Biomaterial Database

Machine learning analyses of antibody somatic mutations predict immunoglobulin light chain toxicity. 2021

Maura Garofalo, and Luca Piccoli, and Margherita Romeo, and Maria Monica Barzago, and Sara Ravasio, and Mathilde Foglierini, and Milos Matkovic, and Jacopo Sgrignani, and Raoul De Gasparo, and Marco Prunotto, and Luca Varani, and Luisa Diomede, and Olivier Michielin, and Antonio Lanzavecchia, and Andrea Cavalli

Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland.

In systemic light chain amyloidosis (AL), pathogenic monoclonal immunoglobulin light chains (LC) form toxic aggregates and amyloid fibrils in target organs. Prompt diagnosis is crucial to avoid permanent organ damage, but delayed diagnosis is common because symptoms usually appear only after strong organ involvement. Here we present LICTOR, a machine learning approach predicting LC toxicity in AL, based on the distribution of somatic mutations acquired during clonal selection. LICTOR achieves a specificity and a sensitivity of 0.82 and 0.76, respectively, with an area under the receiver operating characteristic curve (AUC) of 0.87. Tested on an independent set of 12 LCs sequences with known clinical phenotypes, LICTOR achieves a prediction accuracy of 83%. Furthermore, we are able to abolish the toxic phenotype of an LC by in silico reverting two germline-specific somatic mutations identified by LICTOR, and by experimentally assessing the loss of in vivo toxicity in a Caenorhabditis elegans model. Therefore, LICTOR represents a promising strategy for AL diagnosis and reducing high mortality rates in AL.

UI	MeSH Term	Description	Entries
D007147	Immunoglobulin Light Chains	Polypeptide chains, consisting of 211 to 217 amino acid residues and having a molecular weight of approximately 22 kDa. There are two major types of light chains, kappa and lambda. Two Ig light chains and two Ig heavy chains (IMMUNOGLOBULIN HEAVY CHAINS) make one immunoglobulin molecule.	Ig Light Chains,Immunoglobulins, Light-Chain,Immunoglobulin Light Chain,Immunoglobulin Light-Chain,Light-Chain Immunoglobulins,Chains, Ig Light,Chains, Immunoglobulin Light,Immunoglobulins, Light Chain,Light Chain Immunoglobulins,Light Chain, Immunoglobulin,Light Chains, Ig,Light Chains, Immunoglobulin,Light-Chain, Immunoglobulin
D008958	Models, Molecular	Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.	Molecular Models,Model, Molecular,Molecular Model
D009154	Mutation	Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.	Mutations
D011994	Recombinant Proteins	Proteins prepared by recombinant DNA technology.	Biosynthetic Protein,Biosynthetic Proteins,DNA Recombinant Proteins,Recombinant Protein,Proteins, Biosynthetic,Proteins, Recombinant DNA,DNA Proteins, Recombinant,Protein, Biosynthetic,Protein, Recombinant,Proteins, DNA Recombinant,Proteins, Recombinant,Recombinant DNA Proteins,Recombinant Proteins, DNA
D006801	Humans	Members of the species Homo sapiens.	Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000069550	Machine Learning	A type of ARTIFICIAL INTELLIGENCE that enable COMPUTERS to independently initiate and execute LEARNING when exposed to new data.	Transfer Learning,Learning, Machine,Learning, Transfer
D000075363	Immunoglobulin Light-chain Amyloidosis	A nonproliferative disorder of PLASMA CELLS characterized by excessive production and misfolding of IMMUNOGLOBULIN LIGHT CHAINS that form insoluble amyloid fibrils (see AMYLOID DEPOSITS) in various tissues. Clinical features include LIVER FAILURE; MULTIPLE MYELOMA; NEPHROTIC SYNDROME; RESTRICTIVE CARDIOMYOPATHY, and neuropathies.	Monoclonal Immunoglobulin Deposition Disease,AL Amyloidosis,Amyloidosis, Immunoglobulin Light-chain,Amyloidosis, Primary,Primary Amyloidosis,Primary Systemic Amyloidosis,AL Amyloidoses,Amyloidoses, Primary,Amyloidoses, Primary Systemic,Amyloidosis, Immunoglobulin Light chain,Amyloidosis, Primary Systemic,Immunoglobulin Light chain Amyloidosis,Immunoglobulin Light-chain Amyloidoses,Primary Amyloidoses,Primary Systemic Amyloidoses,Systemic Amyloidoses, Primary,Systemic Amyloidosis, Primary
D000465	Algorithms	A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.	Algorithm
D000595	Amino Acid Sequence	The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.	Protein Structure, Primary,Amino Acid Sequences,Sequence, Amino Acid,Sequences, Amino Acid,Primary Protein Structure,Primary Protein Structures,Protein Structures, Primary,Structure, Primary Protein,Structures, Primary Protein
D000818	Animals	Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA.	Animal,Metazoa,Animalia