Porcine germline genome engineering.

Germline editing, the process by which the genome of an individual is edited in such a way that the change is heritable, has been applied to a wide variety of animals [D. A. Sorrell, A. F. Kolb, Biotechnol. Adv. 23, 431-469 (2005); D. Baltimore et al., Science 348, 36-38 (2015)]. Because of its relevancy in agricultural and biomedical research, the pig genome has been extensively modified using a multitude of technologies [K. Lee, K. Farrell, K. Uh, Reprod. Fertil. Dev. 32, 40-49 (2019); C. Proudfoot, S. Lillico, C. Tait-Burkard, Anim. Front. 9, 6-12 (2019)]. In this perspective, we will focus on using pigs as the model system to review the current methodologies, applications, and challenges of mammalian germline genome editing. We will also discuss the broad implications of animal germline editing and its clinical potential.

The role of mitochondria in the resistance of melanoma to PD-1 inhibitors.

Malignant melanoma is one of the most common tumours and has the highest mortality rate of all types of skin cancers worldwide. Traditional and novel therapeutic approaches, including surgery, targeted therapy and immunotherapy, have shown good efficacy in the treatment of melanoma. At present, the mainstay of treatment for melanoma is immunotherapy combined with other treatment strategies. However, immune checkpoint inhibitors, such as PD-1 inhibitors, are not particularly effective in the clinical treatment of patients with melanoma. Changes in mitochondrial function may affect the development of melanoma and the efficacy of PD-1 inhibitors. To elucidate the role of mitochondria in the resistance of melanoma to PD-1 inhibitors, this review comprehensively summarises the role of mitochondria in the occurrence and development of melanoma, targets related to the function of mitochondria in melanoma cells and changes in mitochondrial function in different cells in melanoma resistant to PD-1 inhibitors. This review may help to develop therapeutic strategies for improving the clinical response rate of PD-1 inhibitors and prolonging the survival of patients by activating mitochondrial function in tumour and T cells.

Mercury Accumulation and Sequestration in a Deglaciated Forest Chronosequence: Insights from Particulate and Mineral-Associated Forms of Organic Matter.

Understanding mercury (Hg) complexation with soil organic matter is important in assessing atmospheric Hg accumulation and sequestration processes in forest ecosystems. Separating soil organic matter into particulate organic matter (POM) and mineral-associated organic matter (MAOM) can help in the understanding of Hg dynamics and cycling due to their very different chemical constituents and associated formation and functioning mechanisms. The concentration of Hg, carbon, and nitrogen contents and isotopic signatures of POM and MAOM in a deglaciated forest chronosequence were determined to construct the processes of Hg accumulation and sequestration. The results show that Hg in POM and MAOM are mainly derived from atmospheric Hg0 deposition. Hg concentration in MAOM is up to 76% higher than that in POM of broadleaf forests and up to 60% higher than that in POM of coniferous forests. Hg accumulation and sequestration in organic soil vary with the vegetation succession. Variations of δ202Hg and Δ199Hg are controlled by source mixing in the broadleaf forest and by Hg sequestration processes in the coniferous forest. Accumulation of atmospheric Hg and subsequent microbial reduction enrich heavier Hg isotopes in MAOM compared to POM due to the specific chemical constituents and nutritional role of MAOM.

Kidney transplantation from triple-knockout pigs expressing multiple human proteins in cynomolgus macaques.

Porcine cells devoid of three major carbohydrate xenoantigens, αGal, Neu5GC, and SDa (TKO) exhibit markedly reduced binding of human natural antibodies. Therefore, it is anticipated that TKO pigs will be better donors for human xenotransplantation. However, previous studies on TKO pigs using old world monkeys (OWMs) have been disappointing because of higher anti-TKO pig antibodies in OWMs than humans. Here, we show that long-term survival of renal xenografts from TKO pigs that express additional human transgenes (hTGs) can be achieved in cynomolgus monkeys. Kidney xenografts from TKO-hTG pigs were transplanted into eight cynomolgus recipients without pre-screening for low anti-pig antibody titers. Two recipients of TKO-hTG xenografts with low expression of human complement regulatory proteins (CRPs) (TKO-A) survived for 2 and 61 days, whereas six recipients of TKO-hTG xenografts with high CRP expression (TKO-B) survived for 15, 20, 71, 135, 265, and 316 days. Prolonged CD4+ T cell depletion and low anti-pig antibody titers, which were previously reported important for long-term survival of αGal knock-out (GTKO) xenografts, were not always required for long-term survival of TKO-hTG renal xenografts. This study indicates that OWMs such as cynomolgus monkeys can be used as a relevant model for clinical application of xenotransplantation using TKO pigs.

Dip-Coating Self-Assembly Fabrication and Polarization Sensitive Photoresponse of Aligned Single-Walled Carbon Nanotube Film.

It is challenging to obtain wafer-scaled aligned films for completely exploiting the promising properties of semiconducting single-walled carbon nanotubes (s-SWCNTs). Aligned s-SWCNTs with a large area can be obtained by combining water evaporation and slow withdrawal-induced self-assembly in a dip-coating process. Moreover, the tunability of deposition morphology parameters such as stripe width and spacing is examined. The polarized Raman results show that s-SWCNTs can be aligned in ±8.6°. The derived two terminal photodetector shows both a high negative responsivity of 41 A/W at 520 nm and high polarization sensitivity. Our results indicate that aligned films with a large area may be useful to electronics- and optoelectronics-related applications.

Mechanisms underlying disruption of oocyte spindle stability by bisphenol compounds.

Accurate chromosome segregation relies on correct chromosome-microtubule interactions within a stable bipolar spindle apparatus. Thus, exposure to spindle disrupting compounds can impair meiotic division and genomic stability in oocytes. The endocrine disrupting activity of bisphenols such as bisphenol A (BPA) is well recognized, yet their damaging effects on spindle microtubules (MTs) is poorly understood. Here, we tested the effect(s) of acute exposure to BPA and bisphenol F (BPF) on assembled spindle stability in ovulated oocytes. Brief (4 h) exposure to increasing concentrations (5, 25, and 50 µg/mL) of BPA or BPF disrupted spindle organization in a dose-dependent manner, resulting in significantly shorter spindles with highly unfocused poles and fragmented pericentrin. The chromosomes remained congressed in an abnormally elongated metaphase-like configuration, yet normal end-on chromosome-MT attachments were reduced in BPF-treated oocytes. Live-cell imaging revealed a rapid onset of bisphenol-mediated spindle MT disruption that was reversed upon compound removal. Moreover, MT stability and regrowth were impaired in BPA-exposed oocytes, with few cold-stable MTs and formation of multipolar spindles upon MT regrowth. MT-associated kinesin-14 motor protein (HSET/KIFC1) labeling along the spindle was also lower in BPA-treated oocytes. Conversely, cold stable MTs and HSET labeling persisted after BPF exposure. Notably, inhibition of Aurora Kinase A limited bisphenol-mediated spindle pole widening, revealing a potential interaction. These results demonstrate rapid MT disrupting activity by bisphenols, which is highly detrimental to meiotic spindle stability and organization. Moreover, we identify an important link between these defects and altered distribution of key spindle associated factors as well as Aurora Kinase A activity.

CRISPR-C: circularization of genes and chromosome by CRISPR in human cells.

Extrachromosomal circular DNA (eccDNA) and ring chromosomes are genetic alterations found in humans with genetic disorders. However, there is a lack of genetic engineering tools to recapitulate and study the biogenesis of eccDNAs. Here, we created a dual-fluorescence biosensor cassette, which upon the delivery of pairs of CRISPR/Cas9 guide RNAs, CRISPR-C, allows us to study the biogenesis of a specific fluorophore expressing eccDNA in human cells. We show that CRISPR-C can generate functional eccDNA, using the novel eccDNA biosensor system. We further reveal that CRISPR-C also can generate eccDNAs from intergenic and genic loci in human embryonic kidney 293T cells and human mammary fibroblasts. EccDNAs mainly forms by end-joining mediated DNA-repair and we show that CRISPR-C is able to generate endogenous eccDNAs in sizes from a few hundred base pairs and ranging up to 207 kb. Even a 47.4 megabase-sized ring chromosome 18 can be created by CRISPR-C. Our study creates a new territory for CRISPR gene editing and highlights CRISPR-C as a useful tool for studying the cellular impact, persistence and function of eccDNAs.

Error-prone meiotic division and subfertility in mice with oocyte-conditional knockdown of pericentrin.

Mouse oocytes lack canonical centrosomes and instead contain unique acentriolar microtubule-organizing centers (aMTOCs). To test the function of these distinct aMTOCs in meiotic spindle formation, pericentrin (Pcnt), an essential centrosome/MTOC protein, was knocked down exclusively in oocytes by using a transgenic RNAi approach. Here, we provide evidence that disruption of aMTOC function in oocytes promotes spindle instability and severe meiotic errors that lead to pronounced female subfertility. Pcnt-depleted oocytes from transgenic (Tg) mice were ovulated at the metaphase-II stage, but show significant chromosome misalignment, aneuploidy and premature sister chromatid separation. These defects were associated with loss of key Pcnt-interacting proteins (γ-tubulin, Nedd1 and Cep215) from meiotic spindle poles, altered spindle structure and chromosome-microtubule attachment errors. Live-cell imaging revealed disruptions in the dynamics of spindle assembly and organization, together with chromosome attachment and congression defects. Notably, spindle formation was dependent on Ran GTPase activity in Pcnt-deficient oocytes. Our findings establish that meiotic division is highly error-prone in the absence of Pcnt and disrupted aMTOCs, similar to what reportedly occurs in human oocytes. Moreover, these data underscore crucial differences between MTOC-dependent and -independent meiotic spindle assembly.

Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA).

SUMMARY: Clustered regularly interspaced short palindromic repeats (CRISPR)-based technologies have revolutionized human genome engineering and opened countless possibilities to basic science, synthetic biology and gene therapy. Albeit the enormous potential of these tools, their performance is far from perfect. It is essential to perform a posterior careful analysis of the gene editing experiment. However, there are no computational tools for genome editing assessment yet, and current experimental tools lack sensitivity and flexibility. We present a platform to assess the quality of a genome editing experiment only with three mouse clicks. The method evaluates next-generation data to quantify and characterize insertions, deletions and homologous recombination. CRISPR Genome Analyzer provides a report for the locus selected, which includes a quantification of the edited site and the analysis of the different alterations detected. The platform maps the reads, estimates and locates insertions and deletions, computes the allele replacement efficiency and provides a report integrating all the information. AVAILABILITY AND IMPLEMENTATION: CRISPR-GA Web is available at http://crispr-ga.net. Documentation on CRISPR-GA instructions can be found at http://crispr-ga.net/documentation.html CONTACT: mguell@genetics.med.harvard.edu.

Optimization of scarless human stem cell genome editing.

Efficient strategies for precise genome editing in human-induced pluripotent cells (hiPSCs) will enable sophisticated genome engineering for research and clinical purposes. The development of programmable sequence-specific nucleases such as Transcription Activator-Like Effectors Nucleases (TALENs) and Cas9-gRNA allows genetic modifications to be made more efficiently at targeted sites of interest. However, many opportunities remain to optimize these tools and to enlarge their spheres of application. We present several improvements: First, we developed functional re-coded TALEs (reTALEs), which not only enable simple one-pot TALE synthesis but also allow TALE-based applications to be performed using lentiviral vectors. We then compared genome-editing efficiencies in hiPSCs mediated by 15 pairs of reTALENs and Cas9-gRNA targeting CCR5 and optimized ssODN design in conjunction with both methods for introducing specific mutations. We found Cas9-gRNA achieved 7-8× higher non-homologous end joining efficiencies (3%) than reTALENs (0.4%) and moderately superior homology-directed repair efficiencies (1.0 versus 0.6%) when combined with ssODN donors in hiPSCs. Using the optimal design, we demonstrated a streamlined process to generated seamlessly genome corrected hiPSCs within 3 weeks.

A public resource facilitating clinical use of genomes.

Rapid advances in DNA sequencing promise to enable new diagnostics and individualized therapies. Achieving personalized medicine, however, will require extensive research on highly reidentifiable, integrated datasets of genomic and health information. To assist with this, participants in the Personal Genome Project choose to forgo privacy via our institutional review board- approved "open consent" process. The contribution of public data and samples facilitates both scientific discovery and standardization of methods. We present our findings after enrollment of more than 1,800 participants, including whole-genome sequencing of 10 pilot participant genomes (the PGP-10). We introduce the Genome-Environment-Trait Evidence (GET-Evidence) system. This tool automatically processes genomes and prioritizes both published and novel variants for interpretation. In the process of reviewing the presumed healthy PGP-10 genomes, we find numerous literature references implying serious disease. Although it is sometimes impossible to rule out a late-onset effect, stringent evidence requirements can address the high rate of incidental findings. To that end we develop a peer production system for recording and organizing variant evaluations according to standard evidence guidelines, creating a public forum for reaching consensus on interpretation of clinically relevant variants. Genome analysis becomes a two-step process: using a prioritized list to record variant evaluations, then automatically sorting reviewed variants using these annotations. Genome data, health and trait information, participant samples, and variant interpretations are all shared in the public domain-we invite others to review our results using our participant samples and contribute to our interpretations. We offer our public resource and methods to further personalized medical research.

Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers.

DNA built from modular repeats presents a challenge for gene synthesis. We present a solid surface-based sequential ligation approach, which we refer to as iterative capped assembly (ICA), that adds DNA repeat monomers individually to a growing chain while using hairpin 'capping' oligonucleotides to block incompletely extended chains, greatly increasing the frequency of full-length final products. Applying ICA to a model problem, construction of custom transcription activator-like effector nucleases (TALENs) for genome engineering, we demonstrate efficient synthesis of TALE DNA-binding domains up to 21 monomers long and their ligation into a nuclease-carrying backbone vector all within 3 h. We used ICA to synthesize 20 TALENs of varying DNA target site length and tested their ability to stimulate gene editing by a donor oligonucleotide in human cells. All the TALENS show activity, with the ones >15 monomers long tending to work best. Since ICA builds full-length constructs from individual monomers rather than large exhaustive libraries of pre-fabricated oligomers, it will be trivial to incorporate future modified TALE monomers with improved or expanded function or to synthesize other types of repeat-modular DNA where the diversity of possible monomers makes exhaustive oligomer libraries impractical.

Quantitative identification of the co-exposure effects of e-waste pollutants on human oxidative stress by explainable machine learning.

Global electronic waste (e-waste) generation continues to grow. The various pollutants released during precarious e-waste disposal activities can contribute to human oxidative stress. This study encompassed 129 individuals residing near e-waste dismantling sites in China, with elevated urinary concentrations of e-waste-related pollutants including heavy metals, polycyclic aromatic hydrocarbons (PAHs), organophosphorus flame retardants (OPFRs), bisphenols (BPs), and phthalate esters (PAEs). Utilizing an explainable machine learning framework, the study quantified the co-exposure effects of these pollutants, finding that approximately 23% and 18% of the variance in oxidative DNA damage and lipid peroxidation, respectively, was attributable to these substances. Heavy metals emerged as the most critical factor in inducing oxidative stress, followed by PAHs and PAEs for oxidative DNA damage, and BPs, OPFRs, and PAEs for lipid peroxidation. The interactions between different pollutant classes were found to be weak, attributable to their disparate biological pathways. In contrast, the interactions among congeneric pollutants were strong, stemming from their shared pathways and resultant synergistic or additive effects on oxidative stress. An intelligent analysis system for e-waste pollutants was also developed, which enables more efficient processing of large-scale and dynamic datasets in evolving environments. This study offered an enticing peek into the intricacies of co-exposure effect of e-waste pollutants.

In Vitro and In Vivo Evaluation of Lactoferrin-Modified Liposomal Etomidate with Enhanced Brain-Targeting Effect for General Anesthesia.

Etomidate is a general anesthetic that has shown good hemodynamic stability without significant cardiovascular or respiratory depression. Despite several kinds of dosage forms having been reported for this drug, formulation types are very limited in clinical practice, and brain-targeted formulations for this central nervous system (CNS) drug have been rarely reported. Moreover, studies on the biocompatibility, toxicity, and anesthetic effects of the etomidate preparations in vivo were inadequate. The present study was to develop lactoferrin-modified liposomal etomidate (Eto-lip-LF) for enhanced drug distribution in the brain and improved anesthetic effects. Eto-lip-LF had good stability for storage and hemocompatibility for intravenous injection. Compared with the non-lactoferrin-containing liposomes, the lactoferrin-modified liposomes had notably enhanced brain-targeting ability in vivo, which was probably realized by the binding of transferrin with the transferrin and lactoferrin receptors highly distributed in the brain. Eto-lip-LF had a therapeutic index of about 25.3, higher than that of many other general anesthetics. Moreover, compared with the commercial etomidate emulsion, Eto-lip-LF could better achieve rapid onset of general anesthesia and rapid recovery from anesthesia, probably due to the enhanced drug delivery to the brain. The above results demonstrated the potential of this lactoferrin-modified liposomal etomidate to become an alternative preparation for clinical general anesthesia.

Testing multiplexed anti-ASFV CRISPR-Cas9 in reducing African swine fever virus.

African swine fever (ASF) is a highly fatal viral disease that poses a significant threat to domestic pigs and wild boars globally. In our study, we aimed to explore the potential of a multiplexed CRISPR-Cas system in suppressing ASFV replication and infection. By engineering CRISPR-Cas systems to target nine specific loci within the ASFV genome, we observed a substantial reduction in viral replication in vitro. This reduction was achieved through the concerted action of both Type II and Type III RNA polymerase-guided gRNA expression. To further evaluate its anti-viral function in vivo, we developed a pig strain expressing the multiplexable CRISPR-Cas-gRNA via germline genome editing. These transgenic pigs exhibited normal health with continuous expression of the CRISPR-Cas-gRNA system, and a subset displayed latent viral replication and delayed infection. However, the CRISPR-Cas9-engineered pigs did not exhibit a survival advantage upon exposure to ASFV. To our knowledge, this study represents the first instance of a living organism engineered via germline editing to assess resistance to ASFV infection using a CRISPR-Cas system. Our findings contribute valuable insights to guide the future design of enhanced viral immunity strategies. IMPORTANCE: ASFV is currently a devastating disease with no effective vaccine or treatment available. Our study introduces a multiplexed CRISPR-Cas system targeting nine specific loci in the ASFV genome. This innovative approach successfully inhibits ASFV replication in vitro, and we have successfully engineered pig strains to express this anti-ASFV CRISPR-Cas system constitutively. Despite not observing survival advantages in these transgenic pigs upon ASFV challenges, we did note a delay in infection in some cases. To the best of our knowledge, this study constitutes the first example of a germline-edited animal with an anti-virus CRISPR-Cas system. These findings contribute to the advancement of future anti-viral strategies and the optimization of viral immunity technologies.

Understanding heavy metal distribution in timberline vegetations: A case from the Gongga Mountain, eastern Tibetan Plateau.

To quantify impacts of vegetation and topographic factors on heavy metal accumulation in montane forests, we assessed the spatial distribution and determined the sources of mercury (Hg), cadmium (Cd), lead (Pb), chromium (Cr), copper (Cu) and zinc (Zn) in timberline forests of Gongga Mountain. Our results show that vegetation type has little impact on the soil Hg, Cd and Pb concentrations. The soil concentrations of Cr, Cu and Zn are controlled by litter return, moss and lichen biomass, and canopy interception, with the highest concentrations in shrub forest. In contrast to other forests, the soil Hg pool in coniferous forest is significantly high due to the elevated Hg concentration and greater biomass production in litter. However, the soil pool sizes of Cd, Cr, Cu and Zn show a distinct increase along the elevation, which are attributed to the elevated heavy metal inputs from litter and moss, as well as the greater cloud water-induced atmospheric heavy metal depositions. The highest Hg concentrations of the aboveground parts of plant are in the foliage and bark, while the concentrations of Cd, Pb, Cr, Cu and Zn in the branch and bark are the highest. The decreased biomass density leads to a downward trend in the total vegetation pool sizes of Hg, Cd, Pb, Cr, Cu and Zn by 0.4-4.4 times with increasing elevation. The statistical analysis finally suggests that Hg, Cd and Pb mainly originate from anthropogenic atmospheric deposition, whereas Cr, Cu and Zn are mainly from natural sources. Our results highlight the importance of vegetation types and terrain conditions on distribution patterns of heavy metal in alpine forests.

Vacuolar H+-ATPase and BZR1 form a feedback loop to regulate the homeostasis of BR signaling in Arabidopsis.

Brassinosteroid (BR) is a vital plant hormone that regulates plant growth and development. BRASSINAZOLE RESISTANT 1 (BZR1) is a key transcription factor in BR signaling, and its nucleocytoplasmic localization is crucial for BR signaling. However, the mechanisms that regulate BZR1 nucleocytoplasmic distribution and thus the homeostasis of BR signaling remain largely unclear. The vacuole is the largest organelle in mature plant cells and plays a key role in maintenance of cellular pH, storage of intracellular substances, and transport of ions. In this study, we uncovered a novel mechanism of BR signaling homeostasis regulated by the vacuolar H+-ATPase (V-ATPase) and BZR1 feedback loop. Our results revealed that the vha-a2 vha-a3 mutant (vha2, lacking V-ATPase activity) exhibits enhanced BR signaling with increased total amount of BZR1, nuclear-localized BZR1, and the ratio of BZR1/phosphorylated BZR1 in the nucleus. Further biochemical assays revealed that VHA-a2 and VHA-a3 of V-ATPase interact with the BZR1 protein through a domain that is conserved across multiple species. VHA-a2 and VHA-a3 negatively regulate BR signaling by interacting with BZR1 and promoting its retention in the tonoplast. Interestingly, a series of molecular analyses demonstrated that nuclear-localized BZR1 could bind directly to specific motifs in the promoters of VHA-a2 and VHA-a3 to promote their expression. Taken together, these results suggest that V-ATPase and BZR1 may form a feedback regulatory loop to maintain the homeostasis of BR signaling in Arabidopsis, providing new insights into vacuole-mediated regulation of hormone signaling.

RLI2 regulates Arabidopsis female gametophyte and embryo development by facilitating the assembly of the translational machinery.

Eukaryotic protein translation is a complex process that requires the participation of different proteins. Defects in the translational machinery often result in embryonic lethality or severe growth defects. Here, we report that RNase L inhibitor 2/ATP-BINDING CASSETTE E2 (RLI2/ABCE2) regulates translation in Arabidopsis thaliana. Null mutation of rli2 is gametophytic and embryonic lethal, whereas knockdown of RLI2 causes pleiotropic developmental defects. RLI2 interacts with several translation-related factors. Knockdown of RLI2 affects the translational efficiency of a subset of proteins involved in translation regulation and embryo development, indicating that RLI2 has critical roles in these processes. In particular, RLI2 knockdown mutant exhibits decreased expression of genes involved in auxin signaling and female gametophyte and embryo development. Therefore, our results reveal that RLI2 facilitates assembly of the translational machinery and indirectly modulates auxin signaling to regulate plant growth and development.

Endogenous calcium enriched hydrochar catalyst derived from water hyacinth for glucose isomerization.

Water hyacinth is a major aquatic plant in ecological restoration which propagates rapidly, whereas its biomass waste lacks value-added utilization routes. To address this problem, we put forth an innovative two-step carbonization strategy to convert water hyacinth to catalyst for isomerization of glucose to fructose. Through combining the hydrothermal carbonization and pyrolysis, catalyst morphology including its carbon substrate and calcium salts was successfully engineered. The prepared hydrochar-based catalyst presented an outstanding catalytic performance, the optimal of which could obtain 31% fructose yield with 89% selectivity at 120 °C for 45 min in water and maintain the reactivity for at least three runs. The catalytic reactivity was derived from the crystallization of endogenous alkaline earth calcium in water hyacinth, which was comparable to catalysts doped with expensive metals. Besides, the equipment and energy requirements for preparation were quite low-demanding (calcined only at 400 °C for 1 h). This study not only pioneers a sustainable way to upcycle aquatic biomass, but also invents a low-cost and efficient catalyst for biorefinery through the production of engineered carbon.