Role of Moonlighting Proteins in Disease: Analyzing the Contribution of Canonical and Moonlighting Functions in Disease Progression.

The term moonlighting proteins refers to those proteins that present alternative functions performed by a single polypeptide chain acquired throughout evolution (called canonical and moonlighting, respectively). Over 78% of moonlighting proteins are involved in human diseases, 48% are targeted by current drugs, and over 25% of them are involved in the virulence of pathogenic microorganisms. These facts encouraged us to study the link between the functions of moonlighting proteins and disease. We found a large number of moonlighting functions activated by pathological conditions that are highly involved in disease development and progression. The factors that activate some moonlighting functions take place only in pathological conditions, such as specific cellular translocations or changes in protein structure. Some moonlighting functions are involved in disease promotion while others are involved in curbing it. The disease-impairing moonlighting functions attempt to restore the homeostasis, or to reduce the damage linked to the imbalance caused by the disease. The disease-promoting moonlighting functions primarily involve the immune system, mesenchyme cross-talk, or excessive tissue proliferation. We often find moonlighting functions linked to the canonical function in a pathological context. Moonlighting functions are especially coordinated in inflammation and cancer. Wound healing and epithelial to mesenchymal transition are very representative. They involve multiple moonlighting proteins with a different role in each phase of the process, contributing to the current-phase phenotype or promoting a phase switch, mitigating the damage or intensifying the remodeling. All of this implies a new level of complexity in the study of pathology genesis, progression, and treatment. The specific protein function involved in a patient's progress or that is affected by a drug must be elucidated for the correct treatment of diseases.

Secondary resistance to anti-EGFR therapy by transcriptional reprogramming in patient-derived colorectal cancer models.

BACKGROUND: The development of secondary resistance (SR) in metastatic colorectal cancer (mCRC) treated with anti-epidermal growth factor receptor (anti-EGFR) antibodies is not fully understood at the molecular level. Here we tested in vivo selection of anti-EGFR SR tumors in CRC patient-derived xenograft (PDX) models as a strategy for a molecular dissection of SR mechanisms. METHODS: We analyzed 21 KRAS, NRAS, BRAF, and PI3K wildtype CRC patient-derived xenograft (PDX) models for their anti-EGFR sensitivity. Furthermore, 31 anti-EGFR SR tumors were generated via chronic in vivo treatment with cetuximab. A multi-omics approach was employed to address molecular primary and secondary resistance mechanisms. Gene set enrichment analyses were used to uncover SR pathways. Targeted therapy of SR PDX models was applied to validate selected SR pathways. RESULTS: In vivo anti-EGFR SR could be established with high efficiency. Chronic anti-EGFR treatment of CRC PDX tumors induced parallel evolution of multiple resistant lesions with independent molecular SR mechanisms. Mutations in driver genes explained SR development in a subgroup of CRC PDX models, only. Transcriptional reprogramming inducing anti-EGFR SR was discovered as a common mechanism in CRC PDX models frequently leading to RAS signaling pathway activation. We identified cAMP and STAT3 signaling activation, as well as paracrine and autocrine signaling via growth factors as novel anti-EGFR secondary resistance mechanisms. Secondary resistant xenograft tumors could successfully be treated by addressing identified transcriptional changes by tailored targeted therapies. CONCLUSIONS: Our study demonstrates that SR PDX tumors provide a unique platform to study molecular SR mechanisms and allow testing of multiple treatments for efficient targeting of SR mechanisms, not possible in the patient. Importantly, it suggests that the development of anti-EGFR tolerant cells via transcriptional reprogramming as a cause of anti-EGFR SR in CRC is likely more prevalent than previously anticipated. It emphasizes the need for analyses of SR tumor tissues at a multi-omics level for a comprehensive molecular understanding of anti-EGFR SR in CRC.

Degradation of CCNK/CDK12 is a druggable vulnerability of colorectal cancer.

Novel treatment options for metastatic colorectal cancer (CRC) are urgently needed to improve patient outcome. Here, we screen a library of non-characterized small molecules against a heterogeneous collection of patient-derived CRC spheroids. By prioritizing compounds with inhibitory activity in a subset of-but not all-spheroid cultures, NCT02 is identified as a candidate with minimal risk of non-specific toxicity. Mechanistically, we show that NCT02 acts as molecular glue that induces ubiquitination of cyclin K (CCNK) and proteasomal degradation of CCNK and its complex partner CDK12. Knockout of CCNK or CDK12 decreases proliferation of CRC cells in vitro and tumor growth in vivo. Interestingly, sensitivity to pharmacological CCNK/CDK12 degradation is associated with TP53 deficiency and consensus molecular subtype 4 in vitro and in patient-derived xenografts. We thus demonstrate the efficacy of targeted CCNK/CDK12 degradation for a CRC subset, highlighting the potential of drug-induced proteolysis for difficult-to-treat types of cancer.

Functional States in Tumor-Initiating Cell Differentiation in Human Colorectal Cancer.

Intra-tumor heterogeneity of tumor-initiating cell (TIC) activity drives colorectal cancer (CRC) progression and therapy resistance. Here, we used single-cell RNA-sequencing of patient-derived CRC models to decipher distinct cell subpopulations based on their transcriptional profiles. Cell type-specific expression modules of stem-like, transit amplifying-like, and differentiated CRC cells resemble differentiation states of normal intestinal epithelial cells. Strikingly, identified subpopulations differ in proliferative activity and metabolic state. In summary, we here show at single-cell resolution that transcriptional heterogeneity identifies functional states during TIC differentiation. Furthermore, identified expression signatures are linked to patient prognosis. Targeting transcriptional states associated to cancer cell differentiation might unravel novel vulnerabilities in human CRC.

The sFlt-1/PlGF ratio as a triage tool to identify superimposed preeclampsia in women with chronic hypertension in emergency rooms.

OBJECTIVES: Assess the usefulness of the sFlt-1/PlGF ratio for the differential diagnosis of uncontrolled chronic hypertension vs. superimposed preeclampsia. STUDY DESIGN: We performed a cross-sectional study from 2015 to 2017 and 42 women with initial diagnosis of superimposed preeclampsia were enrolled in the emergency room. After a 12 week follow up patients were grouped as superimposed preeclampsia (Group A) and uncontrolled chronic hypertension (Group B) according to the American College of Obstetricians and Gynecologist criteria. A group of 33 healthy women paired by gestational age were included as controls (Group C). Maternal serum levels of sFlt-1 and PlGF were measured at enrollment, and the ratios of the groups were compared. MAIN OUTCOME MEASURES: Superimposed preeclampsia vs. uncontrolled chronic hypertension. RESULTS: After follow-up, group distribution was 30 women in Group A, 12 women in Group B, and 25 women in Group C. The sFlt-1/PlGF ratio was higher in women with superimposed preeclampsia than in women with uncontrolled chronic hypertension (215.5 vs. 9.65, p < 0.001). The control group displayed lower ratio values (3.66, p < 0.001). The sFlt-1 concentration was higher in Group A than in Group B (7564 vs. 1281 pg/mL, p < 0.001) and the PlGF level was lower in Group A (34.39 vs. 169 pg/mL, p < 0.001). CONCLUSIONS: The sFlt-1/PlGF ratio exhibits good performance for the differential diagnosis of superimposed preeclampsia vs. uncontrolled chronic hypertension.

Key Clinical Factors Predicting Adipokine and Oxidative Stress Marker Concentrations among Normal, Overweight and Obese Pregnant Women Using Artificial Neural Networks.

Maternal obesity has been related to adverse neonatal outcomes and fetal programming. Oxidative stress and adipokines are potential biomarkers in such pregnancies; thus, the measurement of these molecules has been considered critical. Therefore, we developed artificial neural network (ANN) models based on maternal weight status and clinical data to predict reliable maternal blood concentrations of these biomarkers at the end of pregnancy. Adipokines (adiponectin, leptin, and resistin), and DNA, lipid and protein oxidative markers (8-oxo-2'-deoxyguanosine, malondialdehyde and carbonylated proteins, respectively) were assessed in blood of normal weight, overweight and obese women in the third trimester of pregnancy. A Back-propagation algorithm was used to train ANN models with four input variables (age, pre-gestational body mass index (p-BMI), weight status and gestational age). ANN models were able to accurately predict all biomarkers with regression coefficients greater than R² = 0.945. P-BMI was the most significant variable for estimating adiponectin and carbonylated proteins concentrations (37%), while gestational age was the most relevant variable to predict resistin and malondialdehyde (34%). Age, gestational age and p-BMI had the same significance for leptin values. Finally, for 8-oxo-2'-deoxyguanosine prediction, the most significant variable was age (37%). These models become relevant to improve clinical and nutrition interventions in prenatal care.

Studying the complex expression dependences between sets of coexpressed genes.

Organisms simplify the orchestration of gene expression by coregulating genes whose products function together in the cell. The use of clustering methods to obtain sets of coexpressed genes from expression arrays is very common; nevertheless there are no appropriate tools to study the expression networks among these sets of coexpressed genes. The aim of the developed tools is to allow studying the complex expression dependences that exist between sets of coexpressed genes. For this purpose, we start detecting the nonlinear expression relationships between pairs of genes, plus the coexpressed genes. Next, we form networks among sets of coexpressed genes that maintain nonlinear expression dependences between all of them. The expression relationship between the sets of coexpressed genes is defined by the expression relationship between the skeletons of these sets, where this skeleton represents the coexpressed genes with a well-defined nonlinear expression relationship with the skeleton of the other sets. As a result, we can study the nonlinear expression relationships between a target gene and other sets of coexpressed genes, or start the study from the skeleton of the sets, to study the complex relationships of activation and deactivation between the sets of coexpressed genes that carry out the different cellular processes present in the expression experiments.

Analysis of gene expression for studying tumor progression: the case of glucocorticoid administration.

BACKGROUND: Glucocorticoids are commonly used as adjuvant treatment for side-effects and have anti-proliferative activity in several tumors but, on the other hand, their proliferative effect has been reported in several studies, some of them involving the spread of cancer. We shall attempt to reconcile these incongruities from the genomic and tissue-physiology perspectives with our findings. METHODS: An accurate phenotype analysis of microarray data can help to solve multiple paradoxes derived from tumor-progression models. We have developed a new strategy to facilitate the study of interdependences among the phenotypes defined by the sample clusters obtained by common clustering methods (HC, SOTA, SOM, PAM). These interdependences are obtained by the detection of non-linear expression-relationships where each fluctuation in the relationship implies a phenotype change and each relationship typology implies a specific phenotype interdependence. As a result, multiple phenotypic changes are identified together with the genes involved in the phenotype transitions. In this way, we study the phenotypic changes from microarray data that describe common phenotypes in cancer from different tissues, and we cross our results with biomedical databases to relate the glucocorticoid activity to the phenotypic changes. RESULTS: 11,244 significant non-linear expression relationships, classified into 11 different typologies, have been detected from the data matrix analyzed. From them, 415 non-linear expression relationships were related to glucocorticoid activity. Studying them, we have found the possible reason for opposite effects of some stressor agents like dexamethasone on tumor progression and it has been confirmed by literature. This hidden reason has resulted in being linked with the type of tumor progression of the tissues. In the first type of tumor progression found, new cells can be stressed during proliferation and stressor agents increase tumor proliferation. In the second type, cell stress and tumor proliferation are antagonists so, therefore, stressor agents stop tumor proliferation in order to stress the cells. The non-linear expression relationships among DUSP6, FERMT2, FKBP5, EGFR, NEDD4L and CITED2 genes are used to synthesize these findings.

Association between selected structural defects and chromosomal abnormalities.

OBJECTIVE: To determine the association between some major structural abnormalities detected prenatally by ultrasound and chromosomal abnormalities. MATERIAL AND METHODS: The present study was a retrolective, transversal study. We analyzed case records of patients during the fetal follow-up at the Department of Maternal Fetal Medicine from January 1994 to May 2010 to identify fetal patients with a diagnosis of holoprosencephaly, diaphragmatic hernia, omphalocele, cystic hygroma, hydrops and cardiac defects. We analyzed patients who had a prenatal invasive diagnosis procedure to obtain the odds ratio (OR) for some major isolated anomalies and their different combinations with respect to chromosomal abnormalities. RESULTS: We examined 280 patients with ultrasonographic markers for chromosomal alteration, 197 met inclusion criteria, from which 88 had chromosomal abnormalities. The most frequent diagnosis was trisomy 18 (31.8%), which was followed by trisomy 21 (21.6%), trisomy 13 (21.6%), Turner syndrome (monosomy X) (14.8%) and other chromosomal abnormalities (10.2%). Among the fetuses with nonisolated holoprosencephaly, we obtained an OR of 4.9 95% CI (0.99-24.2) for aneuploidy. Associated omphalocele had an OR of 7.63 95% CI (2.07-46.75), p < 0.01. Interestingly, 62% of aneuploidy cases had associated cardiac defects [OR = 7.7 95% CI (1.4-41.7)]. In addition, associated cystic hygroma had an OR of 2.5 95% CI (0.59-10.91). Heart defects were the most common defects in fetuses with trisomy 18 (57.1%), when they were associated with facial cleft, we had an OR of 11.08 95% CI (2.99-41.11), p < 0.0001. Statistical potency was calculated for each analyzed defect and it was over 80% for all of them but diaphragmatic hernia. CONCLUSIONS: The association of 2 or more structural defects increased the probability of a fetus to be a carrier of a chromosomal disorder; however this was not statistically significative except for associated omphalocele. Heart defects showed the greatest association with all chromosomal abnormalities. The most important association was among heart defect, facial cleft and trisomy 13.

Prenatal prevalence of skeletal dysplasias and a proposal ultrasonographic diagnosis approach.

OBJECTIVE: To determine the prevalence of fetal bone dysplasias diagnosed at the Department of Maternal Fetal Medicine (UNIMEF) of the Instituto Nacional de Perinatologia (INPer); and to describe the most frequent skeletal dysplasias and to propose a diagnostic flow chart. MATERIALS AND METHODS: This is a case series study including skeletal dysplasias cases from January 1995 until December 2009 at the UNIMEF Statistical analysis was performed using SPSS 12 statistical software. RESULTS: A total of 81,892 births were registered at the institution during the study period. The prevalence of bone dysplasia was 8.1 per 10,000 births. We used a diagnostic flow chart that was developed at our institution to diagnose skeletal dysplasias. Micromelia (n = 40, 59.7%) and both rhizomelia and mesomelia (n = 17, 25.3%) were highly prevalent. We found other structural anomalies in 40 cases (61.1%), which were associated with different skeletal dysplasias; these other anomalies were mainly congenital heart diseases (12 cases) with a predominance of ventricular septal defects. There was polyhydramnios in 43.2% of cases. The mean of the gestational age at diagnosis was 24.5 weeks (SD 5.66). The karyotype was obtained in 11.9% (8/67) of cases. A total of 7 stillbirths and 11 neonatal deaths were registered, of which only 10 cases received a necropsy. Births occurred in the third trimester for 88% of cases, of which 85% were born via Cesarean section, whereas in the second trimester, the vaginal approach was chosen in 100% of cases. CONCLUSIONS: The prenatal diagnosis of bone dysplasias is challenging due to the late development of the diagnostic features. Nevertheless, using ultrasonography in a systematic approach, in conjunction with a multidisciplinary approach, is a key factor in the diagnosis of this disease during the fetal period.

[Diffuse cavernous hemangioma of the uterus diagnosed during pregnancy. Case report]. / Hemangioma cavernoso difuso del utero diagnosticado durante el embarazo. Reporte de un caso.

We report the case of a pregnancy of 16 weeks with anemia and a presumptive diagnosis of partial mole. In secondary care this diagnosis was ruled out through ultrasonography and diffuse cysts were found in the myometrium. Spectral Doppler ultrasound showed no flow, but it could be observed with power angiography. Cesarean section was performed at 38 weeks and hysterectomy 24 hours after because of intra-abdominal hemorrhage. Power angiography, spectral Doppler and serum human chorionic gonadotropin are the most useful diagnostic tools in the differential diagnosis of diffuse cavernous hemangioma of the uterus. Postpartum hemorrhage is a likely complication.

[Birth defects associated with increased nuchal translucency]. / Defectos congénitos asociados con translucencia nucal aumentada.

BACKGROUND: Nuchal translucency is widely used to screen for trisomy 21 in the first trimester of pregnancy. It has also been associated with other chromosomal abnormalities, genetic syndromes and congenital defects. OBJECTIVE: To evaluate the perinatal outcome of patients who showed nuchal translucency greater or equal to 95th percentile during the first trimester ultrasound screening, which underwent fetal karyotype. MATERIAL AND METHOD: Case series. Fetuses with nuchal translucency greater or equal to 95th percentile were evaluated by fetal karyotype, second-trimester structural ultrasound scan, fetal echocardiography and postnatal clinical genetic evaluation, attended in the servicio de Genética of the Instituto Nacional de Perinatología Isidro Espinosa de los Reyes. RESULTS: 48 fetuses were evaluated. The karyotype was normal in 39 (81%) and abnormal in 9 (19%) cases of which three had trisomy 21, three monosomy X, two trisomy 18 and one 47,XYY In the cases with normal karyotype, 13 (33%) showed an abnormal second trimester ultrasound scan; among them, 12 had major congenital defects, 5 of them had abnormal cardiac findings that were confirmed by fetal echocardiography. In the group of 26 fetuses with normal karyotype and ultrasound, only 2 patients had minor birth defects. CONCLUSIONS: Increased fetal nuchal translucency is frequently associated with chromosomal abnormalities and several congenital defects, mostly heart defects and genetic syndromes. Our findings are in accordance with other published reports where a complete follow-up of all patients with increased nuchal translucency is recommended even if they have a normal karyotype, due to the increased risk of having other congenital defects or syndromic entities.

PCOPGene-Net: holistic characterisation of cellular states from microarray data based on continuous and non-continuous analysis of gene-expression relationships.

BACKGROUND: Microarray technology is so expensive and powerful that it is essential to extract maximum value from microarray data, specially from large-sample-series microarrays. Our web tools attempt to respond to these researchers' needs by facilitating the possibility to test and formulate from a hypothesis to entire models under a holistic point of view. RESULTS: PCOPGene-Net is a web application for facilitating the study of the relationships among gene expressions under microarray conditions, to classify these conditions and to study their effect on expression relationships. Furthermore, the system guides the researcher in the navigation through the microarray data by providing the most suitable genes and information for the researcher's interests at each moment. We achieve all of these by means of the zoom-out operation, the zoom-in operation, the non-continuous analysis and crossing the PCOPGene results with external data-servers. CONCLUSION: PCOPGene-Net helps to identify cellular states and the genes involved in these. All of that is accomplished in a flexible way, guided by the researcher's interests and taking advantage of the ability of our system to relate gene expressions, even when these relationships are non-continuous and cannot be found using linear or non-linear analytical methods. Currently, our tools are used for tumour-progression study from a holistic point of view.

[Thoracoamniotic shunts and thoracocentesis in fetal therapy]. / Derivaciones toracoamnióticas y toracocentesis en el tratamiento fetal.

BACKGROUND: The not heart thoracic anomalies are caused by different abnormalities in the embryonic period with similar physiopathologic mechanisms. The prenatal treatment by means of decompression can improve substantially the clinical results in these patients. OBJECTIVE: To evaluate, in a qualitative way, the effect of the thoracoamniotic shunts and thoracocentesis in the perinatal outcome in fetuses with not heart thoracic anomalies. METHODS: Twenty-two articles were revised describing 308 cases of fetuses with congenital cystic adenomatoid malformation (CCAM), 25 cases of hydrothorax and 55 cases of broncopulmonary sequestration (BPS). We analyzed the adverse prognostic factors that indicated the treatment election in uterus as well as complications and perinatal outcome. RESULTS: Of the 388 cases of not heart thoracic anomalies, 250 fetuses were managed conservatively, and in 102 fetuses handling in uterus was started. Hydrops was identified as the worst prognostic factor to these fetuses, with a survival rate of 55.7%. The global survival was of 56.5% (155 cases) in the fetuses with CCAM, 98.1% (52 cases) in the fetuses with BPS and of 80% (20 cases) in the fetuses with hydrothorax. CONCLUSIONS: When having a fetus with some of these pathologies, it should be evaluated in an individual and integral way; according to the gestational age when diagnosed, as well as the type of lesion and the presence or absence of fetal dropsy to decide between fetal therapy or expectant handling.

Estudio de las anomalías congénitas: utilidad de la amnioinfusión en la evaluación del embarazo con oligohidramnios severo-anhidramnios / Usefulness of amnioinfusion in server oligohydramnios-amnioinfusion

La infusión intra-amniótica de solución salina ha sido propuesta en los embarazos con oligohidramnios severo o anhidramnios para mejorar el diagnóstico ultrasonográfico en caso de anomalías estructurales; confirmar o exlcuir la ruptura de membranas; y determinar el cariotipo fetal. Se presenta la experiencia con 76 amnioinfusiones prenatales, realizadas en 65 embarazadas con diagnóstico de oligohidramnios severo o anhidramnios con edad gestacional media de 24.4 semanas; se describen los diagnósticos previos y posteriores a las amnioinfusiones. El procedimiento fue exitoso en 71 casos (93.4 por ciento) con la infusión de un volumen medio de 187.3 ml. de solución salina. Antes de la amnioinfusión se realizaron 87 diagnósticos de sospecha de los cuales 77 fueron confirmados post-amnioinfusión (88.5 por ciento), los hallazgos incluyeron: 65 alteraciones estructurales, 8 retardos en el crecimiento y 4 rupturas de membranas. Los diagnósticos excluidos correspondieron a 6 rupturas de membranas y 4 anomalías estructurales. El grupo de anomalías no sospechadas previamente y diagnosticadas post-amnioinfusión incluyó 25 estructurales y 7 cromosómicas. Dentro de las complicaciones se presentaron 7 casos de ruptura prematura de membranas. Se discuten las contribuciones de la amnioinfusión en el diagnóstico prenatal, enfatizando su utilidad para determinar un pronóstico y decidir la conducta más apropiada. Se concluye señalando el papel importante de este procedimiento en la evalución del embarazo con oligohidramnios severo o anhidramnios. Finalmente, se recomienda hacer esfuerzos en futuras investigaciones para establecer una evaluación adecuada y completa acerca de los beneficios y riesgos de este procedimiento diagnóstico, antes de su incorporación a la práctica clínica

Utilidad de los marcadores ultrasonográficos de cromosomopatía / Usefulness of ultrasonographic markers of chromosomopathy

Durante un periodo de tres años y medio, en 132 mujeres embarazadas se diagnosticó la presencia de una amplia variedad de anomalías morfológicas fetales, sugestivas de cromosomopatía, utilizando un equipo de ultrasonido de alta definición y la participación multidisciplinaria. En 95 casos se realizó amniocentesis para estudio del cariotipo fetal. En esta población se determinó la incidencia de cromosomopatía, su contribución al total de las alteraciones cromosómicas diagnosticadas en el periodo de estudio y la expresión fenotípica de las diferentes aneuploidías. Se encontraron 29 cariotipos fetales anormales; 11 con tisomía 18, siete con monosomía del X, cuatro trisomía 21, tres con trisomía 13, uno tetraploidía (29xxyy), uno con mosaico para Turner (45XO 68 por ciento, 46XY 32 por ciento) y dos con inversión en el cromosoma nueve. Del total de las cromosomopatías diagnosticadas en el mismo periodo (N=50), el grupo con anomalías morfológicas representó 49.2 por ciento, mientras que las otras poblaciones de riesgo, de cinco a 15 por ciento. Se diagnosticaron 224 anormalías morfológicas, 43 (19 por ciento) aisladas y 181 (81 por ciento) asociadas. Un número de 80 (36 por ciento) se presentaron en las cromosomopatías. Los marcadores que tuvieron mayor asociación fueron la atresia duodenal, la cardiopatía, la microcefalia, la fosa posterior amplia y el higroma quístico. Se encontró un patrón de marcadores específicos para cada alteración cromosómica. Se concluyó que el ultrasonido puede ser el método más útil para seleccionar el grupo de embarazadas con mayor riesgo de cariotipo anormal