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Correcting common errors in identifying cancer-specific serum peptide signatures.

"Molecular signatures" are the qualitative and quantitative patterns of groups of biomolecules (e.g., mRNA, proteins, peptides, or metabolites) in a cell, tissue, biological fluid, or an entire organism. To apply this concept to biomarker discovery, the measurements should ideally be noninvasive and performed in a single read-out. We have therefore developed a peptidomics platform that couples magnetics-based, automated solid-phase extraction of small peptides with a high-resolution MALDI-TOF mass spectrometric readout (Villanueva, J.; Philip, J.; Entenberg, D.; Chaparro, C. A.; Tanwar, M. K.; Holland, E. C.; Tempst, P. Anal. Chem. 2004, 76, 1560-1570). Since hundreds of peptides can be detected in microliter volumes of serum, it allows to search for disease signatures, for instance in the presence of cancer. We have now evaluated, optimized, and standardized a number of clinical and analytical chemistry variables that are major sources of bias; ranging from blood collection and clotting, to serum storage and handling, automated peptide extraction, crystallization, spectral acquisition, and signal processing. In addition, proper alignment of spectra and user-friendly visualization tools are essential for meaningful, certifiable data mining. We introduce a minimal entropy algorithm, "Entropycal", that simplifies alignment and subsequent statistical analysis and increases the percentage of the highly distinguishing spectral information being retained after feature selection of the datasets. Using the improved analytical platform and tools, and a commercial statistics program, we found that sera from thyroid cancer patients can be distinguished from healthy controls based on an array of 98 discriminant peptides. With adequate technological and computational methods in place, and using rigorously standardized conditions, potential sources of patient related bias (e.g., gender, age, genetics, environmental, dietary, and other factors) may now be addressed.

Algorithms↗

PubMed2004

BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics.

Rice is a major food staple for the world's population and serves as a model species in cereal genome research. The Beijing Genomics Institute (BGI) has long been devoting itself to sequencing, information analysis and biological research of the rice and other crop genomes. In order to facilitate the application of the rice genomic information and to provide a foundation for functional and evolutionary studies of other important cereal crops, we implemented our Rice Information System (BGI-RIS), the most up-to-date integrated information resource as well as a workbench for comparative genomic analysis. In addition to comprehensive data from Oryza sativa L. ssp. indica sequenced by BGI, BGI-RIS also hosts carefully curated genome information from Oryza sativa L. ssp. japonica and EST sequences available from other cereal crops. In this resource, sequence contigs of indica (93-11) have been further assembled into Mbp-sized scaffolds and anchored onto the rice chromosomes referenced to physical/genetic markers, cDNAs and BAC-end sequences. We have annotated the rice genomes for gene content, repetitive elements, gene duplications (tandem and segmental) and single nucleotide polymorphisms between rice subspecies. Designed as a basic platform, BGI-RIS presents the sequenced genomes and related information in systematic and graphical ways for the convenience of in-depth comparative studies (http://rise.genomics.org.cn/).

China↗

PubMed2004

A mammalian artificial chromosome engineering system (ACE System) applicable to biopharmaceutical protein production, transgenesis and gene-based cell therapy.

Mammalian artificial chromosomes (MACs) provide a means to introduce large payloads of genetic information into the cell in an autonomously replicating, non-integrating format. Unique among MACs, the mammalian satellite DNA-based Artificial Chromosome Expression (ACE) can be reproducibly generated de novo in cell lines of different species and readily purified from the host cells' chromosomes. Purified mammalian ACEs can then be re-introduced into a variety of recipient cell lines where they have been stably maintained for extended periods in the absence of selective pressure. In order to extend the utility of ACEs, we have established the ACE System, a versatile and flexible platform for the reliable engineering of ACEs. The ACE System includes a Platform ACE, containing >50 recombination acceptor sites, that can carry single or multiple copies of genes of interest using specially designed targeting vectors (ATV) and a site-specific integrase (ACE Integrase). Using this approach, specific loading of one or two gene targets has been achieved in LMTK(-) and CHO cells. The use of the ACE System for biological engineering of eukaryotic cells, including mammalian cells, with applications in biopharmaceutical production, transgenesis and gene-based cell therapy is discussed.

Animals↗

PubMed2006

Prediction of crossmatch outcome of highly sensitized patients by single and/or multiple antigen bead luminex assay.

BACKGROUND: We used a solid-phase assay to identify human leukocyte antigen (HLA) Class I and II specificities in highly reactive sera, and applied this information to predict crossmatch outcome with greater than 90% accuracy. METHODS: Sera from 20 highly sensitized end-stage renal disease patients reactive to 70-100% of HLA Class I and II antigen panel were analyzed by single and/or multiple antigen flow microparticle bead assay using Luminex platform (Luminex assay). These sera contained antibodies directed against high frequency public HLA class I and/or II epitopes accounting for 70-100% of serum's total reactivity. More than 2,000 complement dependent cytotoxicity (CDC) and 200 flow crossmatches (FLXM) were performed using sera from these patients and deceased donor T and B lymphocytes. RESULTS: Luminex serum analysis was able to correctly predict outcomes of 95% of T and B cell FLXM. In contrast, predictive values for the CDC T and B cell crossmatches by Luminex serum analysis were only 77% and 75%, respectively. The use of serum analysis in donor selection would have reduced the total number of required FLXM by more than 50%. The frequency of negative T cell FLXM was 56% when donors were selected randomly; however, if serum antibody analysis had been used to preselect the donors by excluding donors that were likely to be positive, the frequency of corresponding negative crossmatches would have increased up to 93%. CONCLUSION: This approach to donor selection may allow wider geographic sharing of cadaver donor organs without actually performing the crossmatch.

Antibodies↗

PubMed2003

Physiological control of pituitary hormone secretory-burst mass, frequency, and waveform: a statistical formulation and analysis.

The present study investigates the time-varying control of pituitary hormone secretion over the day and night (D/N). To this end, we implemented an analytical platform designed to reconstruct simultaneously 1) basal (nonpulsatile) secretion, 2) single or dual secretory-burst waveforms, 3) random effects on burst amplitude, 4) stochastic pulse-renewal properties, 5) biexponential elimination kinetics, and 6) experimental uncertainty. The statistical solution is conditioned on a priori pulse-onset times, which are estimated in the first stage. Primary data composed of thyrotropin (TSH) concentrations were monitored over 24 h in 27 healthy adults. According to statistical criteria, 21/27 profiles favored a dual compared with single secretory-burst waveform. An objectively defined waveform change point (D/N boundary) emerged at 2046 (+/-23 min), after which 1) the mass of TSH released per burst increases by 2.1-fold (P < 0.001), 2) TSH secretory-burst frequency rises by 1.2-fold (P < 0.001), 3) the latency to maximal TSH secretion within a burst decreases by 67% (P < 0.001), 4) variability in secretory-burst shape diminishes by 50% (P < 0.001), and 5) basal TSH secretion declines by 17% (P < 0.002). In contrast, the regularity of successive burst times and the slow-phase half-life are stable. In conclusion, nycthemeral mechanisms govern TSH secretory-burst mass, frequency, waveform, and variability but not evidently TSH elimination kinetics or the pulse-timing process. Further studies will be required to assess the generality of the foregoing distinctive control mechanisms in other hypothalamo-pituitary axes.

Adult↗

PubMed1999

Psychotropic drugs in mothers' milk: a comprehensive review of assay methods, pharmacokinetics and of safety of breast-feeding.

Many mentally ill women want to breast-feed their babies but, if they are taking psychotropic drugs, there is very little systematic data upon which to base decisions about whether or not it is safe to do so. We therefore attempt to provide a comprehensive and critical summary of existing case reports and of studies of breast-feeding in relation to commonly used psychotropic drugs. The literature review focuses on the following drugs: antidepressants: tricyclics and serotonin selective reuptake inhibitors (SSRIs); antipsychotic drugs: chlorpromazine, perphenazine, haloperidol and clozapine; mood stabilizers: lithium and carbamazepine; and benzodiazepines. The research literature consists mainly of single case reports and there have been very few attempts at controlled, longitudinal investigations. Findings are often difficult to compare because of differences in methods or because of lack of key information. Most data are available about the tricyclic antidepressants but even here we have found that the reports cover only a grand total of 66 mother-infant pairs. Dilemmas about whether or not to contraindicate breast-feeding arise most commonly in relation to postnatal depression. The findings to date suggest that provided that infants are healthy at the outset it is likely that the benefits of breast-feeding will outweigh potential hazards if their mothers are taking established tricyclic drugs at recommended dose levels. Much less is known about risks associated with SSRI antidepressants or about antipsychotic drugs such as phenothiazines and butyrophenones or mood stabilizers such as carbamazepine, all of which enter breast-milk. Safeguards are suggested for future single case studies, which, as they accumulate, will provide a platform for mounting controlled prospective studies properly to test for any acute toxic effects and for possible long-term adverse effects of such drugs on infants' development. Appendix 1 is a review of assay methods. Appendix 2 examines pharmacokinetic factors in newborn preterm and sick infants with special reference to contraindications to breast-feeding. Appendix 3 is a review of methods for assessing infant health and development.

Adult↗

PubMed2000

Reaction to disturbances of a walking leg during stance.

The ground reaction forces exerted by the legs of freely walking stick insects, Carausius morosus, were recorded during normal and perturbed locomotion. The animals walked along a path into which a three-dimensional force transducer was integrated. The transducer registered all three components of the forces produced by a single leg when, by chance, it walked on the force platform. The stiffness of the walking surface was found to be a critical variable affecting the forces and the trajectories of leg movements during undisturbed walking. The forces produced by a leg were considerably smaller and the trajectories were closer to the body during walking on soft versus stiff surfaces. Perturbations during stance were generated by moving the platform in various directions within the horizontal plane and at two different rates. Perturbations were applied either immediately after leg contact or after a delay of 300 ms. The reactions to these disturbances were compatible with the hypothesis that the velocity of leg movement is under negative feedback control. This interpretation is also supported by comparison with simulations based upon other control schemes. We propose a model circuit that provides a combination of negative and positive feedback control mechanisms to resolve the apparent discrepancies between our results and those of previous studies.

Animals↗

PubMed2004

Molecular recognition of biowarfare agents using micromechanical sensors.

Recent terrorist events have demonstrated that an urgent and widespread need exists for the development of novel sensors for threat detection, especially biowarfare agents. The advent of inexpensive, mass-produced microcantilever sensors promises to bring about a revolution in detection of terrorist threats. Extremely sensitive and highly selective sensors can be developed for using a microcantilever platform. Microcantilevers undergo bending when molecules are adsorbed on a single side. For biowarfare agent detection, specificity is achieved by immobilizing antibodies on one side of the cantilever. Antigen adsorption decreases surface energy and stress, resulting in cantilever deflection.

Antibodies, Bacterial↗

PubMed2001

Accumulation of hippocampal place fields at the goal location in an annular watermaze task.

To explore the plastic representation of information in spatially selective hippocampal pyramidal neurons, we made multiple single-unit recordings in rats trained to find a hidden platform at a constant location in a hippocampal-dependent annular watermaze task. Hippocampal pyramidal cells exhibited place-related firing in the watermaze. Place fields tended to accumulate near the platform, even in probe trials without immediate escape. The percentage of cells with peak activity around the hidden platform was more than twice the percentage firing in equally large areas elsewhere in the arena. The effect was independent of the actual position of the platform in the room frame. It was dissociable from ongoing motor behavior and was not related to linear or angular speed, swim direction, or variation in hippocampal theta activity. There was no accumulation of firing in any particular region in rats that were trained with a variable platform location. These training-dependent effects suggest that regions of particular behavioral significance may be over-represented in the hippocampal spatial map, even when these regions are completely unmarked.

Action Potentials↗

PubMed2001

Percutaneous Approach to Achieve Therapeutic Myocardial Angiogenesis.

Myocardial therapeutic angiogenesis is a novel approach for treating the large number of patients with advanced symptomatic coronary artery disease not amenable to conventional revascularization approaches. Proof of concept has been demonstrated in animal models of myocardial ischemia, and preliminary results suggest possible benefit in clinical trials of direct surgical (transepicardial) delivery of proteins and recombinant genes encoding angiogenic growth factors. Catheter-based intramyocardial gene delivery strategies have been tested in parallel, with the assumption that the less invasive nature and the potential for multiple treatment sessions would make this technique more applicable. Currently, most of the data relating to the catheter-based transendocardial delivery of angiogensis factors are derived from the experience with a single device (Biosense; Johnson & Johnson, Skillman, NJ). Using this injection platform, catheter-based gene delivery was demonstrated in animals to be safe and feasible, with a transfection yield similar to that achieved by the direct transepicardial approach. At the time of this review, more than 45 patients have been enrolled in Phase I clinical trials that evaluate the safety and feasibility of transendocardial delivery of adenovirus and plasmid-mediated gene transfection as well as cellular elements.

Journal Article↗

PubMed1998

Influence of landing on the supination and pronation in the foot joint.

The purpose of this study was to measure the changes of supination and pronation in the ankle joint at landing to quantify the influence of shock attenuation during landing. The subjects did two different motions, jumping down on the force platform from posterior and lateral views. The rear view of single foot contact in a jump from height of 30 and 60 cm showed a landing on the inside of the rear part of the foot (pronation) followed after about 0.03 sec by a rolling outward of the foot (supination). The variables describing changes in three angles of the ankle joint indicated that the standing position was more sensitive on the pronation and supination during ground contact.

Adult↗

PubMed2002

High-throughput detection of submicroscopic deletions and methylation status at 15q11-q13 by a photo-cross-linking oligonucleotide hybridization assay.

BACKGROUND: Current technologies for assessing genetic deletions and duplications of greater than one kilobase are labor-intensive or rely on PCR-based methods, and none offers the ability to simultaneously detect dosage abnormalities, assess 5'-to-3' cytosine-guanosine (CpG) methylation, and interrogate single-nucleotide polymorphisms (SNPs). We describe a high-throughput platform for direct gene-dosage determination capable of concurrent assessment of other forms of gene modification. METHODS: We used a light-activated interstrand nucleic acid cross-linking system (XLnt technology) to determine gene dosage at the 15q11-q13 deletion/duplication locus. We incorporated restriction enzyme digestion of genomic DNA into the method to assess CpG methylation in parallel with gene dosage. For method validation we used DNA from 31 cell lines with previously characterized 15q11-q13 gene dosage and parental origin status. Diagnostic cutoffs were set at 0.5 +/- 0.15, 1 +/- 0.15-0.25, and 2 +/- 0.3. RESULTS: Dosage-only experiments showed discrimination of deletions (n = 21) from healthy controls (NCs; n = 27) in all samples. Five of 49 samples gave results outside of specification. Concurrent evaluation of dosage and CpG methylation yielded dosage results within specification for 18 of 19 deletion and 8 of 12 NC samples. Paternal deletion and NC methylation pattern results were within specification in 17 of 19 and 9 of 12 runs, respectively. No overlap was demonstrated between value sets for the two groups. CONCLUSIONS: The XLnt technology provides a rapid, high-throughput platform for the accurate determination of gene dosage. The flexibility of this technology allows parallel interrogation of gene dosage, CpG methylation, and SNPs.

Chromosomes, Human, Pair 15↗

PubMed2001

Electrospray ionization mass spectrometry-based genotyping: an approach for identification of single nucleotide polymorphisms.

The high frequency of single nucleotide polymorphisms (SNPs) in the human genome makes them ideal genetic markers for mapping, diagnosing disease-related alleles, and identifying SNPs that contribute to drug response differences between individuals. Here we report a novel assay utilizing a single nucleotide primer extension (SNuPE) and electrospray ionization mass spectrometry (ESI-MS) detection for the analysis of SNPs. In contrast to most SNuPE genotyping technologies that detect the extended primer product, the novel Survivor assay detects the unreacted dideoxynucleotides (ddNTPs) remaining or surviving in solution following a SNuPE. This assay involves a simple analysis of the same four ddNTP analytes, regardless of the SNP being investigated, and either single or double-stranded DNA can be used to genotype a SNP, without any labeling requirements of the ddNTPs or oligonucleotide primers. We have tested and blindly validated the Survivor assay by genotyping the C/T SNP at -857 of the human TNFalpha promoter gene. The results obtained are in agreement with the control sequencing data. The results demonstrate that the homogeneous Survivor assay with ESI-MS detection offers advantages in simplicity, accuracy, specificity, and sensitivity. Additional advantages of the method include enhanced hybridization efficiencies in this solution-phase assay and the elimination of immobilized primers for the isolation of single-stranded DNA. With a one-well reaction and an automation platform being developed, the Survivor assay provides a powerful new tool for large-scale SNP analysis and screening.

Base Sequence↗

PubMed2004

Integrated and ultrasensitive gel protein identification.

An integrated gel protein identification technology is developed and demonstrated for the effective ( approximately 90% recovery), rapid (less than 5 min), and sensitive identification (as low as 1 ng gel protein loading) of gel-resolved proteins using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). This integrated technology involves on-line combination of electronic protein transfer with nanoscale proteolytic digestion in a capillary platform, enabling electrokinetic-based protein extraction and stacking, real-time proteolytic cleavage of extracted proteins, and direct deposition of protein digests onto MALDI targets. By revisiting the yeast two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) in similar isoelectric point and molecular mass ranges as studied by Gygi and co-workers (Gygi, S. P.; Corthals, G. L.; Zhang, Y.; Rochon, Y.; Aebersold, R. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 9390-9395), we are additionally able to identify a large number of low abundance proteins with codon adaptation index (CAI) values of <0.2 and increase the proteome coverage to nearly 50%. The CAI value distribution for identified yeast proteins now more closely approximates that predicted for the entire yeast proteome. We further note that the current single-capillary methodology can be easily expanded to a multiplexed capillary platform as a ultrahigh throughput and greatly effective tool for linking 2-D PAGE with MS, particularly for the analysis of low-abundance proteins.

Electrophoresis, Gel, Two-Dimensional↗

PubMed2026

Cross-Platform Concordance in DNA Methylation Based Classification of CNS Tumors.

DNA methylation profiling enables precise classification of pediatric central nervous system (CNS) tumors. Oxford Nanopore Technologies (ONT) offers same-day, single-sample methylation readouts, but its concordance with Illumina EPIC arrays in routine diagnostic tasks remains incompletely defined. We profiled 23 pediatric tumors (18 CNS, 5 non-CNS) by EPIC arrays and ONT. Methylation profiles from both platforms were classified with crossNN (brain model or pan-cancer model); ONT data were additionally classified with Rapid-CNS2 and Sturgeon. We compared (i) classifier agreement with integrated histology (w/o NGS) at family/class levels, (ii) pass-rate above platform-specific score cutoffs, (iii) cross-platform concordance of copy-number variation (CNV), and MGMT promoter methylation status. In CNS cases, ONT and EPIC methylation profiles demonstrated strong correlation, except for a single outlier (P2), which was excluded from further analysis. Comparative assessment of the two platforms showed that: (a) Molecular classification of CNS tumors using the crossNN classifier was consistent with histology (w/o NGS) at the family level in all cases. (b) Copy-number profiles showed high concordance between platforms. (c) MGMT promoter methylation status matched in 94% of cases (16/17). When comparing ONT-specific analysis pipelines using the ONT data, the Rapid-CNS2 pipeline yielded the most reliable class level assignments with 94% (16/17) concordance with the histopathological diagnosis, which marginally exceeded the crossNN and sturgeon classifiers. In non-CNS tumors, the pan-cancer model produced low-confidence outputs with poor agreement with histology (w/o NGS) (only 1/5 concordant), indicating limited readiness for these entities. In conclusion, ONT enables same-day, clinically reliable family-level CNS tumor classification with high concordance to arrays, while EPIC retains a modest class-level edge. A key limitation of ONT is its reliance on fresh-frozen DNA and on classifiers originally built around array-derived CpG sites, rather than on models developed natively from ONT data.

DNA methylation↗

PubMed2005

Noncontact laser microdissection and pressure catapulting: sample preparation for genomic, transcriptomic, and proteomic analysis.

The understanding of the molecular mechanisms of cellular metabolism and proliferation necessitates accurate identification, isolation, and finally characterization of a specific cell or a population of cells and subsequently their subsets of biomolecules. For the simultaneous analysis of thousands of molecular parameters within a single experiment, as realized by DNA, RNA, and protein microarray technologies, a defined number of homogeneous cells derived from a distinct morphological origin is required. Sample preparation is therefore a very crucial step for high-resolution downstream applications. Laser microdissection and laser pressure catapulting (LMPC) enables such pure and homogeneous sample preparation, resulting in an eminent increase in the specificity of molecular analyses. For microdissection, the force of focused laser light is used to excise selected cells or large tissue areas from object slides or from living cell culture down to a resolution of individual single cells and subcellular components like organelles or chromosomes, respectively. After microdissection this sample is directly catapulted into an appropriate collection device. As the entire process works without any mechanical contact, it enables pure sample retrieval from morphologically defined origin without cross contamination. Wherever homogenous samples are required for subsequent analysis of, e.g., cell areas, single cells, or chromosomes, the PALM MicroBeam system is an indispensable tool. The integration of image analysis platforms fully automates screening, identification, and finally subsequent high-throughput sample handling. These samples can be directly linked into versatile downstream applications, such as single-cell mRNA-extraction, different PCR methods, microarray techniques, and many others. Acceleration in sample generation vastly increases the throughput in molecular laboratories and leads to an increasing knowledge about differentially regulated mRNAs and expressed proteins, providing new insights into cellular mechanisms and therefore enabling the development of systems for tumor biomarker identification, early detection of disease-causing alterations, therapeutic targeting and/or patient-tailored therapy.

Animals↗

PubMed2004

Yeast display of antibody fragments: a discovery and characterization platform.

Yeast display of antibody fragments has proven to be an efficient and productive means for directed evolution of single-chain Fv (scFv) antibodies for increased affinity and thermal stability and, more recently, for the display and screening of a non-immune scFv and immune Fab libraries. A major strength of yeast display as a novel antibody discovery platform is the ability to characterize the binding properties, i.e., the affinity and epitope binding characteristics, of a clone without the need for subcloning, expression and purification of the scFv. This review focuses on novel attributes of yeast display for antibody engineering endeavors.

Animals↗

PubMed2005

Increasing detection of polymerase chain reaction (PCR) by isolation of PCR products (IPCRp).

AIM: To develop a method for enhanced polymerase chain reaction (PCR) product detection. METHODS: During the PCR, the double-stranded product is generated with fluorescent dye on one strand, and biotin on the other strand. The product is captured on the streptavidin-coated plates with high efficiency (IPCRp). Washing of the all unamplified compounds, including dye-labeled unincorporated primers, follows the PCR. The targeted dye-labeled PCR product is released by denaturation and loaded on the detection platform. RESULTS: After the application of the IPCRp, the resulting product is highly concentrated targeted dye-labeled single-stranded DNA, free of the unincorporated primers and other PCR artifacts. The strength of the signal of the IPCRp product on detection platform is two- to five-fold higher than the strength of the signal of the conventional PCR product. CONCLUSION: The IPCRp procedure can be accomplished in less than 20 minutes. Efficient isolation of the PCR products has two steps, washing and denaturation. It can increase the yield of targeted PCR product and increase the sensitivity of the detection platform.

DNA↗