New future of cell biology and toxicology: thinking deeper

Emergence of Bias During the Synthesis and Amplification of cDNA for scRNA-seq

The advent of single-cell omics technology has promoted our understanding of the genomic, epigenomic, and transcriptomic heterogeneity in individual cells. Compared to traditional sequencing studies using bulk cells, single-cell transcriptome technology is naturally more dynamic for in depth analysis of genomic variation resulting from cell division and is useful in unraveling the regulatory mechanisms of gene networks in many diseases. However, there are still some limitations of current single-cell RNA sequencing (scRNA-seq) protocols. Biases that arise during the RNA reverse transcription and cDNA pre-amplification steps are the most common problems and play pivotal roles in limiting the quantitative accuracy of scRNA-seq. In this review, we will describe how these biases emerge and impact scRNA-seq protocols. Moreover, we will introduce several current and convenient modified scRNA-seq methods that allow for bias to be decreased and estimated.

Heterogeneity of lipidomic profiles among lung cancer subtypes of patients

Lung cancer is a leading cause of cancer-related deaths with an increasing incidence and poor prognoses. To further understand the regulatory mechanisms of lipidomic profiles in lung cancer subtypes, we measure the profiles of plasma lipidome between health and patients with lung cancer or among patients with squamous cell carcinomas, adenocarcinoma or small cell lung cancer and to correct lipidomic and genomic profiles of lipid-associated enzymes and proteins by integrating the data of large-scale genome screening. Our studies demonstrated that circulating levels of PS and lysoPS significantly increased, while lysoPE and PE decreased in patients with lung cancer. Our data indicate that lung cancer-specific and subtype-specific lipidomics in the circulation are important to understand mechanisms of systemic metabolisms and identify diagnostic biomarkers and therapeutic targets. The carbon atoms, dual bonds or isomerism in the lipid molecule may play important roles in lung cancer cell differentiations and development. This is the first try to integrate lipidomic data with lipid protein-associated genomic expression among lung cancer subtypes as the part of clinical trans-omics. We found that a large number of lipid protein-associated genes significantly change among cancer subtypes, with correlations with altered species and spatial structures of lipid metabolites.

Metabolic Regulation in Mitochondria and Drug Resistance

Mitochondria are generally considered as a powerhouse in a cell where the majority of the cellular ATP and metabolite productions occur. Metabolic rewiring and reprogramming may be initiated and regulated by mitochondrial enzymes. The hypothesis that cellular metabolic rewiring and reprogramming processes may occur as cellular microenvironment is disturbed, resulting in alteration of cell phenotype, such as cancer cells resistant to therapeutics seems to be now acceptable. Cancer metabolic reprogramming regulated by mitochondrial enzymes is now one of the hallmarks of cancer. This chapter provides an overview of cancer metabolism and summarizes progress made in mitochondria-mediated metabolic regulation in cancer drug resistance.

The Significance of Single-Cell Biomedicine in Stem Cells

Clinical application of stem cells (SCs) progresses significantly in the treatment of a large number of diseases, e.g. leukemia, respiratory diseases, kidney disease, cerebral palsy, autism, or autoimmune diseases. Of those, the population, biological phenotypes, and functions of individual SCs are mainly concerned, due to the lack of cell separation and purification processes. The single-cell technology, including microfluidic technology and single-cell genome amplification technology, is widely used to study SCs and gains some recognitions. The present review will address the importance of single-cell technologies in the recognition and heterogeneity of SCs and highlight the significance of current single-cell approaches in the understanding of SC phenotypes. We also discuss the values of single-cell studies to overcome the bottleneck in explore of biological mechanisms and reveal the therapeutic potentials of SCs in diseases, especially tumor-related diseases, as new diagnostic and therapeutic strategies.

The pathophysiological role of mitochondrial oxidative stress in lung diseases

Mitochondria are critically involved in reactive oxygen species (ROS)-dependent lung diseases, such as lung fibrosis, asbestos, chronic airway diseases and lung cancer. Mitochondrial DNA (mtDNA) encodes mitochondrial proteins and is more sensitive to oxidants than nuclear DNA. Damage to mtDNA causes mitochondrial dysfunction, including electron transport chain impairment and mitochondrial membrane potential loss. Furthermore, damaged mtDNA also acts as a damage-associated molecular pattern (DAMP) that drives inflammatory and immune responses. In this review, crosstalk among alveolar epithelial cells, alveolar macrophages and mitochondria is examined. ROS-related transcription factors and downstream cell signaling pathways are also discussed. We conclude that targeting oxidative stress with antioxidant agents, such as thiol molecules, polyphenols and superoxide dismutase (SOD), and promoting mitochondrial biogenesis should be considered as novel strategies for treating lung diseases that currently have no effective treatment options.

Significance of Mitochondria DNA Mutations in Diseases

Mitochondria are essential double-membraned cytoplasmic organelles to support aerobic respiration and produce cellular energy by oxidative phosphorylation (OXPHOS). Mitochondrial functions are controlled by mitochondrial (mtDNA) and nuclear genomes (nDNA). Mutations of mtDNA result in mitochondrial dysfunction and multisystem diseases through compromising OXPHOS function directly by a point mutation or a large-scale mtDNA rearrangement. One or more of OXPHOS complexes are impaired and dysfunctional to affect tissues with high energy demands. mtDNA is more susceptible to oxidative damage and has more mutations than nDNA. Unlike diploid nDNA, mtDNA is a multi-copy genome transmitted and maternally inherited through oocyte. The multi-copy nature of mtDNA easily causes the heteroplasmy as a unique aspect of mtDNA, making mitochondrial diseases more complex and heterogeneous. mtDNA-associated mitochondrial dysfunction plays the important role in the development of multisystemic primary mitochondrial disease, neurodegeneration, and cancer. The present article overviews the occurrence of mtDNA mutation, interactions with other factors, and molecular mechanisms of mtDNA-associated diseases.

Mitochondrial DNA in Telocytes

Telocyte (TC) is a new identified interstitial cell type with a small nuclear and one or several long and thin prolongations with enlargements on them. They were found in many mammals including humans, mouse, rats, dogs, and monkeys and play vital roles in many physiological and pathological conditions. The ultrastructure of mitochondria was observed in TCs, and the alterations were found in TCs from inflammatory ureter tissue. MtDNA is associated with mitochondria normal functions and involved in physiological and pathological processes. However, mitochondria and mtDNA in TCs were not investigated deeply. This review will introduce the origin, distribution, morphology, and functions of TCs and the distribution and functions of TC mitochondria in order to improve a better understanding of the potential functions of mtDNA in TCs.

A global view of regulatory networks in lung cancer: An approach to understand homogeneity and heterogeneity

A number of new biotechnologies are used to identify potential biomarkers for the early detection of lung cancer, enabling a personalized therapy to be developed in response. The combinatorial cross-regulation of hundreds of biological function-specific transcription factors (TFs) is defined as the understanding of regulatory networks of molecules within the cell. Here we integrated global databases with 537 patients with lung adenocarcinoma (ADC), 140 with lung squamous carcinoma (SCC), 9 with lung large-cell carcinoma (LCC), 56 with small-cell lung cancer (SCLC), and 590 without cancer with the understanding of TF functions. The present review aims at the homogeneity or heterogeneity of gene expression profiles among subtypes of lung cancer. About 5, 136, 52, or 16 up-regulated or 19, 24, 122, or 97down-regulated type-special TF genes were identified in ADC, SCC, LCC or SCLC, respectively. DNA-binding and transcription regulator activity associated genes play a dominant role in the differentiation of subtypes in lung cancer. Subtype-specific TF gene regulatory networks with elements should be an alternative for diagnostic and therapeutic targets for early identification of lung cancer and can provide insightful clues to etiology and pathogenesis.

Tomorrow's genome medicine in lung cancer

Tomorrow's genome medicine in lung cancer should focus more on the homogeneity and heterogeneity of lung cancer which play an important role in the development of drug resistance, genetic complexity, as well as confusion and difficulty of early diagnosis and therapy. Chromosome positioning and repositioning may contribute to the sensitivity of lung cancer cells to therapy, the heterogeneity associated with drug resistance, and the mechanism of lung carcinogenesis. The CCCTC-binding factor plays critical roles in genome topology and function, increased risk of carcinogenicity, and potential of lung cancer-specific mediations. Chromosome reposition in lung cancer can be regulated by CCCTC binding factor. Single-cell gene sequencing, as part of genome medicine, was paid special attention in lung cancer to understand mechanical phenotypes, single-cell biology, heterogeneity, and chromosome positioning and function of single lung cancer cells. We at first propose to develop an intelligent single-cell robot of human cells to integrate together systems information of molecules, genes, proteins, organelles, membranes, architectures, signals, and functions. It can be a powerful automatic system to assist clinicians in the decision-making, molecular understanding, risk analyzing, and prognosis predicting.

New strategies for targeting drug combinations to overcome mutation-driven drug resistance

Targeted therapies are suggested as an effective alternative for patients with cancer that harbor mutations, but treatment outcomes are frequently limited by primary or acquired drug resistance. The present review describes potential mechanisms of primary or acquired drug resistances to provide a resource for considering how to be overcome. We focus on strategies of targeted drug combinations to minimize the development of drug resistance within the context how resistance develops. Strategies benefit from the combined use of "omics" technologies, i.e., high-throughput functional genomics data, pharmacogenomics, or genome-wide CRISPR-Cas9 screening, to analyze and design targeted drug combinations for mutation-driven drug resistance. We also introduce new insights towards pathway-centric combined therapies as an alternative to overcome the heterogeneity and benefit patient prognoses.

Regulatory roles of epigenetic modulators, modifiers and mediators in lung cancer

Lung cancer as the leading cause of cancer-related deaths can be initiated and progressed by the interaction between dynamically genetic and epigenetic elements, although mechanisms mediating lung cancer development and progression remain unclear. Tumor progenitor genes may contribute to lung carcinogenesis and cancer progression, are epigenetically disrupted at the early stages of malignancies even before mutations, and alter cell differentiation throughout tumor evolution. The present review explores potential roles and mechanisms of epigenetic modulators, modifiers and mediators in the development of lung cancer. We also overviewed potential mechanisms by which epigenetic modulators, modifiers and mediators control and regulate 3D nuclear architectures, and discussed translational efforts to epigenetic modifications for treatment of lung cancer. Deep understanding of epigenetic modulators, modifiers and mediators will benefit the discovery and development of new diagnostics and therapies for lung cancer.

Effects of anti-human T lymphocyte immune globulins in patients: new or old

Multiple studies demonstrated that anti‐human T lymphocyte immune globulins (ATG) can decrease the incidence of acute and chronic graft rejection in cell or organ transplants. However, further in‐depth study indicates that different subgroups may benefit from either different regimes or alteration of them. Studies among renal transplant patients indicate that low immunological risk patients may not gain the same amount of benefit and thus tilt the risk versus benefit consideration. This may hold true for low immunological risk patients receiving other organ transplants and would be worth further investigation. The recovery time of T cells and natural killer (NK) cells also bears consideration and the impact that it has on the severity and incidence of opportunistic infections closely correlated with the dosage of ATG. The use of lower doses of ATG in combination with other induction medications may offer a solution. The finding that ATG may lose efficacy in cases of multiple transplants or re‐transplants in the case of heart transplants may hold true for other transplantations. This may lead to reconsideration of which induction therapies would be most beneficial in the clinical setting. These studies on ATG done on different patient groups will naturally not be applicable to all, but the evidence accrued from them as a whole may offer us new and different perspectives on how to approach and potentially solve the clinical question of how to best reduce the mortality associated with chronic host‐versus‐graft disease.