MALDI-TOF mass spectrometry

Proteomics-based mass spectrometry profiling of SARS-CoV-2 infection from human nasopharyngeal samples

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the on-going global pandemic of coronavirus disease 2019 (COVID-19) that continues to pose a significant threat to public health worldwide. SARS-CoV-2 encodes four structural proteins namely membrane, nucleocapsid, spike, and envelope proteins that play essential roles in viral entry, fusion, and attachment to the host cell. Extensively glycosylated spike protein efficiently binds to the host angiotensin-converting enzyme 2 initiating viral entry and pathogenesis. Reverse transcriptase polymerase chain reaction on nasopharyngeal swab is the preferred method of sample collection and viral detection because it is a rapid, specific, and high-throughput technique. Alternate strategies such as proteomics and glycoproteomics-based mass spectrometry enable a more detailed and holistic view of the viral proteins and host-pathogen interactions and help in detection of potential disease markers. In this review, we highlight the use of mass spectrometry methods to profile the SARS-CoV-2 proteome from clinical nasopharyngeal swab samples. We also highlight the necessity for a comprehensive glycoproteomics mapping of SARS-CoV-2 from biological complex matrices to identify potential COVID-19 markers.

Comprehensive Assessment of Indian Variations in the Druggable Kinome Landscape Highlights Distinct Insights at the Sequence, Structure and Pharmacogenomic Stratum

India confines more than 17% of the world’s population and has a diverse genetic makeup with several clinically relevant rare mutations belonging to many sub-group which are undervalued in global sequencing datasets like the 1000 Genome data (1KG) containing limited samples for Indian ethnicity. Such databases are critical for the pharmaceutical and drug development industry where diversity plays a crucial role in identifying genetic disposition towards adverse drug reactions. A qualitative and comparative sequence and structural study utilizing variant information present in the recently published, largest curated Indian genome database (IndiGen) and the 1000 Genome data was performed for variants belonging to the kinase coding genes, the second most targeted group of drug targets. The sequence-level analysis identified similarities and differences among different populations based on the nsSNVs and amino acid exchange frequencies whereas a comparative structural analysis of IndiGen variants was performed with pathogenic variants reported in UniProtKB Humsavar data. The influence of these variations on structural features of the protein, such as structural stability, solvent accessibility, hydrophobicity, and the hydrogen-bond network was investigated. In-silico screening of the known drugs to these Indian variation-containing proteins reveals critical differences imparted in the strength of binding due to the variations present in the Indian population. In conclusion, this study constitutes a comprehensive investigation into the understanding of common variations present in the second largest population in the world and investigating its implications in the sequence, structural and pharmacogenomic landscape. The preliminary investigation reported in this paper, supporting the screening and detection of ADRs specific to the Indian population could aid in the development of techniques for pre-clinical and post-market screening of drug-related adverse events in the Indian population.

Recent trends in rapid diagnostic techniques for dermatophytosis

Dermatophytosis is a common contagious disease of both humans and animals. It is caused by a group of filamentous fungi known as dermatophytes, including several genera and various species. An accurate diagnosis of dermatophytes as a causative agent of a skin lesion requires up to one month of conventional laboratory diagnostics. The conventional gold standard diagnostic method is a direct microscopic examination followed by 3 to 4 weeks of Sabouraud's dextrose agar (SDA) culturing, and it may require further post-culturing identification through biochemical tests or microculture technique application. The laborious, exhaustive, and time-consuming gold standard method was a real challenge facing all dermatologists to achieve a rapid, accurate dermatophytosis diagnosis. Various studies developed more rapid, accurate, reliable, sensitive, and specific diagnostic tools. All developed techniques showed more rapidity than the classical method but variable specificities and sensitivities. An extensive bibliography is included and discussed through this review, showing recent variable dermatophytes diagnostic categories with an illustration of weaknesses, strengths, and prospects.

Knowledge and Attitudes of Medical and Health Science Students in the United Arab Emirates toward Genomic Medicine and Pharmacogenomics: A Cross-Sectional Study

Medical and health science students represent future health professionals, and their perceptions are essential to increasing awareness on genomic medicine and pharmacogenomics. Lack of education is one of the significant barriers that may affect health professional’s ability to interpret and communicate pharmacogenomics information and results to their clients. Our aim was to assess medical and health science students’ knowledge, attitudes and perception for a better genomic medicine and pharmacogenomics practice in the United Arab Emirates (UAE). A cross-sectional study was conducted using a validated questionnaire distributed electronically to students recruited using random and snowball sampling methods. A total of 510 students consented and completed the questionnaire between December 2018 and October 2019. The mean knowledge score (SD) for students was 5.4 (±2.7). There were significant differences in the levels of knowledge by the year of study of bachelor’s degree students, the completion status of training or education in pharmacogenomics (PGX) or pharmacogenetics and the completion of an internship or study abroad program (p-values < 0.05. The top two barriers that students identified in the implementation of genomic medicine and pharmacogenomics were lack of training or education (59.7%) and lack of clinical guidelines (58.7%). Concerns regarding confidentiality and discrimination were stated. The majority of medical and health science students had positive attitudes but only had a fair level of knowledge. Stakeholders in the UAE must strive to acquaint their students with up-to-date knowledge of genomic medicine and pharmacogenomics.

HSD3B1 and resistance to androgen-deprivation therapy in prostate cancer: a retrospective, multicohort study

BACKGROUND

HSD3B1 (1245A>C) has been mechanistically linked to castration-resistant prostate cancer because it encodes an altered enzyme that augments dihydrotestosterone synthesis from non-gonadal precursors. We postulated that men inheriting the HSD3B1 (1245C) allele would exhibit resistance to androgen-deprivation therapy (ADT).

METHODS

In this multicohort study, we determined HSD3B1 genotype retrospectively in men treated with ADT for post-prostatectomy biochemical failure and correlated genotype with long-term clinical outcomes. We used data and samples from prospectively maintained prostate cancer registries at the Cleveland Clinic (Cleveland, OH, USA; primary study cohort) and the Mayo Clinic (Rochester, MN, USA; post-prostatectomy and metastatic validation cohorts). In the post-prostatectomy cohorts, patients of any age were eligible if they underwent prostatectomy between Jan 1, 1996, and Dec 31, 2009 (at the Cleveland Clinic; primary cohort), or between Jan 1, 1987, and Dec 31, 2011 (at the Mayo Clinic; post-prostatectomy cohort) and were treated with ADT for biochemical failure or for non-metastatic clinical failure. In the metastatic validation cohort, patients of any age were eligible if they were enrolled at Mayo Clinic between Sept 1, 2009, and July 31, 2013, with metastatic castration-resistant prostate cancer. The primary endpoint was progression-free survival according to HSD3B1 genotype. We did prespecified multivariable analyses to assess the independent predictive value of HSD3B1 genotype on outcomes.

FINDINGS

We included and genotyped 443 patients: 118 in the primary cohort (who underwent prostatectomy), 137 in the post-prostatectomy validation cohort, and 188 in the metastatic validation cohort. In the primary study cohort, median progression-free survival diminished as a function of the number of variant alleles inherited: 6·6 years (95% CI 3·8-not reached) in men with homozygous wild-type genotype, 4·1 years (3·0-5·5) in men with heterozygous variant genotype, and 2·5 years (0·7 to not reached) in men with homozygous variant genotype (p=0·011). Relative to the homozygous wild-type genotype, inheritance of two copies of the variant allele was predictive of decreased progression-free survival (hazard ratio [HR] 2·4 [95% CI 1·1-5·3], p=0·029), as was inheritance of one copy of the variant allele (HR 1·7 [1·0-2·9], p=0·041). Findings were similar for distant metastasis-free survival and overall survival. The effect of the HSD3B1 genotype was independently confirmed in the validation cohorts.

INTERPRETATION

Inheritance of the HSD3B1 (1245C) allele that enhances dihydrotestosterone synthesis is associated with prostate cancer resistance to ADT. HSD3B1 could therefore potentially be a powerful genetic biomarker capable of distinguishing men who are a priori likely to fare favourably with ADT from those who harbour disease liable to behave more aggressively, and who therefore might warrant early escalated therapy.

FUNDING

Prostate Cancer Foundation, National Institutes of Health, US Department of Defense, Howard Hughes Medical Institute, American Cancer Society, Conquer Cancer Foundation of the American Society of Clinical Oncology, Cleveland Clinic Research Programs Committee and Department of Radiation Oncology, Gail and Joseph Gassner Development Funds.

Genotyping of common SIRPB1 copy number variant using Paralogue Ratio Test coupled to MALDI-MS quantification

Copy number variant (CNV) regions have been proven to have a significant impact on gene expression. Some of them have been also found to be associated to different human diseases. CNV genotyping is often prone to error and cross-validation with independent methods is frequently required. The platform of choice depends on whether it is a genome-wide discovery screening or a candidate CNV study, the cohort size and the number of CNVs included in the assay and, finally, the budget available. Here we illustrate a affordable approach to determine the CNV genotype using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and based on the quantitative determination of single nucleotide duplicated mismatches (SNDM) mapping the CNV region and a paralogue genomic region that is used as a two-copy reference. We have genotyped nsv436327, a common CNV mapping SIRPB1 intron 1 that has been associated to human personality behavior. SIRP cluster region was subjected to several ancestral duplication events what makes SIRPB1 CNV genotyping technically challenging. We designed three sets of primer pairs that amplified paralogue regions inside and outside the CNV, containing three SNDMs. Post-PCR extension analyses of sequencing oligonucleotides mapping immediately upstream each SNDM allowed us to quantify using MALDI-MS the proportion of PCR products derived from the CNV region versus the external reference. In contrast to other approaches, setting up this genotyping method requires an affordable investment.

Surface-enhanced laser desorption ionization time-of-flight mass spectrometry used to screen serum diagnostic markers of colon cancer recurrence in situ following surgery

The aim of the present study was to identify specific serum biomarkers in patients with colon cancer recurrence in situ following surgery. The study was conducted at the Renmin Hospital of Wuhan University (Wuhan, China) between January 2012 and January 2014. Surface-enhanced laser desorption ionization time-of-flight mass spectrometry was used to compare and analyze the serum protein profiles of patients with (n=50) and patients without (n=50) recurrence in situ. Biomarker Wizard software was used to analyze and obtain the protein spectrum. In total, nine protein peaks demonstrated statistically significant differences between the recurrence and non-recurrence group (P<0.05), which included two protein peaks (7,731.3 Da and 8,266.5 Da). The two protein peaks were highly expressed in patients with colon cancer recurrence in situ following surgery, but lowly expressed in patients without recurrence. Therefore, the two protein peaks may represent potential biomarkers for the prediction of colon cancer recurrence in situ following surgical treatment.

Quantitative assessment of mutant allele burden in solid tumors by semiconductor-based next-generation sequencing

OBJECTIVES

Identification of tumor-specific somatic mutations has had a significant impact on both disease diagnosis and therapy selection. The ability of next-generation sequencing (NGS) to provide a quantitative assessment of mutant allele burden, in numerous target genes in a single assay, provides a significant advantage over conventional qualitative genotyping platforms.

METHODS

We assessed the quantitative capability of NGS and a primer extension-based matrix-assisted laser desorption ionization-time-of-flight (PE-MALDI) assay and directly correlated NGS mutant allele burden determination to morphologic assessment of tumor percentage in H&E-stained slides.

RESULTS

Our results show a 100% concordance between NGS and PE-MALDI in mutant allele detection and a significant correlation between NGS and PE-MALDI for determining mutant allele burden when mutant allele burden is 10% or more.

CONCLUSIONS

NGS-based mutation screening provides a quantitative assessment comparable to that of PE-MALDI. In addition, NGS also allows for a high degree of multiplexing and uses nanogram quantities of DNA, thereby preserving precious material for future analysis. Furthermore, this study provides evidence that H&E-based morphologic assessment of tumor burden does not correlate to actual tumor mutant allele burden frequency.