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Napolitano G, Has C, Schwerk A, Yuan JH, Ullrich C. Potential of Artificial Intelligence to Accelerate Drug Development for Rare Diseases. Pharmaceut Med 2024; 38:79-86. [PMID: 38315404 DOI: 10.1007/s40290-023-00504-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2023] [Indexed: 02/07/2024]
Abstract
The growth in breadth and depth of artificial intelligence (AI) applications has been fast, running hand in hand with the increasing amount of digital data available. Here, we comment on the application of AI in the field of drug development, with a strong focus on the specific achievements and challenges posed by rare diseases. Data paucity and high costs make drug development for rare diseases especially hard. AI can enable otherwise inaccessible approaches based on the large-scale integration of heterogeneous datasets and knowledge bases, guided by expert biological understanding. Obstacles still exist for the routine use of AI in the usually conservative pharmaceutical domain, which can easily become disillusioned. It is crucial to acknowledge that AI is a powerful, supportive tool that can assist but not replace human expertise in the various phases and aspects of drug discovery and development.
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Affiliation(s)
| | - Canan Has
- Centogene GmbH, Alboinstraße 36-42, 12103, Berlin, Germany
| | - Anne Schwerk
- Beriln Institute of Health Center for Regenerative Therapies (BCRT), Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jui-Hung Yuan
- Beriln Institute of Health Center for Regenerative Therapies (BCRT), Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Carsten Ullrich
- Beriln Institute of Health Center for Regenerative Therapies (BCRT), Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
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2
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Herbst C, Bothe V, Wegler M, Axer-Schaefer S, Audebert-Bellanger S, Gecz J, Cogne B, Feldman HB, Horn AHC, Hurst ACE, Kelly MA, Kruer MC, Kurolap A, Laquerriere A, Li M, Mark PR, Morawski M, Nizon M, Pastinen T, Polster T, Saugier-Veber P, SeSong J, Sticht H, Stieler JT, Thifffault I, van Eyk CL, Marcorelles P, Vezain-Mouchard M, Abou Jamra R, Oppermann H. Heterozygous loss-of-function variants in DOCK4 cause neurodevelopmental delay and microcephaly. Hum Genet 2024; 143:455-469. [PMID: 38526744 PMCID: PMC11043173 DOI: 10.1007/s00439-024-02655-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/09/2024] [Indexed: 03/27/2024]
Abstract
Neurons form the basic anatomical and functional structure of the nervous system, and defects in neuronal differentiation or formation of neurites are associated with various psychiatric and neurodevelopmental disorders. Dynamic changes in the cytoskeleton are essential for this process, which is, inter alia, controlled by the dedicator of cytokinesis 4 (DOCK4) through the activation of RAC1. Here, we clinically describe 7 individuals (6 males and one female) with variants in DOCK4 and overlapping phenotype of mild to severe global developmental delay. Additional symptoms include coordination or gait abnormalities, microcephaly, nonspecific brain malformations, hypotonia and seizures. Four individuals carry missense variants (three of them detected de novo) and three individuals carry null variants (two of them maternally inherited). Molecular modeling of the heterozygous missense variants suggests that the majority of them affect the globular structure of DOCK4. In vitro functional expression studies in transfected Neuro-2A cells showed that all missense variants impaired neurite outgrowth. Furthermore, Dock4 knockout Neuro-2A cells also exhibited defects in promoting neurite outgrowth. Our results, including clinical, molecular and functional data, suggest that loss-of-function variants in DOCK4 probable cause a variable spectrum of a novel neurodevelopmental disorder with microcephaly.
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Affiliation(s)
- Charlotte Herbst
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Viktoria Bothe
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Meret Wegler
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Susanne Axer-Schaefer
- Department of Epileptology, Krankenhaus Mara Bethel Epilepsy Center Medical School OWL, Bielefeld University, Campus Bethel, Bielefeld, Germany
| | | | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Benjamin Cogne
- Service de Génétique Médicale, CHU Nantes, 44000, Nantes, France
- l'institut du Thorax, Nantes Université, CHU Nantes, CNRS, INSERM, 44000, Nantes, France
| | - Hagit Baris Feldman
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anselm H C Horn
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Erlangen National High Performance Computing Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Melissa A Kelly
- HudsonAlpha Clinical Services Lab, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Michael C Kruer
- Barrow Neurological Institute, Phoenix Children's Hospital University of Arizona College of Medicine, Phoenix, USA
| | - Alina Kurolap
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Annie Laquerriere
- Department of Anatomy, Inserm U1245 and CHU Rouen, Univ Rouen Normandie, 76000, Rouen, France
| | - Megan Li
- Invitae Corp, San Francisco, CA, USA
| | - Paul R Mark
- Division of Medical Genetics, Helen DeVos Children's Hospital, Corewell Health, Grand Rapids, MI, USA
| | - Markus Morawski
- Center of Neuropathology and Brain Research, Medical Faculty, Paul Flechsig Institute, University of Leipzig, Leipzig, Germany
| | - Mathilde Nizon
- Service de Génétique Médicale, CHU Nantes, 44000, Nantes, France
- l'institut du Thorax, Nantes Université, CHU Nantes, CNRS, INSERM, 44000, Nantes, France
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, USA
- University of Missouri Kansas City School of Medicine, Kansas City, USA
| | - Tilman Polster
- Department of Epileptology, Krankenhaus Mara Bethel Epilepsy Center Medical School OWL, Bielefeld University, Campus Bethel, Bielefeld, Germany
| | - Pascale Saugier-Veber
- Department of Genetics and Reference Center for Developmental Disorders, Inserm U1245 and CHU Rouen, Univ Rouen Normandie, 76000, Rouen, France
| | - Jang SeSong
- Genomic Medicine Institute, Seoul National University, Seoul, Republic of Korea
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jens T Stieler
- Center of Neuropathology and Brain Research, Medical Faculty, Paul Flechsig Institute, University of Leipzig, Leipzig, Germany
| | - Isabelle Thifffault
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, USA
- University of Missouri Kansas City School of Medicine, Kansas City, USA
| | - Clare L van Eyk
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | | | - Myriam Vezain-Mouchard
- Department of Genetics and Reference Center for Developmental Disorders, Inserm U1245 and CHU Rouen, Univ Rouen Normandie, 76000, Rouen, France
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Henry Oppermann
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany.
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Rahit KMTH, Avramovic V, Chong JX, Tarailo-Graovac M. GPAD: a natural language processing-based application to extract the gene-disease association discovery information from OMIM. BMC Bioinformatics 2024; 25:84. [PMID: 38413851 PMCID: PMC10898068 DOI: 10.1186/s12859-024-05693-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 02/09/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Thousands of genes have been associated with different Mendelian conditions. One of the valuable sources to track these gene-disease associations (GDAs) is the Online Mendelian Inheritance in Man (OMIM) database. However, most of the information in OMIM is textual, and heterogeneous (e.g. summarized by different experts), which complicates automated reading and understanding of the data. Here, we used Natural Language Processing (NLP) to make a tool (Gene-Phenotype Association Discovery (GPAD)) that could syntactically process OMIM text and extract the data of interest. RESULTS GPAD applies a series of language-based techniques to the text obtained from OMIM API to extract GDA discovery-related information. GPAD can inform when a particular gene was associated with a specific phenotype, as well as the type of validation-whether through model organisms or cohort-based patient-matching approaches-for such an association. GPAD extracted data was validated with published reports and was compared with large language model. Utilizing GPAD's extracted data, we analysed trends in GDA discoveries, noting a significant increase in their rate after the introduction of exome sequencing, rising from an average of about 150-250 discoveries each year. Contrary to hopes of resolving most GDAs for Mendelian disorders by now, our data indicate a substantial decline in discovery rates over the past five years (2017-2022). This decline appears to be linked to the increasing necessity for larger cohorts to substantiate GDAs. The rising use of zebrafish and Drosophila as model organisms in providing evidential support for GDAs is also observed. CONCLUSIONS GPAD's real-time analyzing capacity offers an up-to-date view of GDA discovery and could help in planning and managing the research strategies. In future, this solution can be extended or modified to capture other information in OMIM and scientific literature.
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Affiliation(s)
- K M Tahsin Hassan Rahit
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Vladimir Avramovic
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Jessica X Chong
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
- Brotman-Baty Institute, Seattle, WA, 98195, USA
| | - Maja Tarailo-Graovac
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, T2N 4N1, Canada.
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Parker W, Anderson LG, Jones JP, Anderson R, Williamson L, Bono-Lunn D, Konsoula Z. The Dangers of Acetaminophen for Neurodevelopment Outweigh Scant Evidence for Long-Term Benefits. CHILDREN (BASEL, SWITZERLAND) 2023; 11:44. [PMID: 38255358 PMCID: PMC10814214 DOI: 10.3390/children11010044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/20/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024]
Abstract
Based on available data that include approximately 20 lines of evidence from studies in laboratory animal models, observations in humans, correlations in time, and pharmacological/toxicological considerations, it has been concluded without reasonable doubt and with no evidence to the contrary that exposure of susceptible babies and children to acetaminophen (paracetamol) induces many, if not most, cases of autism spectrum disorder (ASD). However, the relative number of cases of ASD that might be induced by acetaminophen has not yet been estimated. Here, we examine a variety of evidence, including the acetaminophen-induced reduction of social awareness in adults, the prevalence of ASD through time, and crude estimates of the relative number of ASD cases induced by acetaminophen during various periods of neurodevelopment. We conclude that the very early postpartum period poses the greatest risk for acetaminophen-induced ASD, and that nearly ubiquitous use of acetaminophen during early development could conceivably be responsible for the induction in the vast majority, perhaps 90% or more, of all cases of ASD. Despite over a decade of accumulating evidence that acetaminophen is harmful for neurodevelopment, numerous studies demonstrate that acetaminophen is frequently administered to children in excess of currently approved amounts and under conditions in which it provides no benefit. Further, studies have failed to demonstrate long-term benefits of acetaminophen for the pediatric population, leaving no valid rationale for continued use of the drug in that population given its risks to neurodevelopment.
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Affiliation(s)
- William Parker
- Department of Psychology and Neuroscience, University of North Carolina, Chapel Hill, NC 27599, USA
- WPLab, Inc., Durham, NC 27707, USA
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | | | | | | | - Lauren Williamson
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099, USA;
| | - Dillan Bono-Lunn
- Department of Public Policy, University of North Carolina, Chapel Hill, NC 27599, USA;
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Carrizosa-Molina T, Casillas-Díaz N, Pérez-Nadador I, Vales-Villamarín C, López-Martínez MÁ, Riveiro-Álvarez R, Wilhelm L, Cervera-Juanes R, Garcés C, Lomniczi A, Soriano-Guillén L. Methylation analysis by targeted bisulfite sequencing in large for gestational age (LGA) newborns: the LARGAN cohort. Clin Epigenetics 2023; 15:191. [PMID: 38093359 PMCID: PMC10717641 DOI: 10.1186/s13148-023-01612-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 12/02/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND In 1990, David Barker proposed that prenatal nutrition is directly linked to adult cardiovascular disease. Since then, the relationship between adult cardiovascular risk, metabolic syndrome and birth weight has been widely documented. Here, we used the TruSeq Methyl Capture EPIC platform to compare the methylation patterns in cord blood from large for gestational age (LGA) vs adequate for gestational age (AGA) newborns from the LARGAN cohort. RESULTS We found 1672 differentially methylated CpGs (DMCs) with a nominal p < 0.05 and 48 differentially methylated regions (DMRs) with a corrected p < 0.05 between the LGA and AGA groups. A systems biology approach identified several biological processes significantly enriched with genes in association with DMCs with FDR < 0.05, including regulation of transcription, regulation of epinephrine secretion, norepinephrine biosynthesis, receptor transactivation, forebrain regionalization and several terms related to kidney and cardiovascular development. Gene ontology analysis of the genes in association with the 48 DMRs identified several significantly enriched biological processes related to kidney development, including mesonephric duct development and nephron tubule development. Furthermore, our dataset identified several DNA methylation markers enriched in gene networks involved in biological pathways and rare diseases of the cardiovascular system, kidneys, and metabolism. CONCLUSIONS Our study identified several DMCs/DMRs in association with fetal overgrowth. The use of cord blood as a material for the identification of DNA methylation biomarkers gives us the possibility to perform follow-up studies on the same patients as they grow. These studies will not only help us understand how the methylome responds to continuum postnatal growth but also link early alterations of the DNA methylome with later clinical markers of growth and metabolic fitness.
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Affiliation(s)
- Tamara Carrizosa-Molina
- Department of Pediatrics, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Avda. Reyes Católicos, 2, 28040, Madrid, Spain
| | - Natalia Casillas-Díaz
- Department of Pediatrics, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Avda. Reyes Católicos, 2, 28040, Madrid, Spain
| | | | | | - Miguel Ángel López-Martínez
- Department of Genetics and Genomics, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Rosa Riveiro-Álvarez
- Department of Genetics and Genomics, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - Larry Wilhelm
- Department of Physiology and Pharmacology, Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Rita Cervera-Juanes
- Department of Physiology and Pharmacology, Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Carmen Garcés
- Lipid Research Laboratory, IIS-Fundación Jiménez Díaz, Madrid, Spain
| | - Alejandro Lomniczi
- Department of Physiology and Biophysics, Dalhousie University School of Medicine, 5850 College Street, Halifax, NS, B3H 4R2, Canada.
| | - Leandro Soriano-Guillén
- Department of Pediatrics, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Avda. Reyes Católicos, 2, 28040, Madrid, Spain.
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Kaldunski ML, Smith JR, Brodie KC, De Pons JL, Demos WM, Gibson AC, Hayman GT, Lamers L, Laulederkind SJF, Thorat K, Thota J, Tutaj MA, Tutaj M, Vedi M, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. Rare disease research resources at the Rat Genome Database. Genetics 2023; 224:iyad078. [PMID: 37119810 PMCID: PMC10411567 DOI: 10.1093/genetics/iyad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/05/2023] [Accepted: 04/19/2023] [Indexed: 05/01/2023] Open
Abstract
Rare diseases individually affect relatively few people, but as a group they impact considerable numbers of people. The Rat Genome Database (https://rgd.mcw.edu) is a knowledgebase that offers resources for rare disease research. This includes disease definitions, genes, quantitative trail loci (QTLs), genetic variants, annotations to published literature, links to external resources, and more. One important resource is identifying relevant cell lines and rat strains that serve as models for disease research. Diseases, genes, and strains have report pages with consolidated data, and links to analysis tools. Utilizing these globally accessible resources for rare disease research, potentiating discovery of mechanisms and new treatments, can point researchers toward solutions to alleviate the suffering of those afflicted with these diseases.
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Affiliation(s)
- Mary L Kaldunski
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jennifer R Smith
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kent C Brodie
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jeffrey L De Pons
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wendy M Demos
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Adam C Gibson
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - G Thomas Hayman
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Logan Lamers
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stanley J F Laulederkind
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ketaki Thorat
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jyothi Thota
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marek A Tutaj
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Monika Tutaj
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mahima Vedi
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shur-Jen Wang
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stacy Zacher
- Finance and Administration, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melinda R Dwinell
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Anne E Kwitek
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Joint Department of Biomedical Engineering, Marquette University & Medical College of Wisconsin, Milwaukee, WI 53226, USA
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Vanselow S, Wahn V, Schuetz C. Activated PI3Kδ syndrome - reviewing challenges in diagnosis and treatment. Front Immunol 2023; 14:1208567. [PMID: 37600808 PMCID: PMC10432830 DOI: 10.3389/fimmu.2023.1208567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/04/2023] [Indexed: 08/22/2023] Open
Abstract
Activated PI3Kδ syndrome (APDS) is a rare inborn error of immunity (IEI) characterized primarily by frequent infections, lymphoproliferation and autoimmunity. Since its initial description in 2013, APDS has become part of the growing group of nearly 500 IEIs affecting various components of the immune system. The two subtypes of APDS - APDS1 and APDS2 - are caused by variants in the PIK3CD and PIK3R1 genes, respectively. Due to the rarity of the disease and the heterogeneous clinical picture, many patients are not diagnosed until years after symptom onset. Another challenge is the large number of PIK3CD and PIK3R1 variants whose functional significance for developing APDS is inconclusive. Treatment of APDS has so far been mostly symptom-oriented with immunoglobulin replacement therapy, immunosuppressive therapies and antibiotic or antiviral prophylaxes. Additionally, allogeneic stem cell transplantation as well as new targeted therapies are options targeting the root cause that may improve patients' quality of life and life expectancy. However, the clinical course of the disease is difficult to predict which complicates the choice of appropriate therapies. This review article discusses diagnostic procedures and current and future treatment options, and highlights the difficulties that physicians, patients and their caretakers face in managing this complex disease. This article is based on cohort studies, the German and US guidelines on the management of primary immunodeficiencies as well as on published experience with diagnosis and compiled treatment experience for APDS.
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Affiliation(s)
- Sven Vanselow
- Infill Healthcare Communication, Königswinter, Germany
| | - Volker Wahn
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine at Charité University Hospital Berlin, Berlin, Germany
| | - Catharina Schuetz
- Medical Faculty of The Technical University (TU) Dresden, Department of Pediatrics, University Hospital Carl Gustav Carus, Dresden, Germany
- University Center for Rare Diseases, University Hospital Carl Gustav Carus, Dresden, Germany
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Exploring the Potential Challenges for Developing Generic Orphan Drugs for Rare Diseases: A Survey of US and European Markets. Value Health Reg Issues 2023; 35:87-94. [PMID: 36921379 DOI: 10.1016/j.vhri.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/08/2022] [Accepted: 01/04/2023] [Indexed: 03/18/2023]
Abstract
OBJECTIVES The US Food and Drug Administration in 1983 and the European Union's European Medicines Agency in 2000 implemented the orphan drug development program for rare diseases. The study aimed to find the potential challenges encountered by generic companies in developing generics for rare diseases. METHODS We performed a thematic analysis, which consists of qualitative and quantitative research. For data analysis of approved orphan drugs, we used statistical methods, and for the industrial case study, we selected 14 generic companies and conducted semistructured interviews related to 10 critical areas of drug development. RESULTS The orphan drug approvals were classified into 4 categories: the number of orphan approvals, pediatric claims, formulation, and therapeutic areas. We analyzed the approvals from 2001 to 2021; the Food and Drug Administration approved 815 drugs and European Medicines Agency approved 258 drugs. The pediatric orphan approvals were analyzed from 2010 to 2021; the average percentage of orphan drugs claim pediatric exclusivity during this period was found to be 31.8%. In formulation, we found the highest percentage of drugs belong to small molecules at 71%. In the therapeutic class, oncology drugs have a majority of approvals at 25%. The industrial case study responses revealed that the major challenge for drug development is the complexity of the disease at 21%, followed by the limited market at 17%. CONCLUSIONS There is a high need for generic orphan drugs in the developing countries. The generic companies can use the opportunities provided by health authorities for the benefit of both the company and the patient perspective.
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Alves VM, Korn D, Pervitsky V, Thieme A, Capuzzi S, Baker N, Chirkova R, Ekins S, Muratov EN, Hickey A, Tropsha A. Knowledge-based approaches to drug discovery for rare diseases. Drug Discov Today 2022; 27:490-502. [PMID: 34718207 PMCID: PMC9124594 DOI: 10.1016/j.drudis.2021.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/13/2021] [Accepted: 10/21/2021] [Indexed: 02/03/2023]
Abstract
The conventional drug discovery pipeline has proven to be unsustainable for rare diseases. Herein, we discuss recent advances in biomedical knowledge mining applied to discovering therapeutics for rare diseases. We summarize current chemogenomics data of relevance to rare diseases and provide a perspective on the effectiveness of machine learning (ML) and biomedical knowledge graph mining in rare disease drug discovery. We illustrate the power of these methodologies using a chordoma case study. We expect that a broader application of knowledge graph mining and artificial intelligence (AI) approaches will expedite the discovery of viable drug candidates against both rare and common diseases.
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Affiliation(s)
- Vinicius M. Alves
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA.,UNC Catalyst for Rare Diseases, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Daniel Korn
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Vera Pervitsky
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Andrew Thieme
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Stephen Capuzzi
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Nancy Baker
- ParlezChem, 123 W Union Street, Hillsborough, NC, 27278, USA
| | - Rada Chirkova
- Department of Computer Science, North Carolina State University, Raleigh, NC, 27695-8206, USA
| | - Sean Ekins
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab 3510 Raleigh, North Carolina 27606, USA
| | - Eugene N. Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA.,Department of Pharmaceutical Sciences, Federal University of Paraiba, Joao Pessoa, PB, Brazil
| | - Anthony Hickey
- UNC Catalyst for Rare Diseases, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA.,Corresponding Authors: Addresses for correspondence: Room 1079, 120 Mason Farm Rd, Genetics Medicine Building, University of North Carolina, Chapel Hill, NC 27514; Telephone: (919) 966-2955; FAX: (919) 966-0204; . 100K Beard Hall, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA; Telephone: (919) 966-2955; FAX: (919) 966-0204;
| | - Alexander Tropsha
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA.,Corresponding Authors: Addresses for correspondence: Room 1079, 120 Mason Farm Rd, Genetics Medicine Building, University of North Carolina, Chapel Hill, NC 27514; Telephone: (919) 966-2955; FAX: (919) 966-0204; . 100K Beard Hall, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA; Telephone: (919) 966-2955; FAX: (919) 966-0204;
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