Causality between COVID-19 and multiple myeloma: a two-sample Mendelian randomization study and Bayesian co-localization.

Infection is the leading cause of morbidity and mortality in patients with multiple myeloma (MM). Studying the relationship between different traits of Coronavirus 2019 (COVID-19) and MM is critical for the management and treatment of MM patients with COVID-19. But all the studies on the relationship so far were observational and the results were also contradictory. Using the latest publicly available COVID-19 genome-wide association studies (GWAS) data, we performed a bidirectional Mendelian randomization (MR) analysis of the causality between MM and different traits of COVID-19 (SARS-CoV-2 infection, COVID-19 hospitalization, and severe COVID-19) and use multi-trait analysis of GWAS(MTAG) to identify new associated SNPs in MM. We performed co-localization analysis to reveal potential causal pathways between diseases and over-representation enrichment analysis to find involved biological pathways. IVW results showed SARS-CoV-2 infection and COVID-19 hospitalization increased risk of MM. In the reverse analysis, the causal relationship was not found between MM for each of the different symptoms of COVID-19. Co-localization analysis identified LZTFL1, MUC4, OAS1, HLA-C, SLC22A31, FDX2, and MAPT as genes involved in COVID-19-mediated causation of MM. These genes were mainly related to immune function, glycosylation modifications and virus defense. Three novel MM-related SNPs were found through MTAG, which may regulate the expression of B3GNT6. This is the first study to use MR to explore the causality between different traits of COVID-19 and MM. The results of our two-way MR analysis found that SARS-CoV-2 infection and COVID-19 hospitalization increased the susceptibility of MM.

A genetically encoded and gate for cell-targeted metabolic labeling of proteins.

We describe a genetic AND gate for cell-targeted metabolic labeling and proteomic analysis in complex cellular systems. The centerpiece of the AND gate is a bisected methionyl-tRNA synthetase (MetRS) that charges the Met surrogate azidonorleucine (Anl) to tRNA(Met). Cellular protein labeling occurs only upon activation of two different promoters that drive expression of the N- and C-terminal fragments of the bisected MetRS. Anl-labeled proteins can be tagged with fluorescent dyes or affinity reagents via either copper-catalyzed or strain-promoted azide-alkyne cycloaddition. Protein labeling is apparent within 5 min after addition of Anl to bacterial cells in which the AND gate has been activated. This method allows spatial and temporal control of proteomic labeling and identification of proteins made in specific cellular subpopulations. The approach is demonstrated by selective labeling of proteins in bacterial cells immobilized in the center of a laminar-flow microfluidic channel, where they are exposed to overlapping, opposed gradients of inducers of the N- and C-terminal MetRS fragments. The observed labeling profile is predicted accurately from the strengths of the individual input signals.

SpyStapler-mediated assembly of nanoparticle vaccines.

The COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has wreaked havoc around the globe, with no end in sight. The rapid emergence of viral mutants, marked by rapid transmission and effective immune evasion, has also posed unprecedented challenges for vaccine development, not least in its speed, mass production, and distribution. Here we report a versatile "plug-and-display" strategy for creating protein vaccines, including those against malaria parasites and SARS-CoV-2, through the combined use of the intrinsically disordered protein ligase SpyStapler and computationally designed viral-like particles. The resulting protein nanoparticles harboring multiple antigens induce potent neutralizing antibody responses in mice, substantially stronger than those induced by the corresponding free antigens. This modular vaccine design enabled by SpyStapler furnishes us with a new weapon for combatting infectious diseases. Electronic Supplementary Material: Supplementary material (further details of the protein sequences, cloning procedures, TEM imaging, ELISA details, and reaction controls) is available in the online version of this article at 10.1007/s12274-022-4951-9.

Directed assembly of genetically engineered eukaryotic cells into living functional materials via ultrahigh-affinity protein interactions.

Engineered living materials (ELMs) are gaining traction among synthetic biologists, as their emergent properties and nonequilibrium thermodynamics make them markedly different from traditional materials. However, the aspiration to directly use living cells as building blocks to create higher-order structures or materials, with no need for chemical modification, remains elusive to synthetic biologists. Here, we report a strategy that enables the assembly of engineered Saccharomyces cerevisiae into self-propagating ELMs via ultrahigh-affinity protein/protein interactions. These yeast cells have been genetically engineered to display the protein pairs SpyTag/SpyCatcher or CL7/Im7 on their surfaces, which enable their assembly into multicellular structures capable of further growth and proliferation. The assembly process can be controlled precisely via optical tweezers or microfluidics. Moreover, incorporation of functional motifs such as super uranyl-binding protein and mussel foot proteins via genetic programming rendered these materials suitable for uranium extraction from seawater and bioadhesion, respectively, pointing to their potential in chemical separation and biomedical applications.

A multishear microfluidic device for quantitative analysis of calcium dynamics in osteoblasts.

Microfluidics is a convenient platform to study the influences of fluid shear stress on calcium dynamics. Fluidic shear stress has been proven to affect bone cell functions and remodelling. We have developed a microfluidic system which can generate four shear flows in one device as a means to study cytosolic calcium concentration ([Ca(2+)](c)) dynamics of osteoblasts. Four shear forces were achieved by having four cell culture chambers with different widths while resistance correction channels compensated for the overall resistance to allow equal flow distribution towards the chambers. Computational simulation of the local shear stress distribution highlighted the preferred section in the cell chamber to measure the calcium dynamics. Osteoblasts showed an [Ca(2+)](c) increment proportional to the intensity of the shear stress from 0.03 to 0.30 Pa. A delay in response was observed with an activation threshold between 0.03 and 0.06 Pa. With computational modelling, our microfluidic device can offer controllable multishear stresses and perform quantitative comparisons of shear stress-induced intensity change of calcium in osteoblasts.

Injectable, photoresponsive hydrogels for delivering neuroprotective proteins enabled by metal-directed protein assembly.

Axon regeneration constitutes a fundamental challenge for regenerative neurobiology, which necessitates the use of tailor-made biomaterials for controllable delivery of cells and biomolecules. An increasingly popular approach for creating these materials is to directly assemble engineered proteins into high-order structures, a process that often relies on sophisticated protein chemistry. Here, we present a simple approach for creating injectable, photoresponsive hydrogels via metal-directed assembly of His6-tagged proteins. The B12-dependent photoreceptor protein CarHC can complex with transition metal ions through an amino-terminal His6-tag, which can further undergo a sol-gel transition upon addition of AdoB12, leading to the formation of hydrogels with marked injectability and photodegradability. The inducible phase transitions further enabled facile encapsulation and release of cells and proteins. Injecting the Zn2+-coordinated gels decorated with leukemia inhibitory factor into injured mouse optic nerves led to prolonged cellular signaling and enhanced axon regeneration. This study illustrates a powerful strategy for designing injectable biomaterials.

Cobalt-Cross-Linked, Redox-Responsive Spy Network Protein Hydrogels.

Although assembly of recombinant proteins by SpyTag/SpyCatcher chemistry has proven to be a versatile approach for creating bioactive hydrogels, the resulting Spy networks often exhibit weak mechanics due to the poor efficiency of interchain cross-linking. Here we leverage metal/ligand (i.e., cobalt/His6-tag) coordination interactions to modulate the bulk mechanics of the protein networks. The drastic difference between the Co2+ and Co3+ complexes in thermodynamic and kinetic properties enabled us to regulate the materials' properties and to immobilize and release recombinant proteins in a redox-dependent manner. The resulting hydrogels are capable of not only supporting cell growth and proliferation, but also influencing specific cell signaling via immobilized growth factors such as leukemia inhibitory factor (LIF). The integrated use of stimuli-responsive metal coordination and SpyTag/SpyCatcher chemistry opens up a new dimension for designing bioactive protein materials.

Genetically Programming Stress-Relaxation Behavior in Entirely Protein-Based Molecular Networks.

We report the synthesis of a series of elastin-like polypeptide (ELP)-based molecular networks through the combined use of the covalent bond-forming SpyTag/SpyCatcher chemistry, physically entangled p53dim domains (Xs), and site-directed mutagenesis. The resulting networks shared similar chemical composition but differed significantly in their viscoelasticity. These materials exhibited excellent compatibility toward encapsulated fibroblasts and stem cells. These results point to a versatile strategy for designing viscoelastic materials by tapping into diverse protein-protein interactions.

Protein Hydrogel Microbeads for Selective Uranium Mining from Seawater.

Practical methods for oceanic uranium extraction have yet to be developed in order to tap into the vast uranium reserve in the ocean as an alternative energy. Here we present a protein hydrogel system containing a network of recently engineered super uranyl binding proteins (SUPs) that is assembled through thiol-maleimide click chemistry under mild conditions. Monodisperse SUP hydrogel microbeads fabricated by a microfluidic device further enable uranyl (UO22+) enrichment from natural seawater with great efficiency (enrichment index, K = 2.5 × 103) and selectivity. Our results demonstrate the feasibility of using protein hydrogels to extract uranium from the ocean.

Microfluidics and microbial engineering.

The combination of microbial engineering and microfluidics is synergistic in nature. For example, microfluidics is benefiting from the outcome of microbial engineering and many reported point-of-care microfluidic devices employ engineered microbes as functional parts for the microsystems. In addition, microbial engineering is facilitated by various microfluidic techniques, due to their inherent strength in high-throughput screening and miniaturization. In this review article, we firstly examine the applications of engineered microbes for toxicity detection, biosensing, and motion generation in microfluidic platforms. Secondly, we look into how microfluidic technologies facilitate the upstream and downstream processes of microbial engineering, including DNA recombination, transformation, target microbe selection, mutant characterization, and microbial function analysis. Thirdly, we highlight an emerging concept in microbial engineering, namely, microbial consortium engineering, where the behavior of a multicultural microbial community rather than that of a single cell/species is delineated. Integrating the disciplines of microfluidics and microbial engineering opens up many new opportunities, for example in diagnostics, engineering of microbial motors, development of portable devices for genetics, high throughput characterization of genetic mutants, isolation and identification of rare/unculturable microbial species, single-cell analysis with high spatio-temporal resolution, and exploration of natural microbial communities.

N-Methyl-D-aspartate receptor-mediated chemotaxis and Ca(2+) signaling in Tetrahymena pyriformis.

Although the ciliate Tetrahymena is a good model for the study of chemotaxis, its profound motility makes it difficult to monitor intracellular calcium (Ca(2+)) changes induced by chemotactic stimuli. In this study, we report a microfluidic-based chemotaxis system generating directional chemotactic gradients under highly viscous conditions, suppressing T. pyriformis motility, and allowing for the stable confocal imaging of changes in intracellular Ca(2+) in the ciliate. Once the viscous condition was achieved, directional chemical gradients were formed inside the center chamber via the release of N-methyl-d-aspartate (NMDA), a known chemoattractant, from the surrounding chemical reservoirs into the center chamber. As a result, intracellular Ca(2+) in the ciliate increased up to three-fold, and its distribution was skewed in the direction of NMDA stimulation. However, the Ca(2+) in ciliates pretreated with phospholipase C (PLC) or phosphatidylinositol-3-kinase (PI3K) blockers did not increase even after stimulation. Additionally, the PI3K blocker induced the secretion of granules, the size of which was dependent on the concentration of the blocker. Collectively, the results indicate that both PLC and PI3K perform pivotal roles in controlling the levels of intracellular Ca(2+) in T. pyriformis during chemotaxis.