Association of rare variants in genes of immune regulation with pediatric autoimmune CNS disease

October 9, 2022

Join us to hear from Dr. Saba Jafarpour of Children’s Hospital Los Angeles about the latest findings in her research of rare neuroimmune disorders.


[00:00:05] Dr. Carlos A. Pardo: Following the trend, it is a great pleasure to introduce another colleague who is the new generation of pediatric neurologists. This is Dr. Jafarpour who is at the Children’s Center here in LA working with Dr. Jonathan Santoro. So, yesterday we mentioned briefly genetics, and this is a very fascinating topic for the future because we are basically going to focus in one area that is going to be the future of neuroimmunology, what we are doing to understand the genetic component in some of the immunological disorders. So, Dr. Saba, thank you so much for taking the time for coming to the meeting and illustrating about genetics.

[00:01:12] Dr. Saba Jafarpour: Thank you very much. Good afternoon, everyone. I’m Saba Jafarpour, one of the neurology residents at Children’s Hospital Los Angeles. I’m going to talk about our research which is in regard to association of rare variants in genes of immune regulation with pediatric autoimmune central nervous system diseases. I’ve listed some of our disclosures here mainly related to Dr. Santora. So, autoimmune central nervous system disorders are a complex group of disorders characterized by immune mediated inflammation in the brain and spinal cord. Despite the differences in presentations and symptoms, there is a significant degree of overlap between these conditions. And we think that they are likely sharing similarities in terms of the underlying mechanisms and the molecular mechanisms that are causing these diseases. And therefore, the genetic underpinning of these disorders should have overlapping similarities.

[00:02:25] But there is not much known in regard to the genetic underpinning of these disorders. Our susceptibility to different diseases is influenced by the unique differences in our DNA and in our genes, and these differences could make us more susceptible or at decreased risk for different conditions. So, that’s why it’s important to understand the genetic differences and the variations that could contribute to increased risk of autoimmune central nervous system disorders. Researchers have been trying to identify the genetic basis of autoimmune CNS disorders, and among these conditions, multiple sclerosis has been most widely investigated. Mainly the common genetic variants or the polymorphisms where the focus of the studies through genome wide association studies.

[00:03:31] However, in the recent years there has been an increasing degree of interest in terms of identifying the rare variants that could also contribute to risk of these diseases. So, as you can see in this figure, the common variants that are identified through genome wide association studies can have moderate or little effect in terms of increasing the risk, but the rare variants can have moderate or strong effects in terms of their contribution to the risk. The rare variants are identified through next generation sequencing techniques such as examining whole genome sequencing. And in comparison, to genome wide association studies, a smaller sample size could be used to identify using the next generation sequencing.

[00:04:32] There is sparsity of data in general and particularly in pediatric population regarding association of rare variants of genes of immune regulation in pediatric and also in adult autoimmune and inflammatory central nervous system disorders. So, in our study we try to answer this question and explore this area in this topic. One of the implications of identifying the genetic variants is that it could actually point us towards the underlying molecular mechanisms, and it could actually shed light in different personalized or targeted treatments that could be used in these conditions. So, we audited the patients who presented to our pediatric neuro immunology and demyelinating disorders clinic at Children’s Hospital of Los Angeles in a 2.5-year period between July of 2019 and December 2021. And we identified 54 patients with pediatric onset autoimmune CNS disorders in whom genetic studies were available.

[00:05:52] The mean age was 13.4 and 55% were female and 50% were Hispanic or Latinx, which is a main population here in Los Angeles, and a great number of our patients have Hispanic background. The distribution of the clinical diagnosis is demonstrated in the pie chart. We included patients with multiple sclerosis as well as MOG associated disorder, autoimmune encephalitis, primary CNS vasculitis, ADEM, transverse myelitis, and some other rare CNS inflammatory conditions such as Susac’s syndrome. We have patients with neurosarcoidosis, inflammatory strokes, and some other inflammatory CNS disorders that are listed here. So, talking about the genetic studies and the methods that were used. So, as you know, all life is encoded in DNA and the sequencing of the DNA or decoding the genome has been one of the most remarkable achievements of the human in the recent years.

[00:07:16] And recently with the advent of next generation sequencing, compared to prior traditional sequencing methods, now we are able to sequence the DNA much faster and with lower cost. So, it has made it much more available and basically has revolutionized the field of genetics in the clinical diagnosis arena. There are different types of next generation sequencing techniques including whole genome sequencing, which as the name implies, it actually looks into the whole genome including the coding and non-coding regions. There is also a whole exam sequencing which looks at the coding regions only, and then there are targeted gene panels or focused exam sequencing which looks into a list of genes that are of interest or of clinical relevance.

[00:08:18] In our study we actually had data using the targeted gene panel which included 155 genes that are implicated in immune regulation. So, 77.8% of the patients included in our study actually did have rare variants of immune regulation genes. We identified 88 unique variants of 55 genes including the ones I’ve listed here. And the most frequent number of variants were identified on 13D gene. Here you can see genes harboring the rare variants identified in our study which are grouped based on the clinical diagnosis. A great number of our patients had MOGAD and MS. So, we identified more gene variants in these groups. But as we include more patients with other diagnosis, we can see that we can identify rare variants of these genes in other diagnosis as well.

[00:09:43] We also looked into the functional effect of these variants and how the variation in the genes could actually change the function of the genes. In order to predict if a variation in the gene can affect the function, there is a scoring system, the CADD score, that predicts the functional effect, and the score of greater than 10 is considered detrimental. So, detrimental effect on the gene function. And a majority of the variants that we identified actually had a high CADD score. The median was 21.3. So, at least half of the variants had CADD score of 21.3 and greater than that. So, that tells us that these variations in the genes are probably interfering with the function of the genes that are implicated in immune regulation.

[00:10:52] The genes that are looked into and they’re listed in the panel are associated with different immune disregulation conditions, but I want to highlight some of these conditions that have neurologic manifestations previously reported and associated with them. So, a couple of these genes, the STXPP2 and the UNC13D genes are associated with familial hemophagocytic lymphohistiocytosis or familial HLH. So, familial HLH is an inflammatory condition in which the immune system actually produces more active immune cells and also excessive amount of immune proteins such as cytokines. So, there is inflammation in different parts of the body, there is fever and also inflammation in the liver and spleen. And also, more than half of the patients with familial HLH have neuroinflammatory findings. So, there is also involvement of the CNS in a great number of these patients.

[00:12:08] Some of the other genes that we found association in terms of rare variants in these genes that were previously reported as a cause of an Aicardi-Goutières syndrome. So, Aicardi-Goutières syndrome is a rare genetic condition that is also affecting brain, spinal cord, and the immune system. And in this condition, the immune system actually turns itself on in a destructive way and it causes damage to the white matter in the CNS. Or it causes leukodystrophy as well as global developmental delays and cognitive delays as a result of the inflammation in the brain. So, one of the other genes that were implicated previously reported in familial but just like all the inflammatory syndrome has been previously reported in MOGAD and as kind of a prognostic factor in MOGAD and also in NMOSD and granulomatous neuroinflammatory conditions as well.

[00:13:32] And NOD2 which is previously well known as the strongest genetic risk factor for Crohn’s disease and has also been reported in association with neuro inflammatory conditions such as Rasmussen’s encephalitis and CNS granulomatosis. So, these are the ones that were previously reported in the literature, but our study shows that it’s previously new data that we acquired from our patients, it supports the fact that these are probably also involved in neuro inflammatory conditions. We also did pathway analysis, basically grouping together genes that are involved in the similar biologic pathways or molecular mechanisms. And one of the pathways that was common among the genes that we found variants in this study was not like signaling pathway.

[00:14:40] So, NOD-like receptors are a group of receptors that are used in innate immune system in response to different kinds of infections. And the function of this pathway is to promote production of pro inflammatory cytokines and chemokines. So, it drives the immune response whenever there is a bacterial or viral infection. The other emerged pathway was the inflammatory bowel disease pathway. So, the molecular mechanism of this pathway also includes the NOD2 signaling pathway. So, similar to what I mentioned previously. I also mentioned about variations in NOD2 being the strongest genetic risk factor for Crohn’s disease. But our data, as well as some other data suggests that there might be association with neuro inflammatory conditions as well. And identification of these pathways could be important because now we can think about specific arms of the immune system that might be more involved in neuro inflammatory conditions, and that can have implications in designing targeted treatments if we know which parts or which pathways are more involved in these conditions.

[00:16:23] So, our data suggests that NOD2 signaling may be an attractive candidate for further investigation and targeting in pediatric and in autoimmune and inflammatory CNS conditions. So, to summarize, the genetic basis of autoimmune and inflammatory CNS disorders remains largely unknown. And in our study, we observed a high rate of identification of rare and low frequency variants in immune regulation genes. We identified 88 unique variants of 55 genes, including the ones listed here. Pathway analysis revealed an enrichment of NOD2 receptor signaling within our patient population. So, these findings may shed light into the underlying mechanisms of autoimmune CNS disorders and have therapeutic implications. I would like to thank my mentor Dr. Jonathan Santoro and my other co-authors at Jones Hospital of Los Angeles. And with that, I am happy to take any questions.

[00:17:50] Audience Member: Two quick questions. Can you share what targeted genetic panel used, was it the same one for all your patients?

[00: 17:56] Dr. Saba Jafarpour: Yeah, it was the Invitae Autoinflammatory and Autoimmunity Syndromes Panel.

[00:18:01] Audience Member: Okay.

[00:18:02] Dr. Saba Jafarpour: Yeah.

[00:18:03] Audience Member: And then I don’t know if you could tell, were many of those conditions autosomal recessive, and was it a homo or heterozygous finding for those patients?

[00:18:11] Dr. Saba Jafarpour: Yeah. So, all of the variants that we found were heterozygous. There are different autosomal dominant or recessive reports with conditions associated with these genes, but our patients didn’t have the phenotype of those conditions. So, that’s why we think this is kind of a separate process probably.

[00:18:33] Audience Member: Great. Thank you.

[00:18:34] Dr. Saba Jafarpour: Thank you.

[00: 18:37] Dr. Carlos A. Pardo: Thank you so much. It was very important source of information. Thank you very much, Saba. Genetics is part of the future in medicine. It has been part of medicine in the past 20 years, but I think that I like that you keep in mind four letters A, T, C, G. Okay. So, those are the four letters that are critical for the DNA. Is that right, Saba? Okay. A, C, T, G, and I will tell you why you need to pay attention to that.