Crucial role of nonspecific interactions in amyloid nucleation

Protein oligomers have been implicated as toxic agents in a wide range of amyloid-related diseases. However, it has remained unsolved whether the oligomers are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct. Analogously, it has not been resolved if the amyloid nucleation process is a classical one-step nucleation process or a two-step process involving prenucleation clusters. We use coarse-grained computer simulations to study the effect of nonspecific attractions between peptides on the primary nucleation process underlying amyloid fibrillization. We find that, for peptides that do not attract, the classical one-step nucleation mechanism is possible but only at nonphysiologically high peptide concentrations. At low peptide concentrations, which mimic the physiologically relevant regime, attractive interpeptide interactions are essential for fibril formation. Nucleation then inevitably takes place through a two-step mechanism involving prefibrillar oligomers. We show that oligomers not only help peptides meet each other but also, create an environment that facilitates the conversion of monomers into the β-sheet–rich form characteristic of fibrils. Nucleation typically does not proceed through the most prevalent oligomers but through an oligomer size that is only observed in rare fluctuations, which is why such aggregates might be hard to capture experimentally. Finally, we find that the nucleation of amyloid fibrils cannot be described by classical nucleation theory: in the two-step mechanism, the critical nucleus size increases with increases in both concentration and interpeptide interactions, which is in direct contrast with predictions from classical nucleation theory.During the process of amyloid formation, normally soluble proteins assemble into fibrils that are enriched in β-sheet content and have diameters of a few nanometers and lengths up to several micrometers. This phenomenon has been implicated in a variety of pathogenic processes, including Alzheimer’s and Parkinson’s diseases, type 2 diabetes, and systemic amyloidoses (1–3). The association with human diseases has largely motivated a long-standing effort to probe the assembly process, and numerous studies have aimed at elucidating the mechanism of amyloid aggregation (4). The basic nature of the aggregation reaction has emerged as a nucleation and growth process (5, 6), where the aggregates are created through a not well-understood primary nucleation event and can grow by recruiting additional peptides or proteins to their ends (7, 8). In this paper, we focus on the nature of this primary step in amyloid nucleation and the fundamental initial events that underlie amyloid formation.Amyloidogenic peptides and proteins, when in their nonpathological cellular form, can range in the structures from mainly α-helical to β-sheet and even random coil, whereas the amyloid forms of proteins possess a generic cross–β-structure (9–14). The formation of amyloid is, hence, accompanied by marked changes in the conformations of the peptides and proteins that undergo this process. A pertinent question is whether this conformational change takes place simultaneously with the nucleation process or whether nucleation takes place first and is then followed by conformational change. These two possible scenarios of nucleation have been extensively discussed in the experimental and theoretical literature (5, 8, 15–19). We will refer in this work to the two scenarios simply as one-step nucleation (1SN), in which the β-sheet–enriched nucleus forms directly from the solution, and two-step nucleation (2SN), where soluble monomers first assemble into disordered oligomers, which subsequently convert into a β-sheet nucleus. Disordered oligomers, ranging in size between dimers and micrometer-sized particles, have been observed in some experiments (20–28). These findings highlight a central question regarding the role of disordered oligomers in fibril formation: are such clusters a necessary step in the process of fibril formation or just a byproduct?From a biological and biomedical perspective, it is important to understand the conditions under which oligomeric clusters form, because such species exhibit high cytotoxicity (1, 29–31). Indeed, there is strong evidence that the disordered oligomers rather than fully grown fibrils are the main pathogenic species in protein aggregation diseases (31–33). As such, defining the role of the prefibrillar oligomers during amyloid formation will be crucial to develop intervention strategies that target these species (1, 30, 34, 35).Mutations in the polypeptide sequence and extrinsic changes in the experimental conditions are known to alter the concentrations of aggregated species, their size, and their cytotoxicity (25, 36–39). For instance, mutations that increase hydrophobicity of the Alzheimer’s β-peptide (Aβ1–42) have a pronounced effect on its aggregation behavior and the size distribution of the resulting oligomers (23–26, 40), promoting toxicity and expediting the fibrillization process. In the same spirit, two extra hydrophobic residues in Aβ1–42 are believed to contribute to the more pronounced oligomerization and faster fibrillization compared with its alloform Aβ1–40 (24, 25, 40). Temperature, pH, and concentration of certain metals also affect oligomerization and pathways of fibrillization (41–44).The common feature of the above experiments is that they modify the internal free energy difference between the soluble and the β-sheet–forming state, also called the β-sheet propensity, which has been extensively studied in the literature (45–48). However, they also modify interactions between peptides that aggregate, a crucial contribution that has not yet been systematically addressed.In this paper, we study the effect of nonspecific interactions between peptides on the amyloid nucleation process. Such nonspecific interactions do not depend on the atomistic details of the amino acids involved, allowing us to address question about amyloid aggregation and nucleation using a coarse-grained model. In particular, generic hydrophobic stretches in the sequence of Aβ have been shown to be sufficient to promote aggregation (49, 50). Mutations of nonpolar residues to other nonpolar residues had little or no effect on aggregation, whereas mutations that reduce charge and/or increase hydrophobicity enhanced it (50, 51). Furthermore, atomic force microscopy measurements have shown that the strength of overall interactions between amyloidogenic proteins correlates with their tendency to aggregate (52, 53).We have performed extensive computer simulations that allowed us to observe both the 1SN and the 2SN mechanisms. These simulations reveal that 1SN and 2SN can be viewed as two limits of the same process, something that several previous studies have suspected (16, 18). Importantly, we observe that only 2SN is possible at low peptide concentrations, comparable with the levels that are found in vivo. Another key observation is that fibril nucleation typically does not proceed through the most prevalent oligomeric species but rather, through an oligomer with a size that is only observed as a result of rare fluctuations. As a consequence, such oligomers will be hard to capture experimentally, although their presence is required for nucleation to take place. Our simulations show that the free energy barrier for fibril nucleation through the two-step mechanism decreases with increasing strength of the interpeptide interactions. Furthermore, the critical nucleus size in the two-step mechanism is found to grow with the increase in the peptide concentrations as well as with stronger interpeptide interactions, which is in direct contrast with the classical nucleation. These results imply that weakening the nonspecific interactions between peptide monomers in solution and thereby, simultaneously increasing both the free energy barrier for oligomer formation and the free energy barrier for peptide conversion at a given oligomer size may be a crucial step in preventing amyloid aggregation.     

Predictive value of ABCB1 polymorphisms G2677T/A, C3435T, and their haplotype in small cell lung cancer patients treated with chemotherapy

Purpose

Multiple drug resistance limits the efficacy of numerous cytotoxic drugs used in the treatment of small cell lung cancer (SCLC). The drug efflux protein ATP-binding cassette transporter B1 (ABCB1) has an important role in this process, and its gene variability may affect chemotherapy outcomes.

Patients and methods

This study aimed to evaluate the associations between ABCB1 polymorphisms G2677T/A, C3435T, and their haplotype with progression-free survival (PFS) and overall survival (OS) in 177 SCLC patients treated with cisplatin–etoposide or cyclophosphamide–epirubicin–vincristine chemotherapy. To determine the ABCB1 genotype, allelic specific TaqMan^? probes were used in a RT-PCR .

Results

Patients carrying the G2677T/A TT?+?TA?+?AA genotypes (24?%) or the C3435T CT?+?TT genotypes (72?%) or the 2677T/A-3435T haplotype (40?%) had a longer PFS (Cox regression, P?=?0.052, 0.037 and 0.037, respectively); these associations persisted also in multivariate analyses (Cox regression, P?=?0.028, 0.037 and 0.030, respectively). Moreover, patients with the C3435T CT?+?TT genotypes had a longer OS both in univariate and multivariate analysis (Cox regression, P?=?0.022 and 0.028, respectively). A trend toward longer OS was noted for the 2677T/A-3435T haplotype (Cox regression, P?=?0.051), but its independent value was not confirmed (Cox regression, P?=?0.071).

Conclusions

Our study reported a possible predictive value of ABCB1 polymorphisms G2677T/A, C3435T, and their haplotype for longer PFS and OS in Caucasian SCLC patients treated with chemotherapy. However, to be implemented into routine clinical practice, ABCB1 polymorphisms require further validation.     

Effects of multivitamin supplementation on DNA damage in lymphocytes from elderly volunteers

The aim of this study was to evaluate the effect of a mixture of vitamins and minerals on oxidative DNA damage and the resistance of DNA to H(2)O(2)-induced DNA strand breaks in lymphocytes from 80 elderly volunteers ex vivo by means of Comet assay. The intervention with vitamin complex decreased significantly the levels of DNA damage. Our results demonstrate that the vitamin complex was able to decrease H(2)O(2)-induced DNA breakage. Our data suggest that the consumption of some vitamins may reduce the effects of oxidative DNA damage and may be useful for attaining healthy aging.     

Solitary colonic metastasis of renal cell carcinoma

We report a rare case of a solitary metastasis of a renal cell carcinoma which manifested as a primary colonic tumour. A 60-year-old male patient who had undergone a right radical nephrectomy 5 years previously for renal cell carcinoma, presented with a history of dyspepsia and pain in the right upper abdomen. A mass on the hepatic flexure was detected by computed tomography and colonoscopy and right hemicolectomy was performed. Postoperative histological examination revealed that the tumour was a metastatic renal cell carcinoma of the clear cell type.     

Lecithostaphylus tylosuri sp. nov. (Digenea, Zoogonidae) from the digestive tract of the needlefish Tylosurus acus imperialis (Teleostei, Belonidae)

Lecithostaphylus tylosuri sp. nov. (Digenea, Zoogonidae) specimen were collected from the digestive tract of Tylosurus acus imperialis (Teleostei, Belonidae) caught off the eastern coast of Tunisia. L. tylosuri is very similar to its closest relatives, L. retroflexus and L. nitens. It can be easily distinguished from L. retroflexus (Molin, 1859) in having a more extensive vitellarium, with follicles reaching from the posterior margin of the acetabulum and extending beyond the posterior margin of the testes and a coiled seminal vesicle. L. tylosuri differs from L. nitens as illustrated by Linton 1898, in having a longer cirrus pouch (0.7 mm vs 0.36 mm, respectively) overlapping the anterior edge of the ventral sucker and a submarginal genital pore (submedian in L. nitens). It’s also different from L. nitens as described by Manter 1947 in the vitelline disposition and in having the greater sucker ratio (1: 1.3–2.1 vs 1: 1.3–1.6, respectively). L. tylosuri differs from L. nitens as reported by Machida and Kuramochi 2000 by the absence of variations in the vitellarium disposition in all specimens. L. tylosuri is more similar to L. nitens from group A (considered synonym of L. ahaaha Yamaguti, 1970 = L. nitens by Bray 1987) by having vitelline follicles extending beyond the testes. L. tylosuri can be distinguished from L. ahaaha by its pedunculate rather than prominent acetabulum and its larger body size (4.10–7.85 mm long and 0.75–1.2 mm large vs 2.1–6 mm long and 0.45–1.1 mm large, respectively). The prevalence of L. tylosuri sp. nov. was negatively correlated with host length (decreasing with host size increasing). Host sex does not seem to affect infection parameters.     

Differential response to lipid peroxidation in male and female mice with age: correlation of antioxidant enzymes matters

The aim of this study was to correlate the activity of superoxide dismutase, catalase and glutathion peroxidase in liver and brain of 1, 4 and 18 months old CBA mice of both sexes. In liver, decreased superoxide dismutase and increased glutathione peroxidase activities were observed during aging in male mice. In brain, the increase of catalase and glutathion peroxidase activity during aging was observed only in female mice. Regardless of tissue examined, different sex-related correlation pattern of antioxidant enzyme activity was demonstrated in young and old mice. The cooperation between antioxidant enzymes becomes more coherent with increased lipid peroxidation concentration in liver and brain of older female mice. On the contrary, in older male mice the link among three antioxidant enzymes becomes weaker, regardless of lipid peroxidation concentration which increased in liver and decreased in brain during aging. In older mice lower partial coefficient of correlation than pair correlation demonstrates the influence of the third party in the cooperation of two antioxidant enzymes. The results imply stronger correlative links in old female than male mice, which might explain why old females are better protected from oxidative stress than males.     

Epithelioid hemangioendothelioma of bone

Epithelioid hemangioendothelioma is a low-grade malignant tumor with a histologic appearance and clinical course between that of a hemangioma and angiosarcoma. It is rarely encountered in the bone. A 48-year-old woman was examined following trauma. A cystic lesion was noted on a plain radiograph of the left foot, destructing the diaphysis of the first metatarsal bone. Magnetic resonance imaging showed a solid intramedullary lesion involving a large part of the bone. Scintigraphic examination showed uptake in the diaphysis of the left tibia and the first metatarsal bone of the left foot. Histopathologic examination showed a neoplastic lesion consisting of atypical endothelial cells lining vascular structures or forming solid nests in a myxoid stroma. The tumor was immunoreactive for factor VIII, CD31, CD34, and vimentin. A diagnosis of epithelioid hemangioendothelioma was made and the patient underwent subtotal resection of the metatarsal bone with reconstruction of the fibula, and a wide resection of the tibial lesion. No recurrences or metastasis were observed during a four-year follow-up.     

Shear-wave sonoelastographic features of invasive lobular breast cancers

AimTo evaluate shear-wave elastographic (SWE) and related gray-scale features of pure invasive lobular breast carcinoma (ILC) and compare them with invasive ductal breast cancers (IDC).MethodsQuantitative SWE features of mean (El-mean), maximum (El-max), minimum (El-min) elasticity values of the stiffest portion of the mass, and lesion-to-fat elasticity ratio (E-ratio) were measured in 40 patients with pure ILC and compared with 75 patients with IDC. Qualitative gray-scale features of lesion size, echogenicity, orientation, and presence of distal shadowing were determined and compared between the groups.ResultsILC were significantly larger than IDC (P = 0.008) and exhibited significantly higher El-max (P = 0.015) and higher El-mean (P = 0.008) than IDC. ILC were significantly more often horizontally oriented, while IDC were significantly more often vertically oriented (P < 0.001); ILC were significantly more often hyperechoic than IDC (P < 0.001). Differences in stiffness between ILC and IDC determined by quantitative SWE parameters were present only in small tumors (≤1.5 cm in size), ie, small ILC had significantly higher El-max (P = 0.030), El-mean (P = 0.014), and El-min (P = 0.045) than small IDC, while tumors larger than 1.5 cm had almost equal stiffness, without significant differences between the groups.ConclusionSpecific histopathologic features of ILC are translated into their qualitative sonographic and quantitative sonoelastographic appearance, with higher stiffness of small ILC compared to small IDC. Gray-scale and sonoelastographic features may help in diagnosing ILC.Invasive ductal cancer (IDC) is the most common breast cancer, while invasive lobular cancer (ILC) is the second most common and accounts for 6%-12% of breast cancers (1-3). ILC differs considerably from IDC by having a unique pathological growth pattern, the so called Indian-file pattern, with sheets of single-cell layers growing along the Cooper ligaments, ductuli, and other breast structures, resembling a spiderweb that diffusely spreads in the breast, producing minor desmoplastic reaction (4,5). This spiderweb-like growth is reflected in imaging features of ILC, as well as in its clinical presentation (6). IDC usually clinically manifests as a firm lump, while ILC usually manifests as a palpable thickening and skin or nipple retraction (3,5). ILC has increased tendency for multifocality and multicentricity, a higher risk of bilateral breast cancer (20%-29%), and older age at onset (7,8). Lymph node metastases are less common in ILC than in IDC of equal size, because ILC tumor cells lack cellular atypia and often have low mitotic rate (9). ILC has the propensity to metastasize to the chest, peritoneum, retroperitoneum, and pelvis (10).Because of its growth pattern of mass infiltrating surrounding tissues, IDC is much more easily detected than ILC also on mammography. ILC has higher false-negative mammographic rates than IDC, since ILC may be invisible or may have quite low mammographic density, and microcalcifications are uncommon (6,11). Due to the higher propensity for multicentric and bilateral lesions, it is generally considered that patients with ILC should be referred to preoperative breast MRI, the best imaging modality to evaluate the tumor extent, while the benefit for preoperative MRI in IDC has not yet been proven (12,13). Fine-needle aspiration is not as sensitive for the diagnosis of ILC as it is for IDC, and core-biopsy should be performed when ILC is suspected, even in cases of palpable lesions (14,15). ILC is associated more often than IDC with positive margins on surgical excision and is more often treated with mastectomy, because of the large size at diagnosis and underestimation of tumor extent with conventional imaging (16).Ultrasound of the breast is widely used in the diagnosis of breast cancer, usually after mammography, and most image-guided core biopsies of breast lesions are routinely performed under the sonographic guidance (17,18). Ultrasound is highly operator-dependent, much more than mammography or MRI. The quality of ultrasonic equipment and transducers is variable, suboptimal examinations are common, and interobserver variability is high; sensitivity of ultrasound in detection of ILC is reported in the range of 68%-88% (6,12,19).Sonoelastography is a relatively new ultrasonographic method, which may help in the detection and differentiation of benign and malignant breast lesions (18,20). Strain elastography allows qualitative estimation of the breast lesion stiffness, while shear-wave elastography (SWE) allows quantification of lesion stiffness in kilopascals (kPa) (18). Multicentric studies found that SWE features can help discriminate breast cancers and benign breast lesions, and breast cancers among themselves (20-22). It was also shown that some IDC, like triple negative breast cancers, differ in their stiffness compared to other IDC (23). Studies evaluating some SWE features of invasive cancers were done in a small number of patients with ILC, but to the best of our knowledge none so far has provided values specific for a larger, homogeneous group of patients with pure ILC (24,25).The aim of this single-center study was to evaluate and establish SWE and related conventional sonographic features of pure ILC of the breast in a group of 40 patients, and to compare these features with the most common invasive breast cancer, IDC. SWE features within ILC group were also correlated with tumor size, extent, histologic grade, and the presence of nodal metastases.