One of the goals of the ACDA is to promote and monitor ACDMPV research by medical professionals around the globe. Since 2001, the ACDA has supported ACDMPV research at Baylor College of Medicine in Houston, Texas, USA through donations of blood samples, tissue samples and funding. Baylor has accumulated the largest collection of DNA and tissue samples related to ACDMPV in the world. In addition, there is increased ACDMPV research occurring world wide as evidenced by the number of published medical journal articles.
The ACDA has worked closely with the National Organization for Rare Disorders (NORD) and their Medical Advisory Board to issue grants for ACDMPV research. In addition, Baylor College of Medicine has applied for and received significant grant funding through the NIH Research Project Grant Program (R01). Below is a description of the NORD Research Grant Program, the NIH Research Project Grant Program (R01) and the various grants issued for ACDMPV research throughout the years.
NORD Research Grant Program
Read the details about the NORD Research Grant Program HERE.
NORD’s Research Grant Program began in 1989 and more than 150 grants have been administered since its inception, including a total of nine grants in support of ACDMPV research as follows:
Funding for NORD grants in support of ACDMPV research is raised solely through the hard work, contributions and fundraising efforts of families affected by ACDMPV.
As described by NORD, “NORD’s Research Grant Program, which is focused on disease-specific grants, provides small “seed money” grants to academic scientists performing basic translational science or studying new treatments or diagnostic tests for rare diseases. The goal of the small studies supported by NORD’s research grants is to provide preliminary data that may one day lead to a treatment (drug, device, or medical food) for patients with rare disorders. Researchers can then use the preliminary data funded by NORD’s research grant program to apply for larger multi-year government grants, or to attract a commercial sponsor who will manufacture the orphan product and get it approved for marketing by the Food & Drug Administration (FDA)….Each research proposal is reviewed by NORD’s Medical Advisory Committee, which recommends funding for the highest scored proposals. After the grant is awarded, NORD monitors the progress of the research, processing biannual reports to NORD’s Medical Advisory Committee.”
The grant cycle is described below [Update as of September 2016: NORD indicates they are in the process of revising the schedule for the grant cycle. We will publish the revised schedule as soon as available.]
NORD 2018 Grant Status
The ACDA and The David Ashwell Foundation are in the process of raising funds, which funds may potentially be applied to a 2018 NORD grant upon review and approval of the distribution of such funds by the ACDA and The David Ashwell Foundation. Please note the minimum amount required for a NORD grant for ACDMPV research has been increased to $35,000 (previously $33,500), effective as of the 2017 grant. Please click HERE to donate.
NORD 2017 Grant Recipient
NORD’s Medical Advisory Committee recommended, and the NORD Board of Directors approved, the awarding of five total research grants in December 2017, including one grant for ACDMPV research in the amount of $50,000 (with funding raised in coordination with the ACDA and The David Ashwell Foundation). The grant was distributed as follows:
Arun Pradhan, PhD
Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
Development of FOXF1-activating small molecule compound for the treatment of Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACDMPV)
NORD 2016 Grant Recipient
NORD’s Medical Advisory Committee recommended, and the NORD Board of Directors approved, the awarding of seven total research grants in February 2017, including one grant for ACDMPV research in the amount of $50,000 (with funding raised in coordination with the ACDA and The David Ashwell Foundation). The grant was distributed as follows:
Przemyslaw Szafranski, Ph.D.
Baylor College of Medicine, Houston, TX
Modeling ACDMPV therapies by targeting negative regulators of FOXF1 and genes outside the SHH pathway.
NORD 2015 Grant Recipients
NORD’s Medical Advisory Committee recommended, and the NORD Board of Directors approved, the awarding of seven total research grants in December 2015, including one grant for ACDMPV research in the amount of $50,000 (with funding raised in coordination with the ACDA and The David Ashwell Foundation). The grant was distributed as follows:
Partha Sen, PhD (primary investigator) and Aaron Hamvas MD (co-investigator)
[NOTE: Due to the relocation of Dr. Sen, he has requested NORD to transfer the entirety of the 2015 grant to his co-recipient, Dr. Hamvas.]
Characterizing the FOXF1 gene network in lung development
The aim of this two year grant is to help understand the role of FOXF1 in ACDMPV and in lung development, along with the development of other organ systems. The overall objective is to understand the genetic basis of ACDMPV that may lead to therapeutic developments of this deadly disorder.
NORD 2014 Grant Recipients
NORD’s Medical Advisory Committee recommended, and the NORD Board of Directors approved, the awarding of six total research grants in December 2014, including two grants for ACDMPV research in the amount of $93,500 each (with funding raised in coordination with the ACDA and The David Ashwell Foundation). As such, of the almost 7,000 rare diseases under NORD’s umbrella, ACDMPV research grants comprised 45% of the total grants awarded by NORD in 2014. The grants were distributed as follows:
1) Csaba Galambos
Children’s Hospital Colorado and University of Colorado Denver
Role of Pericytes and Platelet-Derived Growth Factor-Beta Signaling in the Pathogenesis of Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACDMPV)
One of the grants supported Dr. Csaba Galambos of Children’s Hospital Colorado and University of Colorado Denver. Dr. Galambos is a pediatric pathologist who has worked with the researchers at Baylor College of Medicine in the past. Part of Dr. Partha Sen’s immunohistochemistry study (for his previous grant from NORD) was performed in the laboratories of Dr. Galambos. His current project, “Role of Pericytes and Platelet-Derived Growth Factor-Beta Signaling in the Pathogenesis of Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins,” is an integrative approach utilizing banked human ACDMPV lung tissues, in vivo animal modeling and novel in vitro cell-based methods, to determine whether upregulation of PDFG-B signaling is sufficient to cause defective pulmonary vascular remodeling and PHT, and to identify PDGF-B-driven mechanisms that are responsible for impaired angiogenesis and defective lung growth in ACDMPV.
2) Przemyslaw Szafranski
Baylor College of Medicine
Towards designing ACDMPV therapy: Deciphering epigenetic regulation of FOXF1
The other grant supported Przemyslaw Szafranski of Baylor College of Medicine in Houston. His project, “Towards designing ACDMPV therapy: Deciphering epigenetic regulation of FOXF1,” will identify key lncRNAs and their interactors involved in epigenetic regulation of FOXF1, decipher mechanism of how the expression of FOXF1-controlling lncRNAs, in particular those involved in FOXF1 silencing on the paternal chromosome, is regulated, and identify additional to FOXF1 genes involved in etiology of ACDMPV.
NORD 2012 Grant Recipients
NORD’s Medical Advisory Committee recommended, and the NORD Board of Directors approved, the awarding of five research grants in May 2012 and seven additional grants in November 2012, including two grants for ACDMPV research in the amounts of $61,550 and $42,861 (with funding raised in coordination with the ACDA and The David Ashwell Foundation). The grants were distributed as follows:
1) Partha Sen, PhD
Baylor College of Medicine
To Investigate the Role of FOXF1 in Lung Development, Particularly with Respect to Alvelar Capillary Dysplasia and Misalignment of Pulmonary Veins
One of the grants investigated the role of the FOXF1 gene and its effect on airway branches and sac-like structures of the lungs. This will be accomplished by using siRNA (small interfering RNA) that will knock down the FOXF1 protein. The goal is to provide a better understanding of the FOXF1 protein functions hopefully leading to future therapies for ACDMPV.
2) Przemyslaw Szafranski, PhD
Baylor College of Medicine
Long Noncoding RNAs as Potential Diagnostic and Therapeutic Targets in Patients with Alveolar Capillary Dysplasia
The other grant focused on unraveling the function of novel, identified IncRNAs (noncoding RNAs) identified with ACDMPV in normal and pathological lung development in ACDMPV patients. The goal is to expand tools for ACDMPV diagnostics and gene therapy, while shedding light on the enigmatic role of IncRNA as gene regulators, in general.
Interim progress report summary: Abnormalities in the FOXF1 gene are known to result in ACDMPV. The goal of Dr. Szafranski’s research project is to learn more about how the FOXF1 gene is regulated (controlled). Knowing more about how FOXF1 works should allow him to search for other genetic mutations that can cause ACDMPV. Dr. Szafranski has so far identified several pieces of genetic code (called lncRNA’s) that are located close to FOXF1, are expressed in lung tissue, and which might therefore regulate FOXF1 expression. He is now conducting experiments to see which of these lncRNA’s regulate FOXF1 expression most clearly. He then plans to study the mechanisms by which lncRNA’s regulate FOXF1. He hopes that this work will increase the number of identified genetic abnormalities that have been found to cause ACDMPV and thus assist in prenatal diagnosis and perhaps even treatment for ACDMPV. Thanks to Dr. Simon Ashwell, father to David, for this summary.
NORD 2008 Grant Recipients
NORD’s Medical Advisory Committee recommended, and the NORD Board of Directors approved, the awarding of seven research grants in November 2008, including one grant for ACDMPV research in the amount of $30,000 (with funding raised in coordination with the ACDA). The grant was distributed as follows:
Partha Sen, PhD
Baylor College of Medicine
Genotyping and VEGF188 Expression Study for Further Understanding of the Molecular Basis and Pathophysiology of ACD
NORD 2005 Grant Recipients
NORD’s Medical Advisory Committee recommended, and the NORD Board of Directors approved, the awarding of fourteen research grants in October 2005, including one grant for ACDMPV research in the amount of $30,000 (with funding raised in coordination with the ACDMPV Association). The grant was distributed as follows:
Partha Sen, PhD
Baylor College of Medicine
Recruitment of New Families and Histochemical Studies on the Lung Specimens of Patients with Alveolar Capillary Dysplasia
This grant was used for histological screening on lung tissue samples. This involves comparing the ACDMPV tissue samples to “normal” tissue samples to look for presence or absence of specific proteins that are known to affect lung development. Significant variations in proteins between the ACDMPV and normal tissue samples could provide insight to which gene(s) might be involved and provide a direction for additional research. Genes are responsible for controlling the production of proteins, so variations in certain proteins would implicate problems the corresponding gene(s) that control them.
Since genetics research is very complex field where the possible combinations and interactions of variables that contribute to diseases is mind boggling, techniques are used to limit some variables. For example, in this study, Dr. Langston has a set of criteria for classifying tissue samples as ACDMPV and each sample must meet all the criteria for it to be included in the study. Using this process increases the likelihood that each sample will contain the unique ACDMPV genetic signature and not introduce “noise” into the study. The criteria are:
•misalignment of pulmonary veins
•under development of gas exchange
•deficient capillary number
•lymphatic deficiencies (in about 1/3 of cases)
•thickening of the pulmonary arteries
Another technique being used at Baylor to reduce variables in the comparative study of ACDMPV tissue and “normal” lung tissue is that the “normal” tissue will be from babies that have undergone the same types of medical care (drugs, ventilation, etc.) as the ACDMPV patients in order to minimize any affects from different medicines and treatments.
The study will be looking for 6-8 proteins that are all known to be involved in lung development.
NIH Research Project Grant Program (R01)
Read the details about the NIH Research Project Grant Program (R01) HERE.
The NIH has issued two multi-year R01 grants in support of ACDMPV research as follows:
NIH 2017 Project Information
Title: Epigenomic Dysfunction at 16Q24.1 Vascular Defects and Perinatal Consequences
Project Leader: Pawel Stankiewicz, MD, PhD
Awardee Organization: Baylor College of Medicine
Project Start Date: May 22, 2017
Project End Date: April 30, 2021
Project Number: 1R01HL137203
Description (provided by applicant): Heterozygous genomic deletions and point mutations in the FOXF1 cause alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACDMPV), a neonatally lethal developmental lung disease. The vast majority of ACDMPV patients have additional defects involving heart, gastrointestinal, or genitourinary systems. The mesenchymal FOXF1 transcription factor expressed in the endothelial and smooth muscle cells plays an important role in epithelium-mesenchyme signaling, as a downstream target of Sonic hedgehog pathway. We accumulated the largest collection of ACDMPV samples in the world (N~145 families). Recently, we found that genomic deletions mapping in a protein-coding gene desert ~270 kb upstream to FOXF1 and leaving it intact manifest with the full ACDMPV phenotype. These deletions enabled us to define an ~60 kb tissue-specific enhancer region harboring long non-coding RNAs (lncRNAs), LINC01081 and LINC01082, that are expressed in fetal lungs. Another lncRNA, FENDRR that maps 1.7 kb upstream of FOXF1 in the opposite orientation and likely utilizes the same bi-directional promoter as FOXF1, interacts with chromatin-modifying complex (PRC) 2 to regulate gene expression. Interestingly, homozygous loss of Fendrr, leaving Foxf1 intact, leads to lethal defects of lungs and heart in mouse neonates. Importantly, we found that the FOXF1 locus is imprinted, likely using these lncRNAs; 31/32 of the characterized genomic deletions arose de novo on maternal chromosome 16q24.1. Trisomy 16 in humans, resulting from maternal meiosis I nondisjunction, is the most common prenatal trisomy (>1% of all pregnancies) and lethal unless rescued early embryonically. In one-third of such cases, children with maternal UPD(16) manifest IUGR (attributed to trisomic placenta) and multiple congenital malformations, including heart defects, pulmonary hypoplasia, tracheosophageal fistula, gut malrotation, absent gall bladder, renal agenesis, hydronephrosis, imperforate anus, and single umbilical artery. Interestingly, all the above clinical features, except IUGR, are observed in the vast majority of children with ACDMPV. In contrast, relatively normal phenotype was reported in few patients with paternal UPD(16), and imprinted gene(s) on chromosome 16 were suggested as causative for maternal UPD(16) phenotype. We hypothesize that FOXF1 enhancer and lncRNAs play an important role in genomic imprinting at 16q24.1, which may be responsible for the key features of maternal UPD(16). In aim 1, we will study the role of genomic imprinting of the FOXF1 locus in ACDMPV and UPD(16). In aim 2, we will analyze the function of the FOXF1 enhancer, including the overlapping lncRNAs. In aim 3, we will investigate the function of FENDRR in development and disease of heart, lung, and placenta. The proposed studies would provide a better understanding of the function of distant tissue-specific enhancers in genomic imprinting and the development and disease. This proposal would also elucidate the role of lncRNAs in enhancer function and gene regulation in general, and provide knowledge on this class of promising therapeutic targets.
PUBLIC HEALTH RELEVANCE (provided by applicant): We will elucidate how tissue-specific distant enhancer in chromosome 16q24.1 including long noncoding RNAs (lncRNAs) regulate expression of FOXF1, the gene responsible for a neonatal diffuse developmental disorder of the lungs, alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV), commonly associated with multiple congenital malformations involving the cardiac, gastrointestinal, and genitourinary systems. We will study the role of lncRNAs in genomic imprinting of the FOXF1 locus on chromosome 16q24.1. We will determine whether genomic imprinting at chromosome 16q24.1 is responsible for the phenotype of maternal UPD(16). We will also study the function of lncRNA FENDRR in development of lungs, heart and placenta. LncRNAs are considered promising therapeutic targets and we believe that by manipulating their expression, we may have the potential to correct the lethal phenotype of ACDMPV and UPD(16).
NIH 2010 Project Information
Title: Pathogenetics of the FOX Transcription Factor Gene Cluster on 16Q24.1
Project Leader: Pawel Stankiewicz, MD, PhD
Awardee Organization: Baylor College of Medicine
Project Start Date: May 1, 2010
Project End Date: April 30, 2014
Project Number: 5R01HL101975
DESCRIPTION (provided by applicant): Recently, we have found that haploinsufficiency due to point mutations or genomic deletions of the transcription factor Forkhead Box F1 (FOXF1) on 16q24.1 results in ACDMPV and a broad spectrum of congenital malformations. In addition, we have identified two distinct microdeletions upstream of FOXF1, implicating a position effect in the pathogenesis of the disease. Pleiotropic effects encountered in FOXF1 microdeletions, such as hypoplastic left heart syndrome and gastrointestinal atresias, may be due to haploinsufficiency for the neighboring genes, FOXC2 and FOXL1, both part of the FOX cluster at 16q24.1. Heterozygous Foxf1 mice die from pulmonary hemorrhage with severe defects in lung alveolarization and vasculogenesis along with other organ anomalies, although they do not completely recapitulate ACDMPV in humans. The expression of the Foxf1 gene during development suggests an intriguing pattern of gene regulation. We hypothesize that this complex regulation of Foxf1 may be due to both position effects and genomic imprinting in a tissue- and time-specific manner; ACDMPV can also be caused by disruption of other gene(s) or FOXF1 regulatory elements; and the lung defect in Foxf1 mice can be prevented perinatally by increasing the dosage of the Foxf1 protein in the capillary endothelium and surrounding mesenchyme. We have designed three aims to test these hypotheses. In aim 1, we will dissect gene regulation of FOXF1 in two ways. First, regulatory elements that may be important to the expression of the FOX gene cluster or to FOXF1 specific expression will be identified and tested using reporter assays, ChIP-on-chip, and chromatin conformation capture (3C) techniques. Second, we will analyze the segregation and allele-specific expression of Foxf1 in mice. In aim 2, we will use the knowledge gained from our studies in aim 1 to screen for point mutations and copy-number variations in the regulatory elements identified upstream or downstream to FOXF1 and in the ACDMPV candidate genes. Finally, in aim 3, we will explore therapeutic options by use of adenoviral vector-based Foxf1 gene transfer in peripheral murine lungs. ACDMPV is a lethal disorder and there is no available treatment at the present time. We believe that a gene therapy approach using viral vectors may have the potential to correct the lethal phenotype of ACDMPV patients by reversing the abnormal formation of the lethal capillary defect. Moreover, the risks related to this experimental therapy may be justified from a risk: benefit standpoint and have potential to be translated in the hospital setting.
PUBLIC HEALTH RELEVANCE (provided by applicant): We will unravel the pathogenesis and identify other causative gene(s) responsible for a neonatal diffuse developmental disorder of the lungs, Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV), commonly associated with multiple congenital malformations involving the cardiac, gastrointestinal, and genitourinary systems. This lethal disease has no available treatment at the present time. We believe that a gene therapy approach using viral vectors in mice may have the potential to correct the lethal phenotype of ACDMPV patients by reversing the abnormal formation of the lethal capillary defect.
NIH 2003 Project Information
The first ACDMPV related research grant was to the Baylor College of Medicine research team for a feasibility study on collecting and preparing DNA from ACDMPV families. The specific aims of the research were:
Phase 1: Identify affected individuals, evaluate clinically both patients and family members, analyze the pedigrees, obtain blood and tissue samples and isolate genomic DNA from families with ACDMPV.
Phase 2: Determine the genetic map position of the gene(s) responsible for ACDMPV by conventional linkage analysis in out bred North American families.
Phase 3: Identify the gene responsible for ACDMPV by a combined positional/functional cloning approach and study its DNA sequence, pattern of expression as a prelude to elucidating its role in lung, heart, gut and kidney development.
Baylor received an initial grant for Phase 1 to find and collect tissue samples from ACDMPV patients and blood samples from family members. Primarily through the ACDA families’ authorization for release of tissue samples, the research team assembled the world’s largest collection of ACDMPV tissue samples for study. It also has blood samples from many parents and siblings. During Phase 1, the researchers demonstrated that they could gather the needed tissue and blood samples and they could amplify the DNA to obtain quantities necessary for research.
DNA amplification is a technique where a short, well defined piece of DNA (not an entire DNA structure) is copied to make an exact duplicate of the original. The technique is repeated and the small piece of DNA is amplified many times, in an exponential manner (2 become 4, then 8 then 16 and so on into the millions). With more quantity of DNA available, analysis is made much easier.
Based on this successful Phase 1 feasibility study, Baylor applied for a follow-on research grant to continue the NIH study for the next phase. The application was not approved because NIH reviewers indicated that while the Baylor approach seemed plausible, it was very difficult research and they felt the chance for success was low. Baylor revised and resubmitted the application, but it was again denied.