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

Caracterización estructural de factores de transcripción del tipo MADS en su unión a ADN involucrado en la respuesta a inclinación de Pinus radiata D. Don

120 P.Pinus radiata D. Don es la conífera de mayor importancia en la producción forestal, sustentando cerca del 80% del abastecimiento industrial de la madera en Chile. El crecimiento normal de los árboles puede verse afectado por estrés abiótico, que provocan la pérdida de verticalidad de estos. La tensión física producida en coníferas, a causa de que el tronco busca reorientar su crecimiento vertical, genera madera de compresión, esta se caracteriza por altos niveles de lignina, menor contenido de celulosa y mayor ángulo de micro-fibra, factores que disminuyen la calidad de los productos obtenidos por la industria forestal.La madera de compresión se produce por cambios en la modulación genética de la zona afectada del tronco. Para comprender este fenómeno es necesario estudiar los genes que provocan dichas modificaciones. Se ha visto que el gen xyloglucano endotransglucosilasa/hidrolasa (XTH), que participa de la expansión y formación de la madera, es sobre-expresado en respuesta a la inclinación en el lado inferior del ápice. Por otro lado, estudios previos han mostrado la activación del factor de transcripción del tipo MADS (MCM1, AG, DEFA y SRF) implicado en procesos de desarrollo y biosíntesis de la pared secundaria a tiempos tempranos de la respuesta a inclinación. A su vez, el análisis de la región promotora del gen XTH, mostró que contiene secuencias de respuesta a factores MADS. Por este motivo, se quiso establecer si el factor de transcripción de tipo MADS podría tener alguna relación en la regulación del gen XTH.En esta tesis se estudió con dos factores de transcripción de tipo MADS: denominados PrMADBJ y PrMADBT, cuyos modelos tridimensionales fueron generados utilizando como templado la estructura PDB: 3P57, los monómeros se caracterizaron por presentar una zona coil, 2 alfa hélices y dos beta plegadas anti paralelas. Adicionalmente, se emplearon técnicas de acoplamiento molecular, con las que se pudo determinar que estos factores de transcripción MADS se unen a elementos cis-regulatorios del ADN como dímeros, a través de una zona positivamente cargada de su estructura, las técnicas de acoplamiento y dinámica molecular mostraron que la interacción proteína-ADN era favorable, y que la secuencia denominada CARG4 posee una mejor interacción con los monómeros y homo-dímeros de los PrMADS. Con esto, se pudo demostrar que los residuos positivamente cargados K23, R26, K30 y K31 situados dentro del dominio MADS de la proteína serían los responsables en la interacción ADN-proteína/ABSTRACT:Pinus radiata D. Don is the most important conifer in forest production, sustaining nearly 80% of the industrial wood supply in Chile. The growth of normal trees can be affected by abiotic stress, causing the loss of their verticality. Physical strain produced in conifers, which is caused by the trunk seeking to reorient its vertical growth, generates compression wood. This wood is characterized by high levels of lignin, less cellulose content and a greater angle of micro-fiber, factors that lower the quality of the products obtained by forest industry. Compression wood is produced by changes in the genetic modulation of the affected area in the trunk. To understand this phenomenon, it is necessary to study the genes that cause such changes. It has been found that the gene xyloglucan endotransglucosylase/hydrolase (XTH), involved in the expansion and wood formation is overexpressed in response to the inclination in the lower side of the apex. Furthermore, previous studies have shown the activation of the MADS transcription factor (MCM1, AG, DEFA and SRF), which is predominantly involved in developmental processes and secondary wall biosynthesis in the early stages of the tilt response. In turn, the analysis of the promoter region XTH gene sequences shows that it contains sequences response to MADS. Therefore, this study aims to determine whether the MADS transcription factor plays a key role in XTH gene regulation.A three-dimensional model of two MADS transcription factors (MADBJ and MADBT) were generated using as template the structure PDB: 3P57. Docking were used using HADDOCK program, determining that these MADS transcription factors bind cis-regulatory elements. Docking and molecular dynamics showed that the interaction of a dimer protein and DNA was favorable. Moreover, the sequence CARG4 has a better interaction with the monomers and homo-dimers of PrMADS. It was demonstrated that the positively charged residues K23, R26, K30 and K31 located within the MADS domain of the protein allowed the binding specificity

NOTCH3 gene mutation in a chilean cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy family

Introduction: Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a rare hereditary stroke disorder caused by mutations in the NOTCH3 gene. We report the first Chilean CADASIL family with complete radiological and histological studies. Methods: The family tree was constructed from an autopsy-confirmed confirmed patient, and includes 3 generations. We performed clinical, pathologic, genetic, and radiologic examinations on members of a family with CADASIL. Results: In the second generation, findings compatible with CADASIL were identified in 6 individuals, all of whom had a missense mutation in exon 3 (c.268C>T) resulting in an arginine to cysteine amino acid substitution at position 90 (R90C). In the third generation, a missense mutation was detected in one of the 4 asymptomatic individuals. Conclusions: There are similarities in clinical presentation between this family and previously described Asian and European series with R90C mutations. Detecting genotypes with a gain or loss of cysteine residues opens the door to future gene transfection-based therapies

P2X4 Receptor in Silico and Electrophysiological Approaches Reveal Insights of Ivermectin and Zinc Allosteric Modulation

Protein allosteric modulation is a pillar of metabolic regulatory mechanisms; this concept has been extended to include ion channel regulation. P2XRs are ligand-gated channels activated by extracellular ATP, sensitive to trace metals and other chemicals. By combining in silico calculations with electrophysiological recordings, we investigated the molecular basis of P2X4R modulation by Zn(II) and ivermectin, an antiparasite drug currently used in veterinary medicine. To this aim, docking studies, molecular dynamics simulations and non-bonded energy calculations for the P2X4R in the apo and holo states or in the presence of ivermectin and/or Zn(II) were accomplished. Based on the crystallized Danio rerio P2X4R, the rat P2X4R, P2X2R, and P2X7R structures were modeled, to determine ivermectin binding localization. Calculations revealed that its allosteric site is restricted to transmembrane domains of the P2X4R; the role of Y42 and W46 plus S341 and non-polar residues were revealed as essential, and are not present in the homologous P2X2R or P2X7R transmembrane domains. This finding was confirmed by preferential binding conformations and electrophysiological data, revealing P2X4R modulator specificity. Zn(II) acts in the P2X4R extracellular domain neighboring the SS3 bridge. Molecular dynamics in the different P2X4R states revealed allosterism-induced stability. Pore and lateral fenestration measurements of the P2X4R showed conformational changes in the presence of both modulators compatible with a larger opening of the extracellular vestibule. Electrophysiological studies demonstrated additive effects in the ATP-gated currents by joint applications of ivermectin plus Zn(II). The C132A P2X4R mutant was insensitive to Zn(II); but IVM caused a 4.9 ± 0.7-fold increase in the ATP-evoked currents. Likewise, the simultaneous application of both modulators elicited a 7.1 ± 1.7-fold increase in the ATP-gated current. Moreover, the C126A P2X4R mutant evoked similar ATP-gated currents comparable to those of wild-type P2X4R. Finally, a P2X4/2R chimera did not respond to IVM but Zn(II) elicited a 2.7 ± 0.6-fold increase in the ATP-gated current. The application of IVM plus Zn(II) evoked a 2.7 ± 0.9-fold increase in the ATP-gated currents. In summary, allosteric modulators caused additive ATP-gated currents; consistent with lateral fenestration enlargement. Energy calculations demonstrated a favorable transition of the holo receptor state following both allosteric modulators binding, as expected for allosteric interactions

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-β-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/β-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