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DICER governs characteristics of glioma stem cells and the resulting tumors in xenograft mouse models of glioblastoma. Those models that do exist have questionable clinical relevance. We explored intratumoral heterogeneity produced by AA3 by immunophenotyping xenograft tumors and cultured cells, and characterized marker expression by immunofluorescence and flow cytometry.

Single cell cloning revealed the phenotypic plasticity of AA3, consistent with the intratumoral heterogeneity observed in xenografts. In conclusion, this model is appropriate for studies of the etiology of ovarian hormone independent adenocarcinomas, for identification of therapeutic targets, predictive testing, and drug development. The zebrafish is a widely accepted model to study leukemia. This chapter highlights using transgenic- and xenograft -based models in zebrafish to study a specific leukemogenic mutation and analyze therapeutic responses in vivo.

In vivo bioluminescence imaging using orthotopic xenografts towards patient's derived- xenograft Medulloblastoma models. Medulloblastoma is a cerebellar neoplasia of the central nervous system. Among these, MBgroup are highly metastatic with the worst prognosis. The current standard therapy includes surgery, radiation and chemotherapy. Thus, specific treatments adapted to cure those different molecular subgroups are needed.

The use of orthotopic xenograft models , together with the non-invasive in vivo biolumiscence imaging BLI technology, is emerging during preclinical studies to test novel therapeutics for medulloblastoma treatment. Orthotopic MB xenografts were performed by injection of Daoy-luc cells, that had been previously infected with lentiviral particles to stably express luciferase gene, into the fourth right ventricle of the cerebellum of ten nude mice.

For the implantation, specific stereotactic coordinates were used. Tumor growth was evaluated by quantifying the bioluminescence signals using the integrated fluxes of photons within each area of interest using the Living Images Software Package 3. Finally, histological analysis using hematoxylin-eosin staining was performed to confirm the presence of tumorigenic cells into the cerebellum of the mice. We describe a method to use the in vivo bioluminescent imaging BLI showing the potential to be used to investigate the potential antitumorigenic effects of a drug for in vivo medulloblastoma treatment.

There is a need to develop patient's derived- xenograft PDX model systems to test novel drugs for medulloblastoma treatment within each molecular sub. A human lung xenograft mouse model of Nipah virus infection. While the exact route of transmission to humans is not known, we have previously shown that NiV can efficiently infect human respiratory epithelial cells.

Thus, there is an urgent need for models of henipavirus infection of the human respiratory tract to study the pathogenesis and understand the host responses.

Here, we describe a novel human lung xenograft model in mice to study the pathogenesis of NiV. Following transplantation, human fetal lung xenografts rapidly graft and develop mature structures of adult lungs including cartilage, vascular vessels, ciliated pseudostratified columnar epithelium, and primitive "air" spaces filled with mucus and lined by cuboidal to flat epithelium.

In conclusion, this study demonstrates that NiV can replicate to high titers in a novel in vivo model of the human respiratory tract, resulting in a robust inflammatory response, which is known to be associated with ALI.

This model will facilitate progress in the fundamental understanding of henipavirus pathogenesis and virus-host interactions; it will also provide biologically relevant models for other respiratory viruses. Xenograft model for therapeutic drug testing in recurrent respiratory papillomatosis.

Identifying effective treatment for papillomatosis is limited by a lack of animal models , and there is currently no preclinical model for testing potential therapeutic agents. We hypothesized that xenografting of papilloma may facilitate in vivo drug testing to identify novel treatment options. The xenograft began growing after 5 weeks and was serially passaged over multiple generations.

Each generation showed a consistent log-growth pattern, and in all xenografts , the presence of the human papillomavirus HPV genome was confirmed by polymerase chain reaction PCR. Histopathologic analysis demonstrated that the squamous architecture of the original papilloma was maintained in each generation.

We report here the first successful case of serial xenografting of a tracheal papilloma in vivo with a therapeutic response observed with drug testing. In severely immunocompromised mice, the HPV genome and squamous differentiation of the papilloma can be maintained for multiple generations.

This is a feasible approach to identify therapeutic agents in the treatment of recurrent respiratory papillomatosis. Next generation patient-derived prostate cancer xenograft models. PubMed Central. Research in this area, however, has been seriously hampered by a lack of clinically relevant, experimental in vivo models of the disease.

This technique allows successful development of transplantable, patient-derived cancer tissue xenograft lines not only from aggressive metastatic, but also from localized prostate cancer tissues. The xenografts have been found to retain key biological properties of the original malignancies, including histopathological and molecular characteristics, tumor heterogeneity, response to androgen ablation and metastatic ability.

As such, they are highly clinically relevant and provide valuable tools for studies of prostate cancer progression at cellular and molecular levels, drug screening for personalized cancer therapy and preclinical drug efficacy testing; especially when a panel of models is used to cover a broader spectrum of the disease. These xenograft models could therefore be viewed as next-generation models of prostate cancer.

Combest, Austin J. Rodent studies are a vital step in the development of novel anticancer therapeutics and are used in pharmacokinetic PK , toxicology, and efficacy studies.

Traditionally, anticancer drug development has relied on xenograft implantation of human cancer cell lines in immunocompromised mice for efficacy screening of a candidate compound.

A critical factor influencing the predictability of rodent tumor models is drug PKs, but a comprehensive comparison of plasma and tumor PK parameters among xenograft models , OSTs, GEMMs, and human patients has not been performed.

In this work, we evaluated the plasma and tumor dispositions of an antimelanoma agent, carboplatin, in patients with cutaneous melanoma compared with four different murine melanoma models one GEMM, one human cell line xenograft , and two OSTs. Using microdialysis to sample carboplatin tumor disposition, we found that OSTs and xenografts were poor predictors of drug exposure in human tumors, whereas the GEMM model exhibited PK parameters similar to those seen in human tumors. GEMMs show promise in becoming an improved prediction model for intratumoral PKs and response in patients with solid tumors.

The ideal substitute for the diseased aortic valve is yet to be found. Jude Medical, Inc. Paul, Minn. The first two xenografts require inflow and outflow suturelines; the third xenograft needs a single-sutureline implantation. At follow-up, reintervention on the xenograft was necessary in one patient endocarditis in group 1, none in group 2, and six in group 3 technical cause, group 3; valve tear, group 2.

Maturation of the developing human fetal prostate in a rodent xenograft model. Saffarini, Camelia M. The etiology of prostate cancer is unknown, although both animal and epidemiologic data suggest that early life exposures to various toxicants, may impact DNA methylation status during development, playing an important role.

Methods We have developed a xenograft model to characterize the growth and differentiation of human fetal prostate implants gestational age weeks that can provide new data on the potential role of early life stressors on prostate cancer.

DNA methylation profiles of laser capture micro-dissected tissue demonstrated tissue-specific markers clustered by their location in either the epithelium or stroma of human prostate tissue. Functional classification analysis identified CpG-related gene clusters in methylated epithelial and stromal human xenografts. Conclusion This study of human fetal prostate tissue establishes a xenograft model that demonstrates dynamic growth and maturation, allowing for future mechanistic studies of the developmental origins of later life proliferative prostate disease.

Patient-derived xenografts as preclinical neuroblastoma models. The prognosis for children with high-risk neuroblastoma is often poor and survivors can suffer from severe side effects. Predictive preclinical models and novel therapeutic strategies for high-risk disease are therefore a clinical imperative.

However, conventional cancer cell line-derived xenografts can deviate substantially from patient tumors in terms of their molecular and phenotypic features. Patient-derived xenografts PDXs recapitulate many biologically and clinically relevant features of human cancers.

Importantly, PDXs can closely parallel clinical features and outcome and serve as excellent models for biomarker and preclinical drug development. Here, we review progress in and applications of neuroblastoma PDX models. Neuroblastoma orthotopic PDXs share the molecular characteristics, neuroblastoma markers, invasive properties and tumor stroma of aggressive patient tumors and retain spontaneous metastatic capacity to distant organs including bone marrow.

The recent identification of genomic changes in relapsed neuroblastomas opens up opportunities to target treatment-resistant tumors in well-characterized neuroblastoma PDXs. We highlight and discuss the features and various sources of neuroblastoma PDXs, methodological considerations when establishing neuroblastoma PDXs, in vitro 3D models , current limitations of PDX models and their application to preclinical drug testing.

Glioblastoma is an aggressive primary brain tumor predominantly localized to the cerebral cortex. We developed a panel of patient-derived mouse orthotopic xenografts PDOX for preclinical drug studies by implanting cancer stem cells CSC cultured from fresh surgical specimens intracranially into 8-wk-old female athymic nude mice. Here we optimize the glioblastoma PDOX model by assessing the effect of implantation location on tumor growth, survival, and histologic characteristics.

To trace the distribution of intracranial injections, toluidine blue dye was injected at 4 locations with defined mediolateral, anterioposterior, and dorsoventral coordinates within the cerebral cortex. Glioblastoma CSC from 4 patients and a glioblastoma nonstem-cell line were then implanted by using the same coordinates for evaluation of tumor location, growth rate, and morphologic and histologic features.

Ventricular tumors were associated with a lower tumor growth rate, as measured by in vivo bioluminescence imaging, and decreased survival in 4 of 5 cell lines. In addition, tissue oxygenation, vasculature, and the expression of astrocytic markers were altered in ventricular tumors compared with nonventricular tumors.

Based on this information, we identified an optimal implantation location that avoided the ventricles and favored cortical tumor growth. To assess the effects of stress from oral drug administration, mice that underwent daily gavage were compared with stress-positive and -negative control groups.

Oral gavage procedures did not significantly affect the survival of the implanted mice or physiologic measurements of stress. Our findings document the importance of optimization of the implantation site for. Zebrafish xenograft models of cancer and metastasis for drug discovery.

The zebrafish is increasingly used for cancer modelling , particularly xenografting of human cancer cell lines, and drug discovery, and may provide novel scientific and therapeutic insights. However, this model system remains underexploited.

They summarise previous work investigating the metastatic cascade, such as tumour-induced angiogenesis, intravasation, extravasation, dissemination and homing, invasion at secondary sites, assessing metastatic potential and evaluation of cancer stem cells in zebrafish. However, their ability to sufficiently reproduce and predict the behaviour of human cancer and metastasis remains unproven. For this to be resolved, novel mechanisms must to be discovered in zebrafish that are subsequently validated in humans, and for therapeutic interventions that modulate cancer favourably in zebrafish to successfully translate to human clinical studies.

Halofuginone suppresses growth of human uterine leiomyoma cells in a mouse xenograft model. Does halofuginone HF inhibit the growth of human uterine leiomyoma cells in a mouse xenograft model? HF suppresses the growth of human uterine leiomyoma cells in a mouse xenograft model through inhibiting cell proliferation and inducing apoptosis.

HF can suppress the growth of human uterine leiomyoma cells in vitro. The mouse xenograft model reflects the characteristics of human leiomyomas. Mice were treated with two different doses of HF or vehicle for 4 weeks with six to eight mice per group. Mouse body weight measurements and immunohistochemical analysis of body organs were carried out to assess the safety of HF treatment. Xenografted tumors were measured and analyzed for cellular and molecular changes induced by HF.

Ovarian steroid hormone receptors were evaluated for possible modulation by HF. Treatment of mice carrying human UL xenografts with HF at 0. HF treatment did not change the expression level of ovarian steroid hormone receptors.

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A key step in mass spectrometry MS -based proteomics is the identification of peptides in sequence databases by their fragmentation spectra. Here we describe Andromeda, a novel peptide search engine using a probabilistic scoring model. On proteome data, Andromeda performs as well as Mascot, a widely used commercial search engine, as judged by sensitivity and specificity analysis based on target decoy searches. The algorithms of Andromeda are provided.

Andromeda can function independently or as an integrated search engine of the widely used MaxQuant computational proteomics platform and both are freely available at www. The combination enables analysis of large data sets in a simple analysis workflow on a desktop computer.

For searching individual spectra Andromeda is also accessible via a web server. We demonstrate the flexibility of the system by implementing the capability to identify cofragmented peptides, significantly improving the total number of identified peptides. Andromeda is a peptide search engine based on probabilistic scoring. It performs as well as Mascot, can handle data with arbitrarily high fragment mass accuracy, is able to assign and score complex patterns of post-translational modifications, and accommodates extremely large databases.

Andromeda can function independently or integrated into MaxQuant. This combination enables analysis of large datasets on a desktop computer. Identification of cofragmented peptides improves the number of identified peptides. Figure 1. Three Andromeda configurations: a integrated in MaxQuant, b standalone search engine, and c web server. Figure 2. Memory and disk structure. One small index is kept in memory whose entries point to blocks of multiple entries in the secondary index that is kept on disk.

Each entry of the disk index points to the position of the protein entry in the file containing the complete information for each protein including the amino acid sequence. The protein lists are sorted alphabetically by the protein names. Index and disk entries are sorted by the peptide mass to allow for quick retrieval of all peptide candidates within a given mass interval. Figure 3. Schematic of the peptide scoring algorithm. In particular, all ion types that are used for the scoring can be found in the table on the left.

Figure 4. For the comparison leucine and isoleucine were treated as the same amino acid. Figure 5. Mascot and Andromeda produce the same top-scoring peptide sequence with a Mascot score of 5. Figure 6. Second peptide identification. The blue peptide has been selected for fragmentation at the position of the cross.

The red rectangle indicates the isolation window. Fragments of the two peptides are indicated in blue and green, respectively. Supplemental figures and materials.

We thank other members of our groups in Martinsried and Copenhagen for fruitful discussion and help. We also thank early adopters of Andromeda in other laboratories for helpful feedback.

Proteome Res. View Author Information. Cite this: J. ACS AuthorChoice. Article Views Altmetric -. Citations PDF 3 MB. Abstract High Resolution Image. Synopsis Andromeda is a peptide search engine based on probabilistic scoring. Mass spectrometry MS -based proteomics is becoming a commonly used technology in a wide variety of biological disciplines.

Both the proteomics community and the bioinformatics community have dealt with many areas of this novel field, and there is already a large literature outlining and reviewing the general tasks involved, particular computational aspects of the field and integrated data analysis pipelines. In this context, our group has developed the MaxQuant environment, a computational proteomics workflow that addresses the above tasks with a focus on high accuracy and quantitative data.

It includes peak detection in the raw data, quantification, scoring of peptides and reporting of protein groups. This leads to greatly enhanced peptide mass accuracy that can be used as a filter in database searching. The MaxQuant environment originally used the Mascot peptide search engine 36 to match tandem mass spectra to possible peptide sequences.

Mascot takes a probability based approach to match sequences from a database to tandem mass spectra. We therefore set out to develop a new search engine that would be free of these restrictions. In combination with MaxQuant, the new search engine would then enable analysis of complex data sets on desktop machines by any proteomics researcher or biologist wishing to employ proteomics.

Database searching with fragment mass spectra typically follows one of three approaches: 44, 45 i deriving a partial or full peptide sequence with associated mass information first implemented by PeptideSearch 46 and graph theory based de novo methods 47 , ii autocorrelation between the experimental and a calculated spectrum first used in SEQUEST or iii calculating a probability that the observed number of matches between the calculated and measured fragment masses could have occurred by chance pioneered in Mascot.

We chose the probability based approach based on the binominal distribution probability and started from a score that we had originally developed for analyzing MS 3 data for which no search software was available at the time.

In this paper, we describe the architecture of the Andromeda search engine and its scoring function. We perform a rigorous comparison against the Mascot search engine on several large-scale data sets. The ability of Andromeda to accurately handle many modifications of the same peptide is demonstrated. Materials and Methods. Modifications due to labeling with Lys-8 and Arg can then be taken as fixed.

The benefits of second peptide analysis were investigated using data that was acquired on an LTQ-Orbitrap Velos. Several runs were acquired with varying isolation windows. MaxQuant, version 1. Peptide masses were recalibrated by MaxQuant prior to both Andromeda and Mascot searches.

For the Mascot search using Mascot server version 2. Oxidation of methionine and N-terminal protein acetylation were used as variable modifications for all searches.

A mass tolerance of 6 ppm was used for the peptide mass. To make Mascot and Andromeda searches comparable, we did not use the individual peptide mass tolerances in MaxQuant. A tolerance of 0. The HCD fragment ion data used in the co-fragmentation study were searched with a 20 ppm window in Andromeda. A maximum of two missed cleavages were allowed in all searches. Mascot and Andromeda scores were matched to each other based on raw file name and scan number.

The search was performed against a concatenated target-decoy database with modified reversing of protein sequences as described previously. In Andromeda, the user specifies allowed peptide and protein modifications, enzymes used for protein cleavages and the protein sequence databases to be searched in the program AndromedaConfig. Modifications are specified by their elemental composition. Neutral losses and diagnostic ions can be specified separately for each type of amino acid with the modification in question.

Searches with semispecific enzymes are supported as well, where only one peptide terminus needs to be a cleavage site according to the given protease digestion rule while the other terminus can be an arbitrary position in the protein.

An unspecific search is also supported where both of the peptide termini can be arbitrary positions in a protein. Parse rules for regular expressions as defined in the Microsoft. NET framework msdn. Table 1. Input files for peak lists and parameter values as well as output files for peptide identifications and a tentative protein list are all human-readable text files.

Expressions used for modifications, labels, enzymes and databases must have been defined previously in the AndromedaConfig. For each candidate the peptide sequence, modification state, score, mass, mass deviation and all corresponding protein IDs are given. MaxQuant with Andromeda as the integrated search engine can be downloaded from www. A standalone version of Andromeda is available at www. The source code is provided as Supporting Information 1.

Both applications require Microsoft. NET 3. The Andromeda web server can be accessed at www. Andromeda has been written in the programming language C , using the Microsoft. NET framework version 3. A version of it is fully integrated into the MaxQuant quantitative proteomics platform.