Proteomics of prostate cancer serum and plasma using low and high throughput approaches.

Despite progress, MS-based proteomics in biofluids, especially blood, faces challenges such as dynamic range and throughput limitations in biomarker and disease studies. In this work, we used cutting-edge proteomics technologies to construct label-based and label-free workflows, capable of quantifying approximately 2,000 proteins in biofluids. With 70µL of blood and a single depletion strategy, we conducted an analysis of a homogenous cohort (n = 32), comparing medium-grade prostate cancer patients (Gleason score: 7(3 + 4); TNM stage: T2cN0M0, stage IIB) to healthy donors. The results revealed dozens of differentially expressed proteins in both plasma and serum. We identified the upregulation of Prostate Specific Antigen (PSA), a well-known biomarker for prostate cancer, in the serum of cancer cohort. Further bioinformatics analysis highlighted noteworthy proteins which appear to be differentially secreted into the bloodstream, making them good candidates for further exploration.

Mechanistic safety assessment via multi-omic characterisation of systemic pathway perturbations following in vivo MAT2A inhibition.

The tumour suppressor p16/CDKN2A and the metabolic gene, methyl-thio-adenosine phosphorylase (MTAP), are frequently co-deleted in some of the most aggressive and currently untreatable cancers. Cells with MTAP deletion are vulnerable to inhibition of the metabolic enzyme, methionine-adenosyl transferase 2A (MAT2A), and the protein arginine methyl transferase (PRMT5). This synthetic lethality has paved the way for the rapid development of drugs targeting the MAT2A/PRMT5 axis. MAT2A and its liver- and pancreas-specific isoform, MAT1A, generate the universal methyl donor S-adenosylmethionine (SAM) from ATP and methionine. Given the pleiotropic role SAM plays in methylation of diverse substrates, characterising the extent of SAM depletion and downstream perturbations following MAT2A/MAT1A inhibition (MATi) is critical for safety assessment. We have assessed in vivo target engagement and the resultant systemic phenotype using multi-omic tools to characterise response to a MAT2A inhibitor (AZ'9567). We observed significant SAM depletion and extensive methionine accumulation in the plasma, liver, brain and heart of treated rats, providing the first assessment of both global SAM depletion and evidence of hepatic MAT1A target engagement. An integrative analysis of multi-omic data from liver tissue identified broad perturbations in pathways covering one-carbon metabolism, trans-sulfuration and lipid metabolism. We infer that these pathway-wide perturbations represent adaptive responses to SAM depletion and confer a risk of oxidative stress, hepatic steatosis and an associated disturbance in plasma and cellular lipid homeostasis. The alterations also explain the dramatic increase in plasma and tissue methionine, which could be used as a safety and PD biomarker going forward to the clinic.

Characterization of the Secretome, Transcriptome, and Proteome of Human ß Cell Line EndoC-ßH1.

Early diabetes research is hampered by limited availability, variable quality, and instability of human pancreatic islets in culture. Little is known about the human ß cell secretome, and recent studies question translatability of rodent ß cell secretory profiles. Here, we verify representativeness of EndoC-ßH1, one of the most widely used human ß cell lines, as a translational human ß cell model based on omics and characterize the EndoC-ßH1 secretome. We profiled EndoC-ßH1 cells using RNA-seq, data-independent acquisition, and tandem mass tag proteomics of cell lysate. Omics profiles of EndoC-ßH1 cells were compared to human ß cells and insulinomas. Secretome composition was assessed by data-independent acquisition proteomics. Agreement between EndoC-ßH1 cells and primary adult human ß cells was ∼90% for global omics profiles as well as for ß cell markers, transcription factors, and enzymes. Discrepancies in expression were due to elevated proliferation rate of EndoC-ßH1 cells compared to adult ß cells. Consistently, similarity was slightly higher with benign nonmetastatic insulinomas. EndoC-ßH1 secreted 783 proteins in untreated baseline state and 3135 proteins when stressed with nontargeting control siRNA, including known ß cell hormones INS, IAPP, and IGF2. Further, EndoC-ßH1 secreted proteins known to generate bioactive peptides such as granins and enzymes required for production of bioactive peptides. EndoC-ßH1 secretome contained an unexpectedly high proportion of predicted extracellular vesicle proteins. We believe that secretion of extracellular vesicles and bioactive peptides warrant further investigation with specialized proteomics workflows in future studies.

Proprotein convertase PCSK9 affects expression of key surface proteins in human pancreatic beta cells via intracellular and extracellular regulatory circuits.

Proprotein convertase subtilisin/kexin type 9 (PCSK9) is involved in the degradation of the low-density lipoprotein receptor. PCSK9 also targets proteins involved in lipid metabolism (very low-density lipoprotein receptor), immunity (major histocompatibility complex I), and viral infection (cluster of differentiation 81). Recent studies have also indicated that PCSK9 loss-of-function mutations are associated with an increased incidence of diabetes; however, the expression and function of PCSK9 in insulin-producing pancreatic beta cells remain unclear. Here, we studied PCSK9 regulation and function by performing loss- and gain-of-function experiments in the human beta cell line EndoC-ßH1. We demonstrate that PCSK9 is expressed and secreted by EndoC-ßH1 cells. We also found that PCSK9 expression is regulated by cholesterol and sterol regulatory element-binding protein transcription factors, as previously demonstrated in other cell types such as hepatocytes. Importantly, we show that PCSK9 knockdown using siRNA results in deregulation of various elements of the transcriptome, proteome, and secretome, and increases insulin secretion. We also observed that PCSK9 decreases low-density lipoprotein receptor and very low-density lipoprotein receptor levels via an extracellular signaling mechanism involving exogenous PCSK9, as well as levels of cluster of differentiation 36, a fatty acid transporter, through an intracellular signaling mechanism. Finally, we found that PCSK9 regulates the cell surface expression of PDL1 and HLA-ABC, proteins involved in cell-lymphocyte interaction, also via an intracellular mechanism. Collectively, these results highlight PCSK9 as a regulator of multiple cell surface receptors in pancreatic beta cells.

First Measurement of the Nuclear-Recoil Ionization Yield in Silicon at 100 eV.

We measured the nuclear-recoil ionization yield in silicon with a cryogenic phonon-sensitive gram-scale detector. Neutrons from a monoenergetic beam scatter off of the silicon nuclei at angles corresponding to energy depositions from 4 keV down to 100 eV, the lowest energy probed so far. The results show no sign of an ionization production threshold above 100 eV. These results call for further investigation of the ionization yield theory and a comprehensive determination of the detector response function at energies below the keV scale.

Routine postaccess-closure angiography to detect vascular complications following transfemoral TAVR.

BACKGROUND: Vascular complications following transfemoral TAVR are associated with increased morbidity and mortality. Measures that may mitigate this risk are important. AIM: To evaluate the utility of routine, access-vessel angiography post sheath-removal in the detection and management of complications in patients undergoing transcatheter aortic valve replacement (TAVR). METHODS: This was a retrospective study of 512 consecutive patients who underwent transfemoral TAVR with routine post access-closure angiography from the radial artery. Rates of mild angiographically evident bleeding, bleeding requiring surgery/interventional-radiology, ischemia, 90-day access-site-related events, and major and minor vascular complications using Valve Academic Research Consortium 3 definitions were recorded. RESULTS: Of 512 patients, digital subtraction angiography (DSA) was undertaken via the radial artery in 467 patients (91%). In the remaining patients (9%) DSA was either not attempted, due to concerns regarding kidney disease and contrast volume, or failed due to anatomical factors (aortic tortuosity/calcification). Significant chronic kidney disease was present at baseline in 72.4% of this cohort (stages III-IV or dialysis). Ninety-four percent of cases underwent TAVR using a balloon-expandable platform. Mild iliofemoral extravasation was observed in 7.7% of the DSA cases. These cases were managed by manual compression with none requiring any vascular intervention subsequently. Valve Academic Research Consortium 3 major and minor access-site-related complications were observed in 0.4% and 12.2%, respectively. Access-site-related bleeding and ischemic events requiring interventional-radiology or vascular-surgery were observed in 0.9% and 1.7% of the DSA cases, respectively. No new renal replacement therapy was needed in any of the DSA cases. Discharge to 90-day access-related complications was 0.8%. CONCLUSIONS: Routine post access-closure angiography is feasible via the radial artery in patients undergoing transfemoral TAVR and appears safe. It facilitates early identification of complications and mitigates risk by enabling prompt action to be taken. Larger studies are needed to confirm these findings.

Affi-BAMS™: A Robust Targeted Proteomics Microarray Platform to Measure Histone Post-Translational Modifications.

For targeted protein panels, the ability to specifically assay post-translational modifications (PTMs) in a quantitative, sensitive, and straightforward manner would substantially advance biological and pharmacological studies. The present study highlights the effectiveness of the Affi-BAMS™ epitope-directed affinity bead capture/MALDI MS platform for quantitatively defining complex PTM marks of H3 and H4 histones. Using H3 and H4 histone peptides and isotopically labelled derivatives, this affinity bead and MALDI MS platform achieves a range of >3 orders of magnitude with a technical precision CV of <5%. Using nuclear cellular lysates, Affi-BAMS PTM-peptide capture resolves heterogeneous histone N-terminal PTMs with as little as 100 µg of starting material. In an HDAC inhibitor and MCF7 cell line model, the ability to monitor dynamic histone H3 acetylation and methylation events is further demonstrated (including SILAC quantification). Affi-BAMS (and its capacity for the multiplexing of samples and target PTM-proteins) thus provides a uniquely efficient and effective approach for analyzing dynamic epigenetic histone marks, which is critical for the regulation of chromatin structure and gene expression.

A Survey of Knowledge and Barriers of Healthcare Professionals toward Opioid Analgesics in Cancer Pain Management.

Purpose: Pain is among the most frequent and troubling symptoms in cancer patients. Despite the availability of updated treatment guidelines and effective pharmacological therapies, undertreatment of cancer pain remains a global problem. Opioids are the mainstay analgesics to treat moderate-to-severe cancer pain. The goal of this study was to assess the knowledge and barriers towards opioid analgesics for cancer pain management among healthcare professionals in Oncology Units in Jordan. Methods: A structured questionnaire was administered to healthcare professionals (consultant doctors, resident doctors, pharmacists, and nurses) at three Oncology Units in a cross-sectional study design. Results: A total of 201 healthcare professionals completed the questionnaire. The average age was 34.8 ± 8.1 years (range 23-58) and 49.3% of respondents were nurses. The mean score for the knowledge of opioids was 12.5 ± 3.2 out of 24 points (range 2-20). An acceptable level of knowledge was observed in 50.7% of participants, while 49.3% had poor knowledge. Knowledge items mostly answered incorrectly were related to opioid administration, pharmacology, dosing, adverse events, rotation, and toxicity. Knowledge scores were significantly higher for consultant doctors compared to pharmacists and nurses (p=0.016 and p < 0.001, respectively). Healthcare professionals who handled opioid analgesics had significantly higher mean knowledge scores than those who did not (p=0.012). Linear regression analysis revealed that being a consultant physician has an independent, statistically significant association with higher knowledge scores. Among perceived barriers to using opioids, fear of addiction by patients was the most frequently reported barrier by respondents (79.6%). Other highly recognized barriers were fear of adverse effects by patients (67.2%) and lack of training programs on opioid dosing and monitoring (63.7%). Conclusions: This study revealed major gaps in the knowledge of opioids and pain management among healthcare professionals. There is an urgent need for developing innovative interventions to improve the knowledge of opioid analgesics and the understanding of pain management guidelines among healthcare professionals in Jordan.

Chemical biology approaches to study histone interactors.

Protein-protein interactions (PPIs) in the nucleus play key roles in transcriptional regulation and ensure genomic stability. Critical to this are histone-mediated PPI networks, which are further fine-tuned through dynamic post-translational modification. Perturbation to these networks leads to genomic instability and disease, presenting epigenetic proteins as key therapeutic targets. This mini-review will describe progress in mapping the combinatorial histone PTM landscape, and recent chemical biology approaches to map histone interactors. Recent advances in mapping direct interactors of histone PTMs as well as local chromatin interactomes will be highlighted, with a focus on mass-spectrometry based workflows that continue to illuminate histone-mediated PPIs in unprecedented detail.

Light Dark Matter Search with a High-Resolution Athermal Phonon Detector Operated above Ground.

We present limits on spin-independent dark matter-nucleon interactions using a 10.6 g Si athermal phonon detector with a baseline energy resolution of σ_{E}=3.86±0.04(stat)_{-0.00}^{+0.19}(syst) eV. This exclusion analysis sets the most stringent dark matter-nucleon scattering cross-section limits achieved by a cryogenic detector for dark matter particle masses from 93 to 140 MeV/c^{2}, with a raw exposure of 9.9 g d acquired at an above-ground facility. This work illustrates the scientific potential of detectors with athermal phonon sensors with eV-scale energy resolution for future dark matter searches.

Constraints on Lightly Ionizing Particles from CDMSlite.

The Cryogenic Dark Matter Search low ionization threshold experiment (CDMSlite) achieved efficient detection of very small recoil energies in its germanium target, resulting in sensitivity to lightly ionizing particles (LIPs) in a previously unexplored region of charge, mass, and velocity parameter space. We report first direct-detection limits calculated using the optimum interval method on the vertical intensity of cosmogenically produced LIPs with an electric charge smaller than e/(3×10^{5}), as well as the strongest limits for charge ≤e/160, with a minimum vertical intensity of 1.36×10^{-7} cm^{-2} s^{-1} sr^{-1} at charge e/160. These results apply over a wide range of LIP masses (5 MeV/c^{2} to 100 TeV/c^{2}) and cover a wide range of ßγ values (0.1-10^{6}), thus excluding nonrelativistic LIPs with ßγ as small as 0.1 for the first time.

A baseline survey of community pharmacies' workforce, premises, services and satisfaction with medical practitioners in Jordan.

PURPOSE: The aim of the present study was to describe the local situation in community pharmacies in Jordan by assessing the baseline resources available in terms of workforce, premises and services provided. METHODS: A survey was developed and administered to community pharmacists from Amman, the capital of Jordan, and Irbid, a large city in North Jordan. RESULTS: Three hundred sixty-seven community pharmacists, 167 from Amman and 200 from Irbid, completed the surveys. The community pharmacists were mostly females (66.6%) and predominantly (about three quarters) younger than 30 years old. The community pharmacists were in independent (69.2%) and chain (30.8%) pharmacies. Respondent pharmacists reported delivering medication review services (93.1% of the respondents delivered the service), smoking-cessation services (86.7%), nutrition services (71.5%), blood pressure testing (86.7%), diabetes screening (86.9%) and home delivery (18.8%). Patient counselling is carried out by 94.5% of respondents. Community pharmacists spend most of their time dispensing prescriptions and counselling patients on prescription and non-prescription medicines and chronic diseases. The study also shed the light on a related aspect of practice which was the relationship with local doctors. Only 9.9% of the respondents indicated high satisfaction with their professional relationship with local medical practitioners, 81.6% had a mid-level of satisfaction and 8.5% had the lowest level of satisfaction. CONCLUSION: The present study identified baseline characteristics of the local situation in community pharmacies. The majority of pharmacists dispensed medications, provided counselling, reviewed medications and provided smoking cessation service.

Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted Proteomics.

The ability to quantitatively probe diverse panels of proteins and their post-translational modifications (PTMs) across multiple samples would aid a broad spectrum of biological, biochemical and pharmacological studies. We report a novel, microarray analytical technology that combines immuno-affinity capture with Matrix Assisted Laser Desorption Ionization Mass Spectrometry (MALDI MS), which is capable of supporting highly multiplexed, targeted proteomic assays. Termed "Affinity-Bead Assisted Mass Spectrometry" (Affi-BAMS), this LC-free technology enables development of highly specific and customizable assay panels for simultaneous profiling of multiple proteins and PTMs. While affinity beads have been used previously in combination with MS, the Affi-BAMS workflow uses enrichment on a single bead that contains one type of antibody, generally capturing a single analyte (protein or PTM) while having enough binding capacity to enable quantification within approximately 3 orders of magnitude. The multiplexing capability is achieved by combining Affi-BAMS beads with different protein specificities. To enable screening of bead-captured analytes by MS, we further developed a novel method of performing spatially localized elution of targets from individual beads arrayed on a microscope slide. The resulting arrays of micro spots contain highly concentrated analytes localized within 0.5 mm diameter spots that can be directly measured using MALDI MS. While both intact proteins and protein fragments can be monitored by Affi-BAMS, we initially focused on applying this technology for bottom-up proteomics to enable screening of hundreds of samples per day by combining the robust magnetic bead-based workflow with the high throughput nature of MALDI MS acquisition. To demonstrate the variety of applications and robustness of Affi-BAMS, several studies are presented that focus on the response of 4EBP1, RPS6, ERK1/ERK2, mTOR, Histone H3 and C-MET to stimuli including rapamycin, H2O2, EPO, SU11274, Staurosporine and Vorinostat.

Erratum: First Dark Matter Constraints from a SuperCDMS Single-Charge Sensitive Detector [Phys. Rev. Lett. 121, 051301 (2018)].

This corrects the article DOI: 10.1103/PhysRevLett.121.051301.

Results from the Super Cryogenic Dark Matter Search Experiment at Soudan.

We report the result of a blinded search for weakly interacting massive particles (WIMPs) using the majority of the SuperCDMS Soudan data set. With an exposure of 1690 kg d, a single candidate event is observed, consistent with expected backgrounds. This analysis (combined with previous Ge results) sets an upper limit on the spin-independent WIMP-nucleon cross section of 1.4×10^{-44} (1.0×10^{-44}) cm^{2} at 46 GeV/c^{2}. These results set the strongest limits for WIMP-germanium-nucleus interactions for masses >12 GeV/c^{2}.

First Dark Matter Constraints from a SuperCDMS Single-Charge Sensitive Detector.

We present the first limits on inelastic electron-scattering dark matter and dark photon absorption using a prototype SuperCDMS detector having a charge resolution of 0.1 electron-hole pairs (CDMS HVeV, a 0.93 g CDMS high-voltage device). These electron-recoil limits significantly improve experimental constraints on dark matter particles with masses as low as 1 MeV/c^{2}. We demonstrate a sensitivity to dark photons competitive with other leading approaches but using substantially less exposure (0.49 g d). These results demonstrate the scientific potential of phonon-mediated semiconductor detectors that are sensitive to single electronic excitations.

Comparative point prevalence survey of antimicrobial consumption between a hospital in Northern Ireland and a hospital in Jordan.

BACKGROUND: To assess antimicrobial prescribing in a Northern Ireland hospital (Antrim Area Hospital (AAH)) and compare them with those of a hospital in Jordan (Specialty Hospital). METHODS: Using the Global-PPS approach, the present study surveyed patients admitted to the hospital in 2015, the prescribed antibiotics, and a set of quality control indicators related to antibiotics. RESULTS: Ultimately, 444 and 112 inpatients in the AAH and the Specialty Hospital, respectively, were surveyed. For the medical group, 165 inpatients were prescribed 239 antibiotics in the AAH, while 44 patients in the Specialty Hospital were prescribed 65 antibiotics. In relation to the surgical group, 34 inpatients treated for infection were prescribed 66 antibiotics in the AAH, while 41 patients in the Specialty Hospital treated for infection were prescribed 56 antibiotics. For the medical patients, the most frequently prescribed antibiotics in the AAH were a combination of penicillins (18.8%) and penicillins with extended spectrum (18.8%). For the surgical patients, the most frequently prescribed antibiotics in the AAH were imidazole derivatives (24.2%). For the medical and surgical patients in the Specialty Hospital, the most frequently prescribed antibiotics were third-generation cephalosporins (26.2 and 37.5%, respectively). In medical patients, compliance to guidelines was 92.2% in the Specialty Hospital compared to 72.0% in the AAH (p < 0.001). In surgical patients, compliance to guidelines was 92.7% in the Specialty Hospital compared to 81.8% in the AAH (p = 0.012). CONCLUSIONS: The present study highlighted differences in the utilisation of antimicrobials between two hospitals in two distinct regions and benchmarked antibiotic prescriptions across two hospitals.

New Results from the Search for Low-Mass Weakly Interacting Massive Particles with the CDMS Low Ionization Threshold Experiment.

The CDMS low ionization threshold experiment (CDMSlite) uses cryogenic germanium detectors operated at a relatively high bias voltage to amplify the phonon signal in the search for weakly interacting massive particles (WIMPs). Results are presented from the second CDMSlite run with an exposure of 70 kg day, which reached an energy threshold for electron recoils as low as 56 eV. A fiducialization cut reduces backgrounds below those previously reported by CDMSlite. New parameter space for the WIMP-nucleon spin-independent cross section is excluded for WIMP masses between 1.6 and 5.5 GeV/c^{2}.

Determinants of asthma control among children in Saudi Arabia.

OBJECTIVE: Asthma is the most common chronic disease among children. Uncontrolled asthma may considerably decrease the quality of life for patients and their families. Our objective was to identify possible risk factors for poor asthma control in children. METHODS: A cross-sectional study was conducted among children with asthma aged 4-11 years who attended a pediatric clinic for follow-up visits at one of the major teaching hospitals in Riyadh, Saudi Arabia. Asthma control status was measured by the childhood asthma control test. Multiple logistic regression analysis was performed to explore the relationships between the outcome and exposure variables. RESULTS: Uncontrolled asthma was present in 89 out of 158 children (59.3%). Asthma control improved with the number of siblings. Control improved by 69% with two or three siblings (OR = 0.31, 95% CI = 0.10-0.96) and by 87% with four or more siblings (OR = 0.13, 95% CI = 0.04-0.48). Similarly, asthma control improved with an increased asthma knowledge of the caregiver (OR = 0.87, 95% CI = 0.81-0.93). Household incomes less than SAR 15 000 and sharing a bedroom increased the odds of having uncontrolled asthma by 2.30 (95% CI = 1.02-5.21) and 3.33 (95% CI = 1.33-8.35), respectively. CONCLUSIONS: In addition to knowledge, socioeconomic factors, such as family income, household crowding, and the number of siblings are associated with asthma control among children in Saudi Arabia. Further research is needed to investigate the role of these factors.

Public Patterns and Determinants of Antibiotic Self-Medication and Antibiotic Knowledge in Southern Jordan.

Antibiotic self-medication, which refers to acquisition and using antibiotics to treat infections based on personal experience and/or without a doctor's advice or prescription, is a significant public health issue jeopardizing patient health outcomes. The purpose of the present cross-sectional online survey was to assess the frequency of self-medication among the general public in various geographical locations in southern Jordan, as well as to examine the determinants to self-medication. The survey was distributed through several social media networks over the period November-December 2022, and included demographic information as well as items related to the use and abuse of antibiotics, information sources about antibiotics, the duration of use of antibiotics, and assessment of the public knowledge about appropriate antibiotic use. Inferential analysis, such as the Chi-Square test and logistic regression, were adopted to assess the associations between the different variables with self-medication. A total of 984 respondents were enrolled in the study. Of these, 752 had been using antibiotics during the last year. However, the self-medicating cases were 413 of the 752. The main source of information about the utilization of antibiotics among participants in the survey was pharmacists. The participants commonly (36.0%) tended to use antibiotics until the symptoms disappeared. Nearly half of the respondents reported usually taking antibiotics for treating a runny nose (rhinorrhea). The logistic regression analysis indicated that self-medication with antibiotics was significantly associated with female gender (p-value < 0.001), low educational level (p-value = 0.014), rural living location (p-value 0.003), no health insurance (p-value = 0.001) and occupation (p-value = 0.005). Meanwhile age had no significant relationship to self-medication. Finally, the results revealed poor understanding of key appropriate antibiotic usage, which inevitably influences self-medication practice. It is crucial to come up with several programs and governmental policies to suppress widespread antibiotic self-medication as it will affect the health of future generations of Jordanian citizens.