Academic literature on the topic 'Centre for Biodiscovery'

Biodiscovery from microbial resources can be defined as the exploration of microbial metabolic products to detect, identify and evaluate their potential for medicinal, agricultural and biotechnological operations. Microbial resource centres house microbial compounds produced under different physical and nutritional parameters to maximise the production of metabolites and are subsequently tested in different bioassays to define targeted activity.

A new microbiology support program for Australian microbial resources centres is essential to take full advantage of the exciting information and biological materials emerging from molecular studies of microbiomes. At a time when taxonomic capacity is in decline, culture collections, with the appropriate level of infrastructure support and funding, are well positioned to enhance the outcomes of microbiome research. The importance of microbial biodiversity and its contribution to life on earth have never been more appreciated in the history of science than now. This appreciation came initially through the systematic study of microbial cultures, their ecological interactions, evolution and genetics. But now in the genomics era, uncultured microorganisms and whole microbial biomes are increasingly being studied using advanced DNA sequencing and bioinformatic techniques bringing greater insight into complex microbial communities, revealing interactions between microbes and the host affecting health and wellbeing. However, it should be remembered that the inference of identity and interpretation of functions of members of these uncultured communities relies heavily on knowledge gained from the study of cultured microorganisms. Advances will be greatly enhanced by bringing novel, and other significant, species in these environments into culture for laboratory study and accession into collections for future biodiscovery.

Abstract Abstract 3123 Although cure rates are high for pediatric Burkitt lymphoma (BL), a subset of patients relapses and succumbs to the disease. BL is characterized by translocation of the MYC gene with an immunoglobulin gene, but secondary changes including gain of 1q, gain of 13q, loss of 13q, loss of 17p, and others have been described by both conventional cytogenetic and oligo array CGH approaches. Secondary changes may contribute to the clinical heterogeneity of BL as evidenced by the fact that loss of 13q is associated with a worse prognosis in pediatric BL (Poirel et al., Leukemia 23:323, 2009). However, high resolution, genome-wide copy number analysis has not yet been reported in pediatric BL. The objective of this study was to identify copy number alterations (CNAs) in pediatric BL using a genome-wide approach, and to examine the relationship between CNAs and clinical parameters including outcome. After institutional review board approval, we identified 30 pediatric BL patients treated at Primary Children's Medical Center (n=25, Salt Lake City, UT) and Penn State Hershey Medical Center (n=5, Hershey, PA) with available formalin-fixed, paraffin-embedded (FFPE) diagnostic biopsy specimens. Age, site, and gender data were available for all specimens, and 22/24 of the Utah patients were treated according to the COG 5961 protocol with full clinical information and follow-up available. DNA was isolated from FFPE biopsies containing at least 80% tumor. In addition, germline DNA was isolated from negative staging bone marrow clot sections on Utah patients (n=25) to serve as a pooled normal reference and to provide germline copy number variation data on individual patients. Tumor and paired normal DNA was submitted for Molecular Inversion Probe (MIP) assay (330K Cancer Panel, Affymetrix, Santa Clara, CA). The Nexus Copy Number (BioDiscovery, El Segundo, CA) software package was used to analyze the MIP data with the following stringent call criteria: SNPRank segmentation, 5.0E-4 significance threshold, 1000 kb maximum contiguous probe spacing, minimum of 5 probes per segment, gains ≥ 2.7 copy number value, and loss ≤ 1.3 copy number value. Patients included 23 males and 7 females with a mean age of 8.0 years (range 2 – 18). At presentation, lactate dehydrogenase (LDH) levels ranged from 443 – 13851 U/L and uric acid levels ranged from 1.5 – 13 mg/dL. Patients were Murphy stage I (n=1), II (n=9), III (n=13), and IV (n=2). A total of three patients relapsed (one stage II patient and two stage III patients) and three died (the two stage III patients that relapsed and a different stage II patient who did not have a complete clinical response). 27 of the 30 tumor samples and 22/25 paired normals had adequate DNA for MIP analysis. The 3 tumor samples without adequate DNA were clinically similar to the others. We identified a total of 103 CNAs (defined as change seen in the same cytoband in 1 or more patients), which included 63 gains and 40 copy number losses. 23/27 cases (85%) had at least one gain or loss. We identified 21 recurrent CNAs (same cytoband affected in 2 or more patients), which included 14 gains and 7 losses. We found gains of 1q in 10/27 patients (37%), gains of 13q in 4/27 patients (15%) and losses of 17p in 3/27 patients (11%). Despite a relatively small sample size, deletion of 17p13 was significantly associated with relapse (p=0.041). To our knowledge, this is the first report of high-resolution genome-wide copy number analysis of pediatric BL. Furthermore, we show for the first time that FFPE archived materials can be used for high resolution gene copy number analysis in lymphomas. We identified CNAs in 85% of the pediatric BL cases, which include previously described changes of 1q, 13q, and 17p. Although sample size limited statistical power, deletion of the 17p13 locus was associated with relapse. We plan to extend these studies in a larger sample of patients to evaluate the potential prognostic significance of both the 17p13 locus deletion as well as additional recurrent CNAs. Disclosures: No relevant conflicts of interest to declare.

Abstract Abstract 289 Children with Down syndrome (DS) have an increased risk of developing acute lymphoblastic leukemia (ALL), and consistently demonstrate poorer outcomes due to higher rates of both relapse and treatment-related mortality compared to other children with ALL. The biology of ALL in DS is unique, with lower frequency of the classic cytogenetic lesions generally observed in childhood ALL, and increased frequency of JAK2 mutations and CRLF2 rearrangements, which are not clearly associated with adverse prognosis in DS-ALL. In order to improve risk stratification and identify potential novel therapeutic targets in this vulnerable population, we analyzed 90 DS-ALL cases for prognostically significant copy number abnormalities (CNAs) in a collaborative cohort from the Children's Oncology Group (n=30), St. Jude Children's Research Hospital (n=22), AIEOP (n=16), Texas Children's Cancer Center (n=10), UKALL 2003 (n=6) and an archival UK sample (n=1), and Utah's Primary Children's Medical Center (n=5). Copy number profiling was performed using 500K, 6.0, CytoScan HD, and OncoScan FFPE Express arrays (Affymetrix), and Human CNV370-Duo arrays (Illumina). Gene expression profiling was performed using U133 Plus2.0 arrays (Affymetrix). Copy number was analyzed with Nexus Copy Number (BioDiscovery, Inc.) and gene expression was analyzed with Partek Genomics Suite (Partek, Inc.) and Gene Set Enrichment Analysis (Broad Institute). Deletions of a focal region on 22q11.22 (present in 28.9% of cases, similar to the incidence previously reported in a non-DS cohort [Mangum et al, ASH 2011:741]), and deletions of IKZF1 (present in 20.0% of cases), were significantly associated with poor event-free survival (EFS) (5-year EFS was 88.6 ± 6.3% in wild-type cases [n=31], 68.1 ± 13.3% in cases with deletion of 22q11.22 only [n=15], and 60.0 ± 21.9% in those with deletion of IKZF1 only [n=5]; combined deletion [n=6] was associated with an even poorer EFS (33.3 ± 19.3%, p<0.0001, Figure 1A). Patients were observed to have focal deletions on 22q11.22 spanning up to 235 kb; the most common recurring shared region is just under 10 kb in length, and does not contain known coding genes. Increased number of copies of a 14 kb region in the platelet-derived growth factor receptor alpha gene (PDGFRA), located at 4q12, occurred in 35.5% of cases performed on microarrays containing evaluable probes in this region, and were significantly associated with poor outcome (4-year EFS 87.5 ± 8.3% in wild-type cases [n=20] and 33.9 ± 17.6% in PDGFRA gain cases [n=11], p = 0.004, Figure 1B). Five cases contained 3 copies of PDGFRA, and six cases had at least 4 copies, with no correlation between outcome and number of copies gained. PDGFRA rearrangements and point mutations have been reported in other malignancies, but copy number gain is a novel mechanism of alteration. Cases with a focal 22q11.22 deletion were associated with an increased frequency of CRLF2 rearrangement (75% versus 47%, Fisher's exact p=0.028). No other differences in age, initial WBC, or CRLF2 rearrangement in cases with versus without the focal 22q11.22 deletion, IKZF1 deletion, or PDGFRA gain were present, nor were there significant differences in incidence of focal PDGFRA gains in cases with versus without IKZF1 or 22q11.22 deletions. Gene expression profiling in 27 evaluable cases demonstrated upregulation of genes with kinase activity in 12 cases with either focal 22q11.22 or IKZF1 deletions. This study represents one of the largest collaborative cohorts of DS-ALL for genomic profiling, confirms the poor prognosis associated with IKZF1 deletion (Buitenkamp et al., Leukemia 2012), and identifies two additional genomic loci strongly associated with poor prognosis. If validated in additional DS-ALL cohorts, these findings suggest key lesions that contribute to the poor outcomes observed in this population. These specific genomic changes may improve risk stratification of treatment in children with DS and ALL, and may lead to enhanced sensitivity to tyrosine kinase inhibitors in the estimated 60% of cases bearing one or more of these three lesions. Disclosures: No relevant conflicts of interest to declare.

Background: Richter Transformation (RT) is defined as the transformation of chronic lymphocytic leukemia (CLL) or small lymphocytic lymphoma (SLL) into an aggressive lymphoma. Diffuse large B-cell lymphoma (DLBCL) makes up the vast majority of RT and these patients have a poor prognosis compared to de novo DLBCL (Rossi D, et al. Blood, 2011; 117(12):3391-3401). Prognostic factors include therapy for CLL/SLL prior to transformation, TP53/CDKN2A abnormalities, as well as clonal relationship between CLL/SLL and RT. There are no randomized controlled trials to direct treatment of RT and many centers use clonal relationship to direct treatment decisions including whether or not patients should receive consolidation with autologous or allogeneic stem cell transplantation (Parikh SA, et al. Blood; 123(11): 1647-1657). One method for establishing clonality involves genetic analysis of the immunoglobulin heavy variable chain (IgHV) gene in both the CLL/SLL portion as well as the RT portion by means of IGHV V-D-J sequencing. Whole genome Chromosomal microarray (CMA) provides a method of tracking duplications or deletions of chromosomal segments sometimes referred to as copy number variants (CNVs). CMA is used at our institution to establish chromosomal aberrations at diagnosis for all CLL/SLL patients. This provides prognostic information at diagnosis as well as the ability to track aberrations in the event of progression or transformation of disease. Use of CMA at diagnosis of CLL/SLL and upon transformation to DLBCL (RT) provides a method to determine clonal relationship. It also identifies aberrations involving TP53 and CDKN2A, which are known to be markers of poor prognosis. Methods: We performed a single center retrospective analysis of all patients at MUSC with pathologically confirmed CLL or SLL and Richter transformation between 1/01/2010 to 02/14/2019. We collected baseline demographic, clinical, laboratory, pathology, and outcomes data from the electronic medical record. Chromosomal Microarray Analysis (CMA) was performed on genomic DNA extracted from peripheral blood and fresh or formalin fixed paraffin-embedded lymph node samples using the Infinium HD Human Omni1 BeadChip or the CytoSNP-850K v1.1 BeadChip Array (Illumina, Inc., San Diego, CA). Copy number and genotype data were analyzed using NxClinical (BioDiscovery, Inc) software. Aberrations that were in 100% of cells were considered constitutional and were not included in the data analysis; whereas regions noted to be in less than 100% of cells were considered clonal changes. Results: We identified a total of 24 patients with a diagnosis of Richter transformation to DLBCL with prior history of CLL/SLL. Of these patients, 7 had CMA performed on both the CLL/SLL and RT samples. Clinical characteristics were collected for each patient and are included in table 1. CMA data including deletions, duplications, LOH, loss of TP53 and/or CDKN2A is displayed for each patient in table 2. Six of the 7 patients (85%) had common CMA aberrations identified in the CLL/SLL and RT samples providing evidence of a common clonality. Five of the 7 patients (71%) were identified to have TP53 loss and/or CDKN2A loss by CMA at the time of RT diagnosis. Discussion: Chromosomal microarray was able to provide proof of common clonality in 6 of 7 patients with Richter transformation to DLBCL, which is a poor prognostic feature of RT. It also identified a loss of TP53 and/or CDKN2A in 5 of 7 patients which is also a poor prognostic feature of RT. This information can be used to counsel patients on prognosis and could effect clinical recommendations such as treatment with Allogeneic stem cell transplantation. Institutions with the ability to run CMA should utilize this modality in patients Richter transformation to DLBCL. Disclosures No relevant conflicts of interest to declare.

Abstract Background. Array-based technology has been showing a great impact on clinical cancer cytogenetic, especially on genetically heterogeneous disease, such as MM, where relevant lesions might be the hallmarks of different patients’ subgroups, thus becoming of clinical relevance as well. We present herein the results of a molecular sub-study of the EMN02 phase III study (EMN02_HOVON95) which was designed to compare consolidation therapy Bortezomib, Melphalan and Prednisone versus upfront autologous stem cell transplantation, both applied after induction therapy with bortezomib-cyclophosphamide-dexamethasone (VCD). The sub-study was aimed at developing a comprehensive, high throughput genomic profile to be used to stratify uniformly treated MM patients according to their genomic background at baseline and to perform correlations with response to induction therapy. Patients and methods. Data obtained from 170 patients who consecutively entered the study and received three 21-day cycles of VCD induction therapy were analyzed. Baseline patients’ characteristics, including cytogenetic abnormalities, were comparable with those of 717 patients enrolled by participating Italian centres. Highly purified CD138+ bone marrow plasma cells were profiled by SNPs array (Affymetrix 6.0 and CytoScanHD® chip). ChAS (Affymetrix) and Nexus Copy NumberTM 7.5 (Biodiscovery) software were used to perform Copy Number Alterations (CNAs) analyses and clinical correlations, respectively. Results. After induction therapy, 66 out of 170 (38.8%) patients achieved a very good partial response (VGPR) or better, including 15 (8,8%) who attained a complete response (CR). On the contrary, 104/170 (61.1%) patients achieved <=partial response (PR), including 28 with stable disease (SD). Presenting MM cases were studied by SNPs array in order to compute CNAs and acquired loss of heterozygosity (LOH) in the tumor. The frequency distribution of the more relevant CNAs is summarized in table 1. A subgroup of 13/170 (7.6%) patients was characterized by the absence of any macro CNAs (either gains or losses): these cases were mainly characterized by LOH events on chr. 1, 8 and 16, where putative tumor suppressor genes are located (e.g. PLEKOH1 and SIAH1 on chr.1 and 16, respectively). In order to identify novel chromosomal lesions potentially influencing response to induction therapy, we compared the CNAs profile of the extreme response categories, i.e. CR and SD. Neither the absence of CNAs nor the presences of any of those that are prognostically relevant were significantly linked to response to induction therapy. On the contrary, the following two novel lesions resulted highly significant. A 42.9 Kb CN gain on chr.11q22.1-22.2, which only includes the Hippo pathway mediator YAP1, significantly characterized 6% of patients in CR, as compared to 54% of patients with SD (p=0.002). An extended CN loss on chr.14q13.1-13.3, including genes implicated in the progression on cancer (e.g. NKX2-8), significantly characterized 62.5% of patients who achieved CR, as compared to 4% of those with SD (p<0.001). Conclusions. The reconstruction of high-throughput virtual karyotype by SNPs array in a cohort of homogeneously treated, newly diagnosed, MM patients offered the opportunity to obtain a comprehensive overlook of each patient’s sub-chromosomal anatomy. This allowed both to perform a detailed patients’ stratification at diagnosis and to identify, among the whole spectrum of CNAs, those having an impact on response to induction therapy. Figure 1 Figure 1. Disclosures Palumbo: Bristol-Myers Squibb: Consultancy, Honoraria; Genmab A/S: Consultancy, Honoraria; Celgene: Consultancy, Honoraria; Janssen-Cilag: Consultancy, Honoraria; Millennium Pharmaceuticals, Inc.: Consultancy, Honoraria; Onyx Pharmaceuticals: Consultancy, Honoraria; Array BioPharma: Honoraria; Amgen: Consultancy, Honoraria; Sanofi: Honoraria. Sonneveld:Celgene: Research Funding, Speakers Bureau; Millennium-Takeda: Research Funding; Onyx: Research Funding, Speakers Bureau; Janssen: Speakers Bureau. Cavo:Millenium: Consultancy, Honoraria; BMS: Consultancy, Honoraria; Celgene: Consultancy, Speakers Bureau; Janssen: Consultancy, Speakers Bureau; Onyx: Honoraria.

Abstract Introduction Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare and aggressive hematological malignancy with multi-organ and frequent skin involvement, and poor clinical outcomes. Based on the limited available data, the estimated incidence is 0.44% of all hematologic malignancies, representing less than 1% of acute leukemias, and 0.7% of cutaneous lymphomas. Due to the rarity of this entity, there have been relatively few studies characterizing the molecular profile of BPDCN. We examined a cohort of 51 patients with BPDCN using OncoScan chromosome microarray, which provides genome-wide copy number abnormality (CNA) analysis. Methods An international cohort of BPDCN cases were collected from centers in Brazil (Laboratorio de Patologia, Botucatu), Swtizerland (University of Zurich), France (Hospital St. Louis, Paris), Peru (Instituto Nacional de Enfermedades Neoplasicas, Lima), Canada (Department of Pathology, University of Montreal), Italy (Derpartment of Pathology, University of Bologna), and US (Department of Pathology - The Ohio State University, Department of Hematopathology - MD Anderson Cancer Center; and Department of Pathology - University of Virginia). A total of 58 tissue blocks from 51 patient samples were retrieved. The diagnosis of BPDCN was done and confirmed by at least three independent hematopathologists or dermatopathologists in accordance with the WHO classification (Lyon 2017). For the purpose of the molecular analysis substratification, cases were classified as 'BPDCN' if they were positive for TCF4, and 'BPDCN-like' if they were negative for TCF4. Immunohistochemistry for CD123, CD4, and CD56 was performed in all cases. Exclusion criteria included expression of MPO, lysozyme, CD3, CD19, CD20, CD22, and/or EBV. DNA was extracted from FFPE samples via standard techniques and processed on OncoScan CNV Plus microarray (ThermoFisher Scientific) according to manufacturer's recommended protocol. Copy number abnormalities and select single nucleotide variants and insertions/deletions (74 mutations in 9 genes) were analyzed on Chromosome Analysis Suite software (ChAS v4.1; ThermoFisher Scientific). Additional analysis was performed using Nexus Copy Number (BioDiscovery, version 10.0). Results To date, we have successfully analyzed 45 cases of BPDCN with Oncoscan, revealing widespread CNA in the vast majority of cases (44/45; 98%). Alterations of chromosome 9 were common in this cohort, particularly CNAs involving CDKN2A/B at 9p21.3. Twenty-five cases (56%) demonstrated CNA including CDKN2A/B, with ten of these cases demonstrating a homozygous loss of CDKN2A/B (22%). Alterations of chromosome 13 were also frequently detected with loss of RB1 (located at 13q14.2) detected in 24 cases (53%). The RUNX1 gene (21q22.12) was a common target of CNAs in this cohort, seen in nine cases (20%). Eight of these cases showed a copy number gain of RUNX1, which is a recurrent finding in a variety of hematological malignancies, particularly myeloid neoplasms. The remaining case with RUNX1 CNA showed a focal, homozygous loss of the gene, demonstrating that dysregulation of RUNX1 through CNA is a common event in BPDCN. We observed frequent deletions of ETV6 (53%), IKZF1 (33%), and TP53(16%) in our cohort. The ARHGAP26 gene (5q31.3), which is associated primarily with juvenile myelomonocytic leukemia, was included in CNA in 13 cases (29%), with both gains and losses observed in this cohort. Oncoscan can detect a limited number of single nucleotide variants in nine genes that are frequently mutated in cancers (BRAF, EGFR, IDH1, IDH2, KRAS, NRAS, PIK3CA, PTEN, and TP53). Mutations were detected in ten cases (22%), with NRAS and TP53 variants detected in three cases each and KRAS and IDH2 variants detected in two cases each. Conclusions Our preliminary data demonstrates complex genomic alterations in BPDCN, with the RB1 locus on chromosome 13, the CDKN2A/B locus on chromosome 9, and the ETV6 locus on chromosome 12 most commonly detected. However, widespread genomic alterations were detected involving a variety of cancer-associated genes further characterizing CNA in BPDCN. Analysis of additional BPDCN cases is progress. Disclosures Khoury: Kiromic: Research Funding; Angle: Research Funding; Stemline Therapeutics: Research Funding. Porcu: Viracta: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Innate Pharma: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; BeiGene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Incyte: Research Funding; Daiichi: Honoraria, Research Funding; Kiowa: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Spectrum: Consultancy; DrenBio: Consultancy. Gru: StemLine: Honoraria, Research Funding, Speakers Bureau; CRISPT Therapeutics: Research Funding; Innate Pharma: Research Funding.

Abstract Background Aboriginal peoples have occupied the island continent of Australia for millennia. Over 500 different clan groups or nations with distinctive cultures, beliefs, and languages have learnt to live sustainably and harmoniously with nature. They have developed an intimate and profound relationship with the environment, and their use of native plants in food and medicine is largely determined by the environment they lived in. Over 1511 plant species have been recorded as having been used medicinally in Australia. Most of these medicinal plants were recorded from the Aboriginal communities in Northern Territory, New South Wales, South Australia, and Western Australia. Not much has yet been reported on Aboriginal medicinal plants of Queensland. Therefore, the main aim of this review is to collect the literature on the medicinal plants used by Aboriginal peoples of Queensland and critically assess their ethnopharmacological uses. Methods The information used in this review was collected from archival material and uploaded into the Tropical Indigenous Ethnobotany Centre (TIEC) database. Archival material included botanist’s journals/books and old hard copy books. Scientific names of the medicinal plant species were matched against the ‘World Flora Online Plant List’, and ‘Australian Plant Census’ for currently accepted species names to avoid repetition. An oral traditional medical knowledge obtained through interviewing traditional knowledge holders (entered in the TIEC database) has not been captured in this review to protect their knowledge. Results This review identified 135 species of Queensland Aboriginal medicinal plants, which belong to 103 genera from 53 families, with Myrtaceae being the highest represented plant family. While trees represented the biggest habit, leaves were the most commonly used plant parts. Of 62 different diseases treated by the medicinal plants, highest number of plants are used for treating skin sores and infections. Few plants identified through this review can be found in other tropical countries but many of these medicinal plants are native to Australia. Many of these medicinal plants are also used as bush food by Aboriginal peoples. Conclusion Through extensive literature review, we found that 135 medicinal plants native to Queensland are used for treating 62 different diseases, especially skin infections. Since these medicinal plants are also used as bush food and are rarely studied using the Western scientific protocols, there is a huge potential for bioprospecting and bush food industry.