Molecular pathology of neurodegenerative diseases by cryo-EM of amyloids.

Abnormal assembly of tau, α-synuclein, TDP-43 and amyloid-ß proteins into amyloid filaments defines most human neurodegenerative diseases. Genetics provides a direct link between filament formation and the causes of disease. Developments in cryo-electron microscopy (cryo-EM) have made it possible to determine the atomic structures of amyloids from postmortem human brains. Here we review the structures of brain-derived amyloid filaments that have been determined so far and discuss their impact on research into neurodegeneration. Whereas a given protein can adopt many different filament structures, specific amyloid folds define distinct diseases. Amyloid structures thus provide a description of neuropathology at the atomic level and a basis for studying disease. Future research should focus on model systems that replicate the structures observed in disease to better understand the molecular mechanisms of disease and develop improved diagnostics and therapies.

Amyloid polymorphisms constitute distinct clouds of conformational variants in different etiological subtypes of Alzheimer's disease.

The molecular architecture of amyloids formed in vivo can be interrogated using luminescent conjugated oligothiophenes (LCOs), a unique class of amyloid dyes. When bound to amyloid, LCOs yield fluorescence emission spectra that reflect the 3D structure of the protein aggregates. Given that synthetic amyloid-ß peptide (Aß) has been shown to adopt distinct structural conformations with different biological activities, we asked whether Aß can assume structurally and functionally distinct conformations within the brain. To this end, we analyzed the LCO-stained cores of ß-amyloid plaques in postmortem tissue sections from frontal, temporal, and occipital neocortices in 40 cases of familial Alzheimer's disease (AD) or sporadic (idiopathic) AD (sAD). The spectral attributes of LCO-bound plaques varied markedly in the brain, but the mean spectral properties of the amyloid cores were generally similar in all three cortical regions of individual patients. Remarkably, the LCO amyloid spectra differed significantly among some of the familial and sAD subtypes, and between typical patients with sAD and those with posterior cortical atrophy AD. Neither the amount of Aß nor its protease resistance correlated with LCO spectral properties. LCO spectral amyloid phenotypes could be partially conveyed to Aß plaques induced by experimental transmission in a mouse model. These findings indicate that polymorphic Aß-amyloid deposits within the brain cluster as clouds of conformational variants in different AD cases. Heterogeneity in the molecular architecture of pathogenic Aß among individuals and in etiologically distinct subtypes of AD justifies further studies to assess putative links between Aß conformation and clinical phenotype.

Protein Co-Aggregation Related to Amyloids: Methods of Investigation, Diversity, and Classification.

Amyloids are unbranched protein fibrils with a characteristic spatial structure. Although the amyloids were first described as protein deposits that are associated with the diseases, today it is becoming clear that these protein fibrils play multiple biological roles that are essential for different organisms, from archaea and bacteria to humans. The appearance of amyloid, first of all, causes changes in the intracellular quantity of the corresponding soluble protein(s), and at the same time the aggregate can include other proteins due to different molecular mechanisms. The co-aggregation may have different consequences even though usually this process leads to the depletion of a functional protein that may be associated with different diseases. The protein co-aggregation that is related to functional amyloids may mediate important biological processes and change of protein functions. In this review, we survey the known examples of the amyloid-related co-aggregation of proteins, discuss their pathogenic and functional roles, and analyze methods of their studies from bacteria and yeast to mammals. Such analysis allow for us to propose the following co-aggregation classes: (i) titration: deposition of soluble proteins on the amyloids formed by their functional partners, with such interactions mediated by a specific binding site; (ii) sequestration: interaction of amyloids with certain proteins lacking a specific binding site; (iii) axial co-aggregation of different proteins within the same amyloid fibril; and, (iv) lateral co-aggregation of amyloid fibrils, each formed by different proteins.

A More Accurate Approach to Amyloid Detection and Subtyping: Combining in situ Congo Red Staining and Immunohistochemistry.

Amyloidosis is the result of various, differently approachable diseases. It is vital to subtype the amyloid deposits in order to establish and finally treat the underlying disease properly. Besides the classical staining with Congo red, further procedures like immunohistochemical staining are needed for classification. Here, we present a more accurate approach using Congo red/immunohistochemical double staining easily applicable in routine diagnostics. Modifications of the Congo red staining technique and the immunohistochemical procedures were needed in order to combine both staining procedures on one slide. The evaluation was done using conventional light and fluorescence microscopy. By shortening the staining time for Congo red to 10 s and by modification regarding endogenous peroxidase blockage, accurate results could be obtained for evaluating the Congo red/immunohistochemistry double staining using a fluorescence microscope. Sections of 2 µm instead of 4 µm thickness were superior for evaluation, since they increased staining specificity. The combination of Congo red and immunohistochemistry as in situ double staining on one slide is a feasible approach in the diagnosis of amyloidosis. It allows focusing on the fluorescent Congo red-positive areas when evaluating immunohistochemistry, thus avoiding signing out false-positive results. Additionally, it increases the signal-to-noise ratio of the immunohistochemically stained sections on conventional microscopy.

Machine learning methods can replace 3D profile method in classification of amyloidogenic hexapeptides.

BACKGROUND: Amyloids are proteins capable of forming fibrils. Many of them underlie serious diseases, like Alzheimer disease. The number of amyloid-associated diseases is constantly increasing. Recent studies indicate that amyloidogenic properties can be associated with short segments of aminoacids, which transform the structure when exposed. A few hundreds of such peptides have been experimentally found. Experimental testing of all possible aminoacid combinations is currently not feasible. Instead, they can be predicted by computational methods. 3D profile is a physicochemical-based method that has generated the most numerous dataset - ZipperDB. However, it is computationally very demanding. Here, we show that dataset generation can be accelerated. Two methods to increase the classification efficiency of amyloidogenic candidates are presented and tested: simplified 3D profile generation and machine learning methods. RESULTS: We generated a new dataset of hexapeptides, using more economical 3D profile algorithm, which showed very good classification overlap with ZipperDB (93.5%). The new part of our dataset contains 1779 segments, with 204 classified as amyloidogenic. The dataset of 6-residue sequences with their binary classification, based on the energy of the segment, was applied for training machine learning methods. A separate set of sequences from ZipperDB was used as a test set. The most effective methods were Alternating Decision Tree and Multilayer Perceptron. Both methods obtained area under ROC curve of 0.96, accuracy 91%, true positive rate ca. 78%, and true negative rate 95%. A few other machine learning methods also achieved a good performance. The computational time was reduced from 18-20 CPU-hours (full 3D profile) to 0.5 CPU-hours (simplified 3D profile) to seconds (machine learning). CONCLUSIONS: We showed that the simplified profile generation method does not introduce an error with regard to the original method, while increasing the computational efficiency. Our new dataset proved representative enough to use simple statistical methods for testing the amylogenicity based only on six letter sequences. Statistical machine learning methods such as Alternating Decision Tree and Multilayer Perceptron can replace the energy based classifier, with advantage of very significantly reduced computational time and simplicity to perform the analysis. Additionally, a decision tree provides a set of very easily interpretable rules.

On the amyloid datasets used for training PAFIG--how (not) to extend the experimental dataset of hexapeptides.

BACKGROUND: Amyloids are proteins capable of forming aberrant intramolecular contact sites, characteristic of beta zipper configuration. Amyloids can underlie serious health conditions, e.g. Alzheimer's or Parkinson's diseases. It has been proposed that short segments of amino acids can be responsible for protein amyloidogenicity, but no more than two hundred such hexapeptides have been experimentally found. The authors of the computational tool Pafig published in BMC Bioinformatics a method for extending the amyloid hexapeptide dataset that could be used for training and testing models. They assumed that all hexapeptides belonging to an amyloid protein can be regarded as amylopositive, while those from proteins never reported as amyloid are always amylonegative. Here we show why the above described method of extending datasets is wrong and discuss the reasons why the incorrect data could lead to falsely correct classification. RESULTS: The amyloid classification of hexapeptides by Pafig was confronted with the classification results from different state of the art computational methods and the outputs of all methods were studied by clustering analysis. The clustering methods show that Pafig is an outlier with regard to other approaches. Our study of the statistical patterns of its training and testing datasets showed a strong bias towards STVIIE hexapeptide in their positive part. Different statistical patterns of seemingly amylo-positive and -negative hexapeptides allow for a repeatable classification, which is not related to amyloid propensity of the hexapetides. CONCLUSIONS: Our study on recognition of amyloid hexapeptides showed that occurrence of incidental patterns in wrongly selected datasets can produce falsely correct results of classification. The assumption that all hexapeptides belonging to amyloid protein can be regarded as amylopositive and those from proteins never reported as amyloid are always amylonegative is not supported by any other computational method. This is in line with experimental observations that amyloid propensity of a full protein can result from only one amyloidogenic fragment in this protein, while the occurrence of amyliodogenic part that is well hidden inside the protein may never lead to fibril formation. This leads to the conclusion that Pafig does not provide correct classification with regard to amyloidogenicity.

Structural typing of systemic amyloidoses by luminescent-conjugated polymer spectroscopy.

Most systemic amyloidoses are progressive and lethal, and their therapy depends on the identification of the offending proteins. Here we report that luminescent-conjugated thiophene polymers (LCP) sensitively detect amyloid deposits. The heterodisperse polythiophene acetic acid derivatives, polythiophene acetic acid (PTAA) and trimeric PTAA, emitted yellow-red fluorescence on binding to amyloid deposits, whereas chemically homogeneous pentameric formic thiophene acetic acid emitted green-yellow fluorescence. The geometry of LCPs modulates the spectral composition of the emitted light, thereby reporting ligand-induced steric changes. Accordingly, a screen of PTAA-stained amyloid deposits in histological tissue arrays revealed striking spectral differences between specimens. Blinded cluster assignments of spectral profiles of tissue samples from 108 tissue samples derived from 96 patients identified three nonoverlapping classes, which were found to match AA, AL, and ATTR immunotyping. We conclude that LCP spectroscopy is a sensitive and powerful tool for identifying and characterizing amyloid deposits.

Amyloidotic cardiomyopathy: multidisciplinary approach to diagnosis and treatment.

Amyloidotic cardiomyopathy (ACMP) occurs in the setting of rare genetic diseases, blood dyscrasias, chronic infection and inflammation, and advanced age. Cardiologists are on the front lines of diagnosis of ACMP when evaluating patients with unexplained dyspnea, congestive heart failure, or arrhythmias. Noninvasive detection of diastolic cardiac dysfunction and unexplained left ventricular hypertrophy should be followed by biopsy to demonstrate the presence of amyloid deposits and appropriate genetic, biochemical, and immunologic testing to accurately define the type of amyloid. Growing numbers of treatment options exist for these diseases, and timely diagnosis and institution of therapy is essential for preservation of cardiac function.

Immunologic studies of water-soluble human amyloid fibrils. Comparative studies of eight amyloid preparations.

Eight preparations of soluble amyloid and degraded amyloid (DAM) were compared immunologically. Unlike amyloid fibrils, six of eight preparations of DAM proved to be relatively strong immunogens. Antisera to DAM reacted weakly or not at all with normal human serum or extracts of normal tissues, but were specifically reactive with amyloid fibrils or DAM. Comparative studies of DAM'S from eight different subjects showed some degree of cross-reactivity among them, yet demonstrated that they were not identical. Similar conclusions were obtained by quantitative precipitin and complement fixation analyses. Comparison of the amyloid fibrils with the homologous DAM by complement fixation and absorption studies demonstrated the existence in DAM of antigenic determinants that were lacking or inaccessible in the native fibrils. A search for amyloid precursors and antibodies to amyloid in the sera of 12 patients proved unsuccessful.

Physical, chemical, and ultrastructural studies of water-soluble human amyloid fibrils. Comparative analyses of nine amyloid preparations.

Amyloid fibrils were isolated from the tissues of nine patients with amyloidosis in a state of high purity by homogenization of the tissue followed by extraction with distilled water. Physical, chemical, and ultrastructural studies suggest that amyloid fibrils from different individuals resemble each other, but are not identical. In tissue sections as well as by negative staining of isolated fibrils, morphologic variations were observed. Among the isolated fibrils at least three types were noted. The majority resembled those described previously. However, one subject had two types of fibrils which differed in size and appearance. Most of the preparations sedimented as a single component with a sedimentation coefficient of 45-50S or as a larger polymer. However, two of the preparations had sedimentation coefficients of 8-9S, and a third one had a major 95S component and a minor 9S fraction. While the preparations of amyloid were not sufficiently pure for amino acid analyses, peptide maps demonstrated differences among amyloid preparations from different subjects. The amyloid fibrils in their native state proved to be remarkably resistant to digestion by a number of proteolytic enzymes. Several chemical methods were tried to produce smaller subunits. Of these, the most successful one was the use of 0.1 M NaOH which yielded a smaller, soluble fraction with sedimentation coefficients ranging from 1.1 to 2.8S. Accompanying this degradation, there was little loss of peptides or carbohydrates. Based on the results of the chemical analyses, it is estimated that the subunit produced by sodium hydroxide had a molecular weight of approximately 35,000-40,000.

Amyloid Typing by Mass Spectrometry in Clinical Practice: a Comprehensive Review of 16,175 Samples.

OBJECTIVE: To map the occurrence of amyloid types in a large clinical cohort using mass spectrometry-based shotgun proteomics, an unbiased method that unambiguously identifies all amyloid types in a single assay. METHODS: A mass spectrometry-based shotgun proteomics assay was implemented in a central reference laboratory. We documented our experience of typing 16,175 amyloidosis specimens over an 11-year period from January 1, 2008, to December 31, 2018. RESULTS: We identified 21 established amyloid types, including AL (n=9542; 59.0%), ATTR (n=4600; 28.4%), ALECT2 (n=511; 3.2%), AA (n=463; 2.9%), AH (n=367; 2.3%), AIns (n=182; 1.2%), KRT5-14 (n=94; <1%), AFib (n=71; <1%), AApoAIV (n=57; <1%), AApoA1 (n=56; <1%), AANF (n=47; <1%), Aß2M (n=38; <1%), ASem1 (n=34; <1%), AGel (n=29; <1%), TGFB1 (n=29; <1%), ALys (n=15; <1%), AIAPP (n=13; <1%), AApoCII (n=11; <1%), APro (n=8; <1%), AEnf (n=6; <1%), and ACal (n=2; <1%). We developed the first comprehensive organ-by-type map showing the relative frequency of 21 amyloid types in 31 different organs, and the first type-by-organ map showing organ tropism of 18 rare types. Using a modified bioinformatics pipeline, we detected amino acid substitutions in cases of hereditary amyloidosis with 100% specificity. CONCLUSION: Amyloid typing by proteomics, which effectively recognizes all amyloid types in a single assay, optimally supports the diagnosis and treatment of amyloidosis patients in routine clinical practice.

Amyloid nomenclature 2020: update and recommendations by the International Society of Amyloidosis (ISA) nomenclature committee.

The ISA Nomenclature Committee met electronically before and directly after the XVII ISA International Symposium on Amyloidosis, which, unfortunately, had to be virtual in September 2020 due to the ongoing COVID-19 pandemic instead of a planned meeting in Tarragona in March. In addition to confirmation of basic nomenclature, several additional concepts were discussed, which are used in scientific amyloid literature. Among such concepts are cytotoxic oligomers, protofibrils, primary and secondary nucleation, seeding and cross-seeding, amyloid signature proteins, and amyloid plaques. Recommendations for their use are given. Definitions of amyloid and amyloidosis are confirmed. Possible novel human amyloid fibril proteins, appearing as 'classical' in vivo amyloid, were discussed. It was decided to include fibulin-like extracellular matrix protein 1 (amyloid protein: AEFEMP1), which appears as localised amyloid in portal veins. There are several possible amyloid proteins under investigation, and these are included in a new Table.

An Organ System-Based Approach to Differential Diagnosis of Amyloid Type in Surgical Pathology.

CONTEXT.­: Amyloidosis is an uncommon but important entity. A protein-based classification of amyloidosis defines the underlying disease process, directing clinical management and providing prognostic information. However, in routine surgical pathology there often is no attempt to classify amyloid other than staining to determine light chain-associated amyloidosis. Systemic and localized amyloidosis vary with respect to frequency of organ involvement by different amyloid types, and most amyloid proteins have commercial antibodies available for identification. OBJECTIVE.­: To provide a guide for the likelihood of amyloid type by organ system. DATA SOURCES.­: Literature review based on PubMed searches containing the word amyloid, specifically addressing the prevalence and significance of amyloid proteins in each organ system other than the brain, and the authors' practice experience. CONCLUSIONS.­: In patients with amyloidosis, determination of the responsible protein is critical for appropriate patient care. In large subspecialty practices and reference laboratories with experience in using and analyzing relevant immunohistochemistry, most amyloid proteins can be identified with an organ-specific algorithm. Referring to an organ-based algorithm may be helpful in providing clinicians with a more specific differential diagnosis regarding amyloid type to help guide clinical evaluation and treatment. When the protein cannot be characterized, mass spectrometry can be performed to definitively classify the amyloid type.

[Update on immunohistological classification of amyloidoses]. / Update--Immunhistologische Klassifikation der Amyloidosen.

The exact classification of amyloid in surgical pathology specimens is complicated by the increasing number of amyloid diseases, with more than 25 different currently known amyloid proteins. Special attention has to be paid to distinguishing hereditary amyloidosis from AL amyloidosis. For this reason we started several years ago to search specifically for hereditary amyloidoses by improving the immunohistochemical classification of amyloid with new antibodies and by applying molecular biology. Since then we have found various cases of systemic and local amyloid diseases in Germany, including, AApoAI-, AFib-, AKer-, ALys- and ATTR-amyloidosis, as well as hitherto unknown amyloidoses. Based on an increasing number of referrals we also collected substantial numbers of cases, which allowed a direct comparison of the prevalences of the various amyloid diseases in organ biopsies.

[Amyloid and amyloidoses]. / Amyloid und Amyloidosen.

Amyloid is a pathologic fibrillar aggregation of polypeptides in a cross-beta-sheet conformation. Amyloidoses are caused by the deposition of amyloid and may occur as cerebral and extracerebral disease. More than 29 different amyloid proteins have been identified. Analysis of a Congo red-stained tissue section by polarization microscopy is the gold standard for diagnosing amyloid. Subsequent classification of the amyloid is mandatory and is increasingly supported by molecular biological analyses. In Germany, this recently led to the discovery of several hereditary amyloid diseases. The correct classification of amyloid is of paramount importance. This helps to asses the prognosis and plan patient treatment.

[Amyloidosis in liver biopsies]. / Amyloidose in Leberbiopsien.

INTRODUCTION: We reassessed the histopathology and origin of amyloid in liver biopsies. MATERIALS AND METHODS: All liver biopsies were retrieved from a series of 588 cases with histologically confirmed amyloidosis submitted between February 2006 and January 2009 to the Amyloid Registry of the Charité University Hospital. Liver biopsies had been fixed in formalin and embedded in paraffin. 3-5 microm thick paraffin sections were stained with hematoxylin and eosin and Congo red. Amyloid was classified immunohistochemically, using antibodies directed against amyloid P-component, AA amyloid, apolipoprotein AI, fibrinogen, lysozyme, lambda- and kappa-light chain, and transthyretin. RESULTS: Amyloid was found in 46 liver biopsies (29 men, 17 women; mean age 60 years, range 34-87 years). Immunohistochemical classification succeeded in 42 cases. AL amyloidosis was present in 40 (87%) cases and was further categorized into AL amyloid of lambda-light chain origin in 26 (57%) cases, and kappa-light chain origin in 14 (30%) cases. ATTR and AA amyloidosis were found in a single patient each (2%). In 4 (9%) cases, amyloid remained unclassified. CONCLUSIONS: Hepatic amyloidosis is most commonly AL amyloid of lambda- and kappa-light chain origin and is often associated with marked parenchymal atrophy.

[Biological functions of amyloids: facts and hypotheses].

Amyloids are fibrous protein aggregates which arise due to polymerization of proteins accompanied by their conformational rearrangement and formation of a specific "cross-beta" structure. The interest to amyloids is caused by their relation to a vast group of human and animal diseases called amyloidoses. Some of these diseases caused by prions, a specific type of amyloids, are transmissible. Besides mammals, prion amyloids are described in lower eukaryotes, where they underlie non-chromosomal genetic determinants. Though in humans and animals amyloids are usually associated with pathologies, the increasing number of findings suggests that in some cases acquisition of amyloid or prion form by a protein may be of biological significance. Here, we summarize data on biological significance of prion and nonprion amyloids obtained in a wide range of species, from bacteria to mammals.

Amyloid nomenclature 2018: recommendations by the International Society of Amyloidosis (ISA) nomenclature committee.

The nomenclature committee of the International Society of Amyloidosis (ISA) meets every second year to discuss and formulate recommendations. The conclusions from the discussion at the XVI International Symposium on Amyloidosis in Kumamoto, Japan, 25-29 March 2018 and afterwards are summarized in this Nomenclature Article. From having recommended the use of the designation "amyloid fibril" for in vivo material only, ISA's nomenclature committee now accepts its use more broadly following the international scientific literature. However, it is important always to stress the origin of the ß-fibrils in order to avoid misunderstanding. Given the more broad use of the word "amyloid" several classes of amyloid fibrils may be distinguished. For the medical in vivo situation, and to be included in the amyloid nomenclature list, "amyloid" still means mainly extracellular tissue deposits of protein fibrils, recognized by specific properties, such as green-yellow birefringence after staining with Congo red. It should also be underlined that in vivo amyloid fibrils, in addition to the main protein contain associated compounds, particularly serum amyloid P-component (SAP) and proteoglycans, mainly heparan sulfate proteoglycan. With this definition there are presently 36 human amyloid proteins of which 14 appear only associated with systemic amyloidosis and 19 as localized forms. Three proteins can occur both as localized and systemic amyloidosis. Strictly intracellular aggregates are not included in this list.

Amyloid from a histochemical perspective. A review of the structure, properties and types of amyloid, and a proposed staining mechanism for Congo red staining.

Amyloid is a diverse group of unrelated peptides or proteins that have positive functionality or are associated with various pathologies. Despite vast differences, all amyloids share several features that together uniquely define the group. 1) All amyloids possess a characteristic cross-ß pattern with X-ray diffraction typical of ß-sheet secondary protein structures. 2) All amyloids are birefringent and dichroic under polarizing microscopy after staining with Congo red, which indicates a crystalline-like (ordered) structure. 3) All amyloids cause a spectral shift in the peak wavelength of Congo red with conventional light microscopy due to perturbation of π electrons of the dye. 4) All amyloids show heightened intensity of fluorescence with Congo red, which suggests an unusual degree of packing of the dye onto the substrate. The ß portion of amyloid molecules, the only logical substrate for specific Congo red staining under histochemical conditions, consists of a stack of ß-sheets laminated by hydrophilic and hydrophobic interactions between adjacent pairs. Only the first and last ß-sheets are accessible to dyes. Each sheet is composed of numerous identical peptides running across the width of the sheet and arranged in parallel with side chains in register over the length of the fibril. Two sets of grooves are bordered by side chains. X grooves run perpendicular to the long axis of the fibril; these grooves are short (the width of the sheet) and number in the hundreds or thousands. Y grooves are parallel with the long axis. Each groove runs the entire length of the fibril, but there are very few of them. While Congo red is capable of ionic bonding with proteins via two sulfonic acid groups, physical constraints on the staining solution preclude ionic interactions. Hydrogen bonding between dye amine groups and peptide carbonyls is the most likely primary bonding mechanism, because all ß-sheets possess backbone carbonyls. Various amino acid residues may form secondary bonds to the dye via any of three van der Waals forces. It is possible that Congo red binds within the Y grooves, but that would not produce the characteristic staining features that are the diagnostic hallmarks of amyloid. Binding in the X grooves would produce a tightly packed series of dye molecules over the entire length of the fibril. This would account for the signature staining of amyloid by Congo red: dichroic birefringence, enhanced intensity of fluorescence and a shift in visible absorption wavelength.