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- Demichev, Vadim, et al.
(author)
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A proteomic survival predictor for COVID-19 patients in intensive care
- 2022
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In: PLOS Digital Health. - : Public Library of Science (PLoS). - 2767-3170. ; 1:1 January
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Journal article (peer-reviewed)abstract
- Global healthcare systems are challenged by the COVID-19 pandemic. There is a need to optimize allocation of treatment and resources in intensive care, as clinically established risk assessments such as SOFA and APACHE II scores show only limited performance for predicting the survival of severely ill COVID-19 patients. Additional tools are also needed to monitor treatment, including experimental therapies in clinical trials. Comprehensively capturing human physiology, we speculated that proteomics in combination with new data-driven analysis strategies could produce a new generation of prognostic discriminators. We studied two independent cohorts of patients with severe COVID-19 who required intensive care and invasive mechanical ventilation. SOFA score, Charlson comorbidity index, and APACHE II score showed limited performance in predicting the COVID-19 outcome. Instead, the quantification of 321 plasma protein groups at 349 timepoints in 50 critically ill patients receiving invasive mechanical ventilation revealed 14 proteins that showed trajectories different between survivors and non-survivors. A predictor trained on proteomic measurements obtained at the first time point at maximum treatment level (i.e. WHO grade 7), which was weeks before the outcome, achieved accurate classification of survivors (AUROC 0.81). We tested the established predictor on an independent validation cohort (AUROC 1.0). The majority of proteins with high relevance in the prediction model belong to the coagulation system and complement cascade. Our study demonstrates that plasma proteomics can give rise to prognostic predictors substantially outperforming current prognostic markers in intensive care.
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| 2. |
- Demichev, Vadim, et al.
(author)
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A time-resolved proteomic and prognostic map of COVID-19
- 2021
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In: Cell Systems. - : Elsevier BV. - 2405-4712 .- 2405-4720. ; 12:8, s. 780-794.e7
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Journal article (peer-reviewed)abstract
- COVID-19 is highly variable in its clinical presentation, ranging from asymptomatic infection to severe organ damage and death. We characterized the time-dependent progression of the disease in 139 COVID-19 inpatients by measuring 86 accredited diagnostic parameters, such as blood cell counts and enzyme activities, as well as untargeted plasma proteomes at 687 sampling points. We report an initial spike in a systemic inflammatory response, which is gradually alleviated and followed by a protein signature indicative of tissue repair, metabolic reconstitution, and immunomodulation. We identify prognostic marker signatures for devising risk-adapted treatment strategies and use machine learning to classify therapeutic needs. We show that the machine learning models based on the proteome are transferable to an independent cohort. Our study presents a map linking routinely used clinical diagnostic parameters to plasma proteomes and their dynamics in an infectious disease.
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| 6. |
- Taylor, V. E., et al.
(author)
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Transient Shoaling, Over-Deepening and Settling of the Calcite Compensation Depth at the Eocene-Oligocene Transition
- 2023
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In: Paleoceanography and Paleoclimatology. - 2572-4517 .- 2572-4525. ; 38:6
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Journal article (peer-reviewed)abstract
- The major Cenozoic shift from a shallow (∼3–4 km) to deep (∼4.5 km) calcite compensation depth (CCD) occurred at the Eocene-Oligocene Transition (∼34 Ma), suggesting a strong relationship between calcium carbonate (CaCO3) cycling and Antarctic glaciation. However, the linkages between these two events are debated. Here we present new records of bulk sediment stable isotope and carbonate composition from a depth transect of sites in the low-latitude Pacific Ocean and one site from the South Atlantic Ocean, together with a new benthic foraminiferal stable isotope record (δ13Cb and δ18Ob) from the Pacific where the sedimentary sequence is most expanded. Our records reveal a short-lived (∼300 Kyr) CCD shoaling event closely associated with a negative carbon isotope excursion in the latest Eocene. This event is immediately followed by CCD deepening which occurs in two rapid (∼40 Kyr-long) steps. Our data show that the first of these deepening steps represents recovery from the latest Eocene shoaling event while the second was closely associated with a rapid increase in δ18Ob and shows a distinctive over-deepening and settling pattern to >5 and 4.4 km, respectively. These results, together with good agreement between Pacific and South Atlantic records, strongly suggest that the carbon cycle was perturbed globally shortly before the inception of Antarctic glaciation. Once large-scale Antarctic glaciation was initiated, rapid further change in global seawater chemistry triggered transitory deep ocean carbonate burial fluxes far exceeding their early Oligocene steady state values.
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