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PubMed2026

Intraductal Papillary Squamous Neoplasm (IPSN) of the Pancreas: Histological and Molecular Characterization of a Novel and Distinct Intraductal Cancer Precursor.

We report 6 intraductal papillary squamous neoplasms (IPSNs) of the pancreas, a rare but distinctive tumor whose biological features remain largely unknown. Five cases were investigated using an integrated approach combining histomorphological evaluation, immunohistochemistry, and multiregional molecular profiling through whole-exome DNA sequencing and whole-transcriptome RNA sequencing. Only targeted DNA sequencing was available on a sixth recently diagnosed case. Histologically, the intraductal lesions were characterized by large, confluent papillae with fibrovascular cores lined by multilayered epithelial cells with diffuse squamous differentiation. All cases harbored a concomitant invasive carcinoma. The associated invasive carcinomas consistently included a pancreatic tubular/ductal adenocarcinoma; in 5 cases, a poorly differentiated squamous cell carcinoma was also present, the proportion/features of which met the diagnostic criteria of adenosquamous carcinoma in 2 of them. Genomic analyses revealed that IPSNs and their matched invasive carcinomas shared the majority of somatic alterations, supporting a shared clonal origin for the 2 components. Activating KRAS mutations and biallelic inactivation of CDKN2A were detected in all cases. Recurrent mutations involved members of the SWI/SNF chromatin-remodeling complex and KMT2D. Additionally, FGFR1 and MYC amplifications were identified in 2 distinct cases (1 case each). Molecular alterations restricted to the invasive component involved mediators of the transforming growth factor-β signaling pathway. Transcriptomic profiling demonstrated a basal-like expression pattern in all IPSNs and squamous cell carcinomas, although in 2 cases, the matched pancreatic tubular/ductal adenocarcinoma shifted toward a classical transcriptomic subtype. In conclusion, through integrated histological assessment and multiregional molecular sequencing, we demonstrate that IPSN represents a bona fide precursor of invasive pancreatic cancer, a new addition to the intraductal neoplasms category. This study challenges the current paradigm that pancreatic squamous epithelium plays no role in the initiation of pancreatic carcinogenesis, providing the first evidence of its involvement in early tumorigenic processes and yielding immediate implications for pancreatic tumor classification and biological understanding.

Humans↗

PubMed1990

Molecular symmetry and arrangement of subunits in extracellular hemoglobin from Caenestheria inopinata.

The subunit structure of extracellular hemoglobin from the clam shrimp Caenestheria inopinata was studied using the method of cross-linking by bifunctional reagents followed by SDS/PAGE. Two phases were distinguished in the cross-linking by glutardialdehyde: a fast phase characterized by the appearance of two bands in electrophoresis corresponding to single polypeptide chains and cross-linked chain pairs, and a slow phase where five bands corresponding to even numbers, 2-10, of cross-linked polypeptide chains are observed. Theoretical curves for the distribution of protein among the various cross-linked species were calculated assuming allowed arrangements of ten identical subunits. Equally good descriptions of the cross-linking were provided by two models with dihedral symmetry: a ring arrangement with two types of alternating interactions and a two-layered eclipsed arrangement with one type of interaction between subunits from different layers and another between subunits within the same layer. A way out of the ambiguity was found by carrying out the fast phase of the cross-linking reaction with dimethyl-3,3'-dithiobispropionimidate.2HCl, a bifunctional reagent containing an S-S bond that can be cleaved by 2-mercaptoethanol, following up with glutardialdehyde in the slow phase. The observation in the presence of 2-mercaptoethanol of electrophoretic bands corresponding to trimeric and higher cross-linked polypeptide chain species rules out the alternating ring and confirms the two-layered eclipsed model. The arrangement of subunits found in this work from consecutive cross-linking can account satisfactorily for molecular profiles previously obtained from electron microscopy of Caenestheria hemoglobin.

Animals↗

PubMed2005

Neurodevelopment, neuroplasticity, and new genes for schizophrenia.

Schizophrenia is a complex, debilitating neuropsychiatric disorder. Epidemiological, clinical, neuropsychological, and neurophysiological studies have provided substantial evidence that abnormalities in brain development and ongoing neuroplasticity play important roles in the pathogenesis of the disorder. Complementing these clinical studies, a range of cytoarchitectural, morphometric, ultrastructural, immunochemical, and gene expression methods have been applied in investigations of postmortem brain tissues to characterize the cellular and molecular profile of putative developmental and plastic abnormalities in schizophrenia. While findings have been diverse and many are in need of replication, investigations focusing on higher cortical and limbic brain regions are increasingly demonstrating abnormalities in the structural and molecular integrity of the synaptic complex as well as glutamate-related receptors and signal transduction pathways that play critical roles in brain development, synaptogenesis, and synaptic plasticity. Most exciting have been recent associations of schizophrenia with specific genes, such as neuregulin-1, dysbindin-1, and AKT-1, which are vital to synaptic development, neurotransmission, and plasticity.

Humans↗

PubMed2004

Rapid and sensitive p53 alteration analysis in biopsies from lung cancer patients using a functional assay and a universal oligonucleotide array: a prospective study.

PURPOSE: Molecular profiling of alterations associated with lung cancer holds the promise to define clinical parameters such as response to treatment or survival. Because <5% of small cell lung cancers and <30% of non-small cell lung cancers are surgically resectable, molecular analysis will perforce rely on routinely available clinical samples such as biopsies. Identifying tumor mutations in such samples will require a sensitive and robust technology to overcome signal from excess amounts of normal DNA. EXPERIMENTAL DESIGN: p53 mutation status was assessed from the DNA and RNA of biopsies collected prospectively from 83 patients with lung cancer. Biopsies were obtained either by conventional bronchoscopy or computed tomography-guided percutaneous biopsy. Matched surgical specimens were available for 22 patients. Three assays were used: direct sequencing; a functional assay in yeast; and a newly developed PCR/ligase detection reaction/Universal DNA array assay. RESULTS: Using the functional assay, p53 mutation was found in 62% of biopsies and 64% of surgical specimens with a concordance of 80%. The sensitivity of the functional assay was determined to be 5%. Direct sequencing confirmed mutations in 92% of surgical specimens but in only 78% of biopsies. The DNA array confirmed 100% of mutations in both biopsies and surgical specimens. Using this newly developed DNA array, we demonstrate the feasibility of directly identifying p53 mutations in clinical samples containing <5% of tumor cells. CONCLUSIONS: The versatility and sensitivity of this new array assay should allow additional development of mutation profiling arrays that could be applied to biological samples with a low tumor cell content such as bronchial aspirates, bronchoalveolar lavage fluid, or serum.

Aged↗

PubMed2001

Molecular heterogeneity of oligodendrogliomas suggests alternative pathways in tumor progression.

OBJECTIVE: To identify different genetic molecular profiles in oligodendrogliomas and to evaluate their prognostic significance. METHODS: The main genetic alterations reported in glial tumors were investigated in 26 oligodendrogliomas (10 World Health Organization grade II and 16 World Health Organization grade III). Correlation between identified molecular changes and pathologic grade or clinical course was subsequently analyzed using univariate and multivariate statistical analyses. RESULTS: Loss of heterozygosity (LOH) on chromosome 1p, 19q, and 10; P16/CDKN2A homozygous deletion; EGFR (epidermal growth factor receptor) amplification; and TP53 and PTEN mutations were observed in 14 (54%), 15 (58%), 9 (35%), 7 (27%), 5 (19%), 1 (4%), and 0 cases. LOH 1p and 19q were tightly associated (p < 0.0001). A mutual exclusion was found between LOH 1p/19q and EGFR amplification (p = 0.01), P16/CDKN2A deletions (p = 0.001), or LOH on 10q (p = 0.03), suggesting the existence of distinct genetic subsets in oligodendrogliomas. On univariate analysis, age <50 years (p = 0.002) and LOH 1p (p = 0.01) were associated with a longer progression-free survival (PFS) whereas LOH 10q (p = 0.03) and EGFR amplification (p = 0.007) were associated with a worse PFS. In multivariate analyses, age <50 years (p = 0.001) and LOH 1p (p = 0.006) remained independent predictive factors for PFS. CONCLUSION: These results provide evidence for two alternative molecular pathways of progression in oligodendrogliomas. The first one is associated with loss of 1p and 19q and the second one with P16/CDKN2A deletion, 10q loss, and EGFR amplification. The findings confirm the value of loss of 1p as predictor of longer progression-free survival; in addition, the study demonstrates the unfavorable impact of 10q loss and EGFR amplification on the prognosis.

Adult↗

PubMed2002

Obligate roles for p16(Ink4a) and p19(Arf)-p53 in the suppression of murine pancreatic neoplasia.

Epithelial tumors of the pancreas exhibit a wide spectrum of histologies with varying propensities for metastasis and tissue invasion. The histogenic relationship among these tumor types is not well established; moreover, the specific role of genetic lesions in the progression of these malignancies is largely undefined. Transgenic mice with ectopic expression of transforming growth factor alpha (TGF-alpha) in the pancreatic acinar cells develop tubular metaplasia, a potential premalignant lesion of the pancreatic ductal epithelium. To evaluate the cooperative interactions between TGF-alpha and signature mutations in pancreatic tumor genesis and progression, TGFalpha transgenic mice were crossed onto Ink4a/Arf and/or p53 mutant backgrounds. These compound mutant mice developed a novel pancreatic neoplasm, serous cystadenoma (SCA), presenting as large epithelial tumors bearing conspicuous gross and histological resemblances to their human counterpart. TGFalpha animals heterozygous for both the Ink4a/Arf and the p53 mutation showed a dramatically increased incidence of SCA, indicating synergistic interaction of these alleles. Inactivation of p16(Ink4a) by loss of heterozygosity, intragenic mutation, or promoter hypermethylation was a common feature in these SCAs, and correspondingly, none of the tumors expressed wild-type p16(Ink4a). All tumors sustained loss of p53 or Arf, generally in a mutually exclusive fashion. The tumor incidence data and molecular profiles establish a pathogenic role for the dual inactivation of p16(Ink4a) and p19(Arf)-p53 in the development of SCA in mice, demonstrating that p16(Ink4a) is a murine tumor suppressor. This genetically defined model provides insights into the molecular pathogenesis of SCA and serves as a platform for dissection of cell-specific programs of epithelial tumor suppression.

Animals↗

PubMed1981

Erythrocruorin from the crustacean Caenestheria inopinata. Quaternary structure and arrangement of subunits.

The subunit structure of erythrocruorin from the crustacean Caenestheria inopinata was studied. The native protein was found to have a sedimentation coefficient of 12.0 S and a molecular weight, as determined by sedimentation equilibrium, of 302,000. Iron and heme determinations gave 0.346 and 3.98% corresponding to minimal molecular weights of 16,100 and 15,500, respectively. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis gave one band with mobility corresponding to a molecular weight of 30,000. The molecular weight of the polypeptide chain was determined to be 30,500 by sedimentation equilibrium in 6 M guanidine hydrochloride and 0.1 M 2-mercaptoethanol. Dissociation of the 12S molecule was observed at acidic and alkaline pH. A dissociation species of 2.7 S was isolated and its molecular weight determined to be 28,000 by sedimentation equilibrium. On a molecular weight basis, the native molecule is composed of ten 2.7S subunits, each of which consists of a single polypeptide chain carrying two hemes. We propose a model for the molecule composed of ten spheres, each representing a 2.7S subunit, arranged in two layers stacked in an eclipsed orientation, in five spheres of each layer occupying the vertices of a regular pentagon. Support for this arrangement is provided by a comparison of projections of the model with molecular profiles seen in the electron microscope.

Animals↗

PubMed2002

Nuclear factor kappaB-dependent gene expression profiling of Hodgkin's disease tumor cells, pathogenetic significance, and link to constitutive signal transducer and activator of transcription 5a activity.

Constitutive nuclear nuclear factor (NF)-kappaB activity is observed in a variety of hematopoietic and solid tumors. Given the distinctive role of constitutive NF-kappaB for Hodgkin and Reed-Sternberg (HRS) cell viability, we performed molecular profiling in two Hodgkin's disease (HD) cell lines to identify NF-kappaB target genes. We recognized 45 genes whose expression in both cell lines was regulated by NF-kappaB. The NF-kappaB-dependent gene profile comprises chemokines, cytokines, receptors, apoptotic regulators, intracellular signaling molecules, and transcription factors, the majority of which maintain a marker-like expression in HRS cells. Remarkably, we found 17 novel NF-kappaB target genes. Using chromatin immunoprecipitation we demonstrate that NF-kappaB is recruited directly to the promoters of several target genes, including signal transducer and activator of transcription (STAT)5a, interleukin-13, and CC chemokine receptor 7. Intriguingly, NF-kappaB positively regulates STAT5a expression and signaling pathways in HRS cells, and promotes its persistent activation. In fact, STAT5a overexpression was found in most tumor cells of tested patients with classical HD, indicating a critical role for HD. The gene profile underscores a central role of NF-kappaB in the pathogenesis of HD and potentially of other tumors with constitutive NF-kappaB activation.

Base Sequence↗

PubMed2005

[Molecular protocol for HER2/neu analysis in breast carcinoma].

BACKGROUND: The HER2/neu proto-oncogene is frequently over-expressed in breast cancer and serves as a biological target for trastuzumab therapy. However, there is no consensus regarding the technical aspects to be used to define HER2/neu status in clinical practice. METHODS: The present study was conducted to address this critical issue by prospectively analysing a large cohort of breast cancer patients (n = 222) and using a variety of methods. To define HER2/neu expression, detection of its encoded protein (p185) was performed by comparative immunohistochemical (IHC) analysis using two mouse monoclonal antibodies (mAb CB11 and mAb TAB250). To assess HER2/neu gene amplification, fluorescent in situ hybridisation (FISH) assays with gene-specific probes were conducted. All procedures were applied to de-paraffinised tissue sections of breast tumour samples. RESULTS: Results showed that mAb CB11 had increased sensitivity and specificity (62.5% and 93.4%, respectively) compared to mAb TAB250 (40% and 76.4%, respectively) in defining HER2/neu amplification. We conclude that HER2/neu measurement by IHC using mAb CB11 is an appropriate strategy which provides a high negative predictive value (95.5%) for HER2/neu amplification in cases with low or undetectable p185 expression. Conversely, mAb CB11 has a high positive predictive value (96.2%) for HER2/neu amplification in cases with p185 overexpression. However, cases with moderate p185 expression need to be considered as inconclusive. In such cases, it is necessary to use FISH measurement to evaluate HER2/neu amplification. It is also advisable to conduct FISH if there is discordance between p185 expression and the histopathology classification of the lesion, or molecular profile of the tumour. Finally, even though the false positive rate of IHC assay is <5%, the toxicity and cost of trastuzumab therapy suggest that FISH be used systematically prior to implementation of treatment. CONCLUSION: We suggest the use of a molecular protocol for HER2/neu analysis in this type of tumor.

Adenocarcinoma, Mucinous↗

PubMed2000

Homogeneity of Trypanosoma evansi isolates from domestic and sylvatic mammals from the Pantanal of Mato Grosso.

'Mal de Cadeiras' is a disease which causes great mortality in horses in the Pantanal Matogrossense region, Brazil. The agent of this disease is Trypanosoma evansi, a kinetoplastid flagellate which belongs to the Trypanosomatidae family, classified into the Salivarian section. Transmission occurs mechanically by haematophagous Diptera, mainly by Stomoxys sp. and Tabanus sp. and vampire bats. Outbreaks of Mal de Cadeiras in horses result in economic losses, thus limiting their use in cattle raising. Ten isolates of T. evansi recently derived from coati (Nasua nasua, Carnivora, Procyonidae), horses and dogs were compared, using schizodeme analyses from DNA digested by the restriction enzyme Hin fl. The results showed similar electrophoretic profiles for all isolates from wherever the host came. Homogeneity of isolates from domestic and sylvatic animals suggested two hypotheses: (1) the parasites circulated in only one transmission cycle;, and (2) independent cycles were not established in sufficient time to modify the molecular profiles of the isolates.

Animals↗

PubMed2005

Vascular cell signaling by membrane estrogen receptors.

There is substantial interest in the effects of estrogen on the vascular wall, due to the marked gender difference in the incidence of clinically apparent coronary heart disease (CHD), when comparing premenopausal women with age-matched males. Recent randomized clinical trials unexpectedly failed to demonstrate a hormone replacement therapy (HRT) benefit for CHD secondary or primary prevention in postmenopausal women. There are several possible explanations for these findings, which have created a conundrum in light of the numerous potentially beneficial vascular effects of estrogen demonstrated at the cellular, molecular, and even animal model level. Clinical trials are ongoing, and the dissection of molecular pathways continues. Although estrogen receptors (ERs) are traditionally defined as ligand-activated transcriptional activators or repressors, a phenomenon certainly involved in some of estrogen's beneficial effects on vascular cells, we and others have recently demonstrated the presence of membrane-associated ERs in endothelial cells (EC), and that engagement of this subset of receptors may also contribute to the favorable molecular profile of the endothelium. In this review, we describe evidence for membrane-localized ERs in EC. We discuss features of their membrane targeting, and how they may differ from classical ERs. We also describe the rapid assembly of a membrane-associated molecular complex, comprised of ER, c-Src and the regulatory unit of phosphatidylinositol 3-kinase (PI3K), p85, in response to estrogen. Finally, we describe how this complex triggers sequential enzyme activation, involving endothelial nitric oxide synthase (eNOS), and consequent enhanced basal release of NO, a key modulator of vascular tone and 'healthy' blood vessels.

Animals↗

PubMed2002

Chemoprevention of colorectal carcinogenesis.

The field of cancer prevention is advancing rapidly, largely owing to post-genomic technology that has revolutionized our ability to identify and characterize molecular profiles for cancer. Advances in colorectal cancer screening (e.g., endoscopy, fecal occult blood testing, and mutational analysis) have made the detection and eradication of preinvasive neoplastic lesions the standard of care. Basic and translational sciences are building on these advances, and continue to expose molecular hallmarks of carcinogenesis that can be exploited as targets for molecularly targeted preventive interventions (i.e., chemoprevention). These targets will help identify more effective and better tolerated preventive agents. Carcinogenesis is now recognized as a disease in itself and has become the target of an ever-expanding array of preventive interventions.

Adenomatous Polyposis Coli↗

PubMed2005

Discovery and analysis of pancreatic adenocarcinoma genes using cDNA microarrays.

AIM: To study the pathogenetic processes and the role of gene expression by microarray analyses in expediting our understanding of the molecular pathophysiology of pancreatic adenocarcinoma, and to identify the novel cancer-associated genes. METHODS: Nine histologically defined pancreatic head adenocarcinoma specimens associated with clinical data were studied. Total RNA and mRNA were isolated and labeled by reverse transcription reaction with Cy5 and Cy3 for cDNA probe. The cDNA microarrays that represent a set of 4 096 human genes were hybridized with labeled cDNA probe and screened for molecular profiling analyses. RESULTS: Using this methodology, 184 genes were screened out for differences in gene expression level after nine couples of hybridizations. Of the 184 genes, 87 were upregulated and 97 downregulated, including 11 novel human genes. In pancreatic adenocarcinoma tissue, several invasion and metastasis related genes showed their high expression levels, suggesting that poor prognosis of pancreatic adenocarcinoma might have a solid molecular biological basis. CONCLUSION: The application of cDNA microarray technique for analysis of gene expression patterns is a powerful strategy to identify novel cancer-associated genes, and to rapidly explore their role in clinical pancreatic adenocarcinoma. Microarray profiles provide us new insights into the carcinogenesis and invasive process of pancreatic adenocarcinoma. Our results suggest that a highly organized and structured process of tumor invasion exists in the pancreas.

Adenocarcinoma↗

PubMed2026

Age-stratified mutation patterns in early-onset colorectal cancer reveal distinct molecular features and therapeutic implications.

BACKGROUND: Colorectal cancer (CRC) is increasingly diagnosed in younger adults, with evidence that early-onset cases (age <50 years) differ in the spectrum of prevalent gene mutations compared with older individuals. To evaluate how these age-related differences may inform testing guidelines and therapeutic development, we examined mutation rates of the most prevalent gene mutations across four age-stratified cohorts. PATIENTS AND METHODS: Clinicogenomic data were obtained from Memorial Sloan Kettering Center for Harmonized Onco-genomic Research Dataset and China Pan-Cancer cohorts available in cBioPortal. A total of 6762 samples were analyzed. Mutation frequencies for a comprehensive panel of the 100 most prevalent CRC genes were compared across four age groups: 18-29 (n = 79), 30-39 (n = 402), 40-49 (n = 1064), and ≥50 (n = 5217) using chi-square analysis. False discovery rate (FDR) correction for multiple comparisons was carried out using Benjamini-Hochberg procedure. RESULTS: Statistically significant variation in mutation frequency across age groups was seen in 22 key genes. APC mutations increased with age and were seen in 49.4% of patients in the 18-29 group, 69.7% in 30-39, 73.3% in 40-49, and 75.25% of patients ≥50 (P < 0.001, FDR < 0.001). The oldest cohort was more than three times more likely to have an APC mutation than the youngest [odds ratio (OR) = 3.74, 95% confidence interval (CI) 2.44-5.74, P < 0.001]. In contrast, SMAD4 mutations were twice as common in the youngest age group at 31.6% compared with those over 40, with a prevalence of 17.29% in patients 40-49, and 18.84% in patients over 50 (OR = 2.03, 95% CI 1.26-3.27, P < 0.001, FDR < 0.001). POLE mutations peaked in the 30-39 age group with a prevalence of 10.7% compared with 6.3% in patients aged 18-29, 4.9% in patients aged 40-49, and 5.9% in patients aged ≥50 (P < 0.001, FDR < 0.001). Individuals in the 30-39 group were nearly twice as likely to carry a POLE mutation compared with those over 40 (OR = 1.96, 95% CI 1.41-2.74, P < 0.001). CONCLUSIONS: Differences in mutations of key genes including a lower prevalence of APC mutations and increased SMAD4 mutations in younger individuals provides further supporting evidence that early-onset CRC may represent a distinct biological subtype of CRC. Enrichment of POLE mutations in younger patients highlights the importance of expanded molecular profiling in early-onset CRC, which could help identify patients most likely to benefit from immunotherapy and advance personalized treatment strategies in CRC. Together, these findings reinforce the need to approach early-onset CRC as a distinct biological entity and ensure that appropriate molecular assays are incorporated to guide care.

APC↗

PubMed2026

Molecular Diagnostics for WHO Priority Bacterial Pathogens: A Bibliometric Mapping of Diagnostic Platforms, Resistance Markers, and Antimicrobial Resistance Research Trends.

Antimicrobial resistance (AMR) constrains effective treatment and carries implications for infection control, surveillance, and public health. The World Health Organization (WHO) priority bacterial pathogen framework has intensified the need for diagnostic innovation by redefining research priorities around organisms combining high disease burden with complex resistance profiles. Molecular diagnostics have accordingly moved beyond culture-based workflows, integrating rapid pathogen identification, resistance-marker detection, genomic surveillance, and clinical decision support. The present study conducted a bibliometric mapping of the literature on WHO priority pathogens. Rather than addressing resistance at a general level or a single pathogen or technology, it integrates priority pathogens, molecular platforms, and resistance markers within a single framework, tracing their joint thematic and temporal evolution along an explicit pathogen-platform-marker axis. Scopus-indexed articles and reviews (2000-2025) were retrieved, yielding 1746 publications after screening adapted from the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Analyses used Bibliometrix/Biblioshiny, R, and VOSviewer. The literature expanded markedly after 2018, led by China and the United States. Methicillin-resistant Staphylococcus aureus (MRSA), Mycobacterium tuberculosis, Enterococcus faecium, and the Enterobacterales-carbapenemase axis constituted the principal thematic cores, whereas conventional polymerase chain reaction (PCR)/nucleic acid amplification testing (NAAT) and whole-genome sequencing were the dominant platforms. Overall, the field has evolved from pathogen detection into an AMR-centered translational domain encompassing resistance prediction, genomic epidemiology, surveillance, and clinical decision support. Diagnostic development, stewardship, and surveillance depend on hybrid workflows coupling rapid marker-targeted assays with genome-based characterization, delivering actionable resistance within clinically meaningful timeframes, and extending coverage to underrepresented pathogens and platforms.

Humans↗

PubMed2006

GATHER: a systems approach to interpreting genomic signatures.

MOTIVATION: Understanding the full meaning of the biology captured in molecular profiles, within the context of the entire biological system, cannot be achieved with a simple examination of the individual genes in the signature. To facilitate such an understanding, we have developed GATHER, a tool that integrates various forms of available data to elucidate biological context within molecular signatures produced from high-throughput post-genomic assays. RESULTS: Analyzing the Rb/E2F tumor suppressor pathway, we show that GATHER identifies critical features of the pathway. We further show that GATHER identifies common biology in a series of otherwise unrelated gene expression signatures that each predict breast cancer outcome. We quantify the performance of GATHER and find that it successfully predicts 90% of the functions over a broad range of gene groups. We believe that GATHER provides an essential tool for extracting the full value from molecular signatures generated from genome-scale analyses. AVAILABILITY: GATHER is available at http://gather.genome.duke.edu/

Algorithms↗

PubMed2006

Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development.

BACKGROUND: The histopathologic heterogeneity of lung cancer remains a significant confounding factor in its diagnosis and prognosis-spurring numerous recent efforts to find a molecular classification of the disease that has clinical relevance. METHODS AND FINDINGS: Molecular profiles of tumors from 186 patients representing four different lung cancer subtypes (and 17 normal lung tissue samples) were compared with a mouse lung development model using principal component analysis in both temporal and genomic domains. An algorithm for the classification of lung cancers using a multi-scale developmental framework was developed. Kaplan-Meier survival analysis was conducted for lung adenocarcinoma patient subgroups identified via their developmental association. We found multi-scale genomic similarities between four human lung cancer subtypes and the developing mouse lung that are prognostically meaningful. Significant association was observed between the localization of human lung cancer cases along the principal mouse lung development trajectory and the corresponding patient survival rate at three distinct levels of classical histopathologic resolution: among different lung cancer subtypes, among patients within the adenocarcinoma subtype, and within the stage I adenocarcinoma subclass. The earlier the genomic association between a human tumor profile and the mouse lung development sequence, the poorer the patient's prognosis. Furthermore, decomposing this principal lung development trajectory identified a gene set that was significantly enriched for pyrimidine metabolism and cell-adhesion functions specific to lung development and oncogenesis. CONCLUSIONS: From a multi-scale disease modeling perspective, the molecular dynamics of murine lung development provide an effective framework that is not only data driven but also informed by the biology of development for elucidating the mechanisms of human lung cancer biology and its clinical outcome.

Adenocarcinoma↗

PubMedDate not supplied

Expression profiling of tumor necrosis factor alpha-induced apoptosis-associated genes in human solid tumor cell lines.

BACKGROUND: The induction of genes associated with cellular apoptosis by tumor necrosis factor-alpha (TNF-alpha) in human cancer cell line sof various tissue origins may characterize TNF-alpha responder cell lines/cancers. MATERIALS AND METHODS: Using quantitative real-time polymerase chain reaction (PCR), the comprehensive molecular profiling of genes downstream of the TNF-alpha receptor genes in 91 well-defined human cancer cell lines allowed us to elucidate relationships between TNF-alpha response and the genetic expression profiles of the target cell lines. RESULTS: Among the 52 genes tested, the above average expression of Akt mRNA showed significant correlation with TNF-alpha-induced susceptibility to apoptosis. In addition, multidrug resistance protein 5 (MRP5) and tumor necrosis factor receptor type 1 (TNFR1) mRNA expressions also appear to be possible markers for responsiveness to TNF-alpha. CONCLUSION: These results provide a preliminary basis for the screening for genetic markers that may help to predict a favorable therapeutic outcome, and also to identify patients who may benefit from cytokine therapy.

Apoptosis↗