Proteogenomic Approaches for the Identification of NF1/Neurofibromin-depleted Estrogen Receptor-positive Breast Cancers for Targeted Treatment.

NF1 is a key tumor suppressor that represses both RAS and estrogen receptor-α (ER) signaling in breast cancer. Blocking both pathways by fulvestrant (F), a selective ER degrader, together with binimetinib (B), a MEK inhibitor, promotes tumor regression in NF1-depleted ER+ models. We aimed to establish approaches to determine how NF1 protein levels impact B+F treatment response to improve our ability to identify B+F sensitive tumors. We examined a panel of ER+ patient-derived xenograft (PDX) models by DNA and mRNA sequencing and found that more than half of these models carried an NF1 shallow deletion and generally have low mRNA levels. Consistent with RAS and ER activation, RET and MEK levels in NF1-depleted tumors were elevated when profiled by mass spectrometry (MS) after kinase inhibitor bead pulldown. MS showed that NF1 can also directly and selectively bind to palbociclib-conjugated beads, aiding quantification. An IHC assay was also established to measure NF1, but the MS-based approach was more quantitative. Combined IHC and MS analysis defined a threshold of NF1 protein loss in ER+ breast PDX, below which tumors regressed upon treatment with B+F. These results suggest that we now have a MS-verified NF1 IHC assay that can be used for patient selection as a complement to somatic genomic analysis. Significance: A major challenge for targeting the consequence of tumor suppressor disruption is the accurate assessment of protein functional inactivation. NF1 can repress both RAS and ER signaling, and a ComboMATCH trial is underway to treat the patients with binimetinib and fulvestrant. Herein we report a MS-verified NF1 IHC assay that can determine a threshold for NF1 loss to predict treatment response. These approaches may be used to identify and expand the eligible patient population.

Anthropogenic threats to the Vulnerable Andean Condor in northern South America.

Vultures comprise one of the most threatened groups of birds worldwide. With a total population not exceeding 6700 mature individuals, and in rapid decline across its range, the Andean Condor (Vultur gryphus) is listed as a Vulnerable species in the IUCN red list. Local population extinctions and decline are of particular concern in northern South America, where no more than 340 condors may exist at present. Despite this, no quantitative assessments exist in Ecuador, Colombia, and Venezuela regarding the threats affecting Andean Condor populations. To address this, we compiled records of Andean Condors injured, or killed, between 1979 and 2021. We obtained data of 164 condors affected by different causes of injury, of which 83.5% were reported in Ecuador, 15.2% in Colombia, and 1.2% in Venezuela. Of the total number, 84.7% of the injured individuals died. Between 1979 and 2021, in Ecuador, Colombia and Venezuela, at least 103 Andean Condors were presumably poisoned, 22 were shot, and 39 individuals were affected by other causes. The total number of individuals affected by different causes represents between 48% and 72% of the total population estimated in northern South America. Of great concern is the fact that, between 2007 and 2021, poisoning and shooting together caused the loss of 19-31% of the estimated population of condors in Ecuador, and 7-21% of the estimated population in Colombia. Given the important mortality induced by humans, environmental education programs, socio-ecological research, application of environmental laws, and management strategies based on scientific evidence to prevent and mitigate human-wildlife conflicts are urgently required for effective Andean Condor conservation in northern South America.

Resistance to Neoadjuvant Treatment in Breast Cancer: Clinicopathological and Molecular Predictors.

Neoadjuvant Chemotherapy (NAC) in Breast Cancer (BC) has proved useful for the reduction in tumor burden prior to surgery, allowing for a more extensive breast preservation and the eradication of subjacent micrometastases. However, the impact on prognosis is highly dependent on the establishment of Pathological Complete Response (pCR), in particular for Triple Negative (TN) and Hormonal Receptor negative/Human Epidermal growth factor Receptor 2 positive (HR-/HER2+) subtypes. Several pCR predictors, such as PAM50, Integrative Cluster (IntClust), mutations in PI3KCA, or the Trastuzumab Risk model (TRAR), are useful molecular tools for estimating response to treatment and are prognostic. Major evolution events during BC NAC that feature the Residual Disease (RD) are the loss of HR and HER2, which are prognostic of bad outcome, and stemness and immune depletion-related gene expression aberrations. This dynamic nature of the determinants of response to BC NAC, together with the extensive heterogeneity of BC, raises the need to discern the individual and subtype-specific determinants of resistance. Moreover, refining the current approaches for a comprehensive monitoring of tumor evolution during treatment, RD, and eventual recurrences is essential for identifying new actionable alterations and the integral best management of the disease.

Deciphering HER2 Breast Cancer Disease: Biological and Clinical Implications.

The main obstacle for designing effective treatment approaches in breast cancer is the extensive and the characteristic heterogeneity of this tumor. The vast majority of critical genomic changes occurs during breast cancer progression, creating a significant variability within primary tumors as well as between the primary breast cancer and their metastases, a hypothesis have already demonstrated in retrospective studies (1). A clear example of this is the HER2-positive breast cancer. In these tumors, we can find all of the transcriptional subtypes of breast cancer, even the basal like or luminal A subtypes. Although the HER2-enriched is the most representative transcriptional subtype in the HER2-positive breast cancer, we can find it too in breast cancers with HER2-negative status. This intrinsic subtype shows a high expression of the HER2 and is associated with proliferation-related genes clusters, among other features. Therefore, two hypotheses can be suggested. First, the HER2 amplification can be a well-defined driver event present in all of the intrinsic subtypes, and not a subtype marker isolated. Secondly, HER2-enriched subtype can have a distinctive transcriptional landscape independent of HER2 amplification. In this review, we present an extensive revision about the last highlights and advances in clinical and genomic settings of the HER2-positive breast cancer and the HER2-enriched subtype, in an attempt to improving the knowledge of the underlying biology of both entities and to explaining the intrinsic heterogeneity of HER2-positive breast cancers.

Comparison of the Clinical Sensitivity of the Idylla Platform and the OncoBEAM RAS CRC Assay for KRAS Mutation Detection in Liquid Biopsy Samples.

KRAS mutations are common in colorectal cancer (CRC). In this setting, mutation status determination in circulating-free DNA from blood samples (liquid biopsy) has been shown to be a viable alternative to tissue testing. The objective of this study was to compare the sensitivity of two liquid biopsy methods for detecting KRAS mutations in plasma samples from metastatic CRC patients. Samples with a positive (KRAS-MUT+) result and a mutant allelic fraction (MAF) < 5% according to the OncoBEAM RAS CRC assay were pairly analyzed by the Idylla ctKRAS Mutation Test (n = 116). In a cohort of 71 patients with at least 1 year of follow-up, the progression-free survival (PFS) was determined according to MAF values. Idylla detected KRAS mutations in 81/116 OncoBEAM KRAS-MUT+ samples with MAF < 5% and in 48/79 samples with MAF < 1%. Concordance between OncoBEAM and Idylla significantly improved at higher MAF values. PFS rates at 6 and 12 months tended to be lower in patients with MAF levels between 1% and 5% than in those with levels <1%. OncoBEAM demonstrated greater sensitivity for plasma detection of KRAS mutations than Idylla. Importantly, our data identified a "gray zone" below 1% MAF where Idylla showed reduced KRAS mutation detection, highlighting the importance of an accurate method to provide the mutational status of CRC patients.

Triple negative breast cancer subtypes and pathologic complete response rate to neoadjuvant chemotherapy.

Triple negative breast cancer (TNBC) is a heterogeneous disease with distinct molecular subtypes that differentially respond to chemotherapy and targeted agents. The purpose of this study is to explore the clinical relevance of Lehmann TNBC subtypes by identifying any differences in response to neoadjuvant chemotherapy among them. We determined Lehmann subtypes by gene expression profiling in paraffined pre-treatment tumor biopsies from 125 TNBC patients treated with neoadjuvant anthracyclines and/or taxanes +/- carboplatin. We explored the clinicopathological characteristics of Lehmann subtypes and their association with the pathologic complete response (pCR) to different treatments. The global pCR rate was 37%, and it was unevenly distributed within Lehmann's subtypes. Basal-like 1 (BL1) tumors exhibited the highest pCR to carboplatin containing regimens (80% vs 23%, p=0.027) and were the most proliferative (Ki-67>50% of 88.2% vs. 63.7%, p=0.02). Luminal-androgen receptor (LAR) patients achieved the lowest pCR to all treatments (14.3% vs 42.7%, p=0.045 when excluding mesenchymal stem-like (MSL) samples) and were the group with the lowest proliferation (Ki-67≤50% of 71% vs 27%, p=0.002). In our cohort, only tumors with LAR phenotype presented non-basal-like intrinsic subtypes (HER2-enriched and luminal A). TNBC patients present tumors with a high genetic diversity ranging from highly proliferative tumors, likely responsive to platinum-based therapies, to a subset of chemoresistant tumors with low proliferation and luminal characteristics.

Quantification of proteome changes in bovine muscle from two-dimensional electrophoresis data.

Proteome changes in the longissimus thoracis bovine muscle in response to pre-slaughter stress were assessed on the basis of two-dimensional electrophoresis (2-DE) data. In this study, the bootstrap resampling statistical technique and a new measure of relative change of the volume of 2-DE protein spots are shown to be more efficient than commonly used statistics to reliably quantify changes in protein abundance in stress response. The data are supplied in this article and are related to "Tackling proteome changes in the longissimus thoracis bovine muscle in response to pre-slaughter stress" by Franco et al. [1].

Tackling proteome changes in the longissimus thoracis bovine muscle in response to pre-slaughter stress.

Pre-slaughter stress has adverse effects on meat quality that can lead to the occurrence of Dark Firm Dry (DFD) meat in cattle. This study explores the previously uncharacterized proteome changes linked to pre-slaughter stress in the longissimus thoracis (LT) bovine muscle. Differential proteome profiles of DFD and normal (non-DFD) LT meat samples from male calves of the Rubia Gallega breed were assessed by 2-DE coupled to MS analysis (LC-MS/MS and MALDI TOF/TOF MS). A total of seven structural-contractile proteins (three different myosin light chain isoforms, two fast skeletal myosin light chain 2 isoforms, troponin C type 2 and cofilin-2) and three metabolism enzymes (triosephosphate isomerase, ATP synthase and beta-galactoside alpha-2,6-sialyltransferase) were found to have statistically significant differential abundance in sample groups. In addition, 2-DE in combination with the phosphoprotein-specific fluorescent dye Pro-Q DPS revealed that highly phosphorylated fast skeletal myosin regulatory light chain 2 isoforms underwent the most intense relative change in muscle conversion to DFD meat. Therefore, they appear to be the most sensitive biomarkers of stress just prior to slaughter in Rubia Gallega. Overall, these findings will facilitate a more integrative understanding of the biochemical processes associated with stress in cattle muscle and their effects in meat quality. BIOLOGICAL SIGNIFICANCE: Pre-slaughter stress is a crucial factor in meat production. Animals destined for slaughter are stressed by a variety of endogenous and exogenous factors that negatively affect the complex post-mortem biochemical events underlying the conversion of muscle into meat. The study of the muscle proteome has a great relevance for understanding the molecular mechanisms associated with stress. However, there is no information available on the molecular changes linked to pre-slaughter stress in cattle on the proteome scale. Our study led to the identification of a number of candidate proteins associated with the response to pre-slaughter stress in the LT bovine muscle of the Rubia Gallega breed. The functions of those significantly changed proteins have a clear biological relationship with stress response. These findings contribute to a deeper insight into the molecular pathways that respond to stress in cattle.

Histology and immunochemistry evaluation of autologous translocation of retinal pigment epithelium-choroid graft in porcine eyes.

PURPOSE: To evaluate structure and cellular functionality of retinal pigment epithelium (RPE)-choroid grafts after autologous translocation in porcine eyes. METHODS: Retinal pigment epithelium-choroid grafts were obtained from the nasal midperiphery donor site and translocated to the central area in 12 pigs (12 eyes). Grafts were placed under the central retina through a retinotomy. Ophthalmoscopic and pathological evaluations were performed immediately (n = 1) and at 15 (n = 3) and 30 (n = 3) days after surgery. Untranslocated nasal RPE-choroid grafts were obtained at time of surgery and used as controls. Specimens were evaluated by standard histology and by immunochemical studies of RPE65, CRALBP and GFAP. RESULTS: Five animals were lost to follow-up owing to surgery or anaesthesia complications. Ophthalmoscopic examination revealed that the grafts remained in place at all time-points studied. Fifteen and thirty days postsurgery, some areas of the transplanted RPE maintained a monolayered structure. Retinal pigment epithelium cells were firmly attached to Bruch's membrane and predominantly preserved polarity and pigment distribution. However, RPE65, CRALBP and GFAP patterns of expression and distribution were diminished and modified during follow-up. Ophthalmoscopic retinal detachment and proliferative vitreoretinopathy (PVR), confirmed by microscopic evaluation, complicated all cases at 30 days of follow-up. CONCLUSION: Autologous RPE-choroid grafts survived up to 30 days in porcine eyes. Histological and immunochemical evaluation revealed preserved transplanted RPE cells morphology accompanied by alterations in the immunoreactivity expression of functional proteins, and development of significant PVR. The data presented in this manuscript provide insights into the fate, viability and cellular functionality of the transplanted RPE-choroid graft, serving as foundation for further knowledge and improvement of this technique.

Familial hemiplegic migraine with prolonged global aura: follow-up findings of subtraction ictal SPECT co-registered to MRI (SISCOM).

All authors contributed equally to this work. Susana Arias-Rivas wrote the main paper. Manuel Rodriguez-Yáñez investigated the supplementary data. Julia Cortés and Pablo Aguiar performed the nuclear image studies and analysed and described the neuroimaging results. María Pardo, Rogelio Leira and Jose Castillo jointly conceived the study, followed the patient and prepared the manuscript. Miguel Blanco discussed the results. All authors discussed the results and implications and commented on the manuscript at all stages.

Morphological and physiological responses of two varieties of a highland species (Chenopodium quinoa Willd.) growing under near-ambient and strongly reduced solar UV-B in a lowland location.

Morphological and physiological responses of seedlings to different solar UV-B irradiances were evaluated in two varieties of quinoa (Chenopodium quinoa Willd.), a crop species from Andean region of South America. Cristalina and Chucapaca varieties were grown at 1965m a.s.l in a glasshouse under natural light conditions for 18 days, and then transferred to outdoors under near-ambient (+UV-B) and strongly reduced (-UV-B) solar UV-B radiation. Exposition to -UV-B increased cotyledon area and seedling height in Cristalina variety whereas leaf number decreased compared to +UV-B. By contrast Chucapaca variety was not affected by UV-B treatments. Seedling fresh weight (FW), root length and leaf thickness did not show significant differences between +UV-B and -UV-B treatments. Mesophyll tissue was slightly affected by solar UV-B reduction. Chlorophyll content was differentially affected by UV-B treatments. Under +UV-B the highest value was observed in Cristalina variety, while in Chucapaca it was observed under -UV-B treatment. Chlorophyll content was slightly higher in leaves than in cotyledons, but there was no difference in the distribution pattern. Chlorophyll a/b ratio and carotenoid content did not show significant differences between UV-B treatments. Leaf UVB-absorbing compounds showed significant differences between UV-B treatments in Chucapaca only, while there were no significant differences in Cristalina variety. UVB-absorbing compounds of cotyledons did not show significant differences between +UV-B and -UV-B treatments. Sucrose, glucose and fructose showed different distribution patterns in cotyledons and leaves of the two varieties under near-ambient and strongly reduced UV-B. Results demonstrated that varieties of quinoa exhibit different morphological and physiological responses to changes in solar UV-B irradiance, but these responses cannot be used to predict the sensitivity to solar UV-B during a short-term exposition. Also, this study can be useful to learn about the plasticity of metabolic pathways involved in plant's tolerance to solar UV-B radiation.

Epidermal lignin deposition in quinoa cotyledons in response to UV-B radiations.

UV-B radiation (280-320 nm) is harmful to living organisms and has detrimental effects on plant growth, development and physiology. In this work we examined some mechanisms involved in plant responses to UV-B radiation. Seedlings of quinoa (Chenopodium quinoa Willd.) were exposed to variable numbers of UV-B radiation doses, and the effect on cotyledons was studied. We analyzed (1) cotyledons anatomy and chloroplasts ultrastructure; (2) peroxidase activity involved in the lignification processes; and (3) content of photosynthetic pigments, phenolic compounds and carbohydrates. Exposure to two UV-B doses induced an increase in the wall thickness of epidermal cells, which was associated with lignin deposition and higher activity of the peroxidase. The chloroplast ultrastructure showed an appearance typical of plants under shade conditions, likely in response to reduced light penetration into the mesophyll cells due to the screening effect of epidermal lignin deposition. Exposure to UV-B radiation also led to (1) enhancement in the level of phenolics, which may serve a protective function; (2) strong increase in the fructose content, a fact that might be related to higher requirement of erythrose-4P as a substrate for the synthesis of lignin and phenolics; and (3) reduction in the chlorophyll concentration, evidencing alteration in the photosynthetic system. We propose that the observed lignin deposition in epidermal tissues of quinoa is a resistance mechanism against UV-B radiation, which allows growing of this species in Andean highlands.

O berçário de alto risco e o ruído das incubadoras / High risk newborns and the noise in the incubators

A Academia Americana de Pediatria sugere que o nível de exposiçäo à ruído permitido ao recém-nascido näo ultrapasse os 58 dB (A)(Laura e col., 1986). Este estudo investigou os níveis de ruído aos quais os bebês de alto risco estäo expostos em incubadoras de 3 maternidades: 2 na cidade de Säo Paulo e 1 na cidade do Rio de Janeiro. Na maternidade A foram encontrados níveis que variavam de 63 a 69 dBA de ruído contínuo e de 82 a 91 dB linear de impacto de abertura e de 88 a 92 dB linear de fechamento. Na maternidade B foram encontrados níveis que variavam de 59 a 69 dBA de ruído contínuo, de 76 a 88 dB linear de abertura das portinholas e de 81 a 126 dB linear de fechamento. Na maternidade C foram encontrados níveis que variavam de 63 a 70 dBA, de 91 a 94 na abertura das portinholas e de 98 a 114 dBA no fechamento. Este trabalho apresenta valores que devem ser discutidos por todos os profissionais que trabalham diretamente com os bebês na tentativa de minimizar os níveis de ruídos e os riscos que essa exposiçäo possa oferecer