QPGx-CARES: Qatar pharmacogenetics clinical applications and research enhancement strategies.

Pharmacogenetic (PGx)-informed medication prescription is a cutting-edge genomic application in contemporary medicine, offering the potential to overcome the conventional "trial-and-error" approach in drug prescription. The ability to use an individual's genetic profile to predict drug responses allows for personalized drug and dosage selection, thereby enhancing the safety and efficacy of treatments. However, despite significant scientific and clinical advancements in PGx, its integration into routine healthcare practices remains limited. To address this gap, the Qatar Genome Program (QGP) has embarked on an ambitious initiative known as QPGx-CARES (Qatar Pharmacogenetics Clinical Applications and Research Enhancement Strategies), which aims to set a roadmap for optimizing PGx research and clinical implementation on a national scale. The goal of QPGx-CARES initiative is to integrate PGx testing into clinical settings with the aim of improving patient health outcomes. In 2022, QGP initiated several implementation projects in various clinical settings. These projects aimed to evaluate the clinical utility of PGx testing, gather valuable insights into the effective dissemination of PGx data to healthcare professionals and patients, and identify the gaps and the challenges for wider adoption. QPGx-CARES strategy aimed to integrate evidence-based PGx findings into clinical practice, focusing on implementing PGx testing for cardiovascular medications, supported by robust scientific evidence. The current initiative sets a precedent for the nationwide implementation of precision medicine across diverse clinical domains.

Assessment of Broadly Reactive Responses in Patients With MERS-CoV Infection and SARS-CoV-2 Vaccination.

Importance: In the ongoing COVID-19 pandemic, there remain unanswered questions regarding the nature and importance of the humoral immune response against other coronaviruses. Although coinfection of the Middle East respiratory syndrome coronavirus (MERS-CoV) with the SARS-CoV-2 has not been documented yet, several patients previously infected with MERS-CoV received the COVID-19 vaccine; data describing how preexisting MERS-CoV immunity may shape the response to SARS-CoV-2 following infection or vaccination are lacking. Objective: To characterize the cross-reactive and protective humoral responses in patients exposed to both MERS-CoV infection and SARS-CoV-2 vaccination. Design, Setting, and Participants: This cohort study involved a total of 18 sera samples collected from 14 patients with MERS-CoV infection before (n = 12) and after (n = 6) vaccination with 2 doses of COVID-19 mRNA vaccine (BNT162b2 or mRNA-1273). Of those patients, 4 had prevaccination and postvaccination samples. Antibody responses to SARS-CoV-2 and MERS-CoV were assessed as well as cross-reactive responses to other human coronaviruses. Main Outcomes and Measures: The main outcomes measured were binding antibody responses, neutralizing antibodies, and antibody-dependent cellular cytotoxicity (ADCC) activity. Binding antibodies targeting SARS-CoV-2 main antigens (spike [S], nucleocapsid, and receptor-binding domain) were detected using automated immunoassays. Cross-reactive antibodies with the S1 protein of SARS-CoV, MERS-CoV, and common human coronaviruses were analyzed using a bead-based assay. Neutralizing antibodies (NAbs) against MERS-CoV and SARS-CoV-2 as well as ADCC activity against SARS-CoV-2 were assessed. Results: A total of 18 samples were collected from 14 male patients with MERS-CoV infection (mean [SD] age, 43.8 [14.6] years). Median (IQR) duration between primary COVID-19 vaccination and sample collection was 146 (47-189) days. Prevaccination samples had high levels of anti-MERS S1 immunoglobin M (IgM) and IgG (reactivity index ranging from 0.80 to 54.7 for IgM and from 0.85 to 176.3 for IgG). Cross-reactive antibodies with SARS-CoV and SARS-CoV-2 were also detected in these samples. However, cross-reactivity against other coronaviruses was not detected by the microarray assay. Postvaccination samples showed significantly higher levels of total antibodies, IgG, and IgA targeting SARS-CoV-2 S protein compared with prevaccination samples (eg, mean total antibodies: 8955.0 AU/mL; 95% CI, -5025.0 to 22936.0 arbitrary units/mL; P = .002). In addition, significantly higher anti-SARS S1 IgG levels were detected following vaccination (mean reactivity index, 55.4; 95% CI, -9.1 to 120.0; P = .001), suggesting potential cross-reactivity with these coronaviruses. Also, anti-S NAbs were significantly boosted against SARS-CoV-2 (50.5% neutralization; 95% CI, 17.6% to 83.2% neutralization; P < .001) after vaccination. Furthermore, there was no significant increase in antibody-dependent cellular cytotoxicity against SARS-CoV-2 S protein postvaccination. Conclusions and Relevance: This cohort study found a significant boost in cross-reactive NAbs in some patients exposed to MERS-CoV and SARS-CoV-2 antigens. These findings suggest that isolation of broadly reactive antibodies from these patients may help guide the development of a pancoronavirus vaccine by targeting cross-reactive epitopes between distinct strains of human coronaviruses.

Glioma extracellular vesicles for precision medicine: prognostic and theragnostic application.

EV produced by tumour cells carry a diverse population of proteins, lipids, DNA, and RNA molecules throughout the body and appear to play an important role in the overall development of the disease state, according to growing data. Gliomas account for a sizable fraction of all primary brain tumours and the vast majority of brain malignancies. Glioblastoma multiforme (GBM) is a kind of grade IV glioma that has a very dismal prognosis despite advancements in diagnostic methods and therapeutic options. The authors discuss advances in understanding the function of extracellular vesicles (EVs), in overall glioma growth, as well as how recent research is uncovering the utility of EVs in glioma diagnostics, prognostic and therapeutics approaches.

The QChip1 knowledgebase and microarray for precision medicine in Qatar.

Risk genes for Mendelian (single-gene) disorders (SGDs) are consistent across populations, but pathogenic risk variants that cause SGDs are typically population-private. The goal was to develop "QChip1," an inexpensive genotyping microarray to comprehensively screen newborns, couples, and patients for SGD risk variants in Qatar, a small nation on the Arabian Peninsula with a high degree of consanguinity. Over 108 variants in 8445 Qatari were identified for inclusion in a genotyping array containing 165,695 probes for 83,542 known and potentially pathogenic variants in 3438 SGDs. QChip1 had a concordance with whole-genome sequencing of 99.1%. Testing of QChip1 with 2707 Qatari genomes identified 32,674 risk variants, an average of 134 pathogenic alleles per Qatari genome. The most common pathogenic variants were those causing homocystinuria (1.12% risk allele frequency), and Stargardt disease (2.07%). The majority (85%) of Qatari SGD pathogenic variants were not present in Western populations such as European American, South Asian American, and African American in New York City and European and Afro-Caribbean in Puerto Rico; and only 50% were observed in a broad collection of data across the Greater Middle East including Kuwait, Iran, and United Arab Emirates. This study demonstrates the feasibility of developing accurate screening tools to identify SGD risk variants in understudied populations, and the need for ancestry-specific SGD screening tools.

Exome sequencing of glioblastoma-derived cancer stem cells reveals rare clinically relevant frameshift deletion in MLLT1 gene.

BACKGROUND: Glioblastoma multiforme (GBM) is a heterogeneous CNS neoplasm which causes significant morbidity and mortality. One reason for the poor prognostic outcome of GBM is attributed to the presence of cancer stem cells (CSC) which confer resistance against standard chemo- and radiotherapeutics modalities. Two types of GBM-associated CSC were isolated from the same patient: tumor core- (c-CSC) and peritumor tissue-derived cancer stem cells (p-CSC). Our experiments are focused on glioblastoma-IDH-wild type, and no disease-defining alterations were present in histone, BRAF or other genes. METHODS: In the present study, potential differences in genetic variants between c-CSC versus p-CSC derived from four GBM patients were investigated with the aims of (1) comparing the exome sequences between all the c-CSC or p-CSC to identify the common variants; (2) identifying the variants affecting the function of genes known to be involved in cancer origin and development. RESULTS: By comparative analyses, we identified common gene single nucleotide variants (SNV) in all GBM c-CSC and p-CSC, a potentially deleterious variant was a frameshift deletion at Gln461fs in the MLLT1 gene, that was encountered only in p-CSC samples with different allelic frequency. CONCLUSIONS: We discovered a potentially harmful frameshift deletion at Gln461fs in the MLLT1 gene. Further investigation is required to confirm the presence of the identified mutations in patient tissue samples, as well as the significance of the frameshift mutation in the MLLT1 gene on GBM biology and response to therapy based on genomic functional experiments.

p53 signaling in cancer progression and therapy.

The p53 protein is a transcription factor known as the "guardian of the genome" because of its critical function in preserving genomic integrity. The TP53 gene is mutated in approximately half of all human malignancies, including those of the breast, colon, lung, liver, prostate, bladder, and skin. When DNA damage occurs, the TP53 gene on human chromosome 17 stops the cell cycle. If p53 protein is mutated, the cell cycle is unrestricted and the damaged DNA is replicated, resulting in uncontrolled cell proliferation and cancer tumours. Tumor-associated p53 mutations are usually associated with phenotypes distinct from those caused by the loss of the tumor-suppressing function exerted by wild-type p53protein. Many of these mutant p53 proteins have oncogenic characteristics, and therefore modulate the ability of cancer cells to proliferate, escape apoptosis, invade and metastasize. Because p53 deficiency is so common in human cancer, this protein is an excellent option for cancer treatment. In this review, we will discuss some of the molecular pathways by which mutant p53 proteins might perform their oncogenic activities, as well as prospective treatment methods based on restoring tumor suppressive p53 functions.

Generation of gene edited hiPSC from familial Alzheimer's disease patient carrying N141I missense mutation in presenilin 2.

Alzheimer's disease (AD) is the major cause of dementia worldwide. Early-onset familial AD accounts for about 0.5% of all AD and is caused by single major gene mutations and autosomal dominant inheritance. An N141I missense mutation is associated with a significant increase in basal cell death and apoptosis. In this work we generated hiPSC from skin fibroblasts obtained from an AD patient carrying a N141I missense mutation in PSEN2. The generated iPSC colonies grew and were characterized by pluripotency marker staining; the N141I missense mutation was corrected using genome editing technology.

Pandemic COVID-19 caused by SARS-CoV-2: genetic structure, vaccination, and therapeutic approaches.

We give a summary of SARS-genetic CoV-2's structure and evolution, as well as current attempts to develop efficient vaccine and treatment methods for SARS-CoV-2 infection, in this article. Most therapeutic strategies are based on repurposing of existing therapeutic agents used against various virus infections and focused mainly on inhibition of the virus replication cycle, enhancement of innate immunity, and alleviation of CRS caused by COVID-19. Currently, more than 100 clinical trials on COVID-19 aim to provide robust evidence on the efficacy of the currently available anti-SARS-CoV-2 antiviral substances, such as the nucleotide analogue remdesivir, the antimalarial drug chloroquine, and drugs directed against docking of SARS-CoV-2 to the membrane-associated angiotensin-converting enzyme 2 (ACE2) such as transmembrane protease serine 2 (TMPRSS2). The current vaccination campaign is ongoing worldwide using different types of vaccines such as Pfizer-BioNTech and Moderna, Johnson & Johnson, Oxford-AstraZeneca, Novavax, and others with efficacy ranging from 72-95%. In March 2021 Germany limited the use of the Oxford-AstraZeneca COVID-19 vaccine to people 60 years of age and older due to concerns that it may be causing blood clots. Further study and more data are needed to confirm the safety of different available vaccines.

Current progress in chimeric antigen receptor T cell therapy for glioblastoma multiforme.

Glioblastoma multiforme (GBM) is one of the deadliest brain tumors with an unfavorable prognosis and overall survival of approximately 20 months following diagnosis. The current treatment for GBM includes surgical resections and chemo- and radiotherapeutic modalities, which are not effective. CAR-T immunotherapy has been proven effective for CD19-positive blood malignancies, and the application of CAR-T cell therapy for solid tumors including GBM offers great hope for this aggressive tumor which has a limited response to current treatments. CAR-T technology depends on the use of patient-specific T cells genetically engineered to express specific tumor-associated antigens (TAAs). Interaction of CAR-T cells with tumor cells triggers the destruction/elimination of these cells by the induction of cytotoxicity and the release of different cytokines. Despite the great promise of CAR-T cell-based therapy several challenges exist. These include the heterogeneity of GBM cancer cells, aberrant various signaling pathways involved in tumor progression, antigen escape, the hostile inhibitory GBM microenvironment, T cell dysfunction, blood-brain barrier, and defective antigen presentation. All need to be addressed before full application at the clinical level can begin. Herein we provide a focused review of the rationale for the use of different types of CAR-T cells (including FcγRs), the different GBM-associated antigens, the challenges still facing CAR-T-based therapy, and means to overcome such challenges. Finally, we enumerate currently completed and ongoing clinical trials, highlighting the different ways such trials are designed to overcome specific problems. Exploitation of the full potential of CAR-T cell therapy for GBM depends on their solution.

Willingness to participate in genome testing: a survey of public attitudes from Qatar.

Genomics has the potential to revolutionize medical approaches to disease prevention, diagnosis, and treatment, but it does not come without challenges. The success of a national population-based genome program, like the Qatar Genome Program (QGP), depends on the willingness of citizens to donate samples and take up genomic testing services. This study explores public attitudes of the Qatari population toward genetic testing and toward participating in the QGP. A representative sample of 837 adult Qataris was surveyed in May 2016. Approximately 71% of respondents surveyed reported that they were willing to participate in the activities of the QGP. Willingness to participate was significantly associated with basic literacy in genetics, a family history of genetic diseases, and previous experience with genetic testing through premarital screening. Respondents cited the desire to know more about their health status as the principle motivation for participating, while lack of time and information were reported as the most important barriers. With QGP plans to ramp up the scale of its national operation toward more integration into clinical care settings, it is critical to understand public attitudes and their determinants. The results demonstrate public support but also identify the need for more education and individual counseling that not only provide information on the process, challenges, and benefits of genomic testing, but that also address concerns about information security.

The Implementation of an Integrated Management System at Qatar Biobank.

Qatar Biobank (QBB) is a platform that will make vital health research possible through its collection of samples and information on health and lifestyle from the local population of Qatar. The goal of QBB is to collect, process, store, and finally share high-quality biological samples and associated data for research purposes with the research community. To do this, a series of standardized procedures following evidence-based practices are required, and QBB is achieving this by implementing an integrated management system (IMS) that incorporates ISO 9001: 2015 and ISO 27001: 2013 standards. ISO 9001 is one of the most commonly implemented quality management systems as it is applicable to any size of organization. ISO 27001: 2013 is increasingly popular as organizations look to manage their data and information security, especially in the light of the recent General Data Protection Regulation legislation and an ever-changing digital landscape. QBB has achieved certification in both ISO 9001: 2015 (originally 2008 standard) and ISO 27001: 2013 since 2014. In 2016, during preparations for recertification of both standards in 2017, QBB chose to integrate both of the management systems in preference to running them in parallel, without compromising the goals and objectives of QBB. The IMS has ensured that rigorous processes and controls are implemented to not only manage the quality of internal and external processes and services provided, but the privacy and confidentiality of data collected during a participant visit are consistently protected as well as a proactive approach to identifying and managing risk within the organization. This article will explore the impact of implementing an IMS on the continuous improvement of services within QBB.

Conception, Implementation, and Integration of Heterogenous Information Technology Infrastructures in the Qatar Biobank.

The overall goal of the Qatar Biobank (QBB) is to collect, manage, and distribute high-quality human biospecimens with appropriate clinical and/or research annotation and associated phenotypic data, aiming to be an important and essential resource of medical research and evidence-based health care system policies in Qatar. To manage and collect large volumes of data, the QBB has been investing in a number of information management solutions, trying to avoid inflexibility of traditional systems and accommodate changes in data sources and workflows. This article aims to present the information technology solutions of QBB based on a free, open-source software solution, considered a reliable alternative to commercial solutions. After evaluating the free, open-source software solutions available for biobanks, Onyx from ObiBa was utilized to develop custom components to interface various clinical devices, LIMS and Picture Archiving and Communication System, which has varying integration capabilities. This is a showcase for biobanks to carefully evaluate and select hardware and software to automate their operations providing the functions required for business continuity.

Qatar Biobank: A Paradigm of Translating Biobank Science into Evidence-Based Health Care Interventions.

Biobank science is progressively becoming indispensable for the development of novel diagnostic tools in health care, by pairing standardized high-quality biological samples, phenotypic, and omics data required to best characterize the underlying biological mechanisms of response to therapy and survival. Qatar Biobank (QBB), Qatar's National Repository Centre for biological samples and health information, aligning with these endeavors, has developed a strategic framework to enable biobanking science that can be transformed into tangible health care diagnostic tools. In this concept, QBB works closely with multidisciplinary stakeholders: (1) governmental authorities (n = 2), (2) health providers (n = 3), (3) academic institutions (n = 28), (4) other research institutions (n = 6), and (5) the Qatar National Research Fund, by providing data and biospecimens to research projects. The local community organizes campaigns through social media and interactive events, spreading the concept of biobanking to inform and encourage people to participate. Up to now, QBB has recruited up to 30% of the targeted population and collaborated with 35 national and international research entities contributing to more than 170 research projects. QBB is referring about 53% of its participants to the Hamad general hospital through the integrated information system, revealing the need of new health screening approaches for public health policy makers. QBB contributed to the development of a customized genetic screening microarray tailored to the Qatari population that will be used in research as well as for the screening of variants of medical relevance in Qatar, promoting precision medicine in Qatar's health care system. The QBB strategic plan is a paradigm for the optimal utilization of resources, infrastructure, and investments engaging the local authorities and the research entities, and committing them to data sharing and working together toward the discovery of evidence-based health care interventions.

Quality Matters: A Global Discussion in Qatar.

The International Biobanking Conference titled "Quality Matters: A Global Discussion in Qatar" was held on March 25-27, 2019, in the vibrant city of Doha, Qatar. The 3-day event was organized and hosted by the Qatar Biobank (QBB) and the European, Middle Eastern and African Society for Biopreservation and Biobanking (ESBB), with supporting collaboration from the International Society for Biological and Environmental Repositories (ISBER) and the Biobanking and BioMolecular Resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC). The aim was to highlight the role of biobanking in medical research and advancing health care, as well as improving clinical outcomes. The conference convened experts from across the globe to discuss continuing efforts to harmonize biobanking-related processes to achieve high-quality standards and to support international advancements in medical research for our diverse populations. The scientific agenda drew more than 1000 scientists, researchers, industry experts, and health professionals from five continents. The conference focused on the quality aspect of biobanking through seven sessions over 3 days. Researchers, scientists, and experts from around the world were invited to present, and included special presentations from QBB demonstrating their standing as a leading clinical biobank innovator in support of population and genomic medicine. The 3-day conference concluded with a session on Best Practices and Standards, a topic much in discussion with today's context.

Qatar Biobank Cohort Study: Study Design and First Results.

We describe the design, implementation, and results of the Qatar Biobank (QBB) cohort study for the first 10,000 participants. QBB is a prospective, population-based cohort study in Qatar, established in 2012. QBB's primary goal was to establish a cohort accessible to the local and international scientific community, providing adequate health data and biological samples to enable evidence-based research. The study design is based on an agnostic hypothesis, collecting data using questionnaires, biological samples, imaging data, and -omics. QBB aims to recruit 60,000 participants, men and women, adult (aged ≥18 years) Qataris or long-term residents (≥15 years living in Qatar) and follow up with them every 5 years. Currently, QBB has reached 28% (n = 17,065) of the targeted enrollee population and more than 2 million biological samples. QBB is a multinational cohort including 33 different nationalities, with a relatively young population (mean age, 40.5 years) of persons who are highly educated (50% university-educated) and have high monthly incomes. The 4 main noncommunicable diseases found among the QBB population are dyslipidemia, diabetes, hypertension, and asthma with prevalences of 30.1%, 17.4%, 16.8%, and 9.1%, respectively. The QBB repository can provide data and biological samples sufficient to demonstrate valid associations between genetic and/or environmental exposure and disease development to scientists worldwide.

Cholinergic and dopaminergic neuronal differentiation of human adipose tissue derived mesenchymal stem cells.

Mesenchymal stem cells (MSCs) are multipotent cells that can differentiate into various cell types such as cartilage, bone, and fat cells. Recent studies have shown that induction of MSCs in vitro by growth factors including epidermal growth factor (EGF) and fibroblast growth factor (FGF2) causes them to differentiate into neural like cells. These cultures also express ChAT, a cholinergic marker; and TH, a dopaminergic marker for neural cells. To establish a protocol with maximum differentiation potential, we examined MSCs under three experimental culture conditions using neural induction media containing FGF2, EGF, BMP-9, retinoic acid, and heparin. Adipose-derived MSCs were extracted and expanded in vitro for 3 passages after reaching >80% confluency, for a total duration of 9 days. Cells were then characterized by flow cytometry for CD markers as CD44 positive and CD45 negative. MSCs were then treated with neural induction media and were characterized by morphological changes and Q-PCR. Differentiated MSCs expressed markers for immature and mature neurons; ß Tubulin III (TUBB3) and MAP2, respectively, showing the neural potential of these cells to differentiate into functional neurons. Improved protocols for MSCs induction will facilitate and ensure the reproducibility and standard production of MSCs for therapeutic applications in neurodegenerative diseases.

Differentiation of human olfactory bulb-derived neural stem cells toward oligodendrocyte.

In the central nervous system (CNS), oligodendrocytes are the glial element in charge of myelin formation. Obtaining an overall presence of oligodendrocyte precursor cells/oligodendrocytes (OPCs/OLs) in culture from different sources of NSCs is an important research area, because OPCs/OLs may provide a promising therapeutic strategy for diseases affecting myelination of axons. The present study was designed to differentiate human olfactory bulb NSCs (OBNSCs) into OPCs/OLs and using expression profiling (RT-qPCR) gene, immunocytochemistry, and specific protein expression to highlight molecular mechanism(s) underlying differentiation of human OBNSCs into OPCs/OLs. The differentiation of OBNSCs was characterized by a simultaneous appearance of neurons and glial cells. The differentiation medium, containing cAMP, PDGFA, T3, and all-trans-retinoic acid (ATRA), promotes OBNSCs to generate mostly oligodendrocytes (OLs) displaying morphological changes, and appearance of long cytoplasmic processes. OBNSCs showed, after 5 days in OLs differentiation medium, a considerable decrease in the number of nestin positive cells, which was associated with a concomitant increase of NG2 immunoreactive cells and few O4(+)-OPCs. In addition, a significant up regulation in gene and protein expression profile of stage specific cell markers for OPCs/OLs (CNPase, Galc, NG2, MOG, OLIG1, OLIG2, MBP), neurons, and astrocytes (MAP2, ß-TubulinIII, GFAP) and concomitant decrease of OBNSCs pluripotency markers (Oct4, Sox2, Nestin), was demonstrated following induction of OBNSCs differentiation. Taken together, the present study demonstrate the marked ability of a cocktail of factors containing PDGFA, T3, cAMP, and ATRA, to induce OBNSCs differentiation into OPCs/OLs and shed light on the key genes and pathological pathways involved in this process.