Prasoon Agarwal

Treatment of brain injuries and neurodegenerative disorders is a critical challenge due to poor regenerative capabilities of the central nervous system. The current therapeutic strategies are primarily focussed on treating the symptoms than addressing the core issue of loss of neurons. Despite advances in stem cell therapies and surgical alternatives, they are not always successful due to challenges like immune rejection and limited efficacy. Direct neuronal reprogramming of endogenous somatic cells is a promising approach to restore lost neurons. This review evaluates traditional reprogramming techniques and their limitations, explores novel in-vivo strategies that address older problems, and analyse clinical trial outcomes to identify key knowledge gaps to guide future research. Traditional neuronal reprogramming is based on in-vitro ectopic expression of lineage-specific transcription factors. To overcome hurdles posed by in-vitro reprogramming, such as insertional mutagenesis, and variable efficiency, in-vivo approaches have emerged. These techniques employ small molecules, nonviral gene delivery, and CRISPR-based activation to reduce protocol complexity and improve cell survival. Combined methodologies integrate transcription factor cocktails with epigenetic modifiers, microRNAs, and neurotrophic factors, and show further enhancements. Despite these advances, translation to clinical applications has been modest. Early-phase trials report limited functional improvements and highlight risks of off-target effects, inconsistent delivery specificity, and unresolved immunogenicity. Direct neuronal reprogramming offers a viable strategy for replenishing neuronal cell mass in neurodegenerative diseases and brain injuries through autologous therapy. Novel in-vivo and combined approaches show promise in addressing the shortcomings of traditional methods. However, further preclinical validation, comprehensive safety assessments, and uniform frameworks are essential for clinical translation. Future studies should prioritize refining delivery platforms, minimizing off-target reprogramming events, and developing robust biomarkers to monitor conversion efficiency and functional outcomes.

Background: Circulating tumour cells (CTCs) are unique cells that originate from the main tumor site. They circulate in the bloodstream, and are implicated in metastasis, immune evasion and recurrence in various cancers. Associated biomarkers of importance for CTC detection include epithelial cell adhesion molecule (EpCAM), human epidermal growth factor receptor 2 (HER2), programmed death ligand-1 (PD-L1), cluster of differentiation 45 (CD45) and other cancer-specific biomolecules. Their roles as standalone biomarkers, have been thoroughly examined in CTC detection, isolation and targeting. Methods: This review collates key findings on CTC characteristics and biomarker identification. The most recent CTC isolation and detection technologies are discussed, along with individual approaches based on inclusion and exclusion of cell-specific biomarkers. Emerging treatments integrating CTCs, including nanocarrier-mediated drug delivery, have been analyzed. We have discussed both the physical and research barriers in the current landscape. Results: Recent advances have determined that such biomarkers are more reliable when associated with secondary biomarkers, due to concerns regarding immune evasion and low sensitivity. The identification of these molecules has fast-tracked the development of several groundbreaking technologies. Conclusion: The prognostic and predictive role of CTCs in various cancers revealed promising results. The development of integrative therapeutics can enhance patient survival and quality of life. These advancements depend on addressing key issues, such as molecular characterization and low abundance of CTCs.

Background: Aberrant DNA methylation can lead to the onset of pathological phenotypes and is increasingly being implicated in age-related metabolic diseases. In our preceding study we show that the heterozygous ablation of Pcyt2, the rate limiting enzyme in phosphatidylethanolamine (PE) synthesis, causes an age-dependent development of non-alcoholic steatohepatitis (NASH), and that treatment with the Pcyt2 substrate phosphonoethylamine (PEA) can attenuate phenotypic NASH pathologies. Here, we hypothesize that abnormal DNA methylation patterns underly the development of Pcyt2^+ /- NASH. In this study, we conduct an epigenome-wide methylation analysis to characterize the differential methylation of Pcyt2^+ /- livers and investigate whether the attenuation of NASH with PEA treatment is associated with changes in DNA methylation. Results: Pcyt2^+ /- NASH liver experiences significant alterations in DNA methylation pattens relative to Pcyt2^+ / +. Differentially methylated genes belong to pathways including PI3K-Akt signalling pathway, Foxo signalling pathway, oxidative phosphorylation and insulin signalling/secretion, indicating that epigenetic regulation underlies many of our previously established functional pathological mechanisms of Pcyt2^+ /- NASH. Previously unidentified pathways during Pcyt2 deficiency are highlighted, such as cell cycle regulation and cellular senescence that may contribute to NASH development. Treatment with PEA dramatically attenuates aberrant total and protein-coding DNA methylation patterns by 96%. PEA treatment restored the methylation status of key genes involved in epigenetic modifications and induced differential methylation of genes associated with obesity and T2DM such as Adyc3, Celsr2, Fam63b. Conclusion: The Pcyt2^+ /- liver methylome and transcriptome is altered and likely underlies much of the pathology in Pcyt2^+ /- NASH phenotype. The treatment with PEA significantly attenuates aberrant DNA methylation in Pcyt2^+ /- liver and corrects the DNA methylation of genes involved in the pathogenesis of NASH, indicating its therapeutic potential. This analysis provides critical insight into the epigenetic basis of NASH pathophysiology and suggests diagnostic markers and therapeutic targets.

The antibacterial activity of silver nanoparticles has been well-researched throughout the years, and massive data has been generated describing a specific nanoparticle sample and its antibacterial activity by performing laboratory experiments; however, none have utilized this data to create a means of predicting the antibacterial activity. In this paper, we developed a polynomial equation using machine learning that predicts the antibacterial activity of silver nanoparticles against S. aureus and E. coli. Only studies featuring spherical silver nanoparticles without any surface modifications that may enhance the antibacterial activity were considered, and the studies must test the antibacterial activity in terms of the number of bacterial colonies left after treatment to calculate the efficiency. The equation takes the size and amount of the nanoparticles in a particular sample as inputs and predicts its antibacterial activity in terms of the percentage of bacterial colonies left after treatment. The equation was validated for its accuracy and was found to accurately predict the antibacterial activity based on the values of the relevant features. The study is the first of its kind and contributes to the field by reducing the effort and resource consumption in laboratories and providing a simple and efficient means of predicting antibacterial activity.

Amplification of the MYCN oncogene is found in ~20% of neuroblastoma (NB) cases and correlates with high-risk disease and poor prognosis. Despite the plethora of studies describing the role of MYCN in NB, the exact molecular mechanisms underlying MYCN’s contribution to high-risk disease are not completely understood. Herein, we implemented an integrative approach combining publicly available RNA-Seq and MYCN ChIP-Seq datasets derived from human NB cell lines to define biological processes directly regulated by MYCN in NB. Our approach revealed that MYCN-amplified NB cell lines, when compared to non-MYCN-amplified cell lines, are characterized by reduced expression of genes involved in NOTCH receptor processing, axoneme assembly, and membrane protein proteolysis. More specifically, we found genes encoding members of the γ-secretase complex, which is known for its ability to liberate several intracellular signaling molecules from membrane-bound proteins such as NOTCH receptors, to be down-regulated in MYCN-amplified NB cell lines. Analysis of MYCN ChIP-Seq data revealed an enrichment of MYCN binding at the transcription start sites of genes encoding γ-secretase complex subunits. Notably, using publicly available gene expression data from NB primary tumors, we revealed that the expression of γ-secretase subunits encoding genes and other components of the NOTCH signaling pathway was also reduced in MYCN-amplified tumors and correlated with worse overall survival in NB patients. Genetic or pharmacological depletion of MYCN in NB cell lines induced the expression of γ-secretase genes and NOTCH-target genes. Chemical inhibition of γ-secretase activity dampened the expression of NOTCH-target genes upon MYCN depletion in NB cells. In conclusion, this study defines a set of MYCN-regulated pathways that are specific to MYCN-amplified NB tumors, and it suggests a novel role for MYCN in the suppression of genes of the γ-secretase complex, with an impact on the NOTCH-target gene expression in MYCN-amplified NB.

Glioblastoma multiforme (GBM) cancer stem cells (GSCs) are one of the strongest contributing factors to treatment resistance in GBM. Identification of biomarkers capable of directly affecting these cells within the bulk tumor is a major challenge associated with the development of new targeting strategies. In this study, we focus on understanding the potential of the multifunctional extraordinaire survivin as a biomarker for GSCs. We analyzed the expression profiles of this gene using various publicly available datasets to understand its importance in stemness and other cancer processes. The findings from these studies were further validated using human GSCs isolated from a GBM cell line. In these GSCs, survivin was inhibited using the dietary phytochemical piperine (PIP) and the subsequent effects on stemness, cancer processes and Temozolomide were investigated. In silico analysis identified survivin to be one of the most significant differentially regulated gene in GSCs, in comparison to common stemness markers. Further validation studies on the isolated GSCs showed the importance of survivin in stemness, cancer progression and therapy resistance. Taken together, our study identifies survivin as a more consistent GSC marker and also suggests the possibility of using survivin inhibitors along with standard of care drugs for better therapeutic outcomes.

Background: High doses of doxorubicin put cancer patients at risk for developing dilated cardiomyopathy. Previously, we showed that doxorubicin treatment decreases SIRT3 (sirtuin 3), the main mitochondrial deacetylase and increases protein acetylation in rat cardiomyocytes. Here, we hypothesize that SIRT3 expression can attenuate doxorubicin induced dilated cardiomyopathy in vivo by preventing the acetylation of mitochondrial proteins. Methods: Nontransgenic, M3-SIRT3 (truncated SIRT3; short isoform), and M1-SIRT3 (full-length SIRT3; mitochondrial localized) transgenic mice were treated with doxorubicin for 4 weeks (8 mg/kg body weight per week). Echocardiography was performed to assess cardiac structure and function and validated by immunohistochemistry and immunofluorescence (n=4–10). Mass spectrometry was performed on cardiac mitochondrial peptides in saline (n=6) and doxorubicin (n=5) treated hearts. Validation was performed in doxorubicin treated primary rat and human induced stem cell derived cardiomyocytes transduced with adenoviruses for M3-SIRT3 and M1-SIRT3 and deacetylase deficient mutants (n=4–10). Results: Echocardiography revealed that M3-SIRT3 transgenic mice were partially resistant to doxorubicin induced changes to cardiac structure and function whereas M1-SIRT3 expression prevented cardiac remodeling and dysfunction. In doxorubicin hearts, 37 unique acetylation sites on mitochondrial proteins were altered. Pathway analysis revealed these proteins are involved in energy production, fatty acid metabolism, and oxidative stress resistance. Increased M1-SIRT3 expression in primary rat and human cardiomyocytes attenuated doxorubicin-induced superoxide formation, whereas deacetylase deficient mutants were unable to prevent oxidative stress. Conclusions: Doxorubicin reduced SIRT3 expression and markedly affected the cardiac mitochondrial acetylome. Increased M1-SIRT3 expression in vivo prevented doxorubicin-induced cardiac dysfunction, suggesting that SIRT3 could be a potential therapeutic target for mitigating doxorubicin-induced dilated cardiomyopathy.

It is imperative to identify the mechanisms that confer stemness to the cancer cells for more effective targeting. Moreover, there are not many studies on the link between stemness characteristics and the immune response in tumours. Therefore, in the current study involving GBM, we started with the study of BIRC5 (one of the rare genes differentially expressed in normal and cancer cells) and CXCR4 (gene involved in the survival and proliferation of CSCs). Together, these genes have not been systematically explored. We used a set of 27 promoter methylated regions in GBM. Our analysis showed that four genes corresponding to these regions, namely EOMES, BDNF, HLA-A, and PECAM1, were involved with BIRC5 and CXCR4. Interestingly, we found EOMES to be very significantly involved in stemness and immunology and it was positively correlated to CXCR4. Additionally, BDNF, which was significant in methylation, was negatively correlated to BIRC5.

Integrative multiomics data analysis provides a unique opportunity for the mechanistic understanding of colorectal cancer (CRC) in addition to the identification of potential novel therapeutic targets. In this study, we used public omics data sets to investigate potential associations between microbiome, metabolome, bulk transcriptomics and single cell RNA sequencing datasets. We identified multiple potential interactions, for example 5-aminovalerate interacting with Adlercreutzia; cholesteryl ester interacting with bacterial genera Staphylococcus, Blautia and Roseburia. Using public single cell and bulk RNA sequencing, we identified 17 overlapping genes involved in epithelial cell pathways, with particular significance of the oxidative phosphorylation pathway and the ACAT1 gene that indirectly regulates the esterification of cholesterol. These findings demonstrate that the integration of multiomics data sets from diverse populations can help us in untangling the colorectal cancer pathogenesis as well as postulate the disease pathology mechanisms and therapeutic targets.

Survivin is one of the rare proteins that is differentially expressed in normal and cancer cells and is directly or indirectly involved in numerous pathways required for tumor maintenance. It is expressed in almost all cancers and its expression has been detected at early stages of cancer. These traits make survivin an exceptionally attractive target for cancer therapeutics. Even with these promising features to be an oncotherapeutic target, there has been limited success in the clinical trials targeting survivin. Only recently it has emerged that survivin was not being specifically targeted which could have resulted in the negative clinical outcome. Also, focus of research has now shifted from survivin expression in the overall heterogeneous tumor cell populations to survivin expression in cancer stem cells as these cells have proved to be the major drivers of tumors. Therefore, in this review we have analyzed the expression of survivin in normal and cancer cells with a particular focus on its expression in cancer stem cell compartment. We have discussed the major signaling pathways involved in regulation of survivin. We have explored the current development status of various types of interventions for inhibition of survivin. Furthermore, we have discussed the challenges involving the development of potent and specific survivin inhibitors for cancer therapeutics. Finally we have given insights for some of the promising future anticancer treatments.