Plasma cell-free DNA hydroxymethylation profiling reveals anti-PD-1 treatment response and resistance biology in non-small cell lung cancer.

BACKGROUND: Treatment with immune checkpoint inhibitors (ICIs) targeting programmed death-1 (PD-1) can yield durable antitumor responses, yet not all patients respond to ICIs. Current approaches to select patients who may benefit from anti-PD-1 treatment are insufficient. 5-hydroxymethylation (5hmC) analysis of plasma-derived cell-free DNA (cfDNA) presents a novel non-invasive approach for identification of therapy response biomarkers which can tackle challenges associated with tumor biopsies such as tumor heterogeneity and serial sample collection. METHODS: 151 blood samples were collected from 31 patients with non-small cell lung cancer (NSCLC) before therapy started and at multiple time points while on therapy. Blood samples were processed to obtain plasma-derived cfDNA, followed by enrichment of 5hmC-containing cfDNA fragments through biotinylation via a two-step chemistry and binding to streptavidin coated beads. 5hmC-enriched cfDNA and whole genome libraries were prepared in parallel and sequenced to obtain whole hydroxymethylome and whole genome plasma profiles, respectively. RESULTS: Comparison of on-treatment time point to matched pretreatment samples from same patients revealed that anti-PD-1 treatment induced distinct changes in plasma cfDNA 5hmC profiles of responding patients, as judged by Response evaluation criteria in solid tumors, relative to non-responders. In responders, 5hmC accumulated over genes involved in immune activation such as inteferon (IFN)-γ and IFN-α response, inflammatory response and tumor necrosis factor (TNF)-α signaling, whereas in non-responders 5hmC increased over epithelial to mesenchymal transition genes. Molecular response to anti-PD-1 treatment, as measured by 5hmC changes in plasma cfDNA profiles were observed early on, starting with the first cycle of treatment. Comparison of pretreatment plasma samples revealed that anti-PD-1 treatment response and resistance associated genes can be captured by 5hmC profiling of plasma-derived cfDNA. Furthermore, 5hmC profiling of pretreatment plasma samples was able to distinguish responders from non-responders using T cell-inflamed gene expression profile, which was previously identified by tissue RNA analysis. CONCLUSIONS: These results demonstrate that 5hmC profiling can identify response and resistance associated biological pathways in plasma-derived cfDNA, offering a novel approach for non-invasive prediction and monitoring of immunotherapy response in NSCLC.

Epigenomic Blood-Based Early Detection of Pancreatic Cancer Employing Cell-Free DNA.

BACKGROUND & AIMS: Early detection of pancreatic cancer (PaC) can drastically improve survival rates. Approximately 25% of subjects with PaC have type 2 diabetes diagnosed within 3 years prior to the PaC diagnosis, suggesting that subjects with type 2 diabetes are at high risk of occult PaC. We have developed an early-detection PaC test, based on changes in 5-hydroxymethylcytosine (5hmC) signals in cell-free DNA from plasma. METHODS: Blood was collected from 132 subjects with PaC and 528 noncancer subjects to generate epigenomic and genomic feature sets yielding a predictive PaC signal algorithm. The algorithm was validated in a blinded cohort composed of 102 subjects with PaC, 2048 noncancer subjects, and 1524 subjects with non-PaCs. RESULTS: 5hmC differential profiling and additional genomic features enabled the development of a machine learning algorithm capable of distinguishing subjects with PaC from noncancer subjects with high specificity and sensitivity. The algorithm was validated with a sensitivity for early-stage (stage I/II) PaC of 68.3% (95% confidence interval [CI], 51.9%-81.9%) and an overall specificity of 96.9% (95% CI, 96.1%-97.7%). CONCLUSIONS: The PaC detection test showed robust early-stage detection of PaC signal in the studied cohorts with varying type 2 diabetes status. This assay merits further clinical validation for the early detection of PaC in high-risk individuals.

Magnesium-based bioceramics in orthopedic applications.

Magnesium ions are directly involved in numerous biological mechanisms; for example, they play an important part in the regulation of ion channels, DNA stabilization, enzyme activation and stimulation of cell growth and proliferation. This alkaline earth metal has gained great popularity in orthopedic applications in recent years. Magnesium-based bioceramics include a large group of magnesium containing compounds such as oxides, phosphates and silicates, that are involved in orthopedic applications like bone cements, bone scaffolds or implant coatings. This article aims to give a comprehensive review on different magnesium-based bioceramics, e.g. magnesium phosphates (MgO-P2O5), calcium magnesium phosphates (CaO-MgO-P2O5), and magnesium glasses (SiO2-MgO) with a strong focus on the chemistry and properties of magnesium phosphate containing cements as the main application form. In addition, the processing of magnesium phosphate minerals into macroporous scaffolds for tissue engineering applications by either using traditional porogens or by additive manufacturing approaches are reflected. Finally, the biological in vitro and in vivo properties of magnesium phosphates for bone regeneration are summarized, which show promising results regarding the application as bone replacement material, but still lack in terms of testing in large animal models, load-bearing application sites and clinical data. STATEMENT OF SIGNIFICANCE: Though bone substitutes from calcium phosphates have been investigated for a long time, a new trend is visible in the biomaterials sector: magnesium based bioceramics from magnesium phosphates and silicates due to the special biological significance of magnesium ions in enzymatic activation, cell growth and proliferation, etc. In contrast to pure magnesium implants, such formulations do not release hydrogen during degradation. As with calcium based bioceramics, magnesium based bioceramics are used for the development of diverse applications such as cements, macroporous scaffolds and coatings. From this perspective, we present a systematic overview on diverse kinds of magnesium based bioceramics, their processing regimes for different clinical purposes and their behavior both in vitro and in vivo.

Magnesium substitution in the structure of orthopedic nanoparticles: A comparison between amorphous magnesium phosphates, calcium magnesium phosphates, and hydroxyapatites.

As biocompatible materials, magnesium phosphates have received a lot of attention for orthopedic applications. During the last decade multiple studies have shown advantages for magnesium phosphate such as lack of cytotoxicity, biocompatibility, strong mechanical properties, and high biodegradability. The present study investigates the role of Mg(+2) and Ca(+2) ions in the structure of magnesium phosphate and calcium phosphate nanoparticles. To directly compare the effect of Mg(+2) and Ca(+2) ions on structure of nanoparticles and their biological behavior, three groups of nanoparticles including amorphous magnesium phosphates (AMPs) which release Mg(+2), calcium magnesium phosphates (CMPs) which release Mg(+2) and Ca(+2), and hydroxyapatites (HAs) which release Ca(+2) were studied. SEM, TEM, XRD, and FTIR were used to evaluate the morphology, crystallinity, and chemical properties of the particles. AMP particles were homogeneous nanospheres, whereas CMPs were combinations of heterogeneous nanorods and nanospheres, and HAs which contained heterogeneous nanosphere particles. Cell compatibility was monitored in all groups to determine the cytotoxicity effect of particles on studied MC3T3-E1 preosteoblasts. AMPs showed significantly higher attachment rate than the HAs after 1 day and both AMPs and CMPs showed significantly higher proliferation rate when compared to HAs after 7days. Gene expression level of osteoblastic markers ALP, COL I, OCN, OPN, RUNX2 were monitored and they were normalized to GAPDH housekeeping gene. Beta actin expression level was monitored as the second housekeeping gene to confirm the accuracy of results. In general, AMPs and CMPs showed higher expression level of osteoblastic genes after 7 days which can further confirm the stimulating role of Mg(+2) and Ca(+2) ions in increasing the proliferation rate, differentiation, and mineralization of MC3T3-E1 preosteoblasts.

Rapid coating of AZ31 magnesium alloy with calcium deficient hydroxyapatite using microwave energy.

Due to their unique biodegradability, magnesium alloys have been recognized as suitable metallic implant materials for degradable bone implants and bioresorbable cardiovascular stents. However, the extremely high degradation rate of magnesium alloys in physiological environment has restricted its practical application. This paper reports the use of a novel microwave assisted coating technology to improve the in vitro corrosion resistance and biocompatibility of Mg alloy AZ31. Results indicate that a dense calcium deficient hydroxyapatite (CDHA) layer was uniformly coated on a AZ31 substrate in less than 10min. Weight loss measurement and SEM were used to evaluate corrosion behaviors in vitro of coated samples and of non-coated samples. It was seen that CDHA coatings remarkably reduced the mass loss of AZ31 alloy after 7days of immersion in SBF. In addition, the prompt precipitation of bone-like apatite layer on the sample surface during immersion demonstrated a good bioactivity of the CDHA coatings. Proliferation of osteoblast cells was promoted in 5days of incubation, which indicated that the CDHA coatings could improve the cytocompatibility of the AZ31 alloy. All the results suggest that the CDHA coatings, serving as a protective layer, can enhance the corrosion resistance and biological response of magnesium alloys. Furthermore, this microwave assisted coating technology could be a promising method for rapid surface modification of biomedical materials.

Formation of nanostructured fluorapatite via microwave assisted solution combustion synthesis.

Fluorapatite (FA) has potential applications in dentistry and orthopedics, but its synthesis procedures are time consuming. The goal of the present study is to develop a quick microwave assisted solution combustion synthesis method (MASCS) for the production of FA particles. With this new processing, FA particles were successfully synthesized in minutes. Additionally, unique structures including nanotubes, hexagonal crystals, nanowhiskers, and plate agglomerates were prepared by controlling the solution composition and reaction time. In particular, the as-synthesized FA nanotubes presented a "Y" shape inner channel along the crystal axis. It is supposed that the channel formation is caused by the crystal growth and removal of water soluble salts during processing. The as-synthesized FA nanotubes showed good cytocompatibility, the cells cultured with a higher FA concentration demonstrated greater growth rate. With this new and easily applied MASCS processing application, FA nanoparticles have increased potential in dental and orthopedic applications.

Microwave assisted apatite coating deposition on Ti6Al4V implants.

In this work we report a novel microwave assisted technology to deposit a uniform, ultra-thin apatite coating without any cracks on titanium implants in minutes. This method comprises of conventional biomimetic coating in synergism with microwave irradiation to result in alkaline earth phosphate nucleation. The microwave assisted coating process mainly follows the initial stages of biomimetic coating until the step of the Ca-P nuclei formation. After that, due to microwave irradiation more Ca-P nuclei are formed to cover the whole surface of the implant instead of the growth of deposited Ca-P nuclei to Ca-P globules and coatings. It is interesting to note the doping of Mg(2+) to Ca-P apatite coating can significantly change the properties and performances of as-deposited coatings. The hydrophilicity, physical properties, bioactivity, cell adhesion, and growth capability of as-deposited microwave assisted coatings were investigated. The study shows that this coating technology has great potential in biomedical applications. Additionally, since biomimetic coating can be applied to series of implant materials such as polymer, metals and glass, it is expected this microwave assisted coating technology can also be applied to these materials if they can remains stable at 100 °C, the boiling point of water.

Fabrication of novel poly(lactic acid)/amorphous magnesium phosphate bionanocomposite fibers for tissue engineering applications via electrospinning.

Fibrous bionanocomposites consisting of amorphous magnesium phosphate (AMP) nanospheres and polylactic acid (PLA) were fabricated by electrospinning. There are two important signatures of this paper. First, AMP, as an alternative to well-known calcium phosphate (CaP) materials, is added to PLA as the second phase. To the best of our knowledge, it is the first attempt to fabricate magnesium phosphate (MgP)/biopolymer composite. This is made possible by our previously reported research on the successful synthesis of AMP nanospheres via microwave processing. Second, the sustained release of magnesium and phosphate ions from PLA matrix can stimulate a series of cell responses. The structure of the composites and their bone-like apatite-forming abilities in simulated body fluid (SBF) were examined. Additionally, the effects on the proliferation and differentiation of preosteoblast cells were evaluated by performing in vitro cell culture and monitoring markers such as Osteocalcin (OCN), Osteopontin (OPN), Alkaline phosphatase (ALP) and Collagen type-I (Col I) using real-time polymerase chain reaction (PCR). For better dispersion of AMP in the fibers, a surfactant, 12-hydroxysteric acid (HSA), as previously reported in the literature, was used. However, HSA significantly inhibited the proliferation and differentiation of preosteoblast cells, indicating the potential risk in using HSA in the combination of AMP or MgP in tissue engineering applications.

Vertebrate codon bias indicates a highly GC-rich ancestral genome.

Two factors are thought to have contributed to the origin of codon usage bias in eukaryotes: 1) genome-wide mutational forces that shape overall GC-content and create context-dependent nucleotide bias, and 2) positive selection for codons that maximize efficient and accurate translation. Particularly in vertebrates, these two explanations contradict each other and cloud the origin of codon bias in the taxon. On the one hand, mutational forces fail to explain GC-richness (~60%) of third codon positions, given the GC-poor overall genomic composition among vertebrates (~40%). On the other hand, positive selection cannot easily explain strict regularities in codon preferences. Large-scale bioinformatic assessment, of nucleotide composition of coding and non-coding sequences in vertebrates and other taxa, suggests a simple possible resolution for this contradiction. Specifically, we propose that the last common vertebrate ancestor had a GC-rich genome (~65% GC). The data suggest that whole-genome mutational bias is the major driving force for generating codon bias. As the bias becomes prominent, it begins to affect translation and can result in positive selection for optimal codons. The positive selection can, in turn, significantly modulate codon preferences.