GWAS meta‑analysis of axial spondyloarthritis and Behçet’s disease identifies CXCR6 as a novel MHC‑I‑opathy gene in a Turkish population

Author: Dr. Mohammad Saeed

Dr. Mohammad Saeed is a member of the EULAR MHC-I-opathy group.

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“MHC-I-opathy” is a family of inflammatory disorders with a strong genetic link to HLA-I. These include Axial spondyloarthritis (AxSpA; previously Ankylosing spondylitis (AS) associated with HLA-B27), Behçet’s disease (BD; associated with HLA-B51) and psoriasis. Though the MHC-I genetic associations were discovered about 50 years ago, the pathogenesis of these disorders is not fully understood. To identify immunogenetic pathways for MHC-I-opathies, a cluster-based meta-analysis of AxSpA and BD Genome-wide association studies (GWAS) using OASIS was conducted. Both selected GWAS were from Turkiÿe for homogenous population effect.

OASIS (Objective Assimilation of SNPs Interacting in Synchrony) is a GWAS clustering algorithm, developed by Dr. Mohammad Saeed to identify genes of modest significance. These are often missed in classic analysis that use Manhattan plots to identify significant associations in GWAS. Clustering or binning methods, such as OASIS, increase power by decreasing the number of tests per study.

HLA-I was the only locus that was highly significant (P<1× ­10–8) in both GWAS datasets. OASIS identified 234 independent modestly significant non-HLA loci in the two GWAS datasets (Bonferroni correction: P≤2.14×10⁻4; −log10 P≥3.67). The most signficant genes that this study identified were IL23R (1p31.3), LACC1 (13q14.11) and the novel CXCR6 (3p21.31). These are significantly associated with both AxSpA and BD. All three genes are down-regulated in these MHC-I-opathies. Protein interaction network showed that CXCR6 is part of the interactome of IL23R and LACC1 (P=0.00243). The novel gene, CXCR6, identified here codes for a G-protein coupled receptor expressed in several T-cell subsets and regulate their migration to tissues. A previous biological study showed that CXCR6+ CD8+ T-cells were actively recruited to psoriasis-affected skin. It also showed that TNF-α inhibition, which is part of the therapeutics (such as the biologic medications Eternacept, Adalimumab and Infliximab) for AxSpA and BD, reduced the CXCR6-mediated T-cell recruitment.

In summary, this study identified 15 loci common to both AxSpA and BD that may provide diagnostic and therapeutic targets for MHC-I-opathy. Major candidate genes for MHC-I-opathy identified here are IL23R, LACC1, and CXCR6. By integrating locus-level significance with functional validation in independent expression datasets, we ensured that only statistically robust and biologically relevant associations were highlighted, thereby strengthening the reliability and interpretability of our findings.

Link to the Artcle on Journal website

Cross-Reactivity of SARS-CoV-2 Antibodies With Typhoid Flagellar-H Protein.

Aneela Pasha, Mohammad Saeed

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Figure 2A of the article (Copyright with TMIH Journal) and depicts the molecular overlap between Salmonella typhi Flagellar-H antigen and SARS-CoV-2 RBM antigen. This overlap was eliminated due to the Delta mutation (Figure 2B). This, we hypothesize underlies the antibody cross-reactivity between the two organisms.

COVID-19 affected different regions of the world with varying intensity leading to high mortality in some regions and low in others. This proof-of-concept study presents evidence that one potential infection that may have provided natural herd immunity against COVID-19, due to adaptive heterologous immunity, is Typhoid fever.

During the COVID-19 pandemic several patients presented to ImmunoCure from interior Sindh with COVID-19 symptoms and a positive Typhidot test. They had been treated with antibiotics for Typhoid fever. However, their symptoms and clinical exam was suggestive of mild to moderate COVID-19. After informed consents patients were tested for both SARS-COV-2 antibodies and Typhidot (without charge). We found high correlation between the two tests (~72%).

Dr. Mohammad Saeed suspected antibody cross-reactivity, which occurs when antibody against one antigen (usually a protein) reacts against a different antigen / protein. Usual matching analysis (using the BLAST software) did not show any overlap. However, with specialized analysis involving cutting the protein sequences into small pieces and matching them (k-mer analysis) showed that a 5-amino acid sequence overlapped between SARS-CoV-2 (that causes COVID-19) and Salmonella typhi (that causes Typhoid fever).

This 5-amino acid sequence, NGVEG, was found in the Flagellar-H protein of Salmonella typhi and very interestingly in the critical region of SARS-CoV-2 called the Spike protein. The Spike protein is responsible for the entry of the SARS-CoV-2 virus in the cells and vaccines are also made against it to protect from COVID-19. Moreover, NGVEG was found in the special region of the Spike protein called the Receptor Binding Motif (RBM) which is the critical most region of SARS-CoV-2. The Delta variant of SARS-CoV-2 emerged in India after a super-spreader event and the mortality rate in South Asia and around the world from COVID-19 skyrocketed. This Delta variant contained a mutation E484Q. This mutation targeted the very sequence that overlapped between Salmonella typhi and SARS-CoV-2 i.e. NGVEG, turning it into NGVQG. This single amino acid change, completely altered the 3-dimensional structure of the SARS-CoV-2 RBM as shown in the Figure 2 of the article (above).

We next looked at whether COVID-19 mortality was impacted by Typhoid prevalence. Epidemiological data showed that Typhoid endemic regions, such as Pakistan, Bangladesh and others, had lower COVID-19 mortality than Typhoid non-endemic regions such as Europe and United States.

After the COVID-19 pandemic, the Government of Pakistan permanently banned the use of the Typhidot test due to widespread concerns over false-positive results. This policy action, while driven by diagnostic concerns indirectly supports the idea that cross-reactivity between SARS-CoV-2 and Salmonella typhi was of real-world relevance. Our study brings to light this possibility and attempts to highlight the science-policy interface and the public health implications of diagnostic cross-reactivity in endemic settings.

@AneelaPasha and @DrMSaeed_pk

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Dr. Mohammad Saeed.

Consultant Rheumatology and Immunogenetics. ImmunoCure

Written: 11 August 2018

Since this article was written, Pakistan, like the rest of the world, has undergone several critical phases including COVID-19 pandemic and economic challenges. However, this article could still serve as a guide to physicians wanting to return home. 

The need for this article was felt when many Pakistani doctors abroad and visiting Pakistan had shown deep interest in my experience of moving back to Pakistan. I realize a lot of doctors want to move to their homeland, Pakistan, but having lived abroad for several years, with growing family needs they experience uncertainty and genuine anxiety. Moving back to Pakistan can be the most enriching and rewarding experience of your life. The people and the country need your expertise and you need to feel at home once again, putting your heart and soul into what you love most. This article hopes to provide a general outline for your planned move to Pakistan for reasons of personal growth and development – serving your immediate and extended family, providing your children a culturally relevant environment with strong potential for their educational development and creating meaningful social impact based on your skills.

Your move back to Pakistan should be thought of as a move into your future and not into your past. Your priority of moving close to your parents and extended family is a move into your past. However, your children are growing into the future. Their needs will be different and you will not be satisfied unless you ensure a bright future for your children in Pakistan. Therefore as a first priority you must provide your nuclear family with the same space as you have done for them abroad. As a Physician, you would have lived abroad for a number of years in a nuclear family model. Your family will continue to need their own space and your time. This is only possible if you provide them with a home of their own. Therefore your first priority should be to build a home for your family. The work on this project should start early with savings being directed to it on priority basis, long before your planned move.

The practical steps for home building in Pakistan vary according to your circumstances. However buying a home is usually out of financial reach by a substantial amount. Moreover, land in Pakistan is generally expensive especially in major cities and more so in localities where you may want a lifestyle close to your experience abroad. Also buying property is no trivial task and it will be compounded by the fact that you will still be abroad trying to save up for this major project and not aware of all ground realities in the city of your choice. The best method in this situation would be to work with a reputable bank in Pakistan which deals in home ownership and can accommodate residents abroad in its banking policies such as home loans. This will be a safe and efficient way of buying property in Pakistan even if you can afford to buy directly. Your savings should be enough to make the down payment of your home loan (minimum of 1/3 of the property price). On the other hand you may want to buy land and then build your home yourself with help of family and friends supervising the project, but this is a tedious task. I recommend buying a built house.

The location of your house is critical. I recommend choosing a locality (in the city of your choice) where there are good schools for your children at short driving distances. This will reduce their daily travel time and consequent fatigue, making their move to Pakistan more enjoyable. Your children will be spending a good portion of their day at school. So choose the best environment for them. The move will be stressful for them so the school environment must be supportive of their emotional and development needs. Academics cannot be compromised but a supportive school environment does take priority.

Your savings should be based on the average price of a house in the locality of your choice. Your foreign currency earnings will be a major advantage. You could open a foreign currency account in a reputable Pakistani bank of your choice along with a Rupee current account. This will allow you to transfer your savings in foreign currency to Pakistan, build your credit history for an eventual sizeable home loan from the bank and your Rupee current account will be ready for your home transaction.

All your documents as well as for your spouse and children must be in order. These include National ID cards (also obtain Family certificate from 24-hour NADRA offices), Passports (Pakistani), National Tax ID (FBR), Driver’s license(s), PMDC license (based on your MBBS degree; PG training may be added later). It will be a good idea to hire a Tax lawyer (through your contacts in Pakistan) in advance for all your financial needs. Once this work is done and you have enough money in your foreign currency account for the down-payment, you are ready to hit the long hard road of finding the house you will call home in Pakistan. For this you will need to personally see many houses through multiple estate agents but in reality what you need is one trustworthy agent. Again use your personal contacts but you would have already realized by now that for all you have already done, you would have visited Pakistan several times. Yes, repeated visits are highly recommended for you and your family to acclimatize and get the work done. I did not visit Pakistan for nearly a decade prior to my move and still got everything done but I would not recommend taking this route. Try and visit Pakistan and at each visit get some of the tasks completed. It will ease your move back.

Once you locate the house you want to buy and the deal is made, your bank will review your application for the loan and approve it based on its risk assessment of you. The bank will send its own team to review the property and evaluate its value, ensure proper documentation and provide you its own comprehensive opinion. This is valuable consultancy even if you intend to and have the ability to buy the property in full on your own. The re-payment method that will work best in your favor is what is known as ‘balloon payments’ i.e. payment over and above your monthly installment. The bank loan will be for ~ 20 years. Borrow the least amount of money possible as paying back (with interest / rental options) is always more difficult. Your scheduled payments repay only a very small percentage of your principle loan. Majority (>80%) goes to the ‘rental / interest’ payments initially. So the smaller the loan and the more frequent the balloon payments, the sooner you will own your property and at the least overall cost. You will have to have a cushion for renovation work (especially if you are buying a built house). Of course smaller renovations can be done after having moved into your new home.

Getting the house out of the way is half the move. The other major component is landing a job for yourself. Try and avoid doing exactly that, i.e. get a job; don’t. My advice is that one should do a job in the West and business in the East. It’s more rewarding that way. Remember you are moving from a resourceful region to a resource-limited country. You have to have the creativity to generate your own resources. This is no small task either, perhaps more demanding than the first one and requiring lot more persistence and patience. God be with you! If you do decide on landing a job, negotiate from abroad. Once you are in Pakistan you lose your negotiation power and the salary packages start thinning rapidly. Do not panic. Believe in your own ability and know that what the nation expects you to do is just what you are trained to do and have years of experience in.

The medical profession is very rewarding. If you are a physician you have very basic needs to establish a practice of your own. However the most demanding need is time, which you don’t have in abundance. If you have a property loan to pay off you have to be able to generate substantial amount to pay off the monthly installments as well as pay for your daily needs. Your family and friends may come to your rescue here. If you take a non-interest loan from them to pay off the bank you save majorly on the interest / rental financial leakage, own your property and reduce the earning pressure. On the other hand landing a well paying job for ~ 2y years initially is not a bad idea either. This will help you build your social and professional contacts, maintain a good working relationship with your bank and give you time to settle your family. The usual problem with salaries is that they are not according to your expectations. The reason is that Pakistan healthcare is a resource limited industry with few positions at Consultant level and extreme competition as a result. For an institution to hire a foreign trained Consultant it could easily hire at least two locally trained Consultants if not more. It does not always make good business sense to hire foreign trained Consultants.

Your main dilemma is that just like when you moved to the West you did not have a financial credit history, when you move to the East you do not have a social credit history. Patients do not know you. So you do not have the market. You need a referral base. On salaried positions your hospital provides that referral base. But it is not ideal. You will generally be overworked and your quality of care may be compromised, severely reducing your job satisfaction. Remember after moving to Pakistan you will not be getting any younger. Your energies will deplete rapidly given the volume of responsibilities you will be shouldering.

You could enter a partnership based model such as what we also offer at ImmunoCure. If you are a foreign trained physician Consultant, partnerships offer you our referral base with flexible timings that suit your needs. You grow at your own pace and your patient base grows around you. Within 1-year, provided you dedicate yourself to your practice, your patients will recognize your outstanding care in enough numbers to generate word of mouth referrals. For such group practices trust is key. As long as partners can maintain long term trust and are willing to share their practice base, this model can work and will be the ideal model for returning doctors. The sharing of clinical practice is based on overlap of fields. Either single specialty or clinically overlapping multispecialty groups can be formed. Such group practices will be economically viable and will have tremendous growth potential. The incoming doctor should also ensure a fair share to the residing Consultant. The partnerships should be win-win situations or in technical terms ‘Non-zero sum’. Dynamic share determination is the most equitable and works best for both parties.   

“In the great non-zero sum games of history, if you are part of the problem, you will likely be a victim of the solution.” – Non-Zero. Robert Wright.

One intermediate possibility is that while you are planning to return to Pakistan and making your visits to get the administrative work wrapped up, you may start your partnership on temporary basis. You could then consult on local patients on your visits to Pakistan, experience the clinical environment, evaluate the financial possibilities and gradually build your practice in Pakistan even before landing here permanently.

ImmunoCure extends a warm welcome to you and your family.

Welcome home.

Dr. Mohammad Saeed
M.D, DABIM, Rheumatology (USA)
Consultant Rheumatologist
Musculoskeletal Ultrasound Specialist

ImmunoCure
Suite 102, 1st Floor, Building 24-C, Lane 1,
Ittehad Commercial Area, DHA Phase 6, Karachi, Pakistan
Website: Immunocure.pk
Appointments: 0308-2822712

Dr. Mohammad Saeed was invited to present his research on the ‘Genetics of MHC-I-Opathy’ at the British Society for Rheumatology (BSR) (April 24, 2024). The summary of the research was published in the official BSR Journal, Rheumatology.

The presentation was well-received by the august audience of Rheumatologists and Immunologists at the BSR 2024. A lengthy follow-up meeting was held at the University of Leeds and a collaboration for data and analysis exchange was established with Dr. Mohammad Saeed. University of Leeds has been recognized as a center of excellence in Rheumatology by EULAR (European League against Rheumatism) since 2005.

This research received no funding to perform. However, participation at the BSR 2024 Meeting was sponsored by High-Q and KIAZEN Pharmaceuticals, Pakistan. This was considered Advertising campaign for the Sponsors and declared at the BSR Meeting Oral Presentation. 

Python – The Logo Way (Book)

The book is written with the child in mind to teach programming by drawing using “Logo” concepts. I hope to spark greater creativity in children, make education fun and fulfill the need to learn today’s essential skill, i.e, being able to program and ‘talk to computers’. Therefore, a simple text for an accessible programming language such as Python was much needed.

Dr. Mohammad Saeed

Consultant Rheumatology and Immunogenetics

Twitter: @DrMSaeed_pk

Patients can now order medications, including prescription drugs, by uploading their valid Doctor prescription using our Pharmacy online order form. Home delivery within Karachi is free. Our Pharmacy can deliver your medications to your doorstep where ever you are in Pakistan. 

Payments:            Online Bank transfer              

So, please follow your Doctor’s advice, take your medications as prescribed and follow up on time.

Click Here to Order Medications Online

Lecture #3: “How to choose a Mentor?” by Prof. Anwar Siddiqui

Friday, October 16, 2020. Timing: 3 – 4 pm (Tweet)

Zoom Online Meeting Recorded Video

Language requirement: Both English and Urdu

Lecture #2: “Why do Research?” by Prof. Anwar Siddiqui

Friday, September 25, 2020. Timing: 3 – 4 pm (Tweet)

Recorded Video of Lecture:

Lecture #1: “Research Integrity” by Prof. Anwar Siddiqui

🇵🇰 Happy Independence Day

At ImmunoCure we celebrated this important day with the first Seminar. Prof. Anwar Siddiqui enlightened us with his rich experience and concrete examples on "Research Integrity", a theme that blends with our desire to rise as a nation on solid footings. pic.twitter.com/YcrV6ZV64K

— ImmunoCure (@ImmunoCure_pk) August 14, 2020

Professor Anwar Ali Siddiqui
Consultant Research & Development

Professor, Anwar Ali Siddiqui
BSc (Hons.), MSc, MPhil, PhD (Biochemistry)

Professor Anwar Siddiqui is a distinguished Pakistani academic who has played a major role in developing research in Pakistan. Over 35-years in his capacity as one of the first Faculty at Aga Khan University (AKU), he laid the foundation of teaching and research in the Basic Sciences. He served as Director, Research Office of AKU, as well as the Associate Dean for Research. He also laid the foundation of the AKU PhD program in Health Sciences.

Dr. Siddiqui received his PhD in Biochemistry from Queen’s University of Belfast, Northern Ireland, UK in 1981 and became Professor of Biochemistry, Department of Biological and Biomedical Sciences, AKU in 2001. His major scientific contributions include renal stone matrix proteins and their role in urolithiasis and Hepatitis C and cytomegalovirus viral and host factors in disease complications. Dr. Siddiqui has been a member of numerous professional associations including being a member of the Executive Board of ICCS, HEJ, PMRC, University of Karachi and Institutional Review Board of Dow University of Health Sciences. He has been a member of the planning committee for the Asia Pacific Rim on Research Integrity. Dr. Siddiqui was the recipient of AKU Faculty Development Award, Research Programme at Harvard Medical School, Boston, USA (1989-90) and the Outstanding Teacher Award, AKU, Pakistan (1996).

Prof. Siddiqui has been an active teacher of postgraduates and numerous Masters and PhD students have received their degrees under his supervision. He has taught AKU medical students throughout his career of over three decades. He has organized and facilitated workshops on ‘Research Proposal Development’ for several organizations including PMRC, HEC and the British Council, Pakistan. In the domain of research administration, Dr. Siddiqui’s major contributions include establishment of the Aga Khan University’s Research Office, designing and operations of Biosafety level 2 and 3 Research Laboratories and a Cancer Tissue Biobank, development of various research governing and monitoring policies, TORs including Ethics Review Committee, grant review processes and policies on Authorship and Intellectual property rights as well as responsible conduct of research and research integrity. 

Research Publications

Dr. Mohammad Saeed
Founder & CEO
Consultant Rheumatology and Immunogenetics

Rheumatology Clinic: Mon to Thu and Sat
Timings: 10 am to 5 pm
Appointments: +92 308 282 2712

Dr. Mohammad Saeed, M.D.
Consultant Rheumatology and Immunogenetics
Fellowships (USA): Rheumatology, Musculoskeletal Ultrasound, Genomics, Immunology

Dr. Mohammad Saeed graduated from Aga Khan University Medical College and has Fellowships in Genomics from Northwestern University, Chicago, and Immunology from the University of Arkansas for Medical Sciences (UAMS). He trained in Internal Medicine and Rheumatology at UAMS and has further specialization in Musculoskeletal Ultrasound from Boston University (USSONAR program). He has been faculty at UAMS and Staff Scientist at Nephropath, USA.

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He is an active researcher working on the genetics of lupus and other autoimmune disorders and has previously contributed substantially to Neurogenetics. He has several publications in international journals and has been a member of professional organizations including the American College of Rheumatology, European Lupus Society (SLEuro) and American Society of Human Genetics. He is a member of the Pakistan Society for Rheumatology and Health Research Advisory Board, Pakistan.

Rheumatology deals with inflammation anywhere in the body (kidneys, lungs, brain, and nerves, or even eyes) as well as disorders of joints and bones. These conditions are often difficult to diagnose due to the variety of symptoms they produce in different organ systems. Dr. Saeed has a special interest in patients who have not had a diagnosis despite visiting several doctors. Other common Rheumatologic diseases Dr. Saeed manages, include Osteoporosis and Osteoarthritis, Rheumatoid arthritis, Gout, Systemic lupus erythematosus, Myositis, Reactive arthritis, Psoriasis, and Vasculitis. These conditions can vary from mild to severe disease but have good treatments available especially if diagnosed early.

Research Publications

Curriculum vitae

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