SILAC-based quantitative proteomics using mass spectrometry quantifies endoplasmic reticulum stress in whole HeLa cells

Proteogenetic drug response profiling elucidates targetable vulnerabilities of myelofibrosis

Myelofibrosis is a hematopoietic stem cell disorder belonging to the myeloproliferative neoplasms. Myelofibrosis patients frequently carry driver mutations in either JAK2 or Calreticulin (CALR) and have limited therapeutic options. Here, we integrate ex vivo drug response and proteotype analyses across myelofibrosis patient cohorts to discover targetable vulnerabilities and associated therapeutic strategies. Drug sensitivities of mutated and progenitor cells were measured in patient blood using high-content imaging and single-cell deep learning-based analyses. Integration with matched molecular profiling revealed three targetable vulnerabilities. First, CALR mutations drive BET and HDAC inhibitor sensitivity, particularly in the absence of high Ras pathway protein levels. Second, an MCM complex-high proliferative signature corresponds to advanced disease and sensitivity to drugs targeting pro-survival signaling and DNA replication. Third, homozygous CALR mutations result in high endoplasmic reticulum (ER) stress, responding to ER stressors and unfolded protein response inhibition. Overall, our integrated analyses provide a molecularly motivated roadmap for individualized myelofibrosis patient treatment.

Prediction, Discovery, and Characterization of Plant- and Food-Derived Health-Beneficial Bioactive Peptides

Nature may have the answer to many of our questions about human, animal, and environmental health. Natural bioactives, especially when harvested from sustainable plant and food sources, provide a plethora of molecular solutions to nutritionally actionable, chronic conditions. The spectrum of these conditions, such as metabolic, immune, and gastrointestinal disorders, has changed with prolonged human life span, which should be matched with an appropriately extended health span, which would in turn favour more sustainable health care: "adding years to life and adding life to years". To date, bioactive peptides have been undervalued and underexploited as food ingredients and drugs. The future of translational science on bioactive peptides-and natural bioactives in general-is being built on (a) systems-level rather than reductionist strategies for understanding their interdependent, and at times synergistic, functions; and (b) the leverage of artificial intelligence for prediction and discovery, thereby significantly reducing the time from idea and concept to finished solutions for consumers and patients. This new strategy follows the path from benefit definition via design to prediction and, eventually, validation and production.

Quantitative Structural Proteomics Unveils the Conformational Changes of Proteins under the Endoplasmic Reticulum Stress

Protein structures are decisive for their activities and interactions with other molecules. Global analysis of protein structures and conformational changes cannot be achieved by commonly used abundance-based proteomics. Here, we integrated cysteine covalent labeling, selective enrichment, and quantitative proteomics to study protein structures and structural changes on a large scale. This method was applied to globally investigate protein structures in HEK293T cells and protein structural changes in the cells with the tunicamycin (Tm)-induced endoplasmic reticulum (ER) stress. We quantified several thousand cysteine residues, which contain unprecedented and valuable information of protein structures. Combining this method with pulsed stable isotope labeling by amino acids in cell culture, we further analyzed the folding state differences between pre-existing and newly synthesized proteins in cells under the Tm treatment. Besides newly synthesized proteins, unexpectedly, many pre-existing proteins were found to become unfolded upon ER stress, especially those related to gene transcription and protein translation. Furthermore, the current results reveal that N-glycosylation plays a more important role in the folding process of the tertiary and quaternary structures than the secondary structures for newly synthesized proteins. Considering the importance of cysteine in protein structures, this method can be extensively applied in the biological and biomedical research fields.

Host Cell Signatures of the Envelopment Site within Beta-Herpes Virions

Beta-herpesvirus infection completely reorganizes the membrane system of the cell. This system is maintained by the spatiotemporal arrangement of more than 3000 cellular proteins that continuously adapt the configuration of membrane organelles according to cellular needs. Beta-herpesvirus infection establishes a new configuration known as the assembly compartment (AC). The AC membranes are loaded with virus-encoded proteins during the long replication cycle and used for the final envelopment of the newly formed capsids to form infectious virions. The identity of the envelopment membranes is still largely unknown. Electron microscopy and immunofluorescence studies suggest that the envelopment occurs as a membrane wrapping around the capsids, similar to the growth of phagophores, in the area of the AC with the membrane identities of early/recycling endosomes and the trans-Golgi network. During wrapping, host cell proteins that define the identity and shape of these membranes are captured along with the capsids and incorporated into the virions as host cell signatures. In this report, we reviewed the existing information on host cell signatures in human cytomegalovirus (HCMV) virions. We analyzed the published proteomes of the HCMV virion preparations that identified a large number of host cell proteins. Virion purification methods are not yet advanced enough to separate all of the components of the rich extracellular material, including the large amounts of non-vesicular extracellular particles (NVEPs). Therefore, we used the proteomic data from large and small extracellular vesicles (lEVs and sEVs) and NVEPs to filter out the host cell proteins identified in the viral proteomes. Using these filters, we were able to narrow down the analysis of the host cell signatures within the virions and determine that envelopment likely occurs at the membranes derived from the tubular recycling endosomes. Many of these signatures were also found at the autophagosomes, suggesting that the CMV-infected cell forms membrane organelles with phagophore growth properties using early endosomal host cell machinery that coordinates endosomal recycling.

Pancreatic INS-1 β-Cell Response to Thapsigargin and Rotenone: A Comparative Proteomics Analysis Uncovers Key Pathways of β-Cell Dysfunction

Insulin-secreting β-cells in the pancreatic islets are exposed to various endogenous and exogenous stressing conditions, which may lead to β-cell dysfunction or apoptosis and ultimately to diabetes mellitus. However, the detailed molecular mechanisms underlying β-cell's inability to survive under severe stresses remain to be explored. This study used two common chemical stressors, thapsigargin and rotenone, to induce endoplasmic reticulum (ER) and mitochondria stress in a rat insuloma INS-1 832/13 β-cell line, mimicking the conditions experienced by dysfunctional β-cells. Proteomic changes of cells upon treatment with stressors at IC₅₀ were profiled with TMT-based quantitative proteomics and further verified using label-free quantitive proteomics. The differentially expressed proteins under stress conditions were selected for in-depth bioinformatic analysis. Thapsigargin treatment specifically perturbed unfolded protein response (UPR) related pathways; in addition, 58 proteins not previously linked to the UPR related pathways were identified with consistent upregulation under stress induced by thapsigargin. Conversely, rotenone treatment resulted in significant proteome changes in key mitochondria regulatory pathways such as fatty acid β-oxidation, cellular respiration, citric acid cycle, and respiratory electron transport. Our data also demonstrated that both stressors increased reactive oxygen species production and depleted adenosine triphosphate synthesis, resulting in significant dysregulation of oxidative phosphorylation signaling pathways. These novel dysregulated proteins may suggest an alternative mechanism of action in β-cell dysfunction and provide potential targets for probing ER- and mitochondria stress-induced β-cell death.

Bioinformatic Analysis of Temporal and Spatial Proteome Alternations During Infections

Microbial pathogens have evolved numerous mechanisms to hijack host's systems, thus causing disease. This is mediated by alterations in the combined host-pathogen proteome in time and space. Mass spectrometry-based proteomics approaches have been developed and tailored to map disease progression. The result is complex multidimensional data that pose numerous analytic challenges for downstream interpretation. However, a systematic review of approaches for the downstream analysis of such data has been lacking in the field. In this review, we detail the steps of a typical temporal and spatial analysis, including data pre-processing steps (i.e., quality control, data normalization, the imputation of missing values, and dimensionality reduction), different statistical and machine learning approaches, validation, interpretation, and the extraction of biological information from mass spectrometry data. We also discuss current best practices for these steps based on a collection of independent studies to guide users in selecting the most suitable strategies for their dataset and analysis objectives. Moreover, we also compiled the list of commonly used R software packages for each step of the analysis. These could be easily integrated into one's analysis pipeline. Furthermore, we guide readers through various analysis steps by applying these workflows to mock and host-pathogen interaction data from public datasets. The workflows presented in this review will serve as an introduction for data analysis novices, while also helping established users update their data analysis pipelines. We conclude the review by discussing future directions and developments in temporal and spatial proteomics and data analysis approaches. Data analysis codes, prepared for this review are available from https://github.com/BabuLab-UofR/TempSpac, where guidelines and sample datasets are also offered for testing purposes.

Target identification of natural medicine with chemical proteomics approach: probe synthesis, target fishing and protein identification

Natural products are an important source of new drugs for the treatment of various diseases. However, developing natural product-based new medicines through random moiety modification is a lengthy and costly process, due in part to the difficulties associated with comprehensively understanding the mechanism of action and the side effects. Identifying the protein targets of natural products is an effective strategy, but most medicines interact with multiple protein targets, which complicate this process. In recent years, an increasing number of researchers have begun to screen the target proteins of natural products with chemical proteomics approaches, which can provide a more comprehensive array of the protein targets of active small molecules in an unbiased manner. Typically, chemical proteomics experiments for target identification consist of two key steps: (1) chemical probe design and synthesis and (2) target fishing and identification. In recent decades, five different types of chemical proteomic probes and their respective target fishing methods have been developed to screen targets of molecules with different structures, and a variety of protein identification approaches have been invented. Presently, we will classify these chemical proteomics approaches, the application scopes and characteristics of the different types of chemical probes, the different protein identification methods, and the advantages and disadvantages of these strategies.