A genomic case study of mixed fibrolamellar hepatocellular carcinoma.

BACKGROUND: Mixed fibrolamellar hepatocellular carcinoma (mFL-HCC) is a rare liver tumor defined by the presence of both pure FL-HCC and conventional HCC components, represents up to 25% of cases of FL-HCC, and has been associated with worse prognosis. Recent genomic characterization of pure FL-HCC identified a highly recurrent transcript fusion (DNAJB1:PRKACA) not found in conventional HCC. PATIENTS AND METHODS: We performed exome and transcriptome sequencing of a case of mFL-HCC. A novel BAC-capture approach was developed to identify a 400 kb deletion as the underlying genomic mechanism for a DNAJB1:PRKACA fusion in this case. A sensitive Nanostring Elements assay was used to screen for this transcript fusion in a second case of mFL-HCC, 112 additional HCC samples and 44 adjacent non-tumor liver samples. RESULTS: We report the first comprehensive genomic analysis of a case of mFL-HCC. No common HCC-associated mutations were identified. The very low mutation rate of this case, large number of mostly single-copy, long-range copy number variants, and high expression of ERBB2 were more consistent with previous reports of pure FL-HCC than conventional HCC. In particular, the DNAJB1:PRKACA fusion transcript specifically associated with pure FL-HCC was detected at very high expression levels. Subsequent analysis revealed the presence of this fusion in all primary and metastatic samples, including those with mixed or conventional HCC pathology. A second case of mFL-HCC confirmed our finding that the fusion was detectable in conventional components. An expanded screen identified a third case of fusion-positive HCC, which upon review, also had both conventional and fibrolamellar features. This screen confirmed the absence of the fusion in all conventional HCC and adjacent non-tumor liver samples. CONCLUSION: These results indicate that mFL-HCC is similar to pure FL-HCC at the genomic level and the DNAJB1:PRKACA fusion can be used as a diagnostic tool for both pure and mFL-HCC.

Epigenomic analysis of the HOX gene loci reveals mechanisms that may control canonical expression patterns in AML and normal hematopoietic cells.

HOX genes are highly expressed in many acute myeloid leukemia (AML) samples, but the patterns of expression and associated regulatory mechanisms are not clearly understood. We analyzed RNA sequencing data from 179 primary AML samples and normal hematopoietic cells to understand the range of expression patterns in normal versus leukemic cells. HOX expression in AML was restricted to specific genes in the HOXA or HOXB loci, and was highly correlated with recurrent cytogenetic abnormalities. However, the majority of samples expressed a canonical set of HOXA and HOXB genes that was nearly identical to the expression signature of normal hematopoietic stem/progenitor cells. Transcriptional profiles at the HOX loci were similar between normal cells and AML samples, and involved bidirectional transcription at the center of each gene cluster. Epigenetic analysis of a subset of AML samples also identified common regions of chromatin accessibility in AML samples and normal CD34(+) cells that displayed differences in methylation depending on HOX expression patterns. These data provide an integrated epigenetic view of the HOX gene loci in primary AML samples, and suggest that HOX expression in most AML samples represents a normal stem cell program that is controlled by epigenetic mechanisms at specific regulatory elements.

A multi-level hierarchic Markov process with Bayesian updating for herd optimization and simulation in dairy cattle.

Herd optimization models that determine economically optimal insemination and replacement decisions are valuable research tools to study various aspects of farming systems. The aim of this study was to develop a herd optimization and simulation model for dairy cattle. The model determines economically optimal insemination and replacement decisions for individual cows and simulates whole-herd results that follow from optimal decisions. The optimization problem was formulated as a multi-level hierarchic Markov process, and a state space model with Bayesian updating was applied to model variation in milk yield. Methodological developments were incorporated in 2 main aspects. First, we introduced an additional level to the model hierarchy to obtain a more tractable and efficient structure. Second, we included a recently developed cattle feed intake model. In addition to methodological developments, new parameters were used in the state space model and other biological functions. Results were generated for Dutch farming conditions, and outcomes were in line with actual herd performance in the Netherlands. Optimal culling decisions were sensitive to variation in milk yield but insensitive to energy requirements for maintenance and feed intake capacity. We anticipate that the model will be applied in research and extension.

Relationships between milk protein composition, milk protein variants, and cow fertility traits in Dutch Holstein-Friesian cattle.

Selective breeding can change milk protein composition to improve the manufacturing properties of milk. However, the effects of such breeding strategies on other economically important traits should be investigated before implementation. The objectives of this study were to examine the association between cow fertility traits and (1) milk protein composition and (2) milk protein variants (ß-lactoglobulin, ß-casein, κ-casein, and ß-κ-casein) in commercial Dutch Holstein-Friesian cattle. Data on 1,644 first-lactation cows were analyzed by fitting linear mixed models. Greater relative concentration of α(S1)-casein within total milk protein had a positive phenotypic relationship with nonreturn rates and calving rate after first insemination. Furthermore, results showed virtually no significant relationship between cow fertility and concentration of other milk proteins or milk protein variants. Results of this study can be used to assess the correlated effects of breeding for improved milk protein composition on reproduction, thereby allowing for better evaluation of breeding programs before implementation. Our findings suggest that selecting cows based on milk protein composition or milk protein variants for improved manufacturing properties would have no negative influence on reproductive performance.

Effects of milk fat composition, DGAT1, and SCD1 on fertility traits in Dutch Holstein cattle.

Recently, selective breeding was proposed as a means of changing the fatty acid composition of milk to improve its nutritional quality. Before implementing such breeding objectives, effects on other economically important traits should be investigated. The objectives of this study were to examine 1) the effect of milk fat composition, and 2) the effect of polymorphisms of DGAT1 and SCD1 genes on female fertility in commercial Dutch Holstein-Friesian cattle. Data on 1,745 first-lactation cows were analyzed by fitting linear mixed models. We found that higher concentrations of trans fatty acids within total milk fat negatively affected reproductive performance. Furthermore, results suggested a potential effect of the DGAT1 polymorphism on nonreturn rates for insemination 28 and 56 d after the first service. Our results can be used to assess the correlated effects of breeding for improved milk fat composition on reproduction, thereby allowing for better evaluation of breeding programs before implementation.

Biocompatibility of small-intestinal submucosa in urinary tract as augmentation cystoplasty graft and injectable suspension.

We explored the biocompatibility of fluidized canine small-intestinal submucosa (SIS) for periureteral injection and as a patch graft for bladder augmentation in pigs. Gross evaluation 8 weeks after submucosal injection showed persistence of the nodule. Histologic examination showed thickened submucosa with spindle cells embedded in poorly organized fibrous material. There was no evidence of inflammatory reaction or granuloma formation. Subserosal nodules likewise persisted and demonstrated capillary ingrowth. Grafts of SIS became epithelialized within 3 weeks with maintenance of bladder capacity. Ingrowth of capillaries and smooth muscle could be seen in later specimens. Although further studies with longer follow-up are needed, SIS appears to be a promising graft material in the urinary tract.

Use of noninvasive bioelectric impedance to predict cardiac output in open heart recovery.

Cardiac outputs (CO) measured by bioelectric impedance (Z) and thermodilution (TD) were compared in ten stable, non-ventilated male coronary artery bypass patients (mean age 59 +/- 12 years) in an open heart recovery unit. The measurements were obtained blindly in three sequential body positions (supine, 45 degrees, final supine) using either a calculated value for resistivity (p) (based upon hematocrit with blood sampled at the time of the study) to estimate CO(Z), or assumed values of p = 135.5 omega cm and p = 150 omega cm. The results indicate high correlations between the two measurement methods (range: r = 0.97 to 0.99) in the initial supine position for all resistivity conditions followed by a progressive decline when body position was changed to 45 degrees and supine (range: r = 0.74 to 0.90). The highest overall correlations and closest absolute mean cardiac output values were obtained when p was calculated from actual hematocrit values obtained at the time of the study. Applying a two-way ANOVA to assess the simultaneous effects of method (TD vx. Z) and position change (supine, 45 degrees, supine), no significant main effects or interactions were found when cardiac output values were estimated using the calculated measurement of p. However, significant main effects of method were found when p was assumed to be either 135.5 omega cm (p > or = 0.005) or 150.0 omega cm (p > or = 0.0001), with impedance showing a tendency to overestimate cardiac output. In conclusion, our findings suggest that impedance is a valid method to estimate cardiac output in this subpopulation of patients in open heart recovery provided that p is calculated at the time the study is performed.

Comparison of the effects of pindolol and atenolol on hemodynamic function in systemic hypertension.

A randomized double-blind study was performed on a group of mild hypertensive patients (WHO class I) to compare the hemodynamic effects of pindolol and atenolol. Blood pressure (BP) was monitored with a mercury gauge sphygmomanometer, while cardiac function and peripheral arterial flows were measured by the noninvasive technique of bioelectric impedance. After a 2-week washout period, patients with a diastolic BP greater than 95 mm Hg but less than 114 mm Hg were randomized into the pindolol (29 patients) or atenolol (28) treatment groups. Patients were treated with 1 of the 2 drugs in an incremental fashion for 12 weeks. Cardiovascular function was measured after the washout period and at the end of the 12-week treatment period. Baseline hemodynamics were similar in both groups. The 2 drugs were equally effective in lowering both systolic and diastolic BP. Hemodynamically, pindolol lowered BP by decreasing total peripheral resistance (-406 +/- 145 dynes.s.cm-5) while atenolol decreased cardiac index (-0.2 +/- 0.1 liters/min/m2) associated with a decrease in heart rate (-12 +/- 2 beats/min). Regarding peripheral vascular beds, pindolol lowered arm vascular resistance (-198 +/- 72 mm Hg/liter/min) and leg vascular resistance (-73 +/- 25 mm Hg/liter/min), especially when subjects who did not respond to pindolol were excluded from the analysis. Both arm (5.5 +/- 5.4% increase above baseline) and leg (1.2 +/- 4.4% increase above baseline) arterial flow indexes were maintained with pindolol. Conversely, atenolol decreased the arm arterial flow index (-9,8 +/- 5.6% decrease below baseline), but not significantly and with no change in resistance (+54 +/- 62 mm Hg/liter/min).(ABSTRACT TRUNCATED AT 250 WORDS)