Lineage relationship between prostate adenocarcinoma and small cell carcinoma.

BACKGROUND: Prostate cancer displays different morphologies which, in turn, affect patient outcome. This fact prompted questions about the lineage relationship between differentiated, more treatable prostate adenocarcinoma and poorly differentiated, less treatable non-adenocarcinoma including small cell carcinoma, and the molecular mechanism underlying prostate cancer differentiation. METHODS: Newly available non-adenocarcinoma/small cell carcinoma PDX LuCaP lines were analyzed for expression of stem cell transcription factors (scTF) LIN28A, NANOG, POU5F1, SOX2, which are responsible for reprogramming or de-differentiation. cDNA of these genes were cloned from small cell carcinoma LuCaP 145.1 into expression vectors to determine if they could function in reprogramming. RESULTS: Expression of scTF was detected in small cell carcinoma LuCaP 93, 145.1, 145.2, and non-adenocarcinoma LuCaP 173.1, 173.2A. Transfection of scTF from LuCaP 145.1 altered the gene expression of prostate non-small cell carcinoma cells, as well as fibroblasts. The resultant cells grew in stem-like colonies. Of note was a 10-fold lower expression of B2M in the transfected cells. Low B2M was also characteristic of LuCaP 145.1. Conversely, B2M was increased when stem cells were induced to differentiate. CONCLUSIONS: This work suggested a pathway in the emergence of non-adenocarcinoma/small cell carcinoma from adenocarcinoma through activation of scTF genes that produced cancer de-differentiation.

Maternal obesity and gestational weight gain are modestly associated with umbilical cord DNA methylation.

INTRODUCTION: Maternal obesity (OB) and excessive gestational weight gain (GWG) are strong independent contributors that augment obesity risk in offspring. However, direct evidence of epigenetic changes associated with maternal habitus remains sparse. METHODS: We utilized Bisulfite Amplicon Sequencing (BSAS) to conduct targeted DNA methylation association analysis of maternal obesity and excessive GWG with DNA methylation of select metabolism-related and imprinted genes. Umbilical cord (UC) tissue from infants born to normal weight and overweight/obese women from the Glowing study were utilized (n = 78). RESULTS: In multivariable linear regression adjusted for relevant confounders, Institute on Medicine (IOM) GWG category and infant sex were significantly associated with UC IGFBP1 methylation, while gestation length was significantly associated with UC PRKAA1 methylation. In addition, infant fat mass (%) at 2 weeks of age was significantly associated with umbilical cord methylation of RAPTOR. While regression tree analysis confirmed findings from multivariable models demonstrating that maternal early pregnancy BMI and IOM GWG category are associated with fetal UC DNA methylation patterns for select metabolic and imprinted genes, in general, effect sizes were quite small and statistical significance was not maintained when accounting for multiple testing. DISCUSSION: Our findings suggest that maternal obesity and excessive GWG are weakly correlated with offspring DNA methylation patterns at birth.

Quantitative analysis of genomic DNA degradation in whole blood under various storage conditions for molecular diagnostic testing.

Proper storage of whole blood is crucial for isolating nucleic acids from leukocytes and to ensure adequate performance of downstream assays in the molecular diagnostic laboratory. Short-term and long-term storage recommendations are lacking for successful isolation of genomic DNA (gDNA). Container type (EDTA or heparin), temperature (4 °C and room temperature) and time (1-130 days) were assessed as criterion for sample acceptance policies. The percentage of integrated area (%Ti) between 150 and 10,000 bp from the 2200 TapeStation electropherogram was calculated to measure gDNA degradation. Refrigerated EDTA samples yielded gDNA with low %Ti (high quality). Heparinized samples stored at room temperature yielded gDNA of worst quality. Downstream analysis demonstrated that the quality of the gDNA correlated with the quality of the data; samples with high %Ti generated significantly lower levels of high molecular weight amplicons. Recommendations from these analyses include storing blood samples intended for nucleic acid isolation in EDTA tubes at 4 °C for long term storage (>10 days). gDNA should be extracted within 3 days when blood is stored at room temperature regardless of the container. Finally, refrigerated heparinized samples should not be stored longer than 9 days if expecting high quality gDNA isolates. Laboratories should consider many factors, in addition to the results obtained herein, to update their policies for sample acceptance for gDNA extraction intended for molecular genetic testing.

Distinguishing the interactions in the fructose 1,6-bisphosphate binding site of human liver pyruvate kinase that contribute to allostery.

In the study of allosteric proteins, understanding which effector-protein interactions contribute to allosteric activation is important both for designing allosteric drugs and for understanding allosteric mechanisms. The antihyperglycemic target, human liver pyruvate kinase (hL-PYK), binds its allosteric activator, fructose 1,6-bisphosphate (Fru-1,6-BP), such that the 1'-phosphate interacts with side chains of Arg501 and Trp494 and the 6'-phosphate interacts with Thr444, Thr446, Ser449 (i.e., the 444-449 loop), and Ser531. Additionally, backbone atoms from the 527-533 loop interact with a sugar ring hydroxyl and the two effector phosphate moieties. An effector analogue series indicates that only one phosphate on the sugar is required for activation. However, singly phosphorylated sugars, including Fru-1-P and Fru-6-P, bind with a Kix in the range of 0.07-1 mM. The second phosphate of Fru-1,6-BP causes tight effector binding, because this native effector has a Kix of 0.061 µM. Glucose 1,6-bisphosphate and ribulose 1,5-bisphosphate bind in the 0.07-1 mM range. The contrast with a higher Fru-1,6-BP binding indicates specificity for the fructose sugar conformation. Site-directed random mutagenesis at each residue that contacts bound Fru-1,6-BP showed that a negative charge introduced at position 531 mimics allosteric activation, even in the absence of Fru-1,6-BP. Collectively, analogue and mutagenesis studies are consistent with the 527-533 loop playing a key role in allosteric function. Deletion mutations that shortened the 527-533 loop were expected to prevent formation of hydrogen bonds between backbone atoms on the loop and Fru-1,6-BP. Indeed, Fru-1,6-BP did not activate these loop-shortened mutant proteins. Previous structural comparisons of M1-PYK and M2-PYK indicate that the 527-533 loop makes interactions across a subunit interface when an activator is not present. Mutating the hL-PYK subunit interface interactions among Trp527, Arg528, and Asp499 mimics allosteric activation. Considered with published structures, these results are consistent with (1) the two phosphates of Fru-1,6-BP docking to Arg501/Trp494 and the 444-449 loop, respectively, and (2) the formation of hydrogen bonds among Fru-1,6-BP and backbone atoms of the 527-533 loop pulling this loop away from the subunit interface, which results in breaking of the Trp527-Arg528-Asp499 interactions to elicit an allosteric response.

Molecular and cytogenetic evaluation of a patient with ring chromosome 13 and discordant results.

We describe the case of a male newborn with ring chromosome 13 found to have dysmorphic features, growth retardation, imperforate anus, and ambiguous genitalia. An initial karyotype showed 46,XY,r(13)(p13q34) in the 30 cells analyzed. SNP microarray from peripheral blood revealed not only an 8.14-Mb 13q33.2q34 deletion, but also a duplication of 87.49 Mb suggesting partial trisomy 13q that the patient did not appear to have clinically. Further cytogenetic characterization detected 3 distinct cell lines in the repeated peripheral blood sample: 46,XY,r(13)(p13q34)[89]/ 46,XY,r(13;13)(p13q34)[7]/45,XY,-13[5] and 2 in cultured fibroblasts: 46,XY,r(13)(p13q34)[65]/45,XY,-13[35]. Repeated molecular studies on peripheral blood and fibroblasts, however, failed to document the initially seen partial trisomy 13q. We postulate that the presence of duplicated material may be evidence of the high burden of duplicate rings in peripheral blood at any given time, with the high rates of cell death caused by mitotically unstable double rings accounting for the repeated microarray results that failed to detect any duplications. We emphasize the correlation between both cytogenetic and molecular studies with thorough clinical assessment and suggest that given the high sensitivity of newer molecular cytogenetic techniques, careful interpretation of results is critical in the context of ring chromosomes.

Algal genes in the closest relatives of animals.

The spread of photosynthesis is one of the most important but controversial topics in eukaryotic evolution. Because of massive gene transfer from plastids to the nucleus and because of the possibility that plastids have been lost in evolution, algal genes in aplastidic organisms often are interpreted as footprints of photosynthetic ancestors. These putative plastid losses, in turn, have been cited as support for scenarios involving the spread of plastids in broadscale eukaryotic evolution. Phylogenomic analyses identified more than 100 genes of possible algal origin in Monosiga, a unicellular species from choanoflagellates, a group considered to be the closest protozoan relatives of animals and to be primitively heterotrophic. The vast majority of these algal genes appear to be derived from haptophytes, diatoms, or green plants. Furthermore, more than 25% of these algal genes are ultimately of prokaryotic origin and were spread secondarily to Monosiga. Our results show that the presence of algal genes may be expected in many phagotrophs or taxa of phagotrophic ancestry and therefore does not necessarily represent evidence of plastid losses. The ultimate prokaryotic origin of some algal genes and their simultaneous presence in both primary and secondary photosynthetic eukaryotes either suggest recurrent gene transfer events under specific environments or support a more ancient origin of primary plastids.

Raman spectroscopic investigation of peptide-glycosaminoglycan interactions.

Protein-glycosaminoglycan (GAG) interactions play a central role in tissue engineering and drug delivery. A rapid and efficacious method for screening these interactions is essential. Raman spectroscopy was used to identify chemical interactions and conformational changes occurring upon binding between a synthetic peptide (QRRFMQYSARRF) and two glycosaminoglycans (GAGs), heparin and chondroitin 6-sulfate (C6S). The results identify three main chemical groups that are involved in the binding of the synthetic peptide with heparin and C6S. Tyrosine formed hydrogen bonds with the GAGs via its hydroxyl group. The amide I band demonstrated substantial shifts in Raman wavenumbers when bound to heparin and C6S (Deltaomega=-10.2+/-0.7 cm(-1) and Deltaomega=-11.9+/-0.3 cm(-1), respectively), suggesting that the peptide underwent planar conformational changes after binding occurred. Upon binding to the peptide, the sulfate peak of heparin displayed a substantially greater shift in the Raman wavenumber (-7.5+/-0.5 cm(-1)) than that of C6S (-2.6+/-0.5 cm(-1)). The greater amide I and sulfate band shifts seen during peptide-heparin interactions are indicative of a stronger association compared to that between the peptide and C6S. This observation was confirmed by capillary electrophoresis, which demonstrated a lower dissociation constant (KD) between the peptide and heparin (KD of 19.2+/-3.3 microM) than between the peptide and C6S (26.7+/-2.5 microM). We conclude that the shift in the Raman wavenumbers of amide I and sulfate groups can be used for high-throughput screening of interaction affinities between libraries of peptides and GAGs.