Development and validation of a clinical trial patient stratification assay that interrogates 27 mutation sites in MAPK pathway genes

Somatic mutations identified on genes related to the cancer-developing signaling pathways have drawn attention in the field of personalized medicine in recent years. Treatments developed to target a specific signaling pathway may not be effective when tumor activating mutations occur downstream of the target and bypass the targeted mechanism. For instance, mutations detected in KRAS/BRAF/NRAS genes can lead to EGFR-independent intracellular signaling pathway activation. Most patients with these mutations do not respond well to anti-EGFR treatment. In an effort to detect various mutations in FFPE tissue samples among multiple solid tumor types for patient stratification many mutation assays were evaluated. Since there were more than 30 specific mutations among three targeted RAS/RAF oncogenes that could activate MAPK pathway genes, a custom designed Single Nucleotide Primer Extension (SNPE) multiplexing mutation assay was developed and analytically validated as a clinical trial assay. Throughout the process of developing and validating the assay we overcame many technical challenges which include: the designing of PCR primers for FFPE tumor tissue samples versus normal blood samples, designing of probes for detecting consecutive nucleotide double mutations, the kinetics and thermodynamics aspects of probes competition among themselves and against target PCR templates, as well as validating an assay when positive control tumor tissue or cell lines with specific mutations are not available. We used Next Generation sequencing to resolve discordant calls between the SNPE mutation assay and Sanger sequencing. We also applied a triplicate rule to reduce potential false positives and false negatives, and proposed special considerations including pre-define a cut-off percentage for detecting very low mutant copies in the wild-type DNA background.

Patient segmentation assay for MAPK pathway mutations

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Background: Mutational status of solid tumors is increasingly important for identifying the best treatment options. Tumors harboring activating mutations in RAS and RAF result in constitutive activation of the RAS/MAPK signal transduction pathway and do not respond well to MAPK pathway inhibitors. Scientific attention is mostly focused on the major mutational hotspots in these genes (e.g., KRAS codons 12, 13 and 61, BRAF codon 600). However, there is increasing evidence that other mutations can be tumorigenic. Thus, there is a need for highly sensitive and specific assays to detect these mutations. To address this need, we developed and analytically validated an assay that detects 33 mutations that activate the MAPK pathway. Methods: We constructed a set of multiplexed single nucleotide primer extension (SNPE) assays that detect 33 activating mutations in KRAS, NRAS, or BRAF. The assays were analytically validated using a set of 60 formalin fixed paraffin embedded (FFPE) tissue samples from various tumor types, cell lines, and oligos with specific mutations. Performance was compared to dideoxy sequencing. Discordant calls were resolved with next generation sequencing (NGS). The limit of detection was determined by serial dilution of mutant DNA into wildtype DNA. Results: The developed multiplexed assay requires only 15 ng genomic DNA, relies on established technology, is cost effective, is amenable to high throughput, and can yield a patient eligibility decision in a CLIA lab in 4 days, making it a practical alternative to a NGS-based assay. Since low allele frequency mutations may be critical to patient survival, we devised a replicate strategy to increase the specificity and sensitivity of the assay. We showed that analysis of technical triplicates relative to no replicates increased the sensitivity from 97 to 100% and the specificity from 91 to 100%. Limit of detection varied from 2 -12%, depending on the mutation. Conclusions: We developed a selective and sensitive SNPE assay capable of detecting 33 hotspots in the MAPK pathway. Our approach reduced false positive and false negative calls of low allele frequency samples. The assay has clinical applicability for the selection of patients for early phase clinical studies.

Isolation, structure, and biological activity of Phaeofungin, a cyclic lipodepsipeptide from a Phaeosphaeria sp. Using the Genome-Wide Candida albicans Fitness Test

Phaeofungin (1), a new cyclic depsipeptide isolated from Phaeosphaeria sp., was discovered by application of reverse genetics technology, using the Candida albicans fitness test (CaFT). Phaeofungin is comprised of seven amino acids and a β,γ-dihydroxy-γ-methylhexadecanoic acid arranged in a 25-membered cyclic depsipeptide. Five of the amino acids were assigned with d-configurations. The structure was elucidated by 2D-NMR and HRMS-MS analysis of the natural product and its hydrolyzed linear peptide. The absolute configuration of the amino acids was determined by Marfey's method by complete and partial hydrolysis of 1. The CaFT profile of the phaeofungin-containing extract overlapped with that of phomafungin (3), another structurally different cyclic lipodepsipeptide isolated from a Phoma sp. using the same approach. Comparative biological characterization further demonstrated that these two fungal lipodepsipeptides are functionally distinct. While phomafungin was potentiated by cyclosporin A (an inhibitor of the calcineurin pathway), phaeofungin was synergized with aureobasidin A (2) (an inhibitor of the sphingolipid biosynthesis) and to some extent caspofungin (an inhibitor of glucan synthase). Furthermore, phaeofungin caused ATP release in wild-type C. albicans strains but phomafungin did not. It showed modest antifungal activity against C. albicans (MIC 16-32 μg/mL) and better activity against Aspergillus fumigatus (MIC 8-16 μg/mL) and Trichophyton mentagrophytes (MIC 4 μg/mL). The linear peptide was inactive, suggesting that the macrocyclic depsipeptide ring is essential for target engagement and antifungal activity.

Isolation, structure elucidation, and biological activity of virgineone from Lachnum Wirgineum using the genome-wide Candida albicans fitness test

A glycosylated tetramic acid, virgineone (1), was isolated from saprotrophic Lachnum virgineum. The antifungal activity of the fermentation extract of L. virgineum was characterized in the Candida albicans fitness test as distinguishable from other natural products tested. Bioassay-guided fractionation yielded 1, a tyrosine-derived tetramic acid with a C-22 oxygenated chain and a beta-mannose. It displayed broad-spectrum antifungal activity against Candida spp. and Aspergillus fumigatus with a MIC of 4 and 16 microg/mL, respectively. Virgineone was also identified in a number of Lachnum strains collected from diverse geographies and habitats.

Isolation, structure and biological activity of phomafungin, a cyclic lipodepsipeptide from a widespread tropical Phoma sp

We isolated a cyclic lipodepsipeptide, phomafungin, from a Phoma sp. The distinct antifungal activity of phomafungin in the crude extract was initially discovered by mechanistic profiling in the Candida albicans fitness test. The purified compound contains a 28 member ring consisting of eight amino acids and a beta-hydroxy-gamma-methyl-hexadecanoic acid, and displays a broad spectrum of antifungal activity against Candida spp., Aspergillus fumigatus and Trichophyton mentagrophytes with MIC of 2-8 microg/ml, and toxicity to mice at 25 mg/kg. The linear peptide derived from opening of the lactone ring was devoid of antifungal activity as well as toxicity. Phomafungin has been identified in a number of Phoma spp. collected from Africa and the Indian and Pacific Ocean islands.

Broad spectrum antiprotozoal agents that inhibit histone deacetylase: structure-activity relationships of apicidin. Part 1

Apicidin, a natural product recently isolated at Merck, inhibits both mammalian and protozoan histone deacetylases (HDACs). The conversion of apicidin, a nanomolar inhibitor of HDACs, into a series of side-chain analogues that display picomolar enzyme affinity is described within this structure-activity study.

Broad spectrum antiprotozoal agents that inhibit histone deacetylase: structure-activity relationships of apicidin. Part 2

Recently isolated at Merck, apicidin inhibits both mammalian and protozoan histone deacetylases (HDACs). The conversion of apicidin, a nonselective nanomolar inhibitor of HDACs, into a series of picomolar indole-modified and parasite-selective tryptophan-replacement analogues is described within this structure-activity study.

Synthesis of apicidin-derived quinolone derivatives: parasite-selective histone deacetylase inhibitors and antiproliferative agents

Apicidin's indole was efficiently converted into a series of N-substituted quinolone derivatives by indole N-alkylation followed by a two-step, one-pot, ozonolysis/aldol condensation protocol. The new quinolones exhibited good parasite selectivity and potency both at the level of their molecular target, histone deacetylase, and in their whole cell antiproliferative activity in vitro.

Development of a scintillation proximity assay for histone deacetylase using a biotinylated peptide derived from histone-H4

Measurement of histone deacetylase activity is usually accomplished by incubation of the enzyme(s) with acetate-radiolabeled histones or synthetic peptides based on histone sequences, followed by extraction and quantification of released radiolabeled acetic acid. Consequently, this assay is both time consuming and extremely limiting when large numbers of samples are involved. We have now developed a simple, two-step histone deacetylase assay that is based on the scintillation proximity assay (SPA) principle. A biotinylated [3H]acetyl histone H4 peptide substrate was synthesized and shown to generate a radioactive signal upon binding to streptavidin-coated SPA beads. Incubation of biotinylated [3H]acetyl peptide with HeLa nuclear extract (source of histone deacetylase) resulted in a time- and protein-dependent decrease in the SPA signal, providing a measure of enzyme activity. The histone deacetylase-mediated decrease in SPA counts was accompanied by a proportional appearance in free 3H-labeled acetate in the assay mixture. Histone deacetylase activity measured by SPA was concordant with that determined via the traditional ethyl acetate extraction procedure. Furthermore, a broad range of histone deacetylase inhibitors was demonstrated to have comparable effects on the catalytic activity of the HeLa nuclei enzyme using both assays. The histone deacetylase SPA system described here should be readily applicable for automated high-throughput screening and therefore facilitate the discovery of new inhibitors of histone deacetylases.

Molecular cloning of an avian anti-Müllerian hormone homologue

Anti-Müllerian hormone (AMH) is responsible for regression of the Müllerian ducts in males during embryonic development. This peptide hormone of the transforming growth factor-beta family is also believed to play a broader role in sex determination, affecting differentiation and morphogenesis of the testes. Accordingly, in mammals, AMH is produced at much higher levels in male fetuses than in female fetuses. In contrast, in birds, both male and female embryonic gonads produce AMH at high levels, although in males it is still responsible for regression of the Müllerian ducts. Its persistent expression by the embryonic ovaries and its role in female sex determination in birds is not understood. We have cloned an avian homologue to AMH. Avian AMH cDNA encodes a 644 amino acid protein that is 42% identical to human AMH overall with increased identity at the carboxyl terminus. Similarities to human AMH include motifs of sequence identity, a conserved putative plasmin cleavage site and cysteine alignments, and similar genomic intron/exon structure. Antibodies to recombinant avian AMH cross-react with recombinant human AMH and were used to show that avian AMH is glycosylated as has been shown for the human form. The avian AMH gene is transcribed in both male and female gonads but not in liver, heart, kidney or muscle.

In vivo modulation of thymus-leukemia antigens on mouse leukemia cells and thymocytes: retention of modulating antibody on the cell surface

Inoculation of RADA1, ASL1, and ERLD murine leukemia cells into the peritoneal cavities of (C57BL/6J x A/TL--)F1 mice hyperimmunized against thymus-leukemia (TL) cell-surface antigens rendered most cells insensitive to lysis in vitro by guinea pig complement even in the presence of TL antiserum. Thymocytes of A/J mice were similarly modulated by passive injection of TL antiserum. In all cases, retention of some modulating antibody on the surfaces of most cells modulated in vivo for 1--27 days was indicated by: 1) acquisition of sensitivity of modulated cells to lysis by absorbed rabbit complement; 2) positive immunofluorescence reactions for mouse IgG on the surfaces of modulated cells; and 3) release of cytolytically active TL antibody from cells into the circulation of unimmunized mice following transfer of modulated cells. Reversal of modulation of RADA1 cells was complete in some experiments within 24 hours after transfer to unimmunized mice, by which time all indications of cell-bound TL antibody were lost. These results indicate that even long-term modulation of TL antigenicity in vivo does not result in a complete loss of modulating antibody (presumably attached to TL antigens) from the cell surface.

Antibodies of predetermined specificity to the major charged species of human interleukin 1

The development of highly specific antisera to human interleukin 1 (IL-1) has been an elusive goal hampered mainly by the availability of only limited amounts of pure immunogen. To surmount this difficulty, three peptides of the major charged species of IL-1 (pI 6.8) were synthesized and covalently coupled to keyhole limpet hemocyanin (KLH). All three peptide-KLH conjugates raised rabbit heterologous antisera that bound intact pure IL-1 in a dose-dependent and domain-specific manner. Immunoblot analysis of crude concentrated culture supernatants with these antisera showed each of them to be highly specific for mature 18-kDa IL-1. Immunoblot analysis of monocyte lysates revealed a single 33-kDa band consistent with the size of the IL-1 precursor molecule deduced from cloned cDNA. These reagents should prove to be valuable tools in the localization and measurement of IL-1 in cells and fluids and may permit the separate study of individual IL-1 species as well as discrete domains of intact IL-1 molecules.

Early event of C-type virus budding in cells infected with a Rauscher leukemia virus temperature-sensitive mutant

Surface replicas of ts25-infected cells reveal the organization of virus-specific knobs prior to and during the early stage of budding, and antibody-mediated ferritin labeling suggests a transmembrane association of viral envelope and core components.

Antigenic Modulation in Vitro

The acquisition of resistance by TL antibody-sensitized mouse RADA1 leukemia cells and A/J thymocytes to cytolysis in the presence of fresh TL antiserum and guinea pig C (TL antigenic modulation) required a heat-labile mouse serum factor or factors. Most mouse strains had high levels of serum-modulating activity, but the B6 strain was extremely low, and the AKR/J strain moderately low, in activity. The modulating capacity of mouse serum was also destroyed by treatment with zymosan, an immune complex, and cobra venom factor, and was partially restored to heated serum by freeze-thawing.

Human C component C3, and to a lesser extent C4, promoted modulation of cells presentitized with heated TL antiserum and cobra venom factor-treated normal serum. Similar sensitivity of modulating activity of human C3 and of mouse serum to temperatures below 37°C indicated that an analogous mouse C component, mouse C3, was required for modulation. Successful modulation by C2-deficient human serum and susceptibility of mouse serum activity to zymosan, immune complex, and cobra venom factor treatment indicated involvement of the alternative pathway of C activation. All modulating activity in mouse serum and in human C3 preparations could be absorbed onto and eluted from RADA1 cells and thymocytes. Immunofluorescence analysis indicated specific binding of mouse or human C3 to the cell surface only under conditions promoting modulation.

Modulating activity of human C3, unlike that of mouse serum, was not destroyed by heating, and modulation was achieved with the IgG fraction of TL antiserum and heated human C3, suggesting a contribution of factor B-like, C3-cleaving activity by the cells, resulting in deposition of C3 on the cell surface. Intercalation of C3 into aggregated TL antigen-antibody complexes may be required to achieve modulation.