Applications of CRISPR-Cas9 for advancing precision medicine in oncology: from target discovery to disease modeling.

The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) (CRISPR/Cas9) system is a powerful tool that enables precise and efficient gene manipulation. In a relatively short time, CRISPR has risen to become the preferred gene-editing system due to its high efficiency, simplicity, and programmability at low costs. Furthermore, in the recent years, the CRISPR toolkit has been rapidly expanding, and the emerging advancements have shown tremendous potential in uncovering molecular mechanisms and new therapeutic strategies for human diseases. In this review, we provide our perspectives on the recent advancements in CRISPR technology and its impact on precision medicine, ranging from target identification, disease modeling, and diagnostics. We also discuss the impact of novel approaches such as epigenome, base, and prime editing on preclinical cancer drug discovery.

Functional characterization of Alzheimer's disease genetic variants in microglia.

Candidate cis-regulatory elements (cCREs) in microglia demonstrate the most substantial enrichment for Alzheimer's disease (AD) heritability compared to other brain cell types. However, whether and how these genome-wide association studies (GWAS) variants contribute to AD remain elusive. Here we prioritize 308 previously unreported AD risk variants at 181 cCREs by integrating genetic information with microglia-specific 3D epigenome annotation. We further establish the link between functional variants and target genes by single-cell CRISPRi screening in microglia. In addition, we show that AD variants exhibit allelic imbalance on target gene expression. In particular, rs7922621 is the effective variant in controlling TSPAN14 expression among other nominated variants in the same cCRE and exerts multiple physiological effects including reduced cell surface ADAM10 and altered soluble TREM2 (sTREM2) shedding. Our work represents a systematic approach to prioritize and characterize AD-associated variants and provides a roadmap for advancing genetic association to experimentally validated cell-type-specific phenotypes and mechanisms.

Impact of pharmacogenomics in achieving personalized/precision medicine in the clinical setting: a symposium report.

The Indo-Swiss symposium on pharmacogenomic strategies for the implementation of personalized medicine was conducted as part of the Jawaharlal Institute of Postgraduate Medical Education and Research Integrated Pharmacogenomics Program in Puducherry, India, on 19 November 2022. The symposium was conducted in hybrid mode. The theme of symposium was the impact of pharmacogenomics on the achievement of personalized medicine/precision medicine in the clinical setting. The symposium sought to promote interaction among the participants to initiate future collaborative research projects. The symposium also served as a platform for young researchers to present their research findings as posters to the audience.

Knowledge, Attitude, and Practice of Materiovigilance among Nurses at a Tertiary Care Hospital in South India: A Cross-Sectional Study.

Background and Objective: Inadequate knowledge and underreporting of medical device-associated adverse events (MDAEs) were observed among health-care professionals (HCPs) in studies carried out in other countries. In India, HCP's knowledge, attitude, and practice (KAP) regarding materiovigilance have not been explored extensively. Hence, the present study was carried out to assess KAP of materiovigilance among nurses working in a tertiary care teaching hospital in South India. Materials and Methods: This is a descriptive, cross-sectional study conducted among nurses. A self-administered, validated questionnaire was distributed to 420 nurses. Data were analyzed using the Statistical Package for the Social Sciences software version 21.0. Kruskal-Wallis test was used to compare KAP score of materiovigilance among the study participants. Results: A total of 400 (95.2%) responses were received. About 65.7% (n = 263) of nurses were having adequate knowledge about the various aspects of materiovigilance and 80.5% (n = 322) of nurses had a positive attitude toward MDAE reporting. However, only 18 (4.5%) of nurses have reported about MDAEs. Further, factors such as uncertainty on how to report a MDAE and concerns about their legal issues significantly led to underreporting of MDAEs. Conclusion: The transition of adequate knowledge and positive attitude to good practice of MDAE reporting was lacking among the study participants. Hence, with due consideration of these deficits and the various factors influencing MDAE reporting, it is necessary to conduct periodical workshops and training sessions for HCPs to enhance their spontaneous reporting of MDAEs.

Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function.

TET (ten-eleven translocation) enzymes catalyze the oxidation of 5-methylcytosine bases in DNA, thus driving active and passive DNA demethylation. Here, we report that the catalytic domain of mammalian TET enzymes favor CGs embedded within basic helix-loop-helix and basic leucine zipper domain transcription factor-binding sites, with up to 250-fold preference in vitro. Crystal structures and molecular dynamics calculations show that sequence preference is caused by intrasubstrate interactions and CG flanking sequence indirectly affecting enzyme conformation. TET sequence preferences are physiologically relevant as they explain the rates of DNA demethylation in TET-rescue experiments in culture and in vivo within the zygote and germ line. Most and least favorable TET motifs represent DNA sites that are bound by methylation-sensitive immediate-early transcription factors and octamer-binding transcription factor 4 (OCT4), respectively, illuminating TET function in transcriptional responses and pluripotency support.

Coordinated Transcriptional and Catabolic Programs Support Iron-Dependent Adaptation to RAS-MAPK Pathway Inhibition in Pancreatic Cancer.

The mechanisms underlying metabolic adaptation of pancreatic ductal adenocarcinoma (PDA) cells to pharmacologic inhibition of RAS-MAPK signaling are largely unknown. Using transcriptome and chromatin immunoprecipitation profiling of PDA cells treated with the MEK inhibitor (MEKi) trametinib, we identify transcriptional antagonism between c-MYC and the master transcription factors for lysosome gene expression, the MiT/TFE proteins. Under baseline conditions, c-MYC and MiT/TFE factors compete for binding to lysosome gene promoters to fine-tune gene expression. Treatment of PDA cells or patient organoids with MEKi leads to c-MYC downregulation and increased MiT/TFE-dependent lysosome biogenesis. Quantitative proteomics of immunopurified lysosomes uncovered reliance on ferritinophagy, the selective degradation of the iron storage complex ferritin, in MEKi-treated cells. Ferritinophagy promotes mitochondrial iron-sulfur cluster protein synthesis and enhanced mitochondrial respiration. Accordingly, suppressing iron utilization sensitizes PDA cells to MEKi, highlighting a critical and targetable reliance on lysosome-dependent iron supply during adaptation to KRAS-MAPK inhibition. SIGNIFICANCE: Reduced c-MYC levels following MAPK pathway suppression facilitate the upregulation of autophagy and lysosome biogenesis. Increased autophagy-lysosome activity is required for increased ferritinophagy-mediated iron supply, which supports mitochondrial respiration under therapy stress. Disruption of ferritinophagy synergizes with KRAS-MAPK inhibition and blocks PDA growth, thus highlighting a key targetable metabolic dependency. See related commentary by Jain and Amaravadi, p. 2023. See related article by Santana-Codina et al., p. 2180. This article is highlighted in the In This Issue feature, p. 2007.

TET-mediated DNA hydroxymethylation is negatively influenced by the PARP-dependent PARylation.

BACKGROUND: Poly(ADP-ribosyl)ation (PARylation), a posttranslational modification introduced by PARP-1 and PARP-2, has first been implicated in DNA demethylation due to its role in base excision repair. Recent evidence indicates a direct influence of PARP-dependent PARylation on TET enzymes which catalyse hydroxymethylation of DNA-the first step in DNA demethylation. However, the exact nature of influence that PARylation exerts on TET activity is still ambiguous. In our recent study, we have observed a negative influence of PARP-1 on local TET-mediated DNA demethylation of a single gene and in this study, we further explore PARP-TET interplay. RESULTS: Expanding on our previous work, we show that both TET1 and TET2 can be in vitro PARylated by PARP-1 and PARP-2 enzymes and that TET1 PARylation negatively affects the TET1 catalytic activity in vitro. Furthermore, we show that PARylation inhibits TET-mediated DNA demethylation at the global genome level in cellulo. CONCLUSIONS: According to our findings, PARP inhibition can positively influence TET activity and therefore affect global levels of DNA methylation and hydroxymethylation. This gives a strong rationale for future examination of PARP inhibitors' potential use in the therapy of cancers characterised by loss of 5-hydroxymethylcytosine.

Idax and Rinf facilitate expression of Tet enzymes to promote neural and suppress trophectodermal programs during differentiation of embryonic stem cells.

The Inhibitor of disheveled and axin (Idax) and its ortholog the Retinoid inducible nuclear factor (Rinf) are DNA binding proteins with nuclear and cytoplasmic functions. Rinf is expressed in embryonic stem cells (ESCs) where it regulates transcription of the Ten-eleven translocation (Tet) enzymes, promoting neural and suppressing mesendoderm/trophectoderm differentiation. Here, we find that Idax, which is not expressed in ESCs, is induced upon differentiation. Like Rinf, Idax facilitates neural and silences trophectodermal programs. Individual or combined loss of Idax and Rinf led to downregulation of neural and upregulation of trophectoderm markers during differentiation of ESCs to embryoid bodies as well as during directed differentiation of ESCs to neural progenitor cells (NPCs) and trophoblast-like cells. These defects resemble those of Tet-deficient ESCs. Consistently, Tet genes are direct targets of Idax and Rinf, and loss of Idax and Rinf led to downregulation of Tet enzymes during ESC differentiation to NPCs and trophoblast-like cells. While Idax and Rinf single and double knockout (DKO) mice were viable and overtly normal, DKO embryos had reduced expression of several NPC markers in embryonic forebrains and deregulated expression of selected trophoblast markers in placentas. NPCs derived from DKO forebrains had reduced self-renewal while DKO placentas had increased junctional zone and reduced labyrinth layers. Together, our findings establish Idax and Rinf as regulators of Tet enzymes for proper differentiation of ESCs.

Pharmacovigilance of Antitubercular Therapy in Tuberculosis.

Background Adverse drug reactions (ADRs) to tuberculosis (TB) drugs are a significant concern for medical professionals and health authorities. Adverse events due to drug-resistant TB (DRTB) treatment are among the most important reasons for treatment interruption. Methods This study was an observational study conducted among patients diagnosed with TB (pulmonary/extrapulmonary) receiving antitubercular therapy (ATT) (first line/second-line drugs) irrespective of their age and gender. The patients who consented to participate, registered under National Tuberculosis Elimination Program (NTEP), Puducherry, during the study period from March 2020 to December 2020, were included in the study. The demographic details were recorded from the treatment card, and the participants were provided a diary to note down the adverse events. They were asked to report over the phone or during their visits to treatment centers for the first two months. During the follow-up (irrespective of their treatment phase [intensive/continuation]), the patients were assessed for symptoms and signs of common adverse events. Any adverse events reported by the patient were also recorded and analyzed for causality and severity. Results During the study period, 219 patients were included, of which 92 patients (42%) presented with adverse events. Among the patients with ADRs, 56.5% were males and 43.5% were females. The females were found to be at more risk than males for adverse events with the OR 1.871 (95% CI: 1.066-3.284). GI system was the most common body system involved (39%), followed by musculoskeletal system and skin disorders (24% and 21%), respectively. Most of the adverse events were latent in nature (60.9%), followed by sub-acute onset (28.3%) and acute events (6.5%). Maximum adverse events reported were mild to moderate (71.8%), followed by severe (18.5%). Most of the events were probable in nature (41.3%), and the definite category was 25% as per Naranjo's probability scale. Conclusion The current study shows the frequency of adverse events in patients receiving antitubercular drug therapy. The females were found to be at more risk than males for adverse events. It was found that the GI system was most affected as a known reaction to TB therapy followed by the musculoskeletal system. With more effective pharmacovigilance measures implementation, the adverse events being one of the factors for treatment interruption can be overcome.

Orexin receptors: Targets and applications.

Over the years, elucidating targets from the neural circuits that can be used to treat disorders pertaining to the nervous system and extending their scope to other systems have always proved interesting to researchers. The role of various peptides and neurotransmitters has been elucidated and is being developed as therapeutic targets. Out of these, orexins are neuropeptides produced in the hypothalamus that stimulate a specific type of G-Protein coupled receptors (GPCR) called orexin receptors and bring about various physiological and pathological roles. Orexin receptors are of interest not only because of their wide applications such as insomnia, obesity, and inflammatory disorders but also because of their contribution to promising aspects of drug discovery such as optogenetics and their tremendous growth from the stage of being orphans to orexins. This review will discuss in detail the structure of orexin receptors, their physiological role, and various applications in disease states adding a note on agonists and antagonists and finally summarizing the recent drug approvals in the field.

Is Single-Dose Antimicrobial Prophylaxis Sufficient to Control Infections in Gastrointestinal Oncological Surgeries?

Surgical site infections (SSIs) represent one of the most important complications occurring postoperatively following surgical procedures. The SSI incidence is higher following gastrointestinal (GI) surgeries compared to any other surgery. It contributes to the majority of morbidity and mortality in patients undergoing GI surgeries. The accepted practice worldwide for the prevention and control of SSIs is providing antimicrobial prophylaxis. The appropriate antimicrobial and dose are chosen depending on the microbial flora, complications, and patient risk factors. The objective of this review was to determine the sufficient number of prophylactic antimicrobial doses that would be efficacious and safe in controlling the SSIs following GI oncological surgeries. Single-dose antimicrobial prophylaxis has shown the same efficacy as the multiple-dose antimicrobial regimen in controlling SSIs in esophageal, gastric, and colorectal surgeries. The advantages of a single-dose regimen include less chance of emergence of resistance, less chance for allergies or toxicity, and less cost. The addition of metronidazole with single-dose antimicrobial prophylaxis in colorectal surgery should be considered due to its beneficial effect in further reducing infections. Further randomized controlled trials are needed for the literature to determine the efficacy and safety of single-dose antimicrobial prophylaxis in patients undergoing esophageal and colorectal surgeries. In addition, studies are required to determine the individual effectiveness of metronidazole in controlling SSIs in colorectal surgeries.

National guidelines for gene therapy product (2019): A road-map to gene therapy products development and clinical trials.

The "National Guidelines for Gene Therapy Product (GTP) Development and Clinical Trials" prepared by the Indian Council of Medical Research and Department of Biotechnology in 2019 came as a welcome step in the process of regulation of gene therapy research, as there was a lack of Indian guidelines earlier specific to gene therapy. Indian researchers have taken their step in setting the path of gene therapy research, and this guideline serves to provide the standards starting from its development up to translation to new drug including the ethical, scientific, and regulatory requirements to be followed during the conduct of trial. The Indian guidelines were framed with reference to United States-Food and Drug Administration and European Union guidelines on gene therapy. It is the responsibility of all the stakeholders involved in the development of GTP to adhere to the national guidelines. This review provides an outline of the Indian regulatory guidelines on GTP.

Efficacy and Safety of Eberconazole vs Sertaconazole in Localised Tinea Infection.

BACKGROUND: Topical antifungals especially azole group of drugs are effective agents in the treatment of dermatophytoses producing 100% clinical and mycological cure. Each of them vary having specific characteristics to tackle several clinical challenges like high relapse rate, recurrences and quality of life. AIMS AND OBJECTIVES: To compare the efficacy and safety of Eberconazole and Sertaconazole in tinea infection. MATERIALS AND METHODS: This was a randomized, observer-blinded, parallel-group study conducted at a dermatology out-patient department (OPD) of tertiary care teaching hospital in Puducherry. 85 patients with tinea corporis and tinea cruris infections who visited the dermatology OPD were enrolled in this study. The treatment phase involved two groups receiving either Sertaconazole 2% cream or Eberconazole 1% applied topically twice daily for 4 weeks. At the end of treatment phase, there was a 'follow-up phase' at the end of 4 weeks, where the patients were assessed clinically and mycologically. The data were analyzed using descriptive statistics using MS Excel version 2019 and SPSS version 15 for Windows. RESULTS: The primary efficacy variables namely change in pruritus, erythema, induration, scaling and mycological cure significantly improved in both the groups, as compared to baseline (P < 0.001), in the treatment phase and follow-up phase. Intergroup comparison with respect to pruritus and scaling showed significant difference (P < 0.001), suggestive of better reduction of pruritus and scaling scores at 4 weeks with Sertaconazole when compared to Eberconazole. CONCLUSIONS: Sertaconazole was better than Eberconazole in relieving signs and symptoms of dermatophytoses, especially pruritus, thereby improving patients' quality of life.

Enzymatic Hydroxylation and Excision of Extended 5-Methylcytosine Analogues.

Methylation of cytosine to 5-methylcytosine (mC) is a prevalent reversible epigenetic mark in vertebrates established by DNA methyltransferases (MTases); the methylation mark can be actively erased via a multi-step demethylation mechanism involving oxidation by Ten-eleven translocation (TET) enzyme family dioxygenases, excision of the latter oxidation products by thymine DNA (TDG) or Nei-like 1 (NEIL1) glycosylases followed by base excision repair to restore the unmodified state. Here we probed the activity of the mouse TET1 (mTET1) and Naegleria gruberi TET (nTET) oxygenases with DNA substrates containing extended derivatives of the 5-methylcytosine carrying linear carbon chains and adjacent unsaturated CC bonds. We found that the nTET and mTET1 enzymes were active on modified mC residues in single-stranded and double-stranded DNA in vitro, while the extent of the reactions diminished with the size of the extended group. Iterative rounds of nTET hydroxylations of ssDNA proceeded with high stereo specificity and included not only the natural alpha position but also the adjoining carbon atom in the extended side chain. The regioselectivity of hydroxylation was broken when the reactive carbon was adjoined with an sp1 or sp2 system. We also found that NEIL1 but not TDG was active with bulky TET-oxidation products. These findings provide important insights into the mechanism of these biologically important enzymatic reactions.

Rinf Regulates Pluripotency Network Genes and Tet Enzymes in Embryonic Stem Cells.

The Retinoid inducible nuclear factor (Rinf), also known as CXXC5, is a nuclear protein, but its functions in the context of the chromatin are poorly defined. We find that in mouse embryonic stem cells (mESCs), Rinf binds to the chromatin and is enriched at promoters and enhancers of Tet1, Tet2, and pluripotency genes. The Rinf-bound regions show significant overlapping occupancy of pluripotency factors Nanog, Oct4, and Sox2, as well as Tet1 and Tet2. We found that Rinf forms a complex with Nanog, Oct4, Tet1, and Tet2 and facilitates their proper recruitment to regulatory regions of pluripotency and Tet genes in ESCs to positively regulate their transcription. Rinf deficiency in ESCs reduces expression of Rinf target genes, including several pluripotency factors and Tet enzymes, and causes aberrant differentiation. Together, our findings establish Rinf as a regulator of the pluripotency network genes and Tet enzymes in ESCs.

Antimicrobial Prophylaxis in Instrumented Spinal Fusion Surgery: A Comparative Analysis of 24-Hour and 72-Hour Dosages.

STUDY DESIGN: Prospective study. PURPOSE: To compare the efficacy of 24-hour and 72-hour antibiotic prophylaxis in preventing surgical site infections (SSIs). OVERVIEW OF LITERATURE: Antimicrobial prophylaxis in surgical practice has become a universally accepted protocol for minimizing postoperative complications related to infections. Although prophylaxis is an accepted practice, a debate exists with regard to the antibiotic type and its administration duration for various surgical procedures. METHODS: Our institute is a tertiary care hospital with more than 100 spinal surgeries per year for various spine disorders in the department of orthopedics. We conducted this prospective study in our department from June 2012 to January 2015. A total of 326 patients were enrolled in this study, with 156 patients in the 72-hour antibiotic prophylaxis group (group A) and 170 patients in the 24-hour group (group B). Cefazolin was the antibiotic used in both groups. Two surgeons were involved in conducting all the spinal procedures. Our study compared SSIs among patients undergoing instrumented spinal fusion. RESULTS: The overall rate of SSIs was 1.8% with no statistical difference between the two groups. CONCLUSIONS: The 24-hour antimicrobial prophylaxis is as effective as the 72-hour dosage in instrumented spinal fusion surgery.

Retinol and ascorbate drive erasure of epigenetic memory and enhance reprogramming to naïve pluripotency by complementary mechanisms.

Epigenetic memory, in particular DNA methylation, is established during development in differentiating cells and must be erased to create naïve (induced) pluripotent stem cells. The ten-eleven translocation (TET) enzymes can catalyze the oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and further oxidized derivatives, thereby actively removing this memory. Nevertheless, the mechanism by which the TET enzymes are regulated, and the extent to which they can be manipulated, are poorly understood. Here we report that retinoic acid (RA) or retinol (vitamin A) and ascorbate (vitamin C) act as modulators of TET levels and activity. RA or retinol enhances 5hmC production in naïve embryonic stem cells by activation of TET2 and TET3 transcription, whereas ascorbate potentiates TET activity and 5hmC production through enhanced Fe2+ recycling, and not as a cofactor as reported previously. We find that both ascorbate and RA or retinol promote the derivation of induced pluripotent stem cells synergistically and enhance the erasure of epigenetic memory. This mechanistic insight has significance for the development of cell treatments for regenenerative medicine, and enhances our understanding of how intrinsic and extrinsic signals shape the epigenome.

Genome-wide hydroxymethylcytosine pattern changes in response to oxidative stress.

The TET enzymes convert methylcytosine to the newly discovered base hydroxymethylcytosine. While recent reports suggest that TETs may play a role in response to oxidative stress, this role remains uncertain, and results lack in vivo models. Here we show a global decrease of hydroxymethylcytosine in cells treated with buthionine sulfoximine, and in mice depleted for the major antioxidant enzymes GPx1 and 2. Furthermore, genome-wide profiling revealed differentially hydroxymethylated regions in coding genes, and intriguingly in microRNA genes, both involved in response to oxidative stress. These results thus suggest a profound effect of in vivo oxidative stress on the global hydroxymethylome.

Synthetic epigenetics-towards intelligent control of epigenetic states and cell identity.

Epigenetics is currently one of the hottest topics in basic and biomedical research. However, to date, most of the studies have been descriptive in nature, designed to investigate static distribution of various epigenetic modifications in cells. Even though tremendous amount of information has been collected, we are still far from the complete understanding of epigenetic processes, their dynamics or even their direct effects on local chromatin and we still do not comprehend whether these epigenetic states are the cause or the consequence of the transcriptional profile of the cell. In this review, we try to define the concept of synthetic epigenetics and outline the available genome targeting technologies, which are used for locus-specific editing of epigenetic signals. We report early success stories and the lessons we have learned from them, and provide a guide for their application. Finally, we discuss existing limitations of the available technologies and indicate possible areas for further development.