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June 23, 2019

Clinical Research Update:

I want to thank all of you for your extraordinary support of Schimke Immuno-Osseous Dysplasia (SIOD) research at Stanford University for the last two-and-a-half years.  We are extremely grateful for your entrusting us with getting this novel research program off the ground. This program, to the best of our knowledge, is the only of its kind focused on identifying disease mechanisms in SIOD and translating them into patient therapies.  

As you know, SIOD is due to mutations (changes in the DNA code) for the SMARACAL1 gene. These changes impair the function of the SMARCAL1 protein, which is essential for the cell to make a complete copy of its chromosome DNA before it divides into two daughter cells. Our ultimate goal is to develop therapies that bypass the problem with SMARCAL1 protein function that would benefit patients regardless of whether they have received or are able to receive a hematopoietic stem cell transplant (HSCT) and/or kidney transplant and the particular type(s) of SMARCAL1 gene mutations they have inherited.

As you know well, SIOD results in a number of distinct clinical problems including 1) decreased function of the T-cell immune system; 2) impaired the production of white blood cells by the bone marrow; 3) decreased kidney function resulting in the spilling of protein in the urine and, ultimately, kidney failure; 4) limited function of the growth plate of the bones involved in the growth of the skeleton in maintaining healthy joints, such as those of the hip; and 5) abnormal blood vessel function resulting in premature atherosclerosis and complications such as recurrent migraine headaches.

Currently, we feel that one major translational research priority is to define how impaired/absent SMARCAL1 protein function results in these diverse multi-organ problems characteristic of SIOD. Finding a common mechanism might allow us to develop a common therapy that bypasses these problems for all of the affected organ systems.  Our second major translational research priority is to identify how HSCT and kidney transplantation for SIOD can be performed more safely and effectively using recent technical advances for these procedures. A third research priority is to explore whether drug therapies that are far along in development or already FDA approved for other diseases (also called “repurposing”) could be used to treat some important clinical issues with SIOD patients.

HSCT, Bone Marrow Function, and the Telomere Biology of SIOD

On February 5 of this year, Kruz underwent an HSCT using blood stem cells obtained from Jessica. To the best of our knowledge, this is only the eighth SIOD patient who has undergone HSCT in the world of which four cases has been published in the medical literature. Of the previous seven cases, only one patient has had a successful outcome with HSCT. He received his HSCT at 7 years of age from an HLA-matched brother followed by a kidney transplant from his father; he is now 27 years old and doing well. Thanks to your support we were able to have him and his parents visit the research lab at Stanford, go over his medical history in detail, and obtain blood samples for research. This visit was very helpful in verifying that HSCT for SIOD leads to the normal function of the immune system following the transplant.  

We would also like to emphasize how your support of SIOD research was critically important for designing Kruz’s HSCT conditioning regimen, which makes room in the bone marrow for the donor hematopoietic stem cells to settle and carry out their function. Using your funds, Dr. Elizabeth Lippner in the lab discovered that Kruz, Paizlee, and several other SIOD patients have white blood cells with telomeres at the ends of their chromosomes that are much shorter than normal. Telomeres are special caps made of DNA and protein that are at the ends of all of the DNA chromosomes of the cell to prevent them from being damaged by normal cellular wear-and-tear. Previous work by other scientists using tissue culture cells that were manipulated to have decreased SMARCAL1 protein suggested that SMARCAL1 was involved in both the normal replication of both the main chromosome DNA as well as the telomere ends. Elizabeth was the first to show that the telomere length for blood cells from SIOD patients is very short.

This discovery changed how Dr. Alice Bertaina, decided to prepare Kruz for this HSCT:  She and others in the HSCT field know that patients who have short telomeres because of rare inherited genetic diseases other than SIOD are highly susceptible to bone marrow toxicity following standard HSCT conditioning regimens. To avoid this problem, Kruz received a combination of a low dose of radiation and special drugs for the preparation, an approach that has been used for other patients with telomere length defects. As you know, he did extremely well after the transplant with rapid engraftment of his HSCs and normalization of many of his white blood cell counts. His T cells are also, as expected, gradually increasing indicating that the HSCT is on track for correcting his immune problem. This approach will also be used for Paizlee as part of her upcoming HSCT.    

The discovery of short telomeres also provides an important insight as to why SIOD patients have reduced the production of red and white blood cells by their bone marrow since this is also a feature of genetic diseases other than SIOD that result in short telomeres.  In Kruz’s case, his bone marrow biopsy performed prior to the transplant confirmed that his bone marrow function was markedly reduced and, in fact, was more impaired than we predicted based on his white cell counts in the blood. As you know, Paizlee also has some signs of decreased bone marrow function. Based on Kruz’s response to HSCT, this decreased bone marrow function appears to normalize relatively quickly after the procedure. This linkage between short telomeres and reduced bone marrow function is also important because it raises the possibility that we might be able to treat it in SIOD using drugs that have been helpful for this problem in other telomere deficiency diseases. This would be particularly important for SIOD patients who for various reasons are not candidates for HSCT therapy.

As you know, our plan is for Kruz to also receive a kidney transplant from Jessica once his kidney transplant surgeons feel that he is well-nourished enough to have a speedy recovery after the procedure. We look forward to Paizlee undergoing the same approach of an initial HSCT followed by a renal transplant in which Kyle will be the donor for both. We appreciate how long a road it has been for your family to get to these important steps, and thank all of you for your perseverance and trust in the many doctors and health professionals who are involved in making this happen.

Defining How SMARCAL1 Deficiency Causes SIOD and Developing Clinical Intervention Strategies

SIOD is a complex and poorly understood the disease, and your funding has allowed the lab to jumpstart progress in identifying the underlying mechanisms of how reduced/absent SMARCAL1 protein has such a major adverse impact on diverse processes of the body. Although the discovery that the white blood cells of SIOD patients have shortened telomeres explains their reduced bone marrow function, short telomeres do not appear to explain SIOD’s T-cell immunodeficiency, decreased kidney function, blood vessel problems, and short stature: None of these other medical problems are commonly seen in patients who have genetic disorders that result in short telomeres but have normal SMARCAL1 gene and protein function.   

Thanks to your support, the lab was able to form a research team in Dr. Lippner was joined by  another post-doctoral fellow (Rebecca Saenz, M.D., Ph.D.), a senior research scientist (Girija Dhamdhere, Ph.D.), and a senior research technician (Vasavi Ramachandran, B.S.) to shed light on this mystery. Your funds have also been important for leveraging support for these individuals from other sources, such as grants from the National Institutes of Health and the Stanford Maternal and Child Health Research Institute so that they could focus on researching SIOD. You were recently able to make an additional gift to the Lucile Packard Foundation for Children’s Health for SIOD research and as a result, we will be hiring two new researchers to add to the SIOD team. The first of these will be Dr. Elodie Elkaim, M.D., who trained in one of the premier human immunology programs in the world (Hospital Neckers, Paris, France) under the direction of Dr. Cavazzana and who will be starting in August. We are also seeking another post-doctoral or research scientist to add to the team in order to keep building on our research momentum.

We believe that all of the major clinical problems observed in SIOD ultimately relate to the known role of the SMARCAL1 protein in normal DNA replication in preparation for cell division. Normally, a chromosome strand of DNA replicates in hundreds of little pieces simultaneously that are then stitched together so that there is an intact copy of the chromosome. We hypothesize that when the level of SMARCAL1 protein in the cell is markedly reduced or absent that certain regions (“pieces”) of the chromosomes are no longer effectively duplicated. We expect that this local “stalling” of replication leads to permanent changes in these pieces such that after they are stitched together the genes located in them have reduced function. Genes normally function by producing copies of their DNA sequence called messenger RNAs (mRNAs) that carry the information for the gene to be made into a protein, which actually carries out the gene function. In SIOD we believe that there are a set of genes with reduced mRNA and protein production that ultimately can be traced back to their location in pieces of the chromosome that were difficult to replicate and were structurally altered as a result. For example, we predict that decreased mRNA and protein for these genes in difficult to replicate pieces will account for SIOD’s T-cell dysfunction, kidney disease, blood vessel function abnormalities, and short stature/hip dysplasia.

To test these ideas, we are starting with studies of T cells in SIOD as these are readily obtained from blood samples. The team is determining the level of all of the mRNAs of T cells from Kruz and Paizlee and other SIOD patients compared to unaffected individuals.  Your funding is helping with the costs of our team’s time in isolating the T cells, the chemicals and procedures needed to doing the mRNA sequencing, which is called RNA-Seq and using costs of carrying out the sequencing using special machines at Stanford.

At the same time, we are collaborating with a gifted young scientist, Dr. Maya Kasowski, who is in the Stanford School of Medicine, Department of Pathology, who will determine if the structure of the chromosomes in SIOD T cells differs from those of healthy controls. These studies will use a technique called ATAC-Seq that was invented at Stanford and for which Dr. Kasowski is an expert. She will be looking for areas of the chromosomes that have a structure that makes it hard for the genes they contain to function normally. We anticipate the genes we find with reduced function in the RNA-Seq will be found in the regions that Dr. Kasowski identifies as having an abnormal structure.  

One major problem in SIOD research is that it is difficult to get enough cells from patients to be able to do large scale studies that are typically required for drug development. In an effort to move things faster, we are taking a number of approaches to determine if we can use cells that can be grown in large numbers in the lab for studies of disease mechanism and, ultimately, drug development. For example, Rebecca Saenz in the laboratory has used a technique for gene editing called CRISPR/Cas9 that allows us to take a normal T cell and disrupt its SMARCAL1 gene to determine how this affects the function of the T cell. This approach should improve our understanding of the normal function of SMARCAL1 and how reduced SMARCAL1 function might be overcome by drugs. Similarly, we are using a type of B lymphocyte found in the blood to make a special cell line that can be grown to very large numbers indefinitely. We are making these cell lines from Kruz, Paizlee, and other SIOD patients as well as healthy controls and will see if these can be used for studies of disease mechanism and drug development. Finally, we are making induced pluripotent stem cells (iPSCs) using blood cells from Paizlee and other SIOD patients as well as healthy controls. These iPSCs can be used to make cells that closely resemble T cells, kidney cells, blood vessel cells, and many other tissues. Again, the advantage of having the iPSC system is that we will be able to study SIOD disease mechanisms in many types of tissue and how they can be overcome much more practical than if we were to depend on actually obtaining these tissues from patients, such as from surgical biopsies

We have also been fortunate to have received advice on our research program from a number of Stanford scientists, including Drs. Steven Artandi, Karlene Cimprich, and Stephen Montgomery, who has been generous in providing their time and expertise for free. We plan to include some of these scientists as well as Dr. Kasowski in applying for grant support for joint research projects and programs to substantially increase SIOD translational research activity.     

We are confident that we will be able to submit most of this work for publication by the end of this year, and that this work along with the publication of the short telomere studies will put us in a strong position to apply for funding from the NIH and other granting agencies. In addition, pinpointing exactly which proteins are affected in SIOD may lead to potential therapeutic approaches to overcome the effects of these protein deficiencies.

Thank You for Putting Your Faith in Us

There are so many reasons why the lab owes the success of the exciting research we are conducting for you. Incredibly, you have given more than $1.3 million towards SIOD research. In addition, because of your extraordinary efforts to raise awareness about SIOD, we have heard from families not only in the United States (Oregon, San Diego, Texas, New Jersey, Michigan, and Nebraska) but also in France, Germany, Iran, and China. And it is purely the existence of the Kruzn for Kure Foundation that so many patient families have connected with us. I cannot overstate the impact your advocacy has made not only for our research but for the patient community in general. With such a rare disease it is so hard to get people connected and involved. As you know, we are updating a clinical and research registry of all SIOD patients that was originally started by Dr. Boerkoel. We believe that this registry is of major importance in establishing improved outcomes of patients with SIOD and are grateful for your support of this critical activity.  

I also want to especially thank all of the amazing donors in Muscle Shoals and elsewhere who support the Kruzn for a Kure Foundation. Jessica and Kyle, I’m awed by your commitment, tenacity, and strength in getting this all together! It’s all because you asked us what is necessary to find a way to help these kids and then went out and built the Foundation from scratch. I am immensely grateful that you have put your faith in me and my lab and Dr. Bertaina to do this important work.

Best regards,

David B. Lewis, MD   Professor of Pediatrics, Department of Pediatrics  Chief, Division of Allergy, Immunology, and Rheumatology  Member of the Program in Immunology and the Institute for Immunology, Transplantation, and Infectious Disease  Stanford University School of Medicine

David B. Lewis, MD

Professor of Pediatrics, Department of Pediatrics

Chief, Division of Allergy, Immunology, and Rheumatology

Member of the Program in Immunology and the Institute for Immunology, Transplantation, and Infectious Disease

Stanford University School of Medicine