A tour of 3D genome with a focus on CTCF.

The complex three-dimensional (3D) structure of the genome plays critical roles in the maintenance of genome stability, organization, and dynamics and in regulation of gene expression for understanding molecular mechanisms and diseases. Chromatin maintains biological functions and transcriptional activities through long distance interaction and interactions between loops and enhancers-promoters. We firstly overview the architecture and biology of chromatin and loops, topologically associated domains (TADs) and interactions, and compartments and functions. We specifically focus on CCCTC-binding factor (CTCF) in 3D genome organization and function to furthermore understand the significance of CTCF biology, transcriptional regulations, interactions with cohesin, roles in DNA binding, influences of CTCF degradation, and communication with wings-apart like (Wapl) protein. We also summarize the advanced single cell approaches to further monitor dynamics of CTCF functions and structures in the maintenance of 3D genome organization and function at single cell level.

Lung Cancer Heterogeneity and New Strategies for Drug Therapy.

Lung cancer heterogeneity plays an important role in the development of drug resistance. Comprehensive molecular characterizations of lung cancer can describe hereditary and somatic gene changes, mutation, and heterogeneity. We discuss heterogeneity specificity, characterization, and roles of PIK3CD, TP53, and KRAS, as well as target-driven therapies and strategies applied in clinical trials based on a proposed precise self-validation system. The system is a specifically selected strategy of treatment for patients with cancer gene mutations and heterogeneity based on gene sequencing, following validation of the strategies in the patient's own cancer cells or in patient-derived xenografts using their own cancer cells isolated during surgery or biopsies. These results will be more precise if the drugs used in the strategies are selected through protein structure-guided compound screening or a DNA-encoded chemical library before validation in the patient's own cancer cells. Thus, a deeper understanding of heterogeneity mechanisms and improved validation of the therapeutic strategy will result in more precise treatments for patients.

Correlation between mucin biology and tumor heterogeneity in lung cancer.

Mucins (MUC) are a family consisting of large O-glycoproteins whose primary functions are to protect and lubricate cell epithelial surfaces and contribute to intra- and inter-cellular signal pathways, cell proliferation, growth and apotosis. With the development of new technologies, MUCs begin to be identified as an effective marker in evaluating the tumor heterogeneity in lung cancer. MUCs' diverse expressions in subtypes of lung cancer indicate the inter-tumor heterogeneity. MUCs' mutation may also contribute to the development of intra-heterogeneity and evolution of lung cancer. Understanding MUCs' association with lung cancer heterogeneity and its molecular regulatory mechanism will benefit the development of diagnosis, therapy choice, and prognosis prediction of lung cancer.

Role of epigenetics in lung cancer heterogeneity and clinical implication.

Lung cancer, as a highly heterogeneous disease, can be initiated and progressed through the interaction between permanent genetic mutations and dynamic epigenetic alterations. However, the mediating mechanisms of epigenetics in cancer heterogeneity remain unclear. The evolution of cancer, the existence of cancer stem cells (CSCs) and the phenomenon of epithelial-mesenchymal transition (EMT) have been reported to be involved in lung cancer heterogeneity. In this review, we briefly recap the definition of heterogeneity and concept of epigenetics, highlight the potential roles and mechanisms of epigenetic regulation in heterogeneity of lung cancer, and summarize the diagnostic and therapeutic implications of epigenetic alterations in lung cancer, especially the role of DNA methylation and histone acetylation. Deep understanding of epigenetic regulation in cancer heterogeneity is instrumental to the design of novel therapeutic approaches that target lung cancer.

Detection of single cell heterogeneity in cancer.

Single cell heterogeneity has already been highlighted in cancer classification, diagnosis, and treatment. Recent advanced technologies have gained more ability to reveal the heterogeneity on single cell level. In this review, we listed various detection targets applied in single cell study, including tumor tissue cells, circulating tumor cells (CTCs), disseminated tumor cells (DTCs), circulating tumor DNA (ctDNA), cell-free DNA (cfDNA), and cancer stem cells (CSCs). We further discussed and compared detection methods using these detection targets in different fields to reveal single cell heterogeneity in cancer. We focused not only on the methods that have already been established and validated, but also on newly developed methods. In morphology and phenotype, the methods mainly included cell imaging and immune-staining. In genomics and proteomics, the main methods were single cell sequencing and single cell western blotting. Collectively, from using these methods, we can have a better understanding of the single cell variation, as well as what kind of variation it is and how the variation works. Our observations imply that study on single cell heterogeneity in cancer is an important step to precision medicine. The development of technologies in detection of single cell heterogeneity will be sure to improve the diagnosis and treatment in cancer.

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.

Genomic mechanisms of transformation from chronic obstructive pulmonary disease to lung cancer.

Genetic variations in COPD and lung cancer may be one of the molecular mechanisms responsible for COPD-lung cancer transformation. The present review highlights main genetic variations co-existed in COPD and lung cancer and integrates the varied genes into four molecular mechanisms, e.g. activated cell proliferation pathway, tumor suppressor and DNA repair gene dysfunction, chronic inflammatory microenvironment, and impaired immune response, by which COPD epithelial cells may be transformed into tumorigenic status. We call special attention to further investigate the transformation from COPD to lung cancer and understand the exact molecular mechanisms, to prevent and reduce the increased incidence of COPD and lung cancer. We call direct evidence to show the existence of COPD-lung cancer transformation, since current evidence to support the transformation from COPD to lung cancer is the co-existence of selected genes and proteins in both. We should furthermore explore and understand the homogeneity and heterogeneity of gene mutation, epigenetics, sequencing, and function between COPD and lung cancer. The defining and understanding of COPD-lung cancer transformation will provide new diagnostic and therapeutic biomarkers as a new milestone to prevent and treat lung cancer.

Genome analyses identify the genetic modification of lung cancer subtypes.

Lung cancer is a highly intricate and heterogeneous disease with genomic diversity in each subtype. Global analyses of gene expression and sequencing provided us new understanding of the genetic variation between small cell lung carcinoma (SCLC) and non-small cell lung carcinoma (NSCLC), including adenocarcinoma (ADC), and squamous cell carcinoma (SCC). The genetic variations of lung cancer subtypes in genomic studies were integrated and further analyzed using bioinformatics methods. The lung cancer subtypes share some genetic variations such as the dysfunction of tumor suppressor gene TP53, and also harbor specific variations of their own such as MET in ADC, FGFR1 and FGFR3 in SCC and MYC in SCLC. The activated pathway in lung ADC and SCC mainly focuses on MAPK and PI3K with different key genes of each, respectively, and the activated pathway of SCLC mainly focuses on JAK-STAT pathway. The diagnosis of lung cancer subtypes based on these genetic variations such as SNP was also evaluated. These results provide further insights into the different pathogenesis of lung cancer subtypes.

Roles of tumor heterogeneity in the development of drug resistance: A call for precision therapy.

The drug resistance limits the optimal efficacy of drugs during target therapies for lung cancer and requires the development of precision medicine to identify and develop new highly selective drugs and more precise tailoring of medicine to the target population. Lung cancer heterogeneity as a potential cause of drug resistance to targeted therapy may foster tumor evolution and adaptation and fade personalized-medicine strategies. The present review elucidates the influence of tumor heterogeneity on drug efficacy and resistance, and discusses potential strategies to combat heterogeneity for cancer treatment. There is an urgent need to discover and develop disease- and biology-specific biomarkers for monitoring the existence and occurrence of lung cancer heterogeneity, testing targeted drugs in clinical trials, and implementing precision medicine for patients. Better understanding of lung cancer heterogeneity will strengthen therapeutic strategies and apply precision medicine to cure the disease.

Genome dimensions control biological and toxicological functions; myth or reality?

The multidimensional genome offers a new perspective to understand molecular mechanisms of genotoxicity and provide deeper knowledge of how genome organization and reorganization in dimensions can alter cell sensitivity, tolerance, resistance, or toxicity to drugs, whether drugs per se can influence the 3D architecture of the genome directly or indirectly through transcriptional factors, and how we can improve cell sensitivity to drugs through the reorganization of genome and regulation of gene expression. We address roles of 3D genome organization and reorganization in the pathogenesis and progression of disease by evaluating various methodologies of studying the 3D genome, and in the genome integrity and stability susceptible to chemicals as mechanisms of genotoxicity. We discuss the value of imaging, visualizing, and nuclear proximity ligation-based methods of 3D genome organization to measure spatial proximity and visualize spatial distances between genomic loci. We also list a number of dynamic genome changes during genome function and call for further investigations on the interaction of drugs with genome-specific regulators, key enzymes, or spliceosome.

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.

Potentials of single-cell biology in identification and validation of disease biomarkers.

Single-cell biology is considered a new approach to identify and validate disease-specific biomarkers. However, the concern raised by clinicians is how to apply single-cell measurements for clinical practice, translate the message of single-cell systems biology into clinical phenotype or explain alterations of single-cell gene sequencing and function in patient response to therapies. This study is to address the importance and necessity of single-cell gene sequencing in the identification and development of disease-specific biomarkers, the definition and significance of single-cell biology and single-cell systems biology in the understanding of single-cell full picture, the development and establishment of whole-cell models in the validation of targeted biological function and the figure and meaning of single-molecule imaging in single cell to trace intra-single-cell molecule expression, signal, interaction and location. We headline the important role of single-cell biology in the discovery and development of disease-specific biomarkers with a special emphasis on understanding single-cell biological functions, e.g. mechanical phenotypes, single-cell biology, heterogeneity and organization of genome function. We have reason to believe that such multi-dimensional, multi-layer, multi-crossing and stereoscopic single-cell biology definitely benefits the discovery and development of disease-specific biomarkers.

Regulatory T cells and potential inmmunotherapeutic targets in lung cancer.

Lung cancer and metastasis are two of the most lethal diseases globally and seldom have effective therapies. Immunotherapy is considered as one of the powerful alternatives. Regulatory T cells (Tregs) can suppress the activation of the immune system, maintain immune tolerance to self-antigens, and contribute to immunosuppression of antitumor immunity, which is critical for tumor immune evasion in epithelial malignancies, including lung cancer. The present review gives an overview of the biological functions and regulations of Tregs associated with the development of lung cancer and metastasis and explores the potentials of Treg-oriented therapeutic targets. Subsets and features of Tregs mainly include naturally occurring Tregs (nTregs) (CD4(+) nTregs and CD8(+) nTregs) and adaptive/induced Tregs (CD4(+) iTregs and CD8(+) iTregs). Tregs, especially in circulation or regional lymph nodes, play an important role in the progress and metastasis of lung cancer and are considered as therapeutic targets and biomarkers to predict the survival length and recurrence of lung cancer. Increasing understanding of Tregs' functional mechanisms will lead to a number of clinical trials on the discovery and development of Treg-oriented new therapies. Tregs play important roles in lung cancer and metastasis, and the understanding of Tregs becomes more critical for clinical applications and therapies. Thus, Tregs and associated factors can be potential therapeutic targets for lung cancer immunotherapy.

Single-cell transcriptome in the identification of disease biomarkers: opportunities and challenges.

Single cell transcriptome defined as the entire RNA or polyadenylated products of RNA polymerase II on a cell can describe the gene regulation networks responsible for physiological functions, behaviours, and phenotypes in response to signals and microenvironmental changes. Single cell transcriptome/sequencing has the special power to investigate small groups of differentiating cells, circulating tumour cells, or tissue stem cells. A large number of factors may influence the extent of single-cell heterogeneity within a system. It is the opportunity that the single-cell sequencing can be used for the identification of genetic changes in rare cells, e.g. cancer and tissue stem cells, in clinical samples. The methodologies of single-cell sequencing have been improved and developed with the increase of the understanding and attention. The clinical research and application of the single cell sequencing analysis are expected to identify and validate disease-specific biomarkers, network biomarkers, dynamic network biomarkers. The single cell research and value will be also dependent upon the understanding of genomic heterogeneity, planning and design of study protocol, representative of selected and targeted cells, and sensitivity and repeatability of the methodology. The single cell sequencing can be used to develop new diagnostics, monitor disease progresses, measure responses to therapies, and predict the prognosis of patients, although there are still a large number of challenges and difficulties to be faced. It would be more values and specificities of the single cell sequencing to integrate with the function of cells, organs, and systems of the body, the clinical phenotypes of patients, and the description of clinical bioinformatics.

Challenges of clinical translation from single-cell sequencing to measures in clinical biochemistry of haematology: Definition of immune cell identities.

Peripheral immune cells play important roles in the maintenance of systemic and microenvironmental hemostasis. Measurements of circulating blood cells by single-cell RNA sequencing (scRNA-seq) were proposed as one of the routine measures in clinical biochemistry of hematology. Out of translational challenges, defining precise identities of cell subsets and states is more difficult, due to the complexity of immune cell development, location, regulation, function, and metabolism. It is also a challenge to precisely interpret clinical significance and impact of each cell identity marker gene panel (ciMGPs). ciMGPs have potential to advance the understanding of systemic responses of the disease, identify disease-specific biomarkers, and to define cell heterogeneity. Recently, a large number of peripheral cell subsets and expending/activating states have been identified and validated for use in the fast developments in clinical single cell biomedicine. Defining specificity, measurability, and repeatability of cell subsets/states is important for translation of peripheral scRNA-seq in clinical hematology and biochemistry. The development of standard operating procedure and performance of clinical trials in large populations at various ages, diseases, and therapies will promote the clinical translation of ciMGPs to measures. Thus, defining cell subset/state identities will provide the multi-dimensional and comprehensive readouts of systemic immune cells, the precision monitoring of immune dynamics, and deeper-understanding of the disease and response to therapy.

Discovery in clinical and translational medicine.

With the rapid development of biotechnologies and deep improvement of knowledge, "Discovery" is the initial period and source of innovation of clinical and translational medicine. The international journal of Clinical and Translational Discovery serves to highlight unknown or unclear aspects of clinical and translational medicine-associated knowledge, technologies, mechanisms, and therapies (https://onlinelibrary.wiley.com/journal/27680622). The Discovery aims to define the interaction between genes, proteins, and cells, and explore molecular mechanisms of intercommunication and inter-regulation. More discoveries of technologies and equipment are expected to improve method sensitivity, specificity, stability, analysis, and clinical significance. The first priority of Clinical and Translational Discovery is to turn gene-, protein-, drug-, cell-, and interaction-based discoveries into health advancements. Clinical and Translational Discovery highly focuses on the discoveries of biological therapies and precision medicine-based therapy elicited from computational chemistry, DNA libraries, target-dependent small molecular drugs, high-throughput screening, vaccination, immune therapy, cell implantations, gene editing, and RNA- or protein-based inhibitors. Thus, Clinical and Translational Discovery sincerely welcome you to join and share the rapid development and future successes to come.

Significance of clinical phenomes of patients with COVID-19 infection: A learning from 3795 patients in 80 reports.

A new coronavirus SARS-CoV-2 has caused outbreaks in multiple countries and the number of cases is rapidly increasing through human-to-human transmission. Clinical phenomes of patients with SARS-CoV-2 infection are critical in distinguishing it from other respiratory infections. The extent and characteristics of those phenomes varied depending on the severities of the infection, for example, beginning with fever or a mild cough, progressed with signs of pneumonia, and worsened with severe or even fatal respiratory difficulty in acute respiratory distress syndrome. We summarized clinical phenomes of 3795 patients with COVID-19 based on 80 published reports from the onset of outbreak to March 2020 to emphasize the importance and specificity of those phenomes in diagnosis and treatment of infection, and evaluate the impact on medical services. The data show that the incidence of male patients was higher than that of females and the level of C-reaction protein was increased as well as most patients' imaging included ground-glass opacity. Clinical phenomes of SARS-CoV-2 infection were compared with those of SARS-CoV and MERS-CoV infections. There is an urgent need to develop an artificial intelligence-based machine learning capacity to analyze and integrate radiomics- or imaging-based, patient-based, clinician-based, and molecular measurements-based data to fight the outbreak of COVID-19 and enable more efficient responses to unknown infections in future.

Acute lung injury in patients with COVID-19 infection.

During the 2020 Spring Festival in China, the outbreak of a novel coronavirus, named COVID-19 by WHO, brought on a worldwide panic. According to the clinical data of infected patients, radiologic evidence of lung edema is common and deserves clinical attention. Lung edema is a manifestation of acute lung injury (ALI) and may progress to hypoxemia and potentially acute respiratory distress syndrome (ARDS). Patients diagnosed with ARDS have poorer prognosis and potentially higher mortality. Although no effective treatment is formally approved for COVID-19 infection, support of ventilation with oxygen therapy and sometimes mechanical ventilation is often required. Treatment with systemic and/or local glucocorticoids might be helpful to alleviate the pulmonary inflammation and edema, which may decrease the development and/or consequences of ARDS. In this article, we focus on the lung edema and ALI of patients with this widely transmitted COVID-19 infection in order to provide clinical indications and potential therapeutic targets for clinicians and researchers.

Effects of phosphoinositide 3-kinase on protease-induced acute and chronic lung inflammation, remodeling, and emphysema in rats.

BACKGROUND: Phosphoinositide 3-kinase (PI3K) plays an important role in tissue inflammatory reactions and fibrotic processes. The objective of this study was to evaluate the potential mechanism and therapeutic effects of PI3K inhibitor on pancreatic elastase (PE)-induced acute and chronic lung inflammation, edema, and injury. METHODS: Rats were terminated at 7 or 28 days after an intratracheal challenge with PE and intranasal instillation with a PI3K inhibitor, SHBM1009. Alterations of airway epithelial cells and myofibroblasts were studied in vitro. MEASUREMENTS: Lung inflammation, edema, and injury; emphysema; and tissue remodeling were measured after PE instillation with or without treatment with PI3K inhibitor and budesonide. Cellular biologic functions were monitored. RESULTS: SHBM1009 could prevent PE-induced acute lung inflammation, edema, and injury, and chronic lung inflammation, remodeling, and emphysema. Different patterns of inhibitory effects of SHBM1009 and BEZ235, a dual PI3K/mechanistic target of rapamycin inhibitor, on PE-challenged epithelial cells were observed. PE per se reduced epithelial cell proliferation and stability through the inhibition of cell division rather than promoting cell death, in dose- and time-dependent patterns. Effects of PI3K inhibitors on cells were associated with the severity of PE challenges. CONCLUSIONS: PI3K plays a critical role in the development of acute and chronic lung injury, including the process of tissue remodeling and emphysema. PI3K inhibitors could be new therapeutic alternatives for chronic lung diseases.