Pan-tumor landscape of fibroblast growth factor receptor 1-4 genomic alterations.

BACKGROUND: Selective tyrosine kinase inhibitors targeting fibroblast growth factor receptor (FGFR) 1-4 genomic alterations are in development or have been approved for FGFR-altered cancers (e.g. bladder cancer and advanced intrahepatic cholangiocarcinoma). Understanding FGFR inhibitor-resistance mechanisms is increasingly relevant; we surveyed the pan-tumor landscape of FGFR1-4 genomic alterations [short variants (SVs), gene rearrangements (REs), and copy number alterations (CNAs)], including their association with tumor mutational burden (TMB) and the genomic comutational landscape. PATIENTS AND METHODS: Comprehensive genomic profiling of 355 813 solid tumor clinical cases was performed using the FoundationOne and FoundationOne CDx assays (Foundation Medicine, Inc.) to identify genomic alterations in >300 cancer-associated genes and TMB (determined on ≤1.1 megabases of sequenced DNA). RESULTS: FGFR1-4 SVs and REs occurred in 9603/355 813 (2.7%), and CNAs in 15 078/355 813 (4.2%) samples. Most common FGFR alterations for bladder cancer, intrahepatic cholangiocarcinoma, and glioma were FGFR3 SVs (1051/7739, 13.6%), FGFR2 REs (618/6641, 9.3%), and FGFR1 SVs (239/11 550, 2.1%), respectively. We found several, potentially clinically relevant, tumor-specific associations between FGFR1-4 genomic alterations and other genomic markers. FGFR3 SV-altered bladder cancers and FGFR1 SV-altered gliomas were significantly less likely to be TMB-high versus unaltered samples. FGFR3 SVs in bladder cancer significantly co-occurred with TERT and CDKN2A/B alterations; TP53 and RB1 alterations were mutually exclusive. In intrahepatic cholangiocarcinoma, FGFR2 REs significantly co-occurred with BAP1 alterations, whereas KRAS, TP53, IDH1, and ARID1A alterations were mutually exclusive. FGFR1 SVs in gliomas significantly co-occurred with H3-3A and PTPN11 alterations, but were mutually exclusive with TERT, EGFR, TP53, and CDKN2A/B alterations. CONCLUSIONS: Overall, our hypothesis-generating findings may help to stratify patients in clinical trials and guide optimal targeted therapy in those with FGFR alterations.

Study of the elderly females' voice by phonetography.

This study was carried out to investigate the voice characteristics of 40 healthy females with no voice disorders, ranging in age from 60 to 84 years (X = 68.2+/-5.74 years). Measurements over all the entire phonational range were obtained by phonetography. The subjects were asked to sustain the vowel /a/ in modal register for a minimum of 5 seconds in the highest and lowest intensities after hearing the semitones C, E, G, and A, over all phonational ranges. The results indicated expansion of the low and reduction of high ends of the pitch range, decrease of the pitch numbers of the vocal range, restriction of the lowest and highest limits of the intensity, and reduction of either the maximum phonational range and the phonetogram area. The phonetography technique has shown efficacy to investigate the voice characteristics of elderly females.

Synthesis of (2R, 3R, 4R, 5S)-5-tert-Butyloxycarbonylamino-3,4-Dihydroxy-2-1sopropyl-3,4-O,O-Isopropylidene-6-CyctohexyI-Hexanoic Acid.

The dipeptidic dihydroxyethylene isostere (27, 3R, 4R, 5S)-5-tert-butyloxy-carbonylamino-3,4-dihydroxy-2-isopropyl-3,4-O,O-isoprop-ylidene-6-cyclohexyl-hexanoic acid, 15, is a representative building block of an important class of unnatural dipeptide mimics. This pseudo-dipeptide of Cha-Val is considered to be a transition-state analog mimic that produces potent inhibitors of the enzyme renin when incorporated into angiotensinogen substrate peptide sequence (1). The same strategy has also been proven successful in the development of potent inhibitors of other aspartyl proteases, including HIV protease (2). This synthetic method has been proven successful in the preparation of 100-g-scale quantity of this important building block, which was used in the preparation of a potent HIV protease inhibitory peptidomimetic, PNU-75875, which was proven effective in the treatment of SIV-infected monkeys (3).

A methodology report of a randomized prospective clinical trial to assess velopharyngeal function for speech following palatal surgery.

Cleft lip and palate occurs in approximately 1 in every 750 live human births, making it one of the most common congenital malformations. Surgical closure of the palatal cleft does not always result in a velopharyngeal port capable of supporting normal speech. The University of Florida (UF), in collaboration with the University of São Paulo (USP), is engaging in a 5-year prospective, randomized controlled study to compare velopharyngeal function for speech outcomes between patients undergoing palatoplasty for complete unilateral cleft lip and palate performed using the von Langenbeck procedure with intravelar velarplasty and those receiving the Furlow double-reversing Z-plasty palatoplasty. The von Langenbeck procedure was selected as the time-tested standard against which the Furlow procedure could be judged. The Furlow procedure, a relatively new operation, has been reported to yield substantially higher rates of velopharyngeal competency for speech than have most other reported series and theoretically should result in less disturbance to midfacial growth. A total of 608 patients will be entered into one of two age categories. Inclusion of two age groups will allow a comparison of results between patients having surgery before 1 year of age (9-12 months) and patients undergoing surgery at approximately 1.5 years of age (15-18 months). Speech data will be collected and will be available for definitive analysis throughout the last 3 years of the study. Collection of preliminary growth data will require more than 5 years; growth analysis is anticipated to continue until all patients have reached maturity. The Hospital for Research and Rehabilitation of Patients with Cleft Lip and Palate at the University of São Paulo (USP-HPRLLP) in Bauru, Brazil, is uniquely situated for conducting this study. The well-equipped and modern facilities are staffed by well-trained specialists representing all disciplines in cleft-palate management. In addition, an already existing social services network throughout Brazil will ensure excellent follow-up of study cases. The clinical caseload at this institution currently exceeds 22,000, and more than 1200 new cases are added annually. This project represents a unique opportunity to obtain prospective data from a large number of subjects while controlling the variables that have traditionally plagued cleft-palate studies. This study is designed to determine which of the two proposed surgical procedures is superior in constructing a velum capable of affecting velopharyngeal competency for the development of normal speech.

Novel peptides binding to the Fc-portion of immunoglobulins obtained from a combinatorial phage display peptide library.

Peptides interacting with the Fc portion of human IgG (IgG Fc) were selected from a phage display decapeptide library. The library was selected five times and interacting phage peptides were eluted either with Staphylococcal protein A or at low pH. Individual peptide phage clones were found to interact more strongly with IgG Fc than did either the original library or the wild-type phage. Increasing concentrations of protein A could competitively reduce the interaction of a peptide phage clone (FARLVSSIRY) eluted with protein A to the same level as the original library. Furthermore, when immunoglobulins from chicken, donkey, human, mouse, swine, rabbit, and sheep were included, peptide phage clones FGRLVSSIRY and TWKTSRISIF interacted strongly with human IgG Fc and porcine IgG and weakly with the immunoglobulins obtained from the other species.

Selection of a cyclic nonapeptide inhibitor to alpha-chymotrypsin using a phage display peptide library.

A cyclic nonapeptide library displayed on filamentous bacteriophages was selected 6 times against alpha-chymotrypsin (EC 3.4.21.1) at three different pH conditions (6.5, 7.0, and 7.5). Phage peptide clones from the sixth selection, at all three pH conditions, interacted more strongly with alpha-chymotrypsin than the original library and a wild-type phage did. DNA sequencing of the selected phage peptide clones showed that different cyclic nonapeptide sequences had been selected at the different pH conditions. The oxidized form of the synthetic peptide, Cys-Cys-Phe-Ser-Trp-Arg-Cys-Arg-Cys, selected at pH 7.5, could completely inhibit the enzymatic activity of alpha-chymotrypsin. The structurally related enzymes trypsin (bovine) and elastase (porcine) were only marginally inhibited by the same peptide under the same conditions. The inhibition constant for alpha-chymotrypsin was estimated to be 10(-6) M. Phage clones expressing this peptide had a lower affinity for phenylmethylsulfonylfluoride-modified alpha-chymotrypsin than for natural alpha-chymotrypsin as determined by an enzyme immunosorbent assay. This peptide phage clone was also competitively prevented from binding to alpha-chymotrypsin by the corresponding synthetic oxidized peptide. Collectively, the results suggest that the oxidized form of the selected peptide Cys-Cys-Phe- Ser-Trp-Arg-Cys-Arg-Cys interacts with the active site of alpha-chymotrypsin and acts as a specific inhibitor to the enzyme. To our knowledge, the selected sequence Cys-Cys-Phe-Ser-Trp-Arg-Cys-Arg-Cys has not been found in nature.

Some recent developments in the preparation of novel recognition systems: a recognition site for the selective catalysis of an aldol condensation using molecular imprinting and specific affinity motifs for alpha-chymotrypsin using a phage display peptide library.

Molecular imprinting and phage display library technologies are rapidly being accepted as useful techniques for the generation of ligand-selective recognition motifs. The use of molecular imprinting to produce a novel type II aldolase mimic selective for the cobalt(II)-mediated aldol condensation of benzophenone and acetaldehyde is reported here. Furthermore, peptide motifs have been identified which are acting as 'affinity ligands' selective for the recognition of the enzyme alpha-chymotrypsin using phage display techniques.

Selection of peptides with surface affinity for alpha-chymotrypsin using a phage display library.

Peptides with affinity for the surface of alpha-chymotrypsin (EC 3.4.21.1) were selected from a hexapeptide phage display library consisting of approximately 10(7) different clones. Seven selections were performed and five individual phage clones analysed. Compared to the primary library, the five peptide phage clones all interacted more strongly with alpha-chymotrypsin, and DNA sequencing of the phage clones revealed five different amino acid sequences: Gly-Ala-Val-Ile-Thr-His, Arg-Asp-Ile-Val-Val-Ala, Val-Tyr-Ser-His-Ala-Ser, Gly-Ser-Tyr-Ser-Ala-Gly and Leu-Asp-Ile-Val-Val-Ala. Two of the peptides exhibited 83% identity (i.e. a difference of just one amino acid). The chemically synthesized peptides competitively reduced the binding of the corresponding peptide phage clone to alpha-chymotrypsin. Binding of some of the selected peptide phage clones to alpha-chymotrypsin was also reduced by several of the other non-corresponding synthesized peptides, suggesting that these peptides have common recognition areas on the enzyme. Three of the synthesized peptides were poor substrates of alpha-chymotrypsin and they did not inhibit enzyme activity. Our results suggest that it is possible to select peptides from peptide phage display libraries with affinity for different surface structures on the enzyme, not involved in the biologically active site.

Short-chain dehydrogenases/reductases (SDR).

Short-chain dehydrogenases/reductases (SDR) constitute a large protein family. Presently, at least 57 characterized, highly different enzymes belong to this family and typically exhibit residue identities only at the 15-30% level, indicating early duplicatory origins and extensive divergence. In addition, another family of 22 enzymes with extended protein chains exhibits part-chain SDR relationships and represents enzymes of no less than three EC classes. Furthermore, subforms and species variants are known of both families. In the combined SDR superfamily, only one residue is strictly conserved and ascribed a crucial enzymatic function (Tyr 151 in the numbering system of human NAD(+)-linked prostaglandin dehydrogenase). Such a function for this Tyr residue in SDR enzymes in general is supported also by chemical modifications, site-directed mutagenesis, and an active site position in those tertiary structures that have been characterized. A lysine residue four residues downstream is also largely conserved. A model for catalysis is available on the basis of these two residues. Binding of the coenzyme, NAD(H) or NADP(H), is in the N-terminal part of the molecules, where a common GlyXXXGlyXGly pattern occurs. Two SDR enzymes established by X-ray crystallography show a one-domain subunit with seven to eight beta-strands. Conformational patterns are highly similar, except for variations in the C-terminal parts. Additional structures occur in the family with extended chains. Some of the SDR molecules are known under more than one name, and one of the enzymes has been shown to be susceptible to native, chemical modification, producing reduced Schiff base adducts with pyruvate and other metabolic keto derivatives. Most SDR enzymes are dimers and tetramers. In those analyzed, the area of major subunit contacts involves two long alpha-helices (alpha E, alpha F) in similar and apparently strong subunit interactions. Future possibilities include verification of the proposed reaction mechanism and tracing of additional relationships, perhaps also with other protein families. Short-chain dehydrogenases illustrate the value of comparisons and diversified research in generating unexpected discoveries.

A second class I ribonucleotide reductase in Enterobacteriaceae: characterization of the Salmonella typhimurium enzyme.

The nrdA and nrdB genes of Escherichia coli and Salmonella typhimurium encode the R1 and R2 proteins that together form an active class I ribonucleotide reductase. Both organisms contain two additional chromosomal genes, nrdE and nrdF, whose corresponding protein sequences show some homology to the products of the genes nrdA and nrdB. When present on a plasmid, nrdE and nrdF together complement mutations in nrdA or nrdB. We have now obtained in nearly homogeneous form the two proteins encoded by the S. typhimurium nrdE and nrdF genes (R1E and R2F). They correspond to the R1 and R2 proteins. Each protein is a homodimer. Together they catalyze the reduction of CDP to dCDP, using dithiothreitol or reduced glutaredoxin, but not thioredoxin, as an electron donor. CDP reduction is strongly stimulated by low concentrations of dATP, presumably acting as an allosteric effector. Protein R2F contains an antiferromagnetically coupled dinuclear iron center and a tyrosyl free radical. The E. coli and S. typhimurium chromosome thus have maintained the information for a potentially active additional class I ribonucleotide reductase, whose role in vivo is as yet unknown. The allosteric regulation of this enzyme differs from that of the normally expressed reductase.

Selection of peptides with affinity for single stranded DNA using a phage display library.

A hexapeptide phage library was used to affinity select peptides which interact with single stranded heptaoligonucleotides consisting of cytosine (oligo-C). Selections were performed in two different buffer systems, 50 mM 2[N-Morpholino]ethanesulphonic acid(MES)-buffer, pH 5.5, and 50 mM Tris(hydroxymethyl)-aminomethane, 150 mM NaCl, pH 7.5, respectively. Selection was more successful in 50 mM MES-buffer and three clones with affinity for oligo-C were further investigated. The peptides, Pro-Pro-Pro-Leu-Tyr-Phe, Arg-Phe-Cys-Asp-Thr-Ser and Arg-Ser-Arg-Leu-Ile-Trp, all interacted more strongly with oligo-C compared to the original peptide phage library and wildtype phage. The selected clones also showed different specificity in the interaction with oligo-C, -G, -A and -T.

Normative Speaking Fundamental Frequency (SFF) characteristics of Brazilian male subjects.

The present study was carried out in order to obtain normative Speaking Fundamental Frequency (SFF) data for 150 Brazilian Portuguese-speaking male subjects (mean age, 19.4; range, 17-30) in two different vocal tasks, i.e., oral reading and counting. Mean (+/- SD) SFF was 134.9 +/- 17.9 Hz for oral reading and 130.5 +/- 18.5 Hz for counting. The mean SFF values obtained in this investigation were similar to data reported in previous studies.

Normative Speaking Fundamental Frequency (SFF) characteristics of Brazilian male subjects

The present study was carried out in order to obtain normative Speaking Fundamental Frequency (SFF) data for 150 Brazilian Portuguese-speaking male subjects (mean age, 19.4; range, 17-30) in two different vocal tasks, i.e., oral reading and counting. Mean (+/- SD) SFF was 134.9 +/- 17.9 Hz for oral reading and 130.5 +/- 18.5 Hz for counting. The mean SFF values obtained in this investigation were similar to data reported in previous studies.

Three-dimensional model of NAD(+)-dependent 15-hydroxyprostaglandin dehydrogenase and relationships to the NADP(+)-dependent enzyme (carbonyl reductase).

Modelling the amino acid sequence of NAD(+)-linked 15-hydroxyprostaglandin dehydrogenase into the three-dimensional structure of 3 alpha/20 beta-hydroxysteroid dehydrogenase shows that these two enzymes, as well as the NADP(+)-linked prostaglandin dehydrogenase (identical to carbonyl reductase) have similar conformations, in spite of very limited sequence identity (23-28%). Conservation of tertiary structures is greatest over the first two thirds of the polypeptide chains, where the typical NAD+ binding fold is retained, including the five first beta-strands, with only two short deletions or insertions up to residue 147. The remaining thirds of each of the prostaglandin dehydrogenases have significantly different architecture, including insertions that may contribute to enzyme specificity, and, except for an additional helix (alpha G), are difficult to model. Active site relationships can be evaluated and subunit interactions predicted, suggesting that the alpha E + alpha F two-helix surface constitutes the major subunit interacting area, forming a dimeric unit in the oligomeric enzymes.

Escherichia coli ferredoxin NADP+ reductase: activation of E. coli anaerobic ribonucleotide reduction, cloning of the gene (fpr), and overexpression of the protein.

A specific ribonucleoside triphosphate reductase is induced in anaerobic Escherichia coli. This enzyme, as isolated, lacks activity in the test tube and can be activated anaerobically with S-adenosylmethionine, NADPH, and two previously uncharacterized E. coli fractions. The gene for one of these, previously named dA1, was cloned and sequenced. We found an open reading frame coding for a polypeptide of 248 amino acid residues, with a molecular weight of 27,645 and with an N-terminal segment identical to that determined by direct Edman degradation. In a Kohara library, the gene hybridized between positions 3590 and 3600 on the physical map of E. coli. The deduced amino acid sequence shows a high extent of sequence identity with that of various ferredoxin (flavodoxin) NADP+ reductases. We therefore conclude that dA1 is identical with E. coli ferredoxin (flavodoxin) NADP+ reductase. Biochemical evidence from a bacterial strain, now constructed and overproducing dA1 activity up to 100-fold, strongly supports this conclusion. The sequence of the gene shows an apparent overlap with the reported sequence of mvrA, previously suggested to be involved in the protection against superoxide (M. Morimyo, J. Bacteriol. 170:2136-2142, 1988). We suggest that a frameshift introduced during isolation or sequencing of mvrA caused an error in the determination of its sequence.

Carboxyethyllysine in a protein: native carbonyl reductase/NADP(+)-dependent prostaglandin dehydrogenase.

Two different forms of the monomeric NADP(+)-linked prostaglandin dehydrogenase/carbonyl reductase were purified from human placenta and shown to differ by the modification of a lysine residue. The modified and the unmodified proteins were reproducibly recovered in a ratio of approximately 1:3, and both were chemically stable. The modified form was more acidic (pI approximately 7.4 versus pI approximately 7.7) but indistinguishable from the unmodified form in specificity and activity. Amino acid analysis, sequence analysis, mass spectrometry, and chemical synthesis identified the modified residue as N6-(1-carboxyethyl)lysine with C-2 of propionic acid attached to the side-chain N of Lys-238. This compound can be formed from the lysine residue and pyruvate via a Schiff base and subsequent reduction. The enzyme and its NAD(+)-dependent counterpart are distantly related (23% residue identity) and have the same family assignment to short-chain dehydrogenases. Alignments and model-building into the tertiary structure of 3 alpha/20 beta-hydroxysteroid dehydrogenase show that carbonyl reductase has an extra loop (positions 149-189) that forms a separate extension and replaces a backbone C-terminal beta-strand. This change affects the substrate pocket, explaining the different substrate specificities but conserves residues of known functional importance. Carboxyethyllysine at position 238 corresponds to a proteolysis-sensitive position in several short-chain dehydrogenases, less well-defined in the model but close to a surface, and is compatible with the accessibility and enzyme properties observed.

A possible glycine radical in anaerobic ribonucleotide reductase from Escherichia coli: nucleotide sequence of the cloned nrdD gene.

During anaerobic growth of Escherichia coli an oxygen-sensitive ribonucleoside-triphosphate reductase, different from the aerobic ribonucleoside diphosphate-reductase (EC 1.17.4.1), produces the deoxyribonucleoside triphosphates required for DNA replication. The gene for the anaerobic enzyme has now been cloned and was found to contain a 2136-nucleotide coding region, corresponding to 712 amino acid residues, and an Fnr binding site 228 base pairs upstream of the initiator ATG. The deduced amino acid sequence shows 72% identity to a gene of coliphage T4, sunY, hitherto of unknown function, suggesting that the virus codes for its own anaerobic reductase. The location of an organic free radical formed during activation of the bacterial anaerobic reductase is proposed to be on Gly-681, since the pentapeptide RVCGY at positions 678-682 shows a striking similarity to the C-terminal sequence. RVSGY, of pyruvate formate-lyase. During activation of the anaerobically induced pyruvate formate-lyase, the glycine residue of the pentapeptide becomes an organic radical [Wagner, A. F. V., Frey, M., Neugebauer, F. A., Schäfer, W. & Knappe, J. (1992) Proc. Natl. Acad. Sci. USA 89, 996-1000]. The gene for the anaerobic reductase is located at a position around 96 min on the E. coli genomic map.

Characterization of components of the anaerobic ribonucleotide reductase system from Escherichia coli.

Anaerobic growth of Escherichia coli induces an oxygen-sensitive ribonucleoside triphosphate reductase system, different from the aerobic ribonucleoside diphosphate reductase (EC 1.17.4.1) of aerobic E. coli and higher organisms (Fontecave, M., Eliasson, R., and Reichard, P. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 2147-2151). We have now purified and characterized two proteins from the anaerobic system, provisionally named dA1 and dA3. dA3 is the actual ribonucleoside triphosphate reductase; dA1 has an auxiliary function. From gel filtration, dA1 and dA3 have apparent molecular masses of 27 and 145 kDa, respectively. In denaturing gel electrophoresis, dA3 gives two bands of closely related polypeptides with apparent molecular masses of 77 (beta 1) and 74 (beta 2) kDa. Immunological and structural evidence suggests that beta 2 is a degradation product of beta 1 and that the active enzyme is a dimer of beta 1. dA1 activity coincides on denaturing gels with a band of 29 kDa and thus appears to be a monomer. The reaction requires, in addition, an extract from E. coli heated for 30 min at 100 degrees C. Potassium is one required component, but one or several others remain unidentified and are provisionally designated fraction RT. With dA3, dA1, RT, and potassium ions, CTP reduction shows absolute requirements for S-adenosylmethionine, NADPH (with NADH as a less active substitute), dithiothreitol, and magnesium ions, and is strongly stimulated by ATP, probably acting as an allosteric effector. Micromolar concentrations of several chelators inhibit CTP reduction completely, suggesting the involvement of (a) transition metal(s).

Short-chain dehydrogenases. Proteolysis and chemical modification of prokaryotic 3 alpha/20 beta-hydroxysteroid, insect alcohol and human 15-hydroxyprostaglandin dehydrogenases.

Prokaryotic 3 alpha/20 beta-hydroxysteroid dehydrogenase exhibits one segment sensitive to proteolysis with Glu-C protease and trypsin (cleaving after Glu192 and Arg196, respectively). Cleavage is associated with dehydrogenase inactivation; the presence of NADH offers almost complete protection and substrate (cortisone) gives some protection. Distantly related insect alcohol dehydrogenase is more resistant to proteolysis, but cleavage in a corresponding segment is detectable with Asp-N protease (cleaving before Asp198), while a second site (at Glu243) is sensitive to cleavage with both Glu-C and Asp-N proteases. Combined, the results suggest the presence of limited regions especially sensitive to proteolysis and the possibility of some association between the enzyme active site and the sensitive site(s). Modification of the hydroxysteroid dehydrogenase with tetranitromethane is paralleled by enzyme inactivation. With a 10-fold excess of reagent, labeling corresponds to 1.2 nmol Tyr/nmol protein chain and is recovered largely in Tyr152, with lesser amounts in Tyr251. Tetranitromethane also rapidly inhibits the other two dehydrogenases, but they contain Cys residues, preventing direct correlation with Tyr modification. Together, the proteolysis and chemical modifications highlight three segments of short-chain dehydrogenase subunits, one mid-chain, containing Tyr152 of the steroid dehydrogenase (similar numbers in the other enzymes), strictly conserved and apparently close to the enzyme active site, the other around position 195, sensitive to proteolysis and affected by coenzyme binding, while the third is close to the C-terminus.