Using Drosophila to facilitate the diagnoses of rare human diseases is an area of research that has developed rapidly in the past five years. Technical developments in sequencing human genomes using whole exome (WES) or whole genome sequencing (WGS) have completely changed the landscape of human genetics. It is estimated that there are approximately 30 million people in the US and 400 million worldwide with a rare disease. Many of these patients undergo a diagnostic odyssey and remain undiagnosed for many years. By sequencing their genomes and those of their relatives, we can now discover genetic variations that are rare or ultra-rare. However, considering that there are many polymorphisms in the population, assessing which variant(s) is/are related to the observed symptoms remains a significant challenge. This is precisely where model organisms can contribute and Drosophila is now playing a prominent, strategic role.
The NIH launched the Undiagnosed Diseases Network (UDN) to solicit patients with undiagnosed diseases and try to determine their cause, which are typically genetic in origin. The patients who are enrolled are the most challenging cases in medicine. Twelve clinical sites, a sequencing center, a metabolomics core, and two Model Organisms Screening Centers (MOSC) are supported by the UDN to develop a diagnosis for as many of these patients as possible. To date, over 3,000 patients have applied (https://undiagnosed.hms.harvard.edu/about-us/facts-and-figures/), about 50% have been accepted, and about 30% of the accepted patients have been diagnosed by combining clinical phenotyping, WES or WGS of the proband and 2-3 members of the family, and performing functional studies in worms, flies, or zebrafish. The MOSC Drosophila Core has played a prominent role in this venture and has provided critical data for many of these human genetic diseases (see Table 1). We have also collaborated with the Centers for Mendelian Genomics to assess variant function using Drosophila and facilitate the discovery of new human disease causing genes (Table 1).
Due to the overwhelming success of our strategies, we have been approached by human geneticists from around the world to help in the diagnosis of rare diseases. We are now collaborating with teams in Canada, Pakistan, Belgium, Netherlands, Germany, Switzerland, Korea, Australia, New Zealand, China and several non-UDN participating clinical sites in the USA. Given the quickly expanding number of WES and WGS that are being performed in clinical diagnostic laboratories around the world and the vast number of VUS (variants of unknown significance in genes) as well as variants in genes of unknown significance that are accumulating, there is a strong need to encourage model organism researchers to participate in collaborative research with clinicians. We are working closely with leadership teams for the Canadian Rare Disease Models and Mechanisms Network (RDMM) and related initiatives in Japan (J-RDMM) and the European Union (SolveRD). These publicly funded consortia promote the use of model organisms in rare disease research to engage more model organism researchers around the world to join in this endeavor.
While a precise molecular diagnosis provides a degree of relief and hope to patients who have undergone a diagnostic odyssey, it is just the beginning. Identification of the cellular and biochemical pathways that are at the root of the phenotypes is the most straightforward way to reveal possible drug targets. The fruit fly offers unmatched tools to dissect the molecular pathogenic mechanisms. By rapidly assessing the precise expression pattern and subcellular protein distribution and dynamics, identifying the physical and genetic interactors of the protein/gene of interest, Drosophila researchers can quickly identify potential therapeutic targets. Furthermore, unravelling the molecular players in flies, can potentially identify FDA approved drugs which can then be quickly tested for repurposing. These discoveries have already led to changes in therapeutic approaches in patients, and physicians have applied for compassionate use when appropriate. Discoveries initiated in flies have already altered the treatment for three diseases discovered in the MOSC in collaboration with physicians at BCM, Duke, and Washington University in St. Louis. Hence Drosophila is capable of providing a platform to test existing drugs and develop novel therapeutic approaches.
An important theme that has emerged from functional studies of rare genetic disease is that genes that are affected in pediatric neurological cases (more than 40% of the submitted cases of the UDN) often can provide probing insights into neurodegenerative diseases like Alzheimer's Disease, Parkinson's Disease and Multiple Sclerosis. The observations related to AD and PD are discussed in the previous section.
Table 1. Novel genes or phenotypic expansions identified by the MOSC
| Human gene | Fly gene | Disease | Research Collaborators | Classification |
|---|---|---|---|---|
| ACOX1 | Acox1 | Novel syndrome with ataxia, neuropathy | UDN (BCM/ Wash U) | Phenotypic expansion |
| ANKLE2 | Ankle2 | Microcephaly 16, primary autosomal recessive | CMG (BCM) | Novel gene |
| ARIH1 | ari-1 | Thoracic aortic aneurysms | CMG (U Wash/UT Houston) | Novel gene |
| ATAD3A | belphegor | Harel-Yoon syndrome | CMG (BCM) | Novel gene |
| ATP5F1D | ATP synthase δ | Mitochondrial ATPase synthase deficiency | UDN (Stanford) | Novel gene |
| CACNA1A | cacophony | Early onset developmental delay, ataxia | UDN (TCH) | Phenotypic expansion |
| DNMBP | still life | Vision loss | S. Antonarakis (U Geneva) |
Novel gene |
| DNM1L | Drp1 | Encephalopathy, lethal, due to defective mitochondrial peroxisomal fission 1 | Baylor Genetics | Phenotypic expansion |
| DROSHA | Drosha | Microcephaly, epilepsy | UDN (Duke) | Novel gene |
| EBF3 | knot | Hypotonia, ataxia, and delayed development | UDN (NIH UDP/BCM/TCH) | Novel gene |
| FZR1 | fizzy-related | Epileptic encephalopathy | Peter De Jonghe | Novel gene |
| IRF2BPL | Pits | Neurodevelopmental disorder with regression, abnormal movements, loss of speech and seizures | UDN (Duke/UCLA) | Novel gene |
| MARK3 | par-1 | Vision loss | S. Antonarakis (U Geneva) |
Phenotypic expansion |
| MRPS12 | knockdown | Developmental delay, strabismus, seizures | UDN (Harvard) | Novel gene |
| NR5A1 | ftz-f1 | Non syndromic 46, XX Sex reversal | UDN (BCM/UCLA) | Phenotypic expansion |
| NRD1 | Nardylisin | Global developmental delay, neurodegeneration | UDN (UCLA) | Novel gene |
| OGDHL | Nc73EF | Microcephaly/ataxia; Developmental delay | CMG (BCM) | Novel gene |
| RNF2 | Sce | Microcephaly, hypotonia | UDN (Duke) | Novel gene |
| TBX2 | bifid | Vertebral anomalies, endocrine and T-cell dysfunction | UDN (Duke) | Novel gene |
| TBX3 | bifid | Dysmorphic features, elevated inflammatory markers | UDN (NIH UDP) | Novel gene |
| TENM4 | Ten-m and Ten-a | ID, delayed development | UDN (BCM) | Phenotypic expansion |
| TM2D3 | almondex | Alzheimer's Disease | CHARGE Consortium | Susceptibility locus |
| WDR37 | wdr37 | Epilepsy, developmental delay, dysmorphic features | UDN (NIH) | Novel gene |
Shah PS, Link N, Jang GM, Sharp PP, Zhu T, Swaney DL, Johnson JR, Von Dollen J, Ramage HR, Satkamp L, Newton B, Huttenhain R, Petit MJ, Baum T, Everitt A, Laufman O, Tassetto M, Shales M, Stevenson E, Iglesias GN, Shokat L, Tripathi S, Balasubramaniam V, Webb LG, Aguirre S, Willsey AJ, Garcia-Sastre A, Pollard KS, Cherry S, Gamarnik AV, Marazzi I, Taunton J, Fernandez-Sesma A, Bellen HJ*, Andino R*, Krogan NJ* (2018) Comparative flavivirus-host protein interaction mapping reveals mechanisms of dengue and Zika virus pathogenesis. Cell 175:1931-1945. PMCID: PMC6474419. Recommended by F1000. Covered in Cell 175(7):1728-9, Preview. *Equal Contribution.
Splinter K, Adams DR, Bacino CA, Bellen HJ, Bernstein JA, Cheatle-Jarvela AM, Eng CM, Esteves C, Gahl WA, Hamid R, Jacob HJ, Kikani B, Koeller DM, Kohane IS, Lee BH, Loscalzo J, Luo X, McCray AT, Metz TO, Mulvihill JJ, Nelson SF, Palmer CGS, Phillips JA, 3rd, Pick L, Postlethwait JH, Reuter C, Shashi V, Sweetser DA, Tifft CJ, Walley NM, Wangler MF, Westerfield M, Wheeler MT, Wise AL, Worthey EA, Yamamoto S, Ashley EA, UDN (2018) Effect of genetic diagnosis on patients with previously undiagnosed disease. New England Journal of Medicine 379:2131-2139. PMCID: PMC6481166. Covered in BMJ 363:k4272, Research News.
Marcogliese PC, Shashi V, Spillmann RC, Stong N, Rosenfeld JA, Koenig MK, Martinez-Agosto JA, Herzog M, Chen AH, Dickson PI, Lin HJ, Vera MU, Salamon N, Graham JM, Jr, Ortiz D, Infante E, Steyaert W, Dermaut B, Poppe B, Chung HL, Zuo Z, Lee PT, Kanca O, Xia F, Yang Y, Smith EC, Jasien J, Kansagra S, Spiridigliozzi G, El-Dairi M, Lark R, Riley K, Koeberl DD, Golden-Grant K, UDN, Yamamoto S, Wangler MF, Mirzaa G, Hemelsoet D, Lee B, Nelson SF, Goldstein DB, Bellen HJ*, Pena LDM* (2018) IRF2BPL is associated with neurological phenotypes. American Journal of Human Genetics 103:245-260. PMCID: PMC6081494. *Equal Contribution.
Tan KL, Haelterman NA, Kwartler CS, Regalado ES, Lee PT, Nagarkar-Jaiswal S, Guo DC, Duraine L, Wangler MF, University of Washington Center for Mendelian Genomics, Bamshad MJ, Nickerson DA, Lin G, Milewicz DM, Bellen HJ (2018) Ari-1 regulates myonuclear organization together with Parkin and isassociated with aortic aneurysms. Developmental Cell 45:226-244. PMCID: PMC5920516. Recommended by F1000. Covered in Developmental Cell 45(2):149-50, Preview.
Wang J, Al-Ouran R, Hu Y, Kim SY, Wan YW, Wangler MF, Yamamoto S, Chao HT, Comjean A, Mohr SE, UDN, Perrimon N, Liu Z*, Bellen HJ* (2017) MARRVEL: integration of human and model organism genetic resources to facilitate functional annotation of the human genome. American Journal of Human Genetics 100:843-853. PMCID: PMC5670038. Selected among Best of AJHG 2016-2017. *Equal Contribution.
Yoon WH, Sandoval H, Nagarkar-Jaiswal S, Jaiswal M, Yamamoto S, Haelterman NA, Putluri N, Putluri V, Sreekumar A, Tos T, Aksoy A, Donti T, Graham BH, Ohno M, Nishi E, Hunter J, Muzny DM, Carmichael J, Shen J, Arboleda VA, Nelson SF, Wangler MF, Karaca E, Lupski JR, Bellen HJ (2017) Loss of Nardilysin, a mitochondrial co-chaperone for a-Ketoglutarate Dehydrogenase, promotes mTORC1 activation and neurodegeneration. Neuron 93:115-131. PMCID: PMC5242142.