Ghiam Yamin

All Publications

• Arterial Spin-Labeling and DSC Perfusion Metrics Improve Agreement in Neuroradiologists' Clinical Interpretations of Posttreatment High-Grade Glioma Surveillance MR Imaging-An Institutional Experience. AJNR. American journal of neuroradiology Yamin, G., Tranvinh, E., Lanzman, B. A., Tong, E., Hashmi, S. S., Patel, C. B., Iv, M. 2024

  Abstract

  MR perfusion has shown value in the evaluation of posttreatment high-grade gliomas, but few studies have shown its impact on the consistency and confidence of neuroradiologists' interpretation in routine clinical practice. We evaluated the impact of adding MR perfusion metrics to conventional contrast-enhanced MR imaging in posttreatment high-grade glioma surveillance imaging.This retrospective study included 45 adults with high-grade gliomas who had posttreatment perfusion MR imaging. Four neuroradiologists assigned Brain Tumor Reporting and Data System scores for each examination on the basis of the interpretation of contrast-enhanced MR imaging and then after the addition of arterial spin-labeling-CBF, DSC-relative CBV, and DSC-fractional tumor burden. Interrater agreement and rater agreement with a multidisciplinary consensus group were assessed with κ statistics. Raters used a 5-point Likert scale to report confidence scores. The frequency of clinically meaningful score changes resulting from the addition of each perfusion metric was determined.Interrater agreement was moderate for contrast-enhanced MR imaging alone (κ = 0.63) and higher with perfusion metrics (arterial spin-labeling-CBF, κ = 0.67; DSC-relative CBV, κ = 0.66; DSC-fractional tumor burden, κ = 0.70). Agreement between raters and consensus was highest with DSC-fractional tumor burden (κ = 0.66-0.80). Confidence scores were highest with DSC-fractional tumor burden. Across all raters, the addition of perfusion resulted in clinically meaningful interpretation changes in 2%-20% of patients compared with contrast-enhanced MR imaging alone.Adding perfusion to contrast-enhanced MR imaging improved interrater agreement, rater agreement with consensus, and rater confidence in the interpretation of posttreatment high-grade glioma MR imaging, with the highest agreement and confidence scores seen with DSC-fractional tumor burden. Perfusion MR imaging also resulted in interpretation changes that could change therapeutic management in up to 20% of patients.

  View details for DOI 10.3174/ajnr.A8190

  View details for PubMedID 38453410

• Exploring the performance and explainability of fine-tuned BERT models for neuroradiology protocol assignment. BMC medical informatics and decision making Talebi, S., Tong, E., Li, A., Yamin, G., Zaharchuk, G., Mofrad, M. R. 2024; 24 (1): 40

  Abstract

  Deep learning has demonstrated significant advancements across various domains. However, its implementation in specialized areas, such as medical settings, remains approached with caution. In these high-stake environments, understanding the model's decision-making process is critical. This study assesses the performance of different pretrained Bidirectional Encoder Representations from Transformers (BERT) models and delves into understanding its decision-making within the context of medical image protocol assignment.Four different pre-trained BERT models (BERT, BioBERT, ClinicalBERT, RoBERTa) were fine-tuned for the medical image protocol classification task. Word importance was measured by attributing the classification output to every word using a gradient-based method. Subsequently, a trained radiologist reviewed the resulting word importance scores to assess the model's decision-making process relative to human reasoning.The BERT model came close to human performance on our test set. The BERT model successfully identified relevant words indicative of the target protocol. Analysis of important words in misclassifications revealed potential systematic errors in the model.The BERT model shows promise in medical image protocol assignment by reaching near human level performance and identifying key words effectively. The detection of systematic errors paves the way for further refinements to enhance its safety and utility in clinical settings.

  View details for DOI 10.1186/s12911-024-02444-z

  View details for PubMedID 38326769

  View details for PubMedCentralID 5479722

• Fibrodysplasia ossificans progressiva (FOP) presenting as a rapidly growing non-calcified neck mass. Journal of radiology case reports Yamin, G., Daghighi, S., Mafee, M. 2021; 15 (5): 10-16

  Abstract

  Fibrodysplasia ossificans progressiva (FOP) is an extremely rare autosomal dominant inherited disorder leading to mature ossification within soft tissues. We report a 62-year-old female with a 3-week history of a rapidly enlarging left neck mass with no associated symptoms. A neck CT showed a ~10 cm solid-appearing non-calcified left neck mass that markedly decreased in size on a one-month follow-up neck MRI, but with new extensive edema/intense enhancement in floor of the mouth. Prior radiographs documented hallux valgus and heterotopic ossification of the psoas/paraspinal muscles and shoulder girdle. In this case of FOP, no intervention was implemented and the symptoms improved over time and thus paralleled other such cases for flare-ups. Clinicians should be aware of this rare entity, as it is frequently misdiagnosed as cancer or other benign entities such as infection, resulting in biopsies that can often hasten disease progression.

  View details for DOI 10.3941/jrcr.v15i5.4103

  View details for PubMedID 34276874

  View details for PubMedCentralID PMC8253151

• Assessment of Motor Dysfunction with Virtual Reality in Patients Undergoing [123I]FP-CIT SPECT/CT Brain Imaging Tomography Vu, J. P., Yamin, G., Reyes, Z., Shin, A., Young, A., Litvan, I., Xie, P., Obrzut, S. 2021; 7 (2): 95-106

  View details for DOI 10.3390/tomography7020009

• An Unusual Case of Thiamine Deficiency in a Total Parenteral Nutrition-Dependent Child Secondary to Munchausen by Proxy JPGN Reports Huang, A. C., Herdes, R. E., Yamin, G., Kerner, J. 2021; 2 (1)

  View details for DOI 10.1097/PG9.0000000000000044

• Automated CT registration tool improves sensitivity to change in ventricular volume in patients with shunts and drains. The British journal of radiology Yamin, G. n., Cheecharoen, P. n., Goel, G. n., Sung, A. n., Li, C. Q., Chang, Y. A., McDonald, C. R., Farid, N. n. 2020; 93 (1106): 20190398

  Abstract

  CT is the mainstay imaging modality for assessing change in ventricular volume in patients with ventricular shunts or external ventricular drains (EVDs). We evaluated the performance of a novel fully automated CT registration and subtraction method to improve reader accuracy and confidence compared with standard CT.In a retrospective evaluation of 49 ventricular shunt or EVD patients who underwent sequential head CT scans with an automated CT registration tool (CT CoPilot), three readers were assessed on their ability to discern change in ventricular volume between scans using standard axial CT images versus reformats and subtraction images generated by the registration tool. The inter-rater reliability among the readers was calculated using an intraclass correlation coefficient (ICC). Bland-Altman tests were performed to determine reader performance compared to semi-quantitative assessment using the bifrontal horn and third ventricular width. McNemar's test was used to determine whether the use of the registration tool increased the reader's level of confidence.Inter-rater reliability was higher when using the output of the registration tool (single measure ICC of 0.909 with versus 0.755 without the tool). Agreement between the readers' assessment of ventricular volume change and the semi-quantitative assessment improved with the registration tool (limits of agreement 4.1 vs 4.3). Furthermore, the tool improved reader confidence in determining increased or decreased ventricular volume (p < 0.001).Automated CT registration and subtraction improves the reader's ability to detect change in ventricular volume between sequential scans in patients with ventricular shunts or EVDs.Our automated CT registration and subtraction method may serve as a promising generalizable tool for accurate assessment of change in ventricular volume, which can significantly affect clinical management.

  View details for DOI 10.1259/bjr.20190398

  View details for PubMedID 31825670

  View details for PubMedCentralID PMC7055443

• The false-negative rate of mammography should be calculated in the 1st and 2nd year following a benign screening mammogram. The breast journal Eghtedari, M. n., Al-Shamrani, A. n., Shojaeiadib, N. n., Yamin, G. n., Ojeda-Fournier, H. n. 2020

  View details for DOI 10.1111/tbj.14020

  View details for PubMedID 32815210

• Chronic cough and an atypical pattern of peripheral pulmonary opacities: A case report secondary to suspected drug onset. The Journal of asthma : official journal of the Association for the Care of Asthma Alas, R., Williams, M. T., Yamin, G., Rofoogaran, M. 2018; 55 (1): 106-110

  Abstract

  Chronic eosinophilic pneumonia (CEP) is an idiopathic interstitial lung disease with nonspecific symptoms that involves a complex inflammatory cascade.A 36-year-old prisoner with a history of psoriasis presented with progressive worsening dyspnea, chest pain, and cough. His symptoms started 2-months after starting adalimumab, a tumor necrosis factor (TNF)-inhibitor, for psoriasis treatment.Initial workup revealed 27% eosinophils on complete blood count, elevated IgE levels on bronchoalveolar lavage, and bilateral peripheral lung opacities on imaging. The patient's symptoms and eosinophilia improved markedly after starting corticosteroids. Based on these findings, the patient was diagnosed with CEP.To our knowledge, this is the first case of asthma and CEP in a patient taking adalimumab. We suspect adalimumab unmasked the Th2 cell pathway response that was otherwise suppressed by psoriasis, a primarily Th1 cell pathway disease. The patient's pulmonary changes can be attributed to an eosinophilic asthma phenotype with adalimumab putatively indirectly causing CEP.

  View details for DOI 10.1080/02770903.2017.1313271

  View details for PubMedID 28402696

• Pittsburgh Compound-B (PiB) binds amyloid β-protein protofibrils. Journal of neurochemistry Yamin, G., Teplow, D. B. 2017; 140 (2): 210-215

  Abstract

  The neuropathology of Alzheimer's disease (AD) includes amyloid plaque formation by the amyloid β-protein (Aβ) and intracellular paired helical filament formation by tau protein. These neuropathogenetic features correlate with disease progression and have been revealed in brains of AD patients using positron emission tomography (PET). One of the most useful positron emission tomography imaging agents has been Pittsburgh Compound-B (PiB). However, since its introduction in 2002, substantial evidence has accumulated suggesting that Aβ oligomerization and protofibril formation, rather than fibril formation per se, may be the more important pathogenetic event in AD. Detecting protofibrils and oligomeric forms of Aβ thus may be of value. We report here the results of experiments to determine whether PiB binds to oligomers or protofibrils formed by Aβ40 and Aβ42. We observed strong binding to Aβ42 fibrils, significant binding to protofibrils, and weaker binding to Aβ42 oligomers. PiB also binds Aβ40 fibrils, but its binding to Aβ40 protofibrils and oligomers is substantially lower than for that observed for Aβ42.

  View details for DOI 10.1111/jnc.13887

  View details for PubMedID 27943341

  View details for PubMedCentralID PMC5225051

• Design, Characterization, and Use of a Novel Amyloid β-Protein Control for Assembly, Neurotoxicity, and Gene Expression Studies. Biochemistry Yamin, G., Coppola, G., Teplow, D. B. 2016; 55 (36): 5049-60

  Abstract

  A key pathogenic agent in Alzheimer's disease (AD) is the amyloid β-protein (Aβ), which self-assembles into a variety of neurotoxic structures. Establishing structure-activity relationships for these assemblies, which is critical for proper therapeutic target identification and design, requires aggregation and neurotoxicity experiments that are properly controlled with respect to the Aβ peptide itself. "Reverse" Aβ or non-Aβ peptides suffer from the fact that their biophysical properties are too similar or dissimilar, respectively, to those of native Aβ for them to be appropriate controls. For this reason, we used simple protein design principles to create scrambled Aβ peptides predicted to behave distinctly from native Aβ. We showed that our prediction was true by monitoring secondary structure dynamics with thioflavin T fluorescence and circular dichroism spectroscopy, determining oligomer size distributions, and assaying neurotoxic activity. We then demonstrated the utility of the scrambled Aβ peptides by using them to control experiments examining the effects of Aβ monomers, dimers, higher-order oligomers, and fibrils on gene expression in primary rat hippocampal neurons. Significant changes in gene expression were observed for all peptide assemblies, but fibrils induced the largest changes. Weighted gene co-expression network analysis revealed two predominant gene modules related to Aβ treatment. Many genes within these modules were associated with inflammatory signaling pathways.

  View details for DOI 10.1021/acs.biochem.6b00579

  View details for PubMedID 27505174

• Demonstration of Non-Gaussian Restricted Diffusion in Tumor Cells Using Diffusion Time-Dependent Diffusion-Weighted Magnetic Resonance Imaging Contrast. Frontiers in oncology Hope, T. R., White, N. S., Kuperman, J., Chao, Y., Yamin, G., Bartch, H., Schenker-Ahmed, N. M., Rakow-Penner, R., Bussell, R., Nomura, N., Kesari, S., Bjørnerud, A., Dale, A. M. 2016; 6: 179

  Abstract

  The diffusion-weighted magnetic resonance imaging (DWI) technique enables quantification of water mobility for probing microstructural properties of biological tissue and has become an effective tool for collecting information about the underlying pathology of cancerous tissue. Measurements using multiple b-values have indicated biexponential signal attenuation, ascribed to "fast" (high ADC) and "slow" (low ADC) diffusion components. In this empirical study, we investigate the properties of the diffusion time (Δ)-dependent components of the diffusion-weighted (DW) signal in a constant b-value experiment. A xenograft gliobastoma mouse was imaged using Δ = 11 ms, 20 ms, 40 ms, 60 ms, and b = 500-4000 s/mm(2) in intervals of 500 s/mm(2). Data were corrected for EPI distortions, and the Δ-dependence on the DW-signal was measured within three regions of interest [intermediate- and high-density tumor regions and normal-appearing brain (NAB) tissue regions]. In this study, we verify the assumption that the slow decaying component of the DW-signal is non-Gaussian and dependent on Δ, consistent with restricted diffusion of the intracellular space. As the DW-signal is a function of Δ and is specific to restricted diffusion, manipulating Δ at constant b-value (cb) provides a complementary and direct approach for separating the restricted from the hindered diffusion component. We found that Δ-dependence is specific to the tumor tissue signal. Based on an extended biexponential model, we verified the interpretation of the diffusion time-dependent contrast and successfully estimated the intracellular restricted ADC, signal volume fraction, and cell size within each ROI.

  View details for DOI 10.3389/fonc.2016.00179

  View details for PubMedID 27532028

  View details for PubMedCentralID PMC4970563

• Mass of the Anterior Nasal Septum. JAMA otolaryngology-- head & neck surgery Yamin, G., Shabaik, A., Mafee, M. 2016; 142 (6): 601-2

  View details for DOI 10.1001/jamaoto.2015.3978

  View details for PubMedID 27031377

• Voxel Level Radiologic-Pathologic Validation of Restriction Spectrum Imaging Cellularity Index with Gleason Grade in Prostate Cancer CLINICAL CANCER RESEARCH Yamin, G., Schenker-Ahmed, N. M., Shabaik, A., Adams, D., Bartsch, H., Kuperman, J., White, N. S., Rakow-Penner, R. A., McCammack, K., Parsons, J., Kane, C. J., Dale, A. M., Karow, D. S. 2016; 22 (11): 2668–74

  Abstract

  Restriction spectrum imaging (RSI-MRI), an advanced diffusion imaging technique, can potentially circumvent current limitations in tumor conspicuity, in vivo characterization, and location demonstrated by multiparametric magnetic resonance imaging (MP-MRI) techniques in prostate cancer detection. Prior reports show that the quantitative signal derived from RSI-MRI, the cellularity index, is associated with aggressive prostate cancer as measured by Gleason grade (GG). We evaluated the reliability of RSI-MRI to predict variance with GG at the voxel-level within clinically demarcated prostate cancer regions.Ten cases were processed using whole mount sectioning after radical prostatectomy. Regions of tumor were identified by an uropathologist. Stained prostate sections were scanned at high resolution (75 μm/pixel). A grid of tiles corresponding to voxel dimensions was graded using the GG system. RSI-MRI cellularity index was calculated from presurgical prostate MR scans and presented as normalized z-score maps. In total, 2,795 tiles were analyzed and compared with RSI-MRI cellularity.RSI-MRI cellularity index was found to distinguish between prostate cancer and benign tumor (t = 25.48, P < 0.00001). Significant differences were also found between benign tissue and prostate cancer classified as low-grade (GG = 3; t = 11.56, P < 0.001) or high-grade (GG ≥ 4; t = 24.03, P < 0.001). Furthermore, RSI-MRI differentiated between low and high-grade prostate cancer (t = 3.23; P = 0.003).Building on our previous findings of correlation between GG and the RSI-MRI among whole tumors, our current study reveals a similar correlation at voxel resolution within tumors. Because it can detect variations in tumor grade with voxel-level precision, RSI-MRI may become an option for planning targeted procedures where identifying the area with the most aggressive disease is important. Clin Cancer Res; 22(11); 2668-74. ©2016 AACR.

  View details for DOI 10.1158/1078-0432.CCR-15-2429

  View details for Web of Science ID 000378338200012

  View details for PubMedID 27250935

  View details for PubMedCentralID PMC4896066

• Inhibiting amyloid β-protein assembly: Size-activity relationships among grape seed-derived polyphenols. Journal of neurochemistry Hayden, E. Y., Yamin, G., Beroukhim, S., Chen, B., Kibalchenko, M., Jiang, L., Ho, L., Wang, J., Pasinetti, G. M., Teplow, D. B. 2015; 135 (2): 416-30

  Abstract

  Epidemiological evidence that red wine consumption negatively correlates with risk of Alzheimer's disease has led to experimental studies demonstrating that grape seed extracts inhibit the aggregation and oligomerization of Aβ in vitro and ameliorate neuropathology and behavioral deficits in a mouse model of Alzheimer's disease. The active agent in the extracts is a mixed population of polyphenolic compounds. To evaluate the relative potency of each of these compounds, HPLC was used to fractionate the mixture into monomers, dimers, and oligomers. Each fraction was analyzed for its effect on Aβ conformational dynamics (circular dichroism), oligomerization (zero-length photochemical cross-linking), aggregation kinetics (Thioflavin T fluorescence), and morphology (electron microscopy). The relative activities of each fraction were determined on the basis of molar concentration (mol/L) or mass concentration (g/L). When molar concentration, the number concentration of each polyphenolic compound, was considered, the oligomer fraction was the most potent inhibitor of Aβ oligomerization and aggregation. However, when mass concentration, the number concentration of phenolic groups, was considered, monomers were the most potent inhibitors. To understand these ostensibly contradictory results, a model of polyphenol:Aβ complexation was developed. This model, which was found to be consistent with published X-ray crystallographic studies, offers an explanation for the effects of functional group polyvalency on inhibitor activity. Our data emphasize the importance of an in-depth understanding of the mechanism(s) underlying 'concentration dependence' in inhibitor systems involving polyfunctional agents.

  View details for DOI 10.1111/jnc.13270

  View details for PubMedID 26228682

  View details for PubMedCentralID PMC5639934

• Design and Characterization of Chemically Stabilized Aβ42 Oligomers. Biochemistry Yamin, G., Huynh, T. V., Teplow, D. B. 2015; 54 (34): 5315-21

  Abstract

  A popular working hypothesis of Alzheimer's disease causation is amyloid β-protein oligomers are the key neuropathogenetic agents. Rigorously elucidating the role of oligomers requires the production of stable oligomers of each size. We previously used zero-length photochemical cross-linking to allow stabilization, isolation, and determination of structure-activity relationships of pure populations of Aβ40 dimers, trimers, and tetramers. We also attempted to study Aβ42 but found that Aβ42 oligomers subjected to the same procedures were not completely stable. On the basis of the fact that Tyr is a critical residue in cross-linking chemistry, we reasoned that the chemical accessibility of Tyr10 in Aβ42 must differ from that in Aβ40. We thus chemically synthesized four singly substituted Tyr variants that placed the Tyr in different positions across the Aβ42 sequence. We then studied the stability of the resulting cross-linked oligomers as well as procedures for fractionating the oligomers to obtain pure populations of different sizes. We found that [Phe(10),Tyr(42)]Aβ42 produced stable oligomers yielding highly pure populations of dimers through heptamers. This provides the means to establish formal structure-activity relationships of these important Aβ42 assemblies. In addition, we were able to analyze the dissociation patterns of non-cross-linked oligomers to produce a model for oligomer formation. This work is relevant to the determination of structure-activity relationships that have the potential to provide mechanistic insights into disease pathogenesis.

  View details for DOI 10.1021/acs.biochem.5b00318

  View details for PubMedID 26241378

  View details for PubMedCentralID PMC5104494

• A peptide hairpin inhibitor of amyloid beta-protein oligomerization and fibrillogenesis. Biochemistry Yamin, G., Ruchala, P., Teplow, D. B. 2009; 48 (48): 11329-31

  Abstract

  Amyloid beta-protein (Abeta) self-assembly is linked strongly to Alzheimer's disease. We found that PP-Leu, a tridecapeptide analogue of broad-spectrum antiviral peptides termed theta-defensins, potently inhibits Abeta oligomer and fibril formation. This effect appeared to be mediated through sequestration of the amyloidogenic Abeta peptide in colloid-like assemblies. PP-Leu comprises a turn formed by a d-Pro-l-Pro amino acid dyad and stabilized by a disulfide bond, a motif that was exceptionally resistant to endoproteinase K digestion. This combination of assembly inhibitory activity and protease resistance suggests that PP-Leu may have potential therapeutic value.

  View details for DOI 10.1021/bi901325g

  View details for PubMedID 19877710

• NMDA receptor-dependent signaling pathways that underlie amyloid beta-protein disruption of LTP in the hippocampus. Journal of neuroscience research Yamin, G. 2009; 87 (8): 1729-36

  Abstract

  Alzheimer's disease (AD), the most common neurodegenerative disease in the elderly population, is characterized by the hippocampal deposition of fibrils formed by amyloid beta-protein (A beta), a 40- to 42-amino-acid peptide. The folding of A beta into neurotoxic oligomeric, protofibrillar, and fibrillar assemblies is believed to mediate the key pathologic event in AD. The hippocampus is especially susceptible in AD and early degenerative symptoms include significant deficits in the performance of hippocampal-dependent cognitive abilities such as spatial learning and memory. Transgenic mouse models of AD that express C-terminal segments or mutant variants of amyloid precursor protein, the protein from which A beta is derived, exhibit age-dependent spatial memory impairment and attenuated long-term potentiation (LTP) in the hippocampal CA1 and dentate gyrus (DG) regions. Recent experimental evidence suggests that A beta disturbs N-methyl-D-aspartic acid (NMDA) receptor-dependent LTP induction in the CA1 and DG both in vivo and in vitro. Furthermore, these studies suggest that A beta specifically interferes with several major signaling pathways downstream of the NMDA receptor, including the Ca(2+)-dependent protein phosphatase calcineurin, Ca(2+)/calmodulin-dependent protein kinase II (CaMKII), protein phosphatase 1, and cAMP response element-binding protein (CREB). The influence of A beta on each of these downstream effectors of NMDA is reviewed in this article. Additionally, other mechanisms of LTP modulation, such as A beta attenuation of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor currents, are briefly discussed.

  View details for DOI 10.1002/jnr.21998

  View details for PubMedID 19170166

• Amyloid beta-Protein Assembly as a Therapeutic Target of Alzheimer's Disease CURRENT PHARMACEUTICAL DESIGN Yamin, G., Ono, K., Inayathullah, M., Teplow, D. B. 2008; 14 (30): 3231-3246

  Abstract

  Alzheimer's disease (AD), the most common neurodegenerative disorder in the aged, is characterized by the cerebral deposition of fibrils formed by the amyloid beta-protein (Abeta), a 40-42 amino acid peptide. The folding of Abeta into neurotoxic oligomeric, protofibrillar, and fibrillar assemblies is hypothesized to be the key pathologic event in AD. Abeta is formed through cleavage of the Abeta precursor protein by two endoproteinases, beta-secretase and gamma-secretase, that cleave the Abeta N-terminus and C-terminus, respectively. These facts support the relevance of therapeutic strategies targeting Abeta production, assembly, clearance, and neurotoxicity. Currently, no disease-modifying therapeutic agents are available for AD patients. Instead, existing therapeutics provide only modest symptomatic benefits for a limited time. We summarize here recent efforts to produce therapeutic drugs targeting Abeta assembly. A number of approaches are being used in these efforts, including immunological, nutraceutical, and more classical medicinal chemical (peptidic inhibitors, carbohydrate-containing compounds, polyamines, "drug-like" compounds, chaperones, metal chelators, and osmolytes), and many of these have progressed to phase III clinical trails. We also discuss briefly a number of less mature, but intriguing, strategies that have therapeutic potential. Although initial trials of some disease-modifying agents have failed, we argue that substantial cause for optimism exists.

  View details for Web of Science ID 000261916000004

  View details for PubMedID 19075703

• Familial Alzheimer's disease mutations alter the stability of the amyloid beta-protein monomer folding nucleus. Proceedings of the National Academy of Sciences of the United States of America Grant, M. A., Lazo, N. D., Lomakin, A., Condron, M. M., Arai, H., Yamin, G., Rigby, A. C., Teplow, D. B. 2007; 104 (42): 16522-7

  Abstract

  Amyloid beta-protein (Abeta) oligomers may be the proximate neurotoxins in Alzheimer's disease (AD). Recently, to elucidate the oligomerization pathway, we studied Abeta monomer folding and identified a decapeptide segment of Abeta, (21)Ala-(22)Glu-(23)Asp-(24)Val-(25)Gly-(26)Ser-(27)Asn-(28)Lys-(29)Gly-(30)Ala, within which turn formation appears to nucleate monomer folding. The turn is stabilized by hydrophobic interactions between Val-24 and Lys-28 and by long-range electrostatic interactions between Lys-28 and either Glu-22 or Asp-23. We hypothesized that turn destabilization might explain the effects of amino acid substitutions at Glu-22 and Asp-23 that cause familial forms of AD and cerebral amyloid angiopathy. To test this hypothesis, limited proteolysis, mass spectrometry, and solution-state NMR spectroscopy were used here to determine and compare the structure and stability of the Abeta(21-30) turn within wild-type Abeta and seven clinically relevant homologues. In addition, we determined the relative differences in folding free energies (DeltaDeltaG(f)) among the mutant peptides. We observed that all of the disease-associated amino acid substitutions at Glu-22 or Asp-23 destabilized the turn and that the magnitude of the destabilization correlated with oligomerization propensity. The Ala21Gly (Flemish) substitution, outside the turn proper (Glu-22-Lys-28), displayed a stability similar to that of the wild-type peptide. The implications of these findings for understanding Abeta monomer folding and disease causation are discussed.

  View details for DOI 10.1073/pnas.0705197104

  View details for PubMedID 17940047

  View details for PubMedCentralID PMC2034231

• Characterization of oligomeric intermediates in alpha-synuclein fibrillation: FRET studies of Y125W/Y133F/Y136F alpha-synuclein. Journal of molecular biology Kaylor, J., Bodner, N., Edridge, S., Yamin, G., Hong, D. P., Fink, A. L. 2005; 353 (2): 357-72

  Abstract

  The aggregation of alpha-synuclein is believed to be a critical step in the etiology of Parkinson's disease. A variety of biophysical techniques were used to investigate the aggregation and fibrillation of alpha-synuclein in which one of the four intrinsic Tyr residues was replaced by Trp, and two others by Phe, in order to permit fluorescence resonance energy transfer (FRET) between residues 39 (Tyr) and 125 (Trp). The mutant Y125W/Y133F/Y136F alpha-synuclein (one Tyr, one Trp) showed fibrillation kinetics similar to that of the wild-type, as did the Y125F/Y133F/Y136F (one Tyr, no Trp) and Y39F/Y125W/Y133F/Y136F (no Tyr, one Trp) mutants. Time-dependent changes in FRET, Fourier transform infrared, Trp fluorescence, dynamic light-scattering and other probes, indicate the existence of a transient oligomer, whose population reaches a maximum at the end of the lag time. This oligomer, in which the alpha-synuclein is in a partially folded conformation, is subsequently converted into fibrils, and has physical properties that are distinct from those of the monomer and fibrils. In addition, another population of soluble oligomers was observed to coexist with fibrils at completion of the reaction. The average distance between Tyr39 and Trp125 decreases from 24.9A in the monomer to 21.9A in the early oligomer and 18.8A in the late oligomer. Trp125 remains solvent-exposed in both the oligomers and fibrils, indicating that the C-terminal domain is not part of the fibril core. No FRET was observed in the fibrils, due to quenching of Tyr39 fluorescence in the fibril core. Thus, aggregation of alpha-synuclein involves multiple oligomeric intermediates and competing pathways.

  View details for DOI 10.1016/j.jmb.2005.08.046

  View details for PubMedID 16171820

• Forcing nonamyloidogenic beta-synuclein to fibrillate. Biochemistry Yamin, G., Munishkina, L. A., Karymov, M. A., Lyubchenko, Y. L., Uversky, V. N., Fink, A. L. 2005; 44 (25): 9096-107

  Abstract

  The fibrillation and aggregation of alpha-synuclein is a key process in the formation of intracellular inclusions, Lewy bodies, in substantia nigral neurons and, potentially, in the pathology of Parkinson's disease and several other neurodegenerative disorders. Alpha-synuclein and its homologue beta-synuclein are both natively unfolded proteins that colocalize in presynaptic terminals of neurons in many regions of the brain, including those of dopamine-producing cells of the substantia nigra. Unlike its homologue, beta-synuclein does not form fibrils and has been shown to inhibit the fibrillation of alpha-synuclein. In this study, we demonstrate that fast and efficient aggregation and fibrillation of beta-synuclein can be induced in the presence of a variety of factors. Certain metals (Zn(2+), Pb(2+), and Cu(2+)) induce a partially folded conformation of beta-synuclein that triggers rapid fibrillation. In the presence of these metals, mixtures of alpha- and beta-synucleins exhibited rapid fibrillation. The metal-induced fibrillation of beta-synuclein was further accelerated by the addition of glycosaminoglycans or high concentrations of macromolecular crowding agents. Beta-synuclein also rapidly formed soluble oligomers and fibrils in the presence of pesticides, whereas the addition of low concentrations of organic solvents induced formation of amorphous aggregates. These new findings demonstrate the potential effect of environmental pollutants in generating an amyloidogenic, and potentially neurotoxic, conformation, in an otherwise benign protein.

  View details for DOI 10.1021/bi048778a

  View details for PubMedID 15966733

• Effects of nitration on the structure and aggregation of alpha-synuclein MOLECULAR BRAIN RESEARCH Uversky, V. N., Yamin, G., Munishkina, L. A., Karymov, M. A., Millett, I. S., Doniach, S., Lyubchenko, Y. L., Fink, A. L. 2005; 134 (1): 84-102

  Abstract

  Substantial evidence suggests that the aggregation of the presynaptic protein alpha-synuclein is a key step in the etiology of Parkinson's disease (PD). Although the molecular mechanisms underlying alpha-synuclein aggregation remain unknown, oxidative stress has been implicated in the pathogenesis of PD. Here, we report the effects of tyrosine nitration on the propensity of human recombinant alpha-synuclein to fibrillate in vitro. The properties of nitrated alpha-synuclein were investigated using a variety of biophysical and biochemical techniques, which revealed that nitration led to formation of a partially folded conformation with increased secondary structure relative to the intrinsically disordered structure of the monomer, and to oligomerization at neutral pH. The degree of self-association was concentration-dependent, but at 1 mg/mL, nitrated alpha-synuclein was predominantly an octamer. At low pH, small-angle X-ray scattering data indicated that the nitrated protein was monomeric. alpha-Synuclein fibrillation at neutral pH was completely inhibited by nitrotyrosination and is attributed to the formation of stable soluble oligomers. The presence of heparin or metals did not overcome the inhibition; however, the inhibitory effect was eliminated at low pH. The addition of nitrated alpha-synuclein inhibited fibrillation of non-modified alpha-synuclein at neutral pH. Potential implications of these findings to the etiology of Parkinson's disease are discussed.

  View details for DOI 10.1016/j.molbrainres.2004.11.014

  View details for Web of Science ID 000228321100010

  View details for PubMedID 15790533

• Methionine oxidation, alpha-synuclein and Parkinson's disease. Biochimica et biophysica acta Glaser, C. B., Yamin, G., Uversky, V. N., Fink, A. L. 2005; 1703 (2): 157-69

  Abstract

  The aggregation of normally soluble alpha-synuclein in the dopaminergic neurons of the substantia nigra is a crucial step in the pathogenesis of Parkinson's disease. Oxidative stress is believed to be a contributing factor in this disorder. Because it lacks Trp and Cys residues, mild oxidation of alpha-synuclein in vitro with hydrogen peroxide selectively converts all four methionine residues to the corresponding sulfoxides. Both oxidized and non-oxidized alpha-synucleins have similar unfolded conformations; however, the fibrillation of alpha-synuclein at physiological pH is completely inhibited by methionine oxidation. The inhibition results from stabilization of soluble oligomers of Met-oxidized alpha-synuclein. Furthermore, the Met-oxidized protein also inhibits fibrillation of unmodified alpha-synuclein. The degree of inhibition of fibrillation by Met-oxidized alpha-synuclein is proportional to the number of oxidized methionines. However, the presence of metals can completely overcome the inhibition of fibrillation of the Met-oxidized alpha-synuclein. Since oligomers of aggregated alpha-synuclein may be cytotoxic, these findings indicate that both oxidative stress and environmental metal pollution could play an important role in the aggregation of alpha-synuclein, and hence possibly Parkinson's disease. In addition, if the level of Met-oxidized alpha-synuclein was under the control of methionine sulfoxide reductase (Msr), then this could also be factor in the disease.

  View details for DOI 10.1016/j.bbapap.2004.10.008

  View details for PubMedID 15680224

• Role of individual methionines in the fibrillation of methionine-oxidized alpha-synuclein. Biochemistry Hokenson, M. J., Uversky, V. N., Goers, J., Yamin, G., Munishkina, L. A., Fink, A. L. 2004; 43 (15): 4621-33

  Abstract

  The aggregation of normally soluble alpha-synuclein in the dopaminergic neurons of the substantia nigra is a crucial step in the pathogenesis of Parkinson's disease. Oxidative stress is believed to be a contributing factor in this disorder. We have previously established that oxidation of all four methionine residues in alpha-synuclein (to the sulfoxide, MetO) inhibits fibrillation of this protein in vitro and that the MetO protein also inhibits fibrillation of unmodified alpha-synuclein. Here we show that the degree of inhibition of fibrillation by MetO alpha-synuclein is proportional to the number of oxidized methionines. This was accomplished be selectively converting Met residues into Leu, prior to Met oxidation. The results showed that with one oxidized Met the kinetics of fibrillation were comparable to those for the control (nonoxidized), and with increasing numbers of methionine sulfoxides the kinetics of fibrillation became progressively slower. Electron microscope images showed that the fibril morphology was similar for all species examined, although fewer fibrils were observed with the oxidized forms. The presence of zinc was shown to overcome the Met oxidation-induced inhibition. Interestingly, substitution of Met by Leu led to increased propensity for aggregation (soluble oligomers) but slower formation of fibrils.

  View details for DOI 10.1021/bi049979h

  View details for PubMedID 15078109

• Certain metals trigger fibrillation of methionine-oxidized alpha-synuclein. The Journal of biological chemistry Yamin, G., Glaser, C. B., Uversky, V. N., Fink, A. L. 2003; 278 (30): 27630-5

  Abstract

  The aggregation and fibrillation of alpha-synuclein has been implicated as a key step in the etiology of Parkinson's disease and several other neurodegenerative disorders. In addition, oxidative stress and certain environmental factors, including metals, are believed to play an important role in Parkinson's disease. Previously, we have shown that methionine-oxidized human alpha-synuclein does not fibrillate and also inhibits fibrillation of unmodified alpha-synuclein (Uversky, V. N., Yamin, G., Souillac, P. O., Goers, J., Glaser, C. B., and Fink, A. L. (2002) FEBS Lett. 517, 239-244). Using dynamic light scattering, we show that the inhibition results from stabilization of the monomeric form of Met-oxidized alpha-synuclein. We have now examined the effect of several metals on the structural properties of methionine-oxidized human alpha-synuclein and its propensity to fibrillate. The presence of metals induced partial folding of both oxidized and non-oxidized alpha-synucleins, which are intrinsically unstructured under conditions of neutral pH. Although the fibrillation of alpha-synuclein was completely inhibited by methionine oxidation, the presence of certain metals (Ti3+, Zn2+, Al3+, and Pb2+) overcame this inhibition. These findings indicate that a combination of oxidative stress and environmental metal pollution could play an important role in triggering the fibrillation of alpha-synuclein and thus possibly Parkinson's disease.

  View details for DOI 10.1074/jbc.M303302200

  View details for PubMedID 12754258

• Nitration inhibits fibrillation of human alpha-synuclein in vitro by formation of soluble oligomers. FEBS letters Yamin, G., Uversky, V. N., Fink, A. L. 2003; 542 (1-3): 147-52

  Abstract

  The aggregation of alpha-synuclein in dopaminergic neurons is a critical factor in the etiology of Parkinson's disease (PD). Oxidative and nitrative stress is also implicated in PD. We examined the effect of nitration on the propensity of alpha-synuclein to fibrillate in vitro. Fibril formation of alpha-synuclein was completely inhibited by nitration, due to the formation of stable soluble oligomers (apparently octamers). More importantly the presence of sub-stoichiometric concentrations of nitrated alpha-synuclein led to inhibition of fibrillation of non-modified alpha-synuclein. These observations suggest that nitration of soluble alpha-synuclein may be a protective factor in PD, rather than a causative one.

  View details for DOI 10.1016/s0014-5793(03)00367-3

  View details for PubMedID 12729915

• Methionine oxidation inhibits fibrillation of human alpha-synuclein in vitro. FEBS letters Uversky, V. N., Yamin, G., Souillac, P. O., Goers, J., Glaser, C. B., Fink, A. L. 2002; 517 (1-3): 239-44

  Abstract

  We examined the effect of methionine oxidation of human recombinant alpha-synuclein on its structural properties and propensity to fibrillate. Both oxidized and non-oxidized alpha-synucleins were natively unfolded under conditions of neutral pH, with the oxidized protein being slightly more disordered. Both proteins adopted identical partially folded conformations under conditions of acidic pH. The fibrillation of alpha-synuclein at neutral pH was completely inhibited by methionine oxidation. This inhibitory effect was eliminated at low pH. The addition of oxidized alpha-synuclein to the unoxidized form led to a substantial inhibition of alpha-synuclein fibrillation.

  View details for DOI 10.1016/s0014-5793(02)02638-8

  View details for PubMedID 12062445