A Mouse Brain-based Multi-omics Integrative Approach Reveals Potential Blood Biomarkers for Ischemic Stroke

Abstract

Stroke remains a leading cause of death and disability worldwide. Despite continuous advances, the identification of key molecular signatures in the hyper-acute phase of ischemic stroke is still a primary interest for translational research on stroke diagnosis, prognosis, and treatment. Data integration from high-throughput -omics techniques has become crucial to unraveling key interactions among different molecular elements in complex biological contexts, such as ischemic stroke. Thus, we used advanced data integration methods for a multi-level joint analysis of transcriptomics and proteomics datasets obtained from mouse brains at 2 h after cerebral ischemia. By modeling net-like correlation structures, we identified an integrated network of genes and proteins that are differentially expressed at a very early stage after stroke. We validated 10 of these deregulated elements in acute stroke, and changes in their expression pattern over time after cerebral ischemia were described. Of these, CLDN20, GADD45G, RGS2, BAG5, and CTNND2 were next evaluated as blood biomarkers of cerebral ischemia in mice and human blood samples, which were obtained from stroke patients and patients presenting stroke-mimicking conditions. Our findings indicate that CTNND2 levels in blood might potentially be useful for distinguishing ischemic strokes from stroke-mimicking conditions in the hyper-acute phase of the disease. Furthermore, circulating GADD45G content within the first 6 h after stroke could also play a key role in predicting poor outcomes in stroke patients. For the first time, we have used an integrative biostatistical approach to elucidate key molecules in the initial stages of stroke pathophysiology and highlight new notable molecules that might be further considered as blood biomarkers of ischemic stroke.

Multi-Omics Approach to Elucidate Cerebrospinal Fluid Changes in Dogs with Intervertebral Disc Herniation

“…To obtain an insight into the complex biological processes in IVDH occurring at the molecular level, we used the novel integrative multi-omics approach, involving the integration of high-resolution mass spectrometry-based proteomics and global metabolome profiling data, which has not previously been applied in IVDH in human or veterinary medicine in IVDH. In relation to this current topic, and according to the best authors’ knowledge, IVDH-related proteomic studies have been published to address quantitative analyses of IVD [ 24 ], secretome and proteoglycan in canine NP [ 25 ], as well as gel-based approaches in human CSF in IVDH [ 26 ]. Although there are recent papers reporting multi-omics (e.g., proteomics, metabolomics, transcriptomics and genomics) studies contributing to the identification of potential biomarkers in neurovascular diseases [ 27 ], the use of biostatistical omics data integration is still at an early stage [ 28 ].…”

The bioinformatic identification of proteins with varying levels of post-translational modifications in experimental ischemic stroke in mice

“…Для понимания сути работы необходимо вкратце описать схему эксперимента, поставленного в работе [4] в той части, в которой были исследованы образцы мозга мышей. Авторы использовали модель преходящей церебральной ишемии (tMCAO), провоцируя инфаркт в области средней мозговой артерии 8-ми мышей, лигируя её нейлоновой нитью на 90 мин с последующей реперфузией в течение 30 мин.…”

“…При масс-спектрометрическом анализе каждую пробу предварительно делили на 5 проб электрофорезом в полиакриламидном геле с SDS. Так как в работе [4] авторы не ставили задачей исследование ПТМ, то в качестве модификаций они рассматривали только карбамидметилирование остатков цистеина (особенность пробоподготовки) и спонтанное окисление метионина. Чтобы найти пептиды с такими модификациями, как фосфорилирование и дезаминирование, мы провели идентификацию пептидов заново с использованием программы Peaks Studio X Pro [5]…”

“…Данная работа была выполнена с использованием результатов исследования [4], доступных в базе данных ProteomeXchange (accession code PXD016538). Её авторы применяли комплексный мультиомный подход по выявлению потенциальных биомаркеров в крови мышей с экспериментальным ишемическим инсультом.…”

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Проанализированы экспериментальные данные (Simats A. et al (2020) Molecular & Cellular Proteomics, 19(12), 1921-1936, полученные при использовании комплексного мультиомного подхода по выявлению потенциальных биомаркеров крови при ишемическом инсульте у мышей и доступные в базе данных ProteomeXchange (accession code PXD016538). Идентификация пептидов с посттрансляционными модификациями (ПТМ) была проведена заново.

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