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PubMed2003

New insights into the pathophysiology of multiple myeloma.

For understanding of the pathophysiology of multiple myeloma, features of the malignant clone and changes induced by the bone-marrow microenvironment are equally important. Multiple myeloma plasma cells, which originate from postfollicular B cells, are characterised by complex chromosomal aberrations. Among the earliest genetic events are translocations of the immunoglobulin heavy-chain gene locus, which leads to dysregulation of oncogenes at translocation partner regions (cyclin D1 at 11q13, FGFR3/MMSET at 4p16.3, c-MAF at 16q23, and cyclin D3 at 6p21), and deletions of 13q14, the site of a putative tumour suppressor gene, which is an adverse prognostic indicator. Additional molecular events include epigenetic changes and activation of oncogenes (mutations of N-RAS and K-RAS, and changes in c-MYC), which are usually associated with disease progression. Bone-marrow stromal cells support growth and survival of multiple myeloma cells via various cytokines. Osteoclast activity factors (in particular MIP1alpha) and imbalances between RANKL and osteoprotegerin are major factors for the development of myeloma bone disease. Further characterisation of crucial events in the development of monoclonal gammopathies by novel techniques such as global gene expression profiling will contribute to a molecular classification of multiple myeloma and foster future therapeutic approaches.

Chromosome Aberrations↗

PubMed2000

Variation in the Bemisia tabaci s. l. species complex (Hemiptera: Aleyrodidae) and its natural enemies leading to successful biological control of Bemisia biotype B in the USA.

Parasitoids of the Bemisia tabaci (Gennadius) species complex collected in Spain and Thailand were evaluated as biological control agents of B. tabaci biotype B in cole crops in Texas, USA. Parasitoids were identified by morphological and RAPD-PCR analyses. The most abundant parasitoid from Spain was Eretmocerus mundus Mercet with apparent field parasitism of 39-44%. In Thailand, Encarsia formosa Gahan, E. transvena Timberlake, E. adrianae Lopez-Avila, Eretmocerus sp. 1 and sp. 2 emerged, with apparent field parasitism of 1-65%. Identification and molecular classification of B. tabaci associated with parasitoid collections and in the release site in Texas were accomplished using morphological traits and nucleotide sequence comparison of the mitochondrial cytochrome oxidase I gene (COI) (700-720 bp). Collections of B. tabaci from Thailand grouped separately from B types from Arizona and Florida and the target B type from Texas, USA, a cluster from India, and other New World B. tabaci. The Spanish B. tabaci host of E. mundus which was laboratory and field-tested to achieve biological control of the B type was most closely related to non-B type B. tabaci populations from Spain and Sudan, the latter which formed a second group within the larger clade that also contained the B type cluster. Laboratory tests indicated that E. mundus from Spain parasitized more B. tabaci type B than did Eretmocerus spp. native to Texas and other exotic parasitoids evaluated. Eretmocerus mundus from Spain also successfully parasitized B. tabaci type B when field-released in a 0.94 million ha test area in Texas, and has significantly enhanced control of B. tabaci type B in California, USA. In contrast, parasitoids from Thailand failed to establish in the field in Texas, collectively suggesting a positive correlation between the centres of diversity of compatible parasitoid-host complexes.

Animals↗

PubMedDate not supplied

Periodic systems of molecules as elements of Shchukarev's "supermatrix", i.e. the chemical element periodic system.

Generations of Soviet scientists contributed invaluable insights into molecular classification. Unfortunately, this research is little appreciated in much of the world. Among these workers S. A. Shchukarev was of great importance. His and his followers' legacy includes a host of graphical displays showing enthalpies of formation of gaseous molecules from free atoms DeltaH(a) and standard enthalpies of formation of substances plotted on the atomic number of the central elements, on their oxidation states, their internuclear separations, and other variables for a wide range of molecules. These graphs serve as databases, from which data can be extracted, to moderate precision, visually. We discuss graphs for one very limited set, or "pleiade" (gas-phase oxides of nitrogen), and for three much broader sets, or subsystems (gas-phase fluorides of all main subgroup atoms and oxides of transition-metal atoms in gas-phase and in STP conditions). When dissolved in water, molecules lose their identities but periodicity is echoed in the acids and aquocations that are formed. We show, as an example in tabular form, that redox potentials of high-oxygen acids containing S, Se, and Te change concomitantly with DeltaH(a ) and DeltaH(f) of their hexafluorides. We present graphical evidence that three properties for cations of groups 1-3 (in the short version of the periodic chart) behave similarly and share the periodicity of the elements. One of the properties is related to the ionization potential, which is shown in a tabular example to vary concomitantly with energy of hydration. It was the ultimate goal of S. A. Shchukarev that the transformation of any one graphical database into any other, having different molecules under different conditions, would be made mathematically.

Journal Article↗

PubMed2001

Molecular profiling in prostate cancer.

Prostate cancer is the most diagnosed cancer and the second leading cause of cancer death among men in the United States. Ability to detect this cancer early and availability of better prognostic markers are critical in order to decrease morbidity and mortality of prostate cancer. With the recent development in gene expression analysis methodology, expression profiles of thousands of genes can be generated in tissue samples and cell lines. Comparison of the global gene expression patterns between normal prostate and tumors at different stages may allow us to understand better the molecular mechanism of prostate tumorigenesis and progression. Different cancer cell lines and tissues appear to have different gene expression patterns that provide a new tool to classify tumors. Molecular classification of prostate cancer holds great promise for early detection and prognosis of this disease in the future. In this review, we summarize some of the recent mRNA and protein expression profiling studies performed in prostate cancer. Further, we discuss the potential benefits and limitations of current profiling technology.

Gene Expression Profiling↗

PubMed2000

Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling.

Diffuse large B-cell lymphoma (DLBCL), the most common subtype of non-Hodgkin's lymphoma, is clinically heterogeneous: 40% of patients respond well to current therapy and have prolonged survival, whereas the remainder succumb to the disease. We proposed that this variability in natural history reflects unrecognized molecular heterogeneity in the tumours. Using DNA microarrays, we have conducted a systematic characterization of gene expression in B-cell malignancies. Here we show that there is diversity in gene expression among the tumours of DLBCL patients, apparently reflecting the variation in tumour proliferation rate, host response and differentiation state of the tumour. We identified two molecularly distinct forms of DLBCL which had gene expression patterns indicative of different stages of B-cell differentiation. One type expressed genes characteristic of germinal centre B cells ('germinal centre B-like DLBCL'); the second type expressed genes normally induced during in vitro activation of peripheral blood B cells ('activated B-like DLBCL'). Patients with germinal centre B-like DLBCL had a significantly better overall survival than those with activated B-like DLBCL. The molecular classification of tumours on the basis of gene expression can thus identify previously undetected and clinically significant subtypes of cancer.

Adult↗

PubMed1999

Strain-specific prion-protein conformation determined by metal ions.

In animals infected with a transmissible spongiform encephalopathy, or prion disease, conformational isomers (known as PrPSc proteins) of the wild-type, host-encoded cellular prion protein (PrPc) accumulate. The infectious agents, prions, are composed mainly of these conformational isomers, with distinct prion isolates or strains being associated with different PrPSc conformations and patterns of glycosylation. Here we show that two different human PrPSc types, seen in clinically distinct subtypes of classical Creutzfeldt-Jakob disease, can be interconverted in vitro by altering their metal-ion occupancy. The dependence of PrPSc conformation on the binding of copper and zinc represents a new mechanism for post-translational modification of PrP and for the generation of multiple prion strains, with widespread implications for both the molecular classification and the pathogenesis of prion diseases in humans and animals.

Binding Sites↗

PubMed2005

A unique clonal JAK2 mutation leading to constitutive signalling causes polycythaemia vera.

Myeloproliferative disorders are clonal haematopoietic stem cell malignancies characterized by independency or hypersensitivity of haematopoietic progenitors to numerous cytokines. The molecular basis of most myeloproliferative disorders is unknown. On the basis of the model of chronic myeloid leukaemia, it is expected that a constitutive tyrosine kinase activity could be at the origin of these diseases. Polycythaemia vera is an acquired myeloproliferative disorder, characterized by the presence of polycythaemia diversely associated with thrombocytosis, leukocytosis and splenomegaly. Polycythaemia vera progenitors are hypersensitive to erythropoietin and other cytokines. Here, we describe a clonal and recurrent mutation in the JH2 pseudo-kinase domain of the Janus kinase 2 (JAK2) gene in most (> 80%) polycythaemia vera patients. The mutation, a valine-to-phenylalanine substitution at amino acid position 617, leads to constitutive tyrosine phosphorylation activity that promotes cytokine hypersensitivity and induces erythrocytosis in a mouse model. As this mutation is also found in other myeloproliferative disorders, this unique mutation will permit a new molecular classification of these disorders and novel therapeutical approaches.

Animals↗

PubMed2004

Molecular profiling of breast cancer: clinical implications.

Breast cancers are routinely subcategorised on the basis of clinical stage, cellular morphology and immunohistochemical analysis of a small number of markers. The recent development of gene expression microarray and related technologies provides an opportunity to perform more detailed profiling of the disease. It is anticipated that the molecular classification arising from such studies will be more powerful than its pathological predecessor at confining treatment to those patients who are most likely to benefit. It is likely that this will result in a much less frequent use of adjuvant chemotherapy. Furthermore, of those who do receive it, a higher proportion will benefit. If adopted, this will offer considerable patient benefits in terms of reducing unnecessary toxicity and have major health economic implications.

Breast Neoplasms↗

PubMed2005

Gene expression profiling of colorectal adenomas and early invasive carcinomas by cDNA array analysis.

It is generally accepted that most colorectal carcinomas arise in pre-existing adenomas. Morphologically, colorectal adenomas can be divided into two groups, protruded type and flat type. The aim of this study was to clarify relevant alterations of gene expression associated with the early stage of colorectal carcinogenesis. Using cDNA array, we analysed the expression profiles of 550 cancer-related genes in 36 colorectal adenomas (18 flat-type and 18 protruded-type adenomas) and 14 early invasive carcinomas. Among the 550 genes, we chose 32 genes the average expression levels of which were at least three-fold up- or downregulated in tumour tissues compared with levels in matched normal tissues. A total of 13 and 19 genes were identified as up- and downregulated genes in tumour tissues, respectively. Among the upregulated genes, the average expression levels of E1AF, bone morphogenic protein (BMP)-4, insulin-like growth factor (IGF)-2, inducible nitric oxide synthase (iNOS), tissue inhibitors of metalloproteinase (TIMP)-1, Smad4, and nm23 in tumour tissues were over five times higher than those in matched normal tissues. Colorectal adenomas and early invasive carcinomas were divided into two major clusters by clustering analysis. Moreover, flat- and protruded-type adenomas were divided into two major clusters by clustering analysis. The expression profiles obtained by the cDNA array clearly indicate that colorectal adenomas and early invasive carcinomas have specific expression profiles. Likewise, the gene expression profiles of flat- and protruded-type adenomas are different. These results indicate that molecular classification of early colorectal tumours by a cDNA array is feasible.

Adenoma↗

PubMed2004

BRAF alterations are associated with complex mutational profiles in malignant melanoma.

To evaluate the mutational profiles associated with BRAF mutations in human melanoma, we have studied BRAF, RAS, PTEN, TP53, CDKN2A and CDK4 genes and their expression in melanoma lesions. Owing to the lack of sufficient material from fresh specimens, we employed short-term cell lines obtained from melanoma biopsies. In all, 41 melanoma obtained from eight primary lesions, 20 nodal, 11 cutaneous and two visceral metastases from patients with sporadic (n=31), familial (n=4) and multiple melanoma (n=2) were analysed. The results revealed novel missense mutations in the BRAF, PTEN, CDKN2A and CDK4 genes. Overall, activating mutations of BRAF and loss of functional p16 and ARF were detected in the majority of melanomas (29/41, 36/41 and 29/41, respectively), while PTEN alterations/loss, NRAS and TP53 mutations occurred less frequently (6/41, 6/41 and 10/41, respectively). In the resulting 12 mutational profiles, p16/ARF loss associated with mutated BRAFV599E was the most represented (n=15). In addition, TP53 and PTEN mutations were always accompanied with BRAF alterations, while PTEN loss was found in association with CDKN2A or TP53 mutations in the absence of BRAF activation. The p16/ARFDelta+BRAF/RAS profile was significantly associated with a longer survival, while complex mutational profiles were detected in highly aggressive disease and poor survival. These data support the existence of several molecularly defined melanoma groups which likely reflect different clinical/biological behaviour, thus suggesting that a more extensive molecular classification of melanoma would significantly impact its clinical management.

Adult↗

PubMed2005

Correlation of KIT and platelet-derived growth factor receptor alpha mutations with gene activation and expression profiles in gastrointestinal stromal tumors.

Activating mutations of KIT and platelet-derived growth factor receptor alpha (PDGFRA) are known to be alternative and mutually exclusive genetic events in the development of gastrointestinal stromal tumors (GISTs). We examined the effect of the mutations of these two genes on the gene expression profile of 22 GISTs using the oligonucleotide microarray. Mutations of KIT and PDGFRA were found in 17 cases and three cases, respectively. The remaining two cases had no detectable mutations in either gene. The mutation status of KIT and PDGFRA was directly related to the expression levels of activated KIT and PDGFRA, and was also related to the different expression levels of activated proteins that play key roles in the downstream of the receptor tyrosine kinase III family. To evaluate the impact of mutation status and the importance of the type of mutation in gene expression and clinical features, microarray-derived data from 22 GISTs were interpreted using a principal component analysis (PCA). Three relevant principal component representing mutation of KIT, PDGFRA and chromosome 14q deletion were identified from the interpretation of the oligonucleotide microarray data with PCA. After supervised analysis, there was at least a two fold difference in expression between GISTs with KIT and PDGFRA mutation in 70 genes. Our findings demonstrate that mutations of KIT and PDGFRA affect differential activation and expression of some genes, and can be used for the molecular classification of GISTs.

Adult↗

PubMed2001

Clinical severity of disease, functional disability and health-related quality of life. Three-year follow-up study of 150 Finnish patients with coagulation disorders.

A questionnaire-based follow-up study of 150 Finnish patients with coagulation disorders was conducted to evaluate the changes in clinical manifestation of the disease, pain intensity, functional disability and patient's health-related quality of life, occurring during a 3-year period. Health-related quality of life was assessed using the MOS-36 health survey. The clinical severity of the disease manifestation was estimated using the frequency of bleeding episodes into joints and soft tissue during the previous 12 months. Severity of musculoskeletal morbidity, which reflects simultaneous presence of pain and disability, was estimated using intensity of pain and level of disability. Results showed that clinical severity of the disease remained unchanged during the 3-year period for the majority of patients. Nonetheless, the annual number of bleeds in patients with severe or moderately severe haemophilia was still disconcertingly high and the number of bleeding episodes into soft tissue had increased. The clinical severity of the disease manifestation, rather than the severity of the disease based on molecular classification, was a factor that negatively influenced the intensity of pain (both acute and chronic), as well as level of disability. Severity of musculoskeletal morbidity at time 1 and changes in severity of musculoskeletal morbidity over time were found to be significant predictors of physical role, bodily pain, vitality and social functioning. In conclusion, the disease can be relatively well controlled by the availability of coagulation products, thus stabilizing the clinical severity of the disease manifestation during the 3-year period studied. The findings stress the importance of preventing haemorrhages to avoid resulting permanent joint impairment and disability.

Adolescent↗

PubMed2001

PCR screening for common weak D types shows different distributions in three Central European populations.

BACKGROUND: DNA sequencing showed RHD mutations for all weak D phenotypes investigated in a study from Southwestern Germany. Molecular classification of weak D offers a more reliable basis than serotyping and is relevant for optimal D transfusion strategies. STUDY DESIGN AND METHODS: Sequence-specific primers were designed to detect weak D types 1 to 5 and the partial D phenotype HMi in a modular set for conventional PCR analysis. Alternatively, all reactions were multiplexed into a single tube, and the products were identified after automated capillary electrophoresis by their size and fluorescence. Weak D phenotype samples from 436 donors in the Tyrol (Austria) and Northern Germany were investigated by PCR. RESULTS: More than 90 percent of the weak D types identified by PCR represented type 1, 2, or 3. The distribution among the common types varied between the Tyrol and Northern Germany (p<0.0001). Three new RHD alleles were identified. CONCLUSION: A PCR method of detecting the common weak D types was validated. This PCR system introduces a simple and rapid tool for routine DNA typing of weak D samples. The results confirmed that all weak D phenotype samples identified by current serologic criteria carry altered D proteins.

Alleles↗

PubMed2004

Urinary bladder pathology 2004: an update.

The field of urinary bladder pathology is advancing at a rapid rate, with generation of significant new knowledge on molecular pathogenesis and cell and tissue-based diagnosis. The aim of this presentation is to survey selected, recent advances in this broad field, with specific focus on histologic typing, grading, staging, molecular classification, and reporting on neoplasia of the urinary bladder.

Carcinoma↗

PubMed2006

Molecular diagnosis of chronic liver disease and hepatocellular carcinoma: the potential of gene expression profiling.

Gene expression profile analysis through DNA microarrays and other high-throughput technologies permit simultaneous investigation of all genes within a biologic sample, providing a snapshot of the transcriptional state of healthy or diseased tissue. Although most of the current applications are still geared toward research (study of disease mechanisms/signaling pathways involved, identification of novel oncogenes/tumor suppressor genes), clinical diagnostic applications of this approach are beginning to enter more routine molecular usage. There are clear examples where a group of genes, or "signature," can provide clinically useful information (e.g., cancer prognosis and response to treatment). Importantly, the identification of genes that are up-regulated during tumorigenesis is heralding a new era of targeted molecular therapies in oncology. In addition, the high capacity of the technologies available allow for the identification of new biomarkers for early diagnosis. In the future, gene expression profiling ("disease fingerprinting") is likely to complement liver biopsy in the molecular differential diagnosis of chronic liver diseases and hepatocellular carcinoma (HCC). There has already been some success in the identification of subtypes of HCC based on derived sets of signature gene clusters. Data recently reported have been able to provide the first molecular classification of HCC, although more comprehensive studies are required to confirm these results and translate them into the clinical practice. In fact, variations in gene expression in normal and diseased livers, as well technical factors, are obstacles to the routine use of microarray-based methods in the liver clinic. Continued progress is anticipated in the practical application of gene array methods to refine diagnosis and therapy of HCC.

Carcinoma, Hepatocellular↗

PubMed2004

A prototype antibody microarray platform to monitor changes in protein tyrosine phosphorylation.

Reversible protein phosphorylation is a key regulatory process in all living cells. Deregulation of modification control mechanisms, especially in the case of tyrosine, may lead to malignant transformation and disease. Phosphotyrosine (p-Tyr) accounts for only 0.05% of the total cellular phospho-amino acid content, yet plays an unusually prominent role in eukaryotic signaling, development, and growth. Tracking temporal and positional p-Tyr changes across the cellular proteome, i.e. tyrosine phosphoproteomics, is therefore tremendously valuable. Here, we describe and evaluate a prototype antibody (Ab) microarray platform to monitor changes in protein Tyr phosphorylation. Availability permitting, a virtually unlimited number of Abs, each recognizing a specific cellular protein, may be arrayed on a chip, incubated with total cell or tissue extracts or with biological fluids, and then probed with a fluorescently labeled p-Tyr-specific monoclonal Ab, PY-KD1, specifically generated for this assay as part of the current study. The optimized protocol allowed detection of changes in the Tyr phosphorylation state of selected proteins using submicrogram to low nanogram of total protein extract, amounts that may conceivably be obtained from a thousand to a hundred thousand cells, or less, depending on the cell or tissue type. The assay platform was evaluated by assessing changes in a rationally selected subset of the Tyr phosphoproteome of Bcr-Abl-expressing cells treated with a specific inhibitor, Gleevec, and of epidermal growth factor (EGF)-treated HeLa cells. The results, ratiometric rather than strictly quantitative in nature, conformed with previous identifications of several Bcr-Abl and EGF receptor targets, and associated proteins, as detected by exhaustive mass spectrometric analyses. The Ab microarray method described here offers advantages of low sample and reagent consumption, scalability, detection multiplexing, and potential compatibility with microfluidic devices and automation. The system may hold particular promise for dissecting signaling pathways, molecular classification of tumors, and profiling of novel target-cancer drugs.

Animals↗

PubMed2003

Editorial perspective--advances in B-cell non-Hodgkin's lymphoma.

Radioimmunotherapy (RIT) represents an exciting new therapeutic option for the treatment of B-cell non-Hodgkin's lymphoma (NHL), emerging at a time when significant advances have been made in NHL classification, molecular genetics and treatment. Despite recent treatment advances, including the use of fludarabine phosphate-based combination chemotherapies, able to eradicate minimal residual disease, there remains much room for improvement. The incorporation of RIT into treatment schedules is an attractive option to exploit the extreme sensitivity of lymphoma cells to irradiation. In this supplement, we examine the potential future roles for RIT in the light of past and present therapies, existing RIT clinical data and the unique attributes of radiolabeled monoclonal antibodies.

Algorithms↗

PubMed2000

Ablation of uroplakin III gene results in small urothelial plaques, urothelial leakage, and vesicoureteral reflux.

Urothelium synthesizes a group of integral membrane proteins called uroplakins, which form two-dimensional crystals (urothelial plaques) covering >90% of the apical urothelial surface. We show that the ablation of the mouse uroplakin III (UPIII) gene leads to overexpression, defective glycosylation, and abnormal targeting of uroplakin Ib, the presumed partner of UPIII. The UPIII-depleted urothelium features small plaques, becomes leaky, and has enlarged ureteral orifices resulting in the back flow of urine, hydronephrosis, and altered renal function indicators. Thus, UPIII is an integral subunit of the urothelial plaque and contributes to the permeability barrier function of the urothelium, and UPIII deficiency can lead to global anomalies in the urinary tract. The ablation of a single urothelial-specific gene can therefore cause primary vesicoureteral reflux (VUR), a hereditary disease affecting approximately 1% of pregnancies and representing a leading cause of renal failure in infants. The fact that VUR caused by UPIII deletion seems distinct from that caused by the deletion of angiotensin receptor II gene suggests the existence of VUR subtypes. Mutations in multiple gene, including some that are urothelial specific, may therefore cause different subtypes of primary reflux. Studies of VUR in animal models caused by well-defined genetic defects should lead to improved molecular classification, prenatal diagnosis, and therapy of this important hereditary problem.

Animals↗