High-Throughput Quantitative Analysis of Amino Acids in Freeze-Dried Drops Using Time-of-Flight Secondary Ion Mass Spectrometry.

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) has become a promising analytical tool for molecular profiling in biological applications. However, its ultrahigh vacuum environment and matrix effects hamper the absolute quantitation of solution samples. Herein, we present a rapid high-throughput platform for quantitative ToF-SIMS analysis of amino acids in matrix deposits formed from freeze-dried solution drops through ice sublimation on a parylene film microarray substrate. Droplets of the amino acid solutions, which were mixed with stable isotope-labeled phenylalanine (F*) of high concentration (10 mM), were loaded on wells of the microarray, then frozen and evaporated slowly below the freezing point, forming continuous solid-phase F* matrix deposits. The amino acids (≤500 µM), adequately well dispersed throughout the F* matrix deposits on each well, were quantitatively analyzed by ToF-SIMS in a rapid and high-throughput fashion. The lower limit of quantitation reached below 10 µM.

A comparative study of ammonia solubility in imidazolium-based ionic liquids with different structural compositions.

Four imidazolium-based ionic liquids (ILs) with two cations 1-pentyl-3-butylimidazolium [PBIM]+ and 1-benzyl-3-butylimidazolium tetrafluoroborate [BzBIM]+, and two anions tetrafluoroborate (BF4-) and trifluoromethanesulfonate (OTf-) were synthesized for NH3 solubility enhancement. The structural, thermal, and electrochemical stabilities, ionic conductivity, and viscosity of the four ILs, namely, [PBIM]BF4, [BzBIM]BF4, [PBIM]OTf, and [BzBIM]OTf, were investigated. Due to the intermolecular interaction of the benzyl group attached to the imidazolium ring, [BzBIM]+-based ILs exhibited higher thermal stability but lower ionic conductivity compared to [PBIM]+-based ILs. Further, the NH3 solubility in all ILs was measured using a custom-made setup at temperatures ranging from 293.15 to 323.15 K and pressures ranging from 1 to 5 bar. The effects of the cation and anion structures of ILs, as well as pressure and temperature, on the NH3 solubility in the ILs were also investigated. [PBIM]BF4 showed the best solubility because of its high free volume and low viscosity. Density functional calculations validated the superior NH3 solubility in [PBIM]BF4, attributable to the minimal reorganization of the [cation]anion complex geometry during the solvation process, yielding a low solvation free energy. The findings of this study suggest that ILs exhibit a high NH3 solubility capacity and cation and anion structures considerably affect the NH3 solubility in ILs.

Parallel accumulation-serial fragmentation method for in-depth proteomic analysis of bronchoalveolar lavage fluid collected from patients with nonsmall cell lung cancer.

PURPOSE: Advances in mass spectrometry-based quantitative proteomic analysis have successfully demonstrated the in-depth detection of protein biomarkers in bronchoalveolar lavage fluid (BALF) from patients with lung cancers. Recently, ion mobility technology was incorporated into the mass spectrometers escalating the sensitivity and throughput. Utilizing these advantages, herein, we employed the parallel accumulation-serial fragmentation (PASEF) implanted in a timsTOF Pro mass spectrometer to examine the alteration of BALF proteomes in patients with nonsmall cell lung cancers (NSCLCs). EXPERIMENTAL DESIGN: BALF proteins were processed from patients with NSCLC and analyzed in a timsTOF Pro mass spectrometer with the PASEF method using a peptide input of 100 ng. Label-free mass spectrometry data were analyzed in the FragPipe platform. RESULTS: We quantitated over 1400 proteins from a single injection of 100 ng of peptides per sample with a median of ∼2000 proteins. We were able to find a few potential biomarker proteins upregulated in NSCLC. CONCLUSIONS AND CLINICAL RELEVANCE: The alterations of the BALF proteome landscape vary among patients with NSCLC as previously observed in patients with small-cell lung cancers. The PASEF method has significantly enhanced the sensitivity and throughput, demonstrating its effectiveness in clinical research and application.

Nanobubble Reactivity: Evaluating Hydroxyl Radical Generation (or Lack Thereof) under Ambient Conditions.

Nanobubble (NB) generation of reactive oxygen species (ROS), especially hydroxyl radical (·OH), has been controversial. In this work, we extensively characterize NBs in solution, with a focus on ROS generation (as ·OH), through a number of methods including degradation of ·OH-specific target compounds, electron paramagnetic resonance (EPR), and a fluorescence-based indicator. Generated NBs exhibit consistent physical characteristics (size, surface potential, and concentration) when compared with previous studies. For conditions described, which are considered as high O2 NB concentrations, no degradation of benzoic acid (BA), a well-studied ·OH scavenger, was observed in the presence of NBs (over 24 h) and no EPR signal for ·OH was detected. While a positive fluorescence response was measured when using a fluorescence probe for ·OH, aminophenyl fluorescein (APF), we provide an alternate explanation for the result. Gas/liquid interfacial characterization indicates that the surface of a NB is proton-rich and capable of inducing acid-catalyzed hydrolysis of APF, which results in a false (positive) fluorescence response. Given these negative results, we conclude that NB-induced ·OH generation is minimal, if at all, for conditions evaluated.

Removal of the red tide dinoflagellate Cochlodinium polykrikoides using chemical disinfectants.

For decades, red tide control has been recognized as necessary for mitigating financial damage to fish farms. Chemical disinfectants, frequently used for water disinfection, can reduce the risk of red tides on inland fish farms. This study systematically evaluated four different chemical disinfectants (ozone (O3), permanganate (MnO4-), sodium hypochlorite (NaOCl), and hydrogen peroxide (H2O2)) for their potential use in inland fish farms to control red tides by investigating their (i) inactivation efficacy regarding C. polykrikoides, (ii) total residual oxidant and byproduct formation, and (iii) toxicity to fish. The inactivation efficacy of C. polykrikoides cells by chemical disinfectants from highest to lowest followed the order of O3 > MnO4- > NaOCl > H2O2 for different cell density conditions and disinfectant doses. The O3 and NaOCl treatments generated bromate as an oxidation byproduct by reacting with bromide ions in seawater. The acute toxicity tests of the disinfectants for juvenile red sea bream (Pagrus major) showed that 72-h LC50 values were 1.35 (estimated), 0.39, 1.32, and 102.61 mg/L for O3, MnO4-, NaOCl, and H2O2, respectively. Considering the inactivation efficacy, exposure time of residual oxidants, byproduct formation, and toxicity toward fish, H2O2 is suggested as the most practical disinfectant for controlling red tides in inland fish farms.

Dysregulation of the Wnt/ß-catenin signaling pathway via Rnf146 upregulation in a VPA-induced mouse model of autism spectrum disorder.

Autism spectrum disorder (ASD) is a neurodevelopmental disorder associated with impaired social behavior and communication, repetitive behaviors, and restricted interests. In addition to genetic factors, environmental factors such as prenatal drug exposure contribute to the development of ASD. However, how those prenatal factors induce behavioral deficits in the adult stage is not clear. To elucidate ASD pathogenesis at the molecular level, we performed a high-resolution mass spectrometry-based quantitative proteomic analysis on the prefrontal cortex (PFC) of mice exposed to valproic acid (VPA) in utero, a widely used animal model of ASD. Differentially expressed proteins (DEPs) in VPA-exposed mice showed significant overlap with ASD risk genes, including differentially expressed genes from the postmortem cortex of ASD patients. Functional annotations of the DEPs revealed significant enrichment in the Wnt/ß-catenin signaling pathway, which is dysregulated by the upregulation of Rnf146 in VPA-exposed mice. Consistently, overexpressing Rnf146 in the PFC impaired social behaviors and altered the Wnt signaling pathway in adult mice. Furthermore, Rnf146-overexpressing PFC neurons showed increased excitatory synaptic transmission, which may underlie impaired social behavior. These results demonstrate that Rnf146 is critical for social behavior and that dysregulation of Rnf146 underlies social deficits in VPA-exposed mice.

Oncological and functional outcomes of partial or total laryngopharyngectomy for hypopharyngeal cancer with thyroid or cricoid cartilage invasion.

BACKGROUND: Patients with cartilage invasion in hypopharyngeal squamous cell carcinoma (HPSCC) would benefit from partial laryngopharyngectomy (PLP). AIMS/OBJECTIVES: The purpose of this study was to examine the treatment outcomes of PLP for HPSCC with cartilage invasion, with a focus on the oncological safety and the function preservation. MATERIALS AND METHODS: We performed a retrospective review of 28 patients with HPSCC with thyroid or cricoid cartilage invasion who had undergone upfront surgery and were followed for more than one year between 1993 and 2019. RESULTS: Twelve patients treated with PLP (42.9%) and 16 patients treated with total laryngopharyngectomy (TLP) for cartilage invasion in HPSCC were identified. There was no significant difference in recurrence between the PLP group (7/12, 58.3%) and the TLP group (8/16, 50.0%) (p = .718). PLP was not associated with decreased five-year disease free survival (p = .662) or disease specific survival (p = .883) rates compared to TLP. Nine patients receiving PLP could be decannulated and retained intelligible speech (9/12, 75%). Gastrostomy tubes were placed in the PLP group (5/12, 42.9%) and TLP group (1/16, 6.2%) (p = .057). CONCLUSIONS AND SIGNIFICANCE: PLP appears to be a feasible option for the treatment of thyroid or cricoid cartilage invasion in HPSCC.

Advances in Mass Spectrometry-Based Single Cell Analysis.

Technological developments and improvements in single-cell isolation and analytical platforms allow for advanced molecular profiling at the single-cell level, which reveals cell-to-cell variation within the admixture cells in complex biological or clinical systems. This helps to understand the cellular heterogeneity of normal or diseased tissues and organs. However, most studies focused on the analysis of nucleic acids (e.g., DNA and RNA) and mass spectrometry (MS)-based analysis for proteins and metabolites of a single cell lagged until recently. Undoubtedly, MS-based single-cell analysis will provide a deeper insight into cellular mechanisms related to health and disease. This review summarizes recent advances in MS-based single-cell analysis methods and their applications in biology and medicine.

Porcine Reproductive and Respiratory Syndrome Virus Engineered by Serine Substitution on the 44th Amino Acid of GP5 Resulted in a Potential Vaccine Candidate with the Ability to Produce High Levels of Neutralizing Antibody.

N-linked glycans covering GP5 neutralizing epitopes of porcine reproductive and respiratory syndrome virus (PRRSV) have been proposed to act as a sheath blocking the production of neutralizing antibodies. Herein, we genetically engineered PRRSV with serine (S) substitution on the 44th asparagine (N) on the GP5 ectodomain of PRRSV-2 lineage-1. To evaluate the recombinant PRRSV, in vivo experiments were performed in piglets. The recombinant virus group showed no viremia until 42 days post-inoculation (dpi), and the rectal temperature and average daily weight gain were in the normal range at the same time point as the negative control group. On the 42 dpi, both groups were challenged with the wild-type virus. The recombinant PRRSV group showed lower rectal temperature, viremia, and the lung lesions than that of the negative control group for 19 days post-challenge (dpc). Additionally, the recombinant virus induced 4.50 ± 3.00 (log2) and 8.25 ± 0.96 (log2) of neutralizing antibody before and after challenge, respectively. Taken together, this study confirmed that N44S substitution can create an infectious PRRSV that strongly induces neutralizing antibodies. In addition, the vCSL1-GP5-N44S mutant that we produced was confirmed to have potential as a vaccine candidate, showing good safety and protective effects in pigs.

Predictive factors of distant metastasis in surgically treated HPV-positive tonsil cancer.

BACKGROUND: Human papilloma virus (HPV)-related tonsil cancer is associated with favorable outcomes. OBJECTIVE: The purpose of this study was to define factors affecting distant metastasis in patients with surgically treated HPV-positive tonsil cancer. METHODS: The present study enrolled 76 patients diagnosed with HPV-positive tonsil cancer who underwent primary surgery between January 2010 and December 2021. RESULTS: Twelve (15.7%) patients experienced a distant failure with a median follow-up time of 43 months. Sites of distant metastasis included the lung (n = 10), liver (n = 1), and brain (n = 1). Upon multivariate analysis, an advanced T stage (odds ratio [OR]: 13.94, 95% confidence interval [CI]: 1.29-149.863, p = 0.003) and margin involvement (OR: 5.96, 95% CI: 1.33-26.76, p = 0.02) were independent predictors of distant metastases. The five-year disease-specific survival for the entire cohort was 85%. The multivariate analysis confirmed that distant metastasis (hazard ratio [HR]: 12.688, 95% CI: 3.424-47.016; p < 0.001) and margin involvement (HR: 6.243; 95% CI: 1.681-23.191; p = 0.006) were significant factors associated with the five-year disease-specific survival. CONCLUSION: HPV-positive tonsil cancer patients with an advanced T stage and a positive surgical margin have a substantial risk of distant metastases. Distant metastasis and margin involvement are factors that affect their survival.

Quantitative proteomic analysis of bronchoalveolar lavage fluids from patients with small cell lung cancers.

PURPOSE: Small cell lung cancer (SCLC) is one of the malignant cancers with aggressive progression and poor prognosis. Bronchoalveolar lavage fluid (BALF) has been arising recently as a potential source of biomarkers for lung cancers. In this study, we performed quantitative BALF proteomic analysis to identify potential biomarkers for SCLC. EXPERIMENTAL DESIGN: BALF were collected from tumor-bearing lungs and non-tumor lungs of five SCLC patients. Then, BALF proteomes were prepared for a TMT-based quantitative mass spectrometry analysis. Differentially expressed proteins (DEP) were identified when considering individual variation. Potential SCLC biomarker candidates were validated by immunohistochemistry (IHC). A public database of multiple SCLC cell lines was used to evaluate the correlation of these markers with SCLC subtypes and chemo-drug responses. RESULTS: We identified 460 BALF proteins in SCLC patients and observed considerable individual variation among the patients. Immunohistochemical analysis and bioinformatics resulted in the identification of CNDP2 and RNPEP as potential subtype markers for ASCL1 and NEUROD1, respectively. In addition, CNDP2 was found to be positively correlated with responses to etoposide, carboplatin, and irinotecan. CONCLUSIONS AND CLINICAL RELEVANCE: BALF is an emerging source of biomarkers, making it useful for the diagnosis and prognosis of lung cancers. We characterized the proteomes of paired BALF samples collected from tumor-bearing and non-tumor lungs of SCLC patients. Several proteins were found elevated in tumor-bearing BALF, and especially CNDP2 and RNPEP appeared to be potential indicators for ASLC1-high and NEUROD1-high subtypes of SCLC, respectively. The positive correlation of CNDP2 with chemo-drug responses would help to make decisions for treatment of SCLC patients. These putative biomarkers could be comprehensively investigated for a clinical use towards precision medicine.

Proteogenomic landscape of human pancreatic ductal adenocarcinoma in an Asian population reveals tumor cell-enriched and immune-rich subtypes.

We report a proteogenomic analysis of pancreatic ductal adenocarcinoma (PDAC). Mutation-phosphorylation correlations identified signaling pathways associated with somatic mutations in significantly mutated genes. Messenger RNA-protein abundance correlations revealed potential prognostic biomarkers correlated with patient survival. Integrated clustering of mRNA, protein and phosphorylation data identified six PDAC subtypes. Cellular pathways represented by mRNA and protein signatures, defining the subtypes and compositions of cell types in the subtypes, characterized them as classical progenitor (TS1), squamous (TS2-4), immunogenic progenitor (IS1) and exocrine-like (IS2) subtypes. Compared with the mRNA data, protein and phosphorylation data further classified the squamous subtypes into activated stroma-enriched (TS2), invasive (TS3) and invasive-proliferative (TS4) squamous subtypes. Orthotopic mouse PDAC models revealed a higher number of pro-tumorigenic immune cells in TS4, inhibiting T cell proliferation. Our proteogenomic analysis provides significantly mutated genes/biomarkers, cellular pathways and cell types as potential therapeutic targets to improve stratification of patients with PDAC.

Cntnap2-dependent molecular networks in autism spectrum disorder revealed through an integrative multi-omics analysis.

Autism spectrum disorder (ASD) is a major neurodevelopmental disorder in which patients present with core symptoms of social communication impairment, restricted interest, and repetitive behaviors. Although various studies have been performed to identify ASD-related mechanisms, ASD pathology is still poorly understood. CNTNAP2 genetic variants have been found that represent ASD genetic risk factors, and disruption of Cntnap2 expression has been associated with ASD phenotypes in mice. In this study, we performed an integrative multi-omics analysis by combining quantitative proteometabolomic data obtained with Cntnap2 knockout (KO) mice with multi-omics data obtained from ASD patients and forebrain organoids to elucidate Cntnap2-dependent molecular networks in ASD. To this end, a mass spectrometry-based proteometabolomic analysis of the medial prefrontal cortex in Cntnap2 KO mice led to the identification of Cntnap2-associated molecular features, and these features were assessed in combination with multi-omics data obtained on the prefrontal cortex in ASD patients to identify bona fide ASD cellular processes. Furthermore, a reanalysis of single-cell RNA sequencing data obtained from forebrain organoids derived from patients with CNTNAP2-associated ASD revealed that the aforementioned identified ASD processes were mainly linked to excitatory neurons. On the basis of these data, we constructed Cntnap2-associated ASD network models showing mitochondrial dysfunction, axonal impairment, and synaptic activity. Our results may shed light on the Cntnap2-dependent molecular networks in ASD.

Gate-voltage-induced reversible electrical phase transitions in Mo0.67W0.33Se2 devices.

Tunable electrical phase transitions based on the structural and quantum-state phase transitions in two-dimensional transition-metal dichalcogenides have attracted attention in both semiconducting electronics and quantum electronics applications. Here, we report gate-voltage-induced reversible electrical phase transitions in Mo0.67W0.33Se2 (MoWSe) field-effect transistors prepared on SiO2/Si substrates. In gate-induced depletion regions of the 2H phase, an electrical current resumes flow at 150 K < T < 200 K with decreasing T irrespective of the layer number (n) for MoWSe when n < 20. The newly appearing electron-doped-type conducting channel again enters the 2H-phase region when the back-gate voltage increases, accompanied by the negative differential transconductance for four-layer and monolayer devices or by a deflection point in the transfer curves for a multilayer device. The thermal activation energies of the new conducting and 2H-phase branches differ by one order of magnitude at the same gate voltage for both the four-layer and monolayer cases, indicating that the electrical band at the Fermi level was modified. The hysteresis measurements for the gate voltage were performed with a five-layer device, which confirms the reversible electrical transition behavior. The possible origins of the nucleated conducting phase in the depletion region of the 2H phase of MoWSe are discussed.

Gender-specific differences in central blood pressure and optimal target blood pressure based on the prediction of cardiovascular events.

Background: Hypertension (HBP) is a common disease among both men and women. Central blood pressure (CBP) is a method of evaluating aorta pressure that can assess the intrinsic BP of an individual patient that more closely correlates with cardiovascular disease (CVD) outcomes than peripheral BP parameters. We evaluated gender-specific differences in CBP and optimal target BP based on a composite outcome of CVD, heart failure (HF), and hypertensive complications in patients with HBP. Method: Patients were enrolled from June 2011 to December 2015 and were followed through December 2019. CBP was measured using radial tonometry. The primary endpoint was a composite outcome. Result: The median follow-up period for enrolled patients was 6.5 years. Out of a total of 2,115 patients with an average age of 57.9 ± 13.6 years, 266 patients (12.6%) had events of primary end points during the follow-up period. There was no difference in the lowest BP level between men and women in the incidence of CVD. Among the women (49.6%), 78.1% were postmenopausal. In a multivariable Cox proportional hazards model, CBP and systolic BP showed an increase in risk of 10 and 11%, respectively, with every 10 mmHg increase, and there was a similar trend of 12 and 13%, respectively, in postmenopausal women. However, PP showed an increase in risk of about 2% every 10 mmHg increase, but a tendency to increase risk by 19% in postmenopausal women. Conclusion: This study demonstrated that postmenopausal women will continue to show increased risk for CVD at BP higher than the optimal level. Conversely, there was no increase in CV risk due to menopause at BP values below the optimal level. Therefore, well-controlled BP is more important in postmenopausal women.

Prediction of cardiovascular events by central blood pressure using radial tonometry in type 2 diabetes mellitus patients.

BACKGROUND: High blood pressure (BP) and type 2 diabetes mellitus (T2DM) are major causes of atherosclerotic cardiovascular disease (ASCVD) and heart failure (HF). Central blood pressure (CBP) is more predictive of ASCVD than is brachial BP; however, an association of CBP with ASCVD has not been found in T2DM patients. We evaluated the impact of CBP and the association between optimal level of noninvasively measured CBP and office BP in T2DM patients based on composite outcome of ASCVD, HF, and complications of hypertension. METHODS: Patients were enrolled from June 2011 to December 2015 and were followed up through December 2019. CBP was measured using radial tonometry. The primary endpoints were composite outcome of ASCVD, HF, and hypertension-induced complications such as left ventricular hypertrophy, retinopathy, and proteinuria. RESULTS: During the 6.5-year follow-up period, 515 patients were enrolled in the study. A total of 92 patients (17.9%) developed primary endpoints. The mean age of subjects was 61.3 ± 12.1 years and 55% (n = 283) were male. Patients who developed primary endpoints were older (65.3 ± 9.5 years vs. 60.5 ± 12.4 years) and had lower high-density lipoprotein (36.6 ± 9.4 mg/dL vs. 41.8 ± 11.1 mg/dL), higher CBP (123.6 ± 20.6 mmHg vs. 118.0 ± 20.6 mmHg), and higher pulse pressure (61.3 ± 16.6 mmHg vs. 56.5 ± 15.1 mmHg) than subjects without primary endpoint development. After adjustment for various risk factors, CBP was an independent predictor for primary endpoints (hazard ratio, 1.14; 95% confidence interval, 1.02-1.27; P = 0.016). In addition, the association of CBP and primary endpoints showed a U-shaped curve with the lowest incidence at CBP 118 mmHg and systolic BP about 128 mmHg. CONCLUSIONS: We show the importance of CBP measurements in T2DM patients and present a cutoff value for ASCVD events and hypertension-induced complications.

RNA-sequencing and mass-spectrometry proteomic time-series analysis of T-cell differentiation identified multiple splice variants models that predicted validated protein biomarkers in inflammatory diseases.

Profiling of mRNA expression is an important method to identify biomarkers but complicated by limited correlations between mRNA expression and protein abundance. We hypothesised that these correlations could be improved by mathematical models based on measuring splice variants and time delay in protein translation. We characterised time-series of primary human naïve CD4+ T cells during early T helper type 1 differentiation with RNA-sequencing and mass-spectrometry proteomics. We performed computational time-series analysis in this system and in two other key human and murine immune cell types. Linear mathematical mixed time delayed splice variant models were used to predict protein abundances, and the models were validated using out-of-sample predictions. Lastly, we re-analysed RNA-seq datasets to evaluate biomarker discovery in five T-cell associated diseases, further validating the findings for multiple sclerosis (MS) and asthma. The new models significantly out-performing models not including the usage of multiple splice variants and time delays, as shown in cross-validation tests. Our mathematical models provided more differentially expressed proteins between patients and controls in all five diseases. Moreover, analysis of these proteins in asthma and MS supported their relevance. One marker, sCD27, was validated in MS using two independent cohorts for evaluating response to treatment and disease prognosis. In summary, our splice variant and time delay models substantially improved the prediction of protein abundance from mRNA expression in three different immune cell types. The models provided valuable biomarker candidates, which were further validated in MS and asthma.