White1, J. Li1, W. Liang1, N. Bhagabati1, J. Braisted1, M. Klapa1, T. Currier1, M. Thiagarajan1, A. Sturn1, M. Snuffin2, A. Rezantsev2, D. Popov2, A. Ryltsov2, E. Kostukovich2, I. Borisovsky2, Z. Liu3, A. Vinsavich3, V. Trush3, and J. Quackenbush1,4 1The Institute for Genomic Research, Rockville, MD, 2DataNaut, Bethesda, MD, 3Syntek Systems, Bethesda, MD, and 4Department of Biochemistry, George Washington University, Washington, D.C., USA

TM4: a free, open-source system for microarray data management and analysis.

Microarray experiments are providing unprecedented quantities of genome-wide data on gene-expression patterns. Although this technique has been enthusiastically developed and applied in many biological contexts, the management and analysis of the millions of data points that result from these experiments has received less attention. Sophisticated computational tools are available, but the methods that are used to analyse the data can have a profound influence on the interpretation of the results. A basic understanding of these computational tools is therefore required for optimal experimental design and meaningful data analysis.

/pdf/computational-analysis-of-microarray-data-60m43oybsv.pdf

Computational analysis of microarray data

Calorie restriction (CR) extends lifespan in a wide spectrum of organisms and is the only regimen known to lengthen the lifespan of mammals1,2,3,4. We established a model of CR in budding yeast Saccharomyces cerevisiae. In this system, lifespan can be extended by limiting glucose or by reducing the activity of the glucose-sensing cyclic-AMP-dependent kinase (PKA)5. Lifespan extension in a mutant with reduced PKA activity requires Sir2 and NAD (nicotinamide adenine dinucleotide)5. In this study we explore how CR activates Sir2 to extend lifespan. Here we show that the shunting of carbon metabolism toward the mitochondrial tricarboxylic acid cycle and the concomitant increase in respiration play a central part in this process. We discuss how this metabolic strategy may apply to CR in animals.

/pdf/calorie-restriction-extends-saccharomyces-cerevisiae-2ypqpw38mn.pdf

Calorie restriction extends Saccharomyces cerevisiae lifespan by increasing respiration

The invention provides methods of detecting a nucleic acid. The methods comprise contacting the nucleic acid with one or more types of particles having oligonucleotides attached thereto. In one embodiment of the method, the oligonucleotides are attached to nanoparticles and have sequences complementary to portions of the sequence of the nucleic acid. A detectable change (preferably a color change) is brought about as a result of the hybridization of the oligonucleotides on the nanoparticles to the nucleic acid. The invention also provides compositions and kits comprising particles. The invention further provides methods of synthesizing unique nanoparticle-oligonucleotide conjugates, the conjugates produced by the methods, and methods of using the conjugates. In addition, the invention provides nanomaterials and nanostructures comprising nanoparticles and methods of nanofabrication utilizing nanoparticles. Finally, the invention provides a method of separating a selected nucleic acid from other nucleic acids.

Nanoparticles having oligonucleotides attached thereto and uses therefor

https://www.gastrojournal.org/article/S0016-5085(06)01785-9/pdf

Characterization of HULC, a novel gene with striking up-regulation in hepatocellular carcinoma, as noncoding RNA.

Microarray expression analysis has become one of the most widely used functional genomics tools. Efficient application of this technique requires the development of robust and reproducible protocols. We have optimized all aspects of the process, including PCR amplification of target cDNA clones, microarray printing, probe labeling and hybridization, and have developed strategies for data normalization and analysis.

/pdf/a-concise-guide-to-cdna-microarray-analysis-58fam4z7a0.pdf

A Concise Guide to cDNA Microarray Analysis

Metastasis represents a crucial transition in disease development and progression and has a profound impact on survival for a wide variety of cancers. Cell line models of metastasis have played an important role in developing our understanding of the metastatic process. We used a 19,200-element human cDNA microarray to profile transcription in three paired cell-line models of colorectal tumor metastasis. By correlating expression patterns across these cell lines, we have identified 176 genes that appear to be differentially expressed (greater than 2-fold) in all highly metastatic cell lines relative to their reference. An analysis of these genes reiterates much of our understanding of the metastatic process and suggests additional genes, many of previously uncharacterized function, that may be causatively involved in, or at least prognostic of, metastasis. Northern analysis of a limited number of these genes validates the observed pattern of expression and suggests that further investigation and functional characterization of the identified genes is warranted.

https://cancerres.aacrjournals.org/content/canres/61/21/7792.full.pdf

Identification of Tumor Markers in Models of Human Colorectal Cancer Using a 19,200-Element Complementary DNA Microarray

A concise guide to microarray analysis.

P354: real-world analysis of the risks of thrombotic and bleeding events in patients receiving pegylated asparaginase for treatment of acute lymphoblastic leukemia

Background: The standard remission induction regimen for medically fit patients with acute myeloid leukemia (AML) consists of a backbone of cytarabine & an anthracycline (“7 + 3” therapy). However, the choice & dose of the anthracycline varies between institutions & practitioner preference, particularly in AML with favorable risk cytogenetics. Gemtuzumab ozogamicin (GO) may improve outcomes in this patient population but is associated with increased toxicities. Aims: We aimed to compare the outcomes of 3 cohorts of newly diagnosed AML with favorable cytogenetics who received induction 7 + 3 induction therapy: 1. Standard dose (45 or 60 mg/m2 daunorubicin) (SD); 2. Higher dose (90 mg/m2 daunorubicin or 12 mg/m2 idarubicin) (HD) of anthracycline, 3. 7 + 3 with fractionated GO. Methods: We performed a multicenter retrospective analysis of medically fit patients ≥ 18 yo with favorable risk AML determined using ELN 2017 guidelines from 2015-2020 treated across 6 US academic institutions. Categorical variables were summarized using means and standard deviations. The former was compared using Fisher’s exact test; the latter was compared using either the Wilcoxon text or the Kruskal-Wallis as appropriate. One way ANOVA test was used to compare continuous variables. Kaplan-Meier curves were generated to provide visual summaries of survival and time-to-event data. Results: Our study included 189 treated patients who met eligibility criteria with a median follow up of 2 years. Patients’ characteristics and outcomes are summarized in Table 1. Sixty-nine (37%) received induction with SD, 100 (53%) received HD, and 20 (11%) received GO. Patients in the SD and HD group were younger (median age 50 and 52 yo, respectively) and the majority (>94%) had de novo AML. The rates of composite complete remission in the SD, HD, and GO groups were 66.7%, 70% and 75%, respectively (p=0.761). RFS and OS were similar between all groups (p=0.4 and 0.3, respectively). The rate and duration of cytopenias at day 40 after induction, major bleeding, infections, admission to the intensive care unit, new onset cardiomyopathy (ejection fraction<50%), liver dysfunction and acute renal injury were similar among all groups. No patients developed veno-occlusive disease. Table 1: - Participant Characteristics and Outcomes by Treatment Regimen GON = 20 HDN = 100 SDN = 69 P-value Age in years (standard deviation) 57.75 (9.32) 49.68 (13.67) 51.55 (13.83) 0.038 de novo AML, N (%) 19 (95.0) 94 (94.0) 65 (94.2) 1.000 Disease status after induction 0.812 CR, N (%) 14 (70.0) 66 (66.0) 40 (58.0) CRi, N (%) 0 (0.0) 2 (2.0) 2 (2.9) Persistent, N (%) 1 (5.0) 4 (4.0) 2 (2.9) Composite CR, N (%) 15 (75.0) 70 (70.0) 46 (66.7) 0.761 Admission to ICU, N (%) 4 (20.0) 17 (17.0) 11 (15.9) 0.969 Infections, N (%) 17 (85.0) 74 (74.0) 62 (89.9) 0.082 Major bleeding, N (%) 3 (15.0) 6 (6.0) 4 (5.8) 0.299 VOD, N (%) 0 (0.0) 0 (0.0) 0 (0.0) Transaminitis, N (%) 4 (20.0) 19 (19.0) 19 (27.5) 0.538 Acute renal injury, N (%) 3 (15.0) 19 (19.0) 15 (21.7) 0.962 Cardiomyopathy, N (%) 4 (20.0) 8 (8.0) 5 (7.2) 0.523 Cytopenias at D40 after induction, N (%) 0 (0.0) 7 (7.0) 6 (8.7) 0.542 Image:Summary/Conclusion: Our analysis demonstrated no differences in RFS and OS in patients with AML treated with either GO, HD or SD. In addition, the rates of complications secondary to chemotherapy were similar among all groups. However, a measurable residual disease analysis is ongoing for further characterization of disease response. 

P526: real-world comparison of different treatment modalities for favorable risk acute myeloid leukemia: standard dose anthracycline vs high dose anthracycline vs addition of gemtuzumab ozogamicin

Kristie Abernathy

Papers

A Concise Guide to cDNA Microarray Analysis

Identification of Tumor Markers in Models of Human Colorectal Cancer Using a 19,200-Element Complementary DNA Microarray

A concise guide to microarray analysis.

P354: real-world analysis of the risks of thrombotic and bleeding events in patients receiving pegylated asparaginase for treatment of acute lymphoblastic leukemia

P526: real-world comparison of different treatment modalities for favorable risk acute myeloid leukemia: standard dose anthracycline vs high dose anthracycline vs addition of gemtuzumab ozogamicin