Whole-exome sequencing of cell-free DNA and circulating tumor cells in multiple myeloma.

Liquid biopsies including circulating tumor cells (CTCs) and cell-free DNA (cfDNA) have enabled minimally invasive characterization of many cancers, but are rarely analyzed together. Understanding the detectability and genomic concordance of CTCs and cfDNA may inform their use in guiding cancer precision medicine. Here, we report the detectability of cfDNA and CTCs in blood samples from 107 and 56 patients with multiple myeloma (MM), respectively. Using ultra-low pass whole-genome sequencing, we find both tumor fractions correlate with disease progression. Applying whole-exome sequencing (WES) to cfDNA, CTCs, and matched tumor biopsies, we find concordance in clonal somatic mutations (~99%) and copy number alterations (~81%) between liquid and tumor biopsies. Importantly, analyzing CTCs and cfDNA together enables cross-validation of mutations, uncovers mutations exclusive to either CTCs or cfDNA, and allows blood-based tumor profiling in a greater fraction of patients. Our study demonstrates the utility of analyzing both CTCs and cfDNA in MM.

Effects of two different blends of naturally mycotoxin-contaminated maize meal on growth and metabolic profile in replacement heifers.

The aim of this trial was to assess the effects of the administration of different combinations of mycotoxins in naturally contaminated maize grains on dairy heifer growth, blood measurements and puberty onset. A total of 35 Friesian female heifers were randomly allotted to three experimental groups from 18-21 to 42-45 weeks of age. During the 24-week experimental period (EP), heifers were fed the same diet, but with maize meal derived from three differently contaminated lots: very low contamination, as control (C); medium-low aflatoxin-contaminated (A); and mixed aflatoxin-fumonisin contaminated (A-F). At the end of the EP, they returned to a common diet without contaminated maize, and they were monitored for an additional period of 12 weeks (post-experimental period, PEP). BW, wither height, hip height, body length and heart girth were measured every 4 weeks from the beginning of EP to the end of PEP. At the same time, body condition score was evaluated and blood samples were taken from the jugular vein to be analysed for haematological, serum protein and metabolic profiles. Age at puberty was assessed by measuring weekly plasma progesterone levels from 40 to 52 weeks of age. Body growth measurements were processed both by ANOVA of average daily gain of EP and PEP separately, and by the analysis of growth curve parameters. Haematological, serum protein and metabolic profile were evaluated using a mixed model, taking into account the repeated measurements in time on each animal. Heifers' growth was delayed both in A and A-F groups during EP, as evidenced by the different linear coefficients of the BW growth curve in the three groups. Differently contaminated diets did not affect the haematological profile, so that it can be concluded that these levels of mycotoxin contamination do not determine any specific effect on haematopoiesis and immunity in growing heifers. The main blood marker of mycotoxin chronic toxicity was the γ-glutamyl transferase activity level in plasma, which appeared to be altered even after the removal of mycotoxins. During EP, plasma glucose was lower in the groups fed contaminated diet compared with C. The joint actions of an altered nutritional status and a long-lasting liver damage were probably the causes of the delay in puberty attainment in A and, particularly, in the A-F group. The results from this trial evidenced that a chronic aflatoxin-fumonisin contamination in diets of dairy heifers can determine an important delay in the reproductive career of these animals.

MET and ALK as targets for the treatment of NSCLC.

Cell proliferation, survival, differentiation, migration and metabolism are some of the fundamental cellular processes tightly controlled by the activity of tyrosine-kinase receptors (RTKs). The aberrant signaling of RTKs contributes to cancer growth and survival and has become important target for therapeutic approaches. Well-characterized kinase molecular target in lung cancer, in particular in non-small cell lung cancer (NSCLC), is the activated epidermal growth factor receptor (EGFR) pathway. More recently, the oncogenic role of other two tyrosine-kinases, the hepatocyte growth factor receptor (MET) and the anaplastic lymphoma kinase (ALK), has been recognized. Many different therapeutic strategies have been investigated with the goal to inhibit these receptors, subsequent downstream signaling cascades and arrest tumor growth. This review will discuss the MET and ALK pathways, the different strategies of their inhibition and the potential approaches to overcome acquired resistance to kinase inhibitors in these two genes.

Oncogenic and drug-sensitive NTRK1 rearrangements in lung cancer.

We identified new gene fusions in patients with lung cancer harboring the kinase domain of the NTRK1 gene that encodes the high-affinity nerve growth factor receptor (TRKA protein). Both the MPRIP-NTRK1 and CD74-NTRK1 fusions lead to constitutive TRKA kinase activity and are oncogenic. Treatment of cells expressing NTRK1 fusions with inhibitors of TRKA kinase activity inhibited autophosphorylation of TRKA and cell growth. Tumor samples from 3 of 91 patients with lung cancer (3.3%) without known oncogenic alterations assayed by next-generation sequencing or fluorescence in situ hybridization demonstrated evidence of NTRK1 gene fusions.

Body growth, hematological profile, and clinical biochemistry of heifer calves sired by a bull or its clone.

The aim of this paper was to compare body growth, hematological profile development, and clinical biochemistry in the female progeny of a sire with the female progeny of its clone. Sixteen Friesian female calves, 9 daughters from a tested bull (BULL) and 7 from its somatic cell nuclear transfer clone (CLONE) were monitored from birth to 60 wk of life. Body weight (BW), wither height (WH), hip height (HH), body length (BL), and hearth girth (HG) were measured at birth and 4, 8, 12, 16, 20, 24, 36, and 50 wk. Blood samples were taken from jugular vein at 12 to 48 h from birth and 1, 2, 3, 4, 8, 12, 16, 20, 24, and 36 wks of age, to be analyzed for hematological, serum protein, and metabolic profiles. At the same time, rectal temperature (RT) was recorded. Age at puberty was assessed on surviving heifers by measuring weekly plasma progesterone levels. Data were evaluated using a mixed model, taking into account the repeated measures in time on the calf. For each variable, different covariance structures were tested, choosing the best according to the Akaike's Information Criteria. Significant was set at P < 0.05, and a trend was considered for P < 0.10. At 24 wk of age, WH was lower in CLONE daughters than BULL daughters. Around 20 wk of age, there was a trend for lower BW in CLONE daughters than BULL daughters, confirmed from differences in HG. There was no difference in RT due to sire effect. Blood glucose concentration decreased in both groups during the first 4 wk of life; at birth, only a trend for higher blood glucose in CLONE daughters was recorded, whereas an opposite trend was observed for plasma creatinine. Total leukocyte count did not differ between progenies. Circulating lymphocytes tended to be lower in CLONE than BULL daughters. The neutrophil: lymphocyte ratio tended to be higher in CLONE than BULL calves. No difference was demonstrated for erythrocyte features, whereas mean platelet volume tended to be lower in CLONE than BULL progeny. From these results, there were no differences between progenies from BULL and its clone that suggest welfare problems in the first 6 mo of life.

Improving the yield of circulating tumour cells facilitates molecular characterisation and recognition of discordant HER2 amplification in breast cancer.

BACKGROUND: Circulating tumour cells (CTCs) offer a non-invasive approach to obtain and characterise metastatic tumour cells, but their usefulness has been limited by low CTC yields from conventional isolation methods. METHODS: To improve CTC yields and facilitate their molecular characterisation we compared the Food and Drug Administration-approved CellSearch Epithelial Kit (CEK) to a simplified CTC capture method, CellSearch Profile Kit (CPK), on paired blood samples from patients with metastatic breast (n=75) and lung (n=71) cancer. Molecular markers including Human Epidermal growth factor Receptor 2 (HER2) were evaluated on CTCs by fluorescence in situ hybridisation (FISH) and compared to patients' primary and metastatic cancer. RESULTS: The median cell count from patients with breast cancer using the CPK was 117 vs 4 for CEK (P<0.0001). Lung cancer samples were similar; CPK: 145 cells vs CEK:4 cells (P<0.0001). Recovered CTCs were relatively pure (60-70%) and were evaluable by FISH and immunofluorescence. A total of 10 of 30 (33%) breast cancer patients with HER2-negative primary and metastatic tissue had HER2-amplified CTCs. CONCLUSION: The CPK method provides a high yield of relatively pure CTCs, facilitating their molecular characterisation. Circulating tumour cells obtained using CPK technology demonstrate that significant discordance exists between HER2 amplification of a patient's CTCs and that of the primary and metastatic tumour.

Amplification of EGFR T790M causes resistance to an irreversible EGFR inhibitor.

Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors, gefitinib and erlotinib are effective therapies against mutant non-small cell lung cancers (NSCLCs). Treatment is limited by the development of resistance in part explained by the gain of a secondary EGFR mutation, T790M, at the gatekeeper residue. Irreversible EGFR inhibitors, including PF00299804, are effective in vitro and in vivo against EGFR mutant tumors that contain EGFR T790M and are currently under clinical development. In this study, we generate models of resistance to PF00299804, using cell lines with EGFR T790M and show that the PF00299804-resistant models develop focal amplification of EGFR that preferentially involves the T790M-containing allele. These PF00299804-resistant cell lines remain dependent on EGFR for growth as downregulation of EGFR by shRNA compromises their viability. We show that resistance to PF00299804 arises, at least in part, through selection of a pre-existing EGFR T790M-amplified clone both in vitro and using a xenograft model in vivo. Our findings show that EGFR T790M is a common resistance mechanism to both reversible, and when amplified, the irreversible EGFR kinase inhibitors further emphasizing the need to develop more potent therapies against EGFR T790M. These findings can be used to guide studies of patient tumor specimens from ongoing clinical trials of irreversible EGFR kinase inhibitors.

Evaluation of milk enzymes and electrolytes, plasma metabolites, and oxidative status in twin cows milked in an automatic milking system or twice daily in a conventional milking parlor.

The aim of this paper was to evaluate the effects of automatic milking (AM) on milk enzymes and minerals related to mammary epithelial integrity in comparison with twice-daily conventional milking (CM). One cow from each of 6 pairs of twins was assigned to be milked with AM or with CM throughout first lactation. Milk production was recorded and milk samples were collected at 4, 11, 18, 25, 32, and 39 wk of lactation (WOL) to determine fat and protein content, somatic cell count, pH, plasminogen (pl) and plasmin (Pl) activities, Na, K, and Cl. Body condition score was monitored; blood samples were collected to determine energy-related metabolites in the first third of lactation (14 WOL), and plasma oxidative status throughout lactation. Overall mean and standard deviation of milking frequency (MF) in AM were 2.69 and 0.88, respectively. Milk production, fat and protein contents, and somatic cell count did not differ between milking systems. The pl and pl+Pl activities were lesser in AM than in CM. Milk pH was greater in AM than in CM. Milk Na, K, Na/K ratio, and Cl did not differ across the whole lactation. Milk pH had a positive correlation with milk Pl activity (r = 0.41), Na (r = 0.37), and Cl (r = 0.40) concentration, and negative correlation with the log(10) of pl/Pl ratio (r = -0.47). The milk Na/K ratio had a positive correlation (r = 0.55) with milk Pl activity. Milking system (MS) did not seem to affect mammary epithelial permeability. The differences in enzymatic (proteolytic) activity due to the MS, probably related to daily MF, lead one to suppose that the quality of the protein fraction for the cheese-making process was preserved better with AM than with CM, even if differences in pH might negatively interfere. No difference was detected in BCS, and in plasma concentration of triglycerides and nonesterified fatty acids, whereas plasma cholesterol concentration during the first 10 WOL was lesser in AM than CM. Oxidative status, measured by plasma reactive oxygen metabolites and thiol groups, did not differ between MS throughout the whole lactation. These results suggest that early lactation of AM primiparous cows may give rise to crucial situations: for milk production, when a low MF may impair further mammary cell proliferation; for milk quality, if an irregular MF, with prolonged milking intervals, leads to an increased milk pH with increased conversion of pl to Pl.

Aromatase is differentially expressed in peripheral blood leukocytes from children, and adult female and male subjects.

OBJECTIVE: Aromatase, the key enzyme involved in estrogen synthesis, is expressed in a variety of cells and tissues including human peripheral blood leukocytes (PBLs). The present study was designed to evaluate PBL aromatase gene expression in male and female subjects of different age groups. In addition, differences in gene expression during the follicular and luteal phase of the menstrual cycle in women, and before and after testosterone administration in men, were estimated. DESIGN: Aromatase mRNA and protein were measured in PBLs obtained from young (n = 10) and postmenopausal women (n = 10), men (n = 15), and prepubertal children (n = 10). Aromatase mRNA and protein were also measured during the follicular and luteal phases of the menstrual cycle in women, and before and after the intramuscular administration of 250 mg testosterone enanthate in men. METHODS AND RESULTS: Aromatase mRNA measured by real-time PCR in PBLs from women during the follicular phase was significantly higher than during the luteal phase of the menstrual cycle (P < 0.05). In men, PBL aromatase mRNA values increased significantly following testosterone administration (P < 0.05). PBL mRNA aromatase levels in women during the follicular phase and men after testosterone administration were significantly higher (one-way ANOVA; P < 0.05) than in any other group. Children, postmenopausal women, and women during the luteal phase showed the lowest aromatase mRNA expression. The results of the immunoblot analysis confirmed the data obtained by real-time PCR. A positive correlation between PBL aromatase mRNA values and plasma estradiol and estrone levels during the follicular phase of the menstrual cycle was observed in the group of adult women. No other correlations were found. CONCLUSIONS: The aromatase gene is differentially expressed in PBLs from women, men, and prepubertal children, indicating a sexual dimorphism in the enzyme expression and an important role of sex steroids in the modulation of aromatase gene expression.

Decreased androgen receptor gene methylation in premature pubarche: a novel pathogenetic mechanism?

CONTEXT: Several studies found links between DNA methylation and gene expression. In patients with idiopathic hirsutism, a preferential methylation of the of shorter androgen receptor (AR) alleles was hypothesized to be responsible for the abnormal hair growth. OBJECTIVE: The objective of this study was to assess whether abnormalities in the AR function in both peripheral blood leukocytes (PBLs) and androgen target tissues are present in children with premature pubarche (PP). DESIGN: Human DNA was extracted from PBLs and pubic hair and CAG repeats length and methylation status of the AR gene were analyzed. SETTING: The study was performed at a Pediatric Endocrinology referral clinic. PATIENTS: Twenty-five girls with PP, 23 prepubertal children, and 10 girls with Tanner stage II pubertal development were studied. MAIN OUTCOME MEASURE: The main outcome measures were CAG repeat length and AR methylation pattern in PBLs and pubic hair. RESULTS: In PBLs from PP patients, AR gene methylation was significantly lower (P < 0.01) than that of prepubertal children and similar to that of girls with Tanner II stage pubertal development. A negative correlation between AR gene methylation in PBLs and the age of normal children was detected. PATIENTS with PP exhibited a hair follicle AR methylation pattern similar to that of Tanner stage II girls. The mean number of CAG repeats was lower in PP patients than in prepubertal and Tanner stage II girls, although it was within the normal range for the general population in both groups. CONCLUSIONS: The increased AR gene activity observed in PP patients, as indicated by the reduced AR gene methylation pattern, together with the presence of shorter CAG repeats, might lead to hypersensitivity of the hair follicles to steroid hormones and therefore to the premature development of pubic hair.

Effects of energy and protein allowances in the diets of prepubertal heifers on growth and milk production.

Sixty-one Italian Friesian heifers between 100 and 300 kg of body weight (BW) were fed one of four diets. Heifers that were fed the diet with low energy and low protein received 90% of the amounts of total digestible nutrients (TDN) and crude protein (CP) recommended by the National Research Council for large breed dairy heifers growing at a rate of 0.7 kg/d. Ninety and 110% of recommended amounts of TDN and CP, respectively, were supplied to heifers fed the diet containing low energy and high protein. The diet with high energy and low protein provided 110 and 90% of recommended amounts of TDN and CP, respectively, and heifers fed high energy and high protein received 110% of the recommended amounts of both TDN and CP. When heifers reached 300 kg of BW, all were fed an identical diet. Heifers were bred at approximately 370 kg of BW. The increase of either TDN or CP improved average daily gain (608.1 g/d for heifers fed the low energy and low protein diet; 658.9 g/d for heifers fed the low energy and high protein diet; 794.4 g/d for heifers fed the high energy and low protein diet; and 847.6 g/d for heifers fed the high energy and high protein diet). Milk production through 36 wk of the first lactation was not influenced by the increased TDN or CP in the diet (22.7 kg/d for heifers fed low energy and low protein, 22.2 kg/d for heifers fed low energy and high protein diet, 20.2 kg/d for heifers fed the high energy and low protein diet, and 21.8 kg/d for heifers fed high energy and high protein diet). Results showed that Italian Friesian heifers can tolerate an average daily gain of approximately 800 g from 100 to 300 kg of BW without any detrimental effect on future milk production.