Lucy A Carver PhD and Jan E Schnitzer MD

New Strategies for Discovery of Accessible Tumor Targets How to Validate Targets and Targeting Objectively In Vivo The analytical power and throughput of current genomic and proteomic techniques is unparalleled in the history of medical research. Yet, directly and specifically targeting solid tumors in vivo remains a long-sought yet elusive goal of molecular medicine that should benefit both therapy and diagnostic imaging of cancer. The staggering molecular complexity of solid tumors and other...

References

Untangling the ErbB signalling network. Nat Rev Mol Cell Biol 2001 2(2) 127-137. 2. Fendly BM, Winget M, Hudziak RM, Lipari MT, Napier MA, Ullrich A. Characterization of murine monoclonal antibodies reactive to either the human epidermal growth factor receptor or HER2 neu gene product. Cancer Res 1990 50 1550-1558. 3. Ross J, Fletcher J, Linette G, et al. The Her-2 neu gene and protein in breast cancer 2003 biomarker and target of therapy. Oncologist 2003 8(4) 307-325....

Gene Cutler PhD and Timothy Hoey PhD

Major Public Sequence Databases and Genome Browsers Human Gene Building and Gene Databases Reference Genomes Provide Anchors for Biological Information Information-Intensive Omic Resources Other Internet Resources and Knowledge Integration Cancer is fundamentally a genetic disease caused by a combination of several mutations that make a tumor cell distinct from a normal cell. The new generation of cancer therapies is aimed at targeting this difference, for example, by inhibiting the activity of...

Xiaodong Yang MD PhD Lorin Roskos PhD C Geoffrey Davis PhD and Gisela Schwab MD

Development of XenoMouse Technology Therapeutic Potential of Panitumumab Conclusion References Recent success of antibody therapeutics in oncology has revived a keen interest in the development of monoclonal antibodies (mAbs) for the treatment of cancer. To date, eight mAbs have been approved in the United States for the treatment of hematologi-cal malignancies or solid tumors. The increased success has been largely attributed to advances in antibody technology such as chimerization and...

PSMA Discovery and Mapping

Prostate-specific membrane antigen is a type II membrane glycoprotein, Mr 100,000 Dalton with an intracellular segment (amino acids 1-18), a transmembrane domain (amino acids 19-43) and an extensive extracellular domain (amino acids 44-750) (Fig. 1A). The human PSMA gene was first cloned in Heston's laboratory from lymph node metastatic lesion of adenocarcinoma of prostate (LNCaP) cells (2) and was found to be located in chromosome 11p11-12, which encodes for PSMA transcript expression in the...

Thymidylate Synthase

Thymidylate synthase (TS) is a key enzyme in the de novo synthesis of thymidylate (dTMP), which is needed for the synthesis of DNA. TS is an important target for chemotherapy, and inhibition of TS by FdUMP is considered to be the main mechanism for the action of 5-FU (28). TS expression is a key determinant of 5-FU sensitivity. Preclinical studies in cancer cell lines have demonstrated that overexpression of TS is linked with 5-FU resistance (29). Clinical studies have shown that lower TS mRNA...

Arturo Molina MD

The introduction of the monoclonal antibody rituximab has expanded the treatment options for patients with B-cell non-Hodgkin's lymphoma (NHL). In patients with indolent B-cell lymphomas, rituximab is highly effective both as a single agent and in combination with chemotherapy regimens. Ongoing studies evaluating maintenance ritux-imab therapy and new combinations suggest clinical outcomes defined primarily by improvements in progression-free survival. In chronic leukemia, the use of rituximab...

Inducible Models of Oncogenesis

The lessons learned from the xenograft and metastatic models have been extended to include inducible promoters involved in oncogenesis. An example of an important inducible gene involved in tumor formation is the p53 gene, a tumor suppressor protein that is a potent inducer of apoptosis and cell cycle arrest through transactivation of many genes involved in these pathways. Enhancing, restoring, or activating p53 function in cells is one approach to antitumor therapies. More importantly, p53...

The Classical B71 B72 and CD28 CTLA4 Pathways

Constitutively expressed on na ve peripheral T-cell, CD28 plays an essential role for effective T-cell activation. It delivers a primary costimulatory signal upon the engagement of its ligands B7-1 (CD80) or B7-2 (CD86) expressed on APCs (37). CD28 signaling promotes antigen-specific T-cell proliferation, produces of an array of cytokines, and leads to the differentiation of effector T-cells (37-40). To the contrary, ligation of the homologous CTLA-4 receptor on activated T-cells with the same...

CD30 and CD30 Ligand

CD30 is a 120-kDa type I transmembrane protein that contains six extracellular cys-teine-rich domains (Fig. 1) (9). CD30 is shed in a soluble form (sCD30), which can be detected in sera of patients with CD30+ tumors, autoimmune disease, and viral infection Characteristics of Selected TNF and TNF Receptor Family Members Member Other Names Human Gene Phenotype Associated With Loss of Function OCIF, TR1 Apo2L DR4, Apo2 DR5, KILLER, TRICK2A, TRICKB DcR1, LIT, 9q33 Conflicting data on possible role...

Phase ii trials of bortezomib in solid tumors

Various phase II studies are currently underway in order to evaluate the efficacy and toxicity of bortezomib in an array of neoplasms either as a single agent or in combination with conventional chemotherapy (see Table 2). Many of these trials also include pharmacodynamic and biologic correlative data. Most recently, results from a multicenter phase II study of single-agent bortezomib in patients with metastatic renal cell cancer have been published. Twenty-three patients were enrolled and 21...

Methods for measuring serum psa

Serum PSA is now mostly determined by immunoassays more specifically two-site immunometric sandwich assays. In these methods, commercially available from many suppliers for manual or automated assay systems, two separate antibodies to PSA are incubated with the sample. In heterogeneous assays, one antibody is conjugated to immobilized surface, including various types of particle, and the other antibody is, directly or indirectly, conjugated to a reporter molecule. The reporter molecule can...

Rituximab

The monoclonal antibody rituximab (Rituxan ) has been extensively evaluated in clinical trials, both as a single agent and in combination with chemotherapy, for the treatment of indolent and aggressive B-cell lymphomas, chronic lymphocytic leukemia (CLL), and other lymphoproliferative disorders. In addition, rituximab is an essential component of the ibritumomab tiuxetan (Zevalin ) radioimmunotherapy regimen. Rituximab is approved in the United States for the treatment of patients with relapsed...

Earlystage drug discovery 71 Target Identification and Validation

The majority of reported applications for chemical probes impact the early stages of the drug discovery process. Probes have been used most recently to discover enzyme activities that are regulated during disease-associated events. The hope is that discovery of such regulated enzymes will lead to a better understanding of the disease processes while also identifying new small-molecule drug targets. One of the earliest and most critical steps for a new drug discovery program is picking an...

And Neil H Bander MD

Suitability of Prostate Cancer as Target for mAb-Based Therapy Prostate-Specific Membrane Antigen Development of PSMA-Specific mAbs Clinical Studies References Despite advances in the diagnosis and therapy of prostate carcinoma, it remains a serious medical problem accounting for a large number of malignancies in men each year. Although earlier detection is now possible, many patients develop advanced metastatic disease even when there is no evidence of spread at the time of initial diagnosis...

Arraybased fluorescence hybridization

HCT-116 cells in log-phase growth (d 3, approx 7 106 cells per T75 flask) were either exposed to 100 pg mL of XK469 for 24 h or left untreated. Cells were collected at the end of incubation for RNA extraction for genomic analysis. High-quality RNA is crucial for successful microarray experiments and different standard protocols are available. We used the TRIzol protocol as recommended by the manufacturer (Gibco-BRL). The yield and purity of RNA was determined by gel electrophoresis. RNA...

KGF in Mucositis

Intestine Injury And Regeneration

Epithelia have a hierarchical proliferative organization, with cell loss through differentiation and mechanical stress at the surface, replenished by continuous cell production in the basal epithelial layers. Chemotherapy and radiation directly affect cell proliferation, reducing regeneration of the epithelial lining. The high rate of cellular turnover in the alimentary tract, including the oral mucosa, makes these areas particularly susceptible to damage from cytotoxic therapies. There is...

Selection of Target Candidates

One ofthe issues facing users of high-throughput inference-based methods is deciding which of the many genes and proteins that appear to change significantly are actually causative and targetable with drugs. This applies to mRNA and protein differential analyses as well as genetic association studies. Adam et al. (19) showed a path to generate a subset of targetable proteins from a larger list. In this case, the long list was of plasma-membrane-associated proteins from breast cancer cell lines...

The chemical probe

The ABP has three functional elements the reactive group or warhead a reporter group or attachment site for a reporter group and a linker region connecting these two elements (Fig. 1A). The design and synthesis of class-specific probes that covalently attach to the active sites of enzymes is the first and foremost challenge. Probes must be designed such that they are specifically reactive toward the enzyme(s) of interest yet not reactive toward other molecules present in the complex milieu of...

John R Griffiths Mb Bs Dphil and Marion Stubbs DPhil

The Origins of the Cancer Cell Metabolic Phenotype Metabolic Profile by NMR After Gene Modification Metabolic Profile Studies on HIF-1-Modified Tumors Metabolomics to Assist Drug Discovery Programs Cancer cells exhibit surprisingly uniform metabolic abnormalities, termed the cancer metabolic phenotype. We define six classes of mechanism giving rise to this phenotype mechanisms associated with (1) oncogenesis (2) rapid reproduction (3) stress responses (4) invasiveness and metastasis (5)...

Mucositis

Mucositis is a common, debilitating, and often dose-limiting complication of cancer therapy (1-4). The condition results from the inhibitory effects of chemotherapy and or radiotherapy on rapidly dividing cells, leading to reduction in the renewal capabilities of the basal epithelium. The disease is characterized by sequential mucosal changes, including erythema resulting from inflammation, atrophy, collagen breakdown, and, ultimately, painful ulcerative lesions affecting the alimentary tract,...

William J LaRochelle PhD Richard A Shimkets PhD

2005 Humana Press Inc. 999 Riverview Drive, Suite 208 Totowa, New Jersey 07512 www.humanapress.com All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise without written permission from the Publisher. All articles, comments, opinions, conclusions, or recommendations are those of the author(s), and do not necessarily reflect the views of the...

Unique Enzymatic Functions of PSMA

Prostate-specific membrane antigen is a protein with two unique enzymatic functions, including NAALADase activity (cleaving terminal glutamate from the neuro-dipeptide, N-acetyl-aspartyl- glutamate NAAG and folate hydrolase activity, which cleaves the terminal glutamates from y -linked polyglutamates. NAAG is concentrated in neuronal synapses, whereas folyl-poly-y-glutamates are present in dietary components and PSMA protein on the surface of the brush border epithelium of the small intestine...

PSMAFilamin Interaction

Recently, it has been shown that the cytoplasmic tail of PSMA interacts with the actin-binding protein filamin a (FLNa) (56). PSMA's association with FLNa is necessary for Fig. 4. Schematic showing the PSMA-FLNa interaction within the cells and how such an interaction modulates PSMA function. Which form of PSMA undergoes internalization (monomer or dimer form) is not yet known clearly. In the presence of FLNa, PSMA undergoes internalization to the RECs located at the perinuclear region. In the...

Alternatives to digital karyotyping

Karyotype Steps For Cancer

A recent improvement in the resolution of CGH was achieved by incorporating microarrays in the CGH analysis. Instead of hybridizing the tumor DNA to metaphase spreads of normal cells, the DNA is hybridized to BAC (bacterial artificial chromosome) Fig. 5. SAGE analysis of cancer-specific alterations in gene expression and copy-number changes. Flowchart showing the possible steps and outcomes of a SAGE-based analysis of cancer cell genomes and transcriptomes. Website addresses are as follows...

Transgenic Mice

In the following years, the convergence of experimental mouse embryology and reproduction, with recombinant DNA techniques, permitted manipulation of the mouse at previously barred levels, accelerating discovery. Despite the long and rich chronology of mammalian embryology, it was not until the 1950s and 1960s that successful in vitro culture conditions were determined for the mouse gametes and embryo. Even before the maturation of DNA techniques, there were early attempts to more directly...

Mass Spectrometry

Mass spectrometers consist of three elements an ion source that converts molecules into gas-phase ions, a mass analyzer that separates individual mass-to-charge ratios (m z) of the ionized analytes, and an ion detector that registers the number of ions at each m z value (1-3). The invention ofelectrospray ionization (ESI) and matrix-assisted laser desorp-tion ionization (MALDI) techniques has revolutionized the field of biological mass spectrometry (4,5). The capability of ESI and MALDI to...

Targets of the proteasome

The list of substrate proteins degraded by the UPP reported in the literature is rather extensive and continues to expand with differing levels of impact in cell cycle regulation, apoptosis, and angiogenesis. Proteins involved in cell cycle progression and regulation are among the key substrates for UPP degradation. Included among them are the cyclins (A, B, D, E) (5,11). Cyclins are expressed in a cell-cycle-dependent manner (e.g., cyclins D and E during progression from the G1- to S-phase)...

John B Easton PhD and Peter J Houghton PhD

Cell Cycle Progression Is Regulated by mTOR Inhibition of mTOR Can Cause Apoptosis The Future of mTOR as a Target for Chemotherapy The mammalian target of rapamycin (mTOR) plays a central role in the regulation of cell growth and proliferation by controlling translation in response to nutrients, energy levels, and growth factors. A number of proteins both upstream and downstream in the mTOR signaling pathway have been found to be modified in multiple cancers. As a result, significant interest...

Bcl2

Bcl-2 (B-cell lymphoma gene-2), the first apoptosis inhibitor to be discovered as a proto-oncogene, is the most studied molecule of the Bcl-2 family of proteins in the apoptotic pathway (58,107-109). The gene was cloned from the breakpoint of the t(14 18) translocation in low-grade B-cell lymphoma, where it is juxtaposed to the immunoglobulin heavy-chain gene (58,110). Bcl-2 is constitutively expressed as a result of the chromosomal translocation and promotes cell survival by inhibiting the...

The von Hippel Lindau Gene and RCC

The von Hippel-Lindau disease is a hereditary multisystem cancer syndrome caused by germline mutations of the VHL tumor suppressor gene on the short arm of chromosome 3 (reviewed in ref. 60). The disease predisposes to the development of a variety of highly vascularized benign and malignant tumors of the central nervous system, adrenal glands, pancreas reproductive adnenal organs, and the kidney. VHL disease is the principal cause of inherited RCC. Furthermore, in almost 100 of the sporadic...

Novel therapeutics targeting the trail cell death pathway

Several novel therapeutic agents are being developed to target the TRAIL pathway. Currently, the most advanced of these agents are agonist monoclonal antibodies, either human or chimeric or humanized mouse, directed against either TRAIL-R1 or TRAIL-R2, and recombinant forms of the ligand TRAIL. All of these agents are either in early clinical development (human TRAIL receptor agonist monoclonal antibodies) or in late-stage pre-clinical development (TRAIL, mouse TRAIL receptor agonist monoclonal...

Discovery of Panitumumab

To develop a fully human anti-EGFR mAb, XenoMouse-IgG2 mice were immunized with human epidermoid cervical carcinoma A431 cells that express over one million copies of EGFR per cell on the cell surface. An IgG2 isotype was chosen to avoid potential toxicity resulting from recruitment of antibody effector functions such as antibody-dependent cell-mediated cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC) to normal tissues that express EGFR. The mice were immunized intraperitoneally...

Inhibitors of mTOR Clinical Trials

Based on the preclinical data, a phase I trial evaluating the safety of CCI-779 was implemented (126). The results indicate that with daily intravenous treatment, there are significant grade 3 toxicities, including hypocalcemia, vomiting, thrombocytopenia, and increase in the level of hepatic transaminase. One patient had an objective response (non-small-cell carcinoma), and a number of patients had minor responses or stable disease (cervical carcinoma, uterine carcinoma, renal cell carcinoma,...

Kris F Sachsenmeier PhD and Jonathan A Terrett PhD

Cellular Phenotype in Primary Screening Cellular Phenotype in Secondary Screening Example of Target Validation Using Image-Based Cellular Phenotype Assays Overview References The application of Automated Cell Inc. (ACI) image-based assays of cellular phenotype for target discovery and validation is presented. The need for functional cellular assays as complementary to target discovery strategies that infer a link with disease without demonstrating a cellular phenotype for candidates is...

Ping Wei PhD and Catherine L Farrell PhD

Preclinical Studies of KGF in Epithelial Repair and Regeneration Clinical Development of Palifermin (rHuKGF) Future Studies Acknowledgments References Mucositis is a painful adverse event caused by chemo- and or radiation therapy in cancer patients. It occurs in about 40 of patients receiving chemoradiotherapy and can have profound effects on their quality of life and treatment protocol. Mucositis patients are more susceptible to infections and frequently require longer hospital stays, which...

Gary C Starling PhD William J LaRochelle PhD and Gulshan Ara PhD

Identification and Characterization of PDGF-D PDGF-D in Neoplasia PDGF-D Kidney Development and Function The platelet-derived growth factor (PDGF) family members are molecules that are associated with malignant transformation, neovascularization, and tumor-stromal interactions. Widespread usage of genomic technologies has lead to the identification of a fourth family member, PDGF-D. In this chapter, we focus on the discovery, structure, and function of PDGF-D, a latent, protease-activated...

Clinical Trials Of Prostate Cancer Using HuJ591

Prostate Cancer represents an excellent target, especially for monoclonal antibody-based therapy for the following reasons (64) 1. The prostate is a nonessential organ and its destruction will not harm the host, and the identification of tissue-specific antigens for antibody development is easier than elusive tumor-specific antigens. 2. The sites of prostate metastasis being lymph nodes and bone are sites that receive high levels of circulating antibodies. 3. Metastases are typically of small...

Development of xenomouse technology

The first step toward the creation of the XenoMouse animals that produce human antibodies was to inactivate the endogenous mouse antibody genes. This was achieved through the use of gene-targeting technology to knock out specific segments of the mouse immunoglobulin (Ig) heavy-chain and light-chain loci the J regions of the mouse heavy-chain and of the mouse k light-chain loci were deleted. Consequently, the double-deleted mouse strains exhibited arrested B-cell development and lack of mouse...

Pros and Cons of Reconstitution Models

There are several advantages to reconstitution models. (1) In the reconstituted tissue, the oncogene expressing cells proliferate in a mixture with normal cells, which mimics tumor growth in humans. (2) The reconstitution procedure itself restricts expression of oncogenes to specific cell types. Therefore, any ubiquitous promoter can be used to drive the expression of the oncogenes, whereas tissue-specific promoters are needed in establishing transgenic models. (3) The stroma environment can be...

Psa forms in serum measurement of free or complexed psa

Prostate-specific antigen exists predominantly in circulation as complexes with various protease inhibitors such as arantichymotrypsin (ACT), a2-macroglobulin, and other acute-phase proteins (48). However, complexing with the macroglobulin enfolds the PSA entity totally, resulting in the antigenic loss of PSA in those complexes (49). Thus, the most prevalent form of complexed PSA (cPSA) found in CaP patient sera is the ACT complex (ACT-PSA) (50). Overall in all patient samples, ACT-PSA...

Inhibitors of the Epidermal Growth Factor Receptor System

The epidermal growth factor (EGF) family of type I receptor tyrosine kinases is composed of four structurally related proteins EGFR (erbB-1, HER1) erbB-2 (Her2, Neu), erbB-3 (HER3), and erbB-4 (HER4) (1). The functions of these receptors are intimately interrelated, and their activation by a broad spectrum of ligands* triggers a network of signaling pathways that are involved in cellular proliferation, apoptosis, differentiation, angiogenesis, motility, and invasion. The EGF receptor (EGFR)...

Clinical trial results with avastin 21 Efficacy

Avastin, a humanized monoclonal antibody directed against VEGF A, has emerged as the lead antiangiogenic agent to become part of the armamentarium against metastastic colorectal cancer. The results of a recently completed large, randomized, multicenter, double-blinded clinical trial for untreated metastatic colorectal cancer was presented at the May 2003 American Society of Clinical Oncology meeting (7). Over a 2-yr period, 925 patients were randomized into 3 arms bolus irinotecan...

Pdgfd Pdgfr a and p Pdgfr Transcript Expression in Human Cancer Cell Lines

The mRNA expression profile of PDGFD in cell lines derived from cancers of multiple origins using real-time quantitative RTQ-PCR has been reported (9). The primer probe set utilized was designed to be PDGFD-specific and, as such, did not detect other known PDGF family members. PDGFD was most highly expressed in lung cancer cell lines such as NCI H596, SW900, HOP62, A549, and NCI-UMC-1. Moderate levels of PDGFD were found in ovarian (RL95-2), renal (Caki-2), and in several central nervous system...

Qixin Leng PhD and A James Mixson MD

Endogenous Angiogenic Inhibitors An exciting approach in cancer molecular therapy is the ability to target the developing blood supply of the tumor. In contrast to several other molecular therapy approaches, antiangiogenic molecular therapy can readily access its target the tumor vasculature. Numerous viral and nonviral vectors that target tumor angiogenesis have demonstrated antitumor efficacy in preclinical models in vivo. Molecular therapy strategies that inhibit proangiogenic growth factors...

Gene Identification by EST Database Mining

The Cancer Genome Anatomy Project (CGAP) of the NCI along with other consortiums support sequencing of ESTs from many cancers and their corresponding normal tissues (www.cgap.nci.nih.gov). We use this information to search for new genes and the proteins they encode (7). We search the human EST database (which now contains the sequences of over 5 million ESTs) for DNA sequences that have the following properties (1) expressed in prostate cancers or breast cancers, (2) not associated with known...

The B7H4 and BTLA Pathways

B7-H4 (B7S1, B7x) is the most recent addition to the B7 family (112-114). Human B7-H4 shares 22 and 23 sequence identities with B7-1 and B7-2, respectively. As a common scene for B7 family members, mRNA of B7-H4 also show a wide tissue distribution, whereas surface B7-H4 protein is undetectable in normal tissues (113). Absent from freshly isolated human hematopoietic cells, B7-H4 surface expression can be induced after in vitro activation on T-cell, B-cell, monocyte, and DC (113). Putative...

Multidrug Resistance1 Gene

Cancers treated with multiple anticancer drugs tend to develop or display cross-resistance to many other chemotherapy agents to which they have never been exposed. Several mechanisms contribute to the development of such multidrug resistance, including increased drug efflux from the cell by membrane transporters, activation of drug detoxification enzymes such as glutathione-S-transferase, decreased drug uptake into the cell, and defective apoptotic pathways (reviewed in ref. 23). Human...

NFkB Activation Pathway

Nfkb Pathway

The transcription factor nuclear factor-kB (NF-kB) was the first latent cytoplasmic factor to be discovered and is really at the crossroads of life and death in its central role as a modulator of inflammation, angiogenesis, cell cycle regulation, differentiation, adhesion, migration, and survival (95). It is activated by the same stimuli that induce apoptosis, such as ionizing radiation, chemotherapy, and TNF-a, and, in most cases, counteracts this apoptosis through an inhibitory cell survival...

BRCA1 and BRCA2

Hereditary breast cancer accounts for 5-10 of breast cancers. The majority of familial breast cancers are associated with mutations in BRCA1 or BRCA2, and BRCA1 is mutated in 80 of familial breast and ovarian cancer. These genes are rarely mutated in sporadic breast or ovarian cancers (46). Carriers of mutations in these genes are also at increased risk for prostate and pancreatic cancers, although the risk is lower than for breast cancer (47). BRCA1 and BRCA2 act as a tumor suppressors and...

Human genome assemblies

In February 2001, the International Human Genome Sequencing Consortium (HGSC) and Celera Genomics simultaneously published descriptions of the sequencing, assembly, analysis, and gene annotation of the human genome (13,14). The human genome assembly became a very controversial topic soon afterward. Both in scientific and public discussions, the sequencing and assembly by the public (HGSC) and private (Celera) groups have been portrayed as a race, and the use by Celera of public data to complete...

Malditof and Malditoftof

Matrix-assisted laser desorption ionization is usually coupled to TOF analyzers that measure the collection of ions created by the laser pulse without scanning the mass range. More recently, new configurations of ion sources and mass analyzers have found wide application for protein analysis (22). The use of higher-repetition-rate lasers yielded MS MS rates comparable with, and potentially greater than, liquid chromatography (LC)-ESI-MS MS. To allow the fragmentation of MALDI-generated...

Jimmy C Sung Md Jd Alice Y Lee MS and Timothy J Yeatman MD

Genome, Transcriptome, and Proteome Microarray Technology Analysis of Microarray Data Molecular Classification of Cancer Personalized Medicine One Patient, One Chip References The Human Genome Project is the beginning of a new age in medicine. At the cornerstone of genomic medicine is the diagnosis and treatment of diseases using gene expression. The aim of this chapter is to provide an introduction on the microarray gene profiling technology and its application in the emerging field of...

Balanehru Subramanian PhD Alexander Nakeff PhD and Frederick Valeriote PhD

Array-Based Fluorescence Hybridization Functional Gene Clustering Profile Analysis Technological milestones in genomics have initiated a new approach in the development of novel anticancer drugs to specific genes. However, the heterogeneity of cancer involving multigene complexity calls upon a complementary approach to effectively develop novel anticancer drugs either to specific tumors or with broad range of antitumor activity. Among various techniques, fluorescence in situ hybridization...

Anas Younes MD and Andrea Cerutti MD

Biologic Functions and Signaling Pathways The tumor necrosis factor (TNF) family members are membrane-bound and soluble proteins that play an important physiological role in lymphocyte homeostasis, immunity, inflammation, and calcium metabolism. Abnormalities in the expression or function of these ligands and their receptors have been linked to several human diseases, including autoimmunity and cancer. These observations provided the background for exploring this system to design novel...

Arundhati Ghosh PhD and Warren D W Heston PhD

PSMA Expression in Prostate, Benign Prostate Hyperplasia, and Prostate Cancer Regulation of PSMA Expression and Its Implication in Prostate Cancer Clinical Trials of Prostate Cancer Using HuJ591 Role of Folate Hydrolase in Prostate Cancer References Prostate-specific membrane antigen (PSMA) is a novel marker that represents an excellent ideal cell-surface-bound protein for targeted therapy of prostate cancer and vas-culotoxic therapy of nonprostate solid cancers. Clinical trials using humanized...

The B7H1 PDL1 B7DC PDL2 and PD1 Pathway

Database searching for molecules with similar extracellular domain organization and overall homology with B7-1 and B7-2 has revealed a novel group of B7 family ligands with immune modulation activities (Table 1). For a more comprehensive review, refer to ref. 68. Human B7-H1 (B7 Homologue-1), the third member of B7 family, was identified in 1999 (30). Its extracellular domain shares 22 amino acid sequence identity with both B7-1 and B7-2. The hB7-H1 messenger RNA has a broad tissue...

Recursive partitioning

The recursive partitioning technique is the foundation for tree and forest construction. We will use a genomic application to explain the recursive partitioning process. Suppose that we have data from n units of observations. In microarray data, the unit is usually a tissue sample. Each unit contains a vector of feature measurements or covariates (e.g., expression profiles from a particular gene) and a class label (a normal or tumor tissue). Table 1 illustrates the data structure for...

The Icosl B7H2 and ICOS Pathway

The inducible costimulator (ICOS) was identified by expression cloning using mAb-recognizing activated T-cell surface antigens (95). In human, ICOS, CD28 and CTLA-4 are closely clustered within a 300-kb region on chromosome 2q33, suggesting that they were originated by gene duplications (95). Absent on resting T-cells, both human and mouse ICOS were quickly induced upon T-cell activation (95,96). The crucial role of ICOS in regulating activated T-cells was demonstrated by defective T-cell...

Cre Lox P Conditional Transgenic Systems

The Cre-lox P system is an approach utilized in transgenesis that allows conditional expression of a transgene (see reviews in refs. 36 and43-45). The Cre recombinase enzyme from bacteriophage P1 recognizes 34-bp DNA repeats that are used to flank genomic tar gets to be excised from the genome. The maximum size of the genomic DNA fragment that can be excised has not been defined. Therefore, a single target gene or several linked genes potentially can be altered in a mouse. The directionality of...

KGF in Skin Wound Healing and Hair Loss

The role of KGF in skin wound repair was first suggested by the fact that whereas KGFR is localized to the epithelium, KGF is expressed in the dermis of skin and dramatically up-regulated upon injury (12). Its putative role as a paracrine skin survival factor is substantiated by a number of studies showing its protective function in wound repair and epithelial regeneration (76). KGF significantly increased the rate of re-epithelialization in partial Fig. 2. Effect of KGF on the small intestine...

Contributors

Joan Albanell, MD Medical Oncology Department, ICMHO & IDIBAPS, Hospital Clmic i Provincial de Barcelona, Barcelona, Spain Gulshan Ara, PhD Oncology, Group Leader, Preclinical Development, CuraGen Corporation, Branford, CT Bruce J. Aronow, PhD Division of Pediatric Informatics, Children's Hospital Medical Center and, The University of Cincinnati College of Medicine, Cincinnati, OH Neil H. Bander, MD Department of Urology, Department of Medicine, Weill Medical College of Cornell University,...

Brian Z Ring PhD and Huijun Z Ring PhD

Introduction Toxicity Drug Response Tumor Aggression Target Discovery and Pharmacogenomics Expectations are high that pharmacogenomics, the use of a patient's genetic information to predict response to treatment, will be able to intelligently guide the discovery and development of novel successful pharmaceuticals. Cancer poses a unique challenge in this regard because the multistep carcinogenesis process compounds the diversity already present in the human population. Both inherited and...

Heiko Hermeking PhD

Alterations in Oncogenes and Tumor Suppressor Genes Cause Cancer Oncogenes as Anticancer Drug Targets Techniques Used for Identification of Oncogenic Amplifications From SAGE to LongSAGE Incorporating the Genomic Level Digital Karyotyping Charting Cancer Cell Genomes Validation of Digital Karyotyping Results Further Applications of Digital Karyotyping in Cancer Research Alternatives to Digital Karyotyping References Activated oncogenes are required for the initiation and maintenance of the...

And Cooduvalli S Shashikant PhD

Transgenic Mouse Models and Strategies for Conditional Analysis Using Transgenic Systems to Identify Carcinogens or Develop Therapeutics Conclusions References Cancer research has benefited from the ability to manipulate the mouse genome. Transgenic technology is being used to produce mice with refined genomic mutations that recapitulate cancer development in the human. Transgenic mice have proven valuable in vivo models to address the biological consequences of mutations found in tumors and...

Sheng Yao PhD and Lieping Chen MD PhD

Tumor Evasion of Immune System The B7-CD28 Rapidly Expanding Family of Promising Immunotherapy Targets Perspectives Acknowledgments References To breach host immune defense, cancer cells deploy elaborate tactics to reduce its immunogenicity and to induce immune tolerance. To counter these evasion mechanisms, manipulation of the T-cell cosignaling pathway has become an attractive approach. The B7 family costimulatory molecules deliver crucial signals through receptors on the T-cell surface for...

Systemic and Localized Delivery of Recombinant Adenovirus

A generalized experimental design using systemic delivery of adenovirus was carried out using groups of 8-10 C57BL6 mice. At least three treatment groups were studied in a given experiment (1) mice injected with test adenovirus vector (containing the cDNA of the gene to be tested), (2) mice injected with parental adenovirus vector (containing no cDNA insertion, Av-null), and (3) untreated mice. Mice were injected in the tail vein with approx 1 1011 adenovirus particles (5 108 to 5 109 plaque...

Large Scale Separation Methods in Proteomics

Cells are complicated entities containing a variety of different proteins. Therefore, pre-fractionation of protein mixtures before mass spectrometry analysis is often desirable. Separations can be conducted either before protease digestion to resolve intact protein mixtures into individual component or after protease digestion to reduce the complexity of peptide mixtures to the extent that can be analyzed by a mass spectrometer in maximum capacity (36-38). Both strategies could also incorporate...

Transgenic Mice Expressing Luciferase as an Inducible Reporter of Gene Expression

Ivis Mouse Mcherry

Arguably, whole-cell assays with either constitutive expression of luciferase for cell tracking or inducible expression of luciferase for monitoring gene expression are higher Fig. 1. p53-RE luciferase induction with doxorubicin in vivo. (Courtesy of Dr. Lidia Sambuccetti, Xenogen Corporation see Color Plate 7 following p. 302.) Fig. 1. p53-RE luciferase induction with doxorubicin in vivo. (Courtesy of Dr. Lidia Sambuccetti, Xenogen Corporation see Color Plate 7 following p. 302.) throughput,...

Frank A Scappaticci MD PhD

VEGF as a Target for Cancer Therapy Clinical Trial Results With Avastin What Is the Mechanism for Enhanced Activity of Chemotherapy in Combination With Avastin Combining Targeted Therapies Novel Antiangiogenic Strategies Summary References Promising new antiangiogenic strategies are emerging for the treatment of cancer. Numerous candidate drugs that target vascular endothelial growth factor (VEGF), VEGF receptors (VEGFR), integrins, matrix metalloproteinases, and other blood vessel targets are...

Variants of PSMA

Psma Binding

Prostate-specific membrane antigen is alternatively spliced to produce at least three variants (Fig. 1B), most important of which is PSM', the cDNA of which is identical to PSMA except for a 266-nucleotide region near the 5' end of PSMA cDNA (nucleotides 114380), which codes for the transmembrane region of the protein. Therefore, PSM' is located in the cytoplasm. Su and co-workers (10) used RNAse protection assays to examine the expression of PSMA and PSM' in normal vs benign prostate...

Jeffrey J Martino and Suzie Chen PhD

Genetically Engineered Mouse Models and Drug Discovery and Development Conclusion References Because of the high cost and risk of anticancer drug discovery and development, predictability is highly desirable. Results from a small-animal model system that is highly relevant to a given human tumor are of the highest quality in target identification and validation, in evaluating the efficacy and toxicity, and in targeting the delivery of a therapeutic. Here, we discuss efforts in engineering...

Inhibitors of FLT3

FLT3 (fms-related tyrosine kinases) is a member of the type III split-kinase domain family of RTKs that is expressed by normal bone marrow stem and early progenitor cells (88,89). This receptor, which regulates survival and proliferation of hematopoietic cells, has been recently implicated in acute myeloid leukemia (AML), the most common type of leukemia in adults (90-94). Internal tandem duplications (ITDs) of amino acids within the juxtamembrane domain or point mutations in the activation...

Tapan K Bera PhD Kristi A Egland PhD B K Lee PhD and Ira Pastan MD

Completion of the human genome sequence has opened up an enormous opportunity to researchers all over the world. The Human Genome Project, which includes the expressed sequence tags (EsTs) database and the genome sequence database, provides a huge source of data that can be used to study and identify molecular targets for a wide range of diseases, including cancer. Major efforts must now be devoted to develop strategies by which these databases will be mined efficiently to identify the hidden...

BAF and APRIL

As discussed earlier, BAFF binds with high affinity to three different receptors BAFF-R, TACI, and BCMA. These three receptors activate B-cells mainly through the NF-KB-Rel family of transcription factors (53,81). By recruiting TRAF adaptor proteins, TACI and BCMA activate the IkB kinase (IKK) complex, which includes two catalytic a- and P-subunits and a regulatory y-subunit (82,83). Phosphorylation of IkB, an NF-kB inhibitor that retains p50, p65, and c-Rel NF-KB-Rel proteins in an inactive...

Preclinical Development of Panitumumab

Panitumumab has been evaluated in an extensive series of in vitro assays and in vivo human tumor xenograft models. Panitumumab causes cell cycle arrest at the G0 G1 interphase in vitro and inhibits tumor colony formation (40). Upon binding to the receptor, panitumumab is rapidly internalized, resulting in a marked downregulation of cell surface EGFR in A431 cells (40,41). When the effect on EGFR signaling was evaluated, panitumumab was found to inhibit EGF-induced EGFR tyrosine phosphorylation....

Clinical Development of Panitumumab

Currently available clinical data from phase I and II studies evaluating single-agent therapy with panitumumab are described. In aggregate, available data suggest that panitu-mumab is generally well tolerated, does not require routine premedication, and is associated with a low incidence of infusion-related reactions (< 1 ). Pharmacokinetic variability is low and no HAHA development has been observed in the patients tested to date. Antitumor activity has been observed in patients with solid...

Pharmacogenomics and Cancer

Cancer poses a unique challenge to the emerging promise of pharmacogenomics. The multistep carcinogenesis process further complicates the effects of the genetic diversity already present in the human population. Amplification and deletion seem to provide a majority of the genetic differences in solid tumors (2-4), with translocations also playing significant roles in hematologic cancers. Consequently, to benefit the cancer patient, pharmacogenomics must entail not only an understanding of the...

The B7H3 Pathway

B7-H3, discovered in 2001 as a B7 homolog, remains an orphan B7 family ligand without known receptor (105). Human B7-H3 extracellular domain shares 25 identity with B7-1, 23 with B7-2, and 29 with both B7-H1 and B7-H2. Although B7-H3 mRNA was found in various normal tissues of human and mouse (105), characterization of B7-H3 protein expression remains elusive. It was weakly detected on activated dendritic cells treated by IFN-y or a combination of phorbol myristate acetate (PMA) and ionomycin...

Psma expression in prostate benign prostate hyperplasia and prostate cancer

Prostate Cancer Number Scale

Prostate-specific membrane antigen has been detected in both benign tissue and prostate cancer and is clinically designated as prostate-specific (2). In the past, various methods have been employed to distinguish BPH from among various grades of prostate cancer. By employing in situ hybridization, Kawakami et al. (51) increased expression of PSMA-specific transcripts in poorly differentiated adenocarcinoma in 15 tumors (from a range of Gleason scores). Similarly, by employing...

Regulation of PSMA Expression by PSMA Promoter Enhancer

Psma Prostate Cancer

Prostate-specific membrane antigen has been shown to be increased severalfold in the expression in prostate cancer its expression is suppressed by androgen. Currently, two regulatory elements controlling PSMA expression have been characterized. The proximal Fig. 5. The regulation of PSMA in prostate cancer cells. Negative regulation by androgen receptor and positive regulation by Ca2+ is shown. Polyglutamated folates become enzymatically cleaved to deglu-tamated folates and glutamates. The...

Mercaptopurine and Thiopurine Methyltransferase TPMT

6-Mercaptopurine (6-MP), is one of the most effective drugs for treating children with acute lymphoblastic leukemia (ALL). 6-MP is a prodrug that needs to be activated to 6-thioguanine nucleotides, which can then be incorporated into DNA to induce the antileukemic effect. The enzyme thiopurine methyltransferase (TPMT) converts 6-MP into inactive metabolites. Interindividual variations in TPMT enzyme activity have been observed clinically Patients with reduced TPMT enzyme activity convert more...

Serum psa cutoff in diagnosis of prostate cancer

Even though serum PSA levels increase in men with cancer of the prostate, PSA is not recommended as the only screening procedure for the diagnosis of cancer, because elevated PSA levels also are observed in patients with BPH. DeAntoni et al. showed that 90 of healthy men volunteers in the United States had serum PSA < 4 pg L (70 had < 2 pg L) (23). Of the 10 of that population with PSA > 4 pg L, about one-third would have CaP if the prostate is systematically biopsied (24). Of all CaP...

Apoptosis Markers bcl2 bax AND bclx

Suppression of overexpression of apoptosis genes or downregulation of proapopto-tic genes can promote radioresistant phenotypes. For instance, the protein product of the bcl-2 oncogene enhances cell survival by suppressing apoptosis (26). bax, a related homolog of the bcl-2 protein, can form heterodimers with bcl-2 and, therefore, antagonize its function and promote apoptosis (27,102). Therefore, the combination of overexpression of bcl-2 and low expression of bax are hypothetically associated...

Biochemistry of psa

First described by Wang et al. in 1979 (10), PSA is a single-chain glycoprotein neutral serine protease of240 amino acids secreted by the prostate epithelium and CaP cells (1113). A glycoprotein monomer with a molecular weight of 33,000-34,000, PSA contains 240 amino acids (10-14). Among the many PSA-like kallikreins that have been discovered so far, PSA is named human kallikrein 3 (hK3) (11). PSA is involved in the lysis of seminal coagulum and is one of the predominant proteins present in the...

Novel pathways regulated during e2 senescence

Little is known about the molecular machinery triggering the cellular senescence decision and execution, but a multitude of cellular pathways is likely involved. The above analysis revealed a number of novel candidate gene groups, two of which are depicted in Fig. 3 and discussed here. Coordinate induction of six members and regulators of the Ras-related RAB family of small GTPases, RAB2, 5B, 13, 31, RAB interacting factor and the RAB geranylgeranyltransferase a-subunit might reflect or perhaps...

Role of PDGFD in Various Nephropathies

Mesangioproliferative Diseases P PDGFR has recently been implicated in the pathogenesis of various kidney diseases. Various agents that inhibit P PDGFR signaling either by interfering with ligand binding to the receptor or inhibiting downstream signaling of the receptor have shown activity in various preclinical in vivo models. Perhaps the greatest evidence for a role of P PDGFR agonists in nephritis is seen in mesangioproliferative nephropathies, which include IgA nephritis. IgA...

Pradip Datta PhD DABCC

Serum PSA Cutoff in Diagnosis of Prostate Cancer Methods for Measuring Serum PSA PSA Forms in Serum Measurement of Free or Complexed PSA Issues in PSA Immunoassays Future of PSA References Significant improvement in prostate cancer diagnosis and monitoring of therapy has been made possible by the discovery and use of prostate-specific antigen (PSA) measurement in patient serum. Widespread use of the PSA test has resulted in significant prevention of death from this major cancer disease in...

Ca2Selective Cation Channel TRPV6

The epithelial Ca2+ cation channel TRP family members have been shown to exhibit cellular homeostatic and regulatory functions. Alterations in their expression might be associated with malignant growth. The gene of the Ca2+-selective cation channel CaT-L or TRPV6 is not expressed in benign prostate tissues, including benign prostate hyperplasia, but is upregulated in prostate cancer (68). Fixemer et al. reported very recently on the differential expression of TRPV6 mRNA in prostate tissue...

Arnab Chakravarti MD and Gary Guotang Zhai PhD

Cell Cycle and Proliferation Markers Apoptosis Markers bcl-2, bax, and bcl-x Prostate cancer is responsible for 3 of all deaths in the Western world in men over 55 yr of age. An urgent yet challenging priority in cancer biology is to detect or identify the sequential genetic and epigenetic events early enough through characterizing cancer-associated genes and their protein products. At a specific stage, biomarkers reflect the physiologic state of a cell and might be vital for the identification...

Inducible Transgenic Systems

Restriction of the transgene's expression to a specific time or a specific tissue employs inducible systems. These systems give the investigator control over when and where the putative cancer-causing gene's product is expressed. Gossen and Bujard (38) described a tetracycline-inducible approach modeled on bacterial operons. These systems have been reviewed (8,38-40). Tetracycline, and later doxcycline, was used to remove the tetrepressor from a silenced gene, allowing expression. The gene to...

Cox2 inhibitors in combination with chemotherapy

COX-2 inhibitors have been shown to potentiate cytotoxic actions of a number of chemotherapeutic agents in vitro and to improve their antitumor efficacy in vivo. Hida et al. 62 reported that nimesulide, a COX-2 inhibitor, induced apoptosis and enhanced cytotoxicity of cisplatin and etoposide in lung cancer cells. In another study 156 , a concentration-dependent synergistic effect of COX-2 inhibitors combined with anthracyclines doxorubicin, daunorubicin, and epirubicin as well as when combined...

Endocytic Function of PSMA

Psma Internalization

Prostate-specific membrane antigen, like other cell surface receptors, undergoes inter-nalization constitutively, and such spontaneous internalization is enhanced threefold in a dose-dependent manner by PSMA-specific monoclonal antibody J591 32 . It has been shown very clearly biochemically by using biotinylated cell surface PSMA followed by internalization of the protein , by immunofluorescence analysis or immunoelecton microscopy, that PSMA or the PSMA-antibody complex undergoes...