Transcriptional regulation in model organisms: recent progress and clinical implications

Developing a comprehensive solution aimed to disrupt LARS1/RagD protein-protein interaction

Aminoacyl-tRNA synthetases are crucial enzymes involved in protein synthesis and various cellular physiological reactions. Aside from their standard role in linking amino acids to the corresponding tRNAs, they also impact protein homeostasis by controlling the level of soluble amino acids within the cell. For instance, leucyl-tRNA synthetase (LARS1) acts as a leucine sensor for the mammalian target of rapamycin complex 1 (mTORC1), and may also function as a probable GTPase-activating protein (GAP) for the RagD subunit of the heteromeric activator of mTORC1. In turn, mTORC1 regulates cellular processes, such as protein synthesis, autophagy, and cell growth, and is implicated in various human diseases including cancer, obesity, diabetes, and neurodegeneration. Hence, inhibitors of mTORC1 or a deregulated mTORC1 pathway may offer potential cancer therapies. In this study, we investigated the structural requirements for preventing the sensing and signal transmission from LARS to mTORC1. Building upon recent studies on mTORC1 regulation activation by leucine, we lay the foundation for the development of chemotherapeutic agents against mTORC1 that can overcome resistance to rapamycin. Using a combination of in-silico approaches to develop and validate an alternative interaction model, discussing its benefits and advancements. Finally, we identified a set of compounds ready for testing to prevent LARS1/RagD protein-protein interactions. We establish a basis for creating chemotherapeutic drugs targeting mTORC1, which can conquer resistance to rapamycin. We utilize in-silico methods to generate and confirm an alternative interaction model, outlining its advantages and improvements, and pinpoint a group of novel substances that can prevent LARS1/RagD interactions.Communicated by Ramaswamy H. Sarma.

Canagliflozin interrupts mTOR-mediated inflammatory signaling and attenuates DMBA-induced mammary cell carcinoma in rats

BACKGROUND

Breast cancer prevalence has been globally increasing, therefore, introducing novel interventions in cancer treatment is of a significant importance. The present study was designed to investigate the anti-cancer effect of Canagliflozin (CNG) in an experimental model of DMBA-induced mammary carcinoma in female rats.

METHODS

18 female rats were divided into three experimental groups: Normal control, DMBA control, DMBA+ CNG treated group. DMBA (7.5 mg/kg) was injected subcutaneously in the mammary cells twice weekly for 4 weeks and CNG (10 mg/kg) was orally administered daily for an additional 3 weeks while DMBA control rats only received the vehicle for 3 weeks. Tumors' weight and volume were measured, BRCA-1 and TAC were quantified in serum samples, mTOR, caspase-1, NFκB, IL-1β, NLRP3, GSDMD and MDA were quantified in tumors' homogenates.

RESULTS

CNG treatment increased the BRCA-1 expression, suppressed mTOR inflammatory pathway, attenuated tumor inflammatory mediators; NLRP3, GSDMD, NFκB, IL-1β, suppressed the oxidative stress and inhibited tumor expression of the proliferation biomarker; Ki67.

CONCLUSION

CNG modulated mTOR-mediated signaling pathway and attenuated pyroptotic, inflammatory pathways, suppressed oxidative stress and eventually inhibited DMBA-induced mammary carcinoma proliferation.

Effect of depression disorder on the efficacy and quality of life of first-line chemotherapy combined with immunotherapy in oncogene-driver negative NSCLC patients

Objective

The current research was to assess the relevance between depression disorder and first-line chemotherapy combined with immunotherapy, quality of life in patients with oncogene-driver negative non-small cell cancer (NSCLC).

Methods

NSCLC patients (33 with depression disorder and 34 with no depression disorder) who was received first-line chemotherapy combined with immunotherapy performed Zung Self-rating Depression Scale (SDS) and European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire (EORTC QLQ-C30).

Results

The Progression-Free Survival (PFS) of depression disorder group survivors were lower than these of no depression disorder group survivors (HR, 0.352; 95% CI, 0.201-0.617; P<0.05). The statistical significant was revealed about the Objective Response Rate (ORR) and Disease Control Rate (DCR) in two groups (P<0.05). The quality of life scores of NSCLC patients in no depression disorder group was significantly higher after chemotherapy combined with immunotherapy, and manifested as 92.7 ± 28 vs. 76.3 ± 23.3 (t=8.317, P<0.05), and had a significant difference.

Conclusion

Depression disorder in oncogene-driver negative NSCLC patients influence the curative effect of chemotherapy combined with immunotherapy, and depression disorder was significantly negatively associated with quality of life following chemotherapy combined with immunotherapy.

The Impact of the Microbiome on Resistance to Cancer Treatment with Chemotherapeutic Agents and Immunotherapy

Understanding the mechanisms of resistance to therapy in human cancer cells has become a multifaceted limiting factor to achieving optimal cures in cancer patients. Besides genetic and epigenetic alterations, enhanced DNA damage repair activity, deregulation of cell death, overexpression of transmembrane transporters, and complex interactions within the tumor microenvironment, other mechanisms of cancer treatment resistance have been recently proposed. In this review, we will summarize the preclinical and clinical studies highlighting the critical role of the microbiome in the efficacy of cancer treatment, concerning mainly chemotherapy and immunotherapy with immune checkpoint inhibitors. In addition to involvement in drug metabolism and immune surveillance, the production of microbiota-derived metabolites might represent the link between gut/intratumoral bacteria and response to anticancer therapies. Importantly, an emerging trend of using microbiota modulation by probiotics and fecal microbiota transplantation (FMT) to overcome cancer treatment resistance will be also discussed.

Mesenchymal stem cells: ideal seeds for treating diseases

Mesenchymal stem cells (MSCs), a kind of multipotent stem cells with self-renewal ability and multi-differentiation ability, have become the “practical stem cells” for the treatment of diseases. MSCs have immunomodulatory properties and can be used to treat autoimmune diseases, such as systemic lupus erythematosus (SLE) and Crohn’s disease. MSCs also can be used in cancer and aging. At present, many clinical experiments are using MSCs. MSCs can reduce the occurrence of inflammation and apoptosis of tissue cells, and promote the proliferation of endogenous tissue and organ cells, so as to achieve the effect of repairing tissue and organs. MSCs presumably also play an important role in Corona Virus Disease 2019 (COVID-19) infection.

Sea Urchin as a Universal Model for Studies of Gene Networks

The purple sea urchin Strongylocentrotus purpuratus has been used for over 150 years as a model organism in developmental biology. Using this model species, scientists have been able to describe, in detail, the mechanisms of cell cycle control and cell adhesion, fertilization, calcium signaling, cell differentiation, and death. Massive parallel sequencing of the sea urchin genome enabled the deciphering of the main components of gene regulatory networks during the activation of embryonic signaling pathways. This knowledge helped to extrapolate aberrations in somatic cells that may lead to diseases, including cancer in humans. Furthermore, since many, if not all, developmental signaling pathways were shown to be controlled by non-coding RNAs (ncRNAs), the sea urchin organism represents an attractive experimental model. In this review, we discuss the main discoveries in the genetics, genomics, and transcriptomics of sea urchins during embryogenesis with the main focus on the role of ncRNAs. This information may be useful for comparative studies between different organisms, and may help identify new regulatory networks controlled by ncRNAs.

How wide is the application of genetic big data in biomedicine

In the era of big data, massive genetic data, as a new industry, has quickly swept almost all industries, especially the pharmaceutical industry. As countries around the world start to build their own gene banks, scientists study the data to explore the origins and migration of humans. Moreover, big data encourage the development of cancer therapy and bring good news to cancer patients. Big datum has been involved in the study of many diseases, and it has been found that analyzing diseases at the gene level can lead to more beneficial treatment options than ordinary treatments. This review will introduce the development of extensive data in medical research from the perspective of big data and tumor, neurological and psychiatric diseases, cardiovascular diseases, other applications and the development direction of big data in medicine.

Gut microecology: Why our microbes could be key to our health

The human body contains a large number of microorganisms, and the gut microecology environment contains the largest number and types of microorganisms. The structure and function of gut microbiota are closely related to the health of the human body. In a cascade of studies, the diversity of gut microbiota and its metabolite often found changed in patients or mice model. What kind of gut microbiota that associated with the occurrence or treatment of diseases were also found in many studies. Gut microbiota and its products can affect the function of the human body. Short-chain fatty acids, bile acid, indoles and so on were found can regulate the inflammation, immune response to affect the process of diseases. Immune cells like natural killer T cells, CD3 + T cells were also found had a link to gut microbiota which associated with diseases. Changes in gut microbiota are associated with changes in the body's major systems, such as the digestive system, the endocrine system, the cardiovascular system, the endocrine and metabolic system, the urinary system diseases, the respiratory system and so on. It is of great significance to study gut microecology for the prevention and treatment of various human diseases.

Principles of RNA methylation and their implications for biology and medicine

RNA methylation is a post-transcriptional level of regulation. At present, more than 150 kinds of RNA modifications have been identified. They are widely distributed in messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), noncoding small RNA (sncRNA) and long-chain non-coding RNA (lncRNA). In recent years, with the discovery of RNA methylation related proteins and the development of high-throughput sequencing technology, the mystery of RNA methylation has been gradually revealed, and its biological function and application value have gradually emerged. In this review, a large number of research results of RNA methylation in recent years are collected. Through systematic summary and refinement, this review introduced RNA methylation modification-related proteins and RNA methylation sequencing technologies, as well as the biological functions of RNA methylation, expressions and applications of RNA methylation-related genes in physiological or pathological states such as cancer, immunity and virus infection, and discussed the potential therapeutic strategies.

Cancer neoantigen: Boosting immunotherapy

Tumor neoantigen has a high degree of immunogenicity. As one of the emerging methods of tumor immunotherapy, the vaccine developed against it has served to clinical trials of various solid tumors, especially in the treatment of melanoma. Currently, a variety of immunotherapy methods have been applied to the treatment of the tumor. However, other therapeutic methods have the disadvantages of low specificity and prominent side effects. Treatments require tumor antigen with higher immunogenicity as the target of immune attack. This review will recommend the identification of neoantigen, the influencing factors of neoantigen, and the application of personalized vaccines for neoantigen in metastatic tumors such as malignant melanoma.

How to overcome the side effects of tumor immunotherapy

The incidence of cancer is increasing year by year. Cancer has become one of the health threats of modern people. Simply relying on the surgery, chemotherapy or radiotherapy, not only the survival rate is not high, but also the quality of life of patients is not much better. Fortunately, the emergence and rapid development of cancer immunotherapy have brought more and more exciting results. However, when scientists think it is possible to overcome cancer, they find that not all cancer patients can benefit from immunotherapy, that is to say, the overall efficiency of immunotherapy is not high. Drug resistance and side effects of immunotherapy cannot be ignored. In order to overcome these difficulties, scientists continue to improve the strategy of immunotherapy and find that combination therapy can effectively reduce the incidence of drug resistance. They also found that by reprogramming tumor blood vessels, activating ferroptosis, utilizing thioredoxin, FATP2 and other substances, the therapeutic effect can be improved and side effects can be alleviated. This article reviews the principles of immunotherapy, new strategies to overcome drug resistance of cancer immunotherapy, and how to improve the efficacy of immunotherapy and reduce side effects.

Bone metabolism regulation: Implications for the treatment of bone diseases

Bone cells in the human body are continuously engaged in cellular metabolism, including the interaction between bone cells, the interaction between the erythropoietic cells of the bone marrow and stromal cells, for the remodeling and reconstruction of bone. Osteoclasts and osteoblasts play an important role in bone metabolism. Diseases occur when bone metabolism is abnormal, but little is known about the signaling pathways that affect bone metabolism. The study of these signaling pathways will help us to use the relevant techniques to intervene, so as to improve the condition. The study of these signaling pathways will help us to use the relevant techniques to intervene, so as to improve the condition. I believe they will shine in the diagnosis and treatment of future clinical bone diseases.

Big data-driven precision medicine: Starting the custom-made era of iatrology

Precision medicine is a new therapeutic concept and method emerging in recent years. The rapid development of precision medicine is driven by the development of omics related technology, biological information and big data science. Precision medicine is provided to implement precise and personalized treatment for diseases and specific patients. Precision medicine is commonly used in the diagnosis, treatment and prevention of various diseases. This review introduces the application of precision medicine in eight systematic diseases of the human body, and systematically presenting the current situation of precision medicine. At the same time, the shortcomings and limitations of precision medicine are pointed out. Finally, we prospect the development of precision medicine.

The associations of hub gene polymorphisms in PI3K/AKT/mTOR pathway and Schistosomiasis Japonica infection and hepatic fibrosis

INTRODUCTION

Increasing evidence shows that the PI3K/AKT/mTOR pathway can be activated by a variety of stimulus in immune cells. Schistosomiasis Japonica is a serious threat to human health in some lakes of China.

METHODS

We analyzed the potential associations between the hub gene (PTEN, mTOR, AKT1 and AKT2) polymorphisms of PI3K/AKT/mTOR pathway and S. japonica risk, including infection risk, as well as immunological hepatic fibrosis risk. An immune database named Database of Immune Cell Expression, Expression quantitative trait loci and Epigenomics (DICE) was used to analyze the expression profiles of the hub genes in 15 types of immune cells.

RESULTS

Of them, two SNPs rs2295080 (mTOR) and rs7254617 (AKT2) were found associated with the risk of infection and fibrosis. We also performed a multivariant Cox regression analysis and found that HBV infection may increase hepatic fibrosis in chronic schistosomiasis patients, instead of genetic polymorphisms on PI3K/AKT/mTOR pathway or any other factors. We also found the expressions of mTOR (RICTOR) and AKT2 in T cells were higher than those in monocyte cells. And, the expressions of PTEN, mTOR (RICTOR) and AKT1 reduced both in activated CD4 T cells and activated CD8 T cells.

CONCLUSIONS

We concluded that rs2295080 may be an important marker in the diagnosis of susceptibility to schistosomiasis infection. But HBV infection not rs2295080 could promote immunological liver damage with fibrosis in patients with chronic schistosomiasis infection.

mTOR signaling pathway and mTOR inhibitors in cancer: progress and challenges

Mammalian target of rapamycin (mTOR) regulates cell proliferation, autophagy, and apoptosis by participating in multiple signaling pathways in the body. Studies have shown that the mTOR signaling pathway is also associated with cancer, arthritis, insulin resistance, osteoporosis, and other diseases. The mTOR signaling pathway, which is often activated in tumors, not only regulates gene transcription and protein synthesis to regulate cell proliferation and immune cell differentiation but also plays an important role in tumor metabolism. Therefore, the mTOR signaling pathway is a hot target in anti-tumor therapy research. In recent years, a variety of newly discovered mTOR inhibitors have entered clinical studies, and a variety of drugs have been proven to have high activity in combination with mTOR inhibitors. The purpose of this review is to introduce the role of mTOR signaling pathway on apoptosis, autophagy, growth, and metabolism of tumor cells, and to introduce the research progress of mTOR inhibitors in the tumor field.

Three-dimensional genome: developmental technologies and applications in precision medicine

In the 20th century, our familiar structure of DNA was the double helix. Due to technical limitations, we do not have a good way to understand the finer structure of the genome, let alone its transcriptional regulation. Until the advent of 3C technologies, we were no longer blind to this one. Three-dimensional (3D) genomics is a new subject, which mainly studies the 3D structure and transcriptional regulation of eukaryotic genomes. Now, this field mainly has Hi-C series and CHIA-PET series technologies. Through 3D genomics, we can understand the basic structure of DNA, understand the growth and development of organisms and the occurrence of diseases, so as to promote human medical and health undertakings. The review introduces the main research techniques of 3D genomics and their characteristics, the latest development of 3D genome structure, the relationship between diseases and 3D genome structure, the applications of 3D genome in precision medicine, and the development of the 4D nucleome project.

RNA-based pharmacotherapy for tumors: From bench to clinic and back

RNA therapy is a treatment that regulates cell proteins and cures diseases by affecting the metabolism of mRNAs in cells, which has cut a figure in the studies on various incurable illnesses like hereditary diseases, tumors, etc. In this review, we introduced the discovery and development of RNA therapy and discussed its classification, mechanisms, advantages, and challenges. Moreover, we highlighted how RNA therapy works in killing tumor cells as well as what progresses it has made in related researches. And the development of RNA anti-tumor drugs and the clinical trial process were also included.

GWAS in cancer: progress and challenges

The genome-wide association study (GWAS) is an effective method to detect single-nucleotide polymorphisms (SNPs) of multiple individual genes based on linkage disequilibrium (LD). GWAS examines genotypes and distinguishing gene characteristics that are exhibited in diseases. In the past few decades, more and more literature has reported the results of applying GWAS to study tumors. Although many pleiotropic loci associated with complex phenotypes have been identified by GWAS, the biological functions of many genetic variation loci remain unclear, and the genetic mechanisms of most complex phenotypes cannot be systematically explained. In this article, we will review the new findings of several tumor types, and categorize the new sites and mechanisms that have recently been discovered. We linked the mechanisms of action of various tumors and searched for links to related gene expression pathways. We found that susceptible sites can be divided into hub genes and peripheral genes; the two interact to link gene expression in a variety of diseases.

Cancer immunotherapy: Pros, cons and beyond

Cancer immunotherapy is an innovative treatment for tumors today. In various experiments and clinical studies, it has been found that immunotherapy does have incomparable advantages over traditional anti-tumor therapy, which can prolong progression-free survival (PFS) and overall survival (OS). However, immunotherapy has obvious complexity and uncertainty. Immunotherapy may also cause severe adverse reactions due to an overactive immune system. More effective and fewer adverse reactions immunological checkpoints are still under further exploration. This review gives an overview of recent developments in immunotherapy and indicates a new direction of tumor treatment through analyzing the pros and cons of immunotherapy coupled with keeping a close watch on the development trend of the immunotherapy future.

Microsatellite instability: a review of what the oncologist should know

The patients with high microsatellite instability (MSI-H)/mismatch repair deficient (dMMR) tumors recently have been reported that can benefit from immunotherapy, and MSI can be used as a genetic instability of a tumor detection index. However, many studies have shown that there are many heterogeneous phenomena in patients with MSI tumors in terms of immunotherapy, prognosis and chemotherapy sensitivity. Here we mainly review the research results of MSI detection methods, the mechanisms of MSI occurrence and its relationship with related tumors, aiming to make a brief analysis of the current research status of MSI and provide comparable reference and guidance value for further research in this field.