RESEARCH PRIORITIES

Families of individuals with SATB2-associated syndrome (SAS) recognize the importance of research to better understand SAS and identify possible treatments.

The SATB2 Gene Foundation has created a powerful research asset by developing induced pluripotent stem cells (iPSCs) from patient cells. iPSCs provide cellular models of disease to rapidly advance knowledge and discovery.

Based on high impact needs identified by a recent independent scientific analysis and caregiver input, we have prioritized the following areas in SAS research:

  • speech and language
  • behavior
  • sleep
  • global developmental delays

Additional research priorities include projects on SATB2 function and expression, variations in clinical phenotypes, and symptomatic and/or curative therapeutic interventions.

SAS Stem Cell Biobank

The advantage of a Foundation-sponsored stem cell biobank is that the cell lines will not be held as proprietary by any single laboratory, and we can therefore share iPSCs with qualified researchers around the world in order to continue to advance SAS research. These cells allow researchers to advance our understanding of human-specific disease phenotypes (patient characteristics) and test potential treatments. We have a total of 8 iPSC lines available (4 patient and 4 control lines) through an application and Material Transfer Agreement (MTA).

Experiments with iPSCs typically involve differentiating the stem cells into specific cell types including specific neuronal subtypes (brain cells). These cells allow researchers to study disease mechanisms, for example, how different alterations of the SATB2 gene change neurons derived from iPSCs, and study the effect of the drugs on different cell types, such as neurons derived from iPSCS. This is a necessary first step towards evaluating potential treatments. 

CURRENT RESEARCH

SAS Clinical Registry

We need YOU, parents and caregivers, to help move research FORWARD! Join Dr. Yuri Zarate’s SATB2 clinical registry. We need to fully understand SATB2-associated syndrome in order to develop treatments and recommendations for clinical care. Without rare disease registries such as this one, we would not understand the natural history of these rare conditions. Learn more here or by emailing Dr. Zarate today.

Researchers at Aston University are conducting a questionnaire study to better understand sleep difficulties and how they may be associated with emotion, cognition, and behaviour in children with SATB2-associated syndrome. The study will help to better understand the needs of children with SAS who experience sleep difficulties. Caregivers of children (aged 4-15 years) with a diagnosis of SATB2-associated syndrome are invited to participate, regardless of whether your child currently experiences sleep difficulties. To find out more about the study, please contact the research team or complete an expression of interest form at: https://tinyurl.com/SATB2SleepQEOI.  Please note that this study requires parents/caregivers to be able to complete the questionnaires in English.

RESEARCH AWARDS

Generation of an endogenously tagged SATB2-V5 mouse line

Dr. Kevin A. Peterson, The Jackson Laboratory and Dr. Jennifer L. Fish, University of Massachusetts Lowell

Awarded $5,000 

The SATB2 Gene Foundation is committed to helping researchers build tools and resources to better understand the molecular mechanisms contributing to SATB2-Associated Syndrome (SAS) phenotypes which may ultimately lead to developing better therapeutic strategies. SATB2 is known to interact with both DNA and protein. Further, SATB2 binding to DNA and protein varies between different cell-types and during different stages of life. To enhance the detection of SATB2 interactions in different molecular contexts, we are developing a novel mouse line, SATB2-V5. The addition of the V5 tag to SATB2 protein will improve the efficiency and accuracy of protein isolation and detection. We anticipate this mouse to be available to the research community in the Summer of 2025.

Investigating phosphorylation requirements for SATB2 DNA binding

Awarded $2,500 

SATB2 is a protein that plays a critical role in shaping genetic material and reading other parts of DNA which results in protein production; it is considered a master gene regulator. SATB2 protein binds has several special domains, called CUT domains, that bind to DNA at specific areas. Other proteins act on these CUT domains of SATB2 to turn them on/off  in a process called phosphorylation. We will be using a mouse cell line previously used to study SATB2’s role in bone formation to determine how phosphorylation changes its ability to bind to DNA as well as visualize where in the cell it is located. This is a basic research study that will help determine if SATB2 can be switched on and off in a cell . The future goal would be to repeat this experiment in SATB2 human stem cell lines to see how their SATB2 protein’s function is affected.

Function of SATB2 in the formation of cortical area map

Awarded $15,000

Co-Investigators: Yu-Bing Wang, Postdoctoral Fellow, Ph.D and Pin-Xi Xie, Master Student, B.S.; Tongji University

Studies have shown that different parts of the brain have different brain structures and functions. Individuals with SATB2-Associated Syndrome (SAS) may have intellectual disability, limited or no verbal speech, and behavioral problems, which could be related to specific parts of the brain like the motor and sensory areas. We think that the lack of SATB2 could lead to issues of brain mapping, causing the brain to rely on the wrong brain areas for different functions. This research will look into the changes in the brain area map in mice without SATB2 and see if giving them SATB2 can help to fix the map. Hopefully, this will help us better understand the function of SATB2 in the brain and help inform work towards gene therapy development.

Generation and characterization of neural organoids from SATB2-Associated Syndrome (SAS) iPSC lines

Awarded $15,000

Co-Investigator: Dmitriev Ruslan, Assistant Professor, PhD, Ghent University

This study will focus on understanding the critical role of the SATB2 protein in early human brain development. Currently, we lack a comprehensive understanding of what happens during brain development in individuals affected by SATB2-associated syndrome (SAS). In the past, this was challenging since we did not have the right materials, such as human brain tissue. However, we have made progress by growing small brain-like structures called neural organoids in the lab. These organoids mimic the early stages of human brain development. In this study, we will use neural organoids made from SAS cells donated by the SATB2 Gene Foundation to visualize the effects of SATB2 variants during early brain development.

Investigating mutation-specific mechanisms of SATB2 missense variants to reveal genotype-phenotype correlations in SATB2-associated disorder

Awarded $18,000

Co-Investigator: Joery den Hoed, Postdoctoral Researcher, PhD, Max Planck Institute for Psycholinguistics, Language and Genetics Department

In the last decade, we have made big steps in the clinical application of novel techniques to read DNA sequences, making it now relatively affordable and quick to perform exome or genome sequencing and to search for genetic causes in rare neurodevelopmental diseases. However, interpretation of the (often many) genetic variants that result from these methods remains challenging. For some types of genetic variants, such as deletions of the whole gene, or changes that result in truncation of the protein product, it can be easy to link the variant to disease and predict the effects on the function of the gene, However, for other variants, it can be much harder to do so. Missense variants, genetic changes that replace only one building block in a long chain of amino acids that make up the final protein, are particularly difficult to interpret.

About 30% of individuals with SATB2-associated disorder (SAS) are identified with such missense variants. Given that the symptoms of SAS are variable, different missense variants may have different effects on the function of the SATB2 gene, which could potentially explain some of the variability in clinical outcome. In 2021, together with other colleagues, we developed a set of assays to look at the effects of missense variants on the functions of SATB1, a gene closely related to SATB2. We found that some of these SATB1 missense variants do not result in a loss of function of the gene, but that they instead lead to stronger activity of SATB1.

The current study aims to assay a large number of SATB2 missense variants using a workflow that is comparable to the earlier SATB1-study. This way, we hope to disentangle different functional effects of SATB2 missense variants, gaining a better understanding of the heterogeneity of this genetic variant group at the genetic/molecular level. In collaboration with clinician Yuri Zarate, the results from these functional assays will be mapped to clinical information available for individuals with SAS, to establish relationships between the different SATB2 missense variants and clinical symptoms. These results will aid the interpretation of SATB2 missense variants, increase our understanding of SAS-related disease mechanisms, and potentially result in better genotype-phenotype correlations for SAS.

Functional analysis of SATB2 and disease-associated variants using Drosophila

Awarded $29,938

In this study, the Yamamoto lab is exploring the function of SATB2 in the nervous system and determining functional consequences of pathogenic variants found in patients with SATB2-associated syndrome (SAS) at the molecular level using the fruit fly Drosophila melanogaster. While flies may not be the first experimental animal that comes to people’s minds when studying human diseases, this small insect has made numerous contributions to biomedical sciences in the past century. So far, 10 scientists have been awarded the Nobel Prize in Physiology or Medicine by using fruit flies as a model organism to study fundamental principles of genetics, developmental biology, immunology, and neuroscience. Over the last decade, Dr. Yamamoto has been pioneering the use of fruit flies as ‘living test tubes’ that can provide information on functional consequences of rare genetic variants found in patients with genetic disorders. His lab, in close collaboration with fellow scientists and clinicians around the world, has contributed to the discovery of a number of new genetic disorders. Moreover, his lab has also been harnessing the power of fly genetics to functionally characterize genetic variants that increase the chance of developing common neurological conditions and disorders such as autism spectrum disorders and Alzheimer’s disease.

Through this research award, Dr. Yamamoto is generating a series of mutant and transgenic fly lines to study SAS for the first time in this model system. Flies carry one gene called dve (defective proventriculus) that corresponds to human SATB1 and SATB2. While the function of this gene has been studied in the development of the digestive and reproductive systems in the fly, its role in the nervous system has not been investigated. Using the state-of-the-art genetic technologies such as CRISPR and integrase-mediated transgenesis systems, the lab will ‘humanize’ this fly gene by replacing the fly dve gene with human SATB2. This will provide a foundation to study how different genetic variants found in SAS affects the function of SATB2 in a living organism. Furthermore, the new genetics tools that are being generated will allow scientists to visualize when and where this gene is being expressed in the fly nervous system, providing insights into its function in the developing and mature nervous system. Additional tools available in the Drosophila research community also allow Dr. Yamamoto’s team to overexpress or knockdown the SATB2 homolog in specific neuronal or glial populations to assess its effect on fly behavior. While fruit flies may not necessarily ‘model’ all the symptoms seen in SAS patients, data from such experiments will help scientists to pinpoint the specific role of this gene in the brain. Because experiments in flies can provide a lot of data in a relatively short time frame, such studies complement experiments performed in human-derived cells (iPS cells) and organoids as well as functional studies pursued in mouse models. Dr. Yamamoto’s lab will be collaborating closely with other research grant awardees from the SATB2 Gene Foundation including Drs. Jennifer Fish and Yuri Zarate to accelerate the translation of their findings in fruit flies to mouse models and clinical research.

Metabolic approaches to treatment for SATB2-Associated Syndrome.

Awarded $24,787

Individuals with SATB2-associated syndrome (SAS) present with developmental delay with severe speech deficits, behavioral abnormalities, and bone disease. It has been shown that cells from individuals with SAS present some abnormalities in their metabolism that may be linked to the clinical traits of the syndrome. This project aims to further characterize the metabolic abnormalities in SAS and explore the effect of candidate compounds that could fix them.

In a previous study, researchers tested cells derived from blood samples while this new project aims to assess the metabolic profile of a new group of individuals with SAS utilizing fibroblasts, cells obtained from skin samples. In this way, we plan to exclude that the metabolic abnormalities are limited to a single type of tissue (blood) and thus prove that they are the results of molecular alterations affecting multiple tissues.

We also plan to observe the metabolic effect of raising the expression of the SATB2 gene by altering the conditions of the cell cultures: it has been proved that metabolic distress causes an increase in SATB2 expression, so we will change the conditions in which the cells will grow in order to cause metabolic distress and study the consequential metabolic profile.

Since the previous metabolic findings showed that the cells from people with SAS are less efficient than expected at utilizing certain energy sources, the study will explore the metabolic responses to alternative energy sources, aiming to correct some of the observed metabolic abnormalities. The results of these experiments may be translated into clinical practice by adjusting the diet of individuals with SAS.

The findings from our preliminary study have suggested disruption of certain candidate pathways that may explain both the metabolic abnormalities and the clinical features described in individuals with SAS. Information of previous studies on such pathways has allowed us to select a candidate compound that may correct the negative effects of SATB2 variants on these pathways: therefore, we will add this compound to the cells in our assays and assess their efficacy at correcting the observed metabolic abnormalities.

This study aims to collect important information on the impact of SATB2 variants on metabolic pathways in multiple tissues, improving our knowledge of pathogenic mechanisms underlying SAS, potentially identifying biomarkers that correlate with the onset and severity of SAS features, and identifying novel targets for treatment approaches. Moreover, we will evaluate the efficacy of two independent approaches to SAS treatment: we will explore the impact of alternative energy sources on the metabolism of SAS cells and we will assess the efficacy of a candidate drug at correcting the metabolic abnormalities showed by SAS samples.

Bone geometry deficits in individuals with SATB2-Associated Syndrome.

Awarded $6,580.20

SATB2-associated syndrome (SAS) is a rare disorder caused by alterations in the SATB2 gene. Bone problems such as leg bowing, abnormal curvature of the spine, and fractures have been reported in individuals with SAS. From previous studies, it is also known that individuals with SAS often tend to have weaker bones as documented by x-rays dedicated to measuring bone strength, regardless of the type of genetic change in the SATB2 gene.

To date, the research studies involving bone strength in children with SAS have exclusively utilized a type of x-ray called DXA scan. This study while useful and routinely used, is unable to precisely locate if the deficiency is located in the outer part of the bone (cortical or compact bone, the inner part (trabecular or spongy bone), or both. In this study, we will be using a portable type of X-ray machine that is more accurate in analyzing bone strength call peripheral quantitative computed tomography (pQCT). This technique takes images in a matter of minutes and the results allow us to see what part of the bone is weaker. We will not be evaluating the utility of the pQCT to determine where the bone is weaker but also if it has a higher ability to detect early problems compared to the standard DXA scan.

As part of this study, we will also be evaluating the levels of several bone health markers in the blood to see how they relate to the x-ray findings and if they can be used in routine care of individuals with SAS to predict bone complications.

We expect this study will allow us to gain added insight regarding the bone problems seen in SAS that might contribute to the increased risk for bone fragility in this population while providing better surveillance and management recommendations.

Delineating the regulatory landscape of SATB2-Associated Syndrome.

Awarded $19,708

Gene expression is tightly regulated and involves several (non-coding) key elements such as the promoter anddistal regulatory elements, the enhancers. To switch on the expression of a gene, these enhancer elements physically interact with the promoter of the gene by looping out the intervening DNA sequence.

Recently, we performed an extensive literature review to shed more light on the importance of noncoding structural variations (SVs) in neurodevelopmental disorders (NDDs) (D’haene et al., 2020). In this review we discuss a comprehensive collection of noncoding SVs being at the root of the NDD phenotype in the reported patients. One of the regions in which several noncoding SVs associated with a NDD, have been reported, is the intergenic region downstream of the SATB2 gene.

Previously we determined the interacting elements with the SATB2 promoter. With this proposal we want to determinethe enhancer activity of these interacting regions. We will make use of both in vitro (luciferase assays) and in vivo (zebrafish) assays. The data generated in this project could lead to a better understanding of how SATB2 expression is regulated and subsequently of the causal effect of noncoding SVs in this region. Moreover, these data will be an asset to interpret noncoding variation (in whole genome sequencing (WGS) patient data) in the region downstream of SATB2. In addition, the enhancers that might be validated during this project, are of interest for further research to determine the potential of CRISPR-based strategies targeting these regions to boost SATB2 expression.

Assessment of energy production pathways, metabolism, and hormonal response in SATB2-Associated Syndrome.

Awarded $12,442.28

This study will look at metabolism and hormone response differences in cells from individuals with SAS compared with controls. A series of experiments will evaluate energy metabolism pathways and responses to different concentrations of some hormones by using the Phenotype Mammalian MicroArray (PM-M) platform developed by Biolog™. The utility of this tool has been demonstrated in various neurodevelopmental conditions, in some cases leading to the identification of useful interventions. The investigators hope to identify some potential energy pathways that may play a critical role in how SAS affects individuals and will attempt to develop a profile for individuals with SAS that could be distinctive compared to controls.

Determining SATB2-mediated gene expression in human hippocampal neurons.

Awarded $12,500.00

Research in the Fish lab uses animal (mouse) and cell (mouse and human) models of SATB2-associated syndrome (SAS) to understand the molecular and cellular mechanisms underlying skeletal and neuronal defects typical of SAS. This study will identify changes in gene expression and major gene regulatory pathways altered in neurons among isogenic stem cells with SATB2 mutations (generated with CRISPR/Cas9). A major goal of this project is to identify regulatory pathways that could represent therapeutic targets for SAS patients and will lay the groundwork for future experiments using human induced pluripotent stem cells (hiPSCs) derived from SAS patients.

IPSCS BANK

The SATB2 Gene Foundation requires all applicants for the iPSC (Induced Pluripotent Stem Cells) bank to complete the application and agreement, along with the iPSCs Bank Material Transfer Agreement, in order to access and use the iPSC Bank biological materials. Only SGF approved applicants may have access to the materials. These materials are for research purposes only and are not transferable to any non-approved third party.

Step 1: Complete the application and material transfer agreement (MTA). In addition to the application and MTA, submit the following supporting materials:

a. Lay Statement for the SATB2 Gene Foundation. In a brief paragraph of approximately 10 lines, describe your proposal and it’s significance.

b. Provide a short scientific description of the research you will conduct using these Materials and time frame for proposed completion. An abstract from a research grant is acceptable.

Step 2: Return the completed application, MTA, and supporting materials to the SATB2 Gene Foundation to research@satb2gene.org. Once approved by the SATB2 Gene Foundation Board of Directors, you will receive an email confirming your order.

Step 3: Shipping confirmation. Dr. Jennifer Fish’s laboratory is currently distributing iPSCs. Her laboratory will email you when the sample has shipped, with shipping and tracking information.

Step 4: Shipping charges. Shipment will be charged to the applicant-provided shipping carrier account.

Details of available iPSCs (Currently, there are 4 cell lines with one parental control each, which represent the most common molecular mechanisms of disease).

iPSC Line ID Alteration Originating Cell Type
ID2 Intragenic deletion fibroblast
MID2 fibroblast
ID59 Nonsense: p.R459X fibroblast
MID59 fibroblast
ID100 Missense: p.R389C fibroblast
MID100
SATB22207  Truncating frameshift

c.163delG

p.V55WfsX4

 PBMCs
SATB8383 Control PBMCs

2024 RESEARCH GRANT APPLICATION

The SATB2 Gene Foundation is pleased to announce our Research Grant Program. This grant program is open to research investigators affiliated with an academic institution, hospital system, non-profit institution, or other accredited research institutions based in the United States or internationally. Eligible applicants include post-doctoral fellows, clinical fellows, researchers, physicians, or other associated research professionals with faculty appointments or research positions.

To drive research momentum, the SATB2 Gene Foundation Board is highly interested in research proposals that would create pilot data sufficient to support larger scale grant submissions to other funding sources.

The SATB2 Gene Foundation prioritizes the following areas in SAS research, based on high impact needs identified by a recent independent scientific analysis and caregiver input:

  • Speech and Language
  • Behavior
  • Sleep
  • Global Development Delays

Additional research priorities include projects on SATB2 function and expression, variations in clinical phenotypes, and symptomatic and/or curative therapeutic interventions. We support projects that gather foundational knowledge about SATB2 function, and we also support projects that aim for tangible and immediate clinical applicability.

In addition, the SATB2 Gene Foundation has previously supported other research resources, such as iPSCs for a variety of precise SATB2 mutations.  Please reach out if access to these resources may be helpful to your research.

Schedule for Grant Applications:

  • Delayed to 2025: Program Opens

  • Delayed: Full Applications Due by 11:59pm ET

  • Delayed: Award Announcements to Applicants

  • Delayed: Award Announcements to Public

  • Delayed: Anticipated Project Start

Applications will be reviewed by the SATB2 Gene Foundation Medical and Scientific Advisory Board and the Board of Directors. The grant selection process is unbiased and independent; awards are based solely on scientific merit and expected contributions to the priorities of the SAS community and body of knowledge about SATB2-associated syndrome. Advisors and board members with a conflict of interest will not participate in voting for those specific applications.

If you have any questions regarding the application process, please contact research@satb2gene.org.

Get Started:

HOW YOU CAN HELP

The SATB2 Gene Foundation needs your help in raising the necessary funds to continue to rapidly advance research.

Join us in making an impact on the future of SAS research.  Help us continue to fund innovative SATB2 research, including biobank expansion, experiments on biobanks samples, animal models, and clinical research with the SATB2 registry! Help us accelerate the pathway towards much-needed treatments for our SATB2 patients to improve their quality of life.

Please donate today to support research, on the online giving link please select “SAS Research” on the drop down menu. For additional information, please contact Allison Kaczenski.

Checks with a note of “Research” can mailed to the below address:

  • SATB2 Gene Foundation
    3050 Five Forks Trickum Road Suite D-524
    Lilburn, GA 30047 USA