Clinical and Genotypic Insights Into Higher Prevalence of Palbociclib Associated Neutropenia in Asian Patients.

BACKGROUND: CDK4/6 inhibitors (CDK4/6i) have shown great efficacy in prolonging progression-free survival and is the current standard of care for hormone positive (HR(+)) metastatic breast cancer (mBC). Despite well tolerability and ease of use, the most common side effect of CDK4/6i is myelosuppression, with neutropenia the most prevalent adverse effect. Studies show that the prevalence and severity of neutropenia are more marked in Asian patients, although details remain obscure. METHODS: In this study, we retrospectively analyzed 105 Taiwanese patients who received palbociclib for HR(+) HER2(-) mBC at the Taipei Veterans General Hospital. To investigate a possible genetic association for high prevalence of neutropenia, we queried the Taiwan Biobank with publicly available germline databases (ALFA, gnomAD, ExAC, 1000 Genomes project, HapMap), for the allele frequencies of 4 neutropenia-related SNPs (ABCB1_rs1045642, ABCB1_rs1128503, ERCC1_rs3212986, ERCC1_rs11615) and compared between different ethnicities. In addition, one of the patients was a long-term patient with peritoneal dialysis. We quantified the levels of palbociclib in her serum and peritoneal fluid by liquid chromatography-mass spectrometry (LC-MS). RESULTS: Interestingly, in our cohort, early neutropenia nadir (occurred within 56 days of start) was associated with worse treatment outcome, while occurrence of grade 3/4 neutropenia was associated with better outcome. We observed an extremely high incidence of neutropenia (96.2% any grade, 70.4% grade 3/4). In the analyzed germline databases, we discovered a higher SNP frequency of the T allele in ABCB1_rs1128503, a lower frequency of T allele in ABCB1_rs1045642, and a higher SNP frequency of G allele in ERCC1_rs11615. We observed that palbociclib levels in peritoneal dialysate ranged from around 20-50 ppb, and serum levels reached 100-110 ppb during drug administration and decreased to <10 ppb during discontinuation. CONCLUSION: Our retrospective analysis of real world palbociclib use reveals an association with grade 3/4 neutropenia with better outcome and early neutropenia nadir with worse outcome. Our findings of Asian specific SNPs support a predisposition toward profound and prevalent neutropenia in Asian patients under CDK4/6i. We also report the first pharmacokinetics analysis on a patient with peritoneal dialysis receiving CDK4/6i. In summary, our study provides novel clinical and genotypic insights into CDK4/6i associated neutropenia.

Mapping Lipid C═C Isomer Profiles of Human Gut Bacteria through a Novel Structural Lipidomics Workflow Assisted by Chemical Epoxidation.

The unsaturated lipids produced by human gut bacteria have an extraordinary range of structural diversity, largely because of the isomerism of the carbon-carbon double bond (C═C) in terms of its position and stereochemistry. Characterizing distinct C═C configurations poses a considerable challenge in research, primarily owing to limitations in current bioanalytical methodologies. This study developed a novel structural lipidomics workflow by combining MELDI (meta-chloroperoxybenzoic acid epoxidation for lipid double-bond identification) with liquid chromatography-tandem mass spectrometry for C═C characterization. We utilized this workflow to quantitatively assess more than 50 C═C positional and cis/trans isomers of fatty acids and phospholipids from selected human gut bacteria. Strain-specific isomer profiles revealed unexpectedly high productivity of trans-10-octadecenoic acid by Enterococcus faecalis, Bifidobacterium longum, and Lactobacillus acidophilus among numerous trans-fatty acid isomers produced by gut bacteria. Isotope-tracking experiments suggested that gut bacteria produce trans-10-octadecenoic acid through the isomeric biotransformation of oleic acid in vitro and that such isomeric biotransformation of dietary oleic acid is dependent on the presence of gut bacteria in vivo.

Investigating the Metabolic Heterogeneity of Cancer Cells Using Functional Single-Cell Selection and nLC Combined with Multinozzle Emitter Mass Spectrometry.

Tumor metastasis and cancer recurrence are often a result of cell heterogeneity, where specific subpopulations of tumor cells may be resistant to radio- or chemotherapy. To investigate this physiological and phenotypic diversity, single-cell metabolomics provides a powerful approach at the chemical level, where distinct lipid profiles can be found in different tumor cells. Here, we established a highly sensitive platform using nanoflow liquid chromatography (nLC) combined with multinozzle emitter electrospray ionization mass spectrometry for more in-depth metabolomics profiling. Our platform identified 15 and 17 lipids from individual osteosarcoma (U2OS) and glioblastoma (GBM) cells when analyzing single-cell samples. Additionally, we used the functional single-cell selection (fSCS) pipeline to analyze the subpopulations of cells with a DNA damage response (DDR) in U2OS cells and fast migration in GBM cells. Specifically, we observed a down-regulation of polyunsaturated fatty acids (PUFAs) in U2OS cells undergoing DDR, such as fatty acids FA 20:3; O2 and FA 17:4; O3. Furthermore, ceramides (Cer 38:0; O3) and triglycerides (TG 36:0) were found to be down-regulated in fast-migrating GBM cells compared to the slow-migrating subpopulation. These findings suggest the potential roles of these metabolites and/or lipids in the cellular behavior of the subpopulations.

Next-generation pathology practices with mass spectrometry imaging.

Mass spectrometry imaging (MSI) is a powerful technique that reveals the spatial distribution of various molecules in biological samples, and it is widely used in pathology-related research. In this review, we summarize common MSI techniques, including matrix-assisted laser desorption/ionization and desorption electrospray ionization MSI, and their applications in pathological research, including disease diagnosis, microbiology, and drug discovery. We also describe the improvements of MSI, focusing on the accumulation of imaging data sets, expansion of chemical coverage, and identification of biological significant molecules, that have prompted the evolution of MSI to meet the requirements of pathology practices. Overall, this review details the applications and improvements of MSI techniques, demonstrating the potential of integrating MSI techniques into next-generation pathology practices.

Period measurement of a periodic structure by using a heterodyne grating interferometer.

This paper proposes an alternative method for grating period measurement based on heterodyne grating interferometry. The optical configurations for measuring the period of reflection/transmission gratings were demonstrated, and four commercially available gratings were used to evaluate the effectiveness of the proposed method. Based on the phase-lock technique, the grating period could be obtained immediately through the phase wrapped/unwrapped process. Under precise measurement conditions, the grating period measurement error of the proposed method was better than 1 nm, and the grating period difference between product specifications was less than 1%. In addition, the measurement results of the proposed method also exhibited high similarity with optical microscopy measurements.

A Boron-Dependent Antibiotic Derived from a Calcium-Dependent Antibiotic.

The prevalence of drug-resistant bacterial pathogens foreshadows a healthcare crisis. Calcium-dependent antibiotics (CDAs) are promising candidates to combat infectious diseases as many of them show modes of action (MOA) orthogonal to widespread resistance mechanisms. The calcium dependence is nonetheless one of the hurdles toward realizing their full potential. Using laspartomycin C (LspC) as a model, we explored the possibility of reducing, or even eliminating, its calcium dependence. We report herein a synthetic LspC analogue (B1) whose activity no longer depends on calcium and is instead induced by phenylboronic acid (PBA). In LspC, Asp1 and Asp7 coordinate to calcium to anchor it in the active conformation; these residues are replaced by serine in B1 and condense with PBA to form a boronic ester with the same anchoring effect. Using thin-layer chromatography, MS, NMR, and complementation assays, we demonstrate that B1 inhibits bacterial growth via the same MOA as LspC, i.e., sequestering the cell wall biosynthetic intermediate undecaprenyl phosphate. B1 is as potent and effective as LspC against several Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus. Our success in converting a CDA to a boron-dependent antibiotic opens a new avenue in the design and functional control of drug molecules.

MSIr: Automatic Registration Service for Mass Spectrometry Imaging and Histology.

Mass spectrometry imaging (MSI) is a powerful tool that can be used to simultaneously investigate the spatial distribution of different molecules in samples. However, it is difficult to comprehensively analyze complex biological systems with only a single analytical technique due to different analytical properties and application limitations. Therefore, many analytical methods have been combined to extend data interpretation, evaluate data credibility, and facilitate data mining to explore important temporal and spatial relationships in biological systems. Image registration is an initial and critical step for multimodal imaging data fusion. However, the image registration of multimodal images is not a simple task. The property difference between each data modality may include spatial resolution, image characteristics, or both. The image registrations between MSI and different imaging techniques are often achieved indirectly through histology. Many methods exist for image registration between MSI data and histological images. However, most of them are manual or semiautomatic and have their prerequisites. Here, we built MSI Registrar (MSIr), a web service for automatic registration between MSI and histology. It can help to reduce subjectivity and processing time efficiently. MSIr provides an interface for manually selecting region of interests from histological images; the user selects regions of interest to extract the corresponding spectrum indices in MSI data. In the performance evaluation, MSIr can quickly map MSI data to histological images and help pinpoint molecular components at specific locations in tissues. Most registrations were adequate and were without excessive shifts. MSIr is freely available at https://msir.cmdm.tw and https://github.com/CMDM-Lab/MSIr.

Mitochondria and cytochrome components released into the plasma of severe COVID-19 and ICU acute respiratory distress syndrome patients.

INTRODUCTION: Proteomic analysis of human plasma by LC-ESI-MS/MS has discovered a limited number of new cellular protein biomarkers that may be confirmed by independent biochemical methods. Analysis of COVID-19 plasma has indicated the re-purposing of known biomarkers that might be used as prognostic markers of COVID-19 infection. However, multiple molecular approaches have previously indicated that the SARS-COV2 infection cycle is linked to the biology of mitochondria and that the response to infections may involve the action of heme containing oxidative enzymes. METHODS: Human plasma from COVID-19 and ICU-ARDS was analyzed by classical analytical biochemistry techniques and classical frequency-based statistical approaches to look for prognostic markers of severe COVID-19 lung damage. Plasma proteins from COVID-19 and ICU-ARDS were identified and enumerated versus the controls of normal human plasma (NHP) by LC-ESI-MS/MS. The observation frequency of proteins detected in COVID-19 and ICU-ARDS patients were compared to normal human plasma, alongside random and noise MS/MS spectra controls, using the Chi Square (χ2) distribution. RESULTS: PCR showed the presence of MT-ND1 DNA in the plasma of COVID-19, ICU-ARDS, as well as normal human plasma. Mitochondrial proteins such as MRPL, L2HGDH, ATP, CYB, CYTB, CYP, NDUF and others, were increased in COVID-19 and ICU-ARDS plasma. The apparent activity of the cytochrome components were tested alongside NHP by dot blotting on PVDF against a purified cytochrome c standard preparation for H2O2 dependent reaction with luminol as measured by enhanced chemiluminescence (ECL) that showed increased activity in COVID-19 and ICU-ARDS patients. DISCUSSION: The results from PCR, LC-ESI-MS/MS of tryptic peptides, and cytochrome ECL assays confirmed that mitochondrial components were present in the plasma, in agreement with the established central role of the mitochondria in SARS-COV-2 biology. The cytochrome activity assay showed that there was the equivalent of at least nanogram amounts of cytochrome(s) in the plasma sample that should be clearly detectable by LC-ESI-MS/MS. The release of the luminol oxidase activity from cells into plasma forms the basis of a simple and rapid test for the severity of cell damage and lung injury in COVID-19 infection and ICU-ARDS.

Microbial metabolites regulate social novelty via CaMKII neurons in the BNST.

Social novelty is a cognitive process that is essential for animals to interact strategically with conspecifics based on their prior experiences. The commensal microbiome in the gut modulates social behavior through various routes, including microbe-derived metabolite signaling. Short-chain fatty acids (SCFAs), metabolites derived from bacterial fermentation in the gastrointestinal tract, have been previously shown to impact host behavior. Herein, we demonstrate that the delivery of SCFAs directly into the brain disrupts social novelty through distinct neuronal populations. We are the first to observe that infusion of SCFAs into the lateral ventricle disrupted social novelty in microbiome-depleted mice without affecting brain inflammatory responses. The deficit in social novelty can be recapitulated by activating calcium/calmodulin-dependent protein kinase II (CaMKII)-labeled neurons in the bed nucleus of the stria terminalis (BNST). Conversely, chemogenetic silencing of the CaMKII-labeled neurons and pharmacological inhibition of fatty acid oxidation in the BNST reversed the SCFAs-induced deficit in social novelty. Our findings suggest that microbial metabolites impact social novelty through a distinct neuron population in the BNST.

The Enzymatic Doped/Undoped Poly-Silicon Nanowire Sensor for Glucose Concentration Measurement.

In this work, enzymatic doped/undoped poly-silicon nanowire sensors with different lengths were fabricated using a top-down technique to measure glucose concentration. The sensitivity and resolution of these sensors correlate well with the dopant property and length of nanowire. Experimental results indicate that the resolution is proportional to the nanowire length and dopant concentration. However, the sensitivity is inversely proportional to the nanowire length. The optimum resolution can be better than 0.02 mg/dL for a doped type sensor with length of 3.5 µm. Furthermore, the proposed sensor was demonstrated for 30 applications with similar current-time response and showed good repeatability.

Enzymatic Glucose Fiber Sensor for Glucose Concentration Measurement with a Heterodyne Interferometry.

In this study, we developed a glucose fiber sensor incorporating heterodyne interferometry to measure the phase difference produced by the chemical reaction between glucose and glucose oxidase (GOx). Both theoretical and experimental results showed that the amount of phase variation is inversely proportional to glucose concentration. The proposed method provided a linear measurement range of the glucose concentration from 10 mg/dL to 550 mg/dL. The experimental results indicated that the sensitivity is proportional to the length of the enzymatic glucose sensor, and the optimum resolution can be obtained at a sensor length of 3 cm. The optimum resolution of the proposed method is better than 0.6 mg/dL. Moreover, the proposed sensor demonstrates good repeatability and reliability. The average relative standard deviation (RSD) is better than 10% and satisfied the minimum requirement for point-of-care devices.

Visualizing vinca alkaloids in the petal of Catharanthus roseus using functionalized titanium oxide nanowire substrate for surface-assisted laser desorption/ionization imaging mass spectrometry.

Imaging mass spectrometry (IMS) is a powerful technique that enables analysis of various molecular species at a high spatial resolution with low detection limits. In contrast to the matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) approach, surface-assisted laser desorption/ionization (SALDI) can be more effective in the detection of small molecules due to the absence of interfering background signals in low m/z ranges. We developed a functionalized TiO2 nanowire as a solid substrate for IMS of low-molecular-weight species in plant tissues. We prepared TiO2 nanowires using an inexpensive modified hydrothermal process and subsequently functionalized them chemically with various silane analogs to overcome the problem of superhydrophilicity of the substrate. Chemical modification changed the selectivity of imprinting of samples deposited on the substrate surface and thus improved the detection limits. The substrate was applied to image distribution of the metabolites in very fragile specimens such as the petal of Catharanthus roseus. We observed that the metabolites are distributed heterogeneously in the petal, which is consistent with previous results reported for the C. roseus plant leaf and stem. The intermediates corresponding to the biosynthesis pathway of some vinca alkaloids were clearly shown in the petal. We also performed profiling of petals from five different cultivars of C. roseus plant. We verified the semi-quantitative capabilities of the imprinting/imaging approach by comparing results using the LC-MS analysis of the plant extracts. This suggested that the functionalized TiO2 nanowire substrate-based SALDI is a powerful technique complementary to MALDI-MS.

High-performance miniature linear time-of-flight mass spectrometry as an advantageous tool in a high mass-to-charge range.

A miniature matrix-assisted laser desorption/ionization linear time-of-flight mass spectrometer suitable for the high mass-to-charge (m/z) region is described. The instrument size is roughly 1/50th that of regular instruments, and detailed dimensions and experimental parameters were optimized based on the comprehensive calculation method to provide satisfactory mass resolving power. Observations showed that the performance is limited in the low m/z range and becomes comparable with that of regular instruments in the mid m/z range. In the high m/z range, the miniature instrument provides better mass resolving power and sensitivity than regular instruments, showing superior performance for microbial, protein conjugate, and polymer analyses.

Mass spectrometry-based metabolomic signatures of coral bleaching under thermal stress.

Coral bleaching caused by climate change has resulted in large-scale coral reef decline worldwide. However, the knowledge of physiological response mechanisms of scleractinian corals under high-temperature stress is still challenging. Here, untargeted mass spectrometry-based metabolomics combining with Global Natural Product Social Molecular Networking (GNPS) was utilized to investigate the physiological response of the coral species Pavona decussata under thermal stress. A wide variety of metabolites (including lipids, fatty acids, amino acids, peptides, osmolytes) were identified as the potential biomarkers and subjected to metabolic pathway enrichment analysis. We discovered that, in the thermal-stressed P. decussata coral holobiont, (1) numerous metabolites in classes of lipids and amino acids significantly decreased, indicating an enhanced lipid hydrolysis and aminolysis that contributed to up-regulation in gluconeogenesis to meet energy demand for basic survival; (2) pantothenate and panthenol, two essential intermediates in tricarboxylic acid (TCA) cycle, were up-regulated, implying enhanced efficiency in energy production; (3) small peptides (e.g., Glu-Leu and Glu-Glu-Glu-Glu) and lyso-platelet-activating factor (lysoPAF) possibly implicated a strengthened coral immune response; (4) the down-regulation of betaine and trimethylamine N-oxide (TMAO), known as osmolyte compounds for maintaining holobiont homeostasis, might be the result of disruption of coral holobiont.

Reaction Tracking and High-Throughput Screening of Active Compounds in Combinatorial Chemistry by Tandem Mass Spectrometry Molecular Networking.

Combinatorial synthesis has been widely used as an efficient strategy to screen for active compounds. Mass spectrometry is the method of choice in the identification of hits resulting from high-throughput screenings due to its high sensitivity, specificity, and speed. However, manual data processing of mass spectrometry data, especially for structurally diverse products in combinatorial chemistry, is extremely time-consuming and one of the bottlenecks in this process. In this study, we demonstrated the effectiveness of a tandem mass spectrometry molecular networking-based strategy for product identification, reaction dynamics monitoring, and active compound targeting in combinatorial synthesis. Molecular networking connects compounds with similar tandem mass spectra into a cluster and has been widely used in natural products analysis. We show that both the expected and side products can be readily characterized using molecular networking based on their mass spectrometry fragmentation patterns. Additionally, time-dependent molecular networking was integrated to track reaction dynamics to determine the optimal reaction time to maximize target product yields. We also present a proof-of-concept experiment that successfully identified and isolated active molecules from a dynamic combinatorial library. These results demonstrated the potential of using molecular networking for identifying, tracking, and high-throughput screening of active compounds in combinatorial synthesis.

Labeling and Characterization of Phenol-Containing Glycopeptides Using Chemoselective Probes with Isotope Tags.

Secondary metabolites are structurally diverse natural products (NPs) and have been widely used for medical applications. Developing new tools to enrich NPs can be a promising solution to isolate novel NPs from the native and complex samples. Here, we developed native and deuterated chemoselective labeling probes to target phenol-containing glycopeptides by the ene-type labeling used in proteomic research. The clickable azido-linker was included for further biotin functionalization to facilitate the enrichment of labeled substrates. Afterward, our chemoselective method, in conjunction with LC-MS and MSn analysis, was demonstrated in bacterial cultures. A vancomycin-related phenol-containing glycopeptide was labeled and characterized by our labeling strategy, showing its potential in glycopeptide discovery in complex environments.

In vitro glucose concentration measurement by a reusable enzymatic glucose sensor and a highly stable circular heterodyne polarimeter.

A reliable glucose concentration measurement system was proposed that consisted of a circular heterodyne polarimeter and a reusable enzymatic sensor. The circular heterodyne polarimeter was constructed using a highly stable circular heterodyne light source and a compact alignment-free apparatus that provided phase stability of less than 1° within 20 min. The reusable enzymatic glucose sensor can be reused more than 100 times and retain 90% of its initial performance under optimum storage conditions within a month. The proposed method can be used to determine glucose concentrations in aqueous solutions and human serum. The optimum resolution of the proposed method was approximately 0.88 mg/dl for the glucose solution and 0.68 mg/dl for the serum-based sample.

Measurement of the refractive index of lenses from the maximum phase difference of the total internal reflection with a polarization camera.

The proposed total internal reflection (TIR)-based technique can be used for measuring the refractive index of lenses. Distribution of the phase difference between the s- and p-polarization states of the reflected light induced by TIR can be obtained by a polarization camera. The refractive index of the lens can be determined from the detected maximum phase difference, with the specific measurement equation. Only the maximum phase difference needs to be measured. Information about the incident angle, thickness of the lens, and the matching liquid is not needed. The experimental results demonstrate that the resolution of the system can reach 4.8×10-4RIU.

Design and fabrication of a downlight luminaire with a dual frusto-conical reflector.

A design method and corresponding fabrication procedures are proposed for a dual frusto-conical reflector of a downlight luminaire. The profile of the dual frusto-conical reflector consists of two flat-slant reflective surfaces with slightly different slopes. The optimum dual frusto-conical reflector can be obtained with the proposed design method. The finished product of the dual frusto-conical reflector is fabricated by a 3D printer and followed by surface polishing and reflection paint spraying. The measurement results show that luminaires exhibited 70% optimum illuminance confined within an illumination area of 1.8m2, and the optimum illumination intensity is at 252 lux. The optimum efficiency of the proposed luminaire can reach 158 lm/W for normal-white light-emitting diode (LED) and 119 lm/W for warm-white LED, respectively.

Ambient Ionization Mass Spectrometry Today and Tomorrow: Embracing Challenges and Opportunities.

Ambient ionization mass spectrometry (AIMS) has grown into a group of emerging analytical techniques that allow rapid, real-time, high-throughput, in situ, and in vivo analysis in many scientific fields including biomedicine, pharmaceuticals, and forensic sciences. While dozens of AIMS techniques have been introduced over the past two decades, their broad commercial and industrial use is still restricted by multiple challenges. In this Perspective, we discuss the most relevant technical challenges facing AIMS, i.e., reproducibility, quantitative ability, molecular coverage, sensitivity, and data complexity, and scientists' recent attempts to overcome these hurdles. Furthermore, we present future directions of AIMS from our perspective, including the necessity that efforts should be made to unravel blind biomolecules in routine analysis, the construction of a data depository for AIMS users, the full automation of pipelines for prospect integration in a robotic laboratory, the movement toward on-site tests, and the expansion of outreach to motivate government officials in policymaking. We anticipate that, with progress in these critical but immature areas, AIMS technology will keep evolving to become a more robust and user-friendly set of technologies and, consequently, be translated into everyday life practice.