Multiparametric and accurate functional analysis of genetic sequence variants using CRISPR-Select.

Determining the functional role of thousands of genetic sequence variants (mutations) associated with genetic diseases is a major challenge. Here we present clustered regularly interspaced short palindromic repeat (CRISPR)-SelectTIME, CRISPR-SelectSPACE and CRISPR-SelectSTATE, a set of flexible knock-in assays that introduce a genetic variant in a cell population and track its absolute frequencies relative to an internal, neutral control mutation as a function of time, space or a cell state measurable by flow cytometry. Phenotypically, CRISPR-Select can thereby determine, for example, pathogenicity, drug responsiveness/resistance or in vivo tumor promotion by a specific variant. Mechanistically, CRISPR-Select can dissect how the variant elicits the phenotype by causally linking the variant to motility/invasiveness or any cell state or biochemical process with a flow cytometry marker. The method is applicable to organoids, nontransformed or cancer cell lines. It is accurate, quantitative, fast and simple and works in single-well or 96-well higher throughput format. CRISPR-Select provides a versatile functional variant assay for research, diagnostics and drug development for genetic disorders.

CRISPR/Cas9-mediated knockout of clinically relevant alloantigenes in human primary T cells.

BACKGROUND: The ability of CRISPR/Cas9 to mutate any desired genomic locus is being increasingly explored in the emerging area of cancer immunotherapy. In this respect, current efforts are mostly focused on the use of autologous (i.e. patient-derived) T cells. The autologous approach, however, has drawbacks in terms of manufacturing time, cost, feasibility and scalability that can affect therapeutic outcome or wider clinical application. The use of allogeneic T cells from healthy donors may overcome these limitations. For this strategy to work, the endogenous T cell receptor (TCR) needs to be knocked out in order to reduce off-tumor, graft-versus-host-disease (GvHD). Furthermore, CD52 may be knocked out in the donor T cells, since this leaves them resistant to the commonly used anti-CD52 monoclonal antibody lymphodepletion regimen aiming to suppress rejection of the infused T cells by the recipient. Despite the great prospect, genetic manipulation of human T cells remains challenging, in particular how to deliver the engineering reagents: virus-mediated delivery entails the inherent risk of altering cancer gene expression by the genomically integrated CRISPR/Cas9. This is avoided by delivery of CRISPR/Cas9 as ribonucleoproteins, which, however, are fragile and technically demanding to produce. Electroporation of CRISPR/Cas9 expression plasmids would bypass the above issues, as this approach is simple, the reagents are robust and easily produced and delivery is transient. RESULTS: Here, we tested knockout of either TCR or CD52 in human primary T cells, using electroporation of CRISPR/Cas9 plasmids. After validating the CRISPR/Cas9 constructs in human 293 T cells by Tracking of Indels by Decomposition (TIDE) and Indel Detection by Amplicon Analysis (IDAA) on-target genomic analysis, we evaluated their efficacy in primary T cells. Four days after electroporation with the constructs, genomic analysis revealed a knockout rate of 12-14% for the two genes, which translated into 7-8% of cells showing complete loss of surface expression of TCR and CD52 proteins, as determined by flow cytometry analysis. CONCLUSION: Our results demonstrate that genomic knockout by electroporation of plasmids encoding CRISPR/Cas9 is technically feasible in human primary T cells, albeit at low efficiency.

Strategies for having a more effective and less toxic CAR T-cell therapy for acute lymphoblastic leukemia.

In the recent years, using genetically modified T cells has been known as a rapid developing therapeutic approach due to the heartwarming results of clinical trials with patients suffering from relapsed or refractory (R/R) hematologic malignancies such as R/R Acute Lymphoblastic Leukemia (R/R ALL). One of these renowned approaches is Chimeric antigen receptors (CARs). CARs are synthetic receptors with the ability to be expressed on the surface of T lymphocytes and are specifically designed to target a tumor-associated antigen (TAA) of interest. CAR-expressing T cells have the capability of proliferating and maintaining their immunological functionality in the recipient body but like any other therapeutic approach, the safety, effectiveness, and specificity enhancement of CAR T cells still lingers in the ambiguity arena. Genetic manipulation methods, expansion protocols, infusion dosage, and conditioning regimens are all among crucial factors which can affect the efficacy of CAR T cell-based cancer therapy. In this article, we discuss the studies that have focused on various aspects that affect the efficacy and persistence of CAR T-cell therapy for ALL treatment and provide a widespread overview regarding the practical approaches capable of elevating the effectiveness and lessening the relative toxicities attributed to it.

Novel oleogel formulation based on amaranth oil: Physicochemical characterization.

This study aims to investigate the characteristics of oleogel (OG) produced from amaranth oil at four concentrations of 7%, 9%, 10%, and 12% of the monoglyceride (MG). The physicochemical and structural aspects were performed by using pulsed nuclear magnetic resonance, differential scanning calorimetry, X-ray diffraction, and gas chromatography. The results show that oleogels (OGs) had higher oxidative stability during storage at ambient temperature in comparison with amaranth oil. Moreover, polarized optical microscopy revealed that an increase in percentage of the oleogelator leads to the formation of needle-shaped crystals followed by oil entrapment. Also, MG improves the solid content of amaranth oil from 0.5% to 11% and creates a solid structure in spite of the low solid fat as compared to cocoa butter (CB) (82%), as control sample. Crystals similar to CB were also observed when evaluating the crystalline structure of the OG. The fatty acid ratio and the essential linoleic fatty acid were preserved in the OG by only 2%-6% reduction.

Autism and Probable Prerequisites: Severe and Scheduled Prenatal Stresses at Spotlight.

BACKGROUND: Due to the importance of prenatal maternal stress as environmental factor on autism, the influence of prenatal maternal psychological agitations was assessed in relation with the risk of autism. METHODS: In this case-control study, some mothers of autistic children in Isfahan, central Iran, in 2014, were retrospectively compared with control mothers in terms of quantity, quality, and schedule of exposure to 45 stressful events in a 15-month period. In addition, dividing the stressors into two groups of genome-dependent/independent events, their prevalence was separately scrutinized and compared among patient and control families. RESULTS: Although the child's risk of autism increases significantly with the increase of maternal stress during months 4-7 of pregnancy, the increased stress during months 2-3 of pregnancy can lead to a significant increase in the severity of autism affliction as well as a slight but significant increase in the possibility of LFA in afflicted children (P<0.05). The overall prevalence of genome-dependent stressful events among two patient and control groups was significantly higher than that of genome-independent events (P=0.000), but genome-dependent events led to more stress inpatient families. CONCLUSION: Although the present study consistent with recent findings in the fields of epigenetics and gene-environment interactions can confirm the role of severe and scheduled prenatal stresses in causing autism, it does not deny the necessity of a perspective and wider study in Isfahan and Iran.

Comparative genomics of human stem cell factor (SCF).

Stem cell factor (SCF) is a critical protein with key roles in the cell such as hematopoiesis, gametogenesis and melanogenesis. In the present study a comparative analysis on nucleotide sequences of SCF was performed in Humanoids using bioinformatics tools including NCBI-BLAST, MEGA6, and JBrowse. Our analysis of nucleotide sequences to find closely evolved organisms with high similarity by NCBI-BLAST tools and MEGA6 showed that human and Chimpanzee (Pan troglodytes) were placed into the same cluster. By using JBrowse, we found that SCF in Neanderthal had a single copy number similar to modern human and partly conserved nucleotide sequences. Together, the results approved the gene flow and genetics similarity of SCF among human and P. troglodytes. This may suggest that during evolution, SCF gene transferred partly intact either on the basis of sequence or function from the same ancestors to P. troglodytes, the ancient human like Neanderthal, and then to the modern human.

Environmental factors influencing the risk of autism.

Autism is a developmental disability with age of onset in childhood (under 3 years old), which is characterized by definite impairments in social interactions, abnormalities in speech, and stereotyped pattern of behaviors. Due to the progress of autism in recent decades, a wide range of studies have been done to identify the etiological factors of autism. It has been found that genetic and environmental factors are both involved in autism pathogenesis. Hence, in this review article, a set of environmental factors involved in the occurrence of autism has been collected, and finally, some practical recommendations for reduction of the risk of this devastating disease in children are represented.

RORA and Autism in The Isfahan Population: Is There An Epigenetic Relationship.

OBJECTIVE: Autism is a neurodevelopmental disorder characterized by difficulty in verbal and non-verbal communication, impaired social interaction, and restricted and repetitive behavior. It has been recently introduced as a multigenic disorder with significant epigenetic effects on its pathology. Recently, epigenetic silencing of retinoic acid receptor- related orphan receptor alpha (RORα) gene (which has an essential role in neural tissue development) was shown to have occurred in autistic children due to methylation of its promoter region. This may thus explain a significant part of the molecular pathogenesis of autism. Therefore, we aimed to confirm this finding by implementing a case-control (experimental) study in the population of Isfahan. MATERIALS AND METHODS: The methylation status of a 136 bp sequence of a GpG island (encompassing 13 CpG sites) in the RORA promoter region (positions -200 to -64) as an experimental study was examined in the lymphocyte cells of 30 autistic children after sodium bisulfite treatment using the melting curve analysis-methylation (MCA-Meth) assay compared with normal children. Also, quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analysis was used to estimate the level of mRNA transcripts and to evaluate MCA-Meth analysis results. RESULTS: This study revealed no methylation in the examined promoter regions in both autistic and normal children, with the melting curve of all studied samples being comparable to that of the non-methylated control. The results of MCA-Meth analysis were also consistent with qRT-PCR results. We therefore observed no significant difference in the levels of RORα transcripts in the blood lymphocytes between autistic and healthy children. CONCLUSION: The methylation of the RORA promoter region may not be considered as a common epigenetic risk factor for autism in all populations. Hence, the molecular pathogenesis of autism remains unclear in the population investigated.

TGFBR1 polymorphism and risk of breast cancer in Iranian women.

Numerous epidemiological studies have evaluated the association between transforming growth factor beta receptor type 1 (TGFBR1) polymorphisms and the risk of cancer; however, the results remain inconclusive and controversial. To determine the association between breast cancer risk and the *6A polymorphism of the TGFBR1 gene, a case-control study of 280 breast cancer patients and 280 controls was performed in Iranian women. Our study demonstrates that women who carry the TGFBR1*6A allele are at lower risk of developing breast cancer. The highest protection against breast cancer was observed in 6A/6A homozygotes (OR = 0.32, p = 0.04). A lower frequency of the TGFBR1*6A allele in breast cancer patients may be an important genetic determinant that contributes to a lower risk of breast cancer in Iranian women. The results also showed that the allelic length of TGFBR1 polymorphisms had no significant association with the age at onset or the grade of disease, nor with the expression of progesterone and estrogen receptors and HER2.

Evaluation of anti-tuberculosis induced adverse reactions in hospitalized patients.

BACKGROUND: Tuberculosis has been one of the common diseases of human communities. Besides of disease-related complications, there are serious adverse reactions due to Anti-tuberculosis (Anti-TB) drug therapy. OBJECTIVES: To assess the rate of Adverse Drug Reactions (ADRs) induced by Anti-TB drugs in the infectious disease department for a period of one year. To detect serious and preventable recognized ADRs. METHODS: All patients admitted to the infectious disease department at Imam tertiary teaching hospital in Iran who received Anti-TB drugs from July 2001 to July 2002 entered the study. These patients were monitored for ADRs during hospital stay. The ADRs were then classified based on patients and reactions factors. The causality and severity of the reactions were determined using Naranjo algorithm and Hartwig questionnaire, respectively. RESULTS: During the study period, 83 patients received Anti-TB drugs; of them 44 developed at least one ADR. Total number of 81 ADRs was detected in this study. ADRs were recognized as the major cause of hospital admission in 11 (13.3%) patients. The most frequent system-organ class affected by ADRs was Liver and biliary system (37%). Hepatitis was observed in 21 (25.3%) patients leading to death in two patients. CONCLUSION: Anti-TB drugs could cause significant adverse effects both in quantity and severity leading to hospitalization, prolonged hospital stay and even death. More attention is needed to prevent these reactions.