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Human antibody derivatives against the fibroblast activation protein for tumor stroma targeting of carcinomas.

The fibroblast activation protein (FAP) is selectively expressed on activated fibroblasts of the tumor stroma on more than 90% of lung, breast and colon carcinomas. The high prevalence and abundance of FAP(+) stroma make it a promising target for in vivo diagnosis and therapy of a variety of carcinomas. We describe the humanization of the murine FAP-specific MAb, F19, which has already been clinically used for in vivo diagnostic purposes. Using phage display technology and human V-repertoires, VL and VH regions of F19 were replaced by analogous human V-regions while retaining the original HCDR3 sequence in order to maintain F19 epitope specificity. The resulting human single-chain fragments of immunoglobulin variable regions (scFv 34, scFv 18) showed affinities of 6 nM on cell membrane-bound FAP. scFv 34 was expressed as a bivalent minibody (Mb 34). The antigen-binding characteristics of Mb 34 were comparable to the parental and a complementarity-determining region (CDR)-grafted version of F19. This was revealed by binding competition studies, FACS analyses and immunohistochemistry on various tumor samples including breast, colon and lung carcinomas. Importantly, compared with the CDR-grafted humanized scFv version of F19, the V-regions of the selected human scFv 34 showed sequence identity with the parental antibody (Ab) only over the short, 15-amino acid long HCDR3. Thus, a largely reduced xenoantigenic potential is expected. These human Ab derivatives are suitable to develop novel therapeutic concepts with broad applicability for a wide variety of histological carcinomas based on tumor stroma targeting.

Amino Acid Sequence↗

Effect of multiple oral doses of androgenic anabolic steroids on endurance performance and serum indices of physical stress in healthy male subjects.

Anabolic androgenic steroids (AAS) are doping agents that are mostly used for improvement of strength and muscle hypertrophy. In some sports, athletes reported that the intake of AAS is associated with a better recovery, a higher training load capacity and therefore an increase in physical and mental performances. The purpose of this study was to evaluate, the effect of multiple doses of AAS on different physiological parameters that could indirectly relate the physical state of athletes during a hard endurance training program. In a double blind settings, three groups (n = 9, 8 and 8) were orally administered placebo, testosterone undecanoate or 19-norandrostenedione, 12 times during 1 month. Serum biomarkers (creatine kinase, ASAT and urea), serum hormone profiles (testosterone, cortisol and LH) and urinary catecholamines (noradrenalin, adrenalin and dopamine) were evaluated during the treatment. Running performance was assessed before and after the intervention phase by means of a standardized treadmill test. None of the measured biochemical variables showed significant impact of AAS on physical stress level. Data from exercise testing on submaximal and maximal level did not reveal any performance differences between the three groups or their response to the treatment. In the present study, no effect of multiple oral doses of AAS on endurance performance or bioserum recovery markers was found.

Adult↗

Calcium retention estimated from indicators of skeletal status in adolescent girls and young women.

To determine clinically useful predictors of calcium retention during postpubertal growth, calcium balance, bio-chemical markers of bone turnover, and anthropometric variables were determined in 14 girls aged 11-14 y and in 11 young women aged 19-30 y. Subjects participated in a 3-wk calcium-balance study with a calcium intake of 1332 mg/d. Biochemical markers of bone turnover (serum osteocalcin, total alkaline phosphatase, bone alkaline phosphatase, tartrate-resistant acid phosphatase, and urinary cross-linked N-teleopeptides of type I collagen and hydroxyproline as the creatinine ratios) were measured in fasting samples. Total-body bone mineral density and total-body calcium content were significantly higher in adults than in adolescents (1.17 compared with 1.05 g/cm2 and 1019 compared with 791 g, respectively). At the observed retention of 326 mg/d, adolescents would require 2 y to reach the total bone calcium of the young adults. All biomarkers of bone turnover were strikingly higher in adolescents than in adults and were strongly correlated with calcium retention. A multiple-regression model using a biochemical marker of bone turnover (serum osteocalcin) and postmenarcheal age (a measure of sexual maturation) described 75% of the variability in calcium retention.

Adolescent↗

Transvaginal ultrasound measurement of endometrial thickness as a biomarker for estrogen exposure.

OBJECTIVE: In clinical settings, transvaginal ultrasound has been used to evaluate abnormal vaginal bleeding. Because the endometrium responds to estrogens, endometrial thickness may constitute a biomarker of estrogen status in postmenopausal women. This study aimed to validate the transvaginal ultrasonographic measurement of endometrial thickness as an estrogen biomarker in asymptomatic, postmenopausal women by demonstrating an association between endometrial thickness and risk factors known to be associated with estrogen exposure. METHOD: Endometrial thickness was measured in 1,271 women ages 55 to 74 years who underwent transvaginal ultrasound screening as part of the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial. A questionnaire, completed before screening, provided risk factor information, including reproductive and hormone use histories. RESULTS: Endometrial thickness measurements ranged from 1 to 32 mm (median 3.0 mm). The frequencies of thicker endometrium (> or =3.0 mm), according to body mass index (BMI) quartile, were 55.2%, 66.1%, 69.7%, and 76.7% (P < 0.0001). The frequencies of thicker endometrium were 57.8%, 58.3%, and 82.6% among never users, ex-users, and current users of hormone replacement therapy (HRT), respectively (P < 0.0001). Other factors associated with thicker endometrium included age, marital status, history of uterine fibroids, years since menopause, and history of hypertension. Statistically significant associations were not seen in analyses limited to current HRT users (n = 461). In multiple variable analysis (R2 = 0.08), current HRT use (P < 0.0001) and higher BMI (P < 0.0001) were independently associated with thicker endometrium. CONCLUSION: In postmenopausal women, factors reflecting exogenous (current HRT use) and endogenous (BMI) estrogen exposure were associated with increased endometrial thickness as measured during screening transvaginal ultrasound. Practical limitations related to screening transvaginal ultrasound include measurement variability, lack of information regarding type or dose of HRT, and problems of differentiating true endometrial thickening from unrecognized endometrial polyps or fluid accumulations. Constrained by these limitations, these results partially validate a transvaginal ultrasound measurement of endometrial thickness as a potential biomarker related to estrogen status.

Aged↗

Determinants of the variability of aflatoxin-albumin adduct levels in Ghanaians.

Hepatocellular carcinoma (HCC) is a multifactorial disease with various host and environmental factors involved in its etiology. Of these, aflatoxin exposure has been established as an important risk factor in the development of HCC; the presence of aflatoxin-albumin (AA) adducts in the blood serves as a valuable biomarker of human exposure. In this study, the relationship between a variety of different HCC host factors and the incidence of AA adduct levels was examined in a Ghanaian population at high risk for HCC. These factors included age, gender, hepatitis virus B (HVB) and hepatitis C virus (HCV) status, and genetic polymorphisms in both microsomal epoxide hydrolase (mEH) and glutathione S-transferases (GSTs). Blood samples were analyzed for AA adducts and HBV and HCV status. GSTM1 and GSTT1 deletion polymorphisms and mEH exon 3 and exon 4 single-nucleotide polymorphisms (SNPs) were determined from urine samples. In univariate analysis, age, HBV and HVC status, and GSTT1 and mEH exon 3 genotypes were not associated with AA adduct levels. However, mean adduct levels were significantly higher in both females and individuals typed heterozygous for mEH exon 4 (vs. wild types). Stratification analysis also showed that gender along with mEH exon 4 genotype and HBV status had a significant effect on adduct levels. Both females typed HBsAg+ and males with mEH exon 4 heterozygote genotypes showed significantly higher adduct levels as compared to the HBsAg- and wild types, respectively. Understanding the relationships between these host factors and the variability in aflatoxin-adduct levels may help in identifying susceptible populations in developing countries and for targeting specific public health interventions for the prevention of aflatoxicoses in populations with HCC and chronic liver diseases.

Adult↗

Assessment of estrogenic exposure in brown trout (Salmo trutta) in a Swiss midland river: integrated analysis of passive samplers, wild and caged fish, and vitellogenin mRNA and protein.

This field study examined the vitellogenin (VTG) biomarker response under conditions of low and fluctuating activities of environmental estrogenicity. The present study was performed on immature brown trout (Salmo trutta) exposed to the small river Luetzelmurg, which is located in the prealpine Swiss midland region and receives effluents from a single sewage treatment plant (STP). To understand better factors influencing the relationship between estrogenic exposure and VTG induction, we compared VTG levels in caged (stationary) and feral (free-ranging) fish, VTG levels in fish from up- and downstream of the STP, and two different methods for quantifying VTG (enzyme-linked immunosorbent assay vs real-time reverse transcription-polymerase chain reaction), and we used passive samplers (polar organic chemical integrative sampler [POCIS]) to integrate the variable, bioaccumulative estrogenic load in the river water over time. The POCIS from the downstream site contained approximately 20-fold higher levels of bioassay-derived estrogen equivalents than the POCIS from the upstream site. In feral fish, this site difference in estrogenic exposure was reflected in VTG protein levels but not in VTG mRNA. In contrast, in caged fish, the site difference was evident only for VTG mRNA but not for VTG protein. Thus, the outcome of VTG biomarker measurements varied with the analytical detection method (protein vs mRNA) and with the exposure modus (caged vs feral). Our findings suggest that for environmental situations with low and variable estrogenic contamination, a multiple-assessment approach may be necessary for the assessment of estrogenic exposure in fish.

Animals↗

Model-based approaches to biomarker discovery and evaluation: a multidisciplinary integrated review.

The most common use of any mathematical or statistical model in physiology, pathophysiology, or therapy evaluation is to organize all relevant components characterizing the system behavior into a rigorously testable framework. This approach is widely applied both to the study of complex homeostatic paradigms involving endogenous substances and to the evaluation of the kinetics and dynamics of xenobiotics such as toxicants and drugs. In either case, one seeks a quantitative framework of the system that is consistent with known physiology and pharmacology and is "compatible" (in some meaningful sense) with all available data. The models are then evaluated and subjected to identifiability and validity tests and can then be used to estimate unknown parameters of interest, to make predictions about system behavior, to simulate previously unobserved behavior in response to a putative perturbation, and to aid in further experimental design. In a broader context, however, the focus and ultimate goal of this set of methodologies (whether this is explicitly stated or not) lies in understanding the mechanisms of physiology and pathophysiology and measuring the effect of therapeutic interventions through the accurate quantification of biomarkers of interest. In this review, we attempt to bring together under this comprehensive framework more than four decades of investigation on modeling and simulation in the life sciences (in particular, we will concentrate on the areas of pharmacology, physiology, and bioengineering). We demonstrate that such modeling approaches, when appropriately designed and evaluated, have significant potential and can be used to understand the multiple factors of disease progression and response to therapeutic interventions, the most likely causes of variability in population and individual responses to therapy, and the most appropriate timing of treatment administration. Lastly, they may allow estimation and prediction of significant outcomes in feasibility and clinical studies.

Animals↗

CYP17 and SULT1A1 gene polymorphisms in Indian breast cancer.

BACKGROUND: Breast cancer is the most common cancer among women worldwide. Life-time exposure to steroid hormones, especially estrogen, is a major risk factor for breast cancer. Functional polymorphisms in genes encoding steroid metabolizing enzymes may thus be important as biomarkers of individual susceptibility to breast cancer. The CYP17 and SULT1A1 genes encode for two enzymes involved in hormone biosynthesis and metabolism. Single nucleotide polymorphisms of these genes may result in inter-individual variability in steroid hormone biosynthesis and metabolism thus influence the development of breast cancer. METHODS: We tested this hypothesis by conducting a case - control study on a group of 140 breast cancer cases and 140 healthy age-matched controls. Analysis of CYP17 and SULT1A1 genotypes were done by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP). RESULTS: The genetic polymorphisms of the estrogen-related genes SULT1A1(OR=2.5, 95% CI=1.28-4.98) and CYP17 (OR=4.1, 95= CI=1.78-9.63) were associated with an increased risk of breast cancer among postmenopausal women. Our data also showed evidence for the genetic regulation of serum 17 beta estradiol (E2) levels as measured by ELISA among the premenopausal women with a significant increase in the serum E2 level for the CYP17 A2 variants. CONCLUSION: These results suggest that both CYP17 and SULT1A1 genotypes could be important determinants of breast cancer risk in Indian women and may help in early identification of high risk subjects. Such genotype analysis resulting in a high-risk profile holds considerable promise for individualizing screening, diagnosis and therapeutic intervention in breast cancer.

Adult↗

A pro-B-cell stage characterized by germline Ig transcription without surrogate light chain expression.

B-cell commitment is characterized by the expression of specific membrane proteins and the rearrangement and expression of immunoglobulin (Ig) heavy (H) and light (L) chain genes. At early stages of B-cell development, unrearranged Ig loci are transcribed, which correlates with these regions becoming accessible for Ig gene rearrangement. Some germline transcripts can be translated into protein and potentially play a role in cell signaling during B-cell development. In this report an early stage in human B-cell development is characterized using Epstein-Barr virus (EBV)-transformed cell lines from patients with a severe combined immunodeficiency (SCID). These lines were shown to produce germline constant (C) gene transcripts from the IGH and IGK loci. We demonstrate here that these cells are committed to the B-cell lineage as substantiated by expression of CD79a and CD79b. No surrogate light chain (SLC) gene transcription was detected, indicative of a very early differentiation stage. From these cell lines two types of germline IgV gene transcripts were isolated: a transcript containing the IGKV4-1 gene and a germline IGHV-1 transcript nearly identical to IGHV1/OR15-1 (HC15-1, DP-1), an orphon VH gene on chromosome 15. Germline VH transcripts originating from the VH locus on chromosome 14 could not be detected. It is of interest that, apart from Ig V and C genes (non-functional), V genes that reside outside the Ig locus are a target for the transcription factors that are postulated to initiate Ig gene rearrangement early in B-cell development.

Antigens, CD↗

Peak alignment of urine NMR spectra using fuzzy warping.

Proton nuclear magnetic resonance (1H NMR) spectroscopic analysis of mixtures has been used extensively for a variety of applications ranging from the analysis of plant extracts, wine, and food to the evaluation of toxicity in animals. For example, NMR analysis of urine samples has been used extensively for biomarker discovery and, more simply, for the construction of classification models of toxicity, disease, and biochemical phenotype. However, NMR spectra of complex mixtures typically show unwanted local peak shifts caused by matrix and instrument variability, which must be compensated for prior to statistical analysis and interpretation of the data. One approach is to align the spectral peaks across the data set. An efficient and fast warping algorithm is required as the signals typically contain ca. 32,000-64,000 data points and there can be several thousand spectra in a data set. As demonstrated in our study, the iterative fuzzy warping algorithm fulfills these requirements and can be used on-line for an alignment of the NMR spectra. Correlation coefficients between the aligned and target spectra are used as the evaluation function for the algorithm, and its performance is compared with those of other published warping methods.

Algorithms↗

Population consequences of fipronil and degradates to copepods at field concentrations: an integration of life cycle testing with leslie matrix population modeling.

The predominant data used in ecological risk assessment today are individual-based rather than population-based; yet environmental policies are usually designed to protect populations of threatened species or communities. Most current methods in ecotoxicology are limited by largely logistic/ technology-driven requirements that yield data for a relatively small number of test species and end points that focus on acute lethality or sublethal nonproduction-based parameters (e.g., biomarkers, mutagenesis, genetic change, physiological condition). A contrasting example is presented here showing the predictive ability of meiobenthos-based full life cycle toxicity testing to extrapolate multi-generational effects of chemicals on variables of import to population growth and maintenance. Less than 24-h-old larvae of a meiobenthic copepod were reared individually in 96-well microplate exposures to parent and degradates of the phenylpyrazole insecticide fipronil. Survival, development rates, sex ratio change, fertility, fecundity, and hatching success were tracked daily for 32 d through mating and production of three broods in spiked seawater. These data were then inserted in a Leslie (Lefkovitch) matrix stage-based population growth model to predict relative rates of population increase (lambda) and changes in net population growth with time and toxicant concentration. Field-reported test concentrations produced strong reproductive (52-88%) and net production (40-80%) depressions for parent (at 0.25 and 0.5 microg/L), desthionyl (0.25 and 0.5 microg/L), and sulfide (0.15 microg/L) moieties as compared to controls. Spiked sediment exposures of 65-300 ng of fipronil/g of dry sediment yielded significantly reduced production rates per female that were 67-50% of control production. The consistent reproductively linked impacts of fipronil and its degradation products at the population maintenance levels suggest risks to sediment-dwelling crustaceans at concentrations well below noneffects for most aquatic test species based on risk assessment data from primarily acute and sub-life cycle toxicity tests.

Animals↗

Urinary 5-aminolevulinic acid (ALA) adjusted by creatinine: a surrogate for plasma ALA?

5-Aminolevulinic acid (ALA) is the first intermediate substrate in the heme synthetic pathway and is the substrate of aminolevulinic acid dehydratase (ALAD, porphobilinogen synthase). Because lead effectively inhibits ALAD activity, resulting in accumulation of ALA in urine and blood, urinary ALA (ALAU) has been used as a biomarker for lead exposure or early biologic effect of lead. Intraindividual variation in urinary excretion of ALA requires the use of 24-hour urine samples or adjustment of single urine samples by other normalizing variables, such as urinary creatinine concentration. Previous studies of ALAU concentration have used various adjustment methods; however, few have compared creatinine-adjusted ALAU concentration with ALA concentration in plasma (ALAP) from subjects with low (< 30 micrograms/dL) to moderate (< 60 micrograms/dL) levels of blood lead. To determine if creatinine-adjusted ALAU is associated with ALAP, we measured ALAU, ALAP, and urinary creatinine in 65 Korean lead workers with blood lead concentrations in the range of 14-60 micrograms/dL. ALAU, ALAU/creatinine, or ALAU/log creatinine all correlated with ALAP. However, ALAU/creatinine correlated more closely with ALAP based on Spearman's r (rs = 0.40, P, = 0.0009), supporting the use of ALA/creatinine in single urine samples as a surrogate for ALAP.

Adult↗

Algorithms and tools for data-driven omics integration to achieve multilayer biological insights: a narrative review.

Systems biology is a holistic approach to biological sciences that combines experimental and computational strategies, aimed at integrating information from different scales of biological processes to unravel pathophysiological mechanisms and behaviours. In this scenario, high-throughput technologies have been playing a major role in providing huge amounts of omics data, whose integration would offer unprecedented possibilities in gaining insights on diseases and identifying potential biomarkers. In the present review, we focus on strategies that have been applied in literature to integrate genomics, transcriptomics, proteomics, and metabolomics in the year range 2018-2024. Integration approaches were divided into three main categories: statistical-based approaches, multivariate methods, and machine learning/artificial intelligence techniques. Among them, statistical approaches (mainly based on correlation) were the ones with a slightly higher prevalence, followed by multivariate approaches, and machine learning techniques. Integrating multiple biological layers has shown great potential in uncovering molecular mechanisms, identifying putative biomarkers, and aid classification, most of the time resulting in better performances when compared to single omics analyses. However, significant challenges remain. The high-throughput nature of omics platforms introduces issues such as variable data quality, missing values, collinearity, and dimensionality. These challenges further increase when combining multiple omics datasets, as the complexity and heterogeneity of the data increase with integration. We report different strategies that have been found in literature to cope with these challenges, but some open issues still remain and should be addressed to disclose the full potential of omics integration.

Algorithms↗

Tumor detection through the use of immunoglobulin gene rearrangements combined with tissue in situ hybridization.

Leukemias and lymphomas can now be classified according to the particular immunoglobulin, T-cell receptor, or growth-affecting genes they are expressing. Recognition of the structural alterations of lymphoid DNA has been used to identify neoplasms of previously uncertain lineage, to aid in diagnosis, and to define the state of differentiation of the neoplasm. We have developed a procedurally simple, rapid turnaround technique for using tumor-specific gene alterations as tumor-specific markers. Probes can be constructed that will recognize only the gene expressed in the tumor and not those in any of the normal cells when used with tissue in situ hybridization. We demonstrate the application of direct sequencing of a specific gene of interest from total RNA from a patient with multiple myeloma. A probe is then generated from this sequence and applied directly to patient material.

Base Sequence↗

Development of biomarkers based on diet-dependent metabolic serotypes: characteristics of component-based models of metabolic serotypes.

Our research seeks to identify a serum profile, or serotype, that reflects the systemic physiologic modifications resultant from dietary restriction (DR), in part such that this knowledge can be applied for biomarker studies. Direct comparison suggests that component-based classification algorithms consistently out-perform distance-based metrics for studies of nutritional modulation of metabolic serotype, but are subject to over-fitting concerns. Intercohort differences in the sera metabolome could partially obscure the effects of DR. Further analysis now shows that implementation of component-based approaches (also called projection methods) optimized for class separation and controlled for over-fitting have >97% accuracy for distinguishing sera from control or DR rats. DR's effect on the metabolome is shown to be robust across cohorts, but differs in males and females (although some metabolites are affected in both). We demonstrate the utility of projection-based methods for both sample and variable diagnostics, including identification of critical metabolites and samples that are atypical with respect to both class and variable models. Inclusion of non-statistically different variables enhances classification models. Variables that contribute to these models are sharply dependent on mathematical processing techniques; some variables that do not contribute under one paradigm are powerful under alternative mathematical paradigms. In practical terms, this information may find purpose in other endeavors, such as mechanistic studies of DR. Application of these approaches confirms the utility of megavariate data analysis techniques for optimal generation of biomarkers based on nutritional modulation of physiological processes.

Animals↗