Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications

The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium's collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com, we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form.

1H, 13C, and 15N backbone chemical shift assignments of the C-terminal dimerization domain of SARS-CoV-2 nucleocapsid protein

The current outbreak of the highly infectious COVID-19 respiratory disease is caused by the novel coronavirus SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2). To fight the pandemic, the search for promising viral drug targets has become a cross-border common goal of the international biomedical research community. Within the international Covid19-NMR consortium, scientists support drug development against SARS-CoV-2 by providing publicly available NMR data on viral proteins and RNAs. The coronavirus nucleocapsid protein (N protein) is an RNA-binding protein involved in viral transcription and replication. Its primary function is the packaging of the viral RNA genome. The highly conserved architecture of the coronavirus N protein consists of an N-terminal RNA-binding domain (NTD), followed by an intrinsically disordered Serine/Arginine (SR)-rich linker and a C-terminal dimerization domain (CTD). Besides its involvement in oligomerization, the CTD of the N protein (N-CTD) is also able to bind to nucleic acids by itself, independent of the NTD. Here, we report the near-complete NMR backbone chemical shift assignments of the SARS-CoV-2 N-CTD to provide the basis for downstream applications, in particular site-resolved drug binding studies.

[Differentiated surgical approach for adenocarcinoma of the gastroesophageal junction]

For adenocarcinoma of the gastroesophageal junction (GEJ) the classification of Siewert with its three subtypes is well established as a practical approach to surgical treatment. Transthoracic esophagectomy with gastric tube formation is generally accepted as the surgical standard for adenocarcinoma of the distal esophagus (GEJ type I). Intrathoracic esophagogastrostomy has become the most frequently used anastomotic technique (Ivor Lewis esophagectomy). Both the abdominal and thoracic part can be safely performed with a minimally invasive access. For subcardiac gastric cancer (GEJ type III) transhiatal extended gastrectomy is the resection of choice. For true cardiac carcinomas (GEJ type II) it has not yet been decided which of the abovementioned surgical procedures offers the best long-term survival. If technically possible in terms of a complete resection, transhiatal extended gastrectomy should be preferred because of a better postoperative quality of life. For GEJ type II tumors a minimally invasive approach is not recommended if the extent of resection cannot be safely determined preoperatively.

[Perioperative management of transthoracic oesophagectomies : Fundamentals of interdisciplinary care and new approaches to accelerated recovery after surgery]

Locally advanced carcinomas of the oesophagus require multimodal treatment. The core element of curative therapy is transthoracic en bloc oesophagectomy, which is the standard procedure carried out in most specialized centres. Reconstruction of intestinal continuity is usually achieved with a gastric sleeve, which is anastomosed either intrathoracically or cervically to the remaining oesophagus. This thoraco-abdominal operation is associated with significant postoperative morbidity, not least because of a vast array of pre-existing illnesses in the surgical patient. For an optimal outcome, the careful interdisciplinary selection of patients, preoperative risk evaluation and conditioning are essential. The caseload of the centres correlates inversely with the complication rate. The leading surgical complication is anastomotic leakage, which is diagnosed endoscopically and usually treated with the aid of endoscopic procedures. Pulmonary infections are the most frequent non-surgical complication. Thoracic epidural anaesthesia and perfusion-orientated fluid management can reduce the rate of pulmonary complications. Patients are ventilated protecting the lungs and are extubated as early as possible. Oesophagectomies should only be performed in high-volume centres with the close cooperation of surgeons and anaesthesia/intensive care specialists. Programmes of enhanced recovery after surgery (ERAS) hold further potential for the patient's quicker postoperative recovery. In this review article the fundamental aspects of the interdisciplinary perioperative management of transthoracic oesophagectomy are described.

Genetic damage and repair in human rectal cells for biomonitoring: sex differences, effects of alcohol exposure, and susceptibilities in comparison to peripheral blood lymphocytes

INTRODUCTION

Cells other than lymphocytes may be preferable as surrogate biomarkers during exposure monitoring. In nutritional toxicology, cells from colorectal tissues are particularly relevant for studying associations between food and cancer. Thus, we have previously shown that colonic cells of males have higher levels of DNA damage than females, which (among other factors) could be due to a higher consumption of alcoholic beverages by males. To test this hypothesis, we have performed a first exploratory study to compare DNA damage in rectal cells from biopsies of male patients with alcohol abuse and of male and female controls. Peripheral blood lymphocytes were additionally monitored to assess systemic exposure loads.

METHODS

Cells were isolated and subjected to microgelelectrophoresis +/- endonuclease III to measure DNA breaks and oxidized pyrimidine bases ("comet-assay"). Cell aliquots were treated with H(2)O(2) for 5min in suspension culture and processed immediately or after 60min to determine induced damage and its persistence.

RESULTS

Pooled data from subjects of all groups revealed that oxidative DNA damage in rectal cells directly correlated to damage in lymphocytes. Female controls had lower levels of DNA damage than male controls, confirming the previous studies. An unexpected result was that male alcohol abusers had significantly less genetic damage than male controls. Also, repair was detected in lymphocytes of male alcohol abusers and female controls, but not in male controls.

CONCLUSION

This is the first time the comet-assay has been used to detect genotoxicity in human rectal cells as a biomonitoring tool. Our pilot study confirms earlier reports on sex differences and indicates a good correlation between damage in rectal cells and damage in lymphocytes and implies that alcohol exposure enhances endogenous defence.

Detection of genotoxic effects in human gastric and nasal mucosa cells isolated from biopsy samples

To assess genotoxic burdens from chemicals, it is necessary to relate observations in experimental animals to humans. The success of this extrapolation would be increased by including data on chemical activities in human tissues. Therefore, we have developed techniques to assess DNA damage in human gastric and nasal mucosa (GM, NM) cells. Biopsy samples were obtained during gastroscopy from macroscopically healthy tissue of the stomach or from healthy nasal epithelia during surgery. The specimens were incubated for 30-45 min at 37 degrees C with a digestive solution. We obtained 1.5-8 x 10(6) GM cells and 5-10 x 10(5) NM cells per donor, both with viabilities of 80-95%. The cells were incubated in vitro for 1 hr at 37 degrees C with the test compounds added in their appropriate solvents. In GM cells, we studied N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), sodium dichromate (Na2Cr2O7), nickel sulphate (NiSO4), cadmium sulphate (CdSO4), and lindane. In NM cells, lindane was investigated. Each compound was assessed for DNA damaging activity in cells of at least three different human donor samples using the microgel single cell assay. Similar studies were performed with GM and NM cells obtained from Sprague-Dawley rats. We have found human GM cells to be more sensitive to the genotoxic activity of MNNG than rat GM cells (low effective concentration [LEC] = 0.16 and 0.625 micrograms/ml for human and rat, respectively). Human cells were also more sensitive to the cytotoxic/genotoxic activity of NiSO4 (LEC = 5 and 19 mumoles/ml for human and rat, respectively). CdSO4 was genotoxic in human GM cells (LEC = 0.03-0.125 mumoles/ml), whereas no dose-related genotoxicity was observed in rat GM at concentrations up to 0.5 mumoles/ml. In contrast, approximately equal responses regarding genotoxicity and cytotoxicity were observed in rat and human GM for Na2Cr2O7 (0.25-1 mumoles/ml). Lindane, however, was genotoxic in three out of four rat GM but not in human GM cells (0.5-1 mumoles/ml), whereas it was active in both rat and human NM cells. Together with other recently published in vivo findings, our results with lindane can be interpreted according to a parallelogram approach. In view of possible human exposure situations and the sensitivities of the two target tissues from both species, the data imply that lindane will pose a health risk to humans by inhalation but not by ingestion.

Antigenotoxic properties of lactic acid bacteria in vivo in the gastrointestinal tract of rats

In view of the high incidence of dietary-related tumors, one important research goal is to identify the participating genotoxic carcinogens and the nutritional factors that may counteract their activities. We therefore have further developed a method to assess DNA damage in tumor target tissues of the gastrointestinal tract. Subsequently the prevention of this inducible DNA damage by lactic acid bacteria and by milk products fermented with probiotics was studied as well. The microgel electrophoresis technique was applied to cells of the esophageal, gastric, duodenal, and colonic mucosa. Cells were grouped according to their degree of DNA damage, the simplest measure of which is to discriminate between those with damage (comets) and those without damage. When these cells were isolated from animals treated with a genotoxic carcinogen, N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), and exposed to MNNG for 1-24 hours, it was possible to follow the course of genotoxicity throughout the gastrointestinal tract. After the animals were treated with the lactic acid bacteria under study, it was possible to detect antigenotoxic properties as well. The gavage of 10(10) viable Lactobacillus casei cells in 10 ml of 0.9% NaCl per kilogram body weight immediately before the oral administration of MNNG (5 mg/kg body wt) resulted in a reduction of induced DNA damage in gastric and colonic mucosa cells. A sequential treatment schedule was even more effective: when the animals were treated orally with lactic acid bacteria or yogurt (10 ml/kg body wt) in the morning followed by MNNG (7.5 mg/kg body wt) eight hours later and the colon cells were isolated 16 hours later, the percentages of cells remaining intact were distinctly higher in the combination groups (68 +/- 10 and 68 +/- 19 for L. casei and a "Bio" yogurt, respectively) than in the group receiving only MNNG (45 +/- 17). The effect of heating L. casei was studied and was found to yield less clear-cut effects in preventing genotoxicity. The method is an efficient tool to elucidate antigenotoxic properties of food components in vivo in those target tissues actually afflicted by dietary-related tumors.