Multi-Omics for Biomarker Discovery and Target Validation in Biofluids for Amyotrophic Lateral Sclerosis Diagnosis.

Amyotrophic lateral sclerosis (ALS) is a rare but usually fatal neurodegenerative disease characterized by motor neuron degeneration in the brain and the spinal cord. Two forms are recognized, the familial that accounts for 5-10% and the sporadic that accounts for the rest. New studies suggest that ALS is a highly heterogeneous disease, and this diversity is a major reason for the lack of successful therapeutic treatments. Indeed, only two drugs (riluzole and edaravone) have been approved that provide a limited improvement in the quality of life. Presently, the diagnosis of ALS is based on clinical examination and lag period from the onset of symptoms to the final diagnosis is ∼12 months. Therefore, the discovery of robust molecular biomarkers that can assist in the diagnosis is of major importance. DNA sequencing to identify pathogenic gene variants can be applied in the cases of familial ALS. However, it is not a routinely used diagnostic procedure and most importantly, it cannot be applied in the diagnosis of sporadic ALS. In this expert review, the current approaches in identification of new ALS biomarkers are discussed. The advent of various multi-omics biotechnology platforms, including miRNomics, proteomics, metabolomics, metallomics, volatolomics, and viromics, has assisted in the identification of new biomarkers. The biofluids are the most preferable material for the analysis of potential biomarkers (such as proteins and cell-free miRNAs), since they are easily obtained. In the near future, the biofluid-based biomarkers will be indispensable to classify different ALS subtypes and understand the molecular heterogeneity of the disease.

[1]  Joseph R. Berger,et al.  ALS syndrome in patients with HIV-1 infection , 2006, Journal of the Neurological Sciences.

[2]  A. Al-Chalabi,et al.  Quantification of reverse transcriptase in ALS and elimination of a novel retroviral candidate , 2008, Neurology.

[3]  A. Chiò,et al.  Global Epidemiology of Amyotrophic Lateral Sclerosis: A Systematic Review of the Published Literature , 2013, Neuroepidemiology.

[4]  T. Moens,et al.  Specific biomarkers for C9orf72 FTD/ALS could expedite the journey towards effective therapies , 2017, EMBO Molecular Medicine.

[5]  J. Hardy,et al.  A clinical and pathological study of motor neurone disease on Guam. , 2001, Brain : a journal of neurology.

[6]  H. Sasaki,et al.  Identification of plasma microRNAs as a biomarker of sporadic Amyotrophic Lateral Sclerosis , 2015, Molecular Brain.

[7]  Timothy A. Miller,et al.  Phosphorylated neurofilament heavy chain: A biomarker of survival for C9ORF72‐associated amyotrophic lateral sclerosis , 2017, Annals of neurology.

[8]  P. Andersen,et al.  Neurofilaments in the diagnosis of motoneuron diseases: a prospective study on 455 patients , 2015, Journal of Neurology, Neurosurgery & Psychiatry.

[9]  A. Ludolph,et al.  Systemic dysregulation of TDP-43 binding microRNAs in amyotrophic lateral sclerosis , 2013, Acta Neuropathologica Communications.

[10]  G. Logroscino,et al.  Elevated cerebrospinal fluid neurofilament light levels in patients with amyotrophic lateral sclerosis: a possible marker of disease severity and progression , 2012, European journal of neurology.

[11]  O. Witte,et al.  Neurofilament markers for ALS correlate with extent of upper and lower motor neuron disease , 2017, Neurology.

[12]  P. Wong,et al.  Susceptibility-weighted MRI in mild traumatic brain injury , 2015, Neurology.

[13]  Raquel Manzano,et al.  MicroRNA-206: A Potential Circulating Biomarker Candidate for Amyotrophic Lateral Sclerosis , 2014, PloS one.

[14]  J. Trojanowski,et al.  Phosphorylation of S409/410 of TDP-43 is a consistent feature in all sporadic and familial forms of TDP-43 proteinopathies , 2009, Acta Neuropathologica.

[15]  M. Nordberg,et al.  Metal Concentrations in Cerebrospinal Fluid and Blood Plasma from Patients with Amyotrophic Lateral Sclerosis , 2012, Biological Trace Element Research.

[16]  B. Polsky,et al.  A controlled study of reverse transcriptase in serum and CSF of HIV-negative patients with ALS , 2007, Neurology.

[17]  Inhibition of human endogenous retrovirus-K by antiretroviral drugs , 2017, Retrovirology.

[18]  Alan J. Thomas,et al.  TDP‐43 pathology in Alzheimer's disease, dementia with Lewy bodies and ageing , 2017, Brain pathology.

[19]  J. Trojanowski,et al.  Pathological TDP‐43 distinguishes sporadic amyotrophic lateral sclerosis from amyotrophic lateral sclerosis with SOD1 mutations , 2007, Annals of neurology.

[20]  C. Roodveldt,et al.  The 'Omics' of Amyotrophic Lateral Sclerosis. , 2016, Trends in molecular medicine.

[21]  F. Jessen,et al.  Measuring Compounds in Exhaled Air to Detect Alzheimer's Disease and Parkinson’s Disease , 2015, PloS one.

[22]  Stellan Hjertén,et al.  Highly selective artificial gel antibodies for detection and quantification of biomarkers in clinical samples. II. Albumin in body fluids of patients with neurological disorders. , 2008, Journal of separation science.

[23]  P. Kaňovský,et al.  Cerebrospinal fluid levels of chromogranin A and phosphorylated neurofilament heavy chain are elevated in amyotrophic lateral sclerosis , 2017, Acta neurologica Scandinavica.

[24]  Gavin Giovannoni,et al.  Plasma neurofilament heavy chain levels and disease progression in amyotrophic lateral sclerosis: insights from a longitudinal study , 2014, Journal of Neurology, Neurosurgery & Psychiatry.

[25]  Jochen H Weishaupt,et al.  Serum microRNAs in sporadic amyotrophic lateral sclerosis , 2015, Neurobiology of Aging.

[26]  John L. Robinson,et al.  Co-morbidity of TDP-43 proteinopathy in Lewy body related diseases , 2007, Acta Neuropathologica.

[27]  M. Vinceti,et al.  Elevated Levels of Selenium Species in Cerebrospinal Fluid of Amyotrophic Lateral Sclerosis Patients with Disease-Associated Gene Mutations , 2017, Neurodegenerative Diseases.

[28]  R. Lin,et al.  NF-κB and IRF1 Induce Endogenous Retrovirus K Expression via Interferon-Stimulated Response Elements in Its 5′ Long Terminal Repeat , 2016, Journal of Virology.

[29]  L. Ronnevi,et al.  Increased fragility of erythrocytes from amyotrophic lateral sclerosis (ALS) patients provoked by mechanical stress , 1984, Acta neurologica Scandinavica.

[30]  S. Appel,et al.  Increased lipid peroxidation in sera of ALS patients , 2004, Neurology.

[31]  A. Goris,et al.  EPHA4 is a disease modifier of amyotrophic lateral sclerosis in animal models and in humans , 2012, Nature Medicine.

[32]  M. Sierks,et al.  TDP-43 protein variants as biomarkers in amyotrophic lateral sclerosis , 2017, BMC Neuroscience.

[33]  A. Jeromin,et al.  Biomarkers in Neurodegenerative Diseases. , 2017, Advances in neurobiology.

[34]  I. Mackenzie,et al.  The role of transactive response DNA-binding protein-43 in amyotrophic lateral sclerosis and frontotemporal dementia , 2008, Current opinion in neurology.

[35]  A. Lahunta,et al.  Differential expression of TAR DNA-binding protein (TDP-43) in the central nervous system of horses afflicted with equine motor neuron disease (EMND): a preliminary study of a potential pathologic marker , 2012, Veterinary Research Communications.

[36]  T. Hirayama,et al.  Relationships between disease progression and serum levels of lipid, urate, creatinine and ferritin in Japanese patients with amyotrophic lateral sclerosis: a cross-sectional study. , 2012, Internal medicine.

[37]  John McAnally,et al.  MicroRNA-206 Delays ALS Progression and Promotes Regeneration of Neuromuscular Synapses in Mice , 2009, Science.

[38]  P. Mcgeer,et al.  Colocalization of Transactivation-Responsive DNA-Binding Protein 43 and Huntingtin in Inclusions of Huntington Disease , 2008, Journal of neuropathology and experimental neurology.

[39]  A. Larsson,et al.  A Multiplex Protein Panel Applied to Cerebrospinal Fluid Reveals Three New Biomarker Candidates in ALS but None in Neuropathic Pain Patients , 2016, PloS one.

[40]  M. Burns,et al.  Case-Control Study , 2020, Definitions.

[41]  E. Kremmer,et al.  Poly‐GP in cerebrospinal fluid links C9orf72‐associated dipeptide repeat expression to the asymptomatic phase of ALS/FTD , 2017, EMBO molecular medicine.

[42]  C. Angelini,et al.  Circulating microRNAs as biomarkers of muscle differentiation and atrophy in ALS. , 2016, Clinical neuropathology.

[43]  Stephen A. Goutman,et al.  Amyotrophic lateral sclerosis: mechanisms and therapeutics in the epigenomic era , 2015, Nature Reviews Neurology.

[44]  D. Macgowan,et al.  An ALS-like syndrome with new HIV infection and complete response to antiretroviral therapy , 2001, Neurology.

[45]  D. Burke,et al.  Riluzole therapy for motor neurone disease: An early Australian experience (1996–2002) , 2006, Journal of Clinical Neuroscience.

[46]  Changsong Wang,et al.  Comparative Analysis of VOCs in Exhaled Breath of Amyotrophic Lateral Sclerosis and Cervical Spondylotic Myelopathy Patients , 2016, Scientific reports.

[47]  Y. Kawahara,et al.  TDP-43 promotes microRNA biogenesis as a component of the Drosha and Dicer complexes , 2012, Proceedings of the National Academy of Sciences.

[48]  H. Shang,et al.  Aberration of miRNAs Expression in Leukocytes from Sporadic Amyotrophic Lateral Sclerosis , 2016, Front. Mol. Neurosci..

[49]  M. Nalls,et al.  Genome-wide analysis of the heritability of amyotrophic lateral sclerosis. , 2014, JAMA neurology.

[50]  R. Douville,et al.  TDP-43 regulates endogenous retrovirus-K viral protein accumulation , 2016, Neurobiology of Disease.

[51]  M. Vinceti,et al.  Cerebrospinal fluid of newly diagnosed amyotrophic lateral sclerosis patients exhibits abnormal levels of selenium species including elevated selenite. , 2013, Neurotoxicology.

[52]  L. Petrucelli,et al.  Reduced C9orf72 gene expression in c9FTD/ALS is caused by histone trimethylation, an epigenetic event detectable in blood , 2013, Acta Neuropathologica.

[53]  William T. Hu,et al.  Poly(Gp) Proteins Are A Useful Pharmacodynamic Marker For C9Orf72-Associated Amyotrophic Lateral Sclerosis , 2017 .

[54]  Kevin F. Bieniek,et al.  C9ORF72 repeat expansions in mice cause TDP-43 pathology, neuronal loss, and behavioral deficits , 2015, Science.

[55]  A. Chiò,et al.  Amyotrophic lateral sclerosis outcome measures and the role of albumin and creatinine: a population-based study. , 2014, JAMA neurology.

[56]  A. Al-Chalabi,et al.  Amyotrophic lateral sclerosis , 2017, The Lancet.

[57]  J. González de Aguilar,et al.  Blood Biomarkers for Amyotrophic Lateral Sclerosis: Myth or Reality? , 2014, BioMed research international.

[58]  Xun Hu,et al.  TDP-43 Mutations in Familial and Sporadic Amyotrophic Lateral Sclerosis , 2008, Science.

[59]  S. Signorelli,et al.  Metals and neurodegenerative diseases. A systematic review , 2017, Environmental research.

[60]  M. de Carvalho,et al.  Emerging molecular biomarker targets for amyotrophic lateral sclerosis. , 2016, Clinica chimica acta; international journal of clinical chemistry.

[61]  A. Cagnin,et al.  Diagnostic and Prognostic Biomarkers in Amyotrophic Lateral Sclerosis: Neurofilament Light Chain Levels in Definite Subtypes of Disease , 2017, JAMA neurology.

[62]  I. Evdokimidis,et al.  Cerebrospinal Fluid TAR DNA-Binding Protein 43 Combined with Tau Proteins as a Candidate Biomarker for Amyotrophic Lateral Sclerosis and Frontotemporal Dementia Spectrum Disorders , 2017, Dementia and Geriatric Cognitive Disorders.

[63]  Houeto Jean-Luc [Parkinson's disease]. , 2022, La Revue du praticien.

[64]  O. Resta,et al.  An electronic nose may sniff out amyotrophic lateral sclerosis , 2016, Respiratory Physiology & Neurobiology.

[65]  Xusheng Huang,et al.  Phosphorylated neurofilament heavy chain levels in paired plasma and CSF of amyotrophic lateral sclerosis , 2016, Journal of the Neurological Sciences.

[66]  H. Arai,et al.  Concurrence of TDP-43, tau and α-synuclein pathology in brains of Alzheimer's disease and dementia with Lewy bodies , 2007, Brain Research.

[67]  Albert Ludolph,et al.  Proteomic studies in the discovery of cerebrospinal fluid biomarkers for amyotrophic lateral sclerosis , 2017, Expert review of proteomics.

[68]  C. Dieterich,et al.  Serum microRNAs in patients with genetic amyotrophic lateral sclerosis and pre-manifest mutation carriers. , 2014, Brain : a journal of neurology.

[69]  D. Dickson,et al.  TDP-43 in aging and Alzheimer's disease - a review. , 2011, International journal of clinical and experimental pathology.

[70]  B. Bocca,et al.  Essential trace elements in amyotrophic lateral sclerosis (ALS): Results in a population of a risk area of Italy , 2017, Neurological Sciences.

[71]  M. Lamberti,et al.  Blood Lead, Manganese, and Aluminum Levels in a Regional Italian Cohort of ALS Patients: Does Aluminum Have an Influence? , 2014, Journal of occupational and environmental medicine.

[72]  Adriano Chiò,et al.  State of play in amyotrophic lateral sclerosis genetics , 2013, Nature Neuroscience.

[73]  B. Bocca,et al.  Level of neurotoxic metals in amyotrophic lateral sclerosis: A population-based case–control study , 2015, Journal of the Neurological Sciences.

[74]  H. Tohgi,et al.  Remarkable increase in cerebrospinal fluid 3‐nitrotyrosine in patients with sporadic amyotrophic lateral sclerosis , 1999, Annals of neurology.

[75]  H. Shang,et al.  Blood hemoglobin A1c levels and amyotrophic lateral sclerosis survival , 2017, Molecular Neurodegeneration.

[76]  P. Mccombe,et al.  Serial measurements of phosphorylated neurofilament-heavy in the serum of subjects with amyotrophic lateral sclerosis , 2015, Journal of the Neurological Sciences.

[77]  Lana X. Garmire,et al.  More Is Better: Recent Progress in Multi-Omics Data Integration Methods , 2017, Front. Genet..

[78]  J. Rothstein,et al.  Identification of active loci of a human endogenous retrovirus in neurons of patients with amyotrophic lateral sclerosis , 2011, Annals of neurology.

[79]  A. M. Correia,et al.  Downregulated Glia Interplay and Increased miRNA-155 as Promising Markers to Track ALS at an Early Stage , 2017, Molecular Neurobiology.

[80]  B. Carvalho,et al.  MicroRNAs-424 and 206 are potential prognostic markers in spinal onset amyotrophic lateral sclerosis , 2016, Journal of the Neurological Sciences.

[81]  松崎 敏男 HTLV-1-associated myelopathy (HAM)/tropical spastic paraparesis (TSP) with amyotrophic lateral sclerosis-like manifestations , 2002 .

[82]  Ya-qun Zhao,et al.  Identification of miRNAs as potential new biomarkers for nervous system cancer , 2014, Tumor Biology.

[83]  Dragan Maric,et al.  Human endogenous retrovirus-K contributes to motor neuron disease , 2015, Science Translational Medicine.

[84]  Timothy A. Miller,et al.  Method for widespread microRNA-155 inhibition prolongs survival in ALS-model mice. , 2013, Human molecular genetics.

[85]  M. David,et al.  Neurofilaments as Biomarkers for Amyotrophic Lateral Sclerosis: A Systematic Review and Meta-Analysis , 2016, PloS one.

[86]  H. Akiyama,et al.  Differential diagnosis of amyotrophic lateral sclerosis from Guillain–Barré syndrome by quantitative determination of TDP-43 in cerebrospinal fluid , 2014, The International journal of neuroscience.

[87]  E. Goodall,et al.  Serum miRNAs miR-206, 143-3p and 374b-5p as potential biomarkers for amyotrophic lateral sclerosis (ALS) , 2017, Neurobiology of Aging.

[88]  Xiang Yin,et al.  Blood Volatile Organic Compounds as Potential Biomarkers for Amyotrophic Lateral Sclerosis: an Animal Study in the SOD1 G93A Mouse , 2014, Journal of Molecular Neuroscience.

[89]  H. Tohgi,et al.  Alterations of 3-nitrotyrosine concentration in the cerebrospinal fluid during aging and in patients with Alzheimer's disease , 1999, Neuroscience Letters.

[90]  H. Takata,et al.  Oxidative stress and metal content in blood and cerebrospinal fluid of amyotrophic lateral sclerosis patients with and without a Cu, Zn-superoxide dismutase mutation , 2005, Neurological research.

[91]  A. Al-Chalabi,et al.  Identification of miRNAs as Potential Biomarkers in Cerebrospinal Fluid from Amyotrophic Lateral Sclerosis Patients , 2016, NeuroMolecular Medicine.

[92]  Veeranna,et al.  Neurofilaments and Neurofilament Proteins in Health and Disease. , 2017, Cold Spring Harbor perspectives in biology.

[93]  K. Blennow,et al.  Cerebrospinal fluid levels of free 3-nitrotyrosine are not elevated in the majority of patients with amyotrophic lateral sclerosis or Alzheimer’s disease , 2004, Neurochemistry International.

[94]  S. Schmidt,et al.  Blood levels of trace metals and amyotrophic lateral sclerosis. , 2016, Neurotoxicology.

[95]  G. Comi,et al.  TUBA4A gene analysis in sporadic amyotrophic lateral sclerosis: identification of novel mutations , 2015, Journal of Neurology.

[96]  Tamas Dalmay,et al.  miR-338-3p is over-expressed in blood, CFS, serum and spinal cord from sporadic amyotrophic lateral sclerosis patients , 2014, neurogenetics.

[97]  M. de Carvalho,et al.  Identification of erythrocyte biomarkers in amyotrophic lateral sclerosis. , 2016, Clinical hemorheology and microcirculation.

[98]  H. Haick,et al.  Detection of Alzheimer's and Parkinson's disease from exhaled breath using nanomaterial-based sensors. , 2013, Nanomedicine.

[99]  Bruce L. Miller,et al.  Ubiquitinated TDP-43 in Frontotemporal Lobar Degeneration and Amyotrophic Lateral Sclerosis , 2006, Science.

[100]  H. Shang,et al.  Assessment of a multiple biomarker panel for diagnosis of amyotrophic lateral sclerosis , 2016, BMC Neurology.

[101]  B. De Felice,et al.  A miRNA signature in leukocytes from sporadic amyotrophic lateral sclerosis. , 2012, Gene.

[102]  A. Al-Chalabi,et al.  Detection of serum reverse transcriptase activity in patients with ALS and unaffected blood relatives , 2005, Neurology.

[103]  H. Walach,et al.  Healing of Amyotrophic Lateral Sclerosis: A Case Report , 2017, Complementary Medicine Research.