CRISPR-broad: combined design of multi-targeting gRNAs and broad, multiplex target finding.

In CRISPR-Cas and related nuclease-mediated genome editing, target recognition is based on guide RNAs (gRNAs) that are complementary to selected DNA regions. While single site targeting is fundamental for localized genome editing, targeting to expanded and multiple chromosome elements is desirable for various biological applications such as genome mapping and epigenome editing that make use of different fusion proteins with enzymatically dead Cas9. The current gRNA design tools are not suitable for this task, as these are optimized for defining single gRNAs for unique loci. Here, we introduce CRISPR-broad, a standalone, open-source application that defines gRNAs with multiple but specific targets in large continuous or spread regions of the genome, as defined by the user. This ability to identify multi-targeting gRNAs and corresponding multiple targetable regions in genomes is based on a novel aggregate gRNA scoring derived from on-target windows and off-target sites. Applying the new tool to the genomes of two model species, C. elegans and H. sapiens, we verified its efficiency in determining multi-targeting gRNAs and ranking potential target regions optimized for broad targeting. Further, we demonstrated the general usability of CRISPR-broad by cellular mapping of a large human genome element using dCas9 fused to green fluorescent protein.

Nucleosome binding peptide presents laudable biophysical and in vivo effects.

Chromatin state is highly dependent on the nucleosome binding proteins. Herein, we used a multipronged approach employing biophysical and in vivo experiments to characterize the effects of Nucleosome Binding Peptides (NBPeps) on nucleosome and cell activity. We performed a series of structure-based calculations on the nucleosome surface interaction with GMIP1 (a novel NBPep generated in silico), and HMGN2 (nucleosome binding motif of HMGN2), which contains sites that bind DNA and the acid patch, and also LANA and H4pep (nucleosome binding motif of H4 histone tail) that only bind to the acidic patch. Biochemical assays shows that H4pep, but not HMGN2, GMIP1 and LANA, is highly specific for targeting the nucleosome, with important effects on the final nucleosome structure and robust in vivo effects. These findings suggest that NBPeps might have important therapeutic implications and relevance as tools for chromatin investigation.

Fat nucleosome: Role of lipids on chromatin.

Structural changes in chromatin regulate gene expression and define phenotypic outcomes. Molecules that bind to the nucleosome, the complex of DNA and histone proteins, are key modulators of chromatin structure. Most recently, the formation of condensed chromatin regions based on phase-separation in the cell, a basic physical mechanism, was proposed. Increased understanding of the mechanisms of interaction between chromatin and lipids suggest that small lipid molecules, such as cholesterol and short-chain fatty acids, can regulate important nuclear functions. New biophysical data has suggested that cholesterol interacts with nucleosome through multiple binding sites and affects chromatin structure in vitro. Regardless of the mechanism of how lipids bind to chromatin, there is currently little awareness that lipids may be stored in chromatin and influence its state. Focusing on lipids that bind to nuclear receptors, clinically relevant transcription factors, we discuss the potential interactions of the nucleosome with steroid hormones, bile acids and fatty acids, which suggest that other lipid chemotypes may also impact chromatin structure through binding to common sites on the nucleosome. Herein, we review the main impacts of lipids on the nuclear environment, emphasizing its role on chromatin architecture. We postulate that lipids that bind to nucleosomes and affect chromatin states are likely to be worth investigating as tools to modify disease phenotypes at a molecular level.

Cyclophosphamide administration routine in autoimmune rheumatic diseases: a review / Rotina de administração de ciclofosfamida em doenças autoimunes reumáticas: uma revisão

Abstract Cyclophosphamide is an alkylating agent widely used for the treatment of malignant neoplasia and which can be used in the treatment of multiple rheumatic diseases. Medication administration errors may lead to its reduced efficacy or increased drug toxicity. Many errors occur in the administration of injectable drugs. The present study aimed at structuring a routine for cyclophosphamide use, as well as creating a document with pharmacotherapeutic guidelines for the patient. The routine is schematized in three phases: pre-chemotherapy, administration of cyclophosphamide, and post-chemotherapy, taking into account the drugs to be administered before and after cyclophosphamide in order to prevent adverse effects, including nausea and hemorrhagic cystitis. Adverse reactions can alter laboratory tests; thus, this routine included clinical management for changes in white blood cells, platelets, neutrophils, and sodium, including cyclophosphamide dose adjustment in the case of kidney disease. Cyclophosphamide is responsible for other rare - but serious - side effects, for instance, hepatotoxicity, severe hyponatremia and heart failure. Other adverse reactions include hair loss, amenorrhea and menopause. In this routine, we also entered guidelines to post-chemotherapy patients. The compatibility of injectable drugs with the vehicle used has been described, as well as stability and infusion times. The routine aimed at the rational use of cyclophosphamide, with prevention of adverse events and relapse episodes, factors that may burden the health care system.

Resumo A ciclofosfamida (CFM) é um agente alquilante vastamente usado para o tratamento de neoplasias malignas e pode ser usado no tratamento de diversas doenças reumatológicas. O erro de administração de medicamentos pode levar à diminuição da eficácia ou ao aumento da toxicidade medicamentosa. Diversos erros ocorrem na administração de medicamentos injetáveis. O trabalho objetivou a estruturação de uma rotina do uso de ciclofosfamida, bem como a criação de um documento de orientações farmacoterapêuticas para o paciente. A rotina foi esquematizada em três fases, a pré-quimioterapia (pré-QT), a administração da ciclofosfamida e a pós-quimioterapia (pós-QT), que levaram em consideração os medicamentos que devem ser administrados antes e depois da ciclofosfamida para prevenção aos efeitos adversos, incluindo náusea e cistite hemorrágica. As reações adversas podem alterar os exames laboratoriais e a rotina incluiu manejo clínico para alteração clínica dos leucócitos, das plaquetas, dos neutrófilos e do sódio incluindo o ajuste de dose de ciclofosfamida em caso de insuficiência renal. A ciclofosfamida é responsável por outras reações adversas raras, mas sérias, como hepatotoxicidade, hiponatremia severa e falência cardíaca. Outras reações adversas incluem perda de cabelo, amenorreia e menopausa. A rotina foi composta também por orientações ao paciente pós-QT. A compatibilidade dos medicamentos injetáveis com o veículo foi descrita, bem como o tempo de estabilidade e o tempo de infusão. A rotina visou ao uso racional da ciclofosfamida e prevenir os efeitos adversos e os episódios de recidiva, os quais podem onerar o sistema de saúde.

Cyclophosphamide administration routine in autoimmune rheumatic diseases: a review.

Cyclophosphamide is an alkylating agent widely used for the treatment of malignant neoplasia and which can be used in the treatment of multiple rheumatic diseases. Medication administration errors may lead to its reduced efficacy or increased drug toxicity. Many errors occur in the administration of injectable drugs. The present study aimed at structuring a routine for cyclophosphamide use, as well as creating a document with pharmacotherapeutic guidelines for the patient. The routine is schematized in three phases: pre-chemotherapy, administration of cyclophosphamide, and post-chemotherapy, taking into account the drugs to be administered before and after cyclophosphamide in order to prevent adverse effects, including nausea and hemorrhagic cystitis. Adverse reactions can alter laboratory tests; thus, this routine included clinical management for changes in white blood cells, platelets, neutrophils, and sodium, including cyclophosphamide dose adjustment in the case of kidney disease. Cyclophosphamide is responsible for other rare - but serious - side effects, for instance, hepatotoxicity, severe hyponatremia and heart failure. Other adverse reactions include hair loss, amenorrhea and menopause. In this routine, we also entered guidelines to post-chemotherapy patients. The compatibility of injectable drugs with the vehicle used has been described, as well as stability and infusion times. The routine aimed at the rational use of cyclophosphamide, with prevention of adverse events and relapse episodes, factors that may burden the health care system.