DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to generate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000

The insulin-like growth factor-I receptor kinase inhibitor, NVP-ADW742, suppresses survival and resistance to chemotherapy in acute myeloid leukemia cells

The overexpression of Insulin-like growth factor-I receptor (IGF-IR) is strongly suggested to exert a role in malignant transformation and survival promotion in solid tumors such as breast cancer and prostate cancer, while fewer studies investigated the pathophysiological role of Insulin-like growth factor-I (IGF-I) signaling in acute myeloid leukemia (AML). In this study, we firstly found that the IGF-IR expression level positively correlated with the blast counts in de novo AML patients. Moreover, we observered that inhibitor of IGF-IR by NVP-ADW742, a novel kinase inhibitor of IGF-IR, could induce apoptosis in both HL-60 cell line and primary AML blasts, However, no significant alteration in the cell cycle status was observed in HL-60 cells. Further studies showed that NVP-ADW742 induced Akt dephosphorylation and p38 phosphorylation, decreased the expression of anti-apoptotic protein bcl-2 in HL-60 cells. Besides, we also demostrated that NVP-ADW742 could synergize with ara-C to induce apoptosis in subsets primary drug-resistant AML blasts. Therefore, IGF-IR targeting might be of therapeutic benefit for some AML patients

Discovery of anti-inflammatory dihydroxylated phenolic acids in patients with severe cardiac symptoms and conditions associated with inflammation and hypoxia

Our initial studies detected elevated levels of 3,4-dihydroxyphenyllactic acid (DHPLA) in urine samples of patients with severe cardiac symptoms when compared with healthy subjects. In view of the reported anti-inflammatory properties of DHPLA and related dihydroxylated phenolic acids (DPAs), we embarked on a multi-centre investigation to establish the possible pathophysiological significance and therapeutic implications of these findings. Chinese and Caucasian patients with severe cardiac symptoms and those being treated for conditions associated with inflammation (WBC ≥ 10×109/L or hsCRP ≥ 3.0 mg/L) and/or hypoxia (PaO2 ≤ 75 mmHg) were enrolled, their urine samples were analyzed by HPLC, HPLC-MS, GC-MS and biotransformation assays. DHPLA was detected in urine samples of patients, but undetectable in healthy volunteers. Dynamic monitoring of inpatients undergoing treatment showed their DHPLA levels declined in proportion to their clinical improvement. Proteus vulgaris and P. mirabilis were significantly more abundant in DHPLA-positive patients’ fecal samples than healthy volunteers. In culture, these bacteria were capable of reversible interconversion between DOPA and DHPLA. Furthermore, porcine and rodent organs were able to metabolize DOPA to DHPLA and related phenolic acids. The elevated levels of DHPLA in these patients suggest anti-inflammatory DPAs are generated de novo as part of a human’s defense mechanism against disease. Given that DHPLA isolated from Radix Salvia miltiorrhizae has multi-dimensional pharmacological activities, these data demonstrate not only scientific basis of the ethnopharmacological uses of this medicinal plant but also highlight the therapeutic potential of endogenous, natural or synthetic DPAs and their derivatives in humans

DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to generate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000