Dr. Alkuraia delivers a compelling blueprint for the transition from descriptive to predictive nephrology, effectively synthesizing multi-omics into a coherent clinical strategy. This is a vital masterclass for anyone seeking to understand how molecular precision is finally replacing the trial-and-error tradition of kidney care.
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Deep Dive
Precision Nephrology in the Multi-Omics Era: A New Architecture for Kidney Care.
Added:Hello everyone and welcome to our renal genetics webinar.
And we are focusing on precision medicine today. Precision medicine in nephrology has been lagging a little bit behind other specialities, especially oncology and the rare genetic disorders for many reasons, but I think now we are on our momentum to improve our patient's outcome to precisely, individualizely, and better manage our patients. The greatest advances have occurred in precision medicine with discovery of molecular mechanism and genetic testing in the last couple decades. And now we are using more genomics, transcriptomics, proteomics, metabolomics, and machine learning to predict the disease progression and to treat our patient better. In nephrology field, I think with discovery of upper one associated kidney disease genetic background of different code of GN and nephrotic syndrome, complement mediated disease, precision medicine and atypical HUS, using biomarker for AKI, and trying to find the reason for the unclassified CKD has been phenomenal.
So, hopefully our today's webinar and our upcoming workshop in August will help all of us to understand this challenging process.
Um So, we have great speaker today, Dr. Fawzan Alkuraia, who is a professor of genetics in Alfaisal University, who's going going to give us a very nice presentation how to use precision medicine and the different kind of omics as a new architecture for diagnosing and treating a various kind of kidney disease. Uh then Dr. Nada She's associate professor of nephrology at Ain Shams University is going to give us a very nice case-based discussion. Then our Professor John Sayer and Professor Khalid Al Hasan are going to moderate the session and help us to learn more and more about this genetic testing and this metabolomics and genomics era.
Without further ado, I will let Professor Khalid Al Hasan to introduce our first speaker, Professor Fawzan.
>> Thank you very much Professor Amr for and thanks actually for the World Kidney Academy of arranging such a nice webinars with the free registrations.
Um and it probably this is an going to be an introduction uh today for our upcoming um a workshop, two days workshop which will will be on August and they will encourage our colleagues attendees to to register to this upcoming workshops.
Today, as have been mentioned by my friend Amr, that we get we have my very close friend and actually my classmate but he's so giant guy in his field uh which Professor Fouad Khoury uh and he he going to lighting us about something very peculiar and very important which is the precision medicine in in what's called multiomics era and really and I think all of you like me looking forward to this talk and how we can dive on this important things and in very important field uh that's most of us now we cannot work on many uh parts of our nephrology especially those inherited diseases so that without further due the mics is yours Professor Fouad Khoury >> Good evening everyone. Thank you so much for the very generous introduction and for the very kind invitation. Um it's really exciting to talk about precision medicine but when I talk to you folks in nephrology I think it's best to call it precision nephrology. So much is happening in this space and it's my pleasure to share a few of the developments that I hope you find very helpful and exciting for your field. So for decades nephrology has really relied on a static two-dimensional view of real disease using crude filtration markers and visual biopsies cars to guide our treatment. Today we stand on the precipice of medical revolution driven by multiomics toolbox. By integrating genomics, transcriptomics, proteomics, metabolomics, epigenomics, microbiomics, we can finally stop treating the kidney as an isolated filter and start managing it as a dynamic interconnected ecosystem. Now, each independent omics omics layer acts as a unique lens revealing a completely different dimension of kidney biology allowing us to transition from reactive management to absolute molecular precision.
So, I figured in my first slide I would just introduce you to these different layers of omics to make sure we're all on the same page starting of course with genomics. It's our foundational layer that utilizes advanced genetic sequencing to uncover such things as localized polygenic risk scores that predict your lifetime chronic kidney disease risk, non-invasive genetic diagnosis of monogenic kidney diseases that is increasingly replacing invasive tissue biopsies. Transcriptomics, this layer tracks real-time gene expression using blood and urine RNA signatures to predict active lupus flares, allograft rejection, chronic progression while single-cell RNA sequencing completely redefines our understanding of cellular level kidney pathology.
When it comes to proteomics, here we're talking about a layer that evaluates the dynamic functional protein networks utilizing highly sensitive blood and urine proteomic classifiers that consistently outperform traditional biopsies for early detection of things like acute kidney injury, subclinical rejection, and active fibrotic remodeling.
Metabolomics, another omics layer, it's a very dynamic layer that analyzes small molecule byproducts in bodily fluids including urine to capture instantaneous cellular function mapping distinct metabolic fingerprints that can precisely chart the trajectory of chronic kidney disease progression and identify early drug responses.
Epigenomics, this layer studies how lifestyle and environmental factors and exposures modify gene activity without altering baseline DNA, deploying advanced methylation clocks to predict biological kidney aging alongside highly specific epigenetic biomarkers of progressive tissue fibrosis. And last but not least, the microbiome or microbiomics. This layer profiles the truly genes of microorganisms living within the host, mapping out the complex gut kidney axis to uncover how microbial imbalances directly drive the development of chronic kidney disease, kidney stones, and systemic hypertension. So, what I figured I would do in my talk, I picked a few kidney disorders and I would like to convince you of the value of multiomics in approaching these diseases. And the first of these kidney pathologies is IgA nephropathy.
So, the multiomic approach to IgA nephropathy maps out the gut kidney axis and reveals non-invasive biomarkers for personalized treatment. So, if you look at what the microbiomics layer contributed, it really profiled the gut microbioma or microbiota rather to identify composition changes or what we call dysbiosis. And studies have shown that a reduction in beneficial commensal bacteria and expansion of opportunistic pathogens directly trigger abnormal immune responder responses.
At the genomics layer, we we meaning our community identified over 30 genetic risk loci that direct that are directly involved in maintaining intestinal epithelial barrier and detecting mucosal pathogens highlighting an inherent genetic risk linked to the gut.
Um at the level of the transcriptome and the epigenome, examining the expression of genes and immune cells, this highlighted how genes regulating mucosal immunity and O-glycosylation um are pathologically activated.
And at the level of the glycomics, uh again, it's been identified that there are structural changes of the IgA1 antibodies, uh revealing that there is galactose-deficient IgA1 uh state, which is the core autoantigen of the disease. And at the level of proteomics and metabolomics, by evaluating the protein networks of small molecule byproducts in blood and urine, we are able to connect altered gut metabolites, such as short-chain fatty acids, to kidney inflammation, complement system activation, and mesangial cell damage.
So, what have we learned from deploying this uh multiomics uh uh in in IgA nephropathy? Now, we have learned of the so-called the four-hit pathogenesis model of IgA uh nephropathy, uh along the gut-kidney axis uh perturbation. So, hit number one is that gut-driven autoantigen the dysbiosis of the gut microbiota disrupts the tight junction uh within the intestinal lining, increasing the gut permeability, which is uh uh the other name for leaky gut. Uh and so, bacteria and their toxins translocate across the barrier, hyperactivating B cells in the gut-associated lymphoid tissue, especially in the ileum. Influenced by genetics susceptibility, these B cells overproduce sugar uh uh poorly sugar-coated uh or galactose-deficient IgA1 um autoantibodies. So, hit number two is this auto antibody generation.
And so, the circulating poorly glycosylated Gd-IgA1 acts as a foreign target prompting the immune system to generate IgG or IgA autoantibodies against it. That's hit number two. Now, hit number three is the immune complexes. The autoantigens are the Gd-IgA1 and the autoantibodies bind together in the bloodstream to form circulating pathogenic immune complexes.
Hit number four, that's where you have the kidney injury and the defective sensing. So, these massive complexes deposit in the kidneys glomeruli causing inflammation, cell proliferation, and complement activation. Concurrently, multiomics revealed a lack of the gut microbial metabolites such as acetate downregulated protective metabolic receptors of the kidney crippling the kidney's ability to defend against this inflammatory onslaught.
So, what does that mean to you as clinicians?
Their clinical value is immense. First, we have non-invasive diagnostic profiles, right? So, now we can combine gut microbiome sequencing with serum metabolomics to allow clinicians to build machine learning classifiers. And these models can diagnose or monitor IgA nephropathy progression without relying strictly on painful kidney biopsies. Second, you predict drug response. The metagenomic profiling can accurately predict who will respond to therapy. For instance, an abundance of proteobacteria or Escherichia shigella has been used in multiomics models to predict treatment non-responders with very high accuracy.
And so, when it comes to treatment, you can think of microbiome targeted therapies, right? So, instead of broad immune suppression, uh multi-omics, you know, supports precise gut-targeted therapies. And this include targeted release budesonide, designed to specifically release the medicine in the ileum where the pathogenic B cells cluster, specific probiotics, or to restore the short-chain fatty acids, or narrow-spectrum anti- antibiotics to reduce the circulating immune complexes.
So, that's one example.
And I decided to make my second example something that's particularly relevant to us in Saudi Arabia, which is diabetic kidney disease. We all know how common that is.
And again, the developments in the multi-omics space are just super exciting.
Um the use of multi-omics in DKD represents truly a shift from reactive clinical management to proactive, molecularly driven precision nephrology.
Historically, clinicians relied on crude filtration markers like estimated GFR and urine albumin-creatinine ratio, which only decline, as you know, after irreversible nephron damage has already occurred. A multi-omics paradigm intercepts and predicts DKD through four specific pillars. So, let's start with single-cell analysis and what that taught us about DKD. It taught us about early tubular injury, something we didn't know about. So, traditional diagnostic view is that the glomerulus is the primary site of the of DKD diabetic injury.
However, single-cell RNA sequencing and single-nucleus sequencing have flipped this paradigm, proving that proximal tubular epithelial cells, or TECs, suffer metabolic stress and structural injury much earlier than once thought.
Then you get the maladaptive state, where again, with the help of single-cell transcriptomics, we know that there is epithelial-mesenchymal transition, and this shift into this adaptive uh state is is very, very bad for the kidney. And then you get the tubular damage signature. Again, with this technique, you can have a highly sensitive non-invasive early tubular injury signature way before microalbuminuria manifests or podocyte drop-off is detected.
And at the level of urine proteomics, I don't know if you know this, but more than 70% of urine proteins actually originate directly within the kidney. So you can think of it as a liquid biopsy. And so if you think of a proteomic panel like CDK273 classifier, which is the most clinically validated application of proteomics in kidney disease, this is a panel of 273 urinary peptides that can be used to predict progression years before the the decline in eGFR. And so there is now an early intervention window where with urine proteomics signature, you can detect microstructural changes and extracellular matrix remodeling up to 5 years before a patient starts showing physical drop in eGFR or a rise in standard albumin test.
And so when it comes to the the complement deep or damage, there is also an emerging longitudinal proteomics that maps an influx of urinary complement proteins and tubular interstitial biomarkers.
And so you can actually flag rapid eGFR decliners even if they're classified using your you know, your usual markers as as low risk.
And then when it comes to the metabolomic signature, and again, this is extremely helpful if you're considering putting your patient on SGLT2 inhibitors, like you know, Jardiance. As we know, these are amazingly effective renal protectors, but there is tremendous variation in in response. So, what have we learned from a multi-omics approach? We learned that there is, according to the thrifty fuel hypothesis, that SGLT2 inhibitors prompt the kidney to shift away from inefficient glucose oxidation towards energy-dense substrates. So, responders exhibit a signature increase in circulating ketone bodies, altered branched-chain amino acids, and specific TCA cycle intermediates.
And if you assess the mitochondrial health, again, you can see that true drug responders display a distinct drop in the markers of mitochondrial oxidative stress. And so, prior to even starting the disease, you can have pre-treatment stratification such that you know exactly which patient is going to respond instead of waiting for a few years to test drug efficacy based on whether, you know, structural decline is happening.
And then, of course, genetics the genomics layer is crucial because with the polygenic risk score, you can map the baseline genetic susceptibility.
And so, by aggregating these small risk SNPs, you can actually have a combined polygenic risk score that identifies individuals who are at high risk of developing DKD even if their other traditional biomarkers are telling you otherwise.
And so, by identifying the high-risk phenotype, these patients are genetically predisposed to rapid progression and end-stage kidney disease even if their hemoglobin A1C seemingly is is well controlled. And so, to put this all together, there is this synergistic multi-omics approach to DKD that allows you, starting with a PRS, the polygenic risk score, as a foundational baseline layer, you combine it with real-time dynamic urine proteomics such as the CKD273 273 panel that I told you about, and single-cell shedding data from the urine, and you create a dynamic risk stratification system to identify which diabetic patient requires early aggressive therapeutic blockade.
The third category of disease I'd like to mention, where there's been tremendous utility of multi-omics, is transplant nephrology.
Um so, this is truly fundamentally changing post-transplant surveillance.
Historically, as you know, clinicians relied on a surgeon serum creatinine to trigger an invasive biopsy. Because creatinine only rises after significant structural damage has occurred, this is not going to pick up, you know, subclinical rejection. And so, the the the the multi-omics approach in in in in transplant nephrology presents an an an immense opportunity for precision nephrology. So, let me give you examples of how this is happening practically. Let's start with the so-called donor-derived cell-free DNA or dd-cfDNA.
And I want you to think of it as your tissue injury barometer. So, when a transplanted kidney experiences cellular stress, necrosis, or apoptosis due to an immune attack, it sheds small fragments of double-stranded DNA into the recipient's bloodstream. And with the help of NGS, Uh, you can target single-nucleotide polymorphisms that allow the clinicians to precisely differentiate between the recipient's genetic background and the donor's genetic background. So, how is that put into action? Well, you've got a real-time kinetics, right? Because dd-cfDNA has a very short half-life of less than 180 minutes.
And so, it acts as a real-time molecular sensor of active allograft cell death.
And there's this magic 1% threshold.
If you see the fraction of that cc-fDNA exceeding 1%, that is a very strong predictor of acute rejection.
And what's amazing about this assay is it's incredibly powerful negative predictive value approaching 96%, meaning if it's negative, your patient is very unlikely to be suffering from an antibody-mediated rejection. And so, we can avoid having to do a biopsy to to test that.
The second layer of omics that's super exciting is the chemokine signature. So, while dd-cfDNA measures the physical tissue destruction, the urine chemokine map tells you about the active recruitment of immune cells straight into the graft tissue. And so, when the T cells infiltrate the kidney, the microenvironment responds by secreting specific signaling proteins. And so, you can actually very accurately assess whether your patient has reached immune quiescence by having next-generation immunoassays platforms that track these chemokines to confirm that state of immune quiescence, which helps safely taper the immunosuppressant medications without triggering subclinical immune spikes.
And then, I'd like to mention a word about the proteomics classifier, again something very exciting.
By moving beyond individual markers, we can really observe entire networks in action. And this structure and functional resolution helps distinguish between two primary types of rejection, antibody mediated rejection and T-cell mediated rejection.
And so, because single protein markers often often overlap between infection and rejection, advanced multi-marker panels utilize dozens of protein fragments simultaneously to screen out confounding factors. Just imagine the beauty of having a machine learning model that becomes your classifier that takes all these omics into account in order to give you a very very accurate prediction of what's going on with the health of the of the transplanted kidney. So, it overcomes individual weakness of specific omics layers and it gives you an algorithmic risk stratification.
Um the next disease category I'd like to talk about in the remaining time is the of course I have to mention something monogenic because that's near and dear to my heart and I chose to talk about polycystic kidney disease.
And again, I think it's really fascinating how much our understanding about this disease changed in light of a multi-omics approach.
As you know, historically we viewed polycystic kidney disease as a strictly structural genetic disorder characterized by fluid-filled cysts with with nothing else. But now we know that this is actually a metabolic disease as much as it is a cystic one. So, we know thanks to multi-omics that disease causing variants in PKD1 and PKD2, they actually trigger a cascade of metabolic reprogramming.
How does it work? So, first you get this metabolic shift, right? So, you get a defective, the so-called war almost identical to the Warburg effect that you see in cancer cells, where you see a fuel switch. So, the integrated transcriptomics and metabolomics um revealed a severe down-regulation of fatty acid oxidation and oxidative phosphorylation in cystic tissues.
And the way this is followed is by aerobic glycolysis on hyperdrive. So, to compensate for crippled lipid metabolism, cystic cells heavily favor inefficient aerobic glycolysis, rapidly consuming glucose to generate the biomass and energy required for uninhibited cell division.
And that leads to toxic metabolite accumulation. And and and and and this is secondary to a surge in acylcarnitines and glycolytic intermediates and altered amino acid signatures. And so, this abnormal microenvironment forces fluid secretion into the cyst lumen while provoking the surrounding tissue inflammation.
So, how did this all help us reach to where we are today with tolvaptan as a treatment. We've known for a while that cyclic AMP is crucial in the pathogenesis of polycystic kidney disease, but by integrating these multiomics, now we can pinpoint something amazing about how this is happening, right? So, now we know that by identifying genetic variants in the vasopressin V2 receptor or the V2R, that this actually acts as the primary gas pedal for the intracellular cyclic AMP accumulation in the collecting ducts. And so, this led to the development of tolvaptan. And tolvaptan is a selective V2R antagonist.
So, by blocking vasopressin, tolvaptan drops the intracellular cyclic AMP levels, successfully downregulating the downstream proliferative cascade, and significantly slowing total kidney volume expansion.
The The next disease category I'd like to talk about is a complement-mediated kidney disease, such as atypical hemolytic uremic syndrome and C3 glomerulopathy.
A really poster child for a poster child for what multi-omics has done to revolutionize our understanding of these diseases. So, it turns out, and again, it's a beautiful multi-omics layer, right? So, let's start with the genomics.
So, from genomics, we've learned of loss-of-function variants in genes such as CFH for complement factor H, CFI factor I, and CD46.
And without these functional brakes, the body cannot stop spontaneous alternative complement pathway to take over.
And then, the community also identified gain-of-function variants in C3 and CFB factor B.
And these render these proteins entirely resistant to normal inactivation.
And to top it all off, the community identified copy number variants, such as deletions in CFHR, factor H-related genes, which often drive the development of destructive autoantibodies against the patient's own factor H.
At the level of proteomics, now we can capture active activation signatures.
So, for example, fluid phase versus solid phase profiling. Proteomics tracks whether the destruction is localized to circulating blood or actively planting inside the kidney. And so, a high ratio plasma BA and PB fragments, which are the byproducts of factor B cleavage, they this is this flags severe alternative pathway activity. And then you have the membrane-associated attack complex or MAC. Um so, measuring soluble C5b9 uh is the serum uh or in the serum, rather, um uh or in its physical presence in the kidney biopsy, alerts clinicians to the final terminal phase of cellular lysis and vascular damage. And then, of course, you have the autoantibody detection. Uh and again, with the help of proteomics screen, you can capture something like C3 NEF or C3 nephritic factor autoantibodies, which physically bind to stabilize the C3 convertase, prolonging its half-life, causing relentless, uninhibited C3 consumption.
So, if we look at the pathway profiling of this process, um rather than viewing a complement as a single entity, we can use AI models um that split the cascade in three distinct actionable nodes. And you'll see in a moment how this is very actionable clinically. So, you have the up three uh sorry, upstream or the driver, that's uh where the alternative pathway amplification loop is getting out of whack.
Uh and then you have the midstream, uh where you see uh severe C3 deposition in the glomeruli. And then you have the downstream or the lytic engine, where uh you see uh um um the terminal cleavage of C5 uh into anaphylatoxin C5a and the membrane attack complex. So, how is that going to translate to therapy? Well, depending on which stage your patient is you actually can target your therapy.
For example, you give C5 inhibitors when you know that your patient has a high baseline CFH CFI risk variants coupled with elevated C SC5B9, which indicate dominant downstream vascular damage. And this has really revolutionized the way atypical aHUS is treated. Or you can give C3 inhibitors, which is a perfect match for patients with severe C3 G whose proteomic shows massive localized midstream C3 cleavage and tissue deposition, which effectively halts the central cascade engine before it causes permanent kidney injury. And finally, you give fact factor five factor B inhibitors to individuals whose baseline genomic and plasma BA BB proteomics reveal that the primary issue is in the overactive alternative pathway amplification loop. And again, you you really block the disease very much upstream.
So, let me summarize everything I said in this slide where I tried to be very practical. So, thank you very much. You told us so much about the value of multiomics. In my practice, can you give me a few very very practical examples of how I I can deploy multiomics in my practice as of today, not the future.
Let's start with genomics. Definitely consider genome sequencing if you have unexplained chronic kidney disease in a young adult. Definitely consider genome sequencing if you have someone with a kidney disease and a positive family history, especially in our population where consanguinity increases the likelihood of dealing with autosomal recessive kidney diseases. Definitely consider genome sequencing if you're dealing with an atypical or steroid resistant the syndrome.
How about proteomics and chemokines?
Well, you can actually use them as a liquid biopsy. So, if you're dealing with a patient with diabetic nephropathy with with diabetes, you actually can do very early diabetic nephropathy screening using the likes of CKD273 classifier. So, you actually can detect the the the the pathogenesis of the disease years before microalbuminuria.
You can deploy uh chemokine panels to monitor your patient with lupus nephritis because you actually will see the changes way before you see a drop in eGFR.
And when if you're dealing with a transplant, you can also use proteomics to monitor your patient for for fibrosis without even having to do a biopsy. You can deploy donor-derived cell-free DNA, as I said. You can use it for routine post-transplant rejection surveillance. You can use it to differentiate between rejection versus calcineurin inhibitor toxicity. And you can use it for post-biopsy monitoring. So, really this will be a radical departure from managing advanced organ failure to predict, simulate, and correct renal disease at the atomic level. And if I have a minute, I'd like to conclude with this future slide of where I think things are headed with precision nephrology. If you think what I told you is is futuristic, wait until you hear this. I do believe there will be a routine use of uh what's called digital twin. And so, the ultimate realization of personalized nephrology is the digital twin of a dynamic computational replica of the patient's unique kidney powered by real-time data streams and this will allow virtual modeling and even simulated clinical trials on your patient's digital twin.
There will be AI-driven pathology. This light microscopy that you've heard of, you've probably seen and if you're a pathologist, please don't don't take offense. This will disappear. It will be replaced by spatial single cell transcriptomics powered by AI. So the AI will actually give you an extremely accurate molecular pathology diagnosis without the intervention of a pathologist.
There will be gene therapy for kidney disorders. In fact, there will be genome editing therapies for kidney diseases.
These are being trialed as we speak and and these will involve in vivo editing.
So there will be cure for these monogenic diseases. There will be organoids.
So patient-specific kidney organoids that you can use for high throughput CRISPR screen. So your patient doesn't have to suffer from a trial and error.
You can try that on their organoids. And and I do believe eventually in a population genomic screen as the ultimate way of preventive nephrology. Just imagine a future where you're basically moving the starting line of kidney care from clinic all the way back to birth by having a, you know, universal baseline risk stratification at the time of birth such that you take, you know, very stratified care of individuals based on their genetic risk and the dynamic monitoring that would follow based on the multi-omics I mentioned. I hope I made it on time. I hope you enjoyed this and I look forward to interacting with you in the Q&A session. Thank you very much for your attention.
>> Thank you very much for that. What What a beautiful talk. We just listened to so so attractive and we couldn't even thanks for so keeping us until the end.
So very beautiful. I highly enjoy it.
And I just um I will ask our attendees, please if you have a question, just to throw it in the Q&A. And as I get the instruction from Amr that the question answer would be at the end of this session. So still you have time to put some question.
Actually, myself I have a couple of questions. So uh if you could just um Dr. Fawzan, be patient with us little bit. So at the end we'll we'll give the questions. Um so uh Amr, uh you will go for the next stuff?
>> Yes. Thanks Khalid and uh great presentation, Fawzan.
One of the most beautiful uh demonstrations that I have heard, I think, in the last 10 years. So and I feel now we are not on the 21st century, but uh we are knocking the door for the 22nd century as well. Thank you so much for this advancement uh in in proteomics and multiomics era.
So uh now uh we are going to uh give very brief uh description of our upcoming uh uh workshop. This will be a uh virtual workshop in August. So if Dr. Fawzan can stop sharing his screen, we are going to share the screen and uh to give you uh 2-minute uh instructions about our upcoming uh August 25th-26th uh virtual uh workshop.
Hello, everyone. Um the World Kidney Academy is very glad and honored uh to launch its first urinogenetic uh workshop for 2 days on August 25th and 26 along with the European Society of Pediatric Nephrology, the International Pediatric Nephrology Association, and the Saudi Society of Nephrology and Transplantation. This is the first of its kind uh course, which is will be completely virtual, 100% online masterclass focusing on understanding the basics and advanced knowledge in genetic testing and interpretation of uh genetic studies and trying to apply the basics of uh genetic testing into our clinical practice uh to improve our patient's outcome to precisely and individualized uh treat our patients. So, um very unique uh flagship uh program, and it's going to uh be launched on August 25-26 for 6 hours uh each day. So, 6 + 6 hours, so total of 12 hours, 100% uh virtual and interactive uh platform.
There will be a lot of demonstration, uh case-based discussion, and also clinical case scenarios and MCQs. It's accredited by the American Association of Continuing Medical Education. Again, uh four organization are gathering to give you this up-to-date information in genetic testing and genetic kidney disease. And uh it's not only that, but you will have also access to all of the scientific materials including all the lectures, the recorded lectures in the platform, MCQs, clinical case scenarios, and journal club in our smart platform for 3 months. So, the story doesn't end with the 2 days of workshop. Again, you will also have an access to a bonus scientific materials including articles, chapters in the books that will help you to understand and to apply the renal genetic uh disorders, and understand the genetic testing, and improve your clinical practice. Again, it's the first of its kind, 100% online for 2 days on August 25th and 26th. And uh we are gathering international experts, uh nephrologists, pediatric nephrologists, and geneticists uh from all over the world, as you can see here. Uh we have uh Professor uh Detlef from Belgium, uh Professor Franz Schaefer uh from Germany, and Professor Justine uh Bachita uh from France, Professor Robishrina from USA, along with our founders of this course, Professor Khaled uh Al Hassan, Professor uh Jamila Abdulaziz from um the Saudi Arabia, and Professor Hanan Abdulaziz, Dr. Mahmoud El Sherif, Dr. Muhammad Shalaby, and uh Professor Rasha Samir from Egypt. So, um very good diversity, international experts in the field are going to help you to understand uh the basics and advanced knowledge in genetic kidney disease. And we are targeting all nephrologists, pediatric nephrologists, pediatric and adult nephrology trainees, and general pediatricians as well.
So, if you are interested, please go ahead and register. Here is the QR code, you can scan it. And also, the application code is here, and you can take advantage on the early uh registration code uh early 10 to get 10% uh discount. So, try to use uh the promo code of early 10 that's going to expire soon.
If you have any questions or concerns, can either contact me or contact our project manager, Ms. Farida El Wakil.
Here is her WhatsApp number and her email address. The aim of this course is to make genetic testing easier, very straightforward, and also to help you to apply this knowledge into your clinical practice. So, when you get a patient with inherited kidney disease or possibility of positive genetic testing, you can understand how to interpret it and how to precisely and individually treat your patients to improve their outcome.
Okay, so with that we are going to move to our next speaker and our next speaker is Professor Nahla Tayema. Professor Nahla Tayema is associate professor of nephrology at Ain Shams University and she is going to give us application of genetic testing and genetic kidney disease in our daily nephrology practice. So, we'll see how this omics multi-omics knowledge will help us and she'll be very basic and Professor John Sayer >> is >> Professor Khaled are going to help to give take home message of this case based discussions.
So, without further ado, the microphone is is yours, Professor Nahla.
>> Good evening, everyone.
I'm very honored and thankful for you, Professor Dr. Amr, for inviting me to share in this great webinar.
And I'm a excited to share with you these three real cases.
>> [snorts] >> Um Uh shall I start?
>> Yes, please.
Case one.
You see the screen, right?
Dr. Khalid, can you see the screen?
Dr. Fawzan?
>> Yes, yes, very clear screen.
>> Just go ahead, Nahla, please.
>> Yes, I think you just need to change it to presentation mode, so you can easily flip through the slides.
>> This is in a slideshow mode. Go ahead, Nahla.
>> My first case is How can I open it? I can't.
>> You can see it on the screen. It's already shared in the screen.
>> Can you make it just presentation mode, full screen?
If you can't, it should be fine. Just flip the flip the slide to the second slide.
>> Yes.
Okay.
Uh my first case is for 22-year-old female patient with long history of hypocalcemia, fits, and chronic kidney disease since since she was 2 years old.
And, she presented to our clinic by end-stage kidney disease at 2022.
She was on hemodialysis and uh, presented to us seeking renal transplantation uh, in August 2024.
Her donor was her mom, 45, medicated free.
Uh, she has a positive family history of consanguinity and a positive family history of kidney disease.
And this was the family pedigree uh, to uh, third generation and they chose her mom and dad, they were cousins.
Uh, she has four five sisters.
Uh, the first one is a recipient and presented to us with end-stage kidney disease and she has four more sisters.
Uh, three of them also has chronic kidney disease and hypocalcemia and hypomagnesemia.
Uh, the next step we started with uh, pelvic abdominal ultrasound. We did all investigations and significant was metabolic profile in urine that shows hypocalcemia.
Uh, hypo oxalate level was also low and pelvic abdominal ultrasound showed medullary nephrocalcinosis.
Uh, our next step uh, you know, our important issue is to exclude primary hyperoxaluria which is recurrent post renal transplant after kidney transplantation and may need combined liver and kidney so so we proceeded for genetic test.
We started with the Sanger sequencing for AGXT gene that denotes for uh, primary hyperoxaluria type one and it shows no mutation in this gene but they recommend to do whole exome sequencing to exclude other causes of nephrocalcinosis.
And so we proceeded for a whole exome sequencing and we got the result with homozygous pathogenic variant detected in coding 16 gene and homozygous variant of conflicting interpretation pathogenicity in AGXT gene. Um so we made MDT with geneticist to to to make a decision in this case whether to proceed for renal transplantation only or combined liver and kidney transplantation to protect the graft from recurrence after transplantation. And we decided that after consultation of geneticist, we excluded AGXT mutation that was variant of uncertain significance and she underwent renal transplantation only which till now has any successful transplantation with normal kidney function test and baseline creatinine 1.1 with no evidence of recurrence.
Our second case is the four 12-years-old boy.
His condition is started since he was 9-years-old with nocturnal enuresis, nephrotic syndrome, proteinuria but normal serum creatinine.
Actually he has um He presented to transplant clinic as someone advised him to to start preparation for renal transplantation.
Although normal serum creatinine we made full examination and investigation and history. There was no negative consanguinity, no family history of renal disease except for his younger brother who has the same condition also nephrotic syndrome with normal serum creatinine.
Actually we We with genetic test for this young boy. We examined one of them with whole exam sequencing which and the result revealed CoQ8B variant mutation.
And it was homozygous and this gene mutation encodes for CoQ coenzyme CoQ10 deficiency which is mitochondrial essential for mediates electron transfer necessary for oxidative phosphorylation and ATP production.
This condition is associated with steroid resistant nephrotic syndrome.
And according to this result, we started to treat him as CoQ10 deficient steroid resistant nephrotic syndrome and started with replacement of CoQ10. This condition needs actually high doses of CoQ10 supplementation.
And rarely respond to low doses and this was was the scenario with us and we started with 20 mg per kg per day. Then gives partial improvement then we raise the dose to 40 mg per kg per day. And he showed the partial improvement or market improvement from 5 g proteinuria to 1 g almost with market improvement of symptoms.
He didn't receive any immune suppressants and gets normal growth for both young boys.
Our third case is 420 year 28 years old male patient hypertensive epileptic presented with end-stage kidney disease diagnosed with rhabdomyolysis and acute kidney injury then progressed to end-stage kidney disease.
He presented to us for renal transplantation uh from his brother, 23 years old, medically free.
Uh there was no family history of consanguinity.
Uh they have a family history of renal disease in their sister uh who passed away on dialysis at the age of 21.
Uh we started preparation for renal transplantation, uh then sent for a genetic test to detect the etiology in this family uh and to protect the donor if there is a genetic disease. Uh the result reveals RIR1 uh ryanodine receptor 1 mutation. Uh this gene encodes for malignant hyperthermia uh and abnormal calcium uptake by the muscle.
And after anesthesia consultation for these two donor and recipient, these two brothers, uh it was a risky operation uh because we don't have dantrolene, which is the antidote for this lethal lethal condition, uh malignant hyperthermia, and the operation was postponed.
Although it is variant of uncertain significance, but it's a lethal condition, so we we considered this result except yani although it's variant of uncertain significance, but we uh took it in consideration and postponed the operation.
Uh these were three renal cases, and thank you.
>> Thank you so much, uh Professor Nala.
The floor is yours, uh Professor John Seer and Professor Khaled, to discuss the importance of this genetic testing in these uh three various cases.
>> Yeah, um maybe I'll start. So um thanks very much for the presentations and thanks to Fozan for the uh amazing talk. I think Fozan qualifies as a nephrologist now as well. So um he can give some insight, but um I guess I'll start with the first case.
Um and I would like you to kind of reconsider, you know, whether Sanger sequencing for this single is even worth it and whether, you know, you could consider whole exome or whole genome as first line for someone that you've got um you know, kidney failure presenting at such an early age.
And my other uh question regarding that case is, you know, maybe some deeper phenotyping of that patient in terms of magnesium levels and that might have actually given you, you know, a better diagnostic hunch than um primary hyperoxaluria. I know why you wanted to exclude it, but maybe you'd you'd have come to a, you know, a clearer diagnosis earlier with more phenotypic information.
Any comments about that?
>> Natela, is yours.
Hm.
Uh as regarding magnesium level, she had history of hypermagnesemia since childhood. Um and uh recurrent renal stones. Uh we started uh actually this case presented to us with uh AGXT gene uh Sanger sequencing, but uh our practice uh we didn't start with the Sanger sequencing. We started with whole exome sequencing to exclude uh all causes of um nephrocalcinosis uh to save time and money.
>> Yeah, that makes sense. So you you inherited the patient with already the the Sanger diagnosis. Yeah, okay.
Yeah.
Okay.
>> I I I totally agree with you.
Professor Jamila, I think of us here, she's the first probably published case series about hypomagnesemia, nephro- hypercal- hypercalciuria, nephrocalcinosis with very good number of patients. And unfortunately, we do have in King Faisal probably couples of those have been transplanted.
But once it's confirmed by genetic testing that it is um it's oxalosis or I don't know.
>> And also watch, please, for cardiovascular calcification because magnesium is a major inhibitor of cardiovascular calcification. Uh so this patient uh probably would have a very aggressive uh calcification on their vascular system.
>> Yeah.
>> Yeah.
>> Yeah.
I I guess this there is a word of caution in in families that are consanguineous that you don't get distracted by a single diagnosis and that potentially there's two or three genetic diagnoses in in any family if there's high levels of consanguinity. So, I would you know, that's another reason, I guess, to go for a very broad approach to start with, you know, with exome or genome first approach.
>> Very nice. Let's move to the second case, the QA.
Uh the fish >> Yeah.
So, my comments here was yeah, this this is shows the benefit of an omics approach, doesn't it? That you find a treatment that actually will work in a in a precise way for for a child uh with nephrotic syndrome and prevents um immunosuppressants. So, yeah, I don't think there's, you know, any diet that that the you know, the diagnostics helped and helped change the life of the patient, but um I guess uh um the other learning point would be to, you know, see how how you could adapt that use that information for wider screening of other family members at risk and, you know, you know, newborns uh for example, do you newborn screening on on wider family members. So, can you comment on cascade screening of other siblings and cousins and whoever was at risk in the family?
>> Yes. Sorry, I didn't get the the question.
>> I was just saying did you find any other affected members in the family following cascade testing?
>> No, his brother only.
His young brother only and they have the same treatment and improved.
>> Okay. Okay.
>> And I think also this argue, I mean, many physician would say genetic testing is expensive, it's not available in the developing countries, resource-limited settings. We have to send it out to different uh countries, take time.
But nothing is uh more precious and priceless than the patient's life.
>> Yeah.
>> [clears throat] >> I mean I mean our patients chronic kidney diseases, they are getting sometimes unnecessarily tested I think unnecessarily uh potentially harmful medication that are also expensive. So, I think the overall uh benefit outweigh the risk or the cost.
>> And then just to comment on the third case, I think this case remains unsolved, doesn't it? You've got um two people with unexplained kidney failure.
Um you found a VUS that may or may not be significant, uh but I think this points to the fact that whatever tests you've done have been inconclusive in terms of the kidney disease, so you need to think about, you know, if an exome was done, can you do a genome, can you do a transcriptomic approach, can you you know, involve multiomics, can you re-phenotype the patients, you know, in different ways to get clues? So, I think this VUS, in my mind, yeah, is a caution for the anesthetic, but is not related to the kidney disease.
And so, you should never stop looking, I guess.
>> I believe Nahla is a fan of a genetic testing, so she didn't focus on the downside, she focused on the upside that she saved the vision to life by, you know, finding different diagnosis.
>> Yeah.
>> Very nice. Professor Khaled, um, do you like to close, uh, to give closing remarks for our, uh, fantastic webinar?
>> Yeah, absolutely. I probably, uh, I would be interested to look to the Q&A, uh, for our attendees. So, uh, before we start with that, I, um, I will go back to the talk of, uh, of my friend, uh, Fawzan.
Uh, I was so interested by it, and the good thing, um, the last slide when he talked about, um, uh, transforming all of this in the clinical practice, and actually we do have in King Faisal, we do have, uh, donor driven, uh, free cell DNA, and what we actually give it attractive name, uh, as a project, we call it liquid biopsy.
So, instead of doing the renal biopsy, this is, you call it a liquid biopsy, and to tell you the truth, it's still the standardizing of it, and the cutting the number, and, um, false positive, like inflammation, infections, can give you the positive thing. So, probably we need sometimes on that. Is that right, Fouzan?
>> I I was careful Thank you for raising this issue. I was careful in framing it right. I talked about its incredibly powerful negative predictive value.
So, I didn't spend time talking about the downside of specificity issues, which will keep improving because remember this is only a one layer of omics. You're simply looking at DNA. But if if I'm sure you you paid attention to the rest of it. As I said, you know, you actually can look at a proteomic signature and a transcriptomic signature, and that can dramatically improve the the performance, you know, the accuracy of the test. So, I guess the take-home message of why I didn't want to give a talk on just genomics, I wanted people to start thinking of all these layers. It may sound a little overwhelming to the audience who may not be very familiar, but you know, there's no escaping. This is This is happening, and this will be standard of care. So, you better, you know, get on with it before you're left out. And my take-home message is it's never going to be one layer. It's always going to be a combination in order to improve the accuracy of whatever I say. Think in one slide I made that take-home message. You know, no one layer is sufficient typically. You need all these layers combined. Each layer has its own weaknesses, and thank you for raising one weakness of just relying on DNA for you know, for for for monitoring for graft for donor kidney rejection.
>> Thank you very much. And I I I I completely agree with John. I I felt actually I don't know what this So, probably you did some mistake.
>> Thanks. I had a good teacher in you, right? So, thank you.
>> [laughter] >> And John, you know, collaborating with both of you. So, thank you. You did a good job.
>> [laughter] >> Uh so, the second question for Zanne, we uh we used to request a test, for example, whole exam or whole genome tests. But now, if we if I'm I'm I'm interested to do all the all the layers, is there is way to do this tests? Is it Is it especially specific test can be requested? Special name can be requested? And what do you think the cost of that?
>> So, that's actually what we're developing in the lab. Uh very, very soon, inshallah, within uh the next uh few months, you're going to hear um about the use of long read sequencing in order to provide a multi-omic uh test.
So, you will get very, very high-quality whole genome sequence. And you know, that's another conversation why long read is is different. But the beauty of long read is that you get for free the epigenome layer. And if you throw the RNA in there, you get actually the genome, transcriptome, and epigenome in one go. And uh you know, there's been tremendous uh progress in the uh automation of doing proteomic analysis. Uh you know, there's been uh a major development where Illumina acquired SomaLogic. So, now it's uh much, much easier to do, for example, uh proteomic assay on Illumina.
You can also use uh Olink on Illumina and other platforms. So, a multi-omic test is actually already there. So, without mentioning names, I'm not advertising, there is actually a multi-omic test you can order on a filter paper that does, you know, the the genome, uh the transcriptome, and if there is anything to suggest the potential of a metabolomic uh perturbation, you actually do get the metabolome as well. So, that's already happening and it's only the beginning.
This will become very much routine in the near future.
>> Excellent. So, um another one question that's lead me to another question. We used to say this is an inherent disease or non-inherent disease and this is depending on genomics more than probably other types of the layers. You correct me if I'm I'm wrong. And the classical example for example is the IGA. Is there's no classical inheritance that we know of?
But, it's it's running the families.
It's running the communities. It's well known in Asian. To tell you the truth, initially I thought it's not much in Saudi Arabia until our colleague in transplant they going to going to publish their reports. They found more than half of the donors they do have this. So, do you think inheritance can be in other different layers?
>> Absolutely. So, I'm I'm glad you brought it up. I tried to again, there was so much to cram in 30 minutes. So, I apologize for not being clear.
This is a classical example of a multi-factorial disorder. So, you have genetic predisposition and when I talk about predisposition, I'm not talking about genetic causation. It's different from polycystic kidney disease, right? So, if you get a pathogenic PKD1 or PKD2 variant, you will develop you know, adult onset polycystic kidney disease if you live long enough, right? That's not the case with genetic predisposition. It increases your risk, but you do need as the name implies multi-factorial. You need the right setup. You need, you know, the right exposure. So, it's it's a combination of genes and environment.
So, for sure you're going to find familial clustering, right? Because they do share that genetic predisposition.
But, it's not 1 1 2. It's far more nuanced than that.
It's almost like uh like diabetes, right? There isn't a gene for diabetes.
Of course, there's a monogenic form of diabetes that's very rare, but the common, you know, a garden variety diabetes that you see in clinic, this is uh very rarely monogenic. It's almost always polygenic. And that's the beauty of polygenic risk score I talked about.
You actually, at the time of birth, you know that the this person is in the top centile for risk of diabetes or in the bottom centile uh in terms of risk for diabetes. And that makes big, big difference in the way, you know, you individualize uh your approach to these individuals.
>> Yeah, thank you very much. Um uh from Q&A, we there is two questions, actually. One by Wesley, and he say, "Thanks. Thank you for fantastic lecture." I totally agree with him with that. And one of the worries I have is that uh with and whole whole genome sequencing is very hard to interpret.
Uh there is often a lot of possible pathogenic variant, and to find the truly pathogenic variant can be very problematic at the clinical levels. Your comments, Professor Fouzan.
>> Um several things to offer. Again, time is limited. A um interpretation will become uh better and better as we have more and more genomes. So, for example, you know, this variant of uncertain significance that uh significance that Dr. Nehela talked about, if if just imagine if we were to have hundreds of thousands of Egyptian patients uh in a data bank, this variant could have been easily reclassified as either disease causing or non-disease causing, right? as we sequence more individuals, that problem will become less and less uh uh uh uh uh of an issue. Second, um you know, machine learning is uh has improved a lot and it's really helping us narrow down the list of variants when we try to interpret a genome and write a report for the clinician. Third, you really don't have fear of clinician.
Don't worry about it. That's not your problem. It's the problem of the lab director. It's their job to filter the variants and only give you something meaningful. And lastly, in terms of your worry about identifying too many pathogenic variants, it's almost like saying I'm not going to do MRI for my patient because I can't identify so many bad things and everybody's going to tell you this is crazy. If you think MRI is indicated, you will do the MRI and you will be prepared as a clinician to deal with something you didn't expect. Why is genetics any different? You do genome sequencing on individual. You prepare that individual that, "Hey, I may identify something unrelated to your disease um but I will only return it to you if it's actionable." And that's the recommendation of the ACMG, the American College of Medical Genetics and Genomics, that we don't just give you terrible news. "Oh, by the way, you're going to die tomorrow. There's nothing we're going to do about it." We never do that in genetics. We will tell you, "Hey, you've got this. It could predispose you to cancer but guess what?
There's something can do about it." Or it could predispose you to an arrhythmia uh but there's something we can do about it. So there's actually a very strict list of disorders we're allowed ethically to return to the uh to the patient as secondary findings. Now, when it comes to disease-causing variants related to the patient, obviously we will be returning anything that could be relevant to the patient's pathology and mean that's why after all you, the clinician, asked me and the lab to do genome interpretation because you do want to have a molecular diagnosis for your patient.
>> Wonderful. Very clear. Uh just forgive me for this question. Is uh pharmacogenomics part of the omics multi-layer omics?
>> It's part of genomics, that's for sure.
Um the the thing is um when you and that's another reason why you shouldn't hesitate from doing genomics. You always get uh you know freebies when you do genomics. So you do the genomics for for the patient because of uh you know kidney disease and you identify, oh my gosh, this patient is high risk for malignant hyperthermia. I could save his life uh from you know doing the wrong anesthesia, for example, right? Another thing that is a freebie is a pharmacogenomic profile. If you do the genome, you actually get for free the pharmacogenomic profile of your patient and that is his or hers for life. And so before you prescribe anything, you just go and and and check the profile and >> As as map.
>> the patient. In fact, as you know at King Faisal, it's already um you get an alert. So before you prescribe, you get an alert that oh, your patient is incompatible with this drug. And I do hope this becomes very routine across the hospitals.
>> Yeah, yeah, it's honestly I second what you said. Honestly, it's help us especially for using tacrolimus in transplant patient. A huge variation between the patient uh uh in in metabolizing the FK. It's it's a wonderful uh discussion in addition wonderful talk. So the last uh probably the question is um to Dr. Naela. And uh Muhammad Mansour, he's curious about your uh third case. Was the surgery done later on? Did the malignant hypertension eventually happen?
Dr. Naela.
>> No, we didn't do the surgery as the antidote for this condition is not available.
And uh he's liable to uh malignant hyperthermia which is a lethal condition.
>> Excellent. Thank you very much.
Actually, uh we're a little bit over uh time little bit and I we promise for them that we not take longer but sorry Professor for them because he's little bit sleep earlier than the other soldiers.
>> [laughter] >> Thank you very much all thanks John thanks Nela thanks Amosa thanks everyone and thanks our colleagues that in these four to us very nice and delighting about about us about something very important probably it's going to be the few definitely it's of the future of the medicine.
And again we'll announce the the workshop that's going to happen to August don't miss it.
We going to have giant speakers and well-known speakers so prepare for it and please register. So thank you very much and good night and thank you thank you very much everyone. Thank you see you. Bye.
>> Thank you.
>> Mhm.
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