When science goes viral: The research response during three months of the COVID-19 outbreak

Here we present the results of a bibliometric survey of peer-reviewed and pre-print papers published in the English language on issues related to COVID-19 within the first three months since a cluster of a severe acute respiratory disease of unknown etiology was officially confirmed by the Chinese Center for Disease Control and Prevention on 31 December 2019. A systematic search using PubMed/Medline and Scopus databases and preprint servers was performed. The articles were classified according to their type, subject and country of origin. Up to 31 March 2020, a total of 2062 papers published in 578 peer-reviewed journals and 1425 preprints posted mostly on medRxiv (55.4 %), were identified. The mean number of published journal papers and preprints per day in the considered period was 27 and 12, respectively, and reached a maximum of 51 and 46 per day in March, respectively. The identified articles, journal papers and preprints, mostly covered the epidemiology of COVID-19 (35.7 %), clinical aspects of infection (21.0 %), preventative measures (12.8 %), treatment options (12.5 %), diagnostics (12.2 %), mathematical modeling of disease transmission and mitigation (9.6 %), and molecular biology and pathogenesis of SARS-CoV-2 (8.7 %). The majority of the journal papers were commentaries (38.5 %), reviews (33.6 %) and original research (21.3 %), while preprints predominantly presented original results (89.8 %). Chinese scientists contributed the highest share of original research and were responsible for 32.9 % journal papers and 43.9 % preprints published in the considered period. A high number of contributions was also seen from the United States, the United Kingdom, and Italy. The benefits and potential risks of such a massive publication output are discussed. The scientific response seen during the first 3 months of the COVID-19 outbreak is a demonstration of the capabilities of modern science to react rapidly to emerging global health threats by providing and discussing the essential information for understanding the etiological factor, its spread, preventative measures, and mitigation strategies.

Good or not good: Role of miR-18a in cancer biology

miR-18a is a member of primary transcript called miR-17-92a (C13orf25 or MIR17HG) which also contains five other miRNAs: miR-17, miR-19a, miR-20a, miR-19b and miR-92a. This cluster as a whole shows specific characteristics, where miR-18a seems to be unique. In contrast to the other members, the expression of miR-18a is additionally controlled and probably functions as its own internal controller of the cluster. miR-18a regulates many genes involved in proliferation, cell cycle, apoptosis, response to different kinds of stress, autophagy and differentiation. The disturbances of miR-18a expression are observed in cancer as well as in different diseases or pathological states. The miR-17-92a cluster is commonly described as oncogenic and it is known as 'oncomiR-1', but this statement is a simplification because miR-18a can act both as an oncogene and a suppressor. In this review we summarize the current knowledge about miR-18a focusing on its regulation, role in cancer biology and utility as a potential biomarker.

YRNAs and YRNA-Derived Fragments as New Players in Cancer Research and Their Potential Role in Diagnostics

YRNAs are a type of short, noncoding RNAs. A total of four different transcripts can be distinguished, which are YRNA1, YRNA3, YRNA4 and YRNA5. All YRNAs are relatively small, made up of about 100 nucleotides each. YRNAs are characterized by a stem-loop structure and each part of that structure carries a different function. YRNAs are transcribed in the nucleus by RNA polymerase III. Then, the YRNA molecule is bound to the polyuridine tail of the La protein responsible for both its nuclear retention and protection from degradation. They also bind to the Ro60 protein, making the molecule more stable. In turn, YRNA-derived small RNAs (YsRNAs) are a class of YRNAs produced in apoptotic cells as a result of YRNA degradation. This process is performed by caspase-3-dependent pathways that form two groups of YsRNAs, with lengths of either approximately 24 or 31 nucleotides. From all four YRNA transcripts, 75 well-described pseudogenes are generated as a result of the mutation. However, available data indicates the formation of up to 1000 pseudogenes. YRNAs and YRNA-derived small RNAs may play a role in carcinogenesis due to their altered expression in cancers and influence on cell proliferation and inflammation. Nevertheless, our knowledge is still limited, and more research is required. The main aim of this review is to describe the current state of knowledge about YRNAs, their function and contribution to carcinogenesis, as well as their potential role in cancer diagnostics. To confirm the promising potential of YRNAs and YRNA-derived fragments as biomarkers, their significant role in several tumor types was taken into consideration.

Long Intergenic Non-Coding RNAs in HNSCC: From "Junk DNA" to Important Prognostic Factor

Head and neck squamous cell carcinoma is one of the most common and fatal cancers worldwide. Even a multimodal approach consisting of standard chemo- and radiotherapy along with surgical resection is only effective in approximately 50% of the cases. The rest of the patients develop a relapse of the disease and acquire resistance to treatment. Especially this group of individuals needs novel, personalized, targeted therapy. The first step to discovering such solutions is to investigate the tumor microenvironment, thus understanding the role and mechanism of the function of coding and non-coding sequences of the human genome. In recent years, RNA molecules gained great interest when the complex character of their impact on our biology allowed them to come out of the shadows of the "junk DNA" label. Furthermore, long non-coding RNAs (lncRNA), specifically the intergenic subgroup (lincRNA), are one of the most aberrantly expressed in several malignancies, which makes them particularly promising future diagnostic biomarkers and therapeutic targets. This review contains characteristics of known and validated lincRNAs in HNSCC, such as XIST, MALAT, HOTAIR, HOTTIP, lincRNA-p21, LINC02487, LINC02195, LINC00668, LINC00519, LINC00511, LINC00460, LINC00312, and LINC00052, with a description of their prognostic abilities. Even though much work remains to be done, lincRNAs are important factors in cancer biology that will become valuable biomarkers of tumor stage, outcome prognosis, and contribution to personalized medicine.

cfRNAs as biomarkers in oncology - still experimental or applied tool for personalized medicine already?

Currently, the challenges of contemporary oncology are focused mainly on the development of personalized medicine and precise treatment, which could be achieved through the use of molecular biomarkers. One of the biological molecules with great potential are circulating free RNAs (cfRNAs) which are present in various types of body fluids, such as blood, serum, plasma, and saliva. Also, different types of cfRNA particles can be distinguished depending on their length and function: microRNA (miRNA), PIWI-interacting RNA (piRNA), tRNA-derived RNA fragments (tRFs), circular RNA (circRNA), long non-coding RNA (lncRNA), and messenger RNA (mRNA). Moreover, cfRNAs occur in various forms: as a free molecule alone, in membrane vesicles, such as exosomes, or in complexes with proteins and lipids. One of the modern approaches for monitoring patient's condition is a "liquid biopsy" that provides a non-invasive and easily available source of circulating RNAs. Both the presence of specific cfRNA types as well as their concentration are dependent on many factors including cancer type or even reaction to treatment. Despite the possibility of using circulating free RNAs as biomarkers, there is still a lack of validated diagnostic panels, defined protocols for sampling, storing as well as detection methods. In this work we examine different types of cfRNAs, evaluate them as possible biomarkers, and analyze methods of their detection. We believe that further research on cfRNA and defining diagnostic panels could lead to better and faster cancer identification and improve treatment monitoring.

Diagnostics of Mutations in MMR/EPCAM Genes and Their Role in the Treatment and Care of Patients with Lynch Syndrome

Lynch syndrome (LS), also known as hereditary nonpolyposis colorectal cancer (HNPCC), is a disorder caused by an autosomal dominant heterozygous germline mutation in one of the DNA mismatch repair (MMR) genes. Individuals with LS are at an increased risk of developing colorectal and extracolonic cancers, such as endometrial, small bowel, or ovarian. In this review, the mutations involved with LS and their diagnostic methods are described and compared, as are their current uses in clinical decision making. Nowadays, LS diagnosis is based on a review of family medical history, and when necessary, microsatellite instability (MSI) or/and immunohistochemistry (IHC) analyses should be performed. In the case of a lack of MMR protein expression (dMMR) or MSI-H (MSI-High) detection in tumor tissue, molecular genetic testing can be undertaken. More and more genetic testing for LS is based mainly on next-generation sequencing (NGS) and multiplex ligation-dependent probe amplification (MLPA), which provide better and quicker information about the molecular profile of patients as well as individuals at risk. Testing based on these two methods should be the standard and commonly used. The identification of individuals with mutations provides opportunities for the detection of cancer at an early stage as well as the introduction of proper, more effective treatment, which will result in increased patient survival and reduced costs of medical care.

Central dipsogenic effect of vasopressin

The purpose of the present study was to investigate the possible role of vasopressin (ADH) in the control of thirst. With this aim spontaneous water intake (WI) was examined in conscious dogs after 1) electric stimulation in the basal forebrain causing release of ADH, 2) injection of 0.03, 0.05, 0.10, 0.15, 0.30, and 3.00 mU of ADH into the third cerebral ventricle (3rd V), 3) injection of 0.3, 3.0, and 30 mU of ADH into the lateral cerebral ventricle (LV) and injection of 5.0 and 10.0 mU of ADH into the carotid artery (CA). Stimulation through 10 of 16 electrodes located in various structures of the limbic system caused a significant increase in blood ADH, decrease of urine output, increase in renal free-water reabsorption, nonstimulus-bound drinking, positive water balance, and decrease in plasma osmolality (Posmol). Injection of ADH to the 3rd V caused a significant increase in WI. The maximum WI was observed after injection of 0.10-0.15 mU of ADH. Elevation of WI caused a significant decrease in Posmol 1 h after injection of ADH to the 3rd V. Insignificant increases or no changes in WI were observed when ADH was injected into the LV and CA, respectively. The results suggest that ADH may exert central dipsogenic effects.

Thirst and renal excretion of water and electrolytes during pyrogen fever in dogs

Body temperature, water intake, urine output, sodium and potassium excretion, osmolal and free water clearance, plasma osmolality, sodium and potassium concentrations and osmotic thirst were examined in conscious dogs during pyrogen fever and compared to those found under control conditions. Arterial blood pressure and central venous pressure were also measured in some experiments. Administration of pyrogen produced transient but significant decreases in urine output and striking increases in the spontaneous water intake in some of the experiments in the phase of increasing fever. Arterial blood pressure decreased, whetreas central venous pressure increased at this stage of fever. No significant changes in renal excretion of solutes and free water as well as sodium and potassium were found. Plasma osmolality and sodium concentration increased and potassium concentration decreased unsignificantly both in control and pyrogen experiments. The main finding was that the thirst threshold to osmotic stimuli increased markedly during the phase of stabilized fever may be caused by significant increase in internal body temperature.

Central effects of atrial natriuretic peptide on plasma catecholamines, vasopressin, renin and beta-endorphin and on renal excretory functions in the dog

Atrial natriuretic peptide (ANP) has been identified in the central nervous system and its participation in regulation of various regulatory brain functions has been postulated. To elucidate whether central ANP influences endocrine systems related to blood pressure regulation and renal excretory functions, effects of infusion of ANP at a rate of 120 ng.min-1 into the third cerebral ventricle on plasma level of epinephrine (E), norepinephrine (NE), renin, vasopressin and beta-endorphin as well as on excretion of urine, sodium, potassium (UKV) solutes and free water (CH2O) were investigated in conscious dogs. Significant decrease of plasma E from 77.6 +/- 7.0 to 62.1 +/- 4.8 pg.ml-1 and of NE from 345.5 +/- 20.7 to 286.4 +/- 15.0 pg.ml-1 was found at the end of 30 min lasting ANP infusion. Significant elevation of PRA and UKV and a decrease in CH2O were found 60 min after ANP infusion. No significant changes in other variables were found. In time control experiments plasma hormones concentration and renal excretory functions were not significantly influenced. The results suggest that central ANP may affect the sympatho-adrenal outflow.

Osmotic thirst suppression in dogs exposed to low ambient temperature

Body temperature, urine output, osmotic and free water clearances, plasma osmolality, sodium and potassium concentrations, blood lactate level, osmotic thirst and central blood volume were measured in dogs exposed to cold (+1 to -8 degrees C) for 1-3 hours and compared to those obtained under control conditions at ambient temperatures (18-20 degrees C). In some additional experiments osmotic thirst threshold and arterial blood pressure during intravenous infusion of norepinephrine were also examined. Exposure to low ambient temperature caused an increase in the osmotic thirst threshold and rise in central blood volume. Transient increase in the urine output and free water clearance accompanied by a decrease in the urine osmolality were also observed. No changes were found in rectal temperature, plasma osmolality and plasma sodium concentration. Infusion of norepinephrine elevated the osmotic thirst threshold in a dose-dependent manner. It is concluded that the cold-induced suppression of osmotic thirst may result from the increased central blood volume. A possible involvement of the sympathetic nervous system in the thirst inhibition in low ambient temperature is also considered.

Liquid lncRNA Biopsy for the Evaluation of Locally Advanced and Metastatic Squamous Cell Carcinomas of the Head and Neck

Background: Long non-coding RNA (lncRNA) are RNA molecules that are more than 200 nucleotides long and have the ability to modify the activity of genes. They can be found in both healthy and cancer tissues, as well as in plasma, saliva and other bodily fluids. They can also be used as biomarkers of early detection, prognosis and chemotherapy resistance in several cancer types. Treatment of head and neck squamous cell carcinoma (HNSCC) patients with locally advanced disease is still difficult, and choice of treatment should be based on more precise and available biomarkers, such as those obtained from a liquid biopsy. For improvement of treatment efficacy, identification and clinical implementation of new biomarkers are of the utmost importance. Methods: Plasma samples drawn before (p1) and three cycles post (p2) (TPF: docetaxel, cisplatin, 5-fluorouracil/PF: cisplatin, 5-fluorouracil) chemotherapy from 53 HNSCC patients (17 with locally advanced and 36 with metastatic disease) and 14 healthy volunteers were studied. Expression levels of 90 lncRNA expression were analyzed using the qRT-PCR method, and the obtained results were compared between proper groups. Statistical analyses were carried out using Jupyter Notebooks (5.7.2), Python (ver. 3.6) and GraphPad Prism 8. Results: The study demonstrated the differences between the expressions of several lncRNA in cancer patients' and healthy volunteers' plasma, as well as between locally advanced and metastatic patients' groups. A correlation between the response to systemic therapy and lncRNA expression levels was observed. Patients with a (high/low) expression of Alpha 250 and Emx2os showed statistically significant differences in progression free survival (PFS), as well as for overall survival (OS) depending on the level of Alpha 250, snaR, SNHG1. The univariate and multivariate Cox regression model showed Alpha 250 as the best prognostic factor for HNSCC patients. Conclusions: Liquid biopsies based on lncRNAs are promising diagnostic tools that can be used to differentiate between those with cancer and healthy individuals. Additionally, they can also serve as biomarkers for chemotherapy resistance. An identified, circulating lncRNA Alpha 250 seems to prove the best prognostic biomarker, associated with extended PFS and OS, and should be validated in a larger cohort in the future.

Zinc Finger Proteins in Head and Neck Squamous Cell Carcinomas: ZNF540 May Serve as a Biomarker

Head and neck squamous cell carcinoma (HNSCC) is one of the ten most common cancers. Most cancer cases originate from alcohol and tobacco consumption. However, studies have demonstrated that human papillomavirus (HPV) infection, particularly HPV-16, may also significantly influence disease progression. The KRAB-ZNF family of genes is involved in epigenetic suppression, and its involvement in carcinogenesis is the subject of extensive studies. The available literature data demonstrate that they may play different roles, both as tumor suppressors and oncogenes. In this study, six ZNF genes, ZFP28, ZNF132, ZNF418, ZNF426, ZNF540, and ZNF880, were tested using several in silico approaches based on the TCGA and GEO datasets. Our analyses indicate that the expression of the analyzed ZNFs was significantly downregulated in tumor tissues and depended on tumor localization. The expression levels of ZNFs differed between HPV-positive vs. HPV-negative patients depending on the clinical-pathological parameters. More specifically, the patients with higher levels of ZNF418 and ZNF540 showed better survival rates than those with a lower expression. In addition, the level of ZNF540 expression in HPV-positive (HPV(+)) patients was higher than in HPV-negative (HPV(-)) patients (p < 0.0001) and was associated with better overall survival (OS). In conclusion, we demonstrate that ZNF540 expression highly correlates with HPV infection, which renders ZNF540 a potential biomarker for HNSCC prognosis and treatment.

The effect of barbiturates on 24-h water intake and renal excretion of sodium and water in dogs

The effects of barbiturates on 24-h intakes of water and food and urinary excretion of sodium and potassium as well as on plasma concentration of sodium and potassium and osmolality were examined in dogs placed in metabolism cages and fed with a semiliquid diet. Administration of barbiturates stimulated drinking in a Series of 8 dogs having free access to water. Twenty four-h water intake and water balance increased significantly. Food intake, urinary output and urinary excretion of solutes, sodium and water did not change in this Series. A significant decrease in urine output as well as in osmolal clearance and urinary excretion of sodium was observed in a Series of 7 dogs having water restricted for 24 h following administration of barbiturates. Water balance increased in this Series. The same restriction of water in the dogs which had not received barbiturates did not modify renal excretion of water and electrolytes. Plasma osmolality, sodium and potassium concentrations did not change in either Series of experiments. It is concluded that barbiturates induce positive water balance either by stimulation of drinking when water is freely available or by reduction in urine output when water is restricted. The results suggest that expansion of the body fluids following the increased water intake may abolish reduction in urine output and sodium excretion which otherwise occur after administration of barbiturates.

The World of Pseudogenes: New Diagnostic and Therapeutic Targets in Cancers or Still Mystery Molecules?

Pseudogenes were once considered as “junk DNA”, due to loss of their functions as a result of the accumulation of mutations, such as frameshift and presence of premature stop-codons and relocation of genes to inactive heterochromatin regions of the genome. Pseudogenes are divided into two large groups, processed and unprocessed, according to their primary structure and origin. Only 10% of all pseudogenes are transcribed into RNAs and participate in the regulation of parental gene expression at both transcriptional and translational levels through senseRNA (sRNA) and antisense RNA (asRNA). In this review, about 150 pseudogenes in the different types of cancers were analyzed. Part of these pseudogenes seem to be useful in molecular diagnostics and can be detected in various types of biological material including tissue as well as biological fluids (liquid biopsy) using different detection methods. The number of pseudogenes, as well as their function in the human genome, is still unknown. However, thanks to the development of various technologies and bioinformatic tools, it was revealed so far that pseudogenes are involved in the development and progression of certain diseases, especially in cancer.

Enhancement of osmotic thirst elicited by electric stimulation of the limbic system in dogs

Seven dogs were chronically implanted with 30 electrodes directed at various structures of the basal forebrain. Osmotic thirst threshold (expressed as an increase in plasma osmolality and a decrease in cellular water content caused by an intravenous infusion of 5% NaCl, necessary to induce drinking) was measured during electric stimulation of the basal forebrain and compared to that found under control conditions. Stimulation through 11 electrodes located in the lateral part of the septum (5 locations) and other parts of the limbic system markedly decreased the osmotic thirst threshold. The increment in plasma osmolality necessary to elicit drinking decreased from 9.7 +/- 1.3 to 4.8 +/- 1.2 mmol/kg (n = 11). The volume of water drunk at the thirst threshold did not differ significantly. A significant augmentation of the volume of water drunk during 1 h following infusion of hypertonic saline was observed when the infusion was combined with stimulation of the gyrus rectus, precommissural septum and nucleus accumbens. These and previous results (SZCZEPANSKA-SADOWSKA et al., 1979) suggest that the limbic system of the basal forebrain exerts both excitatory and inhibitory influences on the thirst system. The prolonged poststimulatory overdrinking indicates that enhancement of osmotic thirst cannot be entirely explained by an immediate action of the stimulating current on the neurons of the thirst system.

ZNF643/ZFP69B Exerts Oncogenic Properties and Associates with Cell Adhesion and Immune Processes

The global cancer burden remains high; thus, a better understanding of the molecular mechanisms driving carcinogenesis is needed to improve current prevention and treatment options. We previously detected the ZNF643/ZFP69B gene upregulated in multiple tumors, and we speculated it may play a role in tumor biology. To test this hypothesis, we employed TCGA-centered databases to correlate ZNF643 status with various clinicopathological parameters. We also performed RNA-seq analysis and in vitro studies assessing cancer cell phenotypes, and we searched for ZNF643-bound genomic loci. Our data indicated higher levels of ZNF643 in most analyzed tumors compared to normal samples, possibly due to copy number variations. ZNF643 mRNA correlated with diverse molecular and immune subtypes and clinicopathological features (tumor stage, grade, patient survival). RNA-seq analysis revealed that ZNF643 silencing triggers the deregulation of the genes implicated in various cancer-related processes, such as growth, adhesion, and immune system. Moreover, we observed that ZNF643 positively influences cell cycle, migration, and invasion. Finally, our ChIP-seq analysis indicated that the genes associated with ZNF643 binding are linked to adhesion and immune signaling. In conclusion, our data confirm the oncogenic properties of ZNF643 and pinpoint its impact on cell adhesion and immune processes.

ZNF714 Supports Pro-Oncogenic Features in Lung Cancer Cells

Despite the ongoing progress in diagnosis and treatments, cancer remains a threat to more than one-third of the human population. The emerging data indicate that many Krüppel-associated box zinc finger proteins (KRAB-ZNF) belonging to a large gene family may be involved in carcinogenesis. Our previous study identified Zinc Finger Protein 714 (ZNF714), a KRAB-ZNF gene of unknown function, as being commonly overexpressed in many tumors, pointing to its hypothetical oncogenic role. Here, we harnessed The Cancer Genome Atlas (TCGA)-centered databases and performed functional studies with transcriptomic and methylomic profiling to explore ZNF714 function in cancer. Our pan-cancer analyses confirmed frequent ZNF714 overexpression in multiple tumors, possibly due to regional amplification, promoter hypomethylation, and Nuclear Transcription Factor Y Subunit Beta (NFYB) signaling. We also showed that ZNF714 expression correlates with tumor immunosuppressive features. The in vitro studies indicated that ZNF714 expression positively associates with proliferation, migration, and invasion. The transcriptomic analysis of ZNF714 knocked-down cells demonstrated deregulation of cell adhesion, migration, proliferation, apoptosis, and differentiation. Importantly, we provided evidence that ZNF714 negatively regulates the expression of several known TSGs indirectly via promoter methylation. However, as ZNF714 did not show nuclear localization in our research model, the regulatory mechanisms exerted by ZNF714 require further investigation. In conclusion, our results reveal, for the first time, that ZNF714 may support pro-oncogenic features in lung cancer cells.

Thirst and solute excretion: their effectiveness in osmostatic control of body fluid

The effect of intravenous infusion of hypertonic NaCl at three different rates (series I, 4.0 mmol/min; series II, 8.0 mmol/min; series III, 16.0 mmol/min) on osmotic thirst threshold and postloading restitution of plasma osmolality (Posm) has been determined in dogs. Osmotic thirst threshold increased proportionally to the rate of delivery of the osmotic load. Relative suppression of osmotic thirst at the higher rates of infusion was temporary and largely disappeared within 10 min after the end of hypertonic infusion. During the postloading period excretion of osmotic load and water intake was proportional to the magnitude of the load administered. However, the animals with high osmotic thirst threshold stopped drinking at a higher Posm than those with a low osmotic thirst threshold. In series I and II, Posm decreased during 1 h to a level not significantly different from the preloading value. In each series renal excretion of osmotic load was more important than water intake for restitution of Posm during 1 h. Amount of water ingested during this period was significantly smaller than that theoretically required to restore resting Posm when excretion of osmotic load was not taken into account. However, total amount of water intake and osmotic load excreted during 1 h were together well adjusted to restore preloading Posm.