Characterization by Quantitative Serum Proteomics of Immune-Related Prognostic Biomarkers for COVID-19 Symptomatology

The COVID-19 pandemic caused by SARS-CoV-2 challenges the understanding of factors affecting disease progression and severity. The identification of prognostic biomarkers and physiological processes associated with disease symptoms is relevant for the development of new diagnostic and therapeutic interventions to contribute to the control of this pandemic. To address this challenge, in this study, we used a quantitative proteomics together with multiple data analysis algorithms to characterize serum protein profiles in five cohorts from healthy to SARS-CoV-2-infected recovered (hospital discharge), nonsevere (hospitalized), and severe [at the intensive care unit (ICU)] cases with increasing systemic inflammation in comparison with healthy individuals sampled prior to the COVID-19 pandemic. The results showed significantly dysregulated proteins and associated biological processes and disorders associated to COVID-19. These results corroborated previous findings in COVID-19 studies and highlighted how the representation of dysregulated serum proteins and associated BPs increases with COVID-19 disease symptomatology from asymptomatic to severe cases. The analysis was then focused on novel disease processes and biomarkers that were correlated with disease symptomatology. To contribute to translational medicine, results corroborated the predictive value of selected immune-related biomarkers for disease recovery [Selenoprotein P (SELENOP) and Serum paraoxonase/arylesterase 1 (PON1)], severity [Carboxypeptidase B2 (CBP2)], and symptomatology [Pregnancy zone protein (PZP)] using protein-specific ELISA tests. Our results contributed to the characterization of SARS-CoV-2–host molecular interactions with potential contributions to the monitoring and control of this pandemic by using immune-related biomarkers associated with disease symptomatology.

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Central sensitization in chronic lumbar spine pain – possibilities of therapeutic interventions

Ból ◽

10.5604/01.3001.0014.5098 ◽

2020 ◽

Vol 21 (2) ◽

pp. 45-53

Author(s):

Barbara Kosińska ◽

Paweł Turczyn ◽

Krzysztof Wesołowski ◽

Beata Tarnacka ◽

Małgorzata Malec-Milewska

Keyword(s):

Low Back Pain ◽

Central Sensitization ◽

Diagnostic Tests ◽

Multimodal Therapy ◽

Underlying Mechanism ◽

Therapeutic Interventions ◽

Low Back ◽

Pain Mechanisms ◽

Factors Affecting ◽

Spine Pain

Patients with chronic low back pain are a heterogeneous group. Therapeutic management of these patients should address the underlying mechanism of pain, which can be revealed after performing diagnostic tests. The management of patients with the predominant central sensitization component of includes multimodal therapy consisting of pharmacological and non-pharmacological treatment. An important element is also the identification and exclusion of the most important pathophysiological factors affecting the maintenance of central sensitization mechanisms in each patient. The paper describes pharmacological and non-pharmacological therapeutic options in patients with central sensitization component, considering that these methods may differ significantly in the patients. It should be stated that despite the individualized, multimodal therapy based on pain mechanisms, in some patients substantial pain relief may not be achieved.

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Deep serum proteomics reveal biomarkers and causal candidates for type 2 diabetes

10.1101/633297 ◽

2019 ◽

Cited By ~ 1

Author(s):

Valborg Gudmundsdottir ◽

Valur Emilsson ◽

Thor Aspelund ◽

Marjan Ilkov ◽

Elias F Gudmundsson ◽

...

Keyword(s):

Type 2 Diabetes ◽

Serum Proteins ◽

Protein Profile ◽

Disease Onset ◽

Serum Levels ◽

The Body ◽

Protein Biomarkers ◽

Clinical Value ◽

Serum Proteomics

AbstractThe prevalence of type 2 diabetes mellitus (T2DM) is expected to increase rapidly in the next decades, posing a major challenge to societies worldwide. The emerging era of precision medicine calls for the discovery of biomarkers of clinical value for prediction of disease onset, where causal biomarkers can furthermore provide actionable targets. Blood-based factors like serum proteins are in contact with every organ in the body to mediate global homeostasis and may thus directly regulate complex processes such as aging and the development of common chronic diseases. We applied a data-driven proteomics approach measuring serum levels of 4,137 proteins in 5,438 Icelanders to discover novel biomarkers for incident T2DM and describe the serum protein profile of prevalent T2DM. We identified 536 proteins associated with incident or prevalent T2DM. Through LASSO penalized logistic regression analysis combined with bootstrap resampling, a panel of 20 protein biomarkers that accurately predicted incident T2DM was identified with a significant incremental improvement over traditional risk factors. Finally, a Mendelian randomization analysis provided support for a causal role of 48 proteins in the development of T2DM, which could be of particular interest as novel therapeutic targets.

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Serum proteomics identify potential biomarkers for nasopharyngeal carcinoma sensitivity to radiotherapy

Bioscience Reports ◽

10.1042/bsr20190027 ◽

2019 ◽

Vol 39 (5) ◽

Cited By ~ 2

Author(s):

Guangying Zhang ◽

Kun Zhang ◽

Chao Li ◽

Yanyan Li ◽

Zhanzhan Li ◽

...

Keyword(s):

Nasopharyngeal Carcinoma ◽

Serum Proteins ◽

Sequence Similarity ◽

Predictive Biomarkers ◽

Primary Treatment ◽

Label Free ◽

Discrimination Ability ◽

Serum Proteomics ◽

High Discrimination ◽

Southern University

Abstract Radiotherapy is the primary treatment option for nasopharyngeal carcinoma (NPC). Local recurrence and metastasis caused by radioresistance become a bottleneck of curative effect for patients with NPC. Currently, serum predictive biomarkers of radioresistance are scare. We enrolled NPC patients, who underwent radiotherapy in the Department of Oncology, Xiangya Hospital, Central Southern University, and analyzed the serum proteins profiles in NPC patients using with quantitative label-free proteomics using ultra-definition MS. Patients were divided into those who were radioresistant and radiosensitive by the overall reduction (≤50% or >50%, respectively) in tumor extent. The MS/MS spectrum database search identified 911 proteins and 809 proteins are quantitatable. Eight proteins significantly up-regulated and 12 serum proteins were significantly down-regulated in the radioresistance group compared with radiosensitivity group (P<0.05). Finally, five proteins entered the optimal models, including secreted protein acidic and cysteine rich (SPARC) (P=0.032), serpin family D member 1S (ERPIND1) (P=0.040), complement C4B (C4B) (P=0.017), peptidylprolyl Isomerase B (PPIB) (P=0.042), and family with sequence similarity 173 member A (FAM173A) (P=0.017). In all patient, the area under the curves (AUC) for SPARC, SERPIND, C4B, PPIB, and FAM173A were 0.716 (95% CI: 0.574–0.881), 0.697 (95% CI: 0.837–0.858), 0.686 (95% CI: 0.522–0.850), 0.668 (95% CI: 0.502–0.834) and 0.657 (95% CI: 0.512–0.825), respectively. The AUC of five selected proteins was 0.968 (95% CI: 0.918–1.000) with the sensitivity of 0.941 and the specificity of 0.926. Our result indicated that a panel including five serum protein (SPARC SERPIND1 C4B PPIB FAM173A) based on serum proteomics provided a high discrimination ability for radiotherapy effects in NPC patients. Studies with larger sample size and longer follow-up outcome are required.

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Agricultural transition and land-use change: considerations in the development of irrigated enterprises in the rangelands of northern Australia

The Rangeland Journal ◽

10.1071/rj14129 ◽

2015 ◽

Vol 37 (5) ◽

pp. 445 ◽

Cited By ~ 4

Author(s):

Lisa McKellar ◽

Rosalind H. Bark ◽

Ian Watson

Keyword(s):

Land Use ◽

Field Work ◽

Media Analysis ◽

Irrigated Agriculture ◽

Water Release ◽

Factors Affecting ◽

North West ◽

Agricultural Enterprises ◽

Multiple Data ◽

Learning And Change

The factors affecting the adoption of irrigation by landholders, using a case study of a government-managed irrigation water release in north-west Queensland, Australia, where current land use is dominated by extensive beef-cattle production, were investigated. The study was based on multiple data sources – interview data from family-owned agricultural enterprises, historical and contemporary documents and contemporary media analysis, workshop participation and field work. The study revealed multiple drivers and constraints, which affect the rate, timing and location of adoption of irrigation by family-owned grazing enterprises. The key finding was that there are individual, group and regional interests in irrigation development but that considerable social and individual learning is required for adoption of irrigation to occur. It was found that there is a prominent role for knowledge brokers — as individuals, irrigator groups, and trusted brokers of science information — in facilitating learning and change. An insight, relevant to governments that support irrigation developments is that interventions that aid and support learning can play a role in facilitating the land-use transition for individual grazing properties to irrigated agriculture.

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Prognostic Biomarkers in Breast Cancer: Factors Affecting Immunohistochemical Evaluation

The Breast Journal ◽

10.1111/j.1524-4741.1995.tb00246.x ◽

1995 ◽

Vol 1 (4) ◽

pp. 243-250 ◽

Cited By ~ 18

Author(s):

William E. Grizzle ◽

Russell B. Myers ◽

Denise K. Oelschlager

Keyword(s):

Breast Cancer ◽

Prognostic Biomarkers ◽

Factors Affecting

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Is there a serum proteome signature to predict mortality in severe COVID-19 patients?

10.1101/2021.03.13.21253510 ◽

2021 ◽

Author(s):

Franziska Voellmy ◽

Henk van den Toorn ◽

Riccardo Zenezini Chiozzi ◽

Ottavio Zucchetti ◽

Albetto Papi ◽

...

Keyword(s):

Mortality Risk ◽

Serum Proteins ◽

Trypsin Inhibitors ◽

Protein Abundance ◽

Blood Samples ◽

Serum Proteome ◽

Serum Proteomics ◽

Survivor Group ◽

The Family ◽

Type 3

Here we recorded serum proteome profiles of 33 COVID-19 patients admitted to respiratory and intensive care units because of respiratory failure. We received, for most patients, blood samples just after admission and at two more later timepoints. We focused on serum proteins different in abundance between the group of survivors and non-survivors and observed that a rather small panel of about a dozen proteins were significantly different in abundance between these two groups. The four structurally and functionally related type-3 cystatins AHSG, FETUB, HRG and KNG1 were all more abundant in the survivors. The family of inter-α-trypsin inhibitors, ITIH1, ITIH2, ITIH3 and ITIH4, were all found to be differentially abundant in between survivors and non-survivors, whereby ITIH1 and ITIH2 were more abundant in the survivor group and ITIH3 and ITIH4 more abundant in the non-survivors. ITIH1/ITIH2 and ITIH3/ITIH4 also did show opposite trends in protein abundance during disease progression. This panel of eight proteins, complemented with a few more, may represent a panel for mortality risk assessment and eventually even for treatment, by administration of exogenous proteins possibly aiding survival. Such administration is not unprecedented, as administration of exogenous inter-α-trypsin inhibitors is already used in the treatment of patients with severe sepsis and Kawasaki disease. The mortality risk panel defined here is in excellent agreement with findings in two recent COVID-19 serum proteomics studies on independent cohorts, supporting our findings. This panel may not be unique for COVID-19, as some of the proteins here annotated as mortality risk factors have previously been annotated as mortality markers in aging and in other diseases caused by different pathogens, including bacteria.

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Serum proteomics analysis reveals the thermal fitness of dairy buffalo to chronic heat stress

10.21203/rs.2.13215/v1 ◽

2019 ◽

Author(s):

Liu Ping ◽

Guo Lulu ◽

Mao Huaming ◽

Gu Zhaobing

Keyword(s):

Heat Stress ◽

Oxygen Delivery ◽

Production Efficiency ◽

Serum Proteins ◽

Differentially Expressed ◽

Blood Oxygen ◽

Label Free ◽

Serum Proteomics ◽

Parallel Reaction Monitoring ◽

Dairy Buffalo

Abstract Background: Chronic heat stress (CHS), aggravated by global warming, reduces the production efficiency of the buffalo dairy industry. CHS changes protein abundance, and low-abundant proteins take important roles in biological processes. Results: The objective of the study was to assess differences in low-abundant serum proteins in dairy buffaloes at thermoneutral (TN) or under chronic heat stress (CHS) conditions with proteomic approaches. Six dairy buffaloes as reference animal raised in TN season, and another six dairy buffaloes raised in CHS to discover the molecular mechanism of thermal fitness in hot season with serum proteomics. After the removal of multiple high-abundant proteins in serum, 344 low-abundant proteins were identified in serum with label-free quantification. Of these, 17 low-abundant differentially expressed serum proteins with known functions were detected, and five of these differentially expressed proteins were validated with parallel reaction monitoring. These five proteins were associated with various aspects of heat stress, including decreased heat production, increased blood oxygen delivery, and enhanced natural disease resistance. Conclusions: Lipase (LPL), glutathione peroxidase 3 (GPX3), cathelicidin-2 (CATHL2), ceruloplasmin (CP), and hemoglobin subunit alpha 1 (HBA1) were shown to play cooperative roles in CHS fitness in dairy buffalo. Dairy buffaloes adapt to CHS and hypoxia with high levels of RBCs, HBA1 and CP increased blood oxygen delivery capacity and thermal fitness.

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Explanation and Analysis of the Interaction between Environmental Health Officers and Directors of Food Preparation, Supply and Distribution Centers Based on Game Theory Model in Yazd

Journal of Environmental Health and Sustainable Development ◽

10.18502/jehsd.v4i2.1057 ◽

2019 ◽

Author(s):

Mohsen Pakdaman ◽

Mohammad Taghi Ghaneian ◽

Mohammad Hassan Ehrampoush ◽

Vahid Jafari Nodoshan ◽

Ebrahim Gholami Zarchi

Keyword(s):

Game Theory ◽

Environmental Health ◽

Theory Model ◽

Food Preparation ◽

Behavioral Strategies ◽

Monitoring And Control ◽

Distribution Centers ◽

Factors Affecting ◽

Quantitative Phase ◽

Supply And Distribution

Introduction: Health monitoring and control of food preparation, supply and distribution centers are the responsibility of environmental health officers. Therefore, the present study was conducted to explain the interaction between environmental health officers and providers of food preparation based on the game theory model. Materials and Methods: This research is a descriptive-analytical study in which after the determination of effective factors on the interaction between officers and directors, the so-called 22 games were designed and for each game four behavioral strategies determined and strategies identified as a two-choice I agree, I disagree questionnaire provided to environmental health officers and directors of food preparation, centers to select their desired strategy.. In the quantitative phase, SPSS 22 was used to analyze the data collected by questionnaires in order to determine the percentage of response frequency to each question. Gambit software was used to analyze for determination Nash equilibrium of any Games. Results: In the present study, the factors affecting the interaction between environmental health officers and directors were categorized to 24 subcategories assigned to six categories, and in the quantitative phase, finally, 22 dominant behavior strategies were identified and the final benefit percentage of each actor was determined. Conclusion: Investigating selected strategies by directors suggests that there is a good fit between the rules and health behaviors among the directors. The emphasis on health inspection based on education and counseling and lack of acceptance of the activities of health self-reported companies by the directors and officers are the most important outcomes of this study

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Impact of control technology on fight against COVID-19

MATEC Web of Conferences ◽

10.1051/matecconf/202235502044 ◽

2022 ◽

Vol 355 ◽

pp. 02044

Author(s):

Zihuan Feng ◽

Xun liang ◽

Chengzhen Zhao ◽

Jiachen Wu

Keyword(s):

Information Management ◽

Public Management ◽

Prevention And Control ◽

System Model ◽

Control Technology ◽

Practical Issue ◽

Key Factors ◽

Factors Affecting ◽

Multiple Data ◽

And Control

Since the outbreak of COVID-19, all countries have taken certain measures to restrain the spread of COVID-19. It is a complex and practical issue to study the measures and effects of the epidemic prevention and control. The spread of the epidemic in different countries has certain characteristics, and the prevention and control models and effects in different countries are also different. In this paper, the key factors affecting the prevention effect of COVID-19 were analyzed by integrating multiple data and using interdisciplinary methods of mathematics, statistics and information management science on the basis of public management, and the system model of influencing factors of COVID-19 was constructed.

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CDK9 as an Appealing Target for Therapeutic Interventions

Current Drug Targets ◽

10.2174/1389450119666181026152221 ◽

2019 ◽

Vol 20 (4) ◽

pp. 453-464 ◽

Cited By ~ 12

Author(s):

Shirin Eyvazi ◽

Mohammad Saeid Hejazi ◽

Homan Kahroba ◽

Mozghan Abasi ◽

Reza Eghdam Zamiri ◽

...

Keyword(s):

Transcription Factors ◽

Therapeutic Interventions ◽

Cyclin Dependent Kinase ◽

Serine Threonine Kinase ◽

Threonine Kinase ◽

Physiological Processes ◽

Functional Nature ◽

Cellular Pathways ◽

Rnap Ii ◽

Regulate Gene

Cyclin Dependent Kinase 9 (CDK9) as a serine/threonine kinase belongs to a great number of CDKs. CDK9 is the main core of PTEF-b complex and phosphorylates RNA polymerase (RNAP) II besides other transcription factors which regulate gene transcription elongation in numerous physiological processes. Multi-functional nature of CDK9 in diverse cellular pathways proposes that it is as an appealing target. In this review, we summarized the recent findings on the molecular interaction of CDK9 with critical participant molecules to modulate their activity in various diseases. Furthermore, the presented review provides a rationale supporting the use of CDK9 as a therapeutic target in clinical developments for crucial diseases; particularly cancers will be reviewed.

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