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PubMed2006

Mechanisms of egfr gene transcription modulation: relationship to cancer risk and therapy response.

The epidermal growth factor receptor (EGFR) plays a crucial role in growth, differentiation, and motility of normal as well as cancer cells. For predictive cancer diagnostics and therapeutic targeting of EGFR, it is important to know how the expression level of EGFR is controlled and related to receptor signaling. A novel transcriptional regulation mechanism has been described that depends on the length of a CA repeat in intron 1 [CA simple sequence repeat 1 (CA SSR I)] of the EGFR gene. Thereby, the number of CA repeats is inversely correlated to pre-mRNA synthesis. Indirect evidence for the importance of this mechanism includes the preferential occurrence of amplifications in cancer tissue harboring short CA repeats in this sequence and the discovery of distinct alleles in young breast cancer patients with a family history of the disease and in Japanese breast cancer patients. It can be postulated that the length of the CA repeat influences DNA bendability and, in consequence, the binding of repressor proteins. In summary, it seems that the CA SSR I represents an inherited variable for response to anti-EGFR therapies that could be determined before therapy. Moreover, the potential for synergistic effects with other polymorphism [e.g., EGFR R497K (HER-1 497K) and CCND1 A870G] leading to a simultaneous increase of EGFR signaling activity and expression should be investigated. From a practical perspective, assessment of the CA SSR I number of CA dinucleotide repeats as a predictor for clinical outcome is very attractive because it is a constant feature that does not change over time and can be easily measured in normal and cancer tissues (blood cells, skin, and tumor biopsies) in an assay that is technically simple, objective, and even quantitative.

Breast Neoplasms↗
PubMed2006

Genomic approach to biomarker identification and its recent applications.

This paper discusses selected activities, issues, and challenges in recent development of analytical methods and applications in biomarker identification and validation using state-of-the-art genomic approaches. Molecular profiling via genomics, proteomics, and metabonomics has opened new windows to study disease states and biological systems. It has also provided exciting opportunities for novel applications in clinical research as well as in drug discovery and development. In the past several years, we have witnessed enormous progress resulting particularly from gene expression profiling of mRNA or transcriptomics. After a brief review on technology advances in gene expression profiling using microarrays, I mainly discuss recent developments of the genomic approaches to biomarker identification and validation in two major types of applications. The first type involves examples in cancer diagnostics and prognostics based on tumor gene expression profiling, whereas the second type involves biomarker applications in drug discovery and development. The focus will be on analytical methods and algorithms that have been developed in recent years facilitating biomarker discovery and application by leveraging genome-wide expression profiles derived from microarrays. Technical issues in experimental design, data processing, error modeling, quality control, figures of merit for performance evaluation, and meta-analysis related to biomarker discovery and application are also discussed. A case study of disease outcome prognosis for breast cancer patients based on tumor expression pattern is presented before closing remarks.

Biomarkers↗
PubMed2002

DNA microarray technology: devices, systems, and applications.

In this review, recent advances in DNA microarray technology and their applications are examined. The many varieties of DNA microarray or DNA chip devices and systems are described along with their methods for fabrication and their use. This includes both high-density microarrays for high-throughput screening applications and lower-density microarrays for various diagnostic applications. The methods for microarray fabrication that are reviewed include various inkjet and microjet deposition or spotting technologies and processes, in situ or on-chip photolithographic oligonucleotide synthesis processes, and electronic DNA probe addressing processes. The DNA microarray hybridization applications reviewed include the important areas of gene expression analysis and genotyping for point mutations, single nucleotide polymorphisms (SNPs), and short tandem repeats (STRs). In addition to the many molecular biological and genomic research uses, this review covers applications of microarray devices and systems for pharmacogenomic research and drug discovery, infectious and genetic disease and cancer diagnostics, and forensic and genetic identification purposes. Additionally, microarray technology being developed and applied to new areas of proteomic and cellular analysis are reviewed.

Gene Expression↗
PubMedDate not supplied

Identification and molecular characterization of five novel kallikrein gene 13 (KLK13; KLK-L4) splice variants: differential expression in the human testis and testicular cancer.

The kallikrein gene family is comprised of genes that have either established or potential applications in prostate and breast cancer diagnostics. New members of the human kallikrein gene family have been recently identified. By using the positional candidate gene approach, we were able to clone a novel human serine protease gene that maps to chromosome 19q13.3-q13.4, the location of the kallikrein gene family. We named this gene KLK-L4 (now also known as KLK13). Here, we describe the identification of five new KLK-L4 splice variants which are not expressed in any other tissue except the human testis. We have further established that these splice variants can be detected in normal testis but not in the adjacent matched testicular tumors. In addition, differential expression of the KLK-L4 gene was found in various histological types of testicular cancer. Our results suggest that the KLK-L4 gene is expressed in normal and cancerous testicular tissue; however, its five variants are all expressed in normal tissue but not in testicular tumors. The physiological relevance of these variants and the implications of their differential expression between cancerous and normal tissues are currently unknown.

Alternative Splicing↗
PubMed2025

Single-cell copy number calling and event history reconstruction.

MOTIVATION: Copy number alterations are driving forces of tumour development and the emergence of intra-tumour heterogeneity. A comprehensive picture of these genomic aberrations is therefore essential for the development of personalised and precise cancer diagnostics and therapies. Single-cell sequencing offers the highest resolution for copy number profiling down to the level of individual cells. Recent high-throughput protocols allow for the processing of hundreds of cells through shallow whole-genome DNA sequencing. The resulting low read-depth data poses substantial statistical and computational challenges to the identification of copy number alterations. RESULTS: We developed SCICoNE, a statistical model and MCMC algorithm tailored to single-cell copy number profiling from shallow whole-genome DNA sequencing data. SCICoNE reconstructs the history of copy number events in the tumour and uses these evolutionary relationships to identify the copy number profiles of the individual cells. We show the accuracy of this approach in evaluations on simulated data and demonstrate its practicability in applications to two breast cancer samples from different sequencing protocols. AVAILABILITY AND IMPLEMENTATION: SCICoNE is available at https://github.com/cbg-ethz/SCICoNE.

Single-Cell Analysis↗
PubMed2000

Sentinel node localization by lymphoscintigraphy: a reliable technique with widespread applications.

The concept of the sentinel lymph node (SN) represents an important contribution to guide appropriate surgery of cancer. Diagnostic non-invasive or minimally invasive procedures that provide accurate preoperative staging of the lymph node status are badly needed. The technique of SN biopsy, first developed with the purpose to select melanoma patients for regional node dissection, has been extended to other malignancies. Initial studies in breast carcinoma, conducted with vital blue dye, showed that the SN concept was biologically valid, although SN was missed in up to 30%-40% of cases. If a radioactive tracer is injected close to the tumor, then the SN can be identified by lymphoscintigraphy (LS), and a gamma ray detecting probe (GDP) can be used to locate the skin projection of SN and assist biopsy. These techniques are already used successfully in melanoma and breast carcinoma where the various parameters involved, such as the size of the radioactive particles, the injection site and injection volume, have recently been optimized. In a large series of breast cancer patients, the overall predictive value of the SNs biopsy guided by LS and GDP was 96.8%; in patients with small carcinomas (< 1.2 cm diameter), the concordance between SN and axillary status was 98.6%. In patients with melanoma, LS combined with GDP showed itself to be superior to the blue dye mapping. LS associated with GDP allowed the detection of SN in 98% of cases and 72 SNs in 54 basins were localized. Using blue dye instead, SN was stained only in 80% of patients (50 SNs in 40 basins). Lymphoscintigraphic techniques have shown promising results also in tumors such as vulva and tongue. In conclusion, LS is a simple nuclear medicine technique, relatively inexpensive and well accepted by patients. SN biopsy guided by a GDP is becoming widely adopted for a variety of neoplasms, contributing significantly to the search for less aggressive treatments in patients with early stages of cancer.

Axilla↗
PubMed2004

Operable breast cancer patients with diagnostic delay--oncological and emotional characteristics.

AIMS: Delayed diagnosis in cancer patients often implies presentation with advanced disease with poorer prognosis as a consequence. The aim of the present study was to gain more insight into mechanisms which determine patient delay in the diagnosis of operable breast cancer, stages I and II. METHODS: Patient delay was related to socio-demographic, psychological and clinical-oncological variables in 96 consecutive patients investigated one day before surgery. RESULTS: Patients with a diagnostic delay for one month or more (N=29) reported increased emotional control compared to patients without delay (N=67) (Mean score on Courtauld Emotional Control scale (CEC) 54.5 vs 46.4; p=0.003) and more often grade I tumour (17 out of 29 vs 16 out of 67 patients; p=0.002). Diagnostic delay was predicted independently by tumour differentiation (hazard ratio=5.0; p<0.01 (95% CI: 1.7-14.8)) and emotional control (hazard ratio=5.1; p<0.01 (95% CI: 1.6-16.1)). Multivariate survival analysis with tumour grading and patient delay as covariates showed significant survival effect for tumour differentiation only (hazard ratio=4.4; p<0.05 (95% CI: 1.3-15.4)). CONCLUSION: There seems to be an association between aggressiveness of tumour growth, diagnostic delay and emotional control in patients with early stage breast cancer. Clinical implications of these findings are discussed.

Adaptation, Psychological↗
PubMed1999

Tissue factor assays as diagnostic tools for cancer? Correlation between urinary and monocyte tissue factor activity.

Monocyte and urinary tissue factors (mTF and uTF) are both elevated in a number of pathologic conditions, including cancer. This study validates the best available uTF and mTF assays as diagnostic tools for cancer and examines if uTF levels reflect monocyte activation. Using kinetic chromogenic assays for uTF and mTF (measured on fresh resting cells [baseline], unstimulated cells, and lipopolysaccharide [LPS]-stimulated cells), we assessed TF levels in normal individuals, surgical controls, and patients with benign and malignant diseases. Each benign disease group was stratified as inflammatory or noninflammatory. Controls and benign noninflammatory results were indistinguishable. The malignant and inflammatory groups showed raised uTF levels over controls (p < 0.001). mTF levels differ similarly. For mTF and uTF assays, there was no significant difference between the malignant and inflammatory groups. The relative operating characteristic (ROC) curve plots sensitivity against false positive rate (1-specificity) for all possible cutoff values of a diagnostic test. Assay performance is assessed as the area under the curve (AUC). The ROC curve for the uTF assay displayed both sensitivity and specificity for cancer, the AUC being 0.83. Of the three mTF levels, LPS-stimulated cells gave the optimum curve (AUC = 0.71). uTF showed a weak to moderate association with mTF levels but correlated best and was statistically significant when compared with levels in the LPS-stimulated cells. uTF represents an intrinsic, kidney-derived, physiologic concentration rather than that of preactivated or postactivated monocytes. In conclusion, both uTF and LPS-stimulated mTF levels showed sensitivity and specificity in detecting cancer and inflammatory diseases. However, the two forms of TF appear to be independently derived.

Adolescent↗
PubMed2003

Use of ProteinChip array surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) to identify thymosin beta-4, a differentially secreted protein from lymphoblastoid cell lines.

The identification of proteins differentially expressed between cancer and normal cells is vital for the development of cancer diagnostics, therapeutics and vaccines. Using a ProteinChip Biomarker System (Ciphergen Biosystems, Fremont, CA) which combines ProteinChip technology with time-of-flight mass spectrometry, we have developed a simple method to screen and identify differentially secreted proteins from tumor cell lines. Mass spectra of the range of proteins secreted from normal B-cells were generated along with those secreted from Epstein-Barr virus transformed B-cells. A mass peak at m/z = 4972.1 that was highly over-represented in the transformed B-cell line was chosen for identification and purified by reversed phase chromatography with concomitant monitoring of fractions by SELDI-TOF MS. The resulting purified protein was digested with trypsin and the peptide masses derived from the SELDI-TOF spectrum were used to search the public databases for protein identification. Fragment matching of the resulting peptides identified the protein as thymosin beta-4. Using LC-electrospray ionization MS/MS, the identity of this protein was confirmed. Thymosin beta-4 is a known marker in LCLs establishing the utility of this method to discover and identify proteins differentially expressed between cancers and their matched normal counterparts.

Amino Acid Sequence↗
PubMed1995

Randomized trial of chemoendocrine therapy started before or after surgery for treatment of primary breast cancer.

PURPOSE: To evaluate in a randomized clinical trial systemic chemoendocrine therapy used as primary (neo-adjuvant) treatment before surgery in women with primary operable breast cancer. PATIENTS AND METHODS: Patients aged less than 70 years with clinically palpable, primary operable breast cancer diagnostically confirmed by fine-needle aspiration cytology (FNAC) and suitable for treatment with surgery, radiotherapy, cytotoxic chemotherapy, and tamoxifen were considered eligible. Patients randomized to neoadjuvant treatment received four cycles of chemo-therapy for 3 months before surgery followed by another four cycles after surgery, and were compared with patients randomized to adjuvant therapy who received eight cycles of chemotherapy over 6 months after surgery. RESULTS: Of 212 patients who were randomized to receive either adjuvant (n = 107) or neoadjuvant (n = 105) chemoendocrine therapy, 200 are now assessable for response. The two groups are comparable for age, menopausal status, disease stage, and surgical requirements. The overall clinical response rate was 85%, with a complete histologic response rate of 10%. There was a significant reduction in the requirement for mastectomy in patients who received neoadjuvant treatment (13%) as compared with those who received adjuvant therapy (28%) (P < .005). Symptomatic and hematologic acute toxicity was low and similar for adjuvant and neoadjuvant therapy. The median follow-up period for patients in this trial is 28 months, during which time four patients have relapsed locally and 20, including one of the local relapses, have developed metastatic disease, 19 of whom have died. The follow-up period is too brief to evaluate relapse rate or survival duration. CONCLUSION: This trial confirms previous reports of a high rate of response to neoadjuvant therapy, but is the first to include small primary cancers and to show, in the context of a randomized trial, a reduction in the requirement for mastectomy. Until disease-free and overall survival data are available from the larger National Surgical Adjuvant Breast and Bowel Project (NSABP)-18 trial, such neoadjuvant treatment cannot be recommended outside of a clinical trial.

Adult↗
PubMed1997

The predictive value of serum thyroglobulin in the follow-up of differentiated thyroid cancer.

A strict and careful strategy has to be adopted to cure thyroid cancer. Diagnostic iodine-131 whole-body scan (WBS) and serum thyroglobulin (Tg) are important tools to detect thyroid remnants after thyroidectomy and radioiodine therapy. The aim of this retrospective study was to compare the relative sensitivity of WBS and Tg in the detection of thyroid remnants or metastases and to evaluate the predictive value of Tg in the clinical and scintigraphic course of the disease. Ninety-three patients were followed up after total thyroidectomy and the administration 4-6 weeks later of an ablative dose of 100 or 150 mCi 131I. Eighty-five percent of the patients were free of regional or distant metastases. The follow-up scheme included clinical examination of the patient followed by WBS, Tg, thyroid-stimulating hormone and free thyroxine measurements performed 4 weeks after thyroxine withdrawal and the observance of a low-iodine diet for at least 1 week. WBS (+) patients received a 100- or 150-mCi therapeutic dose of 131I. All patients were further followed up in the same way every 6 months until both WBS and Tg became negative, and thereafter at 1-, 2- and 4-year intervals. Six months after the postoperative radioiodine treatment (first visit), the sensitivity of WBS and Tg was 87% and 26% respectively. Among patients who were WBS(+) at the first visit, 95% of those who were Tg(-) and 47% of those who were Tg(+) had become disease-free at a median of 4 years after surgery (chi2=13.6; P<0.05). Patients whose tests were both positive required more radioiodine to be cured (335+/-90 vs 250+/-95 mCi; P<0.05). Our data indicate that in early diagnosed thyroid cancer, serum Tg measured 6 months after the postoperative 131I ablative dose is less sensitive than WBS for the demonstration of persistence of residual thyroid tissue but provides predictive information on the disease course. WBS(+) and Tg(-) patients are cured earlier and with less radioiodine than those who remain Tg(+).

Adenocarcinoma, Follicular↗
PubMed1979

Gastric and colorectal cancer in Greenland. Diagnostic basis and minimum incidence.

Forty-three gastric cancers, 38 colon cancers, and 26 cancers of the rectum were diagnosed among indigenous Greenlanders in the 20-year period 1955--1974. When cases based on clinical evidence only were excluded, a comparison with Danes showed significant deficits for male gastric cancers for 1960--1964 and female rectal cancers for 1970--1974. For the 20 years as a whole, gastric cancers in females were significantly lower than expected. Eleven clinical gastric cancers, 5 clinical colon cancers, and an additional 34 malignancies suspected of being primary gastrointestinal cancers had not been exhaustively investigated, mainly owing to metastatic spread and old age at the time of diagnosis. It seems reasonable to assume that the incidences of gastric cancer and of colorectal cancer in Greenland did not differ greatly from the incidences in Denmark during the study period in spite of dietary differences. A more regular use of rather simple examinations in the diagnostic routine is necessary for future epidemiological studies.

Age Factors↗
PubMed1997

An ecological study on diet/nutrition and cancer in Japan.

Correlation or ecological studies may be useful in identifying cancer risk factors which are distributed relatively homogeneously within a population, but differ greatly between populations or between different periods within a given population. In Japan, the westernization of dietary habits has progressed remarkably in the last few decades and may have resulted in changes of incidence/mortality rates of diet-related diseases, especially cancer. Based on data from the National Nutritional Survey of Japan (1955-1993) and the vital statistics of Japan (1955-1993), we conducted correlation analyses between food/nutrient intake and cancer mortality. The present study on chronological correlations suggests the relationship between westernized dietary habits and mortality by cancers of the colon, breast, ovary and prostate and also the relationship between traditional Japanese dietary habits and mortality by stomach cancer. Our results suggest the importance of diet in the etiology of diet-related cancer. Further observation and analyses are needed to confirm the relationship between food/nutrient intake and cancer mortality, while also considering the consumption of tobacco and alcohol and improvement in cancer diagnostic and therapeutic techniques.

Diet↗
PubMed1996

Comparison of Cyto-Shuttle and cytocentrifuge as processing methods for nongynecologic cytology specimens.

The Cyto-Shuttle (Cancer Diagnostics, Inc., Fairfax, VA) monolayer preparation method was compared to our routine cytocentrifuge method in 129 fluid cytology cases. A single sample from each case was split and prepared by each method. The Cyto-Shuttle preparation was superior to the cytocentrifuge preparation in 51% of cases, equal to it in 38%, and inferior to it in 11%: bronchial wash/lavage (45 cases), 38%, 49%, 13%; body cavity fluid (39 cases), 72%, 15%, 13%; urine (18 cases), 56%, 44%, 0%: peritoneal washing (16 cases), 44%, 44%, 12%; and miscellaneous (11 cases), 36%, 55%, 9%. Cyto-Shuttle preparations were superior due to decreased background and increased number of cells per slide; fixation and morphology were generally equivalent to cytocentrifuge preparations.

Body Fluids↗
PubMed1999

Role of telomerase in cellular proliferation and cancer.

Telomerase is a cellular reverse transcriptase that helps to provide genomic stability in highly proliferative normal, immortal, and tumor cells by maintaining the integrity of the chromosome ends, the telomeres. The activity of telomerase is associated with the majority of malignant human cancers. Telomerase or another mechanism for telomere maintenance is required for continuous tumor cell proliferation. Telomerase-positive cells that exit the cell cycle via quiescence downregulate telomerase through a transcriptional repression pathway. In the case of cell cycle exit via terminal differentiation, proteolysis of telomerase may also be involved. In response to mitogenic or growth factor signaling, telomerase-competent quiescent cells reenter the cell cycle and express telomerase activity independent of DNA synthesis. Under normal growth conditions, inhibition of telomerase activity in tumor-derived cells results in continued cell division coupled with telomere shortening, eventually followed by cellular senescence or death. Thus, repression of telomerase activity may be a novel adjuvant therapy for the treatment of human cancer and detection of telomerase activity may be important for cancer diagnostics.

Animals↗
PubMed1998

Detection of APC mutations in stool DNA of patients with colorectal cancer by HD-PCR.

In most cases the analysis of DNA mutations in presence of a high excess of wild type DNA fail because of the low sensitivity of the performed method for mutation detection. Here we describe the new high-sensitive and non-radioactive HD-PCR method (for HeteroDuplex-PCR). In opposite to the conventional analytical application the heteroduplex technique is performed to preparatively separate mutated from non-mutated PCR amplified DNA fragments. We used the new method to detect mutations in the tumor suppressor gene APC in stool DNA from patients with sporadic colorectal carcinomas. Since the alteration of the APC gene occurs early in most colorectal tumors, the detection of APC mutations in fecal tumor DNA by HD-PCR may be a powerful tool in non-invasive cancer diagnostics.

Adenoma↗
PubMed2003

Biodistribution and pharmacokinetics of 125I-labeled monoclonal antibody M75 specific for carbonic anhydrase IX, an intrinsic marker of hypoxia, in nude mice xenografted with human colorectal carcinoma.

Carbonic anhydrase IX (CA IX) is frequently expressed in human carcinomas and absent from the corresponding normal tissues. Strong induction by tumor hypoxia predisposes CA IX to serve as a target for cancer diagnostics and therapy. Here we evaluated targeting properties and pharmacokinetics of CA IX-specific monoclonal antibody (MAb) M75. Binding parameters of (125)I-labeled M75, including equilibrium dissociation constant, hypoxia-related binding to various cell lines and internalization, were analyzed in vitro. Biodistribution of (125)I-M75 in nude mice bearing HT-29 human colorectal carcinoma xenografts with hypoxic pattern of CA IX expression was studied by measurements of radioactivity in dissected tissues and macroautoradiography of tissue sections. Pharmacokinetics of intravenously administered (125)I-M75 was described using a 2-compartment model. Blood clearance showed a distribution phase t(1/2)(alpha) = 3.4 hr and an elimination phase t(1/2)(beta) = 55.3 hr postinjection. Despite predominant CA IX localization in less accessible perinecrotic regions, (125)I-M75 exhibited specific accumulation in xenograft, with a mean uptake of 15.3 +/- 3.6% of injected dose per gram of tumor tissue at 48 hr postadministration. Specificity of M75 localization was confirmed by low tumor uptake of control antibody. Altogether, our data demonstrate that M75 MAb is a promising tool for selective immunotargeting of hypoxic human tumors that express CA IX.

Animals↗
PubMed2006

Ki-67 protein is associated with ribosomal RNA transcription in quiescent and proliferating cells.

The nuclear Ki-67 protein (pKi-67) has previously been shown to be exclusively expressed in proliferating cells. As a result, antibodies against this protein are widely used as prognostic tools in cancer diagnostics. Here we show, that despite the strong downregulation of pKi-67 expression in non-proliferating cells, the protein can nevertheless be detected at sites linked to ribosomal RNA (rRNA) synthesis. Although this finding does not argue against the use of pKi-67 as a proliferation marker, it has wide ranging implications for the elucidation of pKi-67 function. Employing the novel antibody TuBB-9, we could further demonstrate that also in proliferating cells, a fraction of pKi-67 is found at sites linked to the rRNA transcription machinery during interphase and mitosis. Moreover, chromatin immunoprecipitation (ChIP) assays provided evidence for a physical association of pKi-67 with chromatin of the promoter and transcribed region of the rRNA gene cluster. These data strongly suggest a role for pKi-67 in the early steps of rRNA synthesis.

Antibodies, Antinuclear↗