Quantifying geographical accessibility to cancer clinical trials in different income landscapes.

BACKGROUND: Clinical trials are increasingly perceived as a therapeutic opportunity for cancer patients. Favoring their concentration in few high-expertise academic centers maximizes quality of data collection but poses an issue of access equality. Analytical tools to quantify trial accessibility are needed to rationalize resources. MATERIALS AND METHODS: We constructed a distance-based accessibility index (dAI) using publicly available data on demographics, cancer incidence and trials. Multiple strategies were applied to mitigate or quantify clear sources of bias: reporting biases by text mining multiple registries; reliability of simple geographical distance by comparison with high-quality travel cost data for Italy; index inflation due to highly heterogeneous cancer incidence by log-transformation. We studied inequalities by Gini index and time trend significance by Mann-Kendall test. We simulated different resource allocation models in representative countries and identified locations where new studies would maximally improve the national index. RESULTS: The dAI approximated well a more realistic but not widely applicable travel cost-based index. Accessibility was unevenly distributed across and within countries (Gini index ∼0.75), with maximal inequalities in high- and upper-middle-income countries (China, United States, Russian Federation). Over time, accessibility increased but less than the total number of trials, most evidently in upper-middle-income countries. Simulations in representative countries (Italy and Serbia) identified ideal locations able to maximally raise the national index. CONCLUSIONS: Access to clinical trials is highly uneven across and within countries and is not mitigated by simple increase in the number of trials; a rational algorithmic approach can be used to mitigate inequalities.

Combining immunotherapy with an epidrug in squamous cell carcinomas of different locations: rationale and design of the PEVO basket trial.

Squamous cell carcinomas (SCCs) are among the most frequent solid tumors in humans. SCCs, related or not to the human papillomavirus, share common molecular features. Immunotherapies, and specifically immune checkpoint inhibitors, have been shown to improve overall survival in multiple cancer types, including SCCs. However, only a minority of patients experience a durable response with immunotherapy. Epigenetic modulation plays a major role in escaping tumor immunosurveillance and confers resistance to immune checkpoint inhibitors. Preclinical evidence suggests that modulating the epigenome might improve the efficacy of immunotherapy. We herein review the preclinical and the clinical rationale for combining immunotherapy with an epidrug, and detail the design of PEVOsq, a basket clinical trial combining pembrolizumab with vorinostat, a histone deacetylase inhibitor, in patients with SCCs of different locations. Sequential blood and tumor sampling will be collected in order to identify predictive and pharmacodynamics biomarkers of efficacy of the combination. We also present how clinical and biological data will be managed with the aim to enable the development of a prospective integrative platform to allow secure and controlled access to the project data as well as further exploitations.

Cytotoxic drugs for patients with breast cancer in the era of targeted treatment: back to the future?

BACKGROUND: Despite current trend of targeted therapy development, cytotoxic agents are a mainstay of treatment of patients with breast cancer. We reviewed recent advances in cytotoxic therapy for patients with metastatic breast cancer (MBC). MATERIALS AND METHODS: Medline searches were conducted for English language studies using the term 'MBC' and 'cytotoxic drugs'. The data search was restricted to the period 2000-2011. RESULTS: Several novel cytotoxic compounds, all microtubule inhibitors, have been approved for clinical use in MBC: (i) nab-paclitaxel, reported to improve tumour response and decrease hypersensitivity reactions in comparison with other taxanes; (ii) ixabepilone, shown to have clinical benefit in taxane- and anthracycline-resistant disease and (iii) eribulin, shown to improve overall survival in heavily pre-treated patients, when compared with best available standard treatment. Agents, such as larotaxel, vinflunine, trabectidin and formulations, including cationic liposomal paclitaxel or paclitaxel poliglumex, are currently under evaluation in phase II/III trials. CONCLUSION: Toxicity and chemotherapy resistance are still major limitations in the treatment of patients with MBC. Further research into new cytotoxic compounds is needed in order to maximise benefit, whilst minimising toxicity.

High rate of stem cell mobilization failure after thalidomide and oral cyclophosphamide induction therapy for multiple myeloma.

Novel agents are increasingly used during induction therapy for multiple myeloma (MM), but there is concern about their potential impact on stem cell mobilization. Regimens containing either thalidomide or cyclophosphamide have little or no impact on stem cell collection. In this retrospective review of 136 patients with newly diagnosed MM, we show that the combination of thalidomide and oral CY with dexamethasone (CTD) during induction therapy impaired stem cell mobilization substantially. Compared with VAD (vincristine, doxorubicin, dexamethasone) and a VAD-like induction regimen, the stem cell collection yield after CTD was decreased by 49% (median 5.0 vs 9.8 × 10(6) CD34+cells/kg, P<0.001). Following CTD, more patients failed to mobilize enough stem cells for one (25.4 vs 5.8%, P=0.002) or two (39.4 vs 15.9%, P=0.002) transplants. These results demonstrate that the combination of thalidomide and oral CY impairs stem cell mobilization and indicate that drugs with no previously reported relevant effect on stem cell mobilization can have a substantial impact when given in combination.

Preferred proline puckerings in cis and trans peptide groups: implications for collagen stability.

The interplay between side-chain and main-chain conformations is a distinctive characteristic of proline residues. Here we report the results of a statistical analysis of proline conformations using a large protein database. In particular, we found that proline residues with the preceding peptide bond in the cis state preferentially adopt a down puckering. Indeed, out of 178 cis proline residues, as many as 145 (81%) are down. By analyzing the 1-4 and 1-5 nonbonding distances between backbone atoms, we provide a structural explanation for the observed trend. The observed correlation between proline puckering and peptide bond conformation suggests a new mechanism to explain the reported shift of the cis-trans equilibrium in proline derivatives. The implications of these results for the current models of collagen stability are also discussed.

Pyramidalization of backbone carbonyl carbon atoms in proteins.

The high accuracy of X-ray analyses at atomic resolution is now able to display subtle deformations from standard geometry of building blocks in proteins. From the analysis of nine ultra-high resolution protein structures, we derived the first experimental evidence that a significant pyramidalization at the main-chain carbonyl carbon atom occurs in proteins. Our findings also show that this pyramidalization is related to the main-chain psi torsion angle. The carbonyl carbon atoms of residues that adopt alphaR and extended conformations show a clear preference for positive and negative pyramidalization, respectively. The agreement between our data and those previously obtained from small molecule structures demonstrates that carbon pyramidalization is an intrinsic property of the peptide structure. Although small in magnitude, the pyramidalization is well preserved in the complex folded state of a macromolecular structure that results from the interplay of many different forces. In addition, this property of the peptide group may have interesting implications for the enzymatic reactions involving the carbonyl carbon atoms.

Productive and nonproductive binding to ribonuclease A: X-ray structure of two complexes with uridylyl(2',5')guanosine.

Guanine-containing mono- and dinucleotides bind to the active site of ribonuclease A in a nonproductive mode (retro-binding) (Aguilar CF, Thomas PJ, Mills A, Moss DS, Palmer RA. 1992. J Mol Biol 224:265-267). Guanine binds to the highly specific pyrimidine site by forming hydrogen bonds with Thr45 and with the sulfate anion located in the P1 site. To investigate the influence of the anion present in the P1 site on retro-binding, we determined the structure of two new complexes of RNase A with uridylyl(2',5')guanosine obtained by soaking two different forms of pre-grown RNase A crystals. In one case, RNase A was crystallized without removing the sulfate anion strongly bound to the active site; in the other, the protein was first equilibrated with a basic solution to displace the anion from the P1 site. The X-ray structures of the complexes with and without sulfate in P1 were refined using diffraction data up to 1.8 A (R-factor 0.192) and 2.0 A (R-factor 0.178), respectively. The binding mode of the substrate analogue to the protein differs markedly in the two complexes. When the sulfate is located in P1, we observe retro-binding; whereas when the anion is removed from the active site, the uridine is productively bound at the B1 site. In the productive complex, the electron density is very well defined for the uridine moiety, whereas the downstream guanine is disordered. This finding indicates that the interactions of guanine in the B2 site are rather weak and that this site is essentially adenine preferring. In this crystal form, there are two molecules per asymmetric unit, and due to crystal packing, only the active site of one molecule is accessible to the ligand. Thus, in the same crystal we have a ligand-bound and a ligand-free RNase A molecule. The comparison of these two structures furnishes a detailed and reliable picture of the structural alterations induced by the binding of the substrate. These results provide structural information to support the hypotheses on the role of RNase A active site residues that have recently emerged from site-directed mutagenesis studies.

Effects of microgravity on the crystal quality of a collagen-like polypeptide.

(Pro-Pro-Gly)(10) is one of the most widely studied collagen polypeptide models. Microgravity crystal growth of (Pro-Pro-Gly)(10) was carried out in the Advanced Protein Crystallization Facility aboard the Space Shuttle Discovery during the STS-95 mission. Crystals were successfully grown in all experiments, using both dialysis and free-interface diffusion methods. The quality of the microgravity-grown crystals and of ground-grown counterparts was assessed by X-ray synchrotron diffraction. Microgravity-grown crystals exhibited a significant improvement in terms of dimensions and resolution limit. As previously reported, crystals were orthorhombic, space group P2(1)2(1)2(1). However, the diffraction pattern showed weak reflections, never previously measured, that were consistent with new unit-cell parameters a = 26.9, b = 26.4, c = 182.5 A. This allowed the derivation of a new model for the arrangement of the triple-helical molecules in the crystals.

Effect of deamidation on folding of ribonuclease A.

The folding of ribonuclease A (RNase A) has been extensively studied by characterizing the disulfide containing intermediates using different experimental conditions and analytical techniques. So far, some aspects still remain unclear such as the role of the loop 65-72 in the folding pathway. We have studied the oxidative folding of a RNase A derivative containing at position 67 the substitution Asn --> isoAsp where the local structure of the loop 65-72 has been modified keeping intact the C65-C72 disulfide bond. By comparing the folding behavior of this mutant to that of the wild-type protein, we found that the deamidation significantly decreases the folding rate and alters the folding pathway of RNase A. Results presented here shed light on the role of the 65-72 region in the folding process of RNase A and also clarifies the effect of the deamidation on the folding/unfolding processes. On a more general ground, this study represents the first characterization of the intermediates produced along the folding of a deamidated protein.

Crystal structure of a collagen-like polypeptide with repeating sequence Pro-Hyp-Gly at 1.4 A resolution: implications for collagen hydration.

The use of polypeptide models has proved to be a valuable tool to obtain accurate information on the collagen triple helix. Here we report the high resolution crystal structure of a collagen-like polypeptide with repeating sequence Pro-Hyp-Gly. The structure has been refined to an R(factor) of 0.137 and an R(free) of 0.163 using synchrotron diffraction data extending up to 1.4 A resolution. The polypeptide triple-helical structure binds a large number of water molecules, in contrast with a previous structure determination at lower resolution. The highly hydrated nature of this polypeptide confirms a number of previous studies conducted both in solution and in the crystal state. In addition, neighboring polypeptide triple helices are directly bound in the crystal through Hyp-Hyp hydrogen-bonding interactions. This finding supports the idea that Hyp residues may be important for the assembly of the triple helices in the collagen fibrils and may stabilize the fibrils by mediating direct contacts between neighboring molecules.

A potential allosteric subsite generated by domain swapping in bovine seminal ribonuclease.

Bovine seminal ribonuclease (BS-RNase) is a peculiar member of the pancreatic-like ribonuclease superfamily endowed with unique biological functions. It has been shown that native BS-RNase is a mixture of two distinct dimeric forms. The most abundant form is characterised by the swapping of the N-terminal helix. Kinetic studies have shown that this dimer is allosterically regulated, whereas the minor component, in which no swapping occurs, exhibits typical Michaelian kinetics. In order to correlate the catalytic properties with the structural features of BS-RNase, we have determined the crystal structure of the BS-RNase swapping dimer complexed with uridylyl(2'-5')guanosine. The structure of the complex was refined to an R value of 0.189 at 1.9 A resolution. Surprisingly, the enzyme binds four dinucleotide molecules, all in a non-productive way. In the two active sites, the guanine base is located in the subsite that is specific for pyrimidines. This unusual binding has been observed also in complexes of RNase A with guanine-containing nucleotides (retro-binding). One of the two additional dinucleotide molecules bound to the enzyme is located on the surface of the protein in a pocket generated by crystal packing; the second was found in a cavity at the interface between the two subunits of the swapping dimer. There are indications that the interface site plays a role in the allosteric regulation exhibited by BS-RNase. This finding suggests that domain swapping may not merely be a mechanism that proteins adopt for the transition from a monomeric to oligomeric state but can be used to achieve modulations in catalytic function.

Activation of diketopiperazine formation by alkylammonium carboxylate salts and aprotic dipolar protophobic solvents.

Diketopiperazine formation from the N-terminal residues of a peptide chain is accelerated by aprotic dipolar protophobic solvents and catalyzed in organic solvents by alkylammonium carboxylate salts. The t1/2 for the first-order reaction of H-Ala-Pro-NH2 x TFA falls from 20 d in methanol to 3.6 min in acetonitrile containing 0.02 mol dm(-3) triethylammonium acetate; for H-Ala-Ala-NH2 x TFA in the same reaction media t1/2 falls from an unmeasurably long time to 1.3 d.

Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2',5')adenosine.

Bovine seminal ribonuclease (BS-RNase) is a unique member of the pancreatic-like ribonuclease superfamily. The native enzyme is a mixture of two dimeric forms with distinct structural features. The most abundant form is characterized by the swapping of N-terminal fragments. In this paper, the crystal structure of the complex between the swapping dimer and uridylyl(2',5')adenosine is reported at 2.06 A resolution. The refined model has a crystallographic R-factor of 0.184 and good stereochemistry. The quality of the electron density maps enables the structure of both the inhibitor and active site residues to be unambiguously determined. The overall architecture of the active site is similar to that of RNase A. The dinucleotide adopts an extended conformation with the pyrimidine and purine base interacting with Thr45 and Asn71, respectively. Several residues (Gln11, His12, Lys41, His119, and Phe120) bind the oxygens of the phosphate group. The structural similarity of the active sites of BS-RNase and RNase A includes some specific water molecules believed to be relevant to catalytic activity. Upon binding of the dinucleotide, small but significant modifications of the tertiary and quaternary structure of the protein are observed. The ensuing correlation of these modifications with the catalytic activity of the enzyme is discussed.

Acid catalysis in the formation of dioxopiperazines from peptides containing tetrahydroisoquinoline-3-carboxylic acid at position 2.

The kinetics of the spontaneous formation of 2,5-dioxopiperazines from peptides containing the Tic (1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid) residue in the 2-position of the sequence has been studied in DMSO and water solution. The reaction is first order in Tic-peptide and subject to general-acid catalysis. Moreover, only the fraction of peptide having the amino terminal group in the deprotonated state reacts with appreciable rate. In pure organic solvent, and in aqueous solution with low buffer concentration, the degradation reaction of Tic-peptides is very low; at 20 degrees C for the peptide H-Tyr-Tic-Phe-Phe-NH2, in DMSO and in neutral water in the absence of buffer, the half-lives (t1/2) are 3 x 10(4) and 1.2 x 10(4) h, respectively. The addition of carboxylic acids or buffers to the reaction solutions markedly increases the reaction rate; in 0.01 m HAc in DMSO and in 0.1 M phosphate buffer in water, pH 7.1, t1/2 values for the tetrapeptide are 61 and 121 h, respectively.

Solid-state conformations of aminosuccinyl peptides: structure of tert-butyloxycarbonyl-L-prolyl-L-aminosuccinyl-glycyl-L-alanine methyl ester (Boc-L-Pro-L-Asu-Gly-L-Ala-OMe). A case of pseudo-translational symmetry.

C20H30N4O8, M(r) = 454.48, monoclinic, P2(1), a = 13.411 (2), b = 12.592 (2), c = 14.710 (1) A, beta = 104.30 (1) degrees, V = 2407 (6) A3, Z = 4, Dx = 1.254 Mg m-3, lambda (Cu K alpha) = 1.5418 A, mu = 0.783 mm-1, F(000) = 968, room temperature, final R = 0.086, wR = 0.080 for 4055 observed reflections. The title compound is a model for the intermediate formed in the deamidation reaction of porcine adrenocorticotropin hormone. The structure presents a pseudo-translational symmetry and was solved by using a modified version of the SIR88 package. In the refinement, few stereochemical restraints were needed to handle the static disorder shown by the C-terminal fragment of one molecule in the asymmetric unit. The conformation of the two independent molecules is almost identical and is a II' beta-bend, stabilized by an intramolecular hydrogen bond. In the crystal, screw-related molecules are linked by hydrogen bonds. The two molecules in the independent unit are related by the translation vector u = 0.4962 (2)a + 0.7310 (2)b + 0.5075 (2)c.

[Desmoid tumors of the abdominal wall]. / Tumori desmoidi della parete addominale.

The authors report their experience in the management of desmoid tumors, rare benign neoplasias, locally aggressive and potentially recurrent after surgery. Etiopathogenetic, diagnostic, and therapeutic features of these tumors are analysed and the value of surgery as well as chemo- or radiotherapy is considered.

Histopathology of spontaneous brain herniations into the middle ear.

Two patients with spontaneous brain herniation into the middle ear have been operated on with a combined otoneurological approach. In case No. 1, two 2 x 3 mm arachnoid tissue herniations were found in the tegmen antri of the left ear. Six years later, a 8 x 9 mm mass consisting of prolapsed brain was removed from the right ear. The histological examination showed normal but disorganized nervous tissue. The surface consisted of middle ear mucosa or modified glial cells. More deeply numerous well preserved neurons and synapses were observed. In case No. 2, a 2 x 1 cm herniation was found in contact with the ossicles and the bony walls of the middle ear. The herniation consisted of partly degenerated nervous tissue which could explain the episode of temporal lobe seizure the patient experienced 8 years before surgery. In the world literature during the last 40 years, 29 cases of spontaneous or idiopathic brain herniation into the middle ear and mastoid have been reported. In 10, the herniations were multiple, as in our case No. 1. Case No. 1 is interesting also because the spontaneous brain herniation was bilateral.

Deamidation via cyclic imide in asparaginyl peptides.

The deamidation reaction of asparaginyl peptides was studied as a function of the pH and sequence. The deamidation of Boc-Asn-Gly-Gly-NH2 and the hydrolysis of the corresponding aminosuccinyl (Asu) peptide, Boc-Asu-Gly-Gly-NH2, were carried out in the pH ranges 5-10, whereas the deamidation of Boc-Asn-Ala-Gly-NH2, Boc-Asn-Gly-Ala-NH2 and Boc-Asn-Ser-Gly-NH2 was studied at pH 8.9 only. In each case, the conversion of the amide side-chain moiety of the Asn to carboxyl group occurs via a succinimide intermediate (Asu), and its breakdown leads to a normal and an isoaspartyl peptide. The kinetic constants of the Asu formation and the hydrolytic step increase markedly at basic pH. The influence of the side chain of the residue next to Asn is also discussed.

The role of the subfornical organ in the drinking behavior of the pigeon.

Pigeons with radiofrequency lesions that damaged the subfornical organ (SFO) (n = 4) or that isolated it from adjacent structures (n = 5), but not sham-lesioned pigeons, were unresponsive to blood-borne (i.p.) ANG II (100 micrograms/pigeon) in the immediate postoperative period and for 60 days thereafter. These animals were less sensitive to hypovolemic challenge (20% PEG), but they responded normally to 24 h of water deprivation and to cellular dehydration. Despite their unresponsiveness to bloodborne ANG II, the lesioned pigeons drank normally to 10 ng of i.c.v. ANG II given as early as 10 days after surgery, and they drank reliably and vigorously but less in total volume to 100 ng i.c.v. They also drank quickly, vigorously, and in normal total volume to i.c.v. tachykinins and bombesins, and to the peripheral (i.p.) bombesins. Peripheral (i.m.) tachykinins produced only low volume and variable drinking in all birds tested regardless of brain damage. The SFO of the pigeon, like that of the mammal, is essential for drinking evoked by blood-borne ANG II and is not necessary for thirst aroused by ANG II acting from within the cerebral ventricles. Lastly, it does not mediate the dipsogenic effects of the tachykinins or the bombesins.

Granuloma associated with fenestrated tracheostomy tubes.

Four cases of granuloma that caused tracheal obstruction have been presented. In each, although for different reasons, a tracheostomy was performed and a fenestrated tube inserted. We conclude that the insertion of a fenestrated tube was the direct cause of the excessive amount of granuloma that caused tracheal obstruction.