help you better understand this technology.

. PRM: In combination with proteomics, screen potential biomarker

Literature 1

Proteomics Screening of biomarkers that distinguish cystic lesions of malignant and malignant pancreatic cancer

Highly Accurate Identification of Cystic Precursor Lesions of Pancreatic Cancer Through Targeted Mass Spectrometry: A Phase IIc Diagnostic Study

Journal of Clinical Oncology

Impact Factor : 44.544 PMID:29166170

Pancreatic cystic lesions are an occasional discovery on imaging , but as many as half of them may be a precursor to pancreatic cancer . Therefore, accurate diagnosis is the key to patient treatment. Currently available diagnostic methods do not reliably identify precancerous and malignant pancreatic cystic lesions. Therefore, the main purpose of this study was to use quantitative proteomic discoveries in multiple cohorts to identify and distinguish precancerous pancreatic cystic lesions (PCL) from significant high-level developmental abnormalities (HGD)/markers of cancer and cystic tumors. Finally, the relevant protein markers were found through PRM detection of targeted proteins: the combination of mucin-5AC and mucin-2 was divided into 97% in the verification cohort, which was significantly higher than the results of the traditional carcinoembryonic antigen and cytology examination. The combined accuracy of mucin-5AC and prostate stem cell antigen (PSCA) in recognition of high-level dysplasia/cancer is 96%. This study will help to promptly diagnose cancer and to intervene or prevent disease early.

Literature 2

DIA Proteomics + PRM Identification of biomarkers for chemotherapy response in advanced lung cancer

Identification of serum biomarkers to predict pemetrexed/platinum chemotherapy efficiency for advanced lung adenocarcinoma patients by data-independent acquisition (DIA) mass spectrometry analysis with parallel reaction monitoring (PRM) verification
Journal : Translational Lung Cancer Research

Impact Factor : 6.496 PMID: 33718037

pemetrexed/platinum chemotherapy is the standard chemotherapy regimen for patients with lung adenocarcinoma , but the efficacy varies greatly. To discover new serum biomarkers to predict the efficacy of pemetrexed/platinum chemotherapy, the authors conducted DIA proteomics tests on serum samples from 20 patients with advanced lung adenocarcinoma who received pemetrexed/platinum chemotherapy. The chemotherapy-responsive group (PR) obtained a total of 23 differential proteins compared with the chemotherapy-responsive group (PD) group, and 7 proteins predicted ROC AUC values ​​for treatment responses were higher than 0.8.To further validate DIA proteomic results, the authors used RPM to detect 16 candidate serum biomarkers in the study cohort of these 20 patients and a new cohort of 22 patients with advanced lung adenocarcinoma (16 PR and 6 PD). PRM validation showed good consistency with DIA proteomics, and 10 differences protein showed similar upregulation or downregulation. Overall, the researchers found potential protein markers that can better respond to advanced lung adenocarcinoma treatment response through DIA proteomics and PRM validation.

. PRM: In combination with proteomics, a simple mechanism study was conducted

Literature 1

Proteomics + phosphorylated proteomics reveal abnormal immunomodulation in patients with new ankylosing spondylitis

Global Proteomics Analyses Reveals Abnormal Immune Regulation in

Patients With New Onset Ankylosing Spondylit

Journal : frontiers in Immunology

Impact factor : 7.561 PMID: 35371008

Ankylosing spondylitis (AS) is a chronic inflammatory disease with high incidence and mortality. In this paper, the researchers tested the proteomics and phosphorylated proteomics of peripheral blood mononuclear cells (PBMCs) in patients with newly developed AS and healthy people, and revealed abnormal immunomodulatory abnormalities in patients with ankylosing spondylitis through bioinformatic analysis. Subsequently, the researchers conducted PRM verification on the differentially changed proteins related to immunomodulation (19 total). The verification results are highly consistent with the proteomic results, and reconfirmed the abnormalities in immunomodulation-related functions. These proteins may serve as candidate markers and new therapeutic targets for AS diagnosis.

Literature 2

Proteomics reveals the response of osteosarcoma cells to IL-6 intervention in Loplatin treatment

Protein and Signaling Pathway Responses to rhIL-6 Intervention Before Lobaplatin Treatment in Osteosarcoma Cells

Journal : Frontiers in Oncology

Influencing factor : 6.244 PMID:33791202

lobaplatin is a third-generation platinum anti-tumor drug, which is widely used in the treatment of osteosarcoma before and after resection. However, lorboplatin resistance will cause treatment failure. The researchers found that osteosarcoma cells became insensitive to loplatin after treatment with exogenous interleukin-6 (IL-6), and the researchers used proteomics to clarify the underlying mechanism.

investigators conducted proteomic detection of osteosarcoma cells in the control group, the Lobacterium-treated group, the recombinant human interleukin-6 (rhIL6) and the Lobacterium-treated group, and verified 31 differential proteins through PRM, among which G3BP1, hFXR1p and FUBP were significantly differentially expressed. Immuno-tissue staining and immunofluorescence staining also showed that these three proteins were highly expressed in specimens of patients with loplatin-resistant osteosarcoma, while negative or weakly expressed in specimens of patients with loplatin-sensitive osteosarcoma. Knockout of FUBP1 showed that the IC50 value of loplatin was significantly reduced in FUBP1-silent cells, indicating that FUBP1 deletion increased the sensitivity of osteosarcoma cells to loplatin. This result reveals the role of FUBP1 in drug sensitivity of osteosarcoma and the potential therapeutic value of increasing osteosarcoma loplatin sensitivity by silencing FUBP1.

. PRM: complementary technology of WB/PCR, verify more proteins at one time

Literature 1

KIF5A-dependent axonal transport defect interferes with trimethyltin chloride (TMT)-induced neurotoxicity

KIF5A-dependent axonal transport deficiency disrupts autophagic flux in trimethyltin chloride-induced neurotoxicity

Journal : Autophagy

Influence factor : 16.016 PMID:32160081

Trimethyltin chloride (TMT) is widely used in the industrial and agricultural fields as a fungicide and plastic stabilizer, and is generally considered to have strong neurotoxicity, especially in the brain hippocampus .However, the mechanism by which TMT induces neurotoxicity is not yet known. In this paper, researchers used proteomics and student-informed analysis to reveal the important role of macroautophagy/ autophagy -lysosome mechanism in TMT-induced neurotoxicity. TMT significantly impairs the autophagy flux by inhibiting lysosomal function, such as inhibiting lysosomal proteolysis, thereby causing autophagy clearance defects, which in turn leads to nerve cell death. Mechanistically, IPA analysis identified a downregulated molecule, KIF5A, which is a key target for TMT-induced impaired autophagy flux. TMT reduces the expression of the KIF5A protein, disrupts the interaction between KIF5A and lysosomes, and impairs lysosomal axonal transport. The researchers' results demonstrate that in TMT-induced neurotoxicity, KIF5A-dependent axonal transport defects lead to autophagy flux damage by interfering with lysosomal function, and regulating KIF5A may be a treatment to combat TMT-induced neurotoxicity.

In this paper, in studying the effect of KIF5A reversing TMT toxicity, the researchers used PRM to target the expression of autophagy-related proteins in TMT-treated KIF5A overexpressing cells, and found that KIF5A reversed the protein changes caused by TMT treatment.

Literature 2

WDR45 participates in neurodegenerative lesions by regulating endoplasmic reticulum homeostasis and neuronal death

WDR45 contributes to neurodegeneration through regulation of ER homeostasis and neuronal death

Journal : Autophagy

Impact factor :16.016 PMID:31204559

β propellin-related neurodegenerative disease (BPAN) is a type of neurodegenerative disease related to iron deposition in brain tissue. It manifests as motor and cognitive developmental delays in childhood, intellectual disability, and continues to adulthood. Exon sequencing discovered WDR45 mutations, but the mechanisms of how WDR45 loss lead to neurodegeneration in BPAN are still unclear. In this study, WDR45 knockout mice were constructed using CRISPR-Cas9 technology, in order to study the pathogenic mechanism of the WDR45 gene based on this model.

To verify whether WDR45 knockdown was successful, the researchers used mRNA qRT-PCR and WB to detect the expression deletion of WDR45's mRNA and protein in the experimental group, respectively. qRT-PCR identified the significant deletion of WDR45, but commercial antibodies could not detect the expression of WDR45 protein in the control group and experimental group. Therefore, the researchers used PRM technology to target WDR45. The PRM results showed that in the experimental group, both specific peptides of WDR45 were significantly deleted, which clarified the deletion of WDR45 protein. Combined mRNA qRT-PCR and PRM-targeted assays demonstrate the researchers' success in WDR45 knockdown. Therefore, PRM is a good technology for targeted protein detection, and researchers can flexibly select protein detection or verification techniques based on the specific situation of the experiment.

Jikai Gene provides PRM and 4D-PRMprotein services to help scientific researchers better conduct protein-related research. For PRM product quotation and cycle, please add Jikai "jikaikefu" on WeChat for consultation.

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·High-throughput sequencing platform divided into conventional Sequencing service and single-cell sequencing service: single-cell sequencing has two platforms: 10x and BD, providing single-cell RNA-seq, single-cell nucleus sequencing, single-cell mixed RNA-seq, single-cell TCR/BCR, single-cell (RNA+ATAC), spatial transcriptome sequencing and other services; routine sequencing service provides meRIP-seq (m6A/m1A/m7G/m5C RNA methylation modification sequencing), acRIP-seq (ac4C RNA acetylation modification sequencing), ATAC-seq, Ribo-seq (translation group sequencing), mRNA/miRNA/LncRNA/circRNA-seq, whole transcriptome sequencing (two libraries/three libraries), exosomal miRNA/LncRNA-seq, WGS/WES, WGBS, RRBS, BSAS and other services.