Circulating proteins to predict COVID-19 severity

Predicting COVID-19 severity is difficult, and the biological pathways involved are not fully understood. To approach this problem, we measured 4701 circulating human protein abundances in two independent cohorts totaling 986 individuals. We then trained prediction models including protein abundances and clinical risk factors to predict COVID-19 severity in 417 subjects and tested these models in a separate cohort of 569 individuals. For severe COVID-19, a baseline model including age and sex provided an area under the receiver operator curve (AUC) of 65% in the test cohort. Selecting 92 proteins from the 4701 unique protein abundances improved the AUC to 88% in the training cohort, which remained relatively stable in the testing cohort at 86%, suggesting good generalizability. Proteins selected from different COVID-19 severity were enriched for cytokine and cytokine receptors, but more than half of the enriched pathways were not immune-related. Taken together, these findings suggest that circulating proteins measured at early stages of disease progression are reasonably accurate predictors of COVID-19 severity. Further research is needed to understand how to incorporate protein measurement into clinical care.

The dynamic changes and sex differences of 147 immune-related proteins during acute COVID-19 in 580 individuals

INTRODUCTION

Severe COVID-19 leads to important changes in circulating immune-related proteins. To date it has been difficult to understand their temporal relationship and identify cytokines that are drivers of severe COVID-19 outcomes and underlie differences in outcomes between sexes. Here, we measured 147 immune-related proteins during acute COVID-19 to investigate these questions.

METHODS

We measured circulating protein abundances using the SOMAscan nucleic acid aptamer panel in two large independent hospital-based COVID-19 cohorts in Canada and the United States. We fit generalized additive models with cubic splines from the start of symptom onset to identify protein levels over the first 14 days of infection which were different between severe cases and controls, adjusting for age and sex. Severe cases were defined as individuals with COVID-19 requiring invasive or non-invasive mechanical respiratory support.

RESULTS

580 individuals were included in the analysis. Mean subject age was 64.3 (sd 18.1), and 47% were male. Of the 147 proteins, 69 showed a significant difference between cases and controls (p < 3.4 × 10-4). Three clusters were formed by 108 highly correlated proteins that replicated in both cohorts, making it difficult to determine which proteins have a true causal effect on severe COVID-19. Six proteins showed sex differences in levels over time, of which 3 were also associated with severe COVID-19: CCL26, IL1RL2, and IL3RA, providing insights to better understand the marked differences in outcomes by sex.

CONCLUSIONS

Severe COVID-19 is associated with large changes in 69 immune-related proteins. Further, five proteins were associated with sex differences in outcomes. These results provide direct insights into immune-related proteins that are strongly influenced by severe COVID-19 infection.

Investigating the informed consent process, therapeutic misconception and motivations of Egyptian research participants: a qualitative pilot study

Few studies have explored the informed consent process among research participants in developing countries. This study aimed to evaluate the informed consent process, therapeutic misconception and motivation for participation among Egyptians participating in clinical trials. In a cross-sectional qualitative pilot study 103 participants in 10 clinical trials responded to a questionnaire. Over 90% agreed they had time to ask questions and received adequate information about the risks prior to consenting. All participants thought the research and the drug would improve their condition; only 46.1% were aware of receiving a non-approved experimental drug and 21.3% of being randomized. Reasons for participation included: better treatment (100%), to benefit society & advance science (85.4%), to receive free drugs (42.6%) and medical care (43.6%), to get hospitalized (15.8%) and to receive money or gifts (4.9%). Investigators need to emphasize the distinction between research and clinical care to address the high rate of therapeutic misconception.

Quasiparticle interference, quasiparticle interactions, and the origin of the charge density wave in 2H-NbSe2

We show that a small number of intentionally introduced defects can be used as a spectroscopic tool to amplify quasiparticle interference in 2H-NbSe2 that we measure by scanning tunneling spectroscopic imaging. We show, from the momentum and energy dependence of the quasiparticle interference, that Fermi surface nesting is inconsequential to charge density wave formation in 2H-NbSe2. We demonstrate that, by combining quasiparticle interference data with additional knowledge of the quasiparticle band structure from angle resolved photoemission measurements, one can extract the wave vector and energy dependence of the important electronic scattering processes thereby obtaining direct information both about the fermiology and the interactions. In 2H-NbSe2, we use this combination to confirm that the important near-Fermi-surface electronic physics is dominated by the coupling of the quasiparticles to soft mode phonons at a wave vector different from the charge density wave ordering wave vector.

Nonequilibrium band mapping of unoccupied bulk states below the vacuum level by two-photon photoemission

We demonstrate angle-resolved, tunable, two-photon photoemission (2PPE) to map a bulk unoccupied band, viz. the Cu sp band 0 to 1 eV below the vacuum level, in the vicinity of the L point. This short-lived bulk band is seen due to the strong optical pump rate, and the observed transition energies and their dispersion with photon energy ℏω, are in excellent agreement with tight-binding band-structure calculations. The variation of the final-state energy with ℏω has a measured slope of ∼1.64 in contrast to values of 1 or 2 observed for 2PPE from two-dimensional states. This unique variation illustrates the significant role of the perpendicular momentum ℏk_{⊥} in 2PPE.

Caviomorph placentation as a model for trophoblast invasion

The guinea pig and its relatives are promising candidates as animal models for studying trophoblast invasion. The origin, migration routes and kinetics of invasive trophoblast cells were examined in two caviomorph species. Histology and immunohistochemistry were done on placentas from 38 guinea pigs of days 20-47 and 13 degus of days 25-51 of gestation. BrdU was used as an in vivo marker for proliferation and for tracing of migration routes in the placenta; it was injected 24h to 15 days before collecting the material. In both species extravillous-like trophoblast cells are derived from proliferating stem cell aggregations in the subplacenta, which are comparable to the cell columns in humans. Migration routes and kinetics under in vivo conditions revealed a mean invasive depth of 300-350 microm/day and a mean life span of the extravillous-like trophoblast of 30 days. The patterns of trophoblast invasion in caviomorphs are analogous to the situation in humans, suggesting that these rodents are appropriate animal models for the study of the dynamics of trophoblast invasion.

[Advantages and disadvantages of the circumferential retinal cryocoagulation before vitrectomy in proliferative diabetic vitreoretinopathy]

BACKGROUND

It is unclear if a circumferential cryocoagulation 4 weeks before pars plana vitrectomy is useful for reducing the risks of surgery such as retinal detachment, secondary glaucomas or rebleeding. Otherwise it seems possible that this surgery itself, done in local anaesthesia, could be an additional risk.

PATIENTS AND METHODS

We retrospectively evaluated the reports of all patients who underwent vitrectomy as primary surgery due to proliferative diabetic vitreoretinopathy between 1997 and 2000. Besides age and sex, all additional surgery (like phacoemulsification, endolaser coagulation, kind of tamponade etc.) and all intra- or postoperative complications were reported after a follow-up of at least 3 months. We created and compared 2 groups of patients, showing in group 1 patients who underwent vitrectomy 4 weeks after cryocoagulation and in group 2 patients undergoing vitrectomy combined with circumferential cryocoagulation.

RESULTS

We evaluated the reports of 226 patients (103 men, 123 women, mean age 58.6 +/- 13.0 years). Follow-up was in the mean 16.3 months. Group 1 contained 150 patients (66.4 %), group 2 76 patients (33.6 %). 63.7 % received air as endotamponade, 8.0 % C(2)F(6) gas, 7.1 % silicon oil and 21.2 % BSS, 34.1 % were operated in combination with phakoemulsification. We observed 9 postoperative retinal detachments (4.0 %), with no significant difference between the two groups (6 detachments in group 1, 2 detachments in group 2). For other surgical risks like rebleeding, rubeosis iridis, secondary glaucoma etc. we also found no statistically significant differences.

CONCLUSION

Circumferential retinal cryocoagulation is a useful preparation before pars plana vitrectomy, when done due to vitreous haemorrhage, because improved resorption lowers the vitrectomy rate. In all other cases it can be done during vitrectomy. Adjuvant circumferential cryocoagulation seems to decrease the risk of postoperative retinal detachments and rebleedings as documented in literature comparison.

Flow cytometric DNA analysis of fresh prostatic resections. Correlation with conventional prognostic parameters in patients with prostate cancer

BACKGROUND

DNA ploidy analysis has been investigated as a prognostic indicator in prostate cancer. Most of the data is derived from retrospective studies using paraffin-embedded tissue. This method has drawbacks related to the quality of DNA histograms and uncontrolled data collection.

METHODS

DNA ploidy analysis of freshly resected prostatic tissue was prospectively compared with conventional prognostic variables in 97 men treated with radical prostatectomy for localized prostate cancer.

RESULTS

Regarding the patients, 31.9% were African American and 66% had pathologic Stages C or D1 disease. Only 9.6% of patients with Stages A2 and B had a prostate-specific antigen (PSA) value greater than 10 ng/ml, whereas 97% of patients with PSA values greater than 20 ng/ml had pathologic Stages C and D1. PSA levels correlated with Gleason score (P = < 0.05); 51% and 100% of patients with Gleason score 5-7 and 8-10, respectively, had PSA values greater than 10 ng/ml. Twenty-two patients (23%) had DNA aneuploid tumors. Comparisons of mechanical to enzymatic cell suspensions indicated that DNA aneuploidy was better preserved in mechanical cell preparations. DNA ploidy correlated with pathologic stage (P = < 0.05) and Gleason score (P = < 0.05). Fifteen of 79 patients (18.9%) with Gleason score 5-7 had DNA aneuploid tumors versus 71.4% of patients with Gleason score 8-10. PSA groups correlated with ploidy status (P = 0.01). Although the majority of patients (19 of 22) with DNA aneuploid tumors had elevated preoperative PSA levels, none had a PSA value greater than 50 ng/ml.

CONCLUSIONS

DNA ploidy analysis correlated with established prognostic indicators in prostate cancer; however, its independent correlation with natural history and treatment outcome must be established for it to have an effect on therapeutic decisions.