Corrigendum: Unraveling patient heterogeneity in complex diseases through individualized co-expression networks: a perspective.

[This corrects the article DOI: 10.3389/fgene.2023.1209416.].

Unraveling patient heterogeneity in complex diseases through individualized co-expression networks: a perspective.

This perspective highlights the potential of individualized networks as a novel strategy for studying complex diseases through patient stratification, enabling advancements in precision medicine. We emphasize the impact of interpatient heterogeneity resulting from genetic and environmental factors and discuss how individualized networks improve our ability to develop treatments and enhance diagnostics. Integrating system biology, combining multimodal information such as genomic and clinical data has reached a tipping point, allowing the inference of biological networks at a single-individual resolution. This approach generates a specific biological network per sample, representing the individual from which the sample originated. The availability of individualized networks enables applications in personalized medicine, such as identifying malfunctions and selecting tailored treatments. In essence, reliable, individualized networks can expedite research progress in understanding drug response variability by modeling heterogeneity among individuals and enabling the personalized selection of pharmacological targets for treatment. Therefore, developing diverse and cost-effective approaches for generating these networks is crucial for widespread application in clinical services.

Transcriptional and Histone Acetylation Changes Associated with CRE Elements Expose Key Factors Governing the Regulatory Circuit in the Early Stage of Huntington's Disease Models.

Huntington's disease (HD) is a disorder caused by an abnormal expansion of trinucleotide CAG repeats within the huntingtin (Htt) gene. Under normal conditions, the CREB Binding Protein interacts with CREB elements and acetylates Lysine 27 of Histone 3 to direct the expression of several genes. However, mutant Htt causes depletion of CBP, which in turn induces altered histone acetylation patterns and transcriptional deregulation. Here, we have studied a differential expression analysis and H3K27ac variation in 4- and 6-week-old R6/2 mice as a model of juvenile HD. The analysis of differential gene expression and acetylation levels were integrated into Gene Regulatory Networks revealing key regulators involved in the altered transcription cascade. Our results show changes in acetylation and gene expression levels that are related to impaired neuronal development, and key regulators clearly defined in 6-week-old mice are proposed to drive the downstream regulatory cascade in HD. Here, we describe the first approach to determine the relationship among epigenetic changes in the early stages of HD. We determined the existence of changes in pre-symptomatic stages of HD as a starting point for early onset indicators of the progression of this disease.

Benefiting from the intrinsic role of epigenetics to predict patterns of CTCF binding.

Motivation: One of the most relevant mechanisms involved in the determination of chromatin structure is the formation of structural loops that are also related with the conservation of chromatin states. Many of these loops are stabilized by CCCTC-binding factor (CTCF) proteins at their base. Despite the relevance of chromatin structure and the key role of CTCF, the role of the epigenetic factors that are involved in the regulation of CTCF binding, and thus, in the formation of structural loops in the chromatin, is not thoroughly understood. Results: Here we describe a CTCF binding predictor based on Random Forest that employs different epigenetic data and genomic features. Importantly, given the ability of Random Forests to determine the relevance of features for the prediction, our approach also shows how the different types of descriptors impact the binding of CTCF, confirming previous knowledge on the relevance of chromatin accessibility and DNA methylation, but demonstrating the effect of epigenetic modifications on the activity of CTCF. We compared our approach against other predictors and found improved performance in terms of areas under PR and ROC curves (PRAUC-ROCAUC), outperforming current state-of-the-art methods.

Differentially Expressed Genes and Signaling Pathways Potentially Involved in Primary Resistance to Chemo-Immunotherapy in Advanced-Stage Gastric Cancer Patients.

Recently, the combination of chemotherapy plus nivolumab (chemo-immunotherapy) has become the standard of care for advanced-stage gastric cancer (GC) patients. However, despite its efficacy, up to 40% of patients do not respond to these treatments. Our study sought to identify variations in gene expression associated with primary resistance to chemo-immunotherapy. Diagnostic endoscopic biopsies were retrospectively obtained from advanced GC patients previously categorized as responders (R) or non-responders (NR). Thirty-four tumor biopsies (R: n = 16, NR: n = 18) were analyzed by 3' massive analysis of cDNA ends (3'MACE). We found >30 differentially expressed genes between R and NRs. Subsequent pathway enrichment analyses demonstrated that angiogenesis and the Wnt-ß-catenin signaling pathway were enriched in NRs. Concomitantly, we performed next generation sequencing (NGS) analyses in a subset of four NR patients that confirmed alterations in genes that belonged to the Wnt/ß-catenin and the phosphoinositide 3-kinase (PI3K) pathways. We speculate that angiogenesis, the Wnt, and the PI3K pathways might offer actionable targets. We also discuss therapeutic alternatives for chemo-immunotherapy-resistant advanced-stage GC patients.

Injuria encefálica aguda en el posoperatorio de cirugía cardíaca / Acute brain injury in the postoperative period of cardiac surgery / Lesão encefálica aguda no pós-operatório de cirurgia cardíaca

Resumen: La injuria encefálica aguda es una de las complicaciones más devastadoras en el posoperatorio de cirugía cardíaca, siendo responsable de un mayor tiempo de asistencia respiratoria mecánica, infecciones pulmonares y por catéteres, dehiscencia esternal, mayor tiempo de estadía hospitalaria, aumento de mortalidad y de costos sanitarios. En el presente trabajo se discuten las diferentes formas de presentación, los factores predisponentes, su fisiopatología, las medidas de prevención y el tratamiento.

Summary: Acute brain injury is one of the most devastating complications in the postoperative period of cardiac surgery, being responsible for a longer time of mechanical ventilation, lung and catheter infections, sternal dehiscence, longer hospital stay, increased mortality and healthcare costs. The present work discusses the different forms of presentation, predisposing factors, their pathophysiology, prevention measures and treatment.

Resumo: O dano cerebral agudo é uma das complicações mais devastadoras no pós-operatório de cirurgia cardíaca, sendo responsável por maior tempo de ventilação mecânica, infecções pulmonares, infecções de cateter, deiscência esternal, maior tempo de internação, aumento da mortalidade e custos de saúde. O presente trabalho discute as diferentes formas de apresentação, fatores predisponentes, sua fisiopatologia, medidas de prevenção e tratamento.

Inhibition of Gsk3b Reduces Nfkb1 Signaling and Rescues Synaptic Activity to Improve the Rett Syndrome Phenotype in Mecp2-Knockout Mice.

Rett syndrome (RTT) is the second leading cause of mental impairment in girls and is currently untreatable. RTT is caused, in more than 95% of cases, by loss-of-function mutations in the methyl CpG-binding protein 2 gene (MeCP2). We propose here a molecular target involved in RTT: the glycogen synthase kinase-3b (Gsk3b) pathway. Gsk3b activity is deregulated in Mecp2-knockout (KO) mice models, and SB216763, a specific inhibitor, is able to alleviate the clinical symptoms with consequences at the molecular and cellular levels. In vivo, inhibition of Gsk3b prolongs the lifespan of Mecp2-KO mice and reduces motor deficits. At the molecular level, SB216763 rescues dendritic networks and spine density, while inducing changes in the properties of excitatory synapses. Gsk3b inhibition can also decrease the nuclear activity of the Nfkb1 pathway and neuroinflammation. Altogether, our findings indicate that Mecp2 deficiency in the RTT mouse model is partially rescued following treatment with SB216763.

Whole exome sequencing of Rett syndrome-like patients reveals the mutational diversity of the clinical phenotype.

Classical Rett syndrome (RTT) is a neurodevelopmental disorder where most of cases carry MECP2 mutations. Atypical RTT variants involve mutations in CDKL5 and FOXG1. However, a subset of RTT patients remains that do not carry any mutation in the described genes. Whole exome sequencing was carried out in a cohort of 21 female probands with clinical features overlapping with those of RTT, but without mutations in the customarily studied genes. Candidates were functionally validated by assessing the appearance of a neurological phenotype in Caenorhabditis elegans upon disruption of the corresponding ortholog gene. We detected pathogenic variants that accounted for the RTT-like phenotype in 14 (66.6 %) patients. Five patients were carriers of mutations in genes already known to be associated with other syndromic neurodevelopmental disorders. We determined that the other patients harbored mutations in genes that have not previously been linked to RTT or other neurodevelopmental syndromes, such as the ankyrin repeat containing protein ANKRD31 or the neuronal acetylcholine receptor subunit alpha-5 (CHRNA5). Furthermore, worm assays demonstrated that mutations in the studied candidate genes caused locomotion defects. Our findings indicate that mutations in a variety of genes contribute to the development of RTT-like phenotypes.

Polycomb PRC2 complex mediates epigenetic silencing of a critical osteogenic master regulator in the hippocampus.

During hippocampal neuron differentiation, the expression of critical inducers of non-neuronal cell lineages must be efficiently silenced. Runx2 transcription factor is the master regulator of mesenchymal cells responsible for intramembranous osteoblast differentiation and formation of the craniofacial bone tissue that surrounds and protects the central nervous system (CNS) in mammalian embryos. The molecular mechanisms that mediate silencing of the Runx2 gene and its downstream target osteogenic-related genes in neuronal cells have not been explored. Here, we assess the epigenetic mechanisms that mediate silencing of osteoblast-specific genes in CNS neurons. In particular, we address the contribution of histone epigenetic marks and histone modifiers on the silencing of the Runx2/p57 bone-related isoform in rat hippocampal tissues at embryonic to adult stages. Our results indicate enrichment of repressive chromatin histone marks and of the Polycomb PRC2 complex at the Runx2/p57 promoter region. Knockdown of PRC2 H3K27-methyltransferases Ezh2 and Ezh1, or forced expression of the Trithorax/COMPASS subunit Wdr5 activates Runx2/p57 mRNA expression in both immature and mature hippocampal cells. Together these results indicate that complementary epigenetic mechanisms progressively and efficiently silence critical osteoblastic genes during hippocampal neuron differentiation.

Mutations in JMJD1C are involved in Rett syndrome and intellectual disability.

PURPOSE: Autism spectrum disorders are associated with defects in social response and communication that often occur in the context of intellectual disability. Rett syndrome is one example in which epilepsy, motor impairment, and motor disturbance may co-occur. Mutations in histone demethylases are known to occur in several of these syndromes. Herein, we aimed to identify whether mutations in the candidate histone demethylase JMJD1C (jumonji domain containing 1C) are implicated in these disorders. METHODS: We performed the mutational and functional analysis of JMJD1C in 215 cases of autism spectrum disorders, intellectual disability, and Rett syndrome without a known genetic defect. RESULTS: We found seven JMJD1C variants that were not present in any control sample (~ 6,000) and caused an amino acid change involving a different functional group. From these, two de novo JMJD1C germline mutations were identified in a case of Rett syndrome and in a patient with intellectual disability. The functional study of the JMJD1C mutant Rett syndrome patient demonstrated that the altered protein had abnormal subcellular localization, diminished activity to demethylate the DNA damage-response protein MDC1, and reduced binding to MECP2. We confirmed that JMJD1C protein is widely expressed in brain regions and that its depletion compromises dendritic activity. CONCLUSIONS: Our findings indicate that mutations in JMJD1C contribute to the development of Rett syndrome and intellectual disability.Genet Med 18 1, 378-385.

Circadian cycle-dependent MeCP2 and brain chromatin changes.

Methyl CpG binding protein 2 (MeCP2) is a chromosomal protein of the brain, very abundant especially in neurons, where it plays an important role in the regulation of gene expression. Hence it has the potential to be affected by the mammalian circadian cycle. We performed expression analyses of mice brain frontal cortices obtained at different time points and we found that the levels of MeCP2 are altered circadianly, affecting overall organization of brain chromatin and resulting in a circadian-dependent regulation of well-stablished MeCP2 target genes. Furthermore, this data suggests that alterations of MeCP2 can be responsible for the sleeping disorders arising from pathological stages, such as in autism and Rett syndrome.

Improvement of the Rett syndrome phenotype in a MeCP2 mouse model upon treatment with levodopa and a dopa-decarboxylase inhibitor.

Rett Syndrome is a neurodevelopmental autism spectrum disorder caused by mutations in the gene coding for methyl CpG-binding protein (MeCP2). The disease is characterized by abnormal motor, respiratory, cognitive impairment, and autistic-like behaviors. No effective treatment of the disorder is available. Mecp2 knockout mice have a range of physiological and neurological abnormalities that resemble the human syndrome and can be used as a model to interrogate new therapies. Herein, we show that the combined administration of Levodopa and a Dopa-decarboxylase inhibitor in RTT mouse models is well tolerated, diminishes RTT-associated symptoms, and increases life span. The amelioration of RTT symptomatology is particularly significant in those features controlled by the dopaminergic pathway in the nigrostratium, such as mobility, tremor, and breathing. Most important, the improvement of the RTT phenotype upon use of the combined treatment is reflected at the cellular level by the development of neuronal dendritic growth. However, much work is required to extend the duration of the benefit of the described preclinical treatment.

Transgenic complementation of MeCP2 deficiency: phenotypic rescue of Mecp2-null mice by isoform-specific transgenes.

Rett syndrome (RTT) is a disorder that affects patients' ability to communicate, move and behave. RTT patients are characterized by impaired language, stereotypic behaviors, frequent seizures, ataxia and sleep disturbances, with the onset of symptoms occurring after a period of seemingly normal development. RTT is caused by mutations in methyl-CpG binding protein 2 (MECP2), an X-chromosome gene encoding for MeCP2, a protein that regulates gene expression. MECP2 generates two alternative splice variants encoding two protein isoforms that differ only in the N-terminus. Although no functional differences have been identified for these splice variants, it has been suggested that the RTT phenotype may occur in the presence of a functional MeCP2-e2 protein. This suggests that the two isoforms might be functionally distinct. Supporting this notion, the two variants show regional and age-related differences in transcript abundance. Here, we show that transgenic expression of either the MeCP2-e1 or MeCP2-e2 splice variant results in prevention of development of RTT-like phenotypic manifestations in a mouse model lacking Mecp2. Our results indicate that the two MeCP2 splice variants can substitute for each other and fulfill the basic functions of MeCP2 in the mouse brain.

Prevalencia de dolor orofacial en la consulta máxilofacial del centro médico San Joaquín de la Pontificia Universidad Católica de Chile / Prevalence of orofacial pain in the maxillofacial consultation of the centro médico San Joaquin, Pontificia Universidad Catílica de Chile

Introducción: Los variados cuadros clínicos que cursan con dolor orofacial, así como las repercusiones en la calidad de vida y la economía, tanto de los pacientes como de los organismos de atención de salud, hace que éstos requieran de un manejo multidisciplinario. Objetivo: Determinar la prevalencia de dolor orofacial como motivo de consulta maxilofacial en el Centro Médico San Joaquín de la Pontificia Universidad Católica de Chile. Material y método: Estudio descriptivo-retrospectivo del total de primeras consultas de Cirugía Maxilofacial entre los años 2007 y 2010. Se obtuvieron características demográficas y clínicas, generales y específicas para dolor orofacial. Resultados: De un total de 818 pacientes, 245 consultas (30 por ciento) fueron por dolor orofacial, de las cuales 174 (71 por ciento) correspondieron a dolor orofacial músculoesquelético. Conclusiones: La prevalencia de dolor orofacial en nuestro estudio fue de un 30 por ciento, cifra que se encuentra dentro de lo estimado en la literatura (1 por ciento a 55 por ciento), destacando el dolor músculoesquelético como el más prevalente. Un enfoque multidisciplinario se hace necesario dada la complejidad de estos pacientes.

Introduction: The varied clinical conditions that present with orofacial pain, and the impact on quality of life and economy of both the patients and health care agencies, make these require a multidisciplinary management. Objective: To determine the prevalence of orofacial pain as the reason for maxillofacial consultation to Centro Médico San Joaquín, Pontificia Universidad Católica de Chile. Material and Method: Retrospective descriptive study of all first consultations of Maxillofacial Surgery between 2007 and 2010. Clinic and demographic characteristics were obtained.Results: Of a total of 818 patients, 245 (30 per cent) consultations were for orofacial pain, of which 174 (71 per cent) were for musculoskeletal orofacial pain. Conclusions: The prevalence of orofacial pain found is similar to that reported in the literature. We found a high prevalence of neuropathic pain in this study. Specialized multidisciplinary approach is necessary for the management of this type of pathology, given the complexity in both the diagnosis and treatment.

Defective body-weight regulation, motor control and abnormal social interactions in Mecp2 hypomorphic mice.

MeCP2 is an abundant protein that binds to methylated cytosine residues in DNA and regulates transcription. Mutations in MECP2 cause Rett syndrome, a severe neurological disorder that affects approximately 1:10 000 females. Mice lacking MeCP2 have been generated and constitute important models of Rett syndrome. However, it is yet unclear whether certain physiological events are sensitive to a decrease, rather than a complete lack of MeCP2. Here we report that a Mecp2 floxed allele (Mecp2(lox)) that was generated to allow conditional mutagenesis behaves as a hypomorph and the corresponding mutant mice exhibit phenotypical alterations including body weight gain, motor abnormalities and altered social behavior. Our data reinforce the view that the central nervous system is extremely sensitive to MeCP2 expression levels and suggest that the 3'-UTR of Mecp2 might contain important elements that contribute to the regulation of its stability or processing.

Cell-specific expression of wild-type MeCP2 in mouse models of Rett syndrome yields insight about pathogenesis.

Rett syndrome (RTT), a leading cause of mental retardation with autistic features in females, is caused by mutations in the gene encoding methyl-CpG-binding protein 2 (MeCP2). RTT is characterized by a diverse set of neurological features that includes cognitive, motor, behavioral and autonomic disturbances. The diverse features suggest that specific neurons contribute to particular phenotypes and raise the question whether restoring MeCP2 function in a cell-specific manner will rescue some of the phenotypes seen in RTT. To address this, we generated transgenic mice expressing inducible MeCP2 under the control of the brain-specific promoters calcium/calmodulin-dependent protein kinase II (CamKII) or neuron-specific enolase (Eno2) and bred them onto mouse models lacking functional MeCP2. Expression of normal MeCP2 in either CamKII or Eno2 distribution was unable to prevent the appearance of most of the phenotypes of the RTT mouse models. These results suggest that most RTT phenotypes are caused either by disruption of complex neural networks involving neurons throughout the brain or by disruption of the function of specific neurons outside of the broad CamKII or Eno2 distribution.