Genome-Wide Patterns of Sequence Divergence of Protein-Coding Genes Between Drosophila buzzatii and D. mojavensis

Evolutionary rates for protein-coding genes are determined not only by natural selection but also by multiple genomic factors including mutation rates, recombination, gene expression levels, and chromosomal location. To investigate the joint effects of different genomic determinants on protein evolution, we compared the coding sequences of 9017 single-copy orthologs between 2 cactophilic species from the Drosophila subgenus, Drosophila mojavensis and D. buzzatii, whose genomes have been previously sequenced. We assessed the impact of 7 genomic determinants, that is, chromosome type, recombination, chromosomal inversions, expression breadth, expression level, gene length, and the number of exons, on divergence rates of protein-coding genes to understand patterns of evolutionary variation. Integrative analysis of these factors revealed that 1) X-linked and autosomal genes evolve at significantly different rates in agreement with the faster-X hypothesis, 2) genes located on the dot chromosome and pericentromeric regions have higher divergence rates, 3) genes located at chromosomes with more fixed inversions have higher pairwise divergence than those located at nearly collinear chromosomes, and 4) gene expression patterns can be considered the strongest determinant of protein evolution. In addition, the number of exons and protein length had a significant effect on pairwise divergence at synonymous sites. All in all, our results show the relative importance of each genomic factor on the rates of protein evolution and functional constraint in these 2 cactophilic Drosophila species.

Correlations between plasma and PET beta-amyloid levels in individuals with subjective cognitive decline: the Fundació ACE Healthy Brain Initiative (FACEHBI)

BACKGROUND

Peripheral biomarkers that identify individuals at risk of developing Alzheimer's disease (AD) or predicting high amyloid beta (Aβ) brain burden would be highly valuable. To facilitate clinical trials of disease-modifying therapies, plasma concentrations of Aβ species are good candidates for peripheral AD biomarkers, but studies to date have generated conflicting results.

METHODS

The Fundació ACE Healthy Brain Initiative (FACEHBI) study uses a convenience sample of 200 individuals diagnosed with subjective cognitive decline (SCD) at the Fundació ACE (Barcelona, Spain) who underwent amyloid florbetaben(18F) (FBB) positron emission tomography (PET) brain imaging. Baseline plasma samples from FACEHBI subjects (aged 65.9 ± 7.2 years) were analyzed using the ABtest (Araclon Biotech). This test directly determines the free plasma (FP) and total plasma (TP) levels of Aβ40 and Aβ42 peptides. The association between Aβ40 and Aβ42 plasma levels and FBB-PET global standardized uptake value ratio (SUVR) was determined using correlations and linear regression-based methods. The effect of the APOE genotype on plasma Aβ levels and FBB-PET was also assessed. Finally, various models including different combinations of demographics, genetics, and Aβ plasma levels were constructed using logistic regression and area under the receiver operating characteristic curve (AUROC) analyses to evaluate their ability for discriminating which subjects presented brain amyloidosis.

RESULTS

FBB-PET global SUVR correlated weakly but significantly with Aβ42/40 plasma ratios. For TP42/40, this observation persisted after controlling for age and APOE ε4 allele carrier status (R2 = 0.193, p = 1.01E-09). The ROC curve demonstrated that plasma Aβ measurements are not superior to APOE and age in combination in predicting brain amyloidosis. It is noteworthy that using a simple preselection tool (the TP42/40 ratio with an empirical cut-off value of 0.08) optimizes the sensitivity and reduces the number of individuals subjected to Aβ FBB-PET scanners to 52.8%. No significant dependency was observed between APOE genotype and plasma Aβ measurements (p value for interaction = 0.105).

CONCLUSION

Brain and plasma Aβ levels are partially correlated in individuals diagnosed with SCD. Aβ plasma measurements, particularly the TP42/40 ratio, could generate a new recruitment strategy independent of the APOE genotype that would improve identification of SCD subjects with brain amyloidosis and reduce the rate of screening failures in preclinical AD studies. Independent replication of these findings is warranted.

FACEHBI: A Prospective Study of Risk Factors, Biomarkers and Cognition in a Cohort of Individuals with Subjective Cognitive Decline. Study Rationale and Research Protocols

BACKGROUND

Long-term longitudinal studies with multimodal biomarkers are needed to delve into the knowledge of preclinical AD. Subjective cognitive decline has been proposed as a risk factor for the development of cognitive impairment. Thus, including individuals with SCD in observational studies may be a cost-effective strategy to increase the prevalence of preclinical AD in the sample.

OBJECTIVES

To describe the rationale, research protocols and baseline characteristics of participants in the Fundació ACE Healthy Brain Initiative (FACEHBI).

DESIGN

FACEHBI is a clinical trial (EudraCT: 2014-000798-38) embedded within a long-term observational study of individuals with SCD.

SETTING

Participants have been recruited at the memory clinic of Fundació ACE (Barcelona) from two different sources: patients referred by a general practitioner and individuals from an Open House Initiative.

PARTICIPANTS

200 individuals diagnosed with SCD with a strictly normal performance in a comprehensive neuropsychological battery.

MEASUREMENTS

Individuals will undergo an extensive neuropsychological protocol, risk factor assessment and a set of multimodal biomarkers including florbetaben PET, structural and functional MRI, diffusion tensor imaging, determination of amyloid species in plasma and neurophthalmologic assessment with optical coherence tomography.

RESULTS

Two hundred individuals have been recruited in 15 months. Mean age was 65.9 years; mean MMSE was 29.2 with a mean of 14.8 years of education.

CONCLUSIONS

FACEHBI is a long-term study of cognition, biomarkers and lifestyle that has been designed upon an innovative symptom-based approach using SCD as target population. It will shed light on the pathophysiology of preclinical AD and the role of SCD as a risk marker for the development of cognitive impairment.

Client and provider factors associated with integration of family planning services among maternal and reproductive health clients in Kigoma Region, Tanzania: a cross-sectional study, April-July 2016

BACKGROUND

Integration of family planning (FP) services into non-FP care visits is an essential strategy for reducing maternal and neonatal mortality through reduction of short birth intervals and unplanned pregnancies.

METHODS

Cross-sectional surveys were conducted across 61 facilities in Kigoma Region, Tanzania, April-July 2016. Multilevel, mixed effects logistic regression analyses were conducted on matched data from providers (n = 330) and clients seeking delivery (n = 935), well-baby (n = 272), pregnancy loss (PL; n = 229), and other routine (postnatal, HIV/STI, other; n = 69) services. Outcomes of interest included receipt of FP information and a modern FP method (significance level p < 0.05).

RESULTS

Clients had significantly greater odds of receiving FP information if the primary reason for seeking care was for PL versus (vs) any other types of care (aOR 1.97), had four or more pregnancies vs fewer (aOR 1.78), and had had a FP discussion with their partner vs no FP discussion (aOR 1.73). Clients had lower odds of receiving FP information if they were aged 40-49 vs 15-19 (aOR 0.50) and reported attending religious services at least weekly vs less frequently (aOR 0.61). Clients of providers who perceived that in-service training had helped vs had not helped job performance (aOR 2.27), and clients of providers having high vs low recent FP training index scores (aOR 1.58) had greater odds of receiving FP information. Clients had greater odds of receiving a modern method when they received information on two or more vs fewer methods (aOR 7.13), had had a FP discussion with their partner vs no discussion (aOR 5.87), if the primary reason for seeking care was for PL vs any other types of care (aOR 4.08), had zero vs one or more live births (aOR 3.92), made their own FP decisions vs not made own FP decisions (aOR 3.17), received FP information from two or more vs fewer sources (aOR 3.12), and were in the middle or high vs the low wealth tercile (aOR 1.99 and 2.30, respectively). Well-baby care clients, Other routine services clients, and married clients had significantly lower odds of receiving a method (aOR 0.14; aOR 0.08; and aOR 0.41, respectively) compared to their counterparts.

CONCLUSIONS

Strategies that better integrate FP into routine care visits, encourage women to have FP discussions with their partners and providers, increase FP training among providers, and expand FP options and sources of information may help reduce the unmet need for FP, and ultimately lower maternal and neonatal mortality.

Identification of Nocardia species from clinical isolates using MALDI-TOF mass spectrometry

The identification of Nocardia isolates still represents a challenge for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) despite its acceptance for most bacterial and fungal isolates. In this study we evaluate the identification of Nocardia isolates using direct spotting and an updated database. Overall, 82 Nocardia isolates belonging to 13 species were identified by DNA sequence analysis of the 16S rRNA and secA1 genes. Nine of these well-characterized isolates from 6 Nocardia species were used to create an in-house library. The remaining 73 isolates were directly spotted on the target plate and on-plate protein extraction was performed. The protein spectra obtained were analyzed by MALDI-TOF MS using the BDAL database (Bruker Daltonics) updated with 6,903 MSPs or the combination of this commercial database and our in-house library. As a result, the use of the commercial database alone and in combination with the in-house library yielded 94.5% and 95.9% of correct species-level identifications, respectively, No isolate was misidentified at the genus level with either database. Besides, the use of the in-house library allowed the species-level identification of a N. otitidiscaviarum isolate that could only be identified at the genus-level with a score value <1.6 using the commercial database. In conclusion, the implementation of the direct spotting method and the in-house database provided a high rate of correct species assignment of Nocardia isolates despite the low number of isolates added. Further addition of well-characterized Nocardia isolates may ensure the rapid, accurate and inexpensive identification of most isolates encountered in the routine of the microbiology laboratory.

Neoadjuvant chemotherapy response influences outcomes in non-colorectal, non-neuroendocrine liver metastases

BACKGROUND

Indications for surgical resection of non-colorectal, non-neuroendocrine (NCNNE) liver metastases are unclear. This study analysed the influence of response to neoadjuvant chemotherapy and the presence of extrahepatic disease (EHD) on outcomes.

METHODS

Patients who underwent hepatic resection for NCNNE liver metastases and who received neoadjuvant chemotherapy at a single centre between 1982 and 2016 were analysed retrospectively. Patients were classified as having no EHD, controlled EHD or non-controlled EHD.

RESULTS

Hepatic resection was performed in 199 patients (81·2 per cent) after partial or complete response to chemotherapy or disease stabilization, and 46 patients (18·8 per cent) after tumour progression. Patients with progressive disease after chemotherapy had worse overall survival than those without (23 versus 50·4 per cent at 5 years; P = 0·004). Median survival was 63·6 (range 31·1-94·8) months for patients without EHD, 34·8 (19·2-49·2) months for those with controlled EHD and 7·2 (1·2-13·2) months for patients with non-controlled EHD (P = 0·004). In multivariable analysis, EHD (P = 0·004), response to chemotherapy (P = 0·004) and resection margins (P = 0·002) were all independent predictors of overall survival, regardless of primary tumour site.

CONCLUSION

The prognosis of patients with NCNNE liver metastases is influenced by preoperative chemotherapy and resectability.

Search for the Exotic Meson X(5568) with the Collider Detector at Fermilab

A search for the exotic meson X(5568) decaying into the B_{s}^{0}π^{±} final state is performed using data corresponding to 9.6  fb^{-1} from pp[over ¯] collisions at sqrt[s]=1960  GeV recorded by the Collider Detector at Fermilab. No evidence for this state is found and an upper limit of 6.7% at the 95% confidence level is set on the fraction of B_{s}^{0} produced through the X(5568)→B_{s}^{0}π^{±} process.

Surgical resection versus systemic therapy for breast cancer liver metastases: Results of a European case matched comparison

BACKGROUND

Resection of breast cancer liver metastases (BCLM) combined with systemic treatment is increasingly accepted but not offered as therapeutic option. New evidence of the additional value of surgery in these patients is scarce while prognoses without surgery remains poor.

PATIENTS AND METHODS

For this case matched analysis, all nationally registered patients with BCLM confined to the liver in the Netherlands (systemic group; N = 523) were selected and compared with patients who received systemic treatment and underwent hepatectomy (resection group; N = 139) at a hepatobiliary centre in France. Matching was based on age, decade when diagnosed, interval to metastases, maximum metastases size, single or multiple tumours, chemotherapy, hormonal or targeted therapy after diagnosis. Based on published guidelines, palliative systemic treatment strategies are similar in both European countries.

RESULTS

Between 1983 and 2013, 3894 patients were screened for inclusion. Overall median follow-up was 80 months (95% CI 70-90 months). The median, 3- and 5-year overall survival of the whole population was 19 months, 29% and 19%, respectively. The resection and systemic group had median survival of 73 vs. 13 months (P < 0.001), respectively. Three and 5-year survival was 18% and 10% for the systemic group and 75% and 54% for the resection group, respectively. After matching, the resection group had a median overall survival of 82 months with a 3- and 5-year overall survival of 81% and 69%, respectively, compared with a median overall survival of 31 months in the systemic group with a 3- and 5-year overall survival of 32% and 24%, respectively (HR 0.28, 95% CI 0.15-0.52; P < 0.001).

CONCLUSIONS

For patients with BCLM, liver resection combined with systemic treatment results in improved overall survival compared to systemic treatment alone. Liver resection should be considered in selected cases.

Abstract P2-09-27: Integrated analysis of PTEN protein expression and PI3KCA mutations as predictors for pathological complete response in HER2-positive breast cancer

Introduction: Anti-HER2 treatment has also influenced the response to neoadjuvant chemotherapy in HER2-positive breast cancer (BC) by increasing the pathologic complete response (pCR) rate. The activation of HER2 signaling causes the downstream activation of the PI3K/AKT/mTOR pathway that plays a crucial role in developing resistance to trastuzumab (T). Therefore, candidate biomarkers with a potential role in the prediction of a pCR and prognosis after anti-HER2 treatment could be selected from this pathway.

Material and Methods: We retrospectively evaluated PTEN protein expression and PI3KCA mutations in core biopsies from HER2-positive patients treated at our institution with neoadjuvant therapy based on anthracyclines, paclitaxel and T. Protein expression was assessed by immunohistochemistry and used as dichotomic variable, PTEN loss was considered if Hscore ≤ 40. The association of PTEN status, PI3KCA mutation and PI3K activation (defined as either PTEN loss and/or presence of PI3KCA) with pathological complete response (ypT0/isN0) and progression-free survival (PFS) was evaluated.

Results: In our database 86 patients with HER2-positive clinical stage II-III BC were identified. Median follow-up was 75.85 months. PTEN was available from 84 (97.7%) and PI3KCA genotype from 67 patients (77.9%). Median age was 47.34, stage III 58.8% and 50% were hormonal receptor (HR) positive. Low PTEN was described in 29.8% tumors and was statistically associated with Grade1-2 and HR positive tumors. PI3KCA mutations (exon 9 and 20) were observed in 23.9% tumors. PI3K activation was detected in 37.5% tumors. Overall, the pCR rate was 53.5%. In low PTEN tumors pCR was 12% and in PTEN-high tumors, it was 72.1% (p&lt;.0001). pCR rate was statistically different between PIK3CA mutant and wild-type tumors (6.3% vs. 51.9%; p&lt;.0001). PI3K activation was statistically associated with lower pCR rate (12.5 vs. 72.9%; p&lt;.0001). In multivariable analysis adjusted for baseline parameters, HR expression (OR 4.170; 95% CI 0.975-17.829;p=0.054) and PI3K activation (OR 45.87; 95% CI8.059-261.101; p&lt;.0001) independently predicted pCR. In univariable analysis clinical, stage III, non-pCR and PI3K activation were correlated with worse PFS. PI3K activation was statistically associated with lower PFS at 5 years (OR 3.813;CI 95%1.369-10.347; p=0.009) in the multivariable analysis.

Conclusions: The study showed the potential role of PIK3CA Genotype and PTEN expression in predicting pCR and prognosis after anthracycline–taxane-based chemotherapy and anti-HER2 treatment.

Citation Format: Gavila J, Gozalbo F, Climent MA, Guerrero AL, Sandiego S, Blanch S, Algarra MA, Soriano V, Guillem V, Ruiz A, Lopez Guerrero JA. Integrated analysis of PTEN protein expression and PI3KCA mutations as predictors for pathological complete response in HER2-positive breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-09-27.

Abstract P4-06-05: Not presented

This abstract was not presented at the symposium.

Abstract P3-09-08: Overeating and breast cancer risk by pathologic subtypes: EpiGEICAM study

Introduction: It has been reported that overeating may be the greatest avoidable cause of cancer in nonsmokers and obesity increases postmenopausal breast cancer (BC) risk. Calorie restriction reduces BC incidence in experimental animals, but the evidence in humans is more limited. This study analyzes the association between female BC risk and excessive or restricted calorie consumption in Spain.

Methods: EpiGEICAM is a multicenter case-control study including 1017 matched pairs (age & town) of incident BC cases and healthy controls in 14 regions in Spain. Participants filled a structured questionnaire. Average calorie intake (cals) during the 5 years previous to diagnosis (cases) or interview (controls) was estimated using a validated 117-item semiquantitative food-frequency questionnaire. Expected calorie intake (cals_exp) was calculated from a linear regression model taking into account the basal metabolic rate (Sabounchi's meta-regression) and the amount of physical activity performed by each woman (5 categories). For each woman the prediction interval (99%) of cals_exp was used to consider her calorie intake as “normal” (NCI) (cals inside this interval –the reference group-), “excesive” (ECI) (cals&gt;upper limit of the interval) or “restricted” (RCI) (cals&lt;lower limit of the interval). The association of ECI and RCI with BC, overall and by pathologic subtype (luminal (ER+ and/or PR+ with HER2-), HER2+ and triple negative), was evaluated using conditional and multinomial logistic regression models, adjusted for age and region (multinomial models), education, body mass index (BMI), smoking, age at menarche & at first birth, menopausal status, previous history of benign breast disease, family history of BC, hormonal replacement therapy (HRT), physical activity and two scores reflecting the participant's adherence to Mediterranean and Western dietary patterns.

Results: After excluding participants with extreme calorie intake, 973 case-control pairs were considered. Average number of calories was higher in BC cases (1990 kcals) than controls (1897 kcals) P=0.001). Women with RCI (cals&lt;80% of the predicted limit) had lower BC risk (OR=0.52, P=0.001), being this effect more marked in premenopausal women (OR=0.36; Pheterogeneity=0.001). On the contrary, women with ECI (cals&gt;40% of the predicted limit) showed increased BC risk (OR=1.92; P=0.001), being this effect stronger in postmenopausal women (OR=2.81; Pheterogenity=0.001). By pathologic subtypes, no statistically significant differences were observed, but ECI (over 40%) was strongly associated with HER2+ tumors (OR=2.05, P=0.021). No differences in the effect of ECI or RCI were observed by levels of BMI, tobacco or HRT.

Conclusion: After taking BMI into account, excessive energy intake increases BC risk, while relative caloric restriction seems to have a protective effect. Moderate calorie restriction, in combination with regular physical activity, could be a good strategy for BC prevention.

Funding:Scientific Foundation of the Spanish Association Against Cancer (AECC), SEOM, FECMA, Cerveza y Salud Foundation, FIS CD110/00018

Citation Format: Pollán M, Castelló A, Martín M, Ruiz A, Casas AM, Baena JM, Antolin S, Ramos M, Garcia-Saénz JA, Muñoz M, Lluch A, de Juan A, Jara C, Sánchez Rovira P, Antón A, Chacón JI, Arcusa A, Jimeno MA, Bezares S, Carrasco E, Pérez-Gómez B, Lope V. Overeating and breast cancer risk by pathologic subtypes: EpiGEICAM study [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-09-08.

Combined Forward-Backward Asymmetry Measurements in Top-Antitop Quark Production at the Tevatron

The CDF and D0 experiments at the Fermilab Tevatron have measured the asymmetry between yields of forward- and backward-produced top and antitop quarks based on their rapidity difference and the asymmetry between their decay leptons. These measurements use the full data sets collected in proton-antiproton collisions at a center-of-mass energy of sqrt[s]=1.96  TeV. We report the results of combinations of the inclusive asymmetries and their differential dependencies on relevant kinematic quantities. The combined inclusive asymmetry is A_{FB}^{tt[over ¯]}=0.128±0.025. The combined inclusive and differential asymmetries are consistent with recent standard model predictions.

Unravelling the mechanisms that determine the uptake and metabolism of magnetic single and multicore nanoparticles in a Xenopus laevis model

Multicore superparamagnetic nanoparticles have been proposed as ideal tools for some biomedical applications because of their high magnetic moment per particle, high specific surface area and long term colloidal stability. Through controlled aggregation and packing of magnetic cores it is possible to obtain not only single-core but also multicore and hollow spheres with internal voids. In this work, we compare toxicological properties of single and multicore nanoparticles. Both types of particles showed moderate in vitro toxicity (MTT assay) tested in Hep G2 (human hepatocellular carcinoma) and Caco-2 (human colorectal adenocarcinoma) cells. The influence of surface chemistry in their biological behavior was also studied after functionalization with O,O'-bis(2-aminoethyl) PEG (2000 Da). For the first time, these nanoparticles were evaluated in a Xenopus laevis model studying their whole organism toxicity and their impact upon iron metabolism. The degree of activation of the metabolic pathway depends on the size and surface charge of the nanoparticles which determine their uptake. The results also highlight the potential of Xenopus laevis model bridging the gap between in vitro cell-based assays and rodent models for toxicity assessment to develop effective nanoparticles for biomedical applications.

[Rectus sheath haematoma: experience in our centre]

BACKGROUND

To describe the clinical characteristics of patients diagnosed with spontaneous abdominal rectus muscle hematoma (RSH), predisposing and precipitating factors, and therapeutic management.

METHOD

Retrospective descriptive study of 46 RSH diagnosed from 2002 to 2016. Epidemiological, clinical, diagnostic tests and treatment were analyzed.

RESULTS

The median age of patients was 81 years, 61% were female. The most frequent triggers were persistent coughing and injection of low molecular weight heparin. Seventy percent were anticoagulated, of which 57% had INR in the supratherapeutic range, and in 45% anticoagulation was definitively discontinued after admission. Forty-one percent presented chronic renal failure; moreover, creatinine at the time of diagnosis was higher than baseline (p <0.001). In most cases, treatment was conservative; interventional radiology was performed on 3 patients (6.5%) and open surgery on 4 (8.7%). Invasive treatment was employed with patients who had larger hematomas and higher transfusion requirements, and this was associated with a longer mean stay (p<0.001).

CONCLUSIONS

RSH is more frequent in elderly patients, treated with acenocumarol and in the supratherapeutic range, and frequently entails permanent suspension of anticoagulant therapy. Renal insufficiency is related to the overdosage of the anticoagulant treatment and to the production of the hematoma. The size of RSH and transfusion requirements are factors that seem to be related to a greater need for invasive treatment through arterial embolization or surgery. Key words. Spontaneous rectus sheath hematoma. Abdominal wall disease. Anticoagulant therapy. Transcatheter embolization. Abdominal pain.

Clinical application of cell, gene and tissue therapies in Spain

Scientific and technical advances in the areas of biomedicine and regenerative medicine have enabled the development of new treatments known as "advanced therapies", which encompass cell therapy, genetics and tissue engineering. The biologic products that can be manufactured from these elements are classified from the standpoint of the Spanish Agency of Medication and Health Products in advanced drug therapies, blood products and transplants. This review seeks to provide scientific and administrative information for clinicians on the use of these biologic resources.