An integrated quantitative proteomics strategy reveals the dual mechanisms of celastrol against acute inflammation

Comprehensive host cell proteins profiling in biopharmaceuticals by a sensitivity enhanced mass spectrometry strategy using TMT-labeling and signal boosting

BACKGROUND

Host Cell Proteins (HCPs) are impurities expressed in host cells during the biopharmaceutical production process, whichmay compromise product quality and potentially leading to immunogenic reactions or other adverse effects. Mass spectrometry (MS)-based strategy is more and more considered as a promising method for HCPs analysis, since it is capable of simultaneously quantifying thousands of proteins in a single test. However, considering the large excess biopharmaceutical product protein present in the system and the extremely low abundance of HCPs, sensitive MS methods are urgently needed in HCPs analysis.

RESULTS

In this work, we introduced a novel approach that leveraged host cell lysate as a boosting channel to enhance the MS signal of the residue HCPs in biopharmaceutical products using isobaric TMT labeling, thereby elevating the low-abundant HCPs to detectable and quantifiable levels of current MS without using enrichment or depletion method to avoid disturbance of the original concentration of the HCPs. Our method surpassed previous benchmarks by identifying a significantly higher number (23844 unique peptides for 3475 proteins) compared to existing records (4541 unique peptides for 848 proteins) for HCPs analysis in RM8671 NIST monoclonal antibody (mAb), demonstrating unparalleled sensitivity and robustness. Furthermore, our workflow successfully identified 44 of 48 UPS1 proteins across a concentration range of 0.32-4.15 ppm in monoclonal antibodies (mAbs), proving its effectiveness for in-depth HCPs analysis in biopharmaceuticals.

SIGNIFICANCE

Present even at sub-ppm levels, HCPs may compromise the stability and safety of product proteins and alter pharmacokinetics or neutralization of therapeutic effects. Our MS signal enhancing method presented an advancement in HCP analysis, combining improved sensitivity and increased scale of HCPs with a streamlined and robust workflow. This method allowed HCPs quantification at <1 ppm level without disturbance of the original HCPs concentration, which is still rare in the field.

Multi-omics analysis of attenuated variant reveals potential evaluation marker of host damaging for SARS-CoV-2 variants

SARS-CoV-2 continues to threaten human society by generating novel variants via mutation and recombination. The high number of mutations that appeared in emerging variants not only enhanced their immune-escaping ability but also made it difficult to predict the pathogenicity and virulence based on viral nucleotide sequences. Molecular markers for evaluating the pathogenicity of new variants are therefore needed. By comparing host responses to wild-type and variants with attenuated pathogenicity at proteome and metabolome levels, six key molecules on the polyamine biosynthesis pathway including putrescine, SAM, dc-SAM, ODC1, SAMS, and SAMDC were found to be differentially upregulated and associated with pathogenicity of variants. To validate our discovery, human airway organoids were subsequently used which recapitulates SARS-CoV-2 replication in the airway epithelial cells of COVID-19 patients. Using ODC1 as a proof-of-concept, differential activation of polyamine biosynthesis was found to be modulated by the renin-angiotensin system (RAS) and positively associated with ACE2 activity. Further experiments demonstrated that ODC1 expression could be differentially activated upon a panel of SARS-CoV-2 variants of concern (VOCs) and was found to be correlated with each VOCs' pathogenic properties. Particularly, the presented study revealed the discriminative ability of key molecules on polyamine biosynthesis as a predictive marker for virulence evaluation and assessment of SARS-CoV-2 variants in cell or organoid models. Our work, therefore, presented a practical strategy that could be potentially applied as an evaluation tool for the pathogenicity of current and emerging SARS-CoV-2 variants.

Self-assembling nanoarchitectonics of size-controllable celastrol nanoparticles for efficient cancer chemotherapy with reduced systemic toxicity

Celastrol, extracted from Tripterygium wilfordii Hook F, is one of the most promising natural extract for cancer treatment. Nevertheless, insufficient tumor retention and severe systemic toxicity still hinder its application. Herein, we report for the first time that Celastrol can directly self-assemble into size-controllable nanoparticles through the anti-solvent method by using different good solvent or by the variation of Celastrol concentrations. In vitro anti-cancer experiment revealed that the as-prepared nanoparticles can kill MCF-7 cells more effectively. Moreover, the nanoparticles can efficiently accumulate in tumors of the tumor bearing mice after tail vein injection. Under the administration of lethal dosage of Celastrol, the tumors are greatly suppressed and the mice maintain the activity. These results demonstrate that anti-solvent method may be a promising strategy to fabricate Celastrol nano-drugs with controllable size and less systemic toxicity for further clinical cancer treatment.

An angled-shape tip-based strategy for highly sensitive proteomic profiling of a low number of cells

Profiling proteins plays an essential role in understanding the functions and dynamic networks in biological systems. Mass spectrometry-based proteomic analysis commonly requires multistep sample processing, which results in severe sample loss. Although the recently developed microproteomic strategies have substantially reduced sample loss via droplet microfluidic technology, specialized equipment and well-trained personnel are needed, which may limit their wide adoption. Here, we report an angled-shape tip-based strategy for rapid sample preparation and sensitive proteomic profiling of small cell populations (<1000 cells). The angled-shape tip provided a 'reactor' for the entire proteomic sample processing workflow, from cell capture and lysis to protein digestion, eliminating the sample transfer-induced protein loss. The angled-shape tip was surface-treated for anti-protein adsorption which further reduced the sample loss. Using this strategy, 1241 ± 38-4110 ± 37 protein groups and 4010 ± 700-34 879 ± 575 peptides were identified from 10-1000 HeLa cells with high quantification reproducibility in only 4.5 h sample processing time, which was superior to the reported methods and commercial kits, especially for <100 cells. This approach was easily accessible, straightforward to operate, and compatible with flow cytometry-based cell sorting. It showed great potential for in-depth proteomic profiling of rare cells (<1000 cells) in both basic biological research and clinical application.

Targeted delivery of celastrol to glomerular endothelium and podocytes for chronic kidney disease treatment

The etiology of chronic kidney disease (CKD) is complex and diverse, which could be briefly categorized to glomerular- or tubular-originated. However, the final outcomes of CKD are mainly glomerular sclerosis, endothelial dysfunction and injury, and chronic inflammation. Thus, targeted delivery of drugs to the glomeruli in order to ameliorate glomerular endothelial damage may help alleviate CKD and help enrich our knowledge. The herb tripterygium wilfordii shows therapeutic effect on kidney disease, and celastrol (CLT) is one of its active ingredients but with strong toxicity. Therefore, based on the unique structure and pathological characteristics of the glomerulus, we designed a targeted delivery system named peptides coupled CLT-phospholipid lipid nanoparticles (PC-PLNs) to efficiently deliver CLT to damaged endothelial cells and podocytes in the glomerulus for CKD treatment and research. PC-PLNs could effectively inhibit inflammation, reduce endothelial damage, alleviate CKD severity, and reduce the toxicity of CLT. We also studied the mechanism of CLT in the treatment of nephropathy and found that CLT can increase the level of NO by increasing eNOS while inhibiting the expression of VCAM-1, thus provides an anti-inflammatory effect. Therefore, our study not only offered an efficient CKD drug formulation for further development, but also provided new medical knowledge about CKD.

ELECTRONIC SUPPLEMENTARY MATERIAL

Supplementary material (attached with all the supporting tables and figures mentioned in this work) is available in the online version of this article at 10.1007/s12274-021-3894-x.

Identification of NLRP3 as a covalent target of 1,6-O,O-diacetylbritannilactone against neuroinflammation by quantitative thiol reactivity profiling (QTRP)

Neuroinflammation plays a key etiological role in the progressive neuronal damage of neurodegenerative diseases. Our phenotypic-based screening discovered 1,6-O,O-diacetylbritannilactone (OABL, 1) from Inula britannica exhibited the potential anti-neuroinflammatory activity as well as a favorable blood-brain barrier penetration. 1 and its active derivative Br-OABL (2) with insert of Br at the C-14 position both modulated TLR4/NF-kB/MAPK pathways. However, proteome-wide identification of 1 binding proteins remains unclear. Here, we employed an adapted isoTOP-ABPP, quantitative thiol reactivity profiling (QTRP) approach, to identify and quantify thiol reactivity binding proteins in murine microglia BV-2 cells. We screened out 15 proteins co-targeted by 1 and 2, which are involved in cellular response to oxidative stress and negative regulation NF-κB transcription factor in biological processes. In site-specific profiling, NLRP3 was identified as a covalent target of 1 and 2 for the first time, and the Cys⁴⁸³ of NLRP3 NACHT domain was identified as one active-site of NLRP3 cysteine residues that can be covalently modified by the α-methylene-γ-lactone moiety. Furthermore, NLRP3 was validated to be directly binded by 1 and 2 by cellular thermo shift assay (CETSA) and activity-based protein profiling (ABPP), and NLRP3 functions were also verified by small interfering RNA approach. Notably, OABL treatment (i.p., 20 mg/kg/day) for 21 days reduced inflammation in 5XFAD mice brain. Together, we applied the QTRP to uncover the binding proteins of OABL in BV-2 cells, among which NLRP3 was revealed as a new covalent target of 1 and 2 against neuroinflammation.