Kedi Cao

The condition of having a healthy, functional proteome is known as protein homeostasis, or proteostasis. Maintaining proteostasis is the province of the proteostasis network, which consists of the cellular components that regulate protein synthesis, folding, localization, and degradation. The proteostasis network is a fundamental functional unit in biology with relevance to many diseases. Despite its importance, the human proteostasis network has until now lacked a precise definition, limiting our ability to interrogate proteostasis, integrate multiomic datasets, compare results across studies, or model proteostasis dysfunction in disease. To address this limitation, we have operationally defined the human proteostasis network by providing a comprehensive, annotated, and manually curated list of its components classified into nine Branches based on their function and localization - cytonuclear proteostasis, ER proteostasis, mitochondrial proteostasis, nuclear proteostasis, proteostasis network regulation, translation, extracellular proteostasis, the autophagy-lysosome pathway, and the ubiquitin-proteasome system - which we present in a series of three manuscripts of which this is the first. Overall, the proteostasis network annotation encompasses 3,151 components described by 4,043 annotations. Here, we present the 1,190 components that make up the first seven of these Branches, which comprise the compartment-based proteostasis network (cytonuclear, ER, mitochondrial, nuclear, and extracellular proteostasis), proteostasis network regulation, and translation. These Branches include chaperones, folding enzymes, systems for trafficking proteins, organelle-specific degradation systems, and the cell's translation machinery. This work provides a framework that will facilitate insights into how proteostasis is preserved in health, lost in aging and disease, and how it could be restored through pharmacological intervention.

Calprotectin, a calcium- and zinc-binding protein that comprises the subunits S100A8 and S100A9, has been extensively studied as a biomarker of gastrointestinal (GI) inflammation through fecal and serum analyses. However, its role in intestinal tissue remains poorly understood because of the limited availability of biopsy specimens. In this study, we analyzed S100A8 and S100A9 messenger RNA (mRNA) expression in 579 intestinal biopsy specimens from allogeneic stem cell transplantation recipients and observed a strong association with acute GI graft-versus-host disease (aGI-GVHD; P< .001). Neutrophil infiltration correlated with the severity of aGI-GVHD (P< .001), and calprotectin expression was strongly linked to Toll-like receptor 4 (TLR4; P< .001) and TLR2 (P< .001) expression. Both TLR4 and aGI-GVHD were associated with elevated calprotectin mRNA levels (P< .001). When patients received broad-spectrum antibiotics at disease onset, calprotectin expression was suppressed (S100A8, P = .001; S100A9, P = .01). GI site–specific differences in calprotectin expression were identified: during severe aGI-GVHD, levels increased up to 30-fold in the small intestine and up to fivefold in the large intestine with respect to mild or no aGI-GVHD, whereas under homeostasis, the large intestine exhibited higher baseline calprotectin (P = .001). The high clinical relevance of this finding is evident from the observation that calprotectin expression was prognostic for transplant-related mortality. Our study suggests that (1) calprotectin is a potential biopsy biomarker in aGI-GvHD and (2) calprotectin expression and neutrophil infiltration possibly indicate translocation of microbiota, which (3) may be modulated by antibiotics.

Scientific workflows automate the analysis of large-scale scientific data, fostering the reuse of data processing operators as well as the reproducibility and traceability of analysis results. In exploratory research, however, workflows are continuously adapted, utilizing a wide range of tools and software libraries, to test scientific hypotheses. Script-based workflow engines cater to the required flexibility through direct integration of programming primitives, but lack abstractions for interactive exploration of the workflow design by a user during workflow execution. In this paper, we study the requirements for the design of interactive workflows through the lens of existing workflow collections. Specifically, we focus on two widely used script-based workflow engines: Snakemake and Nextflow. For Snakemake, we collected workflows from 1602 GitHub repositories that are listed in the Snakemake workflow catalog. For Nextflow, we adopted the nf-core collection with workflows from 94 GitHub repositories as the basis for our study. Using these collections, we present insights on common structures in the design of the workflows. Moreover, we report on results on the language features typically adopted in workflow specification, with a focus on the concepts that are of particular importance for interactive workflows.