A network biology approach to unraveling inherited axonopathies. 2019

Dana M Bis-Brewer, and Matt C Danzi, and Stefan Wuchty, and Stephan Züchner
Dr. John T. Macdonald Foundation Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA.

Inherited axonopathies represent a spectrum of disorders unified by the common pathological mechanism of length-dependent axonal degeneration. Progressive axonal degeneration can lead to both Charcot-Marie-Tooth type 2 (CMT2) and Hereditary Spastic Paraplegia (HSP) depending on the affected neurons: peripheral motor and sensory nerves or central nervous system axons of the corticospinal tract and dorsal columns, respectively. Inherited axonopathies display an extreme degree of genetic heterogeneity of Mendelian high-penetrance genes. High locus heterogeneity is potentially advantageous to deciphering disease etiology by providing avenues to explore biological pathways in an unbiased fashion. Here, we investigate 'gene modules' in inherited axonopathies through a network-based analysis of the Human Integrated Protein-Protein Interaction rEference (HIPPIE) database. We demonstrate that CMT2 and HSP disease proteins are significantly more connected than randomly expected. We define these connected disease proteins as 'proto-modules' and show the topological relationship of these proto-modules by evaluating their overlap through a shortest-path based measurement. In particular, we observe that the CMT2 and HSP proto-modules significantly overlapped, demonstrating a shared genetic etiology. Comparison of both modules with other diseases revealed an overlapping relationship between HSP and hereditary ataxia and between CMT2 + HSP and hereditary ataxia. We then use the DIseAse Module Detection (DIAMOnD) algorithm to expand the proto-modules into comprehensive disease modules. Analysis of disease modules thus obtained reveals an enrichment of ribosomal proteins and pathways likely central to inherited axonopathy pathogenesis, including protein processing in the endoplasmic reticulum, spliceosome, and mRNA processing. Furthermore, we determine pathways specific to each axonopathy by analyzing the difference of the axonopathy modules. CMT2-specific pathways include glycolysis and gluconeogenesis-related processes, while HSP-specific pathways include processes involved in viral infection response. Unbiased characterization of inherited axonopathy disease modules will provide novel candidate disease genes, improve interpretation of candidate genes identified through patient data, and guide therapy development.

UI MeSH Term Description Entries
D002607 Charcot-Marie-Tooth Disease A hereditary motor and sensory neuropathy transmitted most often as an autosomal dominant trait and characterized by progressive distal wasting and loss of reflexes in the muscles of the legs (and occasionally involving the arms). Onset is usually in the second to fourth decade of life. This condition has been divided into two subtypes, hereditary motor and sensory neuropathy (HMSN) types I and II. HMSN I is associated with abnormal nerve conduction velocities and nerve hypertrophy, features not seen in HMSN II. (Adams et al., Principles of Neurology, 6th ed, p1343) Atrophy, Muscular, Peroneal,HMSN Type I,HMSN Type II,Hereditary Motor and Sensory-Neuropathy Type II,Hereditary Motor, and Sensory Neuropathy Type I,Muscular Atrophy, Peroneal,Peroneal Muscular Atrophy,Roussy-Levy Syndrome,Charcot-Marie Disease,Charcot-Marie-Tooth Disease, Autosomal Dominant, With Focally Folded Myelin Sheaths, Type 1A,Charcot-Marie-Tooth Disease, Autosomal Dominant, with Focally Folded Myelin Sheaths, Type 1B,Charcot-Marie-Tooth Disease, Demyelinating, Type 1A,Charcot-Marie-Tooth Disease, Demyelinating, Type 1B,Charcot-Marie-Tooth Disease, Slow Nerve Conduction Type, Linked To Duffy,Charcot-Marie-Tooth Disease, Type 1A,Charcot-Marie-Tooth Disease, Type 1B,Charcot-Marie-Tooth Disease, Type I,Charcot-Marie-Tooth Disease, Type IA,Charcot-Marie-Tooth Disease, Type IB,Charcot-Marie-Tooth Disease, Type II,Charcot-Marie-Tooth Hereditary Neuropathy,Charcot-Marie-Tooth Neuropathy, Type 1A,Charcot-Marie-Tooth Neuropathy, Type 1B,Charcot-Marie-Tooth Syndrome,HMN Distal Type I,HMSN 1A,HMSN 1B,HMSN I,HMSN IA,HMSN IB,HMSN II,HMSN1A,HMSN1B,Hereditary Areflexic Dystasia,Hereditary Motor And Sensory Neuropathy IB,Hereditary Motor and Sensory Neuropathy 1A,Hereditary Motor and Sensory Neuropathy 1B,Hereditary Motor and Sensory Neuropathy IA,Hereditary Type I Motor and Sensory Neuropathy,Neuropathy, Type I Hereditary Motor and Sensory,Neuropathy, Type II Hereditary Motor and Sensory,Roussy Levy Hereditary Areflexic Dystasia,Roussy-Levy Disease,Roussy-Levy Hereditary Areflexic Dystasia,Areflexic Dystasia, Hereditary,Areflexic Dystasias, Hereditary,Atrophies, Peroneal Muscular,Atrophy, Peroneal Muscular,Charcot Marie Disease,Charcot Marie Tooth Disease,Charcot Marie Tooth Disease, Type 1A,Charcot Marie Tooth Disease, Type 1B,Charcot Marie Tooth Disease, Type I,Charcot Marie Tooth Disease, Type IA,Charcot Marie Tooth Disease, Type IB,Charcot Marie Tooth Disease, Type II,Charcot Marie Tooth Hereditary Neuropathy,Charcot Marie Tooth Neuropathy, Type 1A,Charcot Marie Tooth Neuropathy, Type 1B,Charcot Marie Tooth Syndrome,Dystasia, Hereditary Areflexic,Dystasias, Hereditary Areflexic,Hereditary Areflexic Dystasias,Hereditary Motor and Sensory Neuropathy Type II,Hereditary Neuropathy, Charcot-Marie-Tooth,Muscular Atrophies, Peroneal,Peroneal Muscular Atrophies,Roussy Levy Disease,Roussy Levy Syndrome,Syndrome, Charcot-Marie-Tooth,Syndrome, Roussy-Levy
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000465 Algorithms A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task. Algorithm
D015415 Biomarkers Measurable and quantifiable biological parameters (e.g., specific enzyme concentration, specific hormone concentration, specific gene phenotype distribution in a population, presence of biological substances) which serve as indices for health- and physiology-related assessments, such as disease risk, psychiatric disorders, ENVIRONMENTAL EXPOSURE and its effects, disease diagnosis; METABOLIC PROCESSES; SUBSTANCE ABUSE; PREGNANCY; cell line development; EPIDEMIOLOGIC STUDIES; etc. Biochemical Markers,Biological Markers,Biomarker,Clinical Markers,Immunologic Markers,Laboratory Markers,Markers, Biochemical,Markers, Biological,Markers, Clinical,Markers, Immunologic,Markers, Laboratory,Markers, Serum,Markers, Surrogate,Markers, Viral,Serum Markers,Surrogate Markers,Viral Markers,Biochemical Marker,Biologic Marker,Biologic Markers,Clinical Marker,Immune Marker,Immune Markers,Immunologic Marker,Laboratory Marker,Marker, Biochemical,Marker, Biological,Marker, Clinical,Marker, Immunologic,Marker, Laboratory,Marker, Serum,Marker, Surrogate,Serum Marker,Surrogate End Point,Surrogate End Points,Surrogate Endpoint,Surrogate Endpoints,Surrogate Marker,Viral Marker,Biological Marker,End Point, Surrogate,End Points, Surrogate,Endpoint, Surrogate,Endpoints, Surrogate,Marker, Biologic,Marker, Immune,Marker, Viral,Markers, Biologic,Markers, Immune
D015419 Spastic Paraplegia, Hereditary A group of inherited diseases that share similar phenotypes but are genetically diverse. Different genetic loci for autosomal recessive, autosomal dominant, and x-linked forms of hereditary spastic paraplegia have been identified. Clinically, patients present with slowly progressive distal limb weakness and lower extremity spasticity. Peripheral sensory neurons may be affected in the later stages of the disease. (J Neurol Neurosurg Psychiatry 1998 Jan;64(1):61-6; Curr Opin Neurol 1997 Aug;10(4):313-8) Hereditary Spastic Paraplegia,X-Linked, Spastic Paraplegia, Hereditary,Autosomal Dominant Hereditary Spastic Paraplegia,Autosomal Dominant Spastic Paraplegia Hereditary,Autosomal Recessive Hereditary Spastic Paraplegia,Autosomal Recessive Spastic Paraplegia, Hereditary,CMT with Pyramidal Features,Charcot-Marie-Tooth Disease with Pyramidal Features, Autosomal Dominant,HMSN 5,HMSN Type V,HMSN V,HMSN V (Hereditary Motor and Sensory Neuropathy Type V),Hereditary Autosomal Dominant Spastic Paraplegia,Hereditary Autosomal Recessive Spastic Paraplegia,Hereditary Motor And Sensory Neuropathy V,Hereditary Motor and Sensory Neuropathy 5,Hereditary Motor-Sensory Neuropathy with Pyramidal Signs,Hereditary Spastic Paraplegia, Autosomal Recessive,Hereditary X-Linked Recessive Spastic Paraplegia,Hereditary, Spastic Paraplegia, Autosomal Dominant,Hereditary, Spastic Paraplegia, X-Linked Recessive,Hypertrophic Motor-Sensory Neuropathy-Spastic Paraplegia,Paraplegia, Spastic, Hereditary,Peroneal Muscular Atrophy with Pyramidal Features, Autosomal Dominant,Spastic Paraplegia 2,Spastic Paraplegia Type 2,Spastic Paraplegia, Autosomal Dominant, Hereditary,Spastic Paraplegia, Autosomal Recessive, Hereditary,Spastic Paraplegia, Hereditary, Autosomal Dominant,Spastic Paraplegia, Hereditary, Autosomal Recessive,Spastic Paraplegia, Hereditary, X-Linked Recessive,Spastic Paraplegia, X-Linked Recessive, Hereditary,Spastic Paraplegia-Hypertrophic Motor-Sensory Neuropathy,Type V Hereditary Motor and Sensory Neuropathy,X Linked Recessive Hereditary Spastic Paraplegia,X-linked Recessive Hereditary Spastic Paraplegia,Charcot Marie Tooth Disease with Pyramidal Features, Autosomal Dominant,Hereditary Motor Sensory Neuropathy with Pyramidal Signs,Hereditary Spastic Paraplegias,Hereditary X Linked Recessive Spastic Paraplegia,Hypertrophic Motor Sensory Neuropathy Spastic Paraplegia,Paraplegia, Hereditary Spastic,Paraplegias, Hereditary Spastic,Spastic Paraplegia Hypertrophic Motor Sensory Neuropathy,Spastic Paraplegias, Hereditary,Type V, HMSN
D053263 Gene Regulatory Networks Interacting DNA-encoded regulatory subsystems in the GENOME that coordinate input from activator and repressor TRANSCRIPTION FACTORS during development, cell differentiation, or in response to environmental cues. The networks function to ultimately specify expression of particular sets of GENES for specific conditions, times, or locations. Gene Circuits,Gene Modules,Gene Networks,Transcriptional Networks,Gene Module,Circuit, Gene,Circuits, Gene,Gene Circuit,Gene Network,Gene Regulatory Network,Module, Gene,Modules, Gene,Network, Gene,Network, Gene Regulatory,Network, Transcriptional,Networks, Gene,Networks, Gene Regulatory,Networks, Transcriptional,Regulatory Network, Gene,Regulatory Networks, Gene,Transcriptional Network
D060066 Protein Interaction Maps Graphs representing sets of measurable, non-covalent physical contacts with specific PROTEINS in living organisms or in cells. Protein-Protein Interaction Map,Protein-Protein Interaction Network,Protein Interaction Networks,Interaction Map, Protein,Interaction Map, Protein-Protein,Interaction Network, Protein,Interaction Network, Protein-Protein,Map, Protein Interaction,Map, Protein-Protein Interaction,Network, Protein Interaction,Network, Protein-Protein Interaction,Protein Interaction Map,Protein Interaction Network,Protein Protein Interaction Map,Protein Protein Interaction Network,Protein-Protein Interaction Maps,Protein-Protein Interaction Networks
D025941 Protein Interaction Mapping Methods for determining interaction between PROTEINS. Interaction Mapping, Protein,Interaction Mappings, Protein,Mapping, Protein Interaction,Mappings, Protein Interaction,Protein Interaction Mappings

Related Publications

Dana M Bis-Brewer, and Matt C Danzi, and Stefan Wuchty, and Stephan Züchner
December 2020, Genetics in medicine : official journal of the American College of Medical Genetics,
Dana M Bis-Brewer, and Matt C Danzi, and Stefan Wuchty, and Stephan Züchner
January 2007, Molecular systems biology,
Dana M Bis-Brewer, and Matt C Danzi, and Stefan Wuchty, and Stephan Züchner
January 2009, Proceedings of the National Academy of Sciences of the United States of America,
Dana M Bis-Brewer, and Matt C Danzi, and Stefan Wuchty, and Stephan Züchner
January 2024, Pharmaceuticals (Basel, Switzerland),
Dana M Bis-Brewer, and Matt C Danzi, and Stefan Wuchty, and Stephan Züchner
January 2011, Wiley interdisciplinary reviews. Systems biology and medicine,
Dana M Bis-Brewer, and Matt C Danzi, and Stefan Wuchty, and Stephan Züchner
January 2015, PloS one,
Dana M Bis-Brewer, and Matt C Danzi, and Stefan Wuchty, and Stephan Züchner
September 2010, Current opinion in drug discovery & development,
Dana M Bis-Brewer, and Matt C Danzi, and Stefan Wuchty, and Stephan Züchner
January 2023, Frontiers in immunology,
Dana M Bis-Brewer, and Matt C Danzi, and Stefan Wuchty, and Stephan Züchner
January 2012, PLoS computational biology,
Dana M Bis-Brewer, and Matt C Danzi, and Stefan Wuchty, and Stephan Züchner
July 2007, Cellular and molecular life sciences : CMLS,
Copied contents to your clipboard!