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Gastroenteropancreatic Neuroendocrine Carcinoma (GEP-NEC): An Aggressive Disease Course and Limitations for Personalized Oncology.

Neuroendocrine carcinoma (NEC) is a rare, aggressive malignancy with limited treatment options and poor prognosis. We report a male patient diagnosed with a gastroenteropancreatic (GEP)-NEC with synchronous liver metastasis at the time of surgery who underwent a radical resection attempt. Despite radical-intent surgery followed by adjuvant carboplatin/etoposide, early recurrence developed with progression through multiple subsequent chemotherapy lines. During the treatment process, genetic profiling was performed twice to identify actionable genomic targets, with inclusion in the national IMPRESS study as a last resort. Comprehensive genomic profiling revealed TP53 mutation and RB1 loss but no actionable alterations. A patient-derived organoid (PDO) was successfully established from resected tumor tissue and retained key neuroendocrine and proliferative features, with partial genomic concordance to the primary tumor. Differences between the primary and subsequent PDO in variant allele frequencies suggest clonal selection during culture. Exploratory metabolomic profiling of tryptophan pathway metabolites in patient serum and PDO-culture media indicated tumor-associated metabolic alterations. We present clinical and translational efforts in difficult-to-treat NEC, illustrating both the translational challenges and the potential role of PDOs in advancing personalized treatment strategies for a cancer with very limited treatment options.

Gastroenteropancreatic neuroendocrine carcinoma↗

A novel microarray strategy for detecting genes and pathways in microbes with unsequenced genomes.

Expression profile analysis of genes provides valuable information concerning the genetic response of cells to stimuli. We describe an adaptation of this technology that can be used to probe for the expression of specific families of genes in microbial species. In our method a combination of sets of oligonucleotide probes representing fingerprint sequences specific to protein families is used to identify the presence and expression levels of family homologs in a microbial cell. We demonstrate computationally, using exemplars, that when the cDNA complement from an organism is sequentially screened against a set of specific motif oligonucleotides, statistically significant information can be obtained concerning the expression of the corresponding genes. This method can be used to identify specific genes and pathways simultaneously in several organisms of interest even in the absence of sequence information from the organisms.

Computational Biology↗

VAMP: visualization and analysis of array-CGH, transcriptome and other molecular profiles.

MOTIVATION: Microarray-based CGH (Comparative Genomic Hybridization), transcriptome arrays and other large-scale genomic technologies are now routinely used to generate a vast amount of genomic profiles. Exploratory analysis of this data is crucial in helping to understand the data and to help form biological hypotheses. This step requires visualization of the data in a meaningful way to visualize the results and to perform first level analyses. RESULTS: We have developed a graphical user interface for visualization and first level analysis of molecular profiles. It is currently in use at the Institut Curie for cancer research projects involving CGH arrays, transcriptome arrays, SNP (single nucleotide polymorphism) arrays, loss of heterozygosity results (LOH), and Chromatin ImmunoPrecipitation arrays (ChIP chips). The interface offers the possibility of studying these different types of information in a consistent way. Several views are proposed, such as the classical CGH karyotype view or genome-wide multi-tumor comparison. Many functionalities for analyzing CGH data are provided by the interface, including looking for recurrent regions of alterations, confrontation to transcriptome data or clinical information, and clustering. Our tool consists of PHP scripts and of an applet written in Java. It can be run on public datasets at http://bioinfo.curie.fr/vamp AVAILABILITY: The VAMP software (Visualization and Analysis of array-CGH,transcriptome and other Molecular Profiles) is available upon request. It can be tested on public datasets at http://bioinfo.curie.fr/vamp. The documentation is available at http://bioinfo.curie.fr/vamp/doc.

Algorithms↗

Clinicopathological and genetic analysis of primary intraosseous carcinoma not otherwise specified (PIOC NOS).

BACKGROUND: Primary intraosseous carcinoma not otherwise specified (PIOC NOS) is an extremely rare jawbone cancer, accounting for approximately 1-2% of all oral cancers. Considering its rarity, no established standard treatment exists for postoperative recurrence or metastasis. This study aimed to analyse the clinical manifestations of this disease and identify novel genomic abnormalities to aid identification of potential treatment strategies. METHODS: We examined the clinical information of 14 PIOC NOS cases treated at our institution in recent years and compared it with previous reports. Genomic analysis was conducted on seven formalin-fixed paraffin-embedded surgical specimens, assessing 523 DNA and 55 RNA cancer-related genes using next-generation sequencing. RESULTS: Our findings, along with previous literature, revealed the posterior mandible as the primary site in most cases, though this was rarely identified at the time of initial diagnosis. Recurrence within two years of surgery was common. Hotspot mutations in PIK3CA were observed in 60% of cases. Additionally, one patient had high TMB status. CONCLUSIONS: Given the challenges in diagnosis and the potential for rapid recurrence or metastasis, early detection is crucial. Comprehensive genomic profiling is highly desirable, as genomic analysis may direct the development of targeted therapeutic agents to treat relapse.

Humans↗

[Medical applications of genome discovery].

The discovery of the complete base sequence of human genome unveils several perspectives to understand human diseases and develop new therapies. Human genome contains approximately 39,000 genes of which 26,000 code specific proteins that have been identified. There are approximately 1,500 diseases with identified molecular disturbances. Genes can modify signs and symptoms of common diseases. Thus, there are no pure monogenic diseases. Chronic diseases of adults are complex and dependent on multiple factors. Several genes that predispose to chronic degenerative diseases have been identified. This is revealing the complex nature and the interaction of these ailments with the environment. The discovery of bacterial and viral genomic sequences will allow the manufacturing of new vaccines and specific molecular antimicrobials. The new pharmacogenomics will devise treatments for each subject according to her specific genomic profile. The new applications of genomic technology is creating new paradigms in biomedical research such as functional genomics, proteonomics, epigenetic regulation. Gene diagnosis and therapy will considerably improve the future of medicine.

Genetics, Medical↗

High resolution analysis of non-small cell lung cancer cell lines by whole genome tiling path array CGH.

Chromosomal regions harboring tumor suppressors and oncogenes are often deleted or amplified. Array comparative genomic hybridization detects segmental DNA copy number alterations in tumor DNA relative to a normal control. The recent development of a bacterial artificial chromosome array, which spans the human genome in a tiling path manner with >32,000 clones, has facilitated whole genome profiling at an unprecedented resolution. Using this technology, we comprehensively describe and compare the genomes of 28 commonly used non-small cell lung carcinoma (NSCLC) cell models, derived from 18 adenocarcinomas (AC), 9 squamous cell carcinomas and 1 large cell carcinoma. Analysis at such resolution not only provided a detailed genomic alteration template for each of these model cell lines, but revealed novel regions of frequent duplication and deletion. Significantly, a detailed analysis of chromosome 7 identified 6 distinct regions of alterations across this chromosome, implicating the presence of multiple novel oncogene loci on this chromosome. As well, a comparison between the squamous and AC cells revealed alterations common to both subtypes, such as the loss of 3p and gain of 5p, in addition to multiple hotspots more frequently associated with only 1 subtype. Interestingly, chromosome 3q, which is known to be amplified in both subtypes, showed 2 distinct regions of alteration, 1 frequently altered in squamous and 1 more frequently altered in AC. In summary, our data demonstrate the unique information generated by high resolution analysis of NSCLC genomes and uncover the presence of genetic alterations prevalent in the different NSCLC subtypes.

Carcinoma, Non-Small-Cell Lung↗

Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity.

MOTIVATION: One of the major features of genomic DNA sequences, distinguishing them from texts in most spoken or artificial languages, is their high repetitiveness. Variation in the repetitiveness of genomic texts reflects the presence and density of different biologically important messages. Thus, deviation from an expected number of repeats in both directions indicates a possible presence of a biological signal. Linguistic complexity corresponds to repetitiveness of a genomic text, and potential regulatory sites may be discovered through construction of typical patterns of complexity distribution. RESULTS: We developed software for fast calculation of linguistic sequence complexity of DNA sequences. Our program utilizes suffix trees to compute the number of subwords present in genomic sequences, thereby allowing calculation of linguistic complexity in time linear in genome size. The measure of linguistic complexity was applied to the complete genome of Haemophilus influenzae. Maps of complexity along the entire genome were obtained using sliding windows of 40, 100, and 2000 nucleotides. This approach provided an efficient way to detect simple sequence repeats in this genome. In addition, local profiles of complexity distribution around the starts of translation were constructed for 21 complete prokaryotic genomes. We hypothesize that complexity profiles correspond to evolutionary relationships between organisms. We found principal differences in profiles of the GC-rich and other (non-GC-rich) genomes. We also found characteristic differences in profiles of AT genomes, which probably reflect individual species variations in translational regulation. AVAILABILITY: The program is available upon request from Alexander Bolshoy or at http://csweb.haifa.ac.il/library/#complex.

Algorithms↗

Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways.

An expressed sequence tag-based microarray was used to profile genome expression underlying light control of Arabidopsis development. Qualitatively similar gene expression profiles were observed among seedlings grown in different light qualities, including far-red, red, and blue light, which are mediated primarily by phytochrome A, phytochrome B, and the cryptochromes, respectively. Furthermore, light/dark transitions also triggered similar differential genome expression profiles. Most light treatments also resulted in distinct expression profiles in small fractions of the expressed sequence tags examined. The similarly regulated genes in all light conditions were estimated to account for approximately one-third of the genome, with three-fifths upregulated and two-fifths downregulated by light. Analysis of those light-regulated genes revealed more than 26 cellular pathways that are regulated coordinately by light. Thus, light controls Arabidopsis development through coordinately regulating metabolic and regulatory pathways.

Arabidopsis↗

Group C rotaviruses in humans.

Atypical rotaviruses obtained from human feces from Australia, Brazil, and the United Kingdom were shown by a combination of techniques--immunoelectron microscopy, immunofluorescence, genome profile analysis, terminal fingerprint analysis of genome segments, and dot-blot hybridization--to be related to group C porcine rotaviruses. The prevalence of antibody to group C rotaviruses was found to be low in human sera and immunoglobulin pools from six countries. No signs of infection were obtained when one of the human viruses was inoculated into gnotobiotic piglets. We conclude that the atypical human viruses are the first examples of group C rotaviruses in humans.

Animals↗

Functional genomic analysis of cancer metastasis: biologic insights and clinical implications.

Metastasis, the spread of cancer from primary tumors to distant vital organs, has devastating consequences. Lack of effective tools to study this complex problem has hindered the development of accurate prognostic methods and effective treatments for metastatic cancer. In the postgenomic era, the application of genomic profiling methods to the analysis of clinical metastasis samples and animal metastasis models has revolutionized the field of metastasis research. This article reviews recent breakthroughs in the functional genomic analysis of metastasis. In addition, its impacts on our understanding of the molecular basis of metastasis and on clinical practice are discussed.

Animals↗

Balanced-PCR amplification allows unbiased identification of genomic copy changes in minute cell and tissue samples.

Analysis of genomic DNA derived from cells and fresh or fixed tissues often requires whole genome amplification prior to microarray screening. Technical hurdles to this process are the introduction of amplification bias and/or the inhibitory effects of formalin fixation on DNA amplification. Here we demonstrate a balanced-PCR procedure that allows unbiased amplification of genomic DNA from fresh or modestly degraded paraffin-embedded DNA samples. Following digestion and ligation of a target and a control genome with distinct linkers, the two are mixed and amplified in a single PCR, thereby avoiding biases associated with PCR saturation and impurities. We demonstrate genome-wide retention of allelic differences following balanced-PCR amplification of DNA from breast cancer and normal human cells and genomic profiling by array-CGH (cDNA arrays, 100 kb resolution) and by real-time PCR (single gene resolution). Comparison of balanced-PCR with multiple displacement amplification (MDA) demonstrates equivalent performance between the two when intact genomic DNA is used. When DNA from paraffin-embedded samples is used, balanced PCR overcomes problems associated with modest DNA degradation and produces unbiased amplification whereas MDA does not. Balanced-PCR allows amplification and recovery of modestly degraded genomic DNA for subsequent retrospective analysis of human tumors with known outcomes.

Artifacts↗

Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and Arabidopsis.

Genome-wide 70-mer oligonucleotide microarrays of rice (Oryza sativa) and Arabidopsis thaliana were used to profile genome expression changes during light-regulated seedling development. We estimate that the expression of approximately 20% of the genome in both rice and Arabidopsis seedlings is regulated by white light. Qualitatively similar expression profiles from seedlings grown under different light qualities were observed in both species; however, a quantitatively weaker effect on genome expression was observed in rice. Most metabolic pathways exhibited qualitatively similar light regulation in both species with a few species-specific differences. Global comparison of expression profiles between rice and Arabidopsis reciprocal best-matched gene pairs revealed a higher correlation of genome expression patterns in constant light than in darkness, suggesting that the genome expression profile of photomorphogenesis is more conserved. Transcription factor gene expression under constant light exposure was poorly conserved between the two species, implying a faster-evolving rate of transcription factor gene expression in light-grown plants. Organ-specific expression profiles during seedling photomorphogenesis provide genome-level evidence for divergent light effects in different higher plant organs. Finally, overrepresentation of specific promoter motifs in root- and leaf-specific light-regulated genes in both species suggests that these cis-elements are important for gene expression responses to light.

Arabidopsis↗

Identification of two subgroups of mantle cell leukemia with distinct clinical and biological features.

INTRODUCTION: Mantle cell leukemia (MCLeu) has been considered as a leukemic form of mantle cell lymphoma (MCL). However, the presence of certain features rarely observed in MCL, such as transformation to prolymphocytic leukemia (PLL) or indolent clinical course, suggests that MCLeu may represent a distinct disorder. METHODS: Seven cases of MCLeu with t(11;14)(q13;q32) and BCL1-IGH gene rearrangement were ascertained among 140 newly diagnosed chronic B-cell lymphoproliferative disorders with leukemic expression. Comparative genomic hybridization, FISH for specific gene loci, and immunological studies were preformed in them. RESULTS: In comparison with CLL, MCLeu cases had low immunological scores < or =2 with respect to B-CLL (P<0.0001). Expression of CD38 was absent in 43% of MCLeu and in 44% of B-CLL. Comparative genomic hybridization analysis identified genomic imbalances in 86% of MCLeu with a similar pattern than in MCL: gains of 3q, 8q involving MYC gene and 15q, and losses of 6q, 9p, 13q and 17p affecting P53 gene. Differently from MCL and CLL, genomic loss of 8p was frequently detected in MCLeu (83%). Although clinical presentation of MCLeu was indistinguishable from CLL, all patients but one had disease progression within three years. According to the immunologic and genomic profiles, two distinct subgroups of MCLeu were defined: one related to PLL, showing CD38-, deletion of P53, and MYC amplification and another which corresponds to a leukemic form of classical MCL, presenting with CD38+ and normal P53 and MYC status. CONCLUSION: MCLeu and MCL are closely related disorders, as they show similar genomic and molecular patterns. However, the deletion of the short arm of chromosome 8 may represent a specific marker for MCLeu. Two distinct subgroups of MCLeu may also be distinguished according to the immunologic and genomic cell profiles.

ADP-ribosyl Cyclase↗

Ethanol potentiates HIV-1 gp120-induced apoptosis in human neurons via both the death receptor and NMDA receptor pathways.

Neuronal loss is a hallmark of AIDS dementia syndromes. Human immunodeficiency virus type I (HIV-1)-specific proteins may induce neuronal apoptosis, but the signal transduction of HIV-1 gp120-induced, direct neuronal apoptosis remains unclear. Ethanol (EtOH) is considered to be an environmental co-factor in AIDS development. However, whether EtOH abuse in patients with AIDS increases neuronal dysfunction is still uncertain. Using pure, differentiated, and post-mitotic NT2.N-derived human neurons, we investigated the mechanisms of HIV-1 and/or EtOH-related direct neuronal injury and the molecular interactions between HIV-1-specific proteins and EtOH. It was demonstrated that NT2.N neurons were susceptible to HIV-1 Bal (R5-tropic strain) gp120-induced direct cell death. Of importance, EtOH induced cell death in human neurons in a clinically-relevant dose range and EtOH strongly potentiated HIV-1 gp120-induced neuronal injury at low and moderate concentrations. Furthermore, this potentiation of neurotoxicity could be blocked by N-methyl-D-aspartate (NMDA) receptor subunit 2B (NR2B) antagonists. We analyzed human genomic profiles in these human neurons, using Affymetrix genomics technology, to elucidate the apoptotic pathways involved in HIV-1- and EtOH-related neurodegeneration. Our findings indicated significant over-expression of selected apoptosis functional genes. Significant up-regulation of TRAF5 gene expression may play an essential role in triggering potentiation by EtOH of HIV-1 gp120-induced neuronal apoptosis at early stages of interaction. These studies suggested that two primary apoptotic pathways, death receptor (extrinsic) and NMDA receptor (intrinsic)-related programmed cell-death pathways, are both involved in the potentiation by EtOH of HIV-1 gp120-induced direct human neuronal death. Thus, these data suggest rationally-designed, molecular targets for potential anti-HIV-1 neuroprotection.

AIDS Dementia Complex↗

Genomic analysis of prostate carcinoma specimens obtained via ultrasound-guided needle biopsy may be of use in preoperative decision-making.

BACKGROUND: The widespread use of prostate-specific antigen (PSA) testing to screen for prostate carcinoma has led to significant overdiagnosis, due to the frequent detection of indolent malignancies on PSA screening. The detection of abnormal PSA levels typically is followed by ultrasound-guided needle biopsy. Therefore, in an effort to identify genetic markers that augment the information provided by standard histopathologic classification, the authors tested the feasibility of using these minute biopsy samples for genomic profiling via chromosome banding analysis and comparative genomic hybridization (CGH). METHODS: Ultrasound-guided needle biopsy specimens obtained preoperatively from 35 patients with prostate carcinoma were analyzed via chromosome banding analysis (after short-term culturing) and CGH. The findings of these analyses then were analyzed for potential correlations with clinicopathologic parameters. RESULTS: Chromosome banding analysis and CGH were possible in 34 and 33 of the 35 study specimens, respectively. Combined analysis revealed aberrations in 69% of all samples investigated. Copy number losses occurred most commonly at 8p (58% of all abnormal specimens), 16q (42%), and 13q (37%), whereas the only gains detected in more than 1 specimen were those that occurred at 8q (37%). Genomic imbalances and losses at 16q were significantly associated with more poorly differentiated subtypes of prostate carcinoma (P = 0.048 and P = 0.019, respectively), whereas gains at 8q and losses at 16q were significantly correlated with clinically advanced disease (P = 0.048 for the finding of a gain at 8q together with a loss at 16q; P = 0.01 for the finding of either aberration alone). CONCLUSIONS: The authors conclude that genomic analysis of suspected prostate carcinoma specimens obtained via ultrasound-guided needle biopsy is feasible. Thus, it may be possible to use genetic markers to obtain diagnostic and/or prognostic information that is useful in the making of preoperative decisions regarding prostate carcinoma management.

Aged↗

Array-based binary analysis for bacterial typing.

An allele-specific oligonucleotide microarray was developed for rapid typing of pathogens based on analysis of genomic variations. Using a panel of Escherichia coli strains as a model system, selected loci were sequenced to uncover differences, such as single- or multiple-nucleotide polymorphisms as well as insertion/deletions (indels). While typical genomic profiling experiments employ specific sequences targeted to genomic DNA unique to a single strain or virulent gene, the present array is designed to type bacteria based on a patterned signature response across multiple loci. In the signature concept, all strains are interrogated by hybridizing their amplified DNA to an array containing multiple probe sequences. Allele-specific oligonucleotide probe sequences targeting each of these variable regions were synthesized and included in a custom fiber-optic array. For each locus, a set of specific probe sequences is selected, such that hybridization gives a binary signal/no signal response to each of the probes. Using this strategy for multiple loci, many pathogens or microorganisms could be classified using a limited number of probes. Because of the advantages of the fiber-optic array platform over other array formats, including sensitivity and speed, the platform described in this paper is capable of supporting a high-throughput diagnostic strategy.

Bacterial Typing Techniques↗

Analysis of genomic traits of oral and laryngeal cancer: A comparative study.

Oral and laryngeal cancers exhibit overlapping clinical features but distinct genomic profiles. In a study of 60 Head and neck squamous cell carcinomas(HNSCC) cases (30 OSCC, 30 LSCC), NGS revealed TP53 mutations in 70% of oral squamous cell carcinoma (OSCC) and 83% of laryngeal squamous cell carcinoma (LSCC). CDKN2A alterations were more common in OSCC (40%) than LSCC (20%), while PIK3CA mutations were higher in LSCC (30%). NOTCH1 mutations were more frequent in OSCC (27%) than LSCC (10%). Pathway analysis showed disruptions in p53 and PI3K-Akt, with stronger enrichment in LSCC (ES: 3.42). The results suggest site-specific tumor biology influencing therapeutic targets. Molecular profiling is crucial for precision treatment in head and neck cancers.

Oral cancer↗

Operomics: integrated genomic and proteomic profiling of cells and tissues.

In the post-genome era, technologies are becoming available that allow the profiling of tissues and cell populations at multiple levels including genomic (DNA and RNA), proteomic (proteins and peptides) and post-proteomic (eg metabolomic). Operomics refers to the molecular analysis of tissues and cells at the three levels that are connected through the coding process - namely, DNA, RNA and protein. The premise is that no one level or type of analysis fully captures gene expression and that functional changes at the proteome level cannot be simply predicted from analyses at the DNA or RNA levels. An important determinant that weakens a direct link between RNA and protein levels is translational control that differentially regulates mRNA translation. In this paper, the approaches for genomic and proteomic profiling and the contribution of translational control are reviewed.

DNA Methylation↗