A Comparison of cDNA, Oligonucleotide, and Affymetrix GeneChip Gene Expression Microarray Platforms

We have conducted a study to compare the variability in measured gene expression levels associated with three types of microarray platforms. Total RNA samples were obtained from liver tissue of four male mice, two each from inbred strains A/J and C57BL/6J. The same four samples were assayed on Affymetrix Mouse Genome Expression Set 430 GeneChips (MOE430A and MOE430B), spotted cDNA microarrays, and spotted oligonucleotide microarrays using eight arrays of each type. Variances associated with measurement error were observed to be comparable across all microarray platforms. The MOE430A GeneChips and cDNA arrays had higher precision across technical replicates than the MOE430B GeneChips and oligonucleotide arrays. The Affymetrix platform showed the greatest range in the magnitude of expression levels followed by the oligonucleotide arrays. We observed good concordance in both estimated expression level and statistical significance of common genes between the Affymetrix MOE430A GeneChip and the oligonucleotide arrays. Despite their apparently high precision, cDNA arrays showed poor concordance with other platforms

Current Views on Chr10q26 Contribution to Age-Related Macular Degeneration.

Age-related macular degeneration (AMD) is the leading cause of blindness in the global aging population. Familial aggregation and genome-wide association (GWA) studies have identified gene variants associated with AMD, implying a strong genetic contribution to AMD development. Two loci, on human Chr 1q31 and 10q26, respectively, represent the most influential of all genetic factors. While the role of CFH at Chr 1q31 is well established, uncertainty remains about the genes ARMS2 and HTRA1, at the Chr 10q26 locus. Since both genes are in strong linkage disequilibrium, assigning individual gene effects is difficult. In this chapter, we review current literature about ARMS2 and HTRA1 and their relevance to AMD risk. Future studies will be necessary to unravel the mechanisms by which they contribute to AMD

Hematopoietic stem cells and metabolic deterioration in Alström syndrome, a rare genetic model of the metabolic syndrome

Purpose: Alström syndrome (AS) is a rare genetic disease caused by ALMS1 mutations, characterized by short stature, vision and hearing loss. AS patients develop the metabolic syndrome, long-term organ complications, and die prematurely. We explored the association between AS and shortage of hematopoietic stem/progenitor cells (HSPCs), which is linked with metabolic diseases and predict diabetic complications. Methods: We included patients with AS at a national referral Center. We measured HSPCs with flow cytometry at baseline and follow-up. We followed patients up to January 2022 for metabolic worsening and end-organ damage. We evaluated HSPC levels and mobilization as well as bone marrow histology in a murine model of AS. Results: In 23 patients with AS, we found significantly lower circulating HSPCs compared to healthy blood donors (-40%; p = 0.002) and age/sex matched patients (-25%; p = 0.022). Longitudinally, HSPCs significantly declined by further 20% in AS patients over a median of 36 months (IQR 30-44). AS patients who displayed metabolic deterioration over 5.3 years had lower levels of HSPCs both at baseline and at last observation, as compared to those who did not deteriorate. Alms1-mutated mice were obese and insulin-resistant and displayed significantly reduced circulating HSPCs, despite no overt hematological abnormality. Contrary to what observed in diabetic mice, HSPC mobilization and bone marrow structure were unaffected. Conclusion: We found depletion of HSPCs in AS patients, which was recapitulated in Alms1-mutated mice. Larger and longer studies will be needed to establish HSPCs shortage as a driver of metabolic deterioration leading to end-organ damage in AS

Diminished gallbladder motility in rotund leptin-resistant obese mice

Background. Obesity is a risk factor for cholesterol gallstone formation, but the pathogenesis of this phenomenon remains unclear. Most human obesity is associated with diabetes and leptin-resistance. Previous studies from this laboratory have demonstrated that diabetic leptin-resistant (Lepdb) obese mice have low biliary cholesterol saturation indices, enlarged gallbladders and diminished gallbladder response to neurotransmitters. Recently, a novel leptin-resistant mouse strain Leprdb-rtnd (Rotund) has been discovered. Rotund mice are also obese, diabetic, and have an abnormal leptin receptor. Therefore, we tested the hypothesis that leptin-resistant obese Rotund mice would have large gallbladders and reduced biliary motility