Manipulation of TAD reorganization by chemical-dependent genome linking.

Reorganization of topologically associated domain (TAD) is considered to be a novel mechanism for cell fate transitions. Here, we present a protocol to manipulate TAD via abscisic acid (ABA)-dependent genome linking. We use this protocol to merge two adjacent TADs and evaluate the influence on cell fate transitions. The advantages are that the manipulation does not change the genome and is reversible by withdrawing ABA. The major challenge is how to select linking loci for efficient TAD reorganization. For complete details on the use and execution of this protocol, please refer to Wang et al. (2021).

Regulatory forum opinion piece: the role of the toxicologic pathologist in the postgenomic era: challenges and opportunities.

The "omics," high-throughput screening, computational modeling, and database mining revolutions have each arrived with euphoric expectations, considerable hand waving, and promises to set toxicity testing priorities and reduce reliance on conventional animal toxicity and carcinogenicity testing. Reflecting back on prior experience with other predictive approaches and alternatives, what follows the rush to endorse a promising new technology or different approach to toxicity/carcinogenicity testing is years of grinding out data for validation and optimization. Much of what has driven the enthusiasm for each new emerging technology and approach is the costly, labor-intensive, and sometimes irrelevant and inefficient rodent bioassay-testing paradigm. However, no one should expect abandonment of all animal testing for the foreseeable future, especially for agrochemicals and environmental xenobiotic exposures. It is reasonable to anticipate the future will bring still new approaches to safety testing and human risk assessment. In the past, each new approach has not achieved the inflated expectations for safety testing and human risk assessment but often has become a useful research tool with tangible contributions to basic biology and clinical medicine. The toxicologic pathologist is embedded in the matrix of a mixed disciplinary milieu and is faced with some critical challenges and important opportunities in the postgenomic decades ahead. So what advice do we give to the journeyman toxicologic pathologist who will hopefully function effectively in the postgenomic decades ahead? And what advice do we also give to the experienced bench pathologist confronted with emerging technologies each accompanied by a bewildering array of techno-jargon so that he or she can remain effective as a toxicologic pathology practitioner?

Genotipo de los genes VKORC1 y CYP2C9 en la respuesta individual a la warfarina / Genotype of the VKORC1 and CYP2C9 genes in individual response to warfarin

Introducción: la warfarina es un fármaco ampliamente utilizado como anticoagulante oral. Su estrecho rango terapéutico y marcada variabilidad interindividual en la respuesta requieren un control riguroso en su administración para evitar accidentes hemorrágicos. Objetivos: correlacionar las variantes genéticas de CYP2C9*2 y *3 y VKORC1 (C1173T) con la respuesta y los efectos adversos. Material y método: los genotipos CYP2C9*1, *2, *3, y VKORC1 fueron obtenidos por PCR-RFLP y los resultados analizados usando el paquete estadístico SPSS 12.0. Resultados: hay una tendencia a la reducción de dosis en relación con la presencia de alelos polimórficos. Los portadores de CYP2C9*3 requirieron la menor dosis de mantenimiento, seguidos por los portadores de CYP2C9*2 y homocigotos CYP2C9 *1, en ese orden, (4,4±1,0 vesus 5,4±2,3 versus 7,0±3,6 mg/d, p=0,03). Los portadores CYP2C9*3 tuvieron, además, un aumento del riesgo de sobreanticoagulación y requirieron casi el doble de ajustes de dosis para lograr una adecuada anticoagulación. Para VKORC1, los homocigotas T/T necesitaron la dosis más baja, seguidos por los heterocigotas C/T y homocigotas C/C, en ese orden (3,6±0,6 versus 5,5±0,5 y 7,9±0,7 mg/d, p <0,001). Los pacientes T/T tuvieron un mayor riesgo de sobreanticoagulación que los C/T y C/C. El genotipo T/T de VKORC1 produce en todas las combinaciones con CYP2C9 una disminución cercana a 50% de la dosis diaria de warfarina. Conclusiones: se confirma una sensibilidad aumentada a la warfarina en pacientes portadores de alelos *2 y *3 de CYP2C9, y T de VKORC1. Se demuestra un efecto combinado (aproximadamente aditivo) de los alelos variantes de ambos genes.

Summary Introduction: warfarin is a widely used oral anticoagulant. Its narrow therapeutic range (NTR) and its large interindividual variability requires strict control when administered to avoid hemorrhagic accidents. Objectives: to correlate CYP2C9*2 and *3 and VKORC1 (C1173T) genetic variants with response and adverse side effects. Method: CYP2C9*1, *2, *3, and VKORC1 genotypes were obtained by a commonly used PCR-RFLP procedure. The results were analyzed using SPSS 12.0. statistical package. Results: there is a tendency to reduce the dosage in connection with the presence of polymorphic alleles. CYP2C9*3 carriers require the lower maintenance dosage, followed by CYP2C9*2 carriers and then by CYP2C9 *1 homozygotes (4.4±1.0 versus 5.4±2.3 versus 7.0±3.6 mg/d, p=0.03). CYP2C9*3 carriers also showed an increase in the anticoagulation risk, which required almost twice the number of dose adjustments to achieve appropriate anticoagulation. As to VKORC1, T/T homozygotes needed the lowest dose, followed by the C/T heterozygotes, and then by the C/C homozygotes (3.6±0.6 versus 5.5±0.5 and 7.9±0.7 mg/d, p <0,001). Risk of overcoagulation was higher in T/T patients than in C/T or C/C patients. T/T genotype of VKORC1 causes a decrease of nearly 50% in the warfarine daily dosage for all combinations with CYP2C9. Conclusions: we confirmed an increased sensitivity to warfarine in patient carriers of *2 and *3 CYP2C9 alleles and T VKORC1 alleles. We showed a combined effect (approximately accumulative) of variant alleles in both genes.

Résumé Introduction: la warfarine est une drogue très utilisée comme anticoagulant oral. Étant donné son restreint rang thérapeutique et sa remarquable variabilité interindividuelle, un contrôle rigoureux du dosage s’avère indispensable afin d’éviter des accidents hémorragiques. Objectifs: mettre en rapport les variantes génétiques de CYP2C9*2 et *3 et VKORC1 (C1173T) avec la réponse et les effets adverses. Matériel et méthode: les génotypes CYP2C9*1,*2,*3, et VKORC1 résultent par PCR-RFLP et les résultats analysés au moyen du paquet statistique SPSS 12.0. Résultats: il existe une tendance à réduire la dose par la présence d’allèles polymorphiques. Les porteurs de CYP2C9*3 ont requis une dose plus basse de maintien, puis les porteurs de CYP2C9*2 et homozygotes CYP2C9*1, dans cet ordre, (4,4±1,0 versus 7,0±3,6 mg/d, p=0,03). Les porteurs CYP2C9*3 ont aussi subi une augmentation du risque de suranticoagulation et ont requis presque le double d’ajustement de la dose pour atteindre une anticoagulation adéquate. Pour VKORC1, les homozygotes T/T ont requis une dose plus basse, suivis des hétérozygotes C/T et des homozygotes C/C, dans cet ordre (3,6±0,6 versus 5,5±0,5 et 7,9±0,7 mg/d, p <0,001). Les patients T/T ont subi un plus grand risque de suranticoagulation que les C/T et C/C. Le génotype T/T de VKORC1 provoque dans toutes les combinaisons avec CYP2C9 une diminution de 50% environ de la dose par jour de warfarine. Conclusions: on confirme une sensibilité augmentée à la warfarine chez les patients porteurs d’allèles *2 et *3 de CYP2C9, et T de VKORC1. Un effet combiné (à peu près aditif) des allèles variantes des deux gènes reste évident.

Resumo Introdução: a warfarina é uma droga muito usada como anticoagulante oral. Sua administração deve ser controlada rigorosamente para evitar acidentes hemorrágicos devido a uma aplicação terapêutica restrita e a variação da resposta individual. Objetivos: correlacionar as variantes genéticas de CYP2C9*2 e *3 y VKORC1 (C1173T) com a resposta e os efeitos adversos. Material e método: os genótipos CYP2C9*1, *2, *3, e VKORC1 foram obtidos por PCR-RFLP e os resultados foram analisados usando o programa SPSS 12.0. Resultados: observa-se uma tendência à redução da dose na presença de alelos polimórficos. Os portadores de CYP2C9*3 necessitam doses de manutenção mais baixas, seguidos pelos portadores de CYP2C9*2 e homozigotos CYP2C9 *1 (4,4±1,0 versus 5,4±2,3 versus 7,0±3,6 mg/d, p=0,03). Os portadores de CYP2C9*3 apresentaram também um aumento do risco de sobreanticoagulaçao e necessitam o dobro do número de ajustes de dose para obter uma anticoagulaçao adequada. Para VKORC1, os homozigotos T/T necessitaram a dose mais baixa, seguidos pelos heterozigotos C/T e homozigotos C/C (3,6±0,6 versus 5,5±0,5 y 7,9±0,7 mg/d, p <0,001). Os pacientes T/T apresentaram um risco maior de sobreanticoagulação que os C/T e C/C. O genótipo T/T de VKORC1 produz uma redução de aproximadamente 50% da dose diária de warfarina em todas as combinações com CYP2C9. Conclusões: confirma-se a sensibilidade aumentada à warfarina de pacientes portadores de alelos *2 y *3 de CYP2C9, e T de VKORC1. Demonstram-se um efeito combinado (aproximadamente aditivo) dos alelos variantes de ambos os genes.