Minor intron-containing genes as an ancient backbone for viral infection?

Minor intron-containing genes (MIGs) account for <2% of all human protein-coding genes and are uniquely dependent on the minor spliceosome for proper excision. Despite their low numbers, we surprisingly found a significant enrichment of MIG-encoded proteins (MIG-Ps) in protein-protein interactomes and host factors of positive-sense RNA viruses, including SARS-CoV-1, SARS-CoV-2, MERS coronavirus, and Zika virus. Similarly, we observed a significant enrichment of MIG-Ps in the interactomes and sets of host factors of negative-sense RNA viruses such as Ebola virus, influenza A virus, and the retrovirus HIV-1. We also found an enrichment of MIG-Ps in double-stranded DNA viruses such as Epstein-Barr virus, human papillomavirus, and herpes simplex viruses. In general, MIG-Ps were highly connected and placed in central positions in a network of human-host protein interactions. Moreover, MIG-Ps that interact with viral proteins were enriched with essential genes. We also provide evidence that viral proteins interact with ancestral MIGs that date back to unicellular organisms and are mainly involved in basic cellular functions such as cell cycle, cell division, and signal transduction. Our results suggest that MIG-Ps form a stable, evolutionarily conserved backbone that viruses putatively tap to invade and propagate in human host cells.

In-situ cryo-immune engineering of tumor microenvironment with cold-responsive nanotechnology for cancer immunotherapy.

Cancer immunotherapy that deploys the host's immune system to recognize and attack tumors, is a promising strategy for cancer treatment. However, its efficacy is greatly restricted by the immunosuppressive (i.e., immunologically cold) tumor microenvironment (TME). Here, we report an in-situ cryo-immune engineering (ICIE) strategy for turning the TME from immunologically "cold" into "hot". In particular, after the ICIE treatment, the ratio of the CD8+ cytotoxic T cells to the immunosuppressive regulatory T cells is increased by more than 100 times in not only the primary tumors with cryosurgery but also distant tumors without freezing. This is achieved by combining cryosurgery that causes "frostbite" of tumor with cold-responsive nanoparticles that not only target tumor but also rapidly release both anticancer drug and PD-L1 silencing siRNA specifically into the cytosol upon cryosurgery. This ICIE treatment leads to potent immunogenic cell death, which promotes maturation of dendritic cells and activation of CD8+ cytotoxic T cells as well as memory T cells to kill not only primary but also distant/metastatic breast tumors in female mice (i.e., the abscopal effect). Collectively, ICIE may enable an efficient and durable way to leverage the immune system for combating cancer and its metastasis.

The emerging significance of splicing in vertebrate development.

Splicing is a crucial regulatory node of gene expression that has been leveraged to expand the proteome from a limited number of genes. Indeed, the vast increase in intron number that accompanied vertebrate emergence might have aided the evolution of developmental and organismal complexity. Here, we review how animal models for core spliceosome components have provided insights into the role of splicing in vertebrate development, with a specific focus on neuronal, neural crest and skeletal development. To this end, we also discuss relevant spliceosomopathies, which are developmental disorders linked to mutations in spliceosome subunits. Finally, we discuss potential mechanisms that could underlie the tissue-specific phenotypes often observed upon spliceosome inhibition and identify gaps in our knowledge that, we hope, will inspire further research.

Noncovalent reversible binding-enabled facile fabrication of leak-free PDMS microfluidic devices without plasma treatment for convenient cell loading and retrieval.

The conventional approach for fabricating polydimethylsiloxane (PDMS) microfluidic devices is a lengthy and inconvenient procedure and may require a clean-room microfabrication facility often not readily available. Furthermore, living cells can't survive the oxygen-plasma and high-temperature-baking treatments required for covalent bonding to assemble multiple PDMS parts into a leak-free device, and it is difficult to disassemble the devices because of the irreversible covalent bonding. As a result, seeding/loading cells into and retrieving cells from the devices are challenging. Here, we discovered that decreasing the curing agent for crosslinking the PDMS prepolymer increases the noncovalent binding energy of the resultant PDMS surfaces without plasma or any other treatment. This enables convenient fabrication of leak-free microfluidic devices by noncovalent binding for various biomedical applications that require high pressure/flow rates and/or long-term cell culture, by simply hand-pressing the PDMS parts without plasma or any other treatment to bind/assemble. With this method, multiple types of cells can be conveniently loaded into specific areas of the PDMS parts before assembly and due to the reversible nature of the noncovalent bonding, the assembled device can be easily disassembled by hand peeling for retrieving cells. Combining with 3D printers that are widely available for making masters to eliminate the need of photolithography, this facile yet rigorous fabrication approach is much faster and more convenient for making PDMS microfluidic devices than the conventional oxygen plasma-baking-based irreversible covalent bonding method.

Metformin Bicarbonate-Mediated Efficient RNAi for Precise Targeting of TP53 Deficiency in Colon and Rectal Cancers.

Colon and rectal cancers are the leading causes of cancer-related deaths in the United States and effective targeted therapies are in need for treating them. Our genomic analyses show hemizygous deletion of TP53, an important tumor suppressor gene, is highly frequent in both cancers, and the 5-year survival of patients with the more prevalent colon cancer is significantly reduced in the patients with the cancer harboring such deletion, although such reduction is not observed for rectal cancer. Unfortunately, direct targeting TP53 has been unsuccessful for cancer therapy. Interestingly, POLR2A, a gene essential for cell survival and proliferation, is almost always deleted together with TP53 in colon and rectal cancers. Therefore, RNA interference (RNAi) with small interfering RNAs (siRNAs) to precisely target/inhibit POLR2A may be an effective strategy for selectively killing cancer cells with TP53 deficiency. However, the difficulty of delivering siRNAs specifically into the cytosol where they perform their function, is a major barrier for siRNA-based therapies. Here, metformin bicarbonate (MetC) is synthesized to develop pH-responsive MetC-nanoparticles with a unique "bomb" for effective cytosolic delivery of POLR2A siRNA, which greatly facilitates its endo/lysosomal escape into the cytosol and augments its therapeutic efficacy of cancer harboring TP53 deficiency. Moreover, the MetC-based nanoparticles without functional siRNA show notable therapeutic effect with no evident toxicity or immunogenicity.

Trp53 ablation fails to prevent microcephaly in mouse pallium with impaired minor intron splicing.

Minor spliceosome inhibition due to mutations in RNU4ATAC are linked to primary microcephaly. Ablation of Rnu11, which encodes a minor spliceosome snRNA, inhibits the minor spliceosome in the developing mouse pallium, causing microcephaly. There, cell cycle defects and p53-mediated apoptosis in response to DNA damage resulted in loss of radial glial cells (RGCs), underpinning microcephaly. Here, we ablated Trp53 to block cell death in Rnu11 cKO mice. We report that Trp53 ablation failed to prevent microcephaly in these double knockout (dKO) mice. We show that the transcriptome of the dKO pallium was more similar to the control compared with the Rnu11 cKO. We find aberrant minor intron splicing in minor intron-containing genes involved in cell cycle regulation, resulting in more severely impaired mitotic progression and cell cycle lengthening of RGCs in the dKO that was detected earlier than in the Rnu11 cKO. Furthermore, we discover a potential role of p53 in causing DNA damage in the developing pallium, as detection of γH2aX+ was delayed in the dKO. Thus, we postulate that microcephaly in minor spliceosome-related diseases is primarily caused by cell cycle defects.

Bioinspired 3D Culture in Nanoliter Hyaluronic Acid-Rich Core-Shell Hydrogel Microcapsules Isolates Highly Pluripotent Human iPSCs.

Human induced pluripotent stem cells (iPSCs) are ideal for developing personalized medicine. However, the spontaneous differentiation of human iPSCs under conventional 2D and 3D cultures results in significant heterogeneity and compromised quality. Therefore, a method for effectively isolating and expanding high-quality human iPSCs is critically needed. Here, a biomimetic microencapsulation approach for isolating and culturing high-quality human iPSCs is reported. This is inspired by the natural proliferation and development of blastomeres into early blastocyst where the early embryonic stem cells-containing core is enclosed in a semipermeable hydrogel shell known as the zona pellucida (Zona). Blastomere cluster-like human iPSC clusters are encapsulated in a miniaturized (≈10 nanoliter) hyaluronic acid (HA)-rich core of microcapsules with a semipermeable Zona-like hydrogel shell and subsequently cultured to form pluripotent human iPSC spheroids with significantly improved quality. This is indicated by their high expression of pluripotency markers and highly efficient 3D cardiac differentiation. In particular, HA is found to be crucial for isolating the high-quality human iPSCs with the biomimetic core-shell microencapsulation culture. Interestingly, the isolated human iPSCs can maintain high pluripotency even after being cultured again in 2D. These discoveries and the bioinspired culture method may be valuable to facilitate the human iPSC-based personalized medicine.

Methods of Generating Dielectrophoretic Force for Microfluidic Manipulation of Bioparticles.

Manipulation of microscale bioparticles including living cells is of great significance to the broad bioengineering and biotechnology fields. Dielectrophoresis (DEP), which is defined as the interactions between dielectric particles and the electric field, is one of the most widely used techniques for the manipulation of bioparticles including cell separation, sorting, and trapping. Bioparticles experience a DEP force if they have a different polarization from the surrounding media in an electric field that is nonuniform in terms of the intensity and/or phase of the electric field. A comprehensive literature survey shows that the DEP-based microfluidic devices for manipulating bioparticles can be categorized according to the methods of creating the nonuniformity via patterned microchannels, electrodes, and media to generate the DEP force. These methods together with the theory of DEP force generation are described in this review, to provide a summary of the methods and materials that have been used to manipulate various bioparticles for various specific biological outcomes. Further developments of DEP-based technologies include identifying materials that better integrate with electrodes than current popular materials (silicone/glass) and improving the performance of DEP manipulation of bioparticles by combining it with other methods of handling bioparticles. Collectively, DEP-based microfluidic manipulation of bioparticles holds great potential for various biomedical applications.

Deep Learning-Enabled Label-Free On-Chip Detection and Selective Extraction of Cell Aggregate-Laden Hydrogel Microcapsules.

Microfluidic encapsulation of cells/tissues in hydrogel microcapsules has attracted tremendous attention in the burgeoning field of cell-based medicine. However, when encapsulating rare cells and tissues (e.g., pancreatic islets and ovarian follicles), the majority of the resultant hydrogel microcapsules are empty and should be excluded from the sample. Furthermore, the cell-laden hydrogel microcapsules are usually suspended in an oil phase after microfluidic generation, while the microencapsulated cells require an aqueous phase for further culture/transplantation and long-term suspension in oil may compromise the cells/tissues. Thus, real-time on-chip selective extraction of cell-laden hydrogel microcapsules from oil into aqueous phase is crucial to the further use of the microencapsulated cells/tissues. Contemporary extraction methods either require labeling of cells for their identification along with an expensive detection system or have a low extraction purity (<≈30%). Here, a deep learning-enabled approach for label-free detection and selective extraction of cell-laden microcapsules with high efficiency of detection (≈100%) and extraction (≈97%), high purity of extraction (≈90%), and high cell viability (>95%) is reported. The utilization of deep learning to dynamically analyze images in real time for label-free detection and on-chip selective extraction of cell-laden hydrogel microcapsules is unique and may be valuable to advance the emerging cell-based medicine.

Disruption of exon-bridging interactions between the minor and major spliceosomes results in alternative splicing around minor introns.

Vertebrate genomes contain major (>99.5%) and minor (<0.5%) introns that are spliced by the major and minor spliceosomes, respectively. Major intron splicing follows the exon-definition model, whereby major spliceosome components first assemble across exons. However, since most genes with minor introns predominately consist of major introns, formation of exon-definition complexes in these genes would require interaction between the major and minor spliceosomes. Here, we report that minor spliceosome protein U11-59K binds to the major spliceosome U2AF complex, thereby supporting a model in which the minor spliceosome interacts with the major spliceosome across an exon to regulate the splicing of minor introns. Inhibition of minor spliceosome snRNAs and U11-59K disrupted exon-bridging interactions, leading to exon skipping by the major spliceosome. The resulting aberrant isoforms contained a premature stop codon, yet were not subjected to nonsense-mediated decay, but rather bound to polysomes. Importantly, we detected elevated levels of these alternatively spliced transcripts in individuals with minor spliceosome-related diseases such as Roifman syndrome, Lowry-Wood syndrome and early-onset cerebellar ataxia. In all, we report that the minor spliceosome informs splicing by the major spliceosome through exon-definition interactions and show that minor spliceosome inhibition results in aberrant alternative splicing in disease.

Carbon nano-onion-mediated dual targeting of P-selectin and P-glycoprotein to overcome cancer drug resistance.

The transmembrane P-glycoprotein (P-gp) pumps that efflux drugs are a major mechanism of cancer drug resistance. They are also important in protecting normal tissue cells from poisonous xenobiotics and endogenous metabolites. Here, we report a fucoidan-decorated silica-carbon nano-onion (FSCNO) hybrid nanoparticle that targets tumor vasculature to specifically release P-gp inhibitor and anticancer drug into tumor cells. The tumor vasculature targeting capability of the nanoparticle is demonstrated using multiple models. Moreover, we reveal the superior light absorption property of nano-onion in the near infrared region (NIR), which enables triggered drug release from the nanoparticle at a low NIR power. The released inhibitor selectively binds to P-gp pumps and disables their function, which improves the bioavailability of anticancer drug inside the cells. Furthermore, free P-gp inhibitor significantly increases the systemic toxicity of a chemotherapy drug, which can be resolved by delivering them with FSCNO nanoparticles in combination with a short low-power NIR laser irradiation.

Engineering Strategies to Improve Islet Transplantation for Type 1 Diabetes Therapy.

Type 1 diabetes is an autoimmune disease in which the immune system attacks insulin-producing beta cells of pancreatic islets. Type 1 diabetes can be treated with islet transplantation; however, patients must be administered immunosuppressants to prevent immune rejection of the transplanted islets if they are not autologous or not engineered with immune protection/isolation. To overcome biological barriers of islet transplantation, encapsulation strategies have been developed and robustly investigated. While islet encapsulation can prevent the need for immunosuppressants, these approaches have not shown much success in clinical trials due to a lack of long-term insulin production. Multiple engineering strategies have been used to improve encapsulation and post-transplantation islet survival. In addition, more efficient islet cryopreservation methods have been designed to facilitate the scaling-up of islet transplantation. Other islet sources have been identified including porcine islets and stem cell-derived islet-like aggregates. Overall, islet-laden capsule transplantation has greatly improved over the past 30 years and is moving towards becoming a clinically feasible treatment for type 1 diabetes.

Climate change impacts and costs to U.S. electricity transmission and distribution infrastructure.

This study presents a screening-level analysis of the impacts of climate change on electricity transmission and distribution infrastructure of the U.S. In particular, the model identifies changes in performance and longevity of physical infrastructure such as power poles and transformers, and quantifies these impacts in economic terms. This analysis was evaluated for the contiguous U.S, using five general circulation models (GCMs) under two greenhouse gas emission scenarios, to analyze changes in damage and cost from the baseline period to the end of the century with three different adaptation strategies. Total infrastructure costs were found to rise considerably, with annual climate change expenditures increasing by as much as 25%. The results demonstrate that climate impacts will likely be substantial, though this analysis only captures a portion of the total potential impacts. A proactive adaptation strategy resulted in the expected costs of climate change being reduced by as much as 50% by 2090, compared to a scenario without adaptation. Impacts vary across the contiguous U.S. with the highest impacts in parts of the Southeast and Northwest. Improvements and extensions to this analysis would help better inform climate resiliency policies and utility-level planning for the future.

Small-scale forestry and carbon offset markets: An empirical study of Vermont Current Use forest landowner willingness to accept carbon credit programs.

This study investigates the preferences of small forest landowners regarding forest carbon credit programs while documenting characteristics of potentially successful frameworks. We designed hypothetical carbon credit programs with aggregated carbon offset projects and requirements of existing voluntary and compliance protocols in mind. We administered a mail survey to 992 forest landowners in Vermont's Current Use Program utilizing best-worst choice, a novel preference elicitation technique, to elicit their preferences about these programs. We found that small forest landowners see revenue as the most important factor in a carbon credit program and the duration of the program as the least important factor. Landowners reported that shorter program duration, higher revenue, and lower withdrawal penalties positively impact their willingness to accept forest carbon credit programs. Notably, our study includes carbon credit program implementer as a key program attribute, allowing us to quantify landowners' tradeoffs between non-profit, for-profit, and government organizations. Overall, we found that landowners significantly prefer working with a non-profit organization. Based on monetary estimates of willingness-to-accept compensation, our results suggest that aggregated forest carbon offset projects incorporating small forest landowners could be piloted successfully in Vermont by non-profit organizations while maintaining relatively strict guidelines of existing carbon offset protocols.