Comprehensive proteome, phosphoproteome and kinome characterization of luminal A breast cancer.

Background: Breast cancer is one of the most frequently occurring malignant cancers worldwide. Invasive ductal carcinoma (IDC) and invasive lobular carcinoma (ILC) are the two most common histological subtypes of breast cancer. In this study, we aimed to deeply explore molecular characteristics and the relationship between IDC and ILC subtypes in luminal A subgroup of breast cancer using comprehensive proteomics and phosphoproteomics analysis. Methods: Cancer tissues and noncancerous adjacent tissues (NATs) with the luminal A subtype (ER- and PR-positive, HER2-negative) were obtained from paired IDC and ILC patients respectively. Label-free quantitative proteomics and phosphoproteomics methods were used to detect differential proteins and the phosphorylation status between 10 paired breast cancer and NATs. Then, the difference in protein expression and its phosphorylation between IDC and ILC subtypes were explored. Meanwhile, the activation of kinases and their substrates was also revealed by Kinase-Substrate Enrichment Analysis (KSEA). Results: In the luminal A breast cancer, a total of 5,044 high-confidence proteins and 3,808 phosphoproteins were identified from 10 paired tissues. The protein phosphorylation level in ILC tissues was higher than that in IDC tissues. Histone H1.10 was significantly increased in IDC but decreased in ILC, Conversely, complement C4-B and Crk-like protein were significantly decreased in IDC but increased in ILC. Moreover, the increased protein expression of Septin-2, Septin-9, Heterogeneous nuclear ribonucleoprotein A1 and Kinectin but reduce of their phosphorylation could clearly distinguish IDC from ILC. In addition, IDC was primarily related to energy metabolism and MAPK pathway, while ILC was more closely involved in the AMPK and p53/p21 pathways. Furthermore, the kinomes in IDC were primarily significantly activated in the CMGC groups. Conclusions: Our research provides insights into the molecular characterization of IDC and ILC and contributes to discovering novel targets for further drug development and targeted treatment.

Proteome and Glycoproteome Analyses Reveal the Protein N-Linked Glycosylation Specificity of STT3A and STT3B.

STT3A and STT3B are the main catalytic subunits of the oligosaccharyltransferase complex (OST-A and OST-B in mammalian cells), which primarily mediate cotranslational and post-translocational N-linked glycosylation, respectively. To determine the specificity of STT3A and STT3B, we performed proteomic and glycoproteomic analyses in the gene knock-out (KO) and wild-type HEK293 cells. In total, 3961 proteins, 4265 unique N-linked intact glycopeptides and 629 glycosites representing 349 glycoproteins were identified from all these cells. Deletion of the STT3A gene had a greater impact on the protein expression than deletion of STT3B, especially on glycoproteins. In addition, total mannosylated N-glycans were reduced and fucosylated N-glycans were increased in STT3A-KO cells, which were caused by the differential expression of glycan-related enzymes. Interestingly, hyperglycosylated proteins were identified in KO cells, and the hyperglycosylation of ENPL was caused by the endoplasmic reticulum (ER) stress due to the STT3A deletion. Furthermore, the increased expression of the ATF6 and PERK indicated that the unfolded protein response also happened in STT3A-KO cells. Overall, the specificity of STT3A and STT3B revealed that defects in the OST subunit not only broadly affect N-linked glycosylation of the protein but also affect protein expression.

N-glycosylation of GDF15 abolishes its inhibitory effect on EGFR in AR inhibitor-resistant prostate cancer cells.

Castration-resistance of prostate cancer is one of the most challenging clinical problems. In the present study, we have performed proteomics and glycomics using LNCaP model. Growth differentiation factor-15 (GDF15) level is increased in androgen receptor (AR) inhibitor-resistant cells and the inhibitory effect of GDF15 on epithelial growth factor receptor (EGFR) pathway is relieved by GDF15 N70 glycosylation. Interference of GDF15 (siRNA or N70Q dominant negative) or EGFR pathway (inhibitor or siRNA for EGFR, SRC or ERK) decreases the resistant-cell survival in culture and tumor growth in mice. Our study reveals a novel regulatory mechanism of prostate cancer AR inhibitor resistance, raises the possibility of AR/SRC dual-targeting of castration-resistance of prostate cancer, and lays foundation for the future development of selective inhibitors of GDF15 glycosylation.

Exploring the physicochemical role of Pd dopant in promoting Li-ion diffusion dynamics and storage performance of NbS2 at the atomic scale.

The two-dimensional layered niobium disulfide (NbS2), as a kind of anode material for Li-ion batteries, has received great attention because of its excellent electronic conductivity and structural stability. However, its ionic conductivity is far from desirable. Herein, we have proposed an effective way to acquire the rapid promotion of its Li-ion diffusion dynamics from the palladium doping effect. By first-principle calculations, we firstly investigated quantitative relations among lattice constants, mechanical properties, and Pd-doped concentration (x) for Pd doped NbS2 (PdxNbS2). It is found that the interlayer spacing of PdxNbS2 undergoes dramatic expansion, which contributes to affording its large space for Li-ion storage. And Pd0.25NbS2 has the best ductility, exhibiting its excellent destruction-resistant properties. Among PdxNbS2 (x = 0, 0.083, 0.167, 0.250, 0.333, and 0.417), it is also proved that Pd0.25NbS2 is the easiest to be prepared with the introduction of NbPd3 as the raw material for the Pd-dopant and it also exhibits excellent thermal stability at room temperature (300 K). Most importantly, by analysis with the climbing-image nudged elastic band method (CI-NEB), it is revealed that Pd0.25NbS2 shows the lowest Li-ion diffusion energy barrier of 0.26 eV, which is also much lower than that of NbS2 (0.43 eV). This is attributed to the inductive effect of the Pd-dopant in its layered structure, trying to maintain the Li-S six-coordinated structure at the initial state when Li-ions transfer to the saddle point. Accordingly, it induces a small structural difference in coordinate structures between initial states and transition states. Moreover, Pd0.25NbS2 undergoes a less obvious oxidation and reduction reaction, maintaining its excellent structural stability during Li intercalation/deintercalation. Additionally, the theoretical average voltage of Pd0.25NbS2 (1.75 V for Li0.75Pd0.25NbS2vs. Li/Li+) is also much lower than that of NbS2 (2.41 V vs. Li/Li+), implying that it can provide a higher power density. Therefore, our theoretical results pave a distinctive way to develop an ultrahigh-rate and long-life anode material for Li-ion batteries.

Exploring the Efficient Na/K Storage Mechanism and Vacancy Defect-Boosted Li+ Diffusion Based on VSe2/MoSe2 Heterostructure Engineering.

As typical 2D materials, VSe2 and MoSe2 both play a complementary role in Li/Na/K storage. Therefore, we designed and optimized the VSe2/MoSe2 heterostructure to gain highly efficient Li/Na/K-ion batteries. Most importantly, achieving fast Li/Na/K-ion diffusion kinetics in the interlayer of VSe2/MoSe2 is a key point. First of all, first-principles calculations were carried out to systematically investigate the packing structure, mechanical properties, band structure, and Li/Na/K storage mechanism. Our calculated results suggest that a large interlayer spacing (3.80 Å), robust structure, and metallic character pave the way for achieving excellent charge-discharge performance for the VSe2/MoSe2 heterostructure. Moreover, V and Mo ions both suffer a very mild redox reaction even if Li/Na/K ions fill the interlayer space. These structures were all further verified to show thermal stability (300 K) by means of the AIMD method. By analyzing the Li/Na/K diffusion behavior and the effect of vacancy defect on the structural stability and energy barrier for Li interlayer diffusion, it is found that the VSe2/MoSe2 heterostructure exhibits very low-energy barriers for Na/K interlayer diffusion (0.21 eV for Na and 0.11 eV for K). Compared with the VSe2/MoSe2 heterostructure, the V0.92Se1.84/MoSe2 heterostructure not only can still maintain a stable structure and metallic character but also has much lower energy barrier for Li interlayer diffusion (0.07 vs 0.48 eV). These discoveries also break new ground to eliminate the obstacles preventing Li+ diffusion in the interlayer of other heterostructure materials. Besides, both VSe2/MoSe2 and V0.92Se1.84/MoSe2 heterostructures have low average open-circuit voltage (OCV) values during Li/Na/K interlayer diffusion (1.07 V for V0.92Se1.84/MoSe2 vs Li+, 0.86 V for VSe2/MoSe2 vs Na+, and 0.54 V for VSe2/MoSe2 vs K+), such low OCV values are beneficial for anode materials with excellent electrochemical properties. The above findings offer a new route to design anode materials for Li/Na/K-ion batteries.

Comprehensive Analysis of the Glycome and Glycoproteome of Bovine Milk-Derived Exosomes.

Bovine milk-derived exosomes (BMDEs) have potential applications in the pharmaceutical industry as drug delivery carriers. A comprehensive analysis of protein glycosylation in exosomes is necessary to elucidate the process of targeted delivery. In this work, free oligosaccharides (FOSs), O-glycans, and N-glycans in BMDEs and whey were first analyzed through multiple derivation strategies. In summary, 13 FOSs, 44 O-glycans, and 94 N-glycans were identified in bovine milk. To analyze site-specific glycosylation of glycoproteins, a one-step method was used to enrich and characterize intact glycopeptides. A total of 1359 proteins including 114 glycoproteins were identified and most of these were located in the exosomes. Approximately 95 glycopeptides were initially discovered and 5 predicted glycosites were confirmed in BMDEs. Collectively, these findings revealed the characterization and distribution of glycans and glycoproteins in BMDEs, providing insight into the potential applications of BMDEs in drug delivery and food science.