Protocol for Testing the Effects of ssDNA Aptamer in HeLa and MCF-7

Conventional approaches for treating tumors encompass chemotherapy, radiotherapy, and surgery. However, these methods come with their limitations when applied in clinical practice. Aptamers are often referred to as "chemical antibodies" and consist of short DNA or RNA molecules, designed to bind to a wide range of targets, including proteins or nucleic acid structures. They exhibit strong affinities and remarkable specificity for their target molecules, making them capable of functioning as therapeutic agents to directly impede tumor cell proliferation. This approach helps minimize the harm to normal cells, thus reducing toxicity through decreased side effects. Here we report the procedure to develop ssDNA aptamer and investigate its ability to inhibit cancer cell proliferation in HeLa and MCF-7 cancer cell lines.

DirectedCHO: A new miniaturized directed evolution process for phenotype stability trial test of CHO cells before bioreactor scale-up

Most of the biopharmaceuticals that are currently on the market are expressed using the Chinese Hamster Ovary (CHO) cell lines. However, the production yield of these biopharmaceuticals is affected due to CHO cellular heterogeneity and challenges in adaptability during the bioreactor scale-up stage. In this communication, we report the protocol for the miniaturized directed evolution process for CHO cells. The results of the directed evolution process would guide adapting the CHO cell line before bioreactor scale-up. With our approach, we have established the protocol that can be used to streamline superior CHO cell lines for biopharmaceutical production which would be the first of its kind in Africa. Our directed evolution protocol includes a method for a low-cost multiplex directed evolution process that can be used on CHO cells using 20 stressors in 8 concentrations and provides stable trial results for the scale-up process. Using our process, we can provide a simple consumable kit that manufacturers can use for the CHO cell phenotype stability test before the scale-up process. With our approach, we would further develop a platform that can streamline superior CHO cell lines for biopharmaceutical production. This approach would be the first of its kind in South Africa/ Africa.

Recent advances in genome annotation and synthetic biology for the development of microbial chassis

This article provides an overview of microbial host selection, synthetic biology, genome annotation, metabolic modeling, and computational methods for predicting gene essentiality for developing a microbial chassis. This article focuses on lactic acid bacteria (LAB) as a microbial chassis and strategies for genome annotation of the LAB genome. As a case study, Lactococcus lactis is chosen based on its well-established therapeutic applications such as probiotics and oral vaccine development. In this article, we have delineated the strategies for genome annotations of lactic acid bacteria. These strategies also provide insights into streamlining genome reduction without compromising the functionality of the chassis and the potential for minimal genome chassis development. These insights underscore the potential for the development of efficient and sustainable synthetic biology systems using streamlined microbial chassis with minimal genomes.

Treatment Strategies for Multiple Myeloma Treatment and the Role of High-Throughput Screening for Precision Cancer Therapy

In the past few years, development of approved drug candidates has improved the disease management of multiple myeloma (MM). However, due to drug resistance, some of the patients do not respond positively, while some of the patients acquire drug resistance, thereby these patients eventually relapse. Hence, there are no other therapeutic options for multiple myeloma patients. Therefore, this necessitates a precision-based approach to multiple myeloma therapy. The use of patient's samples to test drug sensitivity to increase efficacy and reduce treatment-related toxicities is the goal of functional precision medicine. Platforms such as high-throughput-based drug repurposing technology can be used to select effective single drug and drug combinations based on the efficacy and toxicity studies within a time frame of couple of weeks. In this article, we describe the clinical and cytogenetic features of MM. We highlight the various treatment strategies and elaborate on the role of high-throughput screening platforms in a precision-based approach towards clinical treatment.

Aptamer-Based Tumor-Targeted Diagnosis and Drug Delivery

Early cancer identification is crucial for providing patients with safe and timely therapy. Highly dependable and adaptive technologies will be required to detect the presence of biological markers for cancer at very low levels in the early stages of tumor formation. These techniques have been shown to be beneficial in encouraging patients to develop early intervention plans, which could lead to an increase in the overall survival rate of cancer patients. Targeted drug delivery (TDD) using aptamer is promising due to its favorable properties. Aptamer is suitable for superior TDD system candidates due to its desirable properties including a high binding affinity and specificity, a low immunogenicity, and a chemical composition that can be simply changed.Due to these properties, aptamer-based TDD application has limited drug side effect along with organ damages. The development of aptasensor has been promising in TDD for cancer cell treatment. There are biomarkers and expressed molecules during cancer cell development; however, only few are addressed in aptamer detection study of those molecules. Its great potential of attachment of binding to specific target molecule made aptamer a reliable recognition element. Because of their unique physical, chemical, and biological features, aptamers have a lot of potential in cancer precision medicine.In this review, we summarized aptamer technology and its application in cancer. This includes advantages properties of aptamer technology over other molecules were thoroughly discussed. In addition, we have also elaborated the application of aptamer as a direct therapeutic function and as a targeted drug delivery molecule (aptasensor) in cancer cells with several examples in preclinical and clinical trials.

Application of Drug Repurposing-Based Precision Medicine Platform for Leukaemia Patient Treatment

Drug resistance in leukaemia is a major problem that needs to be addressed. Precision medicine provides an avenue to reduce drug resistance through a personalised treatment plan. It has helped to better stratify patients based on their molecular profile and therefore improved the sensitivity of patients to a given therapeutic regimen. However, therapeutic options are still limited for patients who have already been subjected to many lines of chemotherapy. The process of designing and developing new drugs requires significant resources, including money and time. Drug repurposing has been explored as an alternative to identify effective drug(s) that could be used to target leukaemia and lessen the burden of drug resistance. The drug repurposing process usually includes preclinical studies with drug screening and clinical trials before approval. Although most of the repurposed drugs that have been identified are generally safe for leukaemia treatment, they seem not to be good candidates for monotherapy but could have value in combination with other drugs, especially for patients who have exhausted therapeutic options. In this review, we highlight precision medicine in leukaemia and the role of drug repurposing. Specifically, we discuss the several screening methods via chemoinformatic, in vitro, and ex vivo that have facilitated and accelerated the drug repurposing process.

Advances in CRISPR-Cas9 for the Baculovirus Vector System: A Systematic Review

The baculovirus expression vector systems (BEVS) have been widely used for the recombinant production of proteins in insect cells and with high insert capacity. However, baculovirus does not replicate in mammalian cells; thus, the BacMam system, a heterogenous expression system that can infect certain mammalian cells, was developed. Since then, the BacMam system has enabled transgene expression via mammalian-specific promoters in human cells, and later, the MultiBacMam system enabled multi-protein expression in mammalian cells. In this review, we will cover the continual development of the BEVS in combination with CRPISPR-Cas technologies to drive genome-editing in mammalian cells. Additionally, we highlight the use of CRISPR-Cas in glycoengineering to potentially produce a new class of glycoprotein medicines in insect cells. Moreover, we anticipate CRISPR-Cas9 to play a crucial role in the development of protein expression systems, gene therapy, and advancing genome engineering applications in the future.

Ex vivo drug sensitivity screening in multiple myeloma identifies drug combinations that act synergistically

The management of multiple myeloma (MM) is challenging: an assortment of available drug combinations adds complexity to treatment selection, and treatment resistance frequently develops. Given the heterogeneous nature of MM, personalized testing tools are required to identify drug sensitivities. To identify drug sensitivities in MM cells, we established a drug testing pipeline to examine ex vivo drug responses. MM cells from 44 patients were screened against 30 clinically relevant single agents and 44 double and triple drug combinations. We observed variability in responses across samples. The presence of gain(1q21) was associated with low sensitivity to venetoclax, and decreased ex vivo responses to dexamethasone reflected the drug resistance observed in patients. Less heterogeneity and higher efficacy was detected with many combinations compared to the corresponding single agents. We identified new synergistic effects of melflufen plus panobinostat using low concentrations (0.1-10 nM and 8 nM, respectively). In agreement with clinical studies, clinically approved combinations, such as triple combination of selinexor plus bortezomib plus dexamethasone, acted synergistically, and synergies required low drug concentrations (0.1 nM bortezomib, 10 nM selinexor and 4 nM dexamethasone). In summary, our drug screening provided results within a clinically actionable 5-day time frame and identified synergistic drug efficacies in patient-derived MM cells that may aid future therapy choices.

Micro and nanofluidics for high throughput drug screening

In this book chapter, we elaborate on the state-of-the-art technology developments in high throughput screening, microfluidics and nanofluidics. This book chapter further elaborated on the application of microfluidics and nanofluidics for high throughput drug screening with respect to communicable diseases and non-communicable diseases such as cancer. As a future perspective, there is tremendous potential for microfluidics and nanofluidics to be applied in high throughput drug screening which could be applied for various biotechnology applications such as in cancer precision medicine, point-of-care diagnostics and imaging. With the integration of Fourth industrial revolution (4IR) technologies with micro and nanofluidics technologies, it envisioned that such integration along with digital health would enable next generation technology development in medical field.

Patents and technology transfer in CRISPR technology

CRISPR technology has revolutionized biological research in the last decade and many academic institutions and companies have patented CRISPR systems and applications. Several patents have been filed for various applications of CRISPR in different industries such as agriculture, synthetic biology, bio-nanotechnology and precision medicine. Despite tremendous pressure on the technology transfer teams, several startups and spin-out companies are already using CRISPR technologies for commercial applications. In this chapter, we discuss the different CRISPR nucleases and their applications. Secondly, we detail our current opinion and perspective on the CRISPR patent and technology landscape for non-mammalian systems. We present two case-studies on CRISPR diagnostics companies, SHERLOCK and Mammoth Biosciences, who are currently at the forefront of establishing diagnostics platforms for coronavirus (SARS-CoV-2) detection. Finally, our chapter identifies future advancements and possible challenges that CRISPR technology might face in non-mammalian systems.

Development of insect cell line using CRISPR technology

In this chapter, we delineated the methods of CRISPR technology that has been used for the development of engineered insect cell line. We elaborated on how CRISPR/Cas9 genome editing in Drosophila melanogaster, Bombyx mori, Spodoptera frugiperda (Sf9 and Sf21), and Mosquitoes enabled the use of model or non-model insect system in various biological and medical applications. Also, the application of synthetic baculovirus genome along with CRISPR/Cas9 vector system to enable genome editing of insect cell systems for treatment of communicable and non-communicable diseases.

Patents, ethics, biosafety and regulation using CRISPR technology

In this review chapter, we provide full comprehensive analysis on the patent, ethics and biosafety regulation with respect to the application of CRISPR technology in mammalian systems. We focused on recent development in CRISPR technology and its patent landscape between countries such as US, European Union, China and Australia. Further, we emphasized on the current scenarios on the ethics regulations with respect to CRISPR research, its applicability in patent and technology transfer. Finally, we elaborated on the biosafety regulation on CRISPR/Cas9 technology application in both mammalian and non-mammalian host system.

Drug Sensitivity and Drug Repurposing Platform for Cancer Precision Medicine

One of the critical Global challenges in achieving the UN Sustainable Development Goals 3 Good Health and Well Being is optimizing drug discovery and translational research for unmet medical need in both communicable and non-communicable diseases. Recently, the WHO reports there has been a shift from communicable diseases to non-communicable diseases with respect to being the leading cause of death globally and particularly in low- and middle-income countries such as South Africa. Hence, there is current drive to establish functional precision medicine program that addresses the unmet medical need using high throughput drug sensitivity and drug repurposing platform. Here, this paper serves as a perspective to showcase the recent development in high throughput drug sensitivity screening platform for the cancer precision medicine. We also elaborate on the benefit and applications of high-throughput drug screening platform for Precision Medicine. From a future perspective, this paper aims to showcase the possibility to integrate existing high-throughput drug sensitivity screening platform with the newly developed platform technologies such as microfluidics based single cell drug screening.

Correction to: Prevalence and Risk Factors of Hypertension in the Vietnamese Elderly

The author affiliations for Deepak B. Thimiri Govinda Raj which previously read.

Step-by-Step Protocol for Superparamagnetic Nanoparticle-Based Endosome and Lysosome Isolation from Eukaryotic Cell

Here, we report our step-by-step protocol for superparamagnetic nanoparticle (SPMNP)-based endosome and lysosome isolation from HeLa. Briefly, we synthesized SPMNP 1.0 with iron oxide (Fe₃O₄) core using thermal decomposition method. Further, we performed ligand-exchange strategy for surface functionalization of SPMNP 1.0 with dimercaptosuccinic acid (DMSA). Thus, we generated DMSA-SPMNP 2.0 and used DMSA-SPMNP 2.0 to isolate endosomes and lysosome from HeLa cells. Using our SPMNP subcellular fractionation protocol, we are able to isolate high-pure-high-yield lysosomes using DMSA-SPMNP 2.0 for lysosome proteomics and lipidomics in order to better understand subcellular compartments.

Method for Evaluating Neuromodulatory Properties of Dental Pulp Stem Cell as an In Vitro Model for Parkinson's Disease

Several research groups have utilized dental pulp stem cells for numerous studies as treatment modality for Parkinson's disease (PD). However, the roles of dental pulp stem cells in governing the Parkinson's disease inflammatory microenvironment remain to be evaluated. In this article, we elaborate the method where we can investigate the effects of dental pulp stem cells on neurons and microglia in an in vitro inflammatory microenvironment.

BacMam System for Rapid Recombinant Protein Expression in Mammalian Cells

Baculovirus expression vector system (BEVS) is an established technology for recombinant protein expression in insect cells. Further, BEVS-mediated gene transduction of mammalian cells (BacMam) is emerging as a technique for high level recombinant protein expression in mammalian cells. Here, we describe generic method in using BEVS as a BacMam for rapid recombinant protein expression in mammalian cells.

Synthesis of Hybrid Gold Nanoparticle (AuNP) Functionalized Superparamagnetic Nanoparticles (SPMNPs) for Efficient Coupling of Biomolecules

Recently, we reported our methodology for isolating plasma membrane and lysosome from eukaryotic cell using superparamagnetic nanoparticles (SPMNPs). Here in this article, we report a step-by-step protocol for synthesis of hybrid gold nanoparticle (AuNP), surface functionalization of AuNPs on superparamagnetic nanoparticles (SPMNPs), and potential use of hybrid AuNP-SPMNP for efficient coupling of biomolecules.

Step-by-Step Protocol for Superparamagnetic Nanoparticle-Based Plasma Membrane Isolation from Eukaryotic Cell

Here, we elaborate our detailed protocol for synthesis, functionalization, and application of superparamagnetic nanoparticle (SPMNP) for plasma membrane and lysosome isolation. We used standard thermal decomposition-based synthesis of iron oxide (Fe₃O₄) core SPMNP 1.0. Using ligand addition methodology, we surface functionalized SPMNP 1.0 with phospholipids and generated phospholipid-SPMNP 2.0. Further we used NH₂-phospholipid-SPMNP 2.0 to isolate plasma membrane. Using our SPMNP subcellular fractionation protocol, we are able to isolate high-pure-high-yield plasma membrane using NH₂-phospholipid-SPMNP 2.0. As a future perspective, we propose to use SPMNP on clinical patient samples and perform mass spectrometry-based proteomics, lipidomics, and glycomics for early cancer diagnosis.

An Update on Anti-CD137 Antibodies in Immunotherapies for Cancer

The selective expression of CD137 on cells of the immune system (e.g., T and DC cells) and oncogenic cells in several types of cancer leads this molecule to be an attractive target to discover cancer immunotherapy. Therefore, specific antibodies against CD137 are being studied and developed aiming to activate and enhance anti-cancer immune responses as well as suppress oncogenic cells. Accumulating evidence suggests that anti-CD137 antibodies can be used separately to prevent tumor in some cases, while in other cases, these antibodies need to be co-administered with other antibodies or drugs/vaccines/regents for a better performance. Thus, in this work, we aim to update and discuss current knowledge about anti-cancer effects of anti-CD137 antibodies as mono- and combined-immunotherapies.

The effects of green tea on lipid metabolism and its potential applications for obesity and related metabolic disorders - An existing update

Obesity is one of the top global issues, which induces several serious health consequences both physically and mentally, such as type 2 diabetes, cardiovascular diseases, dyslipidemia, eating disorders, depression and stress. However, the effective therapy to prevent and treat obesity and overweight, up to now, cannot be found nowadays. Several methods/medicines namely diet control, energy balance, environmental changes, genetic and stem cell therapies, new drugs/chemicals have been extensively studied to enhance the ability to control bodyweight and prevent obesity. Of all the aforementioned methods, green tea, used as a daily beverage, has shown beneficial impacts for the health, especially its anti-obesity effects. Available evidence shows that green tea can interrupt lipid emulsification, reduce adipocyte differentiation, increase thermogenesis, and reduce food intake, thus green tea improves the systemic metabolism and decreases fat mass. Here, we highlight and sum up the update investigations of anti-obesity effect of green tea as well as discuss the potential application of them for preventing obesity and its related metabolic disorders.

Surface functionalization dependent subcellular localization of Superparamagnetic nanoparticle in plasma membrane and endosome

In this article, we elaborate the application of thermal decomposition based synthesis of Fe₃O₄ superparamagnetic nanoparticle (SPMNP) in subcellular fractionation context. Here, we performed surface functionalization of SPMNP with phospholipids and dimercaptosuccinic acid. Surprisingly, we observed surface functionalization dependent SPMNP localization in subcellular compartments such as plasma membrane, endosomes and lysosomes. By using SPMNP based subcellular localization with pulse-chase methodology, we could use SPMNP for high pure-high yield organelle (plasma membrane, endosomes and lysosome) fractionation. Further, SPMNP that are distinctly localized in subcellular compartments can be used as technology for subcellular fractionation that can complement existing tools for cell biology research. As a future perspective, isolated magnetic organelles can be extended to protein/protein complex purification for biochemical and structural biology studies.

Designer nanoparticle: nanobiotechnology tool for cell biology

This article discusses the use of nanotechnology for subcellular compartment isolation and its application towards subcellular omics. This technology review significantly contributes to our understanding on use of nanotechnology for subcellular systems biology. Here we elaborate nanobiotechnology approach of using superparamagnetic nanoparticles (SPMNPs) optimized with different surface coatings for subcellular organelle isolation. Using pulse-chase approach, we review that SPMNPs interacted differently with the cell depending on its surface functionalization. The article focuses on the use of functionalized-SPMNPs as a nanobiotechnology tool to isolate high quality (both purity and yield) plasma membranes and endosomes or lysosomes. Such nanobiotechnology tool can be applied in generating subcellular compartment inventories. As a future perspective, this strategy could be applied in areas such as immunology, cancer and stem cell research.

OmniBac: universal multigene transfer plasmids for baculovirus expression vector systems

Current baculovirus expression vector systems (BEVS) rely on either using homologous recombination or site specific transposition (Tn7 transposition) to obtain recombinant baculovirus. Each approach has its own merits. To date, the choice of transfer plasmids limited expression of target proteins to only one of the two types of BEVS. Here we describe OmniBac, comprising novel universal multigene transfer plasmids that can access all BEVS currently in use for protein production in the community. Detailed protocols are presented for integrating OmniBac plasmids into baculoviral genomes used for heterologous protein production in insect cells.

Gene gymnastics: Synthetic biology for baculovirus expression vector system engineering

Most essential activities in eukaryotic cells are catalyzed by large multiprotein assemblies containing up to ten or more interlocking subunits. The vast majority of these protein complexes are not easily accessible for high resolution studies aimed at unlocking their mechanisms, due to their low cellular abundance and high heterogeneity. Recombinant overproduction can resolve this bottleneck and baculovirus expression vector systems (BEVS) have emerged as particularly powerful tools for the provision of eukaryotic multiprotein complexes in high quality and quantity. Recently, synthetic biology approaches have begun to make their mark in improving existing BEVS reagents by de novo design of streamlined transfer plasmids and by engineering the baculovirus genome. Here we present OmniBac, comprising new custom designed reagents that further facilitate the integration of heterologous genes into the baculovirus genome for multiprotein expression. Based on comparative genome analysis and data mining, we herein present a blueprint to custom design and engineer the entire baculovirus genome for optimized production properties using a bottom-up synthetic biology approach.

A novel strategy for the comprehensive analysis of the biomolecular composition of isolated plasma membranes

We manufactured a novel type of lipid-coated superparamagnetic nanoparticles that allow for a rapid isolation of plasma membranes (PMs), enabling high-resolution proteomic, glycomic and lipidomic analyses of the cell surface. We used this technology to characterize the effects of presenilin knockout on the PM composition of mouse embryonic fibroblasts. We found that many proteins are selectively downregulated at the cell surface of presenilin knockout cells concomitant with lowered surface levels of cholesterol and certain sphingomyelin species, indicating defects in specific endosomal transport routes to and/or from the cell surface. Snapshots of N-glycoproteomics and cell surface glycan profiling further underscored the power and versatility of this novel methodology. Since PM proteins provide many pathologically relevant biomarkers representing two-thirds of the currently used drug targets, this novel technology has great potential for biomedical and pharmaceutical applications.