Genomic Evolution of Oligometastatic Clear Cell Renal Cell Carcinoma Presenting Two Decades Following Radical Nephrectomy

Metachronous oligometastatic clear cell renal cell carcinoma may take many years before becoming clinically apparent. Herein we report regional lymph node recurrence of clear cell renal cell carcinoma more than two decades following radical nephrectomy. Chromosomal microarray analysis demonstrated multiple chromosomal alterations, including 3pq deletion shared by the original and recurrent tumors, and 17p deletion containing the TP53 gene present only in the latter. Sequencing of 1550 genes revealed mutations of VHL in both the primary and metastasis and BAP1 only in the metastatic lesion. These findings genetically link the original and recurrent tumors and suggest that VHL, TP53, and BAP1 alterations played an evolutionary role in recurrence decades after initial resection.

Leukemic presentation and progressive genomic alterations of MCD/C5 diffuse large B-cell lymphoma (DLBCL)

Diffuse large B-cell lymphoma (DLBCL) is a heterogenous group of lymphoid malignancies. Based on gene expression profiling, it has been subdivided into germinal center (GC)-derived and activated B-cell (ABC) types. Advances in molecular methodologies have further refined the subclassification of DLBCL, based on recurrent genetic abnormalities. Here, we describe a distinct case of DLBCL that presented in leukemic form. DNA sequencing targeting 275 genes revealed pathogenically relevant mutations of CD79B, MyD88, TP53, TBL1XR1, and PIM1 genes, indicating that this lymphoma would be best classified as MCD/C5 DLBCL, an ABC subtype. Despite an initial good clinical response to BTK inhibitor ibrutinib, anti-CD20 antibody rituxan, alkylating agent bendamustine, and hematopoietic stem-cell transplant, the lymphoma relapsed, accompanied by morphologic and molecular evidence of disease progression. Specifically, the recurrent tumor developed loss of TP53 heterozygosity (LOH) and additional chromosomal changes central to ABC DLBCL pathogenesis, such as PRDM1 loss. Acquired resistance to ibrutinib and rituxan was indicated by the emergence of BTK and FOXO1 mutations, respectively, as well as apparent activation of alternative cell-activation pathways, through copy-number alterations (CNAs), detected by high-resolution chromosomal microarrays. In vitro, studies of relapsed lymphoma cells confirmed resistance to standard BTK inhibitors but sensitivity to vecabrutinib, a noncovalent inhibitor active against both wild-type as well as mutated BTK. In summary, we provide in-depth molecular characterization of a de novo leukemic DLBCL and discuss mechanisms that may have contributed to the lymphoma establishment, progression, and development of drug resistance.

Validation of a Molecular Diagnostic Test for Circulating Tumor DNA by Next-Gen Sequencing

A modified version of the PGDx elioTM Plasma Resolve assay was validated as a laboratory-developed test (LDT) for clinical use in the Molecular Diagnostics Laboratory at Fox Chase Cancer Center. The test detects single nucleotide variants (SNVs) and small insertions and deletions (indels) in 33 target genes using fragmented genomic DNA extracted from plasma. The analytical performance of this assay was assessed with reference standard DNA and 29 samples from cancer patients and detected 66 SNVs and 23 indels. Using 50 ng of input DNA, the sensitivity was 95.5% to detect SNVs at 0.5% allele frequency, and the specificity was 92.3%. The sensitivity to detect indels at 1% allele frequency was 70.4%. A cutoff of 0.25% variant allele frequency (VAF) was set up for diagnostic reporting. An inter-laboratory study of concordance with an orthologous test resulted in a positive percent agreement (PPA) of 91.7%.

Clinical Validation of an Alternative Specimen Collection Kit for SARS-CoV-2 Testing at Fox Chase Cancer Center

Background

Supply chain disruptions during the COVID-19 pandemic have affected the availability of components for specimen collection kits to detect SARS-CoV-2. Plastic injection molding offers a rapid and cheap method for mass production of swabs for upper respiratory tract sampling. Local production of virus transport medium increases flexibility to assemble sample collection kits if the medium provides appropriate stability for SARS-CoV-2 detection.

Methods

A locally produced virus transport medium and a novel injection molded plastic swab were validated for SARS-CoV-2 detection by reverse-transcription quantitative polymerase chain reaction. Both components were compared to standard counterparts using viral reference material and representative patient samples.

Results

Clinical testing showed no significant differences between molded and flocked swabs. Commercial and in-house virus transport media provided stable test results for over 40 days of specimen storage and showed no differences in test results using patient samples.

Conclusions

This collection kit provides new supply chain options for SARS-CoV-2 testing.

Justifying integration of liquid biopsy into routine molecular diagnostics to complement tissue genomic profiling: Experience at Fox Chase Cancer Center

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Background: Plasma-based liquid biopsy has rapidly evolved from a novel research tool toward translation into clinical use for many diseases including cancer. While there are still some gaps regarding standardization and clinical utility, as tissue next-gen sequencing had previously faced and overcome, there is a growing body of evidence supporting integration of liquid biopsy into standard of care as a diagnostic tool for precision oncology. Selected from a larger cohort, several cases are presented here illustrating the use of the PGDx elio plasma resolve assay to profile circulating tumor DNA (ctDNA) from patients whose tumor and matched normal DNA had also been characterized by a next-generation sequencing panel. Methods: The PGDx elio plasma resolve assay and bioinformatics detects single and multi-nucleotide variants in 33 genes, select amplifications and translocations, as well as microsatellite instability by sequencing on the Illumina NextSeq 500/550 platform. DNA from matched tumor and normal FFPE samples were assessed using the 275 gene Molecular Diagnostics Laboratory’s Comprehensive Cancer Panel (CCP), also on the NextSeq platform. Selected cases represent the range of diagnostic utility that might be expected from ctDNA. Results: Across all cases, there were varying levels of concordance between tissue and plasma as well as novel variants in the plasma that were not present in the tissue DNA demonstrating the benefit of incorporating ctDNA profiling to capture critical genomic information. In one rectal adenocarcinoma case, DNA variants from the primary tumor were detected in ctDNA eight months later during evaluation of a recurrent tumor, suggesting that plasma profiling might have provided early biomarker detection of recurrence. An aggressive and recurrent melanoma, however, showed no concordance between ctDNA and tumor DNA variants, indicating that some tumors may not shed sufficient DNA into the bloodstream to make ctDNA clinically relevant. Another case of melanoma had concordant detection of the driver BRAF V600E mutation in tumor and ctDNA, but ctDNA also contained a pathogenic ATM truncation not observed in the tumor sample. Current clinical trials are investigating the combination of PARP- and ATR-inhibiting drugs, which causes excessive DNA damage and cell death in the context of ATM-deficient cancers. Conclusions: These cases show that combined tissue and ctDNA profiling at the time of initial diagnosis can reveal tumor heterogeneity or distinct metastases not observed in a selected tissue sample, and that profiling during and after therapy may provide early detection of recurrence, appearance of resistance mutations, or monitoring of measurable residual disease.

Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study

Assessing the reproducibility, accuracy and utility of massively parallel DNA sequencing platforms remains an ongoing challenge. Here the Association of Biomolecular Resource Facilities (ABRF) Next-Generation Sequencing Study benchmarks the performance of a set of sequencing instruments (HiSeq/NovaSeq/paired-end 2 × 250-bp chemistry, Ion S5/Proton, PacBio circular consensus sequencing (CCS), Oxford Nanopore Technologies PromethION/MinION, BGISEQ-500/MGISEQ-2000 and GS111) on human and bacterial reference DNA samples. Among short-read instruments, HiSeq 4000 and X10 provided the most consistent, highest genome coverage, while BGI/MGISEQ provided the lowest sequencing error rates. The long-read instrument PacBio CCS had the highest reference-based mapping rate and lowest non-mapping rate. The two long-read platforms PacBio CCS and PromethION/MinION showed the best sequence mapping in repeat-rich areas and across homopolymers. NovaSeq 6000 using 2 × 250-bp read chemistry was the most robust instrument for capturing known insertion/deletion events. This study serves as a benchmark for current genomics technologies, as well as a resource to inform experimental design and next-generation sequencing variant calling.

Low saliva pH can yield false positives results in simple RT-LAMP-based SARS-CoV-2 diagnostic tests

Diagnosis of any infectious disease is vital for opportune treatment and to prevent dissemination. RT-qPCR tests for detection of SARS-CoV-2, the causative agent for COVID-19, are ideal in a hospital environment. However, mass testing requires cheaper and simpler tests, especially in settings that lack sophisticated machinery. The most common current diagnostic method is based on nasopharyngeal sample collection, RNA extraction, and RT-qPCR for amplification and detection of viral nucleic acids. Here, we show that samples obtained from nasopharyngeal swabs in VTM and in saliva can be used with or without RNA purification in an isothermal loop-mediated amplification (LAMP)-based assay, with 60-93% sensitivity for SARS-CoV-2 detection as compared to standard RT-qPCR tests. A series of simple modifications to standard RT-LAMP published methods to stabilize pH fluctuations due to salivary acidity resulted in a significant improvement in reliability, opening new avenues for efficient, low-cost testing of COVID-19 infection.

Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP)

The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines. Here, we highlight the different ongoing projects that we have been working on, as well as details on the various methods we use to characterize the microbiome and metagenome of these complex samples. In particular, we present data of a novel multienzyme extraction protocol that we developed, called Polyzyme or MetaPolyZyme. Presently, the XMP is characterizing sample sites around the world with the intent of discovering new species, genes, and gene clusters. Once a project site is complete, the resulting data will be publically available. Sites include Lake Hillier in Western Australia, the "Door to Hell" crater in Turkmenistan, deep ocean brine lakes of the Gulf of Mexico, deep ocean sediments from Greenland, permafrost tunnels in Alaska, ancient microbial biofilms from Antarctica, Blue Lagoon Iceland, Ethiopian toxic hot springs, and the acidic hypersaline ponds in Western Australia.

Combined RT-qPCR of mRNA and microRNA Targets within One Fluidigm Integrated Fluidic Circuit

The ability to profile expression levels of a large number of mRNAs and microRNAs (miRNAs) within the same sample, using a single assay method, would facilitate investigations of miRNA effects on mRNA abundance and streamline biomarker screening across multiple RNA classes. A protocol is described for reverse transcription of long RNA and miRNA targets, followed by preassay amplification of the pooled cDNAs and quantitative PCR (qPCR) detection for a mixed panel of candidate RNA biomarkers. The method provides flexibility for designing custom target panels, is robust over a range of input RNA amounts, and demonstrated a high assay success rate.

A genome-wide association study of early spontaneous preterm delivery

Preterm birth is the leading cause of infant morbidity and mortality. Despite extensive research, the genetic contributions to spontaneous preterm birth (SPTB) are not well understood. Term controls were matched with cases by race/ethnicity, maternal age, and parity prior to recruitment. Genotyping was performed using Affymetrix SNP Array 6.0 assays. Statistical analyses utilized PLINK to compare allele occurrence rates between case and control groups, and incorporated quality control and multiple-testing adjustments. We analyzed DNA samples from mother-infant pairs from early SPTB cases (20(0/7)-33(6/7) weeks, 959 women and 979 neonates) and term delivery controls (39(0/7)-41(6/7) weeks, 960 women and 985 neonates). For validation purposes, we included an independent validation cohort consisting of early SPTB cases (293 mothers and 243 infants) and term controls (200 mothers and 149 infants). Clustering analysis revealed no population stratification. Multiple maternal SNPs were identified with association P-values between 10×10(-5) and 10×10(-6). The most significant maternal SNP was rs17053026 on chromosome 3 with an odds ratio (OR) 0.44 with a P-value of 1.0×10(-6). Two neonatal SNPs reached the genome-wide significance threshold, including rs17527054 on chromosome 6p22 with a P-value of 2.7×10(-12) and rs3777722 on chromosome 6q27 with a P-value of 1.4×10(-10). However, we could not replicate these findings after adjusting for multiple comparisons in a validation cohort. This is the first report of a genome-wide case-control study to identify single nucleotide polymorphisms (SNPs) that correlate with SPTB.

Genome wide nucleosome mapping for HSV-1 shows nucleosomes are deposited at preferred positions during lytic infection

HSV is a large double stranded DNA virus, capable of causing a variety of diseases from the common cold sore to devastating encephalitis. Although DNA within the HSV virion does not contain any histone protein, within 1 h of infecting a cell and entering its nucleus the viral genome acquires some histone protein (nucleosomes). During lytic infection, partial micrococcal nuclease (MNase) digestion does not give the classic ladder band pattern, seen on digestion of cell DNA or latent viral DNA. However, complete digestion does give a mono-nucleosome band, strongly suggesting that there are some nucleosomes present on the viral genome during the lytic infection, but that they are not evenly positioned, with a 200 bp repeat pattern, like cell DNA. Where then are the nucleosomes positioned? Here we perform HSV-1 genome wide nucleosome mapping, at a time when viral replication is in full swing (6 hr PI), using a microarray consisting of 50mer oligonucleotides, covering the whole viral genome (152 kb). Arrays were probed with MNase-protected fragments of DNA from infected cells. Cells were not treated with crosslinking agents, thus we are only mapping tightly bound nucleosomes. The data show that nucleosome deposition is not random. The distribution of signal on the arrays suggest that nucleosomes are located at preferred positions on the genome, and that there are some positions that are not occupied (nucleosome free regions -NFR or Nucleosome depleted regions -NDR), or occupied at frequency below our limit of detection in the population of genomes. Occupancy of only a fraction of the possible sites may explain the lack of a typical MNase partial digestion band ladder pattern for HSV DNA during lytic infection. On average, DNA encoding Immediate Early (IE), Early (E) and Late (L) genes appear to have a similar density of nucleosomes.

Metagenomic assay for identification of microbial pathogens in tumor tissues

Screening for thousands of viruses and other pathogenic microorganisms, including bacteria, fungi, and parasites, in human tumor tissues will provide a better understanding of the contributory role of the microbiome in the predisposition for, causes of, and therapeutic responses to the associated cancer. Metagenomic assays designed to perform these tasks will have to include rapid and economical processing of large numbers of samples, supported by straightforward data analysis pipeline and flexible sample preparation options for multiple input tissue types from individual patients, mammals, or environmental samples. To meet these requirements, the PathoChip platform was developed by targeting viral, prokaryotic, and eukaryotic genomes with multiple DNA probes in a microarray format that can be combined with a variety of upstream sample preparation protocols and downstream data analysis. PathoChip screening of DNA plus RNA from formalin-fixed, paraffin-embedded tumor tissues demonstrated the utility of this platform, and the detection of oncogenic viruses was validated using independent PCR and deep sequencing methods. These studies demonstrate the use of the PathoChip technology combined with PCR and deep sequencing as a valuable strategy for detecting the presence of pathogens in human cancers and other diseases.

IMPORTANCE

This work describes the design and testing of a PathoChip array containing probes with the ability to detect all known publicly available virus sequences as well as hundreds of pathogenic bacteria, fungi, parasites, and helminths. PathoChip provides wide coverage of microbial pathogens in an economical format. PathoChip screening of DNA plus RNA from formalin-fixed, paraffin-embedded tumor tissues demonstrated the utility of this platform, and the detection of oncogenic viruses was validated using independent PCR and sequencing methods. These studies demonstrate that the PathoChip technology is a valuable strategy for detecting the presence of pathogens in human cancers and other diseases.

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study

High-throughput RNA sequencing (RNA-seq) greatly expands the potential for genomics discoveries, but the wide variety of platforms, protocols and performance capabilitites has created the need for comprehensive reference data. Here we describe the Association of Biomolecular Resource Facilities next-generation sequencing (ABRF-NGS) study on RNA-seq. We carried out replicate experiments across 15 laboratory sites using reference RNA standards to test four protocols (poly-A-selected, ribo-depleted, size-selected and degraded) on five sequencing platforms (Illumina HiSeq, Life Technologies PGM and Proton, Pacific Biosciences RS and Roche 454). The results show high intraplatform (Spearman rank R > 0.86) and inter-platform (R > 0.83) concordance for expression measures across the deep-count platforms, but highly variable efficiency and cost for splice junction and variant detection between all platforms. For intact RNA, gene expression profiles from rRNA-depletion and poly-A enrichment are similar. In addition, rRNA depletion enables effective analysis of degraded RNA samples. This study provides a broad foundation for cross-platform standardization, evaluation and improvement of RNA-seq.

Development of a genotyping microarray for studying the role of gene-environment interactions in risk for lung cancer

A microarray (LungCaGxE), based on Illumina BeadChip technology, was developed for high-resolution genotyping of genes that are candidates for involvement in environmentally driven aspects of lung cancer oncogenesis and/or tumor growth. The iterative array design process illustrates techniques for managing large panels of candidate genes and optimizing marker selection, aided by a new bioinformatics pipeline component, Tagger Batch Assistant. The LungCaGxE platform targets 298 genes and the proximal genetic regions in which they are located, using ≈ 13,000 DNA single nucleotide polymorphisms (SNPs), which include haplotype linkage markers with a minimum allele frequency of 1% and additional specifically targeted SNPs, for which published reports have indicated functional consequences or associations with lung cancer or other smoking-related diseases. The overall assay conversion rate was 98.9%; 99.0% of markers with a minimum Illumina design score of 0.6 successfully generated allele calls using genomic DNA from a study population of 1873 lung-cancer patients and controls.

Evidence of a gene-environment interaction that predisposes to spontaneous preterm birth: a role for asymptomatic bacterial vaginosis and DNA variants in genes that control the inflammatory response

OBJECTIVE

We determined whether an environmental exposure to bacterial vaginosis (BV) modified genetic susceptibilities for spontaneous preterm delivery within genes that regulate the inflammatory response.

STUDY DESIGN

Maternal DNA samples and vaginal smears for Gram staining were collected from 743 women (68 preterm births). We used a 1536-single nucleotide polymorphism (SNP) custom chip to study associations between genotype distributions and preterm birth.

RESULTS

For 8 SNPs in 3 genes (protein kinase C alpha, fms-like tyrosine kinase 1, and interleukin 6), the odds ratios for preterm birth ranged from 1.9-4.0 among women with susceptible genotypes who were BV positive. The odds ratios for preterm birth were 2.0-5.0 times greater among women who were BV positive than among women who were BV negative. The significance of these differences was demonstrated by logistic regression analyses for genotype/BV interaction.

CONCLUSION

These results demonstrate that the risk of preterm delivery that is associated with tag SNPs in genes that regulate the inflammatory response is modified by an environmental exposure such as bacterial vaginosis.

Global genomic analysis reveals rapid control of a robust innate response in SIV-infected sooty mangabeys

Natural SIV infection of sooty mangabeys (SMs) is nonprogressive despite chronic virus replication. Strikingly, it is characterized by low levels of immune activation, while pathogenic SIV infection of rhesus macaques (RMs) is associated with chronic immune activation. To elucidate the mechanisms underlying this intriguing phenotype, we used high-density oligonucleotide microarrays to longitudinally assess host gene expression in SIV-infected SMs and RMs. We found that acute SIV infection of SMs was consistently associated with a robust innate immune response, including widespread upregulation of IFN-stimulated genes (ISGs) in blood and lymph nodes. While SMs exhibited a rapid resolution of ISG expression and immune activation, both responses were observed chronically in RMs. Systems biology analysis indicated that expression of the lymphocyte inhibitory receptor LAG3, a marker of T cell exhaustion, correlated with immune activation in SIV-infected RMs but not SMs. Our findings suggest that active immune regulatory mechanisms, rather than intrinsically attenuated innate immune responses, underlie the low levels of immune activation characteristic of SMs chronically infected with SIV.

Gene expression subtypes in patients with chronic fatigue syndrome/myalgic encephalomyelitis

Chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME) is a multisystem disease, the pathogenesis of which remains undetermined. We set out to determine the precise abnormalities of gene expression in the blood of patients with CFS/ME. We analyzed gene expression in peripheral blood from 25 patients with CFS/ME diagnosed according to the Centers for Disease Control and Prevention diagnostic criteria and 50 healthy blood donors, using a microarray with a cutoff fold difference of expression of >or=2.5. Genes showing differential expression were further analyzed in 55 patients with CFS/ME and 75 healthy blood donors, using quantitative polymerase chain reaction. Differential expression was confirmed for 88 genes; 85 were upregulated, and 3 were downregulated. Highly represented functions were hematological disease and function, immunological disease and function, cancer, cell death, immune response, and infection. Clustering of quantitative polymerase chain reaction data from patients with CFS/ME revealed 7 subtypes with distinct differences in Medical Outcomes Survey Short Form-36 scores, clinical phenotypes, and severity.

Inverted end-Hall-type low-energy high-current gaseous ion source

A novel approach to low-energy, high-current, gaseous ion beam generation was explored and an ion source based on this technique has been developed. The source utilizes a dc high-current (up to 20 A) gaseous discharge with electron injection into the region of ion generation. Compared to the conventional end-Hall ion source, the locations of the discharge anode and cathode are inverted: the cathode is placed inside the source and the anode outside, and correspondingly, the discharge current is in the opposite direction. The discharge operates in a diverging axial magnetic field, similar to the end-Hall source. Electron generation and injection is accomplished by using an additional arc discharge with a "cold" (filamentless) hollow cathode. Low plasma contamination is achieved by using a low discharge voltage (avoidance of sputtering), as well as by a special geometric configuration of the emitter discharge electrodes, thereby filtering (removing) the erosion products stemming from the emitter cathode. The device produces a dc ion flow with energy below 20 eV and current up to 2.5 A onto a collector of 500 cm(2) at 25 cm from the source edge, at a pressure > or =0.02 Pa and gas flow rate > or =14 SCCM. The ion energy spread is 2 to 3 eV (rms). The source is characterized by high reliability, low maintenance, and long lifetime. The beam contains less than 0.1% of metallic ions. The specific electric energy consumption is 400 eV per ion registered at the collector. The source operates with noble gases, nitrogen, oxygen, and hydrocarbons. Utilizing biasing, it can be used for plasma sputtering, etching, and other ion technologies.

Assessing the significance of conserved genomic aberrations using high resolution genomic microarrays

Genomic aberrations recurrent in a particular cancer type can be important prognostic markers for tumor progression. Typically in early tumorigenesis, cells incur a breakdown of the DNA replication machinery that results in an accumulation of genomic aberrations in the form of duplications, deletions, translocations, and other genomic alterations. Microarray methods allow for finer mapping of these aberrations than has previously been possible; however, data processing and analysis methods have not taken full advantage of this higher resolution. Attention has primarily been given to analysis on the single sample level, where multiple adjacent probes are necessarily used as replicates for the local region containing their target sequences. However, regions of concordant aberration can be short enough to be detected by only one, or very few, array elements. We describe a method called Multiple Sample Analysis for assessing the significance of concordant genomic aberrations across multiple experiments that does not require a-priori definition of aberration calls for each sample. If there are multiple samples, representing a class, then by exploiting the replication across samples our method can detect concordant aberrations at much higher resolution than can be derived from current single sample approaches. Additionally, this method provides a meaningful approach to addressing population-based questions such as determining important regions for a cancer subtype of interest or determining regions of copy number variation in a population. Multiple Sample Analysis also provides single sample aberration calls in the locations of significant concordance, producing high resolution calls per sample, in concordant regions. The approach is demonstrated on a dataset representing a challenging but important resource: breast tumors that have been formalin-fixed, paraffin-embedded, archived, and subsequently UV-laser capture microdissected and hybridized to two-channel BAC arrays using an amplification protocol. We demonstrate the accurate detection on simulated data, and on real datasets involving known regions of aberration within subtypes of breast cancer at a resolution consistent with that of the array. Similarly, we apply our method to previously published datasets, including a 250K SNP array, and verify known results as well as detect novel regions of concordant aberration. The algorithm has been fully implemented and tested and is freely available as a Java application at http://www.cbil.upenn.edu/MSA.

Cancer is a genetic disease caused by genomic mutations that confer an increased ability to proliferate and survive in a specific environment. It is now known that many regions of genomic DNA are deleted or amplified in specific cancer types. These aberrations are believed to occur randomly in the genome. If these aberrations overlap more than would be expected by chance across individual occurrences of the cancer this suggests a selective pressure on this aberration. These conserved aberrations likely represent regions that are important for the development, progression, and survival of a specific cancer type in its environment. We present a method for identifying these conserved aberrations within a class of samples. The applications for this method include accurate high resolution mapping of aberrations characteristic of cancer subtypes as well as other genetic diseases and determination of conserved copy number variations in the population. With the use of high resolution microarray methods we have profiled different tumor types. We have been able to create high resolution profiles of conserved aberrations in specific cancer types. These conserved aberrations are prime targets for cancer therapies and many of these regions have already been used to develop effective cancer therapeutics.

Differential expression of miRNAs in papillary thyroid carcinoma compared to multinodular goiter using formalin fixed paraffin embedded tissues

microRNAs (miRNAs) are approximately 22 nt RNAs that negatively regulate target gene expression. Their dysregulation has been implicated in the pathogenesis of a number of human cancers, including papillary thyroid carcinoma (PTC). Whereas previous studies using microarray technologies have largely relied on the ability to procure fresh tissue at the time of surgery to characterize miRNA signatures in PTC, we exploited the ability to procure sufficient miRNA from formalin-fixed paraffin-embedded (FFPE) tissue to describe a series of miRNAs whose expression is dysregulated in PTC compared to benign proliferative multinodular goiter (MNG). We identified 13 miRNAs upregulated and 26 miRNAs downregulated in PTC versus MNG. These include miRNA-21, miRNA-31, miRNA-221, and miRNA-222. Their dysregulation was further validated by real time RT-PCR analysis in an independent set of FFPE tissues. Many of these have previously been described in fresh tissue studies as altered in PTC, confirming the utility of this approach. These results further highlight the applicability of miRNA expression patterns as potential markers of human cancer, and our results suggest that FFPE tissues are suitable resources for such miRNA expression analyses. The ability to utilize FFPE tissue in the molecular characterization of human malignancy will unlock a rich resource for future cancer studies.

Multiorgan engraftment and differentiation of human cord blood CD34+ Lin- cells in goats assessed by gene expression profiling

To investigate multitissue engraftment of human primitive hematopoietic cells and their differentiation in goats, human CD34+ Lin- cord blood cells transduced with a GFP vector were transplanted into fetal goats at 45-55 days of gestation. GFP+ cells were detected in hematopoietic and nonhematopoietic organs including blood, bone marrow, spleen, liver, kidney, muscle, lung, and heart of the recipient goats (1.2-36% of all cells examined). We identified human beta2 microglobulin-positive cells in multiple tissues. GFP+ cells sorted from the perfused liver of a transplant goat showed human insulin-like growth factor 1 gene sequences, indicating that the engrafted GFP+ cells were of human origin. A substantial fraction of cells engrafted in goat livers expressed the human hepatocyte-specific antigen, proliferating cell nuclear antigen, albumin, hepatocyte nuclear factor, and GFP. DNA content analysis showed no evidence for cellular fusion. Long-term engraftment of GFP+ cells could be detected in the blood of goats for up to 2 yr. Microarray analysis indicated that human genes from a variety of functional categories were expressed in chimeric livers and blood. The human/goat xenotransplant model provides a unique system to study the kinetics of hematopoietic stem cell engraftment, gene expression, and possible stem cell plasticity under noninjured conditions.

RAKE and LNA-ISH reveal microRNA expression and localization in archival human brain

microRNAs (miRNAs) are small (approximately 22 nucleotide) regulatory RNAs which play fundamental roles in many biological processes. Recent studies have shown that the expression of many miRNAs is altered in various human tumors and some miRNAs may function as oncogenes or tumor suppressor genes. However, with the exception of glioblastoma multiforme, the expression of miRNAs in brain tumors is unknown. Furthermore, methods to profile miRNAs from formalin-fixed, paraffin-embedded (FFPE) archival tissues or to study their cellular and subcellular localization in FFPE tissues have been lacking. Here we report the coordinated miRNA expression analysis from the tissue level to the subcellular level, using the RAKE (RNA-primed, array-based, Klenow Enzyme) miRNA microarray platform in conjunction with Locked Nucleic Acid (LNA)-based in situ hybridization (LNA-ISH) on archival FFPE human brains and oligodendroglial tumors. The ability to profile miRNAs from archival tissues at the tissue level, by RAKE microarrays, and at the cellular level by LNA-ISH, will accelerate studies of miRNAs in human diseases.

Single‐Nucleotide Polymorphisms Associated with Symptomatic Infection and Differential Human Gene Expression in Healthy Seropositive Persons Each Implicate the Cytoskeleton, Integrin Signaling, and Oncosuppression in the Pathogenesis of Human Parvovirus B19 Infection

This study was undertaken to further examine the role of the host response to parvovirus B19 in the development of symptoms and consequences of viral persistence. Genomic DNA from 42 patients with symptomatic B19 infection was analyzed using the HuSNP assay (Affymetrix), and the results were compared with those from analysis of 53 healthy control individuals. Fifty-seven single-nucleotide polymorphisms were identified that were significantly associated with symptomatic infection. Total RNA from peripheral blood mononuclear cells from 57 B19-seropositive and 13 B19-seronegative donors was analyzed by hybridization to a single-color microarray representing 9522 human genes. Ninety-two genes were shown to be differentially expressed. Differential expression was confirmed in 6 of 38 genes (SKIP, MACF1, SPAG7, FLOT1, c6orf48, and RASSF5) tested using real-time quantitative polymerase chain reaction in a different group of healthy subjects. Genes identified in both studies play a functional role in the cytoskeleton, integrin signaling, and oncosuppression, themes that have been shown to be important in parvovirus infections.

Microarray-based, high-throughput gene expression profiling of microRNAs

MicroRNAs (miRNAs) are small regulatory RNAs that serve fundamental biological roles across eukaryotic species. We describe a new method for high-throughput miRNA detection. The technique is termed the RNA-primed, array-based Klenow enzyme (RAKE) assay, because it involves on-slide application of the Klenow fragment of DNA polymerase I to extend unmodified miRNAs hybridized to immobilized DNA probes. We used RAKE to study human cell lines and brain tumors. We show that the RAKE assay is sensitive and specific for miRNAs and is ideally suited for rapid expression profiling of all known miRNAs. RAKE offers unique advantages for specificity over northern blots or other microarray-based expression profiling platforms. Furthermore, we demonstrate that miRNAs can be isolated and profiled from formalin-fixed paraffin-embedded tissue, which opens up new opportunities for analyses of small RNAs from archival human tissue. The RAKE assay is theoretically versatile and may be used for other applications, such as viral gene profiling.

Transcript profiling during preimplantation mouse development

Studies using low-resolution methods to assess gene expression during preimplantation mouse development indicate that changes in gene expression either precede or occur concomitantly with the major morphological transitions, that is, conversion of the oocyte to totipotent 2-cell blastomeres, compaction, and blastocyst formation. Using microarrays, we characterized global changes in gene expression and used Expression Analysis Systematic Explorer (EASE) to identify biological and molecular processes that accompany and likely underlie these transitions. The analysis confirmed previously described processes or events, but more important, EASE revealed new insights. Response to DNA damage and DNA repair genes are overrepresented in the oocyte compared to 1-cell through blastocyst stages and may reflect the oocyte's response to selective pressures to insure genomic integrity; fertilization results in changes in the transcript profile in the 1-cell embryo that are far greater than previously recognized; and genome activation during 2-cell stage may not be as global and promiscuous as previously proposed, but rather far more selective, with genes involved in transcription and RNA processing being preferentially expressed. These results validate this hypothesis-generating approach by identifying genes involved in critical biological processes that can be the subject of a more traditional hypothesis-driven approach.

Genomic identification of direct target genes of LEAFY

The switch from vegetative to reproductive development in plants necessitates a switch in the developmental program of the descendents of the stem cells in the shoot apical meristem. Genetic and molecular investigations have demonstrated that the plant-specific transcription factor and meristem identity regulator LEAFY (LFY) controls this developmental transition by inducing expression of a second transcription factor, APETALA1, and by regulating the expression of additional, as yet unknown, genes. Here we show that the additional LFY targets include the APETALA1-related factor, CAULIFLOWER, as well as three transcription factors and two putative signal transduction pathway components. These genes are up-regulated by LFY even when protein synthesis is inhibited and, hence, appear to be direct targets of LFY. Supporting this conclusion, cis-regulatory regions upstream of these genes are bound by LFY in vivo. The newly identified LFY targets likely initiate the transcriptional changes that are required for the switch from vegetative to reproductive development in Arabidopsis.

Learning words from knowledgeable versus ignorant speakers: links between preschoolers' theory of mind and semantic development

Two studies addressed whether children consider speakers' knowledge states when establishing initial word-referent links. In Study 1, forty-eight 3- and 4-year-olds were taught two novel words by a speaker who expressed either knowledge or ignorance about the words' referents. Children showed better word learning when the speaker was knowledgeable. In Study 2, forty-eight 3- and 4-year-olds were taught two novel words by a speaker who expressed uncertainty about their referents. Whether the uncertainty truly reflected ignorance, however, differed across conditions. In one condition, the speaker said he made the object himself and thus, he was knowledgeable. In the other condition, the speaker stated that the object was made by a friend and thus, expressed ignorance about it. Four-year-olds learned better in the speaker-made than in the friend-made condition; 3-year-olds, however, showed relatively poor learning in both conditions. These findings suggest that theory-of-mind developments impact word learning.

Infants parse dynamic action

As observers of human behavior, infants are faced with a complex flow of motion in which pauses are rare and only occasionally coincide with boundaries between intentional actions. Two studies investigated whether, despite such complexity, 10- to 11-month-old infants (N = 16 for each study) possess skills for parsing ongoing behavior along boundaries correlated with the initiation and completion of intentions. After being familiarized with digitized sequences of continuous everyday action, infants showed renewed interest in test versions in which motion paused in the midst of an actor's pursuit of intentions (interrupting test videos). In contrast, pauses that suspended motion at intention boundary points (completing test videos) sparked no such renewed interest on infants' part. Moreover, basic salience differences between the two types of test videos were not the source of infants' increased interest when intentions were interrupted (Study 2). These findings demonstrate that infants readily detect disruptions of the structure inherent in intentional action, and hence parse ongoing behavior with respect to such structure. Such parsing skill is likely a prerequisite to the development of genuine intentional understanding.

Evidence for referential understanding in the emotions domain at twelve and eighteen months

Infants as young as 12 months readily modulate their behavior toward novel, ambiguous objects based on emotional responses that others display. Such social-referencing skill offers powerful benefits to infants' knowledge acquisition, but the magnitude of these benefits depends on whether they appreciate the referential quality of others' emotional messages, and are skilled at using cues to reference (e.g., gaze direction, body posture) to guide their interpretation of such messages. Two studies demonstrated referential understanding in 12- and 18-month-olds' responses to another's emotional outburst. Infants relied on the presence versus absence of referential cues to determine whether an emotional message should be linked with a salient, novel object in the first study (N = 48), and they actively consulted referential cues to disambiguate the intended target of an affective display in the second study (N = 32). These findings provide the first experimental evidence of such sophisticated referential abilities in 12-month-olds, as well as the first evidence that infant social referencing at any age actually trades on referential understanding.

Further evidence of associations of type a personality scores and driving-related attitudes and behaviors

The present study examined the effects of Type A personality on specific self-reported driving attitudes and behaviors when operating a motor vehicle. 102 undergraduate students completed the student version of the Jenkins Activity Survey (Form T) and several questionnaires asking participants about their driving history, driving attitudes, and driving behaviors. When the full range of Type A scores were examined, Type A personality was significantly related to more traffic accidents, greater frequency of breaking traffic laws, higher impatience when driving, more displays of aggression on the road, and engaging in more risky driving behaviors (rs<.17). When extreme Type A and Type B scores were compared, Type A drivers reported being involved in significantly more motor vehicle accidents and reported displaying more aggression on the road. Further research should examine actual behavioral data using more diverse samples to validate the results.

Do children with autism use the speaker's direction of gaze strategy to crack the code of language?

Normal toddlers infer the referent of a novel word by consulting the speaker's direction of gaze. That is, they use the Speaker's Direction of Gaze (SDG) strategy. This is a far more powerful strategy than the alternative, the Listener's Direction of Gaze (LDG) strategy. In Study 1 we tested if children with autism, who have well-documented impairments in joint attention, used the SDG or the LDG strategy to learn a novel word for a novel object. Results showed that although 70.6% of children with mental handicap passed the test by making the correct mapping between a novel word and a novel object, via the SDG strategy, only 29.4% of children with autism did so. Instead, their reliance on the LDG strategy led to mapping errors. In Study 2 a group of normal children, whose chronological age (24 months old) was equated with the verbal mental age of the 2 clinical groups in Study 1, was tested using a similar procedure. Results showed that 79% of this normal group passed the test by making the correct mapping between a novel word and a novel object using the SDG strategy. Taken together, the results from both studies suggest that children with autism are relatively insensitive to a speaker's gaze direction as an index of the speaker's intention to refer. This result is consistent with previous findings showing that children with autism are relatively "blind" to the mentalistic significance of the eyes. Discussion centers on how the absence of an SDG strategy might disrupt specific aspects of language development in autism.

Infants' reliance on a social criterion for establishing word-object relations

The language children hear presents them with a multitude of co-occurrences between words and things in the world, and they must repeatedly determine which among these manifold co-occurrences is relevant. Social factors--such as cues regarding the speaker's referential intent--might serve as one guide to whether word-object covariation should be registered. In 2 studies, infants (15-20 months and 18-20 months in Studies 1 and 2, respectively) heard novel labels at a time when they were investigating a single novel object; in one case the label was uttered by a speaker seated within the infant's view and displaying concurrent attention to the novel toy (coupled condition), whereas in the other case the label emanated from a speaker seated out of the infant's view (decoupled condition). In both studies, subsequent comprehension questions indicated that infants of 18-20 months registered a stable link between label and object in the coupled conditions, but not in the decoupled condition, despite the fact that covariation between label and object was equivalent in the 2 conditions. Thus, by 18-20 months children are inclined to establish a mapping between word and object only when a speaker displays signs of referring to that object.

Isolation and characterization of cDNAs encoding transcription factor IIB from Arabidopsis and soybean

Clones containing the complete coding regions for transcription factor IIB (TFIIB) were isolated from cDNA libraries of Arabidopsis and soybean. The predicted protein sequences for TFIIB from these two species are highly homologous and contain the same structural motifs and organization as seen in other eukaryotes and Archaebacteria. Southern and Northern blots and primer extension for Arabidopsis TFIIB indicate a low copy number gene encodes a transcript of 1400 nt with a leader of 180 nt. Phylogeny analysis places the plant proteins into one group nearly equidistant from metazoans, fungi, and Archaebacteria.

Infants' ability to draw inferences about nonobvious object properties: evidence from exploratory play

Generalizing knowledge about nonobvious object properties often involves inductive inference. For example, having discovered that a particular object can float, we may infer that other objects of similar appearance likewise float. In this research, exploratory play served as a window on early inductive capability. In the first study, 48 infants between 9 and 16 months explored pairs of novel toys in 2 test conditions: violated expectation (two similar toys were presented in sequence, the first toy produced an interesting nonobvious property, such as a distinctive sound or movement, while the second toy was invisibly altered such that it failed to produce the nonobvious property available in the first toy), and interest control (two similar-looking toys were presented in sequence, neither of which produced the interesting property). Infants quickly and persistently attempted to reproduce the interesting property when exploring the second toy of the violated expectation condition relative to the first toy of the interest control condition (a baseline estimate) or the second toy of the interest control condition (an estimate of simple disinterest). The second study, with 40 9-16-months-olds, confirmed these results and also indicated a degree of discrimination on infants' part: Infants seldom expected toys of radically different appearance to possess the same nonobvious property. The findings indicate that infants as young as 9 months can draw simple inferences about nonobvious object properties after only brief experience with just 1 exemplar.

Infants' ability to consult the speaker for clues to word reference

This research examines whether infants actively seek information from a speaker regarding the referent of the speaker's utterance. Forty-eight infants (in three age groups: 1;2-1;3, 1;4-1;5, and 1;6-1;7) heard novel labels for novel objects in two situations: follow-in labelling (the experimenter looked at and labelled the toy of the infant's focus) vs. discrepant labelling (the experimenter looked at and labelled a different toy than that of the infant's focus). Subsequently, half of the infants were asked comprehension questions (e.g. 'Where's the peri?'). The other half were asked preference questions (e.g. 'Where's the one you like?'), to ensure that their comprehension performance was not merely the result of preferential responding. The comprehension results revealed developmental change in both (a) infants' ability to establish new word-object mappings (infants aged 1;2-1;3 failed to establish stable word-object links even in follow-in labelling), and (b) infants' ability to pinpoint the correct referent during discrepant labelling (only infants aged 1;6-1;7 succeeded). Thus the period between 1;2 and 1;7 represents a time of change in infants' ability to establish new word-object mappings: infants are becoming increasingly adept at acquiring new labels under minimal learning conditions.

Clarifying the role of shape in children's taxonomic assumption

When asked to find a new referent of a novel label children tend to ignore thematic relations (e.g., the relation between a spider and its web) and focus instead on taxonomic relations (e.g., the relation between a spider and a snake). The precise nature of children's taxonomic assumption has not been clear, however. One possibility is that the taxonomic assumption reduces to a "similar-shape rule": perhaps children tend to select objects of the same taxonomic kind when asked to extend new labels simply because these objects are more similar in shape than objects which are only thematically related. Sixty children between 3 and 5 years of age participated in three studies which examined children's attention to thematic relations, similarity of shape, and taxonomic relations when extending novel object labels. The findings indicated that shape has some primacy in children's expectations about object label reference, yet when shape is not available as a guide, children also take taxonomic kind into consideration when searching for new referents of novel labels. Thus children make use of a relatively rich and somewhat varied set of expectations to guide their inferences about object label reference.

Infants' contribution to the achievement of joint reference

This research examines whether infants actively contribute to the achievement of joint reference. One possibility is that infants tend to link a a label with whichever object they are focused on when they hear the label. If so, infants would make a mapping error when an adult labels a different object than the one occupying their focus. Alternatively, infants may be able to use a speaker's nonverbal cues (e.g., line of regard) to interpret the reference of novel labels. This ability would allow infants to avoid errors when adult labels conflict with infants' focus. 64 16-19-month-olds were taught new labels for novel toys in 2 situations. In follow-in labeling, the experimenter looked at and labeled a toy at which infants were already looking. In discrepant labeling, the experimenter looked at and labeled a different toy than the one occupying infants' focus. Infants' responses to subsequent comprehension questions revealed that they (a) successfully learned the labels introduced during follow-in labeling, and (b) displayed no tendency to make mapping errors after discrepant labeling. Thus infants of only 16 to 19 months understand that a speaker's nonverbal cues are relevant to the reference of object labels; they already can contribute to the social coordination involved in achieving joint reference.

The effects of anions on the kinetics of reductive elimination of iron from monoferrictransferrins by thiols

The kinetics of reductive elimination of iron from the human serum monoferric transferrins by thioglycollate (TG), 3-mercaptopropionate (MP), cysteine (Cys), cysteamine (Cym) and 2-mercaptoethanol (ME) have been studied at 37 degrees C using bathophenanthroline sulphonate (BPS) as the ferrous ion acceptor. Analysis of the entire course of the reaction was possible only with thioglycollate since the other thiols cause eventual protein precipitation; in these cases, initial rates were used. The rate of iron release is linearly dependent on thiol concentration at low concentrations of reductant (less than approx. 0.2 M) and increases more rapidly with higher concentrations (up to 0.5-0.75 M). The thiols fall into two distinct groups, with TG, MP and Cys reacting at approx. the same rate, which is an order of magnitude faster than the reaction with Cym and ME. The carboxylate functionality present in the first group may be responsible for the faster reaction rate, by competitively weakening the interaction between the protein and synergistic anion. The pH-dependence of the rate of reductive elimination appears to depend on ionizable functionalities on both the protein and reducing agent. The addition of NaCl, NaClO4, NaHCO3 and Na2HPO4 increases the rate of iron release from the monoferric transferrins. The last two have particularly large accelerating effects and, in the case of the N-terminal monoferrictransferrin, gave saturation kinetics, suggesting that the observed effect is due to conformational changes in the protein caused by binding of ions. The role of the Fe-synergistic anion complex in the transferrins as a 'trapped intermediate' is considered.

Priorities in children's expectations about object label reference: form over color

Young children show considerable interest in color similarity; thus we might expect them to use color as a basis for generalizing object labels. However, natural language observations suggest they do not: children tend to overextend labels based on form similarity and rarely, if ever, overextend labels to objects that share only color. Perhaps, then, children give form priority over color in their expectations about object-label reference. This hypothesis was investigated in 2 studies. In a first study, 40 2- and 3-year-olds sorted 10 sets of 3 pictures that contrasted form with color. Children participated in 1 of 2 conditions: half of the children were shown a target object and asked to "find another one" from among the two choice objects, while the other children heard a novel label for the target (e.g., "See this zom?") and were asked to extend the label (e.g., "Can you find another zom?"). 3-year-olds sorted almost exclusively on the basis of form in both conditions, while 2-year-olds performed differently in the 2 conditions: they frequently chose the color match when labels were absent, but selected by form rather than color when asked to extend a novel label. A second study replicated these findings with novel objects that were real rather than pictured. This study also suggested that 3-year-olds grant color some role in their decisions about object-label reference as long as form differences are reduced to a tolerable level. In sum, young children expect form to be more important than color for guiding object-label reference, even though they may find color interesting when not asked to extend labels. This expectation helps explain the speed and relative ease with which children acquire object labels.

Establishing word-object relations: a first step

This work explores how infants in the early phases of acquiring language come to establish an initial mapping between objects and their labels. If infants are biased to attend more to objects in the presence of language, that could help them to note word-object object pairings. To test this, a first study compared how long 18 10-14-month-old infants looked at unfamiliar toys when labeling phrases accompanied their presentation, versus when no labeling phrases were provided. As predicted, labeling the toys increased infants' attention to them. A second study examined whether the presence of labeling phrases increased infants' attention to objects over and above what pointing, a powerful nonlinguistic method for directing infants' attention, could accomplish on its own. 22 infants from 2 age groups (10-14- and 17-20-month-olds) were shown pairs of unfamiliar toys in 2 situations: (a) in a pointing alone condition, where the experimenter pointed a number of times at one of the toys, and (b) in a labeling + pointing condition, where the experimenter labeled the target toy while pointing to it. While the pointing occurred, infants looked just as long at the target toy whether or not it was labeled. During a subsequent play period in which no labels were uttered, however, infants gazed longer at the target toys that had been labeled than at those that had not. Thus language can increase infants' attention to objects beyond the time that labeling actually occurs. These studies do not pinpoint which aspects of labeling behavior contribute to the attentional facilitation effect that was observed. In any case, however, this tendency for language to sustain infants' attention to objects may help them learn the mappings between words and objects.

Hemes and hemoproteins. 5: Kinetics of the peroxidatic activity of microperoxidase-8: model for the peroxidase enzymes

The peroxidatic activity of the heme octapeptide from cytochrome c, microperoxidase-8 (MP-8), was assayed at 25 degrees C under conditions where formation of Compound I is rate limiting. In the pH range 6-9, the reaction rate increased linearly with a slope close to unity. The active form of the substrate is the hydroperoxide anion, HO2-, and an extrapolated second-order rate constant was obtained for the reaction of aquoMP-8 with HO2- of 3.7 X 10(8) M-1 sec-1, which is close to the second-order rate constants reported for reaction of the peroxidase enzymes with H2O2. Comparison with published data shows that the Fe3+ ion of MP-8 reacts as expected with simple anions, electrons, and HO2-, while the analogous reactions of the enzymes all show a requirement for one H+. We conclude that the peroxidase enzymes activate H2O2 under physiological conditions through a pH-independent, H+-coupled binding of the required H2O2-. The peroxidase activity of MP-8 can be increased more than tenfold by the presence of the guanidinium ion, which is ascribed to formation of the ion-pair GuaH+HO2-; this suggests a role for the invariant distal Arg in the enzymes.

Hemes and hemoproteins. 3. The reaction of microperoxidase-8 with cyanide: comparison with aquocobalamin and hemoproteins

The monomeric heme octapeptide from cytochrome c, microperoxidase-8, (MP-8), coordinates CN- with log K = 7.55 +/- 0.04 at 25 degrees C in 20% (v/v) aqueous methanol. Log K values are independent of pH between 6 and 9. A spectrophotometric titration of cyanoMP-8 between pH 5.5 and 13.8 gave a single pKa greater than or equal to 13.5 ascribed to ionization of the proximal His ligand. A study of the kinetics of the reaction of MP-8 with cyanide between pH 5.5 and 12, at 25 degrees C and mu = 0.1, indicates that formation of cyanoMP-8 occurs via three routes: attack of CN- on Fe(III) (k1 = 6.0 +/- 0.3 X 10(5) M-1 sec-1); attack of HCN on Fe(III) (k2 = 4.8 +/- 2.0 X 10(3) M-1 sec-1), followed by deprotonation and isomerization to form the C-bound species; and displacement of OH- by CN- when the proximal His ligand is ionized (k5 = 1.8 +/- 0.1 X 10(5) M-1 sec-1). These results are compared with available data for the reaction of cyanide with aquocobalamin and with various hemoproteins.

Hemes and hemeproteins, 2: The pH-dependent equilibria of microperoxidase-8 and characterization of the coordination sphere of Fe(III)

Titration of the monomeric heme octapeptide from horse heart cytochrome c, microperoxidase-8 (MP-8) from pH 1 to pH 13 in 20% (v/v) methanol-water solutions, mu = 0.1, at 25 degrees C shows three reversible concentration-independent pKs (4.43 +/- 0.09; 8.90 +/- 0.03; 10.48 +/- 0.09) which are ascribed to successive proton loss from the conjugate acid of His (and its coordination to Fe(III)), bound H2O, and from bound His to form an imidazolate complex, respectively. The equilibrium constant for coordination of imidazole between pH 5.5 and 7.0 is independent of pH (logK = 4.45) which proves that His-18 is coordinated to Fe(III) in aqueous solution.

Hemes and hemoproteins. 1: Preparation and analysis of the heme-containing octapeptide (microperoxidase-8) and identification of the monomeric form in aqueous solution

The heme-octapeptide from cytochrome c, Microperoxidase-8 (MP-8), was prepared by peptic and tryptic digestion of horse heart cytochrome c and purified by gel permeation chromatography in about 50% yield. Conditions for the identification of MP-8 by TLC and analysis by HPLC are described. Study of the concentration-dependence of the absorption spectrum showed that at concentrations of less than or equal to 2.5 X 10(-5) M in aqueous solution at pH 7, 25 degrees C and mu = 0.1, MP-8 exists as an equilibrium mixture of monomers and dimers with KD = 1.17 +/- 0.02 X 10(5) M-1, decreasing to 1.21 +/- 0.02 X 10(4) M-1 and 2.16 +/- 0.21 X 10(3) M-1 in 20% and 50% (v/v) methanol:water mixtures, respectively. Comparison of the Soret region spectrum of monomeric MP-8 with other hemoproteins suggests that it is six-coordinate in aqueous solution with water and His as axial ligands.

The effect of human serum transferrin and milk lactoferrin on hydroxyl radical formation from superoxide and hydrogen peroxide

The effect of transferrins on hydroxyl radical formation from the superoxide anion and hydrogen peroxide generated by the xanthine-xanthine oxidase system has been studied by EPR using 5,5-dimethyl-1-pyrroline N-oxide as a spin trap. Neither diferriclactoferrin nor diferrictransferrin were found capable of promoting hydroxyl radical formation via the Haber-Weiss reaction even in the presence of EDTA in concentrations up to 1 mM. Activity observed by other authors may have been due to the presence of extraneous iron or an active protein impurity. Partially saturated transferrin and lactoferrin present in normal subjects may protect cells from damage by binding iron that might catalyze hydroxyl radical formation from superoxide and hydrogen peroxide. In any event, the hydroxyl radical formation observed in active neutrophils during phagocytosis cannot be associated with lactoferrin activity.

Protein-free models for the proton-coupled reduction of haemoproteins

Reduction of the bis-pilocarpate-haemin complex at pH greater than or equal to 10 involves the simultaneous uptake of an electron by the Fe(III) ion and a proton by the pendant alkoxide group of an axial ligand. This provides a protein-free model for reactions such as the proton-coupled reduction of cytochromes which involve cooperative Coulombic interaction between two non-bonded sites.