bluuebunny/crossref_metadata_2025 huggingface dataset:
Intra-Tumoral Expression of SLC7A11 Is Associated with Immune Microenvironment, Drug Resistance, and Prognosis in Cancers: A Pan-Cancer Analysis
Authors: He Jiajun , Ding Hongjian , Li Huaqing , Pan Zhiyu , Chen Qian
Published: December 2021

While many anti-cancer modalities have shown potent efficacy in clinical practices, cancer prevention, timely detection, and effective treatment are still challenging. As a newly recognized iron-dependent cell death mechanism characterized by excessive generation of lipid peroxidation, ferroptosis is regarded as a potent weapon in clearing cancer cells. The cystine/glutamate antiporter solute carrier family 7 member 11 (SLC7A11) is the core target for ferroptosis regulation, the overexpression of which dictates downregulated sensitivity to ferroptosis in cancer cells. Hence, we elaborated the pan-cancer level bioinformatic study and systematically elucidated the role of intra-tumoral expression of SLC7A11 in the survival of cancer patients and potential immunotherapeutic response. Specifically, 25/27 (92.6%) cancers were featured with upregulated SLC7A11 expression, where SLC7A11 overexpression is a risk factor for worse overall survival in 8 cancers. We also validated SLC7A11 expression in multiple pancreatic cancer cell lines in vitro and found that it was upregulated in most pancreatic cancer cell lines (p < 0.05). Single-cell sequencing method revealed the SLC7A11 was majorly expressed in cancer cells and mononuclear cells. To further explore the function of SLC7A11 in cancer progression, we analyzed the influence on cell proliferation after the knockdown or knockout of SLC7A11 by either CRISPR or RNAi methods. Besides, the association between SLC7A11 and drug resistance was characterized using bioinformatic approaches as well. We also analyzed the association between the expression of SLC7A11 in multi-omics level and the intra-tumoral infiltration of immune cells based on cell annotation algorithms. Moreover, the relationship between SLC7A11 and the expression of MHC, immune stimulators, immune inhibitors as well as the response to immunotherapy was investigated. In addition, the SLC7A11 expression in colon adenocarcinoma, uterine corpus endometrial carcinoma, and stomach adenocarcinoma (STAD) is also positively associated with microsatellite instability and that in head and neck squamous cell carcinoma, STAD, and prostate adenocarcinoma is positively associated with neoantigen level, which further revealed the potential relationship between SLC7A11 and immunotherapeutic response.
PseUdeep: RNA Pseudouridine Site Identification with Deep Learning Algorithm
Authors: Zhuang Jujuan , Liu Danyang , Lin Meng , Qiu Wenjing , Liu Jinyang , Chen Size
Published: December 2021

Background: Pseudouridine (Ψ) is a common ribonucleotide modification that plays a significant role in many biological processes. The identification of Ψ modification sites is of great significance for disease mechanism and biological processes research in which machine learning algorithms are desirable as the lab exploratory techniques are expensive and time-consuming.

Results: In this work, we propose a deep learning framework, called PseUdeep, to identify Ψ sites of three species: H. sapiens, S. cerevisiae, and M. musculus. In this method, three encoding methods are used to extract the features of RNA sequences, that is, one-hot encoding, K-tuple nucleotide frequency pattern, and position-specific nucleotide composition. The three feature matrices are convoluted twice and fed into the capsule neural network and bidirectional gated recurrent unit network with a self-attention mechanism for classification.

Conclusion: Compared with other state-of-the-art methods, our model gets the highest accuracy of the prediction on the independent testing data set S-200; the accuracy improves 12.38%, and on the independent testing data set H-200, the accuracy improves 0.68%. Moreover, the dimensions of the features we derive from the RNA sequences are only 109,109, and 119 in H. sapiens, M. musculus, and S. cerevisiae, which is much smaller than those used in the traditional algorithms. On evaluation via tenfold cross-validation and two independent testing data sets, PseUdeep outperforms the best traditional machine learning model available. PseUdeep source code and data sets are available at https://github.com/dan111262/PseUdeep.
Committed Human CD23-Negative Light-Zone Germinal Center B Cells Delineate Transcriptional Program Supporting Plasma Cell Differentiation
Authors: Santamaria Kathleen , Desmots Fabienne , Leonard Simon , Caron Gersende , Haas Marion , Delaloy Céline , Chatonnet Fabrice , Rossille Delphine , Pignarre Amandine , Monvoisin Céline , Seffals Marine , Lamaison Claire , Cogné Michel , Tarte Karin , Fest Thierry
Published: December 2021

B cell affinity maturation occurs in the germinal center (GC). Light-zone (LZ) GC B cells (BGC-cells) interact with follicular dendritic cells (FDCs) and compete for the limited, sequential help from T follicular helper cells needed to escape from apoptosis and complete their differentiation. The highest-affinity LZ BGC-cells enter the cell cycle and differentiate into PCs, following a dramatic epigenetic reorganization that induces transcriptome changes in general and the expression of the PRDM1 gene in particular. Human PC precursors are characterized by the loss of IL-4/STAT6 signaling and the absence of CD23 expression. Here, we studied the fate of human LZ BGC-cells as a function of their CD23 expression. We first showed that CD23 expression was restricted to the GC LZ, where it was primarily expressed by FDCs; less than 10% of tonsil LZ BGC-cells were positive. Sorted LZ BGC-cells left in culture and stimulated upregulated CD23 expression but were unable to differentiate into PCs – in contrast to cells that did not upregulate CD23 expression. An in-depth analysis (including single-cell gene expression) showed that stimulated CD23-negative LZ BGC-cells differentiated into plasmablasts and time course of gene expression changes delineates the transcriptional program that sustains PC differentiation. In particular, we identified a B cell proliferation signature supported by a transient MYC gene expression. Overall, the CD23 marker might be of value in answering questions about the differentiation of normal BGC-cells and allowed us to propose an instructive LZ BGC-cells maturation and fate model.
The Role of Extracellular Vesicles as a Shared Disease Mechanism Contributing to Multimorbidity in Patients With COPD
Authors: Reid Laura V. , Spalluto C. Mirella , Watson Alastair , Staples Karl J. , Wilkinson Tom M. A.
Published: December 2021

Chronic obstructive pulmonary disease (COPD) is one of the leading causes of death worldwide. Individuals with COPD typically experience a progressive, debilitating decline in lung function as well as systemic manifestations of the disease. Multimorbidity, is common in COPD patients and increases the risk of hospitalisation and mortality. Central to the genesis of multimorbidity in COPD patients is a self-perpetuating, abnormal immune and inflammatory response driven by factors including ageing, pollutant inhalation (including smoking) and infection. As many patients with COPD have multiple concurrent chronic conditions, which require an integrative management approach, there is a need to greater understand the shared disease mechanisms contributing to multimorbidity. The intercellular transfer of extracellular vesicles (EVs) has recently been proposed as an important method of local and distal cell-to-cell communication mediating both homeostatic and pathological conditions. EVs have been identified in many biological fluids and provide a stable capsule for the transfer of cargo including proteins, lipids and nucleic acids. Of these cargo, microRNAs (miRNAs), which are short 17-24 nucleotide non-coding RNA molecules, have been amongst the most extensively studied. There is evidence to support that miRNA are selectively packaged into EVs and can regulate recipient cell gene expression including major pathways involved in inflammation, apoptosis and fibrosis. Furthermore changes in EV cargo including miRNA have been reported in many chronic diseases and in response to risk factors including respiratory infections, noxious stimuli and ageing. In this review, we discuss the potential of EVs and EV-associated miRNA to modulate shared pathological processes in chronic diseases. Further delineating these may lead to the identification of novel biomarkers and therapeutic targets for patients with COPD and multimorbidities.
TC2N: A Novel Vital Oncogene or Tumor Suppressor Gene In Cancers
Authors: Li Hanyang , Fang He , Chang Li , Qiu Shuang , Ren Xiaojun , Cao Lidong , Bian Jinda , Wang Zhenxiao , Guo Yi , Lv Jiayin , Sun Zhihui , Wang Tiejun , Li Bingjin
Published: December 2021

Several C2 domain-containing proteins play key roles in tumorigenesis, signal transduction, and mediating protein–protein interactions. Tandem C2 domains nuclear protein (TC2N) is a tandem C2 domain-containing protein that is differentially expressed in several types of cancers and is closely associated with tumorigenesis and tumor progression. Notably, TC2N has been identified as an oncogene in lung and gastric cancer but as a tumor suppressor gene in breast cancer. Recently, a large number of tumor-associated antigens (TAAs), such as heat shock proteins, alpha-fetoprotein, and carcinoembryonic antigen, have been identified in a variety of malignant tumors. Differences in the expression levels of TAAs between cancer cells and normal cells have led to these antigens being investigated as diagnostic and prognostic biomarkers and as novel targets in cancer treatment. In this review, we summarize the clinical characteristics of TC2N-positive cancers and potential mechanisms of action of TC2N in the occurrence and development of specific cancers. This article provides an exploration of TC2N as a potential target for the diagnosis and treatment of different types of cancers.
IL-1β and the Intestinal Epithelial Tight Junction Barrier
Authors: Kaminsky Lauren W. , Al-Sadi Rana , Ma Thomas Y.
Published: December 2021

The intestinal epithelial tight junction (TJ) barrier controls the paracellular permeation of contents from the intestinal lumen into the intestinal tissue and systemic circulation. A defective intestinal TJ barrier has been implicated as an important pathogenic factor in inflammatory diseases of the gut including Crohn’s disease, ulcerative colitis, necrotizing enterocolitis, and celiac disease. Previous studies have shown that pro-inflammatory cytokines, which are produced during intestinal inflammation, including interleukin-1β (IL-1β), tumor necrosis factor-α, and interferon-γ, have important intestinal TJ barrier-modulating actions. Recent studies have shown that the IL-1β-induced increase in intestinal TJ permeability is an important contributing factor of intestinal inflammation. The IL-1β-induced increase in intestinal TJ permeability is mediated by regulatory signaling pathways and activation of nuclear transcription factor nuclear factor-κB, myosin light chain kinase gene activation, and post-transcriptional occludin gene modulation by microRNA and contributes to the intestinal inflammatory process. In this review, the regulatory role of IL-1β on intestinal TJ barrier, the intracellular mechanisms that mediate the IL-1β modulation of intestinal TJ permeability, and the potential therapeutic targeting of the TJ barrier are discussed.
Cutaneous Neuroimmune Interactions of TSLP and TRPV4 Play Pivotal Roles in Dry Skin-Induced Pruritus
Authors: Lee Wook-Joo , Shim Won-Sik
Published: December 2021

Dry skin is a symptom of skin barrier dysfunction that evokes pruritus; however, the cutaneous neuroimmune interactions underlying dry skin-induced pruritus remain unclear. Therefore, we aimed to elucidate the mechanisms underlying dry skin-induced pruritus. To this end, an acetone/ethanol/water (AEW)-induced mouse model of dry skin was used in this study. We observed that the production of thymic stromal lymphopoietin (TSLP) significantly increased in the keratinocytes of AEW mice. Importantly, treatment with an antagonist of transient receptor potential cation channel subfamily V member 4 (TRPV4), HC067047, ameliorated dry skin conditions in AEW mice. The symptoms of dry skin were significantly reduced in Trpv4 knockout (KO) mice following treatment with AEW. The increase in the intracellular calcium levels by TSLP in the dorsal root ganglia (DRG) of Trpv4 KO mice was also significantly attenuated. The spontaneous scratching bouts were significantly decreased in both the HC067047-treated and Trpv4 KO AEW mice. Importantly, the TSLP-dependent release of tryptase from the mast cells was significantly reduced in both the HC067047-treated mice and Trpv4 KO AEW mice. Notably, inhibition of the TSLP-induced signaling pathway in DRG selectively reduced the spontaneous scratching bouts in AEW mice. Overall, the results demonstrated that the cutaneous neuroimmune interactions of TSLP and TRPV4 play pivotal roles in dry skin-induced pruritus.
Tilapia Piscidin 4 (TP4) Reprograms M1 Macrophages to M2 Phenotypes in Cell Models of Gardnerella vaginalis-Induced Vaginosis
Authors: Liu Chia-Wen , Su Bor-Chyuan , Chen Jyh-Yih
Published: December 2021

Gardnerella vaginalis is associated with bacterial vaginosis (BV). The virulence factors produced by G. vaginalis are known to stimulate vaginal mucosal immune response, which is largely driven by activated macrophages. While Tilapia piscidin 4 (TP4), an antimicrobial peptide isolated from Nile tilapia, is known to display a broad range of antibacterial functions, it is unclear whether TP4 can affect macrophage polarization in the context of BV. In this study, we used the culture supernatants from G. vaginalis to stimulate differentiation of THP-1 and RAW264.7 cells to an M1 phenotype. The treatment activated the NF-κB/STAT1 signaling pathway, induced reactive nitrogen and oxygen species, and upregulated inflammatory mediators. We then treated the induced M1 macrophages directly with a non-toxic dose of TP4 or co-cultured the M1 macrophages with TP4-treated vaginal epithelial VK2 cells. The results showed that TP4 could not only decrease pro-inflammatory mediators in the M1 macrophages, but it also enriched markers of M2 macrophages. Further, we found that direct treatment with TP4 switched M1 macrophages toward a resolving M2c phenotype via the MAPK/ERK pathway and IL-10-STAT3 signaling. Conversely, tissue repair M2a macrophages were induced by TP4-treated VK2 cells; TP4 upregulated TSG-6 in VK2 cells, which subsequently activated STAT6 and M2a-related gene expression in the macrophages. In conclusion, our results imply that TP4 may be able to attenuate the virulence of G. vaginalis by inducing resolving M2c and tissue repair M2a macrophage polarizations, suggesting a novel strategy for BV therapy.
A Host-Restricted Self-Attenuated Influenza Virus Provides Broad Pan-Influenza A Protection in a Mouse Model
Authors: Kim Minjin , Cheong Yucheol , Lee Jinhee , Lim Jongkwan , Byun Sanguine , Jang Yo Han , Seong Baik Lin
Published: December 2021

Influenza virus infections can cause a broad range of symptoms, form mild respiratory problems to severe and fatal complications. While influenza virus poses a global health threat, the frequent antigenic change often significantly compromises the protective efficacy of seasonal vaccines, further increasing the vulnerability to viral infection. Therefore, it is in great need to employ strategies for the development of universal influenza vaccines (UIVs) which can elicit broad protection against diverse influenza viruses. Using a mouse infection model, we examined the breadth of protection of the caspase-triggered live attenuated influenza vaccine (ctLAIV), which was self-attenuated by the host caspase-dependent cleavage of internal viral proteins. A single vaccination in mice induced a broad reactive antibody response against four different influenza viruses, H1 and rH5 (HA group 1) and H3 and rH7 subtypes (HA group 2). Notably, despite the lack of detectable neutralizing antibodies, the vaccination provided heterosubtypic protection against the lethal challenge with the viruses. Sterile protection was confirmed by the complete absence of viral titers in the lungs and nasal turbinates after the challenge. Antibody-dependent cellular cytotoxicity (ADCC) activities of non-neutralizing antibodies contributed to cross-protection. The cross-protection remained robust even after in vivo depletion of T cells or NK cells, reflecting the strength and breadth of the antibody-dependent effector function. The robust mucosal secretion of sIgA reflects an additional level of cross-protection. Our data show that the host-restricted designer vaccine serves an option for developing a UIV, providing pan-influenza A protection against both group 1 and 2 influenza viruses. The present results of potency and breadth of protection from wild type and reassortant viruses addressed in the mouse model by single immunization merits further confirmation and validation, preferably in clinically relevant ferret models with wild type challenges.
Antibody Response and Safety After mRNA-1273 SARS-CoV-2 Vaccination in Peritoneal Dialysis Patients – the Vienna Cohort
Authors: Beilhack Georg , Monteforte Rossella , Frommlet Florian , Gaggl Martina , Strassl Robert , Vychytil Andreas
Published: December 2021

Background

Dialysis patients are at high risk for a severe clinical course after infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Safety and early immune responses after mRNA-based vaccination have been reported mostly in patients on hemodialysis (HD), whereas reports of peritoneal dialysis (PD) patients remain rare.

Methods

In this retrospective observational study, 39 PD patients had received two doses of the mRNA-1273 Moderna® vaccine. We analyzed SARS-CoV-2 Spike (S) antibody titers 4 weeks after each dose of mRNA-1273 and report local and systemic side effects in PD patients that occurred within one week after each mRNA-1273 dose. Using a quantile regression model we examined factors that might influence SARS-CoV-2 S antibody levels in PD patients.

Results

Four weeks after the first dose of mRNA-1273 vaccine 33 of 39 (84.6%) PD patients seroconverted and presented with 6.62 U/mL (median; IQR 1.57-22.5) anti-SARS-CoV-2 S antibody titers. After the second dose, 38 of 39 (97.4%) PD patients developed anti-SARS-CoV-2 S antibodies and titers increased significantly (median 968 U/mL; IQR 422.5-2500). Pain at the injection site was the most common local adverse event (AE) (71%). Systemic AEs occurring after the first dose were mostly fatigue (33%) and headache (20%). No severe systemic AEs were reported after the first injection. After the second dose the incidence and the severity of the systemic AEs increased. The most common systemic AEs were: fatigue (40.5%), headache (22.5%), joint pain (20%), myalgia (17.5%) and fever (13%). Lower Davies Comorbidity Score (p=0.04) and shorter dialysis vintage (p=0.017) were associated with higher antibody titers after the first dose. Patients with higher antibody titers after the first dose tended to have higher antibody titers after the second dose (p=1.53x10-05).

Conclusions

Peritoneal dialysis patients in this cohort had a high seroconversion rate of 97.4%, showed high antibody titers after full vaccination and tolerated the anti-SARS-CoV-2 mRNA-1273 vaccine well without serious adverse events.
Soluble Urokinase Plasminogen Activator Receptor (suPAR) as a Biomarker of Systemic Chronic Inflammation
Authors: Rasmussen Line Jee Hartmann , Petersen Jens Emil Vang , Eugen-Olsen Jesper
Published: December 2021

Systemic chronic inflammation (SCI) is persistent, health-damaging, low-grade inflammation that plays a major role in immunosenescence and in development and progression of many diseases. But currently, there are no recognized standard biomarkers to assess SCI levels alone, and SCI is typically measured by combining biomarkers of acute inflammation and infection, e.g., CRP, IL-6, and TNFα. In this review, we highlight 10 properties and characteristics that are shared by the blood protein soluble urokinase plasminogen activator receptor (suPAR) and SCI, supporting the argument that suPAR is a biomarker of SCI: (1) Expression and release of suPAR is upregulated by immune activation; (2) uPAR and suPAR exert pro-inflammatory functions; (3) suPAR is associated with the amount of circulating immune cells; (4) Blood suPAR levels correlate with the levels of established inflammatory biomarkers; (5) suPAR is minimally affected by acute changes and short-term influences, in contrast to many currently used markers of systemic inflammation; (6) Like SCI, suPAR is non-specifically associated with multiple diseases; (7) suPAR and SCI both predict morbidity and mortality; (8) suPAR and SCI share the same risk factors; (9) suPAR is associated with risk factors and outcomes of inflammation above and beyond other inflammatory biomarkers; (10) The suPAR level can be reduced by anti-inflammatory interventions and treatment of disease. Assessing SCI has the potential to inform risk for morbidity and mortality. Blood suPAR is a newer biomarker which may, in fact, be a biomarker of SCI since it is stably associated with inflammation and immune activation; shares the same risk factors as many age-related diseases; is both elevated by and predicts age-related diseases. There is strong evidence that suPAR is a prognostic marker of adverse events, morbidity, and mortality. It is associated with immune activity and prognosis across diverse conditions, including kidney disease, cardiovascular disease, cancer, diabetes, and inflammatory disorders. Thus, we think it likely represents a common underlying disease-process shared by many diseases; that is, SCI. We review the supporting literature and propose a research agenda that can help test the hypothesis that suPAR indexes SCI, with the potential of becoming the new gold standard for measuring SCI.
An Immunocompetent Microphysiological System to Simultaneously Investigate Effects of Anti-Tumor Natural Killer Cells on Tumor and Cardiac Microtissues
Authors: Nguyen Oanh T. P. , Misun Patrick M. , Lohasz Christian , Lee Jihyun , Wang Weijia , Schroeder Timm , Hierlemann Andreas
Published: December 2021

Existing first-line cancer therapies often fail to cope with the heterogeneity and complexity of cancers, so that new therapeutic approaches are urgently needed. Among novel alternative therapies, adoptive cell therapy (ACT) has emerged as a promising cancer treatment in recent years. The limited clinical applications of ACT, despite its advantages over standard-of-care therapies, can be attributed to (i) time-consuming and cost-intensive procedures to screen for potent anti-tumor immune cells and the corresponding targets, (ii) difficulties to translate in-vitro and animal-derived in-vivo efficacies to clinical efficacy in humans, and (iii) the lack of systemic methods for the safety assessment of ACT. Suitable experimental models and testing platforms have the potential to accelerate the development of ACT. Immunocompetent microphysiological systems (iMPS) are microfluidic platforms that enable complex interactions of advanced tissue models with different immune cell types, bridging the gap between in-vitro and in-vivo studies. Here, we present a proof-of-concept iMPS that supports a triple culture of three-dimensional (3D) colorectal tumor microtissues, 3D cardiac microtissues, and human-derived natural killer (NK) cells in the same microfluidic network. Different aspects of tumor-NK cell interactions were characterized using this iMPS including: (i) direct interaction and NK cell-mediated tumor killing, (ii) the development of an inflammatory milieu through enrichment of soluble pro-inflammatory chemokines and cytokines, and (iii) secondary effects on healthy cardiac microtissues. We found a specific NK cell-mediated tumor-killing activity and elevated levels of tumor- and NK cell-derived chemokines and cytokines, indicating crosstalk and development of an inflammatory milieu. While viability and morphological integrity of cardiac microtissues remained mostly unaffected, we were able to detect alterations in their beating behavior, which shows the potential of iMPS for both, efficacy and early safety testing of new candidate ACTs.
Proteomics and Organoid Culture Reveal the Underlying Pathogenesis of Hashimoto’s Thyroiditis
Authors: Xiao Hui , Liang Jianqing , Liu Sunqiang , Zhang Qiongyue , Xie Famin , Kong Xingyu , Guo Shanshan , Wang Ruwen , Fu Rong , Ye Zhiqi , Li Yun , Zhang Shuang , Zhang Li , Kaudimba Keneilwe Kenny , Wang Ru , Kong Xingxing , Zhao Bing , Zheng Xuqin , Liu Tiemin
Published: December 2021

Hashimoto’s thyroiditis (HT) is an autoimmune disease, and its incidence continues to rise. Although scientists have studied this disease for many years and discovered the potential effects of various proteins in it, the specific pathogenesis is still not fully comprehended. To understand HT and translate this knowledge to clinical applications, we took the mass spectrometric analysis on thyroid tissue fine-needle puncture from HT patients and healthy people in an attempt to make a further understanding of the pathogenesis of HT. A total of 44 proteins with differential expression were identified in HT patients, and these proteins play vital roles in cell adhesion, cell metabolism, and thyroxine synthesis. Combining patient clinical trial sample information, we further compared the transient changes of gene expression regulation in HT and papillary thyroid carcinoma (PTC) samples. More importantly, we developed patient-derived HT and PTC organoids as a promising new preclinical model to verify these potential markers. Our data revealed a marked characteristic of HT organoid in upregulating chemokines that include C-C motif chemokine ligand (CCL) 2 and CCL3, which play a key role in the pathogenesis of HT. Overall, our research has enriched everyone’s understanding of the pathogenesis of HT and provides a certain reference for the treatment of the disease.
Regulatory T Cells as Predictors of Clinical Course in Hospitalised COVID-19 Patients
Authors: Caldrer Sara , Mazzi Cristina , Bernardi Milena , Prato Marco , Ronzoni Niccolò , Rodari Paola , Angheben Andrea , Piubelli Chiara , Tiberti Natalia
Published: December 2021

Background

The host immune response has a prominent role in the progression and outcome of SARS-CoV-2 infection. Lymphopenia has been described as an important feature of SARS-CoV-2 infection and has been associated with severe disease manifestation. Lymphocyte dysregulation and hyper-inflammation have been shown to be associated with a more severe clinical course; however, a T cell subpopulation whose dysfunction correlate with disease progression has yet to be identify.

Methods

We performed an immuno-phenotypic analysis of T cell sub-populations in peripheral blood from patients affected by different severity of COVID-19 (n=60) and undergoing a different clinical evolution. Clinical severity was established based on a modified WHO score considering both ventilation support and respiratory capacity (PaO2/FiO2 ratio). The ability of circulating cells at baseline to predict the probability of clinical aggravation was explored through multivariate regression analyses.

Results

The immuno-phenotypic analysis performed by multi-colour flow cytometry confirmed that patients suffering from severe COVID-19 harboured significantly reduced circulating T cell subsets, especially for CD4+ T, Th1, and regulatory T cells. Peripheral T cells also correlated with parameters associated with disease severity, i.e., PaO2/FiO2 ratio and inflammation markers. CD4+ T cell subsets showed an important significant association with clinical evolution, with patients presenting markedly decreased regulatory T cells at baseline having a significantly higher risk of aggravation. Importantly, the combination of gender and regulatory T cells allowed distinguishing between improved and worsened patients with an area under the ROC curve (AUC) of 82%.

Conclusions

The present study demonstrates the association between CD4+ T cell dysregulation and COVID-19 severity and progression. Our results support the importance of analysing baseline regulatory T cell levels, since they were revealed able to predict the clinical worsening during hospitalization. Regulatory T cells assessment soon after hospital admission could thus allow a better clinical stratification and patient management.
Deciphering DNA Methylation in HIV Infection
Authors: Arumugam Thilona , Ramphal Upasana , Adimulam Theolan , Chinniah Romona , Ramsuran Veron
Published: December 2021

With approximately 38 million people living with HIV/AIDS globally, and a further 1.5 million new global infections per year, it is imperative that we advance our understanding of all factors contributing to HIV infection. While most studies have focused on the influence of host genetic factors on HIV pathogenesis, epigenetic factors are gaining attention. Epigenetics involves alterations in gene expression without altering the DNA sequence. DNA methylation is a critical epigenetic mechanism that influences both viral and host factors. This review has five focal points, which examines (i) fluctuations in the expression of methylation modifying factors upon HIV infection (ii) the effect of DNA methylation on HIV viral genes and (iii) host genome (iv) inferences from other infectious and non-communicable diseases, we provide a list of HIV-associated host genes that are regulated by methylation in other disease models (v) the potential of DNA methylation as an epi-therapeutic strategy and biomarker. DNA methylation has also been shown to serve as a robust therapeutic strategy and precision medicine biomarker against diseases such as cancer and autoimmune conditions. Despite new drugs being discovered for HIV, drug resistance is a problem in high disease burden settings such as Sub-Saharan Africa. Furthermore, genetic therapies that are under investigation are irreversible and may have off target effects. Alternative therapies that are nongenetic are essential. In this review, we discuss the potential role of DNA methylation as a novel therapeutic intervention against HIV.
Perspectives on Marine Data Science as a Blueprint for Emerging Data Science Disciplines
Authors: Verwega Maria-Theresia , Trahms Carola , Antia Avan N. , Dickhaus Thorsten , Prigge Enno , Prinzler Martin H. U. , Renz Matthias , Schartau Markus , Slawig Thomas , Somes Christopher J. , Biastoch Arne
Published: December 2021

Earth System Sciences have been generating increasingly larger amounts of heterogeneous data in recent years. We identify the need to combine Earth System Sciences with Data Sciences, and give our perspective on how this could be accomplished within the sub-field of Marine Sciences. Marine data hold abundant information and insights that Data Science techniques can reveal. There is high demand and potential to combine skills and knowledge from Marine and Data Sciences to best take advantage of the vast amount of marine data. This can be accomplished by establishing Marine Data Science as a new research discipline. Marine Data Science is an interface science that applies Data Science tools to extract information, knowledge, and insights from the exponentially increasing body of marine data. Marine Data Scientists need to be trained Data Scientists with a broad basic understanding of Marine Sciences and expertise in knowledge transfer. Marine Data Science doctoral researchers need targeted training for these specific skills, a crucial component of which is co-supervision from both parental sciences. They also might face challenges of scientific recognition and lack of an established academic career path. In this paper, we, Marine and Data Scientists at different stages of their academic career, present perspectives to define Marine Data Science as a distinct discipline. We draw on experiences of a Doctoral Research School, MarDATA, dedicated to training a cohort of early career Marine Data Scientists. We characterize the methods of Marine Data Science as a toolbox including skills from their two parental sciences. All of these aim to analyze and interpret marine data, which build the foundation of Marine Data Science.
Warming Threatens to Propel the Expansion of the Exotic Seagrass Halophila stipulacea
Authors: Wesselmann Marlene , Chefaoui Rosa M. , Marbà Núria , Serrao Ester A. , Duarte Carlos M.
Published: December 2021

The spread of exotic species to new areas can be magnified when favored by future climatic conditions. Forecasting future ranges using species distribution models (SDMs) could be improved by considering physiological thresholds, because models solely based on occurrence data cannot account for plasticity due to acclimation of individuals to local conditions over their life-time or to adaptation due to selection within local populations. This is particularly relevant for the exotic seagrassHalophila stipulacea, which colonized the Mediterranean Sea a century ago and shifted its thermal niche, coping with a colder regime. Here, we used two hybrid models combining correlative SDMs with the thermal limits for growth of native and exoticH. stipulaceapopulations to predict the distribution of the species in its native (Indian Ocean and Red Sea) and exotic ranges (Mediterranean Sea and Caribbean Sea) under two scenarios forecasting limited (RCP 2.6) and severe (RCP 8.5) future climate changes by 2050 and 2100. Then, we assessed the differences between hybrid models based on native Red Sea thermal limits (niche conservatism: 17–36°C) and on exotic Mediterranean thermal limits (local adaptation: 14–36°C). At the Mediterranean exotic range, the local adaptation hybrid model accurately agreed with the present distribution of the species while the niche conservatism-based hybrid model failed to predict 87% of the current occurrences of the species. By contrast, both hybrid models predicted similar species distributions for the native range and exotic Caribbean range at present and projected thatH. stipulaceawill maintain its current worldwide under all future greenhouse gas emission scenarios. The hybrid model based on Mediterranean thermal limits projected the expansion ofH. stipulaceathrough the western Mediterranean basin (except the gulf of Leon) under the most severe scenario (RCP 8.5) by 2100, increasing its distribution by 50% in the Mediterranean. The future expansion ofH. stipulaceais related to its capacity to cope with warm waters and it may become a relevant species in the future, particularly under the projected decline of native Mediterranean seagrasses, resulting in important shifts in seagrass communities and overall ecosystem functions.
Response of Microbial Communities on Culturing Plates of Post-settlement Sea Cucumbers to Seawater Acidification and Warming
Authors: Zhang Hongxia , Song Mingshan , Wang Lili , Zhang Anguo , Yang Xiaolong , Liu Yongjian , Yuan Xiutang
Published: December 2021

Seawater acidification and warming have been found to affect the early life of many marine organisms, but their effects on the microbial community in the environment related to the early development stage of aquaculture species have been rarely investigated. To understand how seawater acidification and warming impact the microbial community in aquaculture systems, we designed four microcosms to monitor and characterize the microbial composition on the corrugated plates in the Apostichopus japonicus culture tanks during its post-settlement stage. High-throughput 16S rRNA sequencing revealed that the bacterial community composition varied significantly in different periods of incubation. The bacterial diversity and community composition were obviously changed by seawater acidification and warming in the early period and then tended to revert to the level of the control group. Acidification significantly increased the relative abundance of dominant families Rhodobacteraceae and Flavobacteriaceae in the early period, suggesting that microbiota could increase the abundance of predominant taxa to adapt to increased CO2 concentration and reconstruct a stable community structure. No interaction effect of both factors was observed in the combined group. Results reveal that the microbial communities on the corrugated plates in A. japonicus culture tank were affected in the early period of incubation, and could then acclimatize to the increased CO2 and temperature. This study provides new insights into the variation and adaptation responses of the microbiota in aquaculture systems to seawater acidification and warming.
Importance of Autoimmune Responses in Progression of Retinal Degeneration Initiated by Gene Mutations
Authors: Adamus Grazyna
Published: December 2021

Inherited retinal diseases (IRDs) are clinically and genetically heterogeneous rare disorders associated with retinal dysfunction and death of retinal photoreceptor cells, leading to blindness. Among the most frequent and severe forms of those retinopathies is retinitis pigmentosa (RP) that affects 1:4,000 individuals worldwide. The genes that have been implicated in RP are associated with the proteins present in photoreceptor cells or retinal pigment epithelium (RPE). Asymmetric presentation or sudden progression in retinal disease suggests that a gene mutation alone might not be responsible for retinal degeneration. Immune responses could directly target the retina or be site effect of immunity as a bystander deterioration. Autoantibodies against retinal autoantigens have been found in RP, which led to a hypothesis that autoimmunity could be responsible for the progression of photoreceptor cell death initiated by a genetic mutation. The other contributory factor to retinal degeneration is inflammation that activates the innate immune mechanisms, such as complement. If autoimmune responses contribute to the progression of retinopathy, this could have an implication on treatment, such as gene replacement therapy. In this review, we provide a perspective on the current role of autoimmunity/immunity in RP pathophysiology.
In vivo Imaging of Retina and Choroid in Guinea Pigs
Authors: Dong Li , Li Yi Fan , Jiang Xue , Lan Yin Jun , Shao Lei , Jonas Jost B. , Wei Wen Bin
Published: December 2021

Purpose: To evaluate the feasibility of in-vivo imaging of the retina and choroid using spectral domain optical coherence tomography (OCT) in guinea pigs.

Methods: The study included 19 pigmented guinea pigs (age: 3–4 weeks) which underwent sonographic axial length measurements and OCT imaging. At study end, the animals were sacrificed and histomorphometric examinations of the retina and choroid were performed. We assessed the reproducibility of the OCT measurements and compared in-vivo measurements to histomorphometric data.

Results: The mean thickness of the retina and choroid near the optic nerve head was 175.6 ± 25.8 and 63.4 ± 16.5 μm, respectively, and mean Bruch's membrane opening (BMO) diameter was 831 ± 121 μm. The intra-observer comparison of measurements of retinal thickness (intraclass correlation coefficient (ICC) = 0.92, 95% CI: 0.86–0.96; P < 0.001), choroidal thickness (ICC = 0.92, 95% CI: 0.86–0.96; P < 0.001), and BMO diameter (ICC = 0.92, 95% CI: 0.86–0.96; P < 0.001) showed a high correlation. A high agreement was present also for the inter-observer reproducibility of the measurements of retinal thickness (Pearson correlation coefficient (R) = 0.98; P < 0.001), choroidal thickness (R = 0.96; P < 0.001), and BMO diameter (R = 0.98; P < 0.001). The Bland-Altman plots showed that 2.6% (1/38), 5.3% (2/38), and 7.9% (3/38) of the measurement points of retinal thickness, choroidal thickness and BMO diameter, respectively, were located outside of the 95% limits of agreement. The OCT-based thickness measurements of retina and choroid were significantly higher than those measured by histomorphometry (both P-values <0.01).

Conclusion: OCT-based in-vivo morphometric imaging of the retina and choroid in guinea pigs is feasible with an acceptable intra-observer repeatability and inter-observer reproducibility.
Cost-Effectiveness of Conbercept vs. Ranibizumab for Age-Related Macular Degeneration, Diabetic Macular Edema, and Pathological Myopia: Population-Based Cohort Study and Markov Model
Authors: Cui Zhuang , Zhou Wei , Chang Qinxue , Zhang Tiantian , Wang Hui , Meng Xiangda , Liu Yuanyuan , Yan Hua
Published: December 2021

Background: With the advent of aging society of China, fundus diseases related to pathological neovascularization, including age-related macular degeneration (AMD), diabetic macular edema (DME), and pathological myopia (PM), have become an increasingly serious medical and health problems. As effective drugs of the treatment, conbercept and ranibizumab have been commonly used and covered by the national basic medical insurance in China. However, the pharmacoeconomic evaluation of conbercept vs. ranibizumab for DME and PM remains lacking. This study would assess the cost-effectiveness of conbercept and ranibizumab for the treatment of AMD, DME, and PM from the perspective of Chinese payers.

Methods: A Markov chain model was constructed based on the visual conditions of the patient indicated by the number of letters in best corrected visual acuity (BCVA). We conducted models based on real-world scenario to calculate the cost per the quality-adjusted life-year (QALY) gained. A 1-year cycle length and a 10-year simulation treatment were applied and the number of injections of conbercept and ranibizumab was assumed to the average number within 10 years. Transition probabilities, costs, utility data, and other parameters were obtained from literature searches. A 3.5% discounting rate was applied for both the costs and utilities.

Results: The incremental cost-effectiveness ratios (ICERs) were more favorable for conbercept than ranibizumab in treatment of AMD, DME, and PM, with associated ICER of 66,669 renminbi (RMB), −258,813 RMB, and −373,185 RMB per QALY gained. Compared with ranibizumab, the incremental effectiveness of conbercept in treatment of AMD, DME, and PM was −0.665 QALYs, 0.215 QALYs, and 0.029 QALYs, respectively. The sensitivity analysis showed the same findings, although the ICER is sensitive to the costs of this program.

Conclusion: Under the current Chinese healthcare setting, conbercept is suitable and cost-effective in treatment of AMD, DME, and PM compared with ranibizumab.
MCC Regulator of WNT Signaling Pathway (MCC) Is a Podocyte Essential Gene
Authors: Song Hui , Zhuang Lulu , Xu Xiaodong , Shi Jingsong , Hu Weixin , Liu Zhihong , Shi Shaolin
Published: December 2021

Podocytes are an integral part of the glomerular filtration barrier. Many genes are already known to be essential for podocyte survival, structure and function, but there are more podocyte essential genes to be identified. By single-cell RNA-seq of mouse podocytes, we detected the expression of gene encoding MCC regulator of WNT signaling pathway (MCC) in majority of the podocytes and speculated that MCC is essential for podocytes. We confirmed MCC expression in mouse podocytes and further showed its expression in human podocytes. To experimentally prove the essentiality of MCC for podocytes, we knocked down MCC in cultured podocytes and found marked morphological change of cell shape, cytoskeletal F-actin stress fiber disruption, increased apoptosis, and downregulation of podocyte essential genes, CD2AP and WT1, demonstrating that MCC is essential for podocytes. Since MCC has been implicated in cell cycle and β-catenin signaling, we examined the expression of cell cycle related genes and activity of β-catenin in the MCC knockdown podocytes, but did not find significant changes. To further explore the mechanism underlying the role of MCC in podocytes, we performed RNA-sequencing and bioinformatics analysis of MCC knockdown podocytes and found a significant enrichment of the regulated genes in lamellipodia formation. Consistently, we found that MCC is present in lamellipodia and MCC knockdown resulted in loss of lamellipodia in the cells. Lastly, we found that MCC was downregulated in podocytes treated with puromycin aminonucleosides and in glomeruli of diabetic mice and FSGS patients, implicating MCC is involved in the development of podocytopathy and proteinuria. In conclusion, MCC is potentially essential for podocytes and its downregulation may be involved in podocytopathy.
Sex-Specific Differences in the Association Between Race/Ethnicity and NAFLD Among US Population
Authors: Shaheen Magda , Schrode Katrina M. , Pan Deyu , Kermah Dulcie , Puri Vishwajeet , Zarrinpar Ali , Elisha David , Najjar Sonia M. , Friedman Theodore C.
Published: December 2021

Non-alcoholic fatty liver disease (NAFLD) is spreading worldwide, with a racial/ethnic disparity. We examined the gender role in the racial/ethnic difference in NAFLD in the US population. We analyzed data for 3,292 individuals ≥18 years old from NHANES 2017–2018, a representative sample of the non-institutionalized adult population in the US. Exclusions were subjects with elevated transferrin level, chronic hepatitis B or C, excessive alcohol use, or prescription medications that might cause hepatic steatosis. NAFLD was diagnosed by FibroScan® using controlled attenuation parameter (CAP) values: S0 <238, S1 = 238–259, S2 = 260–290, S3 >290. Data were analyzed using Chi square and multinomial regression. The overall prevalence of NAFLD was 47.9% [S2 = 16.1%, and S3 = 31.8%]. The prevalence of S3 was highest among Mexican Americans (46%), lowest among Blacks (22.7%), 29.9% in other Hispanics and 32.1% in Whites (p < 0.05). It was higher among Mexican American males (54.1%) compared to Mexican American females (37.7%) (p < 0.05). In the adjusted model, Mexican Americans were two times more likely than Whites to have S2 and S3 (p < 0.05). Only male Mexican Americans had higher odds of S2 and S3 relative to male White (p < 0.05). Males had higher odds of S3 relative to non-menopausal females (p < 0.05). There was no difference in the odds of S2 or S3 NAFLD among the menopausal females with or without hormone therapy relative to non-menopausal females (p > 0.05). While Mexican Americans had the highest prevalence of severe NAFLD relative to the other racial/ethnic groups, only male Mexican Americans, but not females, had higher likelihood of both moderate and severe NAFLD relative to Whites. Interventions that specifically target Mexican American males are needed to increase awareness about NAFLD and its prevention.
The Programmed Cell Death of Macrophages, Endothelial Cells, and Tubular Epithelial Cells in Sepsis-AKI
Authors: Li Chao , Wang Wei , Xie Shuai-shuai , Ma Wen-xian , Fan Qian-wen , Chen Ying , He Yuan , Wang Jia-nan , Yang Qin , Li Hai-di , Jin Juan , Liu Ming-ming , Meng Xiao-ming , Wen Jia-gen
Published: December 2021

Sepsis is a systemic inflammatory response syndrome caused by infection, following with acute injury to multiple organs. Sepsis-induced acute kidney injury (AKI) is currently recognized as one of the most severe complications related to sepsis. The pathophysiology of sepsis-AKI involves multiple cell types, including macrophages, vascular endothelial cells (ECs) and renal tubular epithelial cells (TECs), etc. More significantly, programmed cell death including apoptosis, necroptosis and pyroptosis could be triggered by sepsis in these types of cells, which enhances AKI progress. Moreover, the cross-talk and connections between these cells and cell death are critical for better understanding the pathophysiological basis of sepsis-AKI. Mitochondria dysfunction and oxidative stress are traditionally considered as the leading triggers of programmed cell death. Recent findings also highlight that autophagy, mitochondria quality control and epigenetic modification, which interact with programmed cell death, participate in the damage process in sepsis-AKI. The insightful understanding of the programmed cell death in sepsis-AKI could facilitate the development of effective treatment, as well as preventive methods.