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RNA (New York, N.Y.) Aug 2020In recent years, RNA-sequencing (RNA-seq) has emerged as a powerful technology for transcriptome profiling. For a given gene, the number of mapped reads is not only... (Review)
Review
In recent years, RNA-sequencing (RNA-seq) has emerged as a powerful technology for transcriptome profiling. For a given gene, the number of mapped reads is not only dependent on its expression level and gene length, but also the sequencing depth. To normalize these dependencies, RPKM (reads per kilobase of transcript per million reads mapped) and TPM (transcripts per million) are used to measure gene or transcript expression levels. A common misconception is that RPKM and TPM values are already normalized, and thus should be comparable across samples or RNA-seq projects. However, RPKM and TPM represent the relative abundance of a transcript among a population of sequenced transcripts, and therefore depend on the composition of the RNA population in a sample. Quite often, it is reasonable to assume that total RNA concentration and distributions are very close across compared samples. Nevertheless, the sequenced RNA repertoires may differ significantly under different experimental conditions and/or across sequencing protocols; thus, the proportion of gene expression is not directly comparable in such cases. In this review, we illustrate typical scenarios in which RPKM and TPM are misused, unintentionally, and hope to raise scientists' awareness of this issue when comparing them across samples or different sequencing protocols.
Topics: Gene Expression; Gene Expression Profiling; High-Throughput Nucleotide Sequencing; Humans; RNA; Sequence Analysis, RNA
PubMed: 32284352
DOI: 10.1261/rna.074922.120 -
Journal of Pharmacological Sciences Apr 2005In patients with hypoalbuminemia, the total serum concentration of valproic acid may offer poor clinical information; however, very few clinical laboratories routinely...
In patients with hypoalbuminemia, the total serum concentration of valproic acid may offer poor clinical information; however, very few clinical laboratories routinely analyze the free concentration of the drug. The aim of this study was to design a procedure to normalize the total concentration of valproic acid according to the level of serum albumin and using previously published free fraction values. In 121 adult patients, with albumin levels of 18 - 41 g/L, the total concentration of valproic acid was normalized using the derived equation: C(N) = alpha(H)C(H)/6.5, where alpha(H) is the free fraction of the drug corresponding to the patient's particular albuminemia and C(H) is the total concentration of valproic acid. The value of 6.5 corresponds to the free fraction of the drug for a serum albumin of 42 g/L (percentile 50 of the reference range). For total concentrations lower than 75 mg/L, the predicted normalized valproic acid concentrations were reasonably concordant with the observed normalized concentrations calculated using the data from a protein-binding study. In a significant number of cases, subtherapeutic concentrations of the drug became therapeutic and even supratherapeutic when corrected according to the albumin levels. Furthermore, cases with therapeutic drug concentrations frequently became supratherapeutic when normalized. The limitations and clinical applications of the proposed formula for normalizing the total concentration of valproic acid are presented. It is concluded that it may be useful for the posological management of hypoalbuminemic patients when the free concentration of the drug is not available, and decisions have to be made based on the total serum concentration.
Topics: Adult; Blood Chemical Analysis; Humans; Hypoalbuminemia; Middle Aged; Protein Binding; Reference Values; Serum Albumin; Valproic Acid
PubMed: 15840952
DOI: 10.1254/jphs.fpe04007x -
Current Treatment Options in Neurology 2022This article introduces fundamental concepts in circadian biology and the neuroscience of sleep, reviews recent studies characterizing circadian rhythm and sleep... (Review)
Review
PURPOSE OF REVIEW
This article introduces fundamental concepts in circadian biology and the neuroscience of sleep, reviews recent studies characterizing circadian rhythm and sleep disruption among critically ill patients and potentially links to functional outcomes, and draws upon existing literature to propose therapeutic strategies to mitigate those harms. Particular attention is given to patients with critical neurologic conditions and the unique environment of the neuro-intensive care unit.
RECENT FINDINGS
Circadian rhythm disruption is widespread among critically ill patients and sleep time is reduced and abnormally fragmented. There is a strong association between the degree of arousal suppression observed at the bedside and the extent of circadian disruption at the system (e.g., melatonin concentration rhythms) and cellular levels (e.g., core clock gene transcription rhythms). There is a paucity of electrographically normal sleep, and rest-activity rhythms are severely disturbed. Common care interventions such as neurochecks introduce unique disruptions in neurologic patients. There are no pharmacologic interventions proven to normalize circadian rhythms or restore physiologically normal sleep. Instead, interventions are focused on reducing pharmacologic and environmental factors that perpetuate disruption.
SUMMARY
The intensive care environment introduces numerous potent disruptors to sleep and circadian rhythms. Direct neurologic injury and neuro-monitoring practices likely compound those factors to further derange circadian and sleep functions. In the absence of direct interventions to induce normalized rhythms and sleep, current therapy depends upon normalizing external stimuli.
PubMed: 35855215
DOI: 10.1007/s11940-022-00724-5 -
Applied Network Science 2020Finding graph indices which are unbiased to network size and density is of high importance both within a given field and across fields for enhancing comparability of...
Finding graph indices which are unbiased to network size and density is of high importance both within a given field and across fields for enhancing comparability of modern network science studies. The degree variance is an important metric for characterising network degree heterogeneity. Here, we provide an analytically valid normalisation of degree variance to replace previous normalisations which are either invalid or not applicable to all networks. It is shown that this normalisation provides equal values for graphs and their complements; it is maximal in the star graph (and its complement); and its expected value is constant with respect to density for Erdös-Rényi (ER) random graphs of the same size. We strengthen these results with model observations in ER random graphs, random geometric graphs, scale-free networks, random hierarchy networks and resting-state brain networks, showing that the proposed normalisation is generally less affected by both network size and density than previous normalisation attempts. The closed form expression proposed also benefits from high computational efficiency and straightforward mathematical analysis. Analysis of 184 real-world binary networks across different disciplines shows that normalised degree variance is not correlated with average degree and is robust to node and edge subsampling. Comparisons across subdomains of biological networks reveals greater degree heterogeneity among brain connectomes and food webs than in protein interaction networks.
PubMed: 32626822
DOI: 10.1007/s41109-020-00273-3 -
Frontiers in Cell and Developmental... 2022Immunotherapies modulate the function of immune cells to eradicate cancer cells through various mechanisms. These therapies are successful across a spectrum of cancers,... (Review)
Review
Immunotherapies modulate the function of immune cells to eradicate cancer cells through various mechanisms. These therapies are successful across a spectrum of cancers, but they are curative only in a subset of patients. Indeed, a major obstacle to the success of immunotherapies is the immunosuppressive nature of the tumor microenvironment (TME), comprising the stromal component and immune infiltrate of tumors. Importantly, the TME in most solid cancers is characterized by sparsely perfused blood vessels resulting from so-called pathological angiogenesis. In brief, dysregulated development of new vessels results in leaky tumor blood vessels that inefficiently deliver oxygen and other nutrients. Moreover, the occurrence of dysregulated fibrosis around the lesion, known as pathological desmoplasia, further compresses tumor blood vessels and impairs blood flow. TME normalization is a clinically tested treatment strategy to reverse these tumor blood vessel abnormalities resulting in stimulated antitumor immunity and enhanced immunotherapy efficacy. TME normalization includes vascular normalization to reduce vessel leakiness and reprogramming of cancer-associated fibroblast to decompress vessels. How immunotherapies themselves normalize the TME is poorly understood. In this review, we summarize current concepts and progress in TME normalization. Then, we review observations of immunotherapy-induced TME normalization and discuss the considerations for combining vascular normalizing and immunotherapies. If TME could be more completely normalized, immunotherapies could be more effective in more patients.
PubMed: 35712656
DOI: 10.3389/fcell.2022.908389 -
Annual Review of Physiology Feb 2019Abnormal blood and lymphatic vessels create a hostile tumor microenvironment characterized by hypoxia, low pH, and elevated interstitial fluid pressure. These... (Review)
Review
Abnormal blood and lymphatic vessels create a hostile tumor microenvironment characterized by hypoxia, low pH, and elevated interstitial fluid pressure. These abnormalities fuel tumor progression, immunosuppression, and treatment resistance. In 2001, we proposed a novel hypothesis that the judicious use of antiangiogenesis agents-originally developed to starve tumors-could transiently normalize tumor vessels and improve the outcome of anticancer drugs administered during the window of normalization. In addition to providing preclinical and clinical evidence in support of this hypothesis, we also revealed the underlying molecular mechanisms. In parallel, we demonstrated that desmoplasia could also impair vascular function by compressing vessels, and that normalizing the extracellular matrix could improve vascular function and treatment outcome in both preclinical and clinical settings. Here, we summarize the progress made in understanding and applying the normalization concept to cancer and outline opportunities and challenges ahead to improve patient outcomes using various normalizing strategies.
Topics: Animals; Humans; Hypoxia; Neoplasms; Neovascularization, Pathologic; Tumor Microenvironment
PubMed: 30742782
DOI: 10.1146/annurev-physiol-020518-114700 -
Journal of the International... 2019Antiretroviral therapy (ART) is considered the treatment that enables people living with HIV (PLHIV) to lead a "normal life". In spite of the availability of free...
Antiretroviral therapy (ART) is considered the treatment that enables people living with HIV (PLHIV) to lead a "normal life". In spite of the availability of free treatment, patients in resource-poor settings may continue to incur additional costs to realize a normal and full life. This article describes the monetary expenses and psychosocial distress people on free ART bear to live normally. We conducted in-depth interviews with 50 PLHIV on ART. We found that the demands of treatment, poverty, stigma, and health-system constraints interplay to necessitate that PLHIV bear continuous monetary and psychosocial costs to realize local values that define normal life. In the context, access to free medicines is not sufficient to enable PLHIV in resource-poor settings to normalize life. Policy makers and providers should consider proactively complementing free ART with mechanisms that empower PLHIV economically, enhance their problem-solving capacities, and provide an enabling environment if the objective of normalizing life is to be achieved.
Topics: Adult; Anti-Retroviral Agents; Female; HIV Infections; Health Resources; Humans; Life Style; Male; Middle Aged; Social Stigma; Stress, Psychological; Uganda; Young Adult
PubMed: 31266380
DOI: 10.1177/2325958219859654 -
JCI Insight Jun 2023Tumor vascular normalization prevents tumor cells from breaking through the basement membrane and entering the vasculature, thereby inhibiting metastasis initiation. In...
Tumor vascular normalization prevents tumor cells from breaking through the basement membrane and entering the vasculature, thereby inhibiting metastasis initiation. In this study, we report that the antitumor peptide JP1 regulated mitochondrial metabolic reprogramming through AMPK/FOXO3a/UQCRC2 signaling, which improved the tumor microenvironment hypoxia. The oxygen-rich tumor microenvironment inhibited the secretion of IL-8 by tumor cells, thereby promoting tumor vascular normalization. The normalized vasculature resulted in mature and regular blood vessels, which made the tumor microenvironment form a benign feedback loop consisting of vascular normalization, sufficient perfusion, and an oxygen-rich microenvironment, prevented tumor cells from entering the vasculature, and inhibited metastasis initiation. Moreover, the combined therapy of JP1 and paclitaxel maintained a certain vascular density in the tumor and promoted tumor vascular normalization, increasing the delivery of oxygen and drugs and enhancing the antitumor effect. Collectively, our work highlights the antitumor peptide JP1 as an inhibitor of metastasis initiation and its mechanism of action.
Topics: Humans; Interleukin-8; Neovascularization, Pathologic; Neoplasms; Paclitaxel; Oxygen; Tumor Microenvironment
PubMed: 37192004
DOI: 10.1172/jci.insight.161675 -
OncoTargets and Therapy 2018Vascular normalization is a new concept of targeting angiogenesis to restore vessel structure and function and to increase blood perfusion and delivery of drugs. It has... (Review)
Review
Vascular normalization is a new concept of targeting angiogenesis to restore vessel structure and function and to increase blood perfusion and delivery of drugs. It has been confirmed that vascular normalization can decrease relapse and benefit other cancer therapy, including chemotherapy, radiotherapy, and immune cell therapy. The key point of this therapy is to inhibit pro-angiogenic factors and make it be balanced with anti-angiogenic factors, resulting in a mature and normal vessel characteristic. Vascular endothelial growth factor (VEGF) is a key player in the process of tumor angiogenesis, and inhibiting VEGF is a primary approach to tumor vessel normalization. Herein, we review newly uncovered mechanisms governing angiogenesis and vascular normalization of cancer and place emphasis on targeting VEGF pathway to normalize the vasculature. Also, important methods to depress VEGF pathway and make tumor vascular are discussed.
PubMed: 30410348
DOI: 10.2147/OTT.S172042 -
Cancer Cell International Sep 2023The tumor vasculature was different from the normal vasculature in both function and morphology, which caused hypoxia in the tumor microenvironment (TME). Previous... (Review)
Review
The tumor vasculature was different from the normal vasculature in both function and morphology, which caused hypoxia in the tumor microenvironment (TME). Previous anti-angiogenesis therapy had led to a modest improvement in cancer immunotherapy. However, antiangiogenic therapy only benefitted a few patients and caused many side effects. Therefore, there was still a need to develop a new approach to affect tumor vasculature formation. The CD93 receptor expressed on the surface of vascular endothelial cells (ECs) and its natural ligands, MMRN2 and IGFBP7, were now considered potential targets in the antiangiogenic treatment because recent studies had reported that anti-CD93 could normalize the tumor vasculature without impacting normal blood vessels. Here, we reviewed recent studies on the role of CD93, IGFBP7, and MMRN2 in angiogenesis. We focused on revealing the interaction between IGFBP7-CD93 and MMRN2-CD93 and the signaling cascaded impacted by CD93, IGFBP7, and MMRN2 during the angiogenesis process. We also reviewed retrospective studies on CD93, IGFBP7, and MMRN2 expression and their relationship with clinical factors. In conclusion, CD93 was a promising target for normalizing the tumor vasculature.
PubMed: 37660019
DOI: 10.1186/s12935-023-03044-z