Halima Alnaqbi’s PhD research addresses the gap in Arab representation in global genome data and establishes preliminary framework for organ and bone marrow transplantation in the UAE.��

Organ transplantation is one of the greatest advances in modern medicine and is the only life-saving strategy for patients with end-stage organ failure. Unfortunately, the need for organ donors is much greater than the number of people who donate.

The human immune system, however, poses a significant barrier to success when organs are transplanted from one individual to another. Rejection is caused by the immune system identifying the transplant as foreign, triggering a response that will ultimately destroy the transplanted organ. Donor and recipient are carefully matched prior to transplantation to minimize the risk of rejection, using tissue typing and blood group markers, but research into the population-specific genome can also play a larger role.

Dr. Halima Alnaqbi has successfully completed her PhD in Immunogenetics with her thesis focusing on enhancing the existing organ transplantation system to include Arab ethnic groups. This was the first research to identify conserved extended haplotypes (CEHs) in Arabs using high-resolution HLA pedigree-phased haplotypes. Dr. Alnaqbi, Dr. Guan Tay, Dr. Sarah Chehadeh, and Dr. Habiba Alsafar, Director of the KU Biotechnology Center, published this research in.

The human leukocyte antigen (HLA) complex, also known as the major histocompatibility complex (MHC), is a set of genes that code for cell surface proteins essential for the acquired immune system to recognize foreign molecules. It is the set of genes that determines compatibility for organ transplant, among many other things, and has garnered attention for its high level of allele variety among populations.

With more than 7000 alleles, the HLA complex is the most polymorphic region of the human genome. Studies have already examined the HLA complexes of various populations for many medical purposes, including populations where particular HLA types are very common and could potentially be identified as hot spots for severe disease, endemic persistence, or pathogen emergence. Proper understanding of the population-specific HLA complex is instrumental for making informed medical decisions.

“Unfortunately, there is a dearth of information about the structure of the MHC in Arab populations, especially for those who reside in Gulf countries,” Dr. Alnaqbi said. “The structure and content of the MHC region in Arab populations remain poorly characterized, posing challenges when establishing disease association studies in ethnic groups that inhabit the region and reducing the capacity to translate genetic research into clinical practice. We wanted to address the knowledge gap and characterize CEHs in the United Arab Emirates population.”

Conserved extended haplotypes refer to the conserved, long stretches of DNA that occur in people from the same population or ancestry. A haplotype is a physical grouping of genomic variants that tend to be inherited together and extended haplotypes provide most of the markers for HLA-associated autoimmune diseases. Previous disease association studies have been dominated by analyses based on populations of European ancestries, but this is gradually changing, allowing researchers to fill the knowledge gaps in disease risk predictions in some ethnic groups. The genome structure of Arab populations from the Middle East, however, remains poorly characterized.

“Although often grouped for their shared language, history, and culture, the populations of the Arabian Peninsula represent a genetically diverse group,” Dr. Alnaqbi said. “With the United Arab Emirates recently establishing its national organ registry program, this study provides insights on the MHC of the UAE population, which is important for matching recipients to appropriate donors.”

To contribute to the available data on Arab populations, Dr. Alnaqbi analyzed MHC alleles and haplotype frequencies in consenting volunteers from the UAE. Families were randomly recruited from different parts of the UAE and all participants were UAE nationals. The research found sections of genetic code were shared between the participants, identifying conserved extended HLA haplotypes in the population.

Dr. Alnaqbi said. “We need more effort into studying the MHC region of the Arabian population to offer better healthcare and benefit from the new paradigm of healthcare represented by personalized and precision medicine.”

Jade Sterling
Science Writer
15 June 2022

The post PhD Research Helps Reduce Organ Transplant Risk Using New Insights to Emirati Genome appeared first on Khalifa University.

Researchers in the UAE have found that some bacteria in the gut may impact the severity of Covid-19 infections. Certain types of anti-inflammatory bacteria linked to fatty acids metabolism in the intestines strengthen the body’s immune response, indicating that the makeup of the gut microbiome may influence the severity of infection and susceptibility to the SARS-CoV-2 virus.��

Read the Arabic story here:

The human gut houses a complex community of microbes, a dynamic population of microorganisms that differs from one person to another and impacts the balance of the whole human body. Evidence suggests the human microbiome even modulates the systemic immune response: in some patients suffering from other respiratory illnesses, the gut microbiota affects the immunity and inflammation in the lungs. It’s possible that a similar link exists between Covid-19 and the body’s gut microbiome. A team of researchers explored the role of gut microbiome diversity and its potential as an intervention target in modifying Covid-19 outcomes.

Dr. Mohammad Al Bataineh, Assistant Professor of Molecular Biology and Genetics, Dr. Habiba Alsafar, Associate Professor of Molecular Biology and Genetics and Director of the Khalifa University Center for Biotechnology, and six other KU researchers collaborated with a team of researchers who make up the UAE Covid-19 Collaborative Partnership to investigate the microbiomes of patients presenting with Covid-19. Their results were published in

The gut microbiome exists in a symbiotic relationship with its host, facilitating digestion and aiding in the delivery of essential nutrients to the cells making up the gastrointestinal tract. It helps protect against pathogenic microbes and plays a role in preserving intestinal homeostasis by modulating local and systemic immune responses. It keeps the local immune system in a perpetual vigilant state and remains relatively stable throughout life.

Although most people with Covid-19 recover within weeks of infection, some experience symptoms long after testing negative. Studies show that up to 75 percent of patients hospitalized with Covid-19 described at least one symptom six months after discharge, including respiratory, gastrointestinal, and memory symptoms, as well as fatigue. Although the exact causes for this are unknown, there is increasing evidence that the gut is linked to the severity of infection and that changes to the microbiome persist after the disease passes.

“The role of the human gut microbiome in health and disease conditions is yet to be fully understood. The gastrointestinal symptoms have been linked to the dysbiosis of the intestinal microbiome, where the normal gut bacterial makeup is altered,” Dr. Al Bataineh said. “Invading viruses can alter our immune responses – responses that are usually regulated by the microbiota in the gut. The infections interrupt the normal programming, and create a microenvironment that helps allow these pathogens to proliferate. We think the Covid-19 virus works in this way, altering the regulatory functions of microorganisms in the GI tract. Patients with Covid-19 tend to have lower levels of the beneficial microbes. Whether this is an association or causation is yet to be established.”

“Alterations in the gut microbiome are quite common among people with infectious diseases,” Dr. Alsafar explained. “We weren’t surprised to see this association with Covid-19 too. A substantial portion of patients presented with gastrointestinal symptoms, and when we identified that Covid-19 patients shed viral RNA in their stool, this was another indication that the virus was getting into the gut.”

SARS-CoV-2, the virus causing Covid-19, enters the human body by binding to a protein called ACE2. ACE2 is present in all people, but the quantity of this protein can vary among individuals and in different tissues and cells throughout the body, including the lungs, small intestine and the nasal cavity.

“The most important connection between the gut microbiome and Covid-19 is the involvement of the ACE2 receptor,” Dr. Alsafar explained. “SARS-CoV-2 enters cells through ACE2 receptors, which regulate the gut microbiota, and when disturbed by infection, cause a dysregulation of the intestinal system.”

It is understandable, then, that higher ACE2 expression in the body is correlated with higher infectivity, suggesting that increased ACE2 levels may predispose individuals to Covid-19. In a healthy gut, bacteria called Bacteroidetes are known as ‘good’ bacteria and downregulate the expression of the ACE2 receptor; this has a protective role in Covid-19 infections as it minimizes the amount of ACE2 receptors on the cell surfaces, meaning there are fewer potential entry points for the SARS-CoV-2 virus.

Unfortunately, patients with Covid-19 are more likely to present with lower levels of these commensal bacteria and higher levels of what are known as ‘opportunistic pathogens’. Together, the imbalance results in the gastrointestinal symptoms prevalent in Covid-19 patients, and these perturbations persist even after patients recover.

The data indicates a direct correlation between the composition of the gut microbiome and Covid-19 infection severity. Meaning, the microbial ecosystem before and during infection can help predict severity and mediate the immune response. However, since the gut microbiota were only sampled after they were infected with the virus, the research team was unable to determine whether pre-existing gut dysbiosis contributed to the severe symptoms, or whether the Covid-19 infection itself was the cause of the gut dysbiosis.

“This is very similar to the chicken and the egg question: which came first?” Dr. Alsafar said.

In addition, we know that dietary changes happen when patients fall ill: when people feel tired, diets often shift towards higher energy food in the hope it will help tackle their symptoms. These dietary changes also come with a change in the direct components of the microbiome, so it’s also possible this contributes to the changes in the gut. However, the participants in this study shared similar lifestyle and dietary habits, including dietary fiber intake.

The research team found that various differences in the microbiome could explain susceptibility and infection severity. Gender has been found to significantly correlate with overall microbiome variation, which may partially explain why men are more likely to contract Covid-19. At the same time, gut microbiota changes with age, with the elderly more likely to have lower levels of protective ‘good’ bacteria. One of these bacteria is Lachnospiraceae, which plays an essential role in gut barrier function and immune tolerance, especially among local inflammation. This commensal bacteria may be protecting the younger population from infection.

Lachnospiraceae also produce butyrate, a fatty acid that can strengthen immune response.

“Fatty acids play various critical cellular functions and are implicated in several stages of viral replication,” Dr. Alsafar explained. “They are directly linked to coronavirus spread and multiplication, and we found lower levels of the good bacteria that produce them in patients with Covid-19.”

Further longitudinal studies would be beneficial to understanding the relationship between Covid-19 susceptibility and changes in the gut microbiome, but this study represents the first to investigate a Middle Eastern cohort. The results show a significant compositional and functional shift in the gut microbiota of Covid-19 patients, suggesting interventions that target the gut could be used to mediate Covid-19 infection.

Jade Sterling
Science Writer
22 February 2022

The post Can You Stomach It? The Link between Covid-19 and the Gut Microbiome appeared first on Khalifa University.

Khalifa University’s Dr. Habiba Alsafar and a collaborative team of UAE researchers have identified eight host-specific genetic factors with a ‘highly plausible’ genetic association with hospitalized cases of Covid-19. The findings may be able to help researchers discover therapeutic approaches to combatting the virus responsible for an enormous health and economic burden worldwide.��

One of the great mysteries of the Covid-19 pandemic was why some people only contracted a mild disease, but for others it was a fatal infection. The variation in consequences range from asymptomatic to life-threatening, viral pneumonia and acute respiratory distress syndrome. Although some factors correlating to disease severity have been established, these risk factors alone do not explain all of the variability seen.

A research team in the UAE has found that the genetic makeup of an individual contributes to the susceptibility and response to viral infection. Although environmental, clinical and social factors affect the chance of exposure to the SARS-CoV-2 virus, host genetics seem to play a significant role in the severity of the disease. The research team involved consisted of Dr. Habiba AlSafar, Associate Professor and Director of the KU Center for Biotechnology (BTC), with Dr. Mira Mousa, and Research Associates Hema Vurivi and Hussein Kannout, all from the BTC. They collaborated with a team from Sheikh Khalifa Medical City, Dubai Health Authority, and the University of Western Australia and the work has been published in.

In a cross-sectional study, the research team looked at 646 patients who contracted Covid-19, 482 of whom were hospitalized with acute respiratory distress syndrome, pneumonia, severe complications, or who needed supplemental oxygen therapy. Upon examination of their genetic information, they identified eight genes expressed in the lungs are very likely to be associated with hospitalization in Covid-19 cases.

Risk factors, disease management and access to health systems do contribute to the wide variety in Covid-19 symptoms seen but multiple genome-wide association studies have demonstrated a link between the patient’s genetic makeup and their vulnerability to severe Covid-19 infection.

Previous work by Dr. AlSafar with researchers in the UAE found that infection with Covid-19 can affect the expression of various genes known to be associated with inflammatory and oxidation activities in the body. Genes that caused the production of reactive oxygen species – a type of unstable molecule that contains oxygen and that easily reacts with other molecules in a cell – were significantly upregulated, while genes that affected antioxidant production – molecules that fight free radicals in the body – were downregulated.

Now, a further eight genes have been discovered with a ‘highly plausible’ genetic association with hospitalization cases of Covid-19, thanks to the first genome-wide association study (GWAS) in the United Arab Emirates.

“Identifying genetic variants associated with Covid-19 severity may uncover novel biological insights into diseases pathogenesis and identify mechanistic targets for therapeutic and vaccine development,” Dr. AlSafar explained. “We can identify which individuals may have a greater risk of being hospitalized and improved treatments to target these patients specifically.”

The team designed their approach to uncover genetic variants shared across ancestry groups, discovering that while the eight genes were largely driven by effects in the populations with European ancestry, the effects were similar in multiple ancestral populations, demonstrating the chances of those variants modulating the risk of infection and severity in different populations.

The eight genes were all found in the lungs and are associated with tumor progression, emphysema and airway obstruction within the lung. In hospitalized Covid-19 patients, these genes were associated with respiratory failure that required invasive mechanical ventilation. Some of the genes were also found to be associated with inflammation in the lungs, further validating previous work that indicated inflammatory responses in the lungs influence Covid-19 susceptibility and severity.

While further studies are needed to fully establish the roles these eight genes play, these findings suggest that genetic diversity may be an important factor in determining why different people have different lung responses to SARS-CoV-2, and thus differing severity of Covid-19. Some of these associations could lead to therapeutic approaches, or therapies designed to improve overall health rather than merely treat symptoms, due to their expression in the lungs.

“The sample size for this study was small so caution should be exercised in translating the findings into genetic tests and clinical application,” Dr. AlSafar added. “However, based on our study, one gene, VWA8, has a 3-fold risk of being associated to hospitalized Covid-19 phenotypes. This gene is linked to types of emphysema and deformities in the lungs.

“We need to conduct further studies on worldwide population genetics to see if we can identify these genes in other populations. Then, we can begin to develop population-specific therapeutics to mitigate this worldwide challenge.”

Jade Sterling
Science Writer
24 January 2022

The post Eight Genes Found to Influence Covid-19 Severity appeared first on Khalifa University.

The study shows that certain types of anti-inflammatory bacteria and fatty acids in the intestines strengthen the body’s immune response

Scientists in the UAE have found that some bacteria in the gut may reduce the severity of Covid-19 in infected people.

The study carried out by scientists at the University of Sharjah, Khalifa University of Science and Technology in Abu Dhabi, and other institutions, said the make-up of the gut microbiome may influence the severity of the disease and the body’s immune response.

The work is among the latest of many studies of the relationship between the gut microbiome and Covid-19, some of which have analysed how diet influences a person’s ability to fend off the coronavirus.

The study, published in��Frontiers in Microbiology, looked at 86 infected people and another 57 without the disease.

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Research to Support Accurate Classification of Genome Variants for Development of Preventative Healthcare System

A team of scientists from Khalifa University of Science and Technology has completed a significant local genome study that will contribute to nationwide efforts to build a high-quality, comprehensive reference genome for the UAE population.

The first phase of the study — the description of the first whole genome sequences of UAE nationals — was completed in 2019. Subsequently, in 2020, the researchers completed the second phase which described the nature of the genetic diversity found among UAE nationals. This year, the researchers completed the third phase of the UAE reference genome, which supports a broader understanding of the genome composition of the nation.

Following advancements in DNA sequencing and analysis techniques since renowned scientist Craig Venter and his colleagues published the first whole human genome sequence at the turn of this century, the genome study has become part of a major area of research at Khalifa University.

The Khalifa University scientists recently published a report titled ‘A population-specific Major Allele Reference Genome from the United Arab Emirates population’ in the international journal, Frontiers in Genetics. The study was authored by Dr. Habiba Alsafar, Associate Professor, Department of Genetics and Molecular Biology, Dr. Andreas Henschel, Associate Professor, Electrical Engineering and Computer Science, with Dr. Gihan Daw Elbait and Dr. Guan Tay, from the Center for Biotechnology.

Dr. Arif Sultan Al Hammadi, Executive Vice-President, Khalifa University, said: “Our researchers have published the first whole genome of a UAE national and have followed it up with this reference genome.�� This will advance our understanding of the genomes of the UAE population, improving the ability of researchers and clinicians to identify genetic causes of diseases that are common in the UAE and the region. This is a stellar achievement in the field of medicine and healthcare, as this will become a fundamental tool that will advance genome and public health research in the UAE, and contribute to nationwide efforts, being led by the recently formed UAE Genomics Council to incorporate genomics into the healthcare ecosystem of the UAE.”��

The ethnic composition of the population of a nation contributes to its genetic uniqueness.�� Consequently, it is important to define national reference genomes of its people to avoid any confounding effects which are linked to the use of reference genomes from other national genome sequencing efforts. A total of 1,028 UAE nationals were recruited for this study, as part of the 1,000 UAE genome project that was conceived by the research team when the Center of Biotechnology was founded in 2015. Of these, 129 samples were selected as individuals that are most representative of the genetic diversity of the UAE for construction of the UAERG.

“Despite achieving this major milestone in a relatively short period of time, our work to improve our understanding of how genes contribute to health continues,” said Dr. Alsafar and added, “Our next challenge is to decode the genome data to identify genetic markers that better predict the likelihood of disease.”

Precision medicine has the potential to profoundly improve the practice of medicine. The goal is to enable clinicians to quickly, efficiently and accurately predict the most appropriate course of action for a patient; a pre-emptive strike to prevent or delay the onset of disease.�� However, the practice of precision medicine and personalized healthcare is a complex science as it is influenced by a range of factors such as the environment and the inherent characteristics within an individual. Genetics is an important contributor to this complexity and genome science will play a key role in the rollout of future national health programs.

Since the establishment of the Center for Biotechnology (BTC), its primary mission sought to address a gap in knowledge relating to the specific genomic features of the UAE population.�� In 2018, the BTC team outlined a vision for a National Arab Genome project for the UAE in the Journal of Human Genetics. The aim was to address the deficiency in genome data on the UAE population to improve our understanding of genome variants that are unique to the population of the nation.�� The team led by eminent geneticist Dr. Alsafar, proceeded with the bold ambition to sequence Emirati nationals to provide a reference upon which clinical decisions can be made.

In 2019, Dr. Alsafar led the team that described the first Whole Genomes Sequences (WGS) of two UAE nationals in Nature Publishing Group’s Scientific Report.�� “It was important to achieve this milestone, as the whole genome sequences provided a starting point for construction of a UAE reference panel which will lead to improvements in the delivery of precision medicine, which we hope will eventually lead to improvements in the quality of life of UAE nationals” said Dr Alsafar.

Despite reporting on the first genome of a UAE national, the Khalifa University team continued to sequence samples provided by UAE nationals for research. In mid-2020, the team followed up the report of the first UAE Whole Genome Sequence with two papers in Frontiers in Genetics. These studies showed that the contemporary population of the UAE arose from gradual admixture through complex and long term interactions between local communities of the area that is now the UAE and the people of neighbouring regions.

The seven emirates that formed the UAE in 1971 were once sheikhdoms that were homes of communities that existed for centuries. These communities lived on the southern routes of human migration within the Arabian Peninsula. Some of the inhabitants of the region encountered people who led a nomadic lifestyle, travelling widely into and out of neighbouring African, Asian and European states. As these nomadic communities passed through this region, traces of genetic impressions of the populations that they encountered in their travels were left behind.

As researchers continue to probe the secrets entwined in the genome of the UAE population, the construction of this reference genome is intended to drive the developing paradigm that is precision medicine, specifically clinical practice that embraces prevention rather than treating disease once it has taken hold.

Clarence Michael
English Editor Specialist
5 July 2021

The post Khalifa University Researchers Complete Reference Genome Study for the UAE appeared first on Khalifa University.

Health challenges remain one of the long-standing issues in the Arab region but biomedical computing research is one way to tackle these challenges.��

By Dr. Ahsan H. Khandoker

Read Arabic story��.

A combination of factors is driving the growth in demand for healthcare in the Middle East, including aging populations, longer life expectancies, and sedentary lifestyles that lead to an increase in obesity, cancer, and diabetes.

Thanks to recent advances in computing technology, biomedical computing has become one of the most influential research areas worldwide. There has been an explosion in the volume of biomedical data generated by the technologies involved in modern healthcare, but these volumes of data pose great analytical challenges in the quest to infer the knowledge buried within.

Researchers across the Arab region have successfully advanced a diverse spectrum of biomedical computing applications, as well as stimulating commercial interest. In an article published in, a journal for the Association of Computing Machinery, my colleagues and I shed light on these notable research efforts and demonstrate how this research addresses healthcare issues in the region. We focus on three main areas of biomedical computing: biomedical imaging, biomedical signal analysis, and bioinformatics.

Biomedical image analysis has been used extensively in the Arab world due to the region’s strong prevalence of diseases that rely on imaging techniques for accurate diagnosis. Across the region, numerous research groups have published work in this area, using various machine learning techniques. Research includes localization of cardiac structures using magnetic resonance imaging (MRI), computer-aided diagnosis for understanding tumor behavior, and diagnosis of Alzheimer’s disease using diffusion tensor images. With the onset of the Covid-19 pandemic, many researchers have also proposed methods for fast and accurate CT image segmentation, which is crucial to the diagnosis of Covid-19.

Biomedical signal analysis is another area that is key, given the advances in the technology of recording different physiological signals from the human body. These signals can be used in diagnosing various diseases as well as modulating the function of different organs. The Khalifa University Biomedical Signal Processing research group is developing non-invasive fetal phonocardiogram, as well as adult electrocardiogram (ECG) signal processing techniques to prevent stillbirths and sudden cardiac deaths.

Cardiovascular disease represents a leading cause of death in the Arab region, as well as worldwide, and the KU team is proud to contribute to the global research efforts to diagnose and predict cardiac arrhythmia complications. The team has developed a new device presenting a novel algorithm to predict a heart attack long before its onset, and successfully developed the first proof-of-concept, low-cost phonocardiogram sensor that can detect fetal heart sounds and give a reliable estimation of the fetal heart rate and its variability.

Brain signal analysis is another notable research direction pursued in biomedical computing applications. Researchers have identified and characterized the brain networks associated with cognitive deficits in patients, with neurological pathologies such as Alzheimer’s disease understood to be caused by alterations in these brain networks. This research could complement current Alzheimer’s Disease diagnostic metrics, especially at early stages of the disease.

Another study has proposed a technique to assess the mental capacity to preserve attention for long durations, with the technique able to monitor changes in the communication patterns among different brain regions with reduced attention. Biomedical signal analysis research in the region has resulted in influential and diverse contributions that aim to resolve multiple technical challenges in the field and address several population health issues.

Researchers in the field of bioinformatics have leveraged high-performance computational methods to tackle hereditary diseases prevalent in the region. There have been multiple efforts to develop national genome programs, with the projects focusing on unravelling the mutations responsible for inherited disorders in the population. The Emirati project, for example, has characterized 1,000 individual genomes with aspirations to eventually cover the entire population of the country. This bioinformatics research has the potential to dramatically enhance the quality of life of millions of people around the Arab region.

Built upon the success demonstrated in different biomedical computing tracks, the Arab region has witnessed a strong momentum for entrepreneurial activities in many sectors, for example, the work of the KU Biomedical Signal Processing research group that resulted in a UAE-based start-up company licensed to commercialize their phonogram technology for fetal wellbeing at home, called Medical Advanced Research Project (MARP ).

Research in biomedical computing is stimulating the budding culture of entrepreneurship and new ventures across the region, opening avenues of development that could magnify the outcomes of the biomedical computing research community in the region. Much of this work is being undertaken by Khalifa University’s Healthcare Engineering Innovation Group (HEIG) and Biotechnology Center (BTC).

Dr. Ahsan H. Khandoker is an Associate Professor of the Department of Biomedical Engineering at Khalifa University.��

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Researchers from Khalifa University have been investigating the specific genome variants that may point to risk factors for certain diseases and seeking to understand how these genetic variations can help develop more personalized treatment plans.

Read Arabic story here:��

Researchers from Khalifa University have recently published a number of articles investigating the nuances of the Emirati genome, following their research published last year describing the sequence of the first complete Emirati genome. They have since been investigating the specific genome variants that may point to risk factors for certain diseases and seeking to understand how these genetic variations can help develop more personalized treatment plans.

Much of the team’s attention has been focused on the genetic risk factors for metabolic syndrome, in particular type 2 diabetes. The discovery and mapping of the complete human genome in 2003 introduced the possibility of individualizing medicine to a person’s physical and genetic makeup, with plans for more population-specific genomic analyses to gain context-specific insights. Evidence is now increasingly suggesting that a patient’s unique genetic profile can be used to detect the onset of a disease and possibly even prevent it.

Dr. Habiba Alsafar, Director of KU’s Biotechnology Center and Associate Professor of Genetics and Molecular Biology, has been studying the unique genomic variants in the UAE population that are associated with diabetes, hypertension, increased cholesterol levels and obesity. Metabolic syndrome is a cluster of conditions occurring together, increasing risk of heart disease, stroke and type 2 diabetes.

The UAE has a high prevalence of metabolic syndrome, which may be linked to genetic risk factors in the local population. However, the association between metabolic syndrome as a phenotype and key genetic variants in the UAE has not been investigated in depth until now.

Dr. Alsafar and her team found clear links between metabolic syndrome and specific genetic and metabolic risk factors, providing an insight into possible causes of disease development. Several gene variants were found to be associated with a predisposition to developing metabolic syndrome, providing clues for disease mechanisms.

“In one study, we found that patients with metabolic syndrome had higher rates of type 2 diabetes, hypertension and dyslipidaemia, a medical condition that refers to abnormal levels of lipids in the blood,” explained Dr. Alsafar. “We noticed that waist circumference and type 2 diabetes were key risk factors for metabolic syndrome and that individuals who developed metabolic syndrome had a higher rate of clinical complications.”

Diabetes mellitus is a group of metabolic diseases, all of which are characterized by high blood glucose levels. It is a major public health problem, particularly type 2 diabetes, which is commonly associated with obesity. Diabetes tends to run in families with genetic factors contributing to its development.

The UAE has a high prevalence of diabetes, consistently ranking among the top five most affected countries in the world. Recent genome-wide association studies have identified more than 400 locations on particular chromosomes that are associated with susceptibility to type 2 diabetes disease. In-depth examination of the Emirati genome in particular could help pinpoint the exact genes that could be contributing to this prevalence.

In another study, the team found that genetic variants of one particular gene, known as TCF7L2, were associated with an increased susceptibility to type 2 diabetes, especially in Emirati males.

“Knowledge of specific risk markers in a population, including at risk genotypes, will help identify individuals who are more likely to develop metabolic syndrome. The ability to do so early, even prior�� to development of symptoms, could mean we can delay or even prevent its onset,” explained Dr. Alsafar.

The population in the UAE is also particularly prone to coronary artery disease.�� Previous studies having shown strong genetic associations between heart disease and type 2 diabetes. A further study by the team examined the genomes of a cohort from the Arab population of the UAE to replicate previously reported significant genetic associations. The study aimed to investigate how these genes are associated with twelve cardio-metabolic traits that may influence the development of the two diseases. The team did replicate these results, adding significant credence to the research, and also noted that some genes are associated with these diseases regardless of ethnic background. They also detected new links between the diseases with height and with blood type.

Knowledge of an individual’s susceptibility to a disease improves diagnosis and means more informed decisions can be made for a patient’s treatment, potentially helping them avoid metabolic syndrome altogether.����

Through these projects, Dr. Alsafar and her team are contributing to the global body of information and research on how to use context-specific genomic information to advance the understanding of medical conditions, improve treatment and promote healthy lifestyle habits.��

Jade Sterling
Science Writer
18 November 2020

The post Diving into the Emirati Genome to Determine the Genes Associated with Metabolic Syndrome appeared first on Khalifa University.

Read Arabic story .

Researchers hope stem cells will one day be effective in treating many medical conditions and diseases for which few treatments exist given that stem cells offer the potential to repair, restore, replace and regenerate cells.

Despite the successes seen so far, there are several major challenges that must be addressed before stem cells can be used as cell therapies to treat a wider range of diseases. One of these challenges, investigated by a team from Khalifa University, is the pathway by which stem cells self-renew or differentiate.

In a recently published in Stem Cells, Dr. Abdulrahim Sajini, Assistant Professor of Biomedical Engineering, along with Dr. James McElhinney, Post-Doctoral Fellow, and Dr. Ayesha Hasan, Assistant Professor of Biomedical Engineering, cover exciting insights into how small modifications to gene expression controls can influence this pathway.

Stem cells are the foundation for every organ and tissue in the body. All stem cells can self-renew, dividing indefinitely to produce more of the same stem cell, or differentiate, developing into specialized cells.

“The unique properties of stem cells make them well suited for regenerative medicine,” explained Dr. Sajini. “Stem cell therapies have shown considerable promise in the treatment of a diverse variety of medical issues, including regrowth of cartilage for osteoarthritis, pancreatic beta cell regeneration for diabetes and neural stem cell transplant for spinal cord injury.”

Before stem cells can be used more extensively in regenerative medicine, they need more study. Researchers need to first learn more about how stem cells behave and how they generate different types of human cells. The KU team reviewed the different types of stem cells and the unique epitranscriptome roles associated with them.

RNA is responsible for coding, decoding, regulating and expressing genes held within our DNA. Recently RNA was found to interact with various modifiers within our cells that can affect whether a gene is expressed or not. This is known as the ‘epitranscriptome’, which can be thought of as an extra layer of instructions for the RNA similar to epigenetics in DNA.

There are different types of stem cells, found during embryonic or adult development, with slightly different properties. Embryonic stem cells are the most pluripotent, meaning they can develop into any cell making up the body, which makes sense as all humans begin as embryos. However, this pluripotency requires multi-layer regulation check points, with the epitranscriptome playing a crucial role in maintaining the plasticity required for embryonic stem cells to self-renew or differentiate. In contrast, germline stem cells are unipotent cells that only give rise to haploid gamete cells.

“Stem cells are unique cells that have an inherent ability to self-renew or differentiate,” explained Dr. McElhinney. “Both fate decisions are strongly regulated at the molecular level via intricate signalling pathways. These pathways were thought to be governed by the action of transcription factors but now, small non-coding RNAs (ncRNAs) and their post-transcriptional modifications have emerged as additional regulatory layers with essential roles in this process.”

“Research into the epitranscriptome signatures in stem cells has revealed the emerging importance of an expanding set of ncRNAs in regulating cell biology. Moreover, these RNAs have been found to be extensively decorated with chemical modifications that comprise a complex regulatory layer on their functionality. As a fundamental governor of cell behavior, elucidating the epitranscriptome would represent a significant step forward to addressing challenges faced by stem cell therapies.”

There are many challenges associated with stem cell therapies. For example, the embryonic stem cells available today are likely to be rejected by the body; adult stem cells on the other hand are difficult to grow in the lab and can only be found in small quantities in their niche.

Currently, the only established therapy using stem cells is hematopoietic stem cell transplants to treat people with conditions such as leukemia and lymphoma—a bone marrow transplantation in most cases as hematopoietic stem cells are those responsible for making blood cells.

One important challenge is deciphering the imbalances in homeostasis that result in the development of cancer stem cells. Some stem cells form tumors after transplantation as pluripotency is linked to tumor formation. Recently, the epitranscriptome has emerged as a major regulator of stem cell biology and the KU team predicts that small ncRNA modifications will play a key part in future stem cell therapies.

“Most often, the onset of cancer appears linked to dysregulation in gene profiles,” explained Dr. Al Marzooqi. “There, the epitranscriptome of small ncRNAs is being directly implicated in the development of tumors by regulating the transcriptome of cancer stem cells. These small ncRNAs are being recognized for their potential to serve as biomarkers with diagnostic potential but the translation of these potential benefits to clinical applications is an ongoing effort. There’s no doubt that understanding how these small ncRNAs impact oncogenesis will help to identify how cancer develops and lead to more personalised approaches in its treatment.”

Jade Sterling
Science Writer
2 November 2020

The post Khalifa University Research Team Investigates the Future of Stem Cell Therapies appeared first on Khalifa University.

A team of researchers from Khalifa University has developed a portable Covid-19 testing kit, no larger than your average smartphone. The new kit is both portable and can deliver the results in 45 minutes only.

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Dr. Anas Alazzam, Associate Professor of Mechanical Engineering and member of the System-on-Chip Lab (SoCL) is the primary investigator for the project with Dr. Habiba AlSafar, Director of the Khalifa University Center for Biotechnology and Associate Professor of Genetics and Molecular Biology, as co-principal investigator. The research team includes the Postdoctoral Researchers Dr. Waqas Waheed, and Dr. Sueda Saylan, along with Research Associate Hussein Kannout.

While PCR testing is always highly accurate, and the gold standard for detecting viruses, it can be complex to use. The researchers at KU used the Loop-mediated Isothermal Amplification method (LAMP) to provide a rapid, sensitive, and specific detection of the Covid-19 virus. It is faster than the conventional PCR method and uses primers that target two specific regions of the viral RNA. The majority of PCR methods rely on thermal cycling where the reactants are exposed to repeated cycles of heating and cooling to start the RNA replication process. While laboratory PCR tests require a programmable thermocycler, LAMP can be carried out with a simple heat block, making it much more amenable to portable testing.

As complicated as this sounds, it’s all completed within the device and needs minimal knowledge to operate. For the KU testing kit, there is no need for any sophisticated equipment as the kit performs Covid-19 detection directly from a patient’s swab. A simple color change shows the result: pink for negative, yellow for positive.

Currently in the clinical validation stage, this testing kit can detect active infections in 45 minutes, meaning it can be used in rapid testing while being cost-effective at the same time.

When the coronavirus pandemic is over, the kits remain useful, as they can be used with any virus detecting primer. The LAMP method will still replicate the RNA to make it testable and then the sample can be tested with a reagent looking for the influenza virus, for example.

Primers to detect an infectious agent can be produced quickly once the viral sequence is known, so if a new virus were to emerge, this PCR test from the team at Khalifa University would be able to detect it.

Jade Sterling
Science Writer
2 October 2020

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