From genetic variability to phenotypic expression of blood group systems

A deep learning approach to prediction of blood group antigens from genomic data

BACKGROUND

Deep learning methods are revolutionizing natural science. In this study, we aim to apply such techniques to develop blood type prediction models based on cheap to analyze and easily scalable screening array genotyping platforms.

METHODS

Combining existing blood types from blood banks and imputed screening array genotypes for ~111,000 Danish and 1168 Finnish blood donors, we used deep learning techniques to train and validate blood type prediction models for 36 antigens in 15 blood group systems. To account for missing genotypes a denoising autoencoder initial step was utilized, followed by a convolutional neural network blood type classifier.

RESULTS

Two thirds of the trained blood type prediction models demonstrated an F1-accuracy above 99%. Models for antigens with low or high frequencies like, for example, Cw, low training cohorts like, for example, Cob, or very complicated genetic underpinning like, for example, RhD, proved to be more challenging for high accuracy (>99%) DL modeling. However, in the Danish cohort only 4 out of 36 models (Cob, Cw, D-weak, Kpa) failed to achieve a prediction F1-accuracy above 97%. This high predictive performance was replicated in the Finnish cohort.

DISCUSSION

High accuracy in a variety of blood groups proves viability of deep learning-based blood type prediction using array chip genotypes, even in blood groups with nontrivial genetic underpinnings. These techniques are suitable for aiding in identifying blood donors with rare blood types by greatly narrowing down the potential pool of candidate donors before clinical grade confirmation.

Transfusion in critical care: Past, present and future

Anaemia and coagulopathy are common in critically ill patients and are associated with poor outcomes, including increased risk of mortality, myocardial infarction, failure to be liberated from mechanical ventilation and poor physical recovery. Transfusion of blood and blood products remains the corner stone of anaemia and coagulopathy treatment in critical care. However, determining when the benefits of transfusion outweigh the risks of anaemia may be challenging in some critically ill patients. Therefore, the European Society of Intensive Care Medicine prioritised the development of a clinical practice guideline to address anaemia and coagulopathy in non-bleeding critically ill patients. The aims of this article are to: (1) review the evolution of transfusion practice in critical care and the direction for future developments in this important area of transfusion medicine and (2) to provide a brief synopsis of the guideline development process and recommendations in a format designed for busy clinicians and blood bank staff. These clinical practice guidelines provide recommendations to clinicians on how best to manage non-bleeding critically ill patients at the bedside. More research is needed on alternative transfusion targets, use of transfusions in special populations (e.g., acute neurological injury, acute coronary syndromes), use of anaemia prevention strategies and point-of-care interventions to guide transfusion strategies.

Detergent-free isolation of native red blood cell membrane complexes

Over the past few decades, studies on the red blood cell (RBC) membrane gave rise to increasingly sophisticated although divergent models of its structural organization, since investigations were often performed in denaturing conditions using detergents. To access soluble isolated RBC membrane complexes with the preservation of their interactions and conformations, we decided to apply the recent SMALP (Styrene Maleic Acid Lipid Particles) technology to RBC ghosts. Depending on the ionic strength of buffers in which ghost membranes were resuspended, the isolated proteins within SMALPs could differ on Coomassie-stained gels, but with few changes when compared to ghost membrane SDS lysates. We subsequently produced SMALPs derived from ghosts from two different blood group phenotypes, RhD-positive and RhD-negative, both types of RBC expressing the RhCE proteins but only RhD-positive cells being able to express the RhD proteins. This allowed the isolation, by size exclusion chromatography (SEC), of soluble fractions containing the Rh complex, including the RhD protein or not, within SMALPs. The use a conformation-dependent anti-RhD antibody in immunoprecipitation studies performed on SEC fractions of SMALPs containing Rh proteins clearly demonstrated that the RhD protein, which was only present in SMALPs prepared from RhD-positive RBC ghosts, has preserved at least one important conformational RhD epitope. This approach opens new perspectives in the field of the erythroid membrane study, such as visualization of RBC membrane complexes in native conditions by cryo-electron microscopy (CryoEM) or immuno-tests with conformation-dependent antibodies against blood group antigens on separated and characterized SMALPs containing RBC membrane proteins.

The role of genomics in transfusion medicine

PURPOSE OF REVIEW

To summarize recent advances in red blood cell (RBC) blood group genotyping, with an emphasis on advances in the use of NGS next generation sequencing (NGS) to detect clinically relevant blood group gene variation.

RECENT FINDINGS

Genetic information is useful in predicting RBC blood group antigen expression in several clinical contexts, particularly, for patients at high-risk for allosensitization, such as multiple transfused patients. Blood group antigen expression is directed by DNA variants affecting multiply genes. With over 300 known antigens, NGS offers the attractive prospect of comprehensive blood group genotyping. Recent studies from several groups show that NGS reliably detects blood group gene single nucleotide variants (SNVs) with good correlation with other genetic methods and serology. Additionally, new custom NGS methods accurately detect complex DNA variants, including hybrid RH alleles. Thus, recent work shows that NGS detects known and novel blood group gene variants in patients, solves challenging clinical cases, and detects relevant blood group variation in donors.

SUMMARY

New work shows that NGS is particularly robust in identifying SNVs in blood group genes, whereas custom genomic tools can be used to identify known and novel complex structural variants, including in the RH system.

Electron paramagnetic resonance oximetry as a novel approach to monitor the effectiveness and quality of red blood cell transfusions

BACKGROUND

The goal of red blood cell transfusion is to improve tissue oxygenation. Assessment of red blood cell quality and individualised therapeutic needs can be optimised using direct oxygen (O₂) measurements to guide treatment. Electron paramagnetic resonance oximetry is capable of accurate, repeatable and minimally invasive measurements of tissue pO₂. Here we present preclinical proof-of-concept of the utility of electron paramagnetic resonance oximetry in an experimental setting of acute blood loss, transfusion, and post-transfusion monitoring.

MATERIALS AND METHODS

Donor rat blood was collected, leucocyte-reduced, and stored at 4 °C in AS-3 for 1, 7 and 14 days. Red blood cell morphology, O₂ equilibrium, p50 and Hill numbers from O₂ binding and dissociation curves were evaluated in vitro. Recipient rats were bled and maintained at a mean arterial pressure of 30-40 mmHg and hind limb muscle (biceps femoris) pO₂ at 25-50% of baseline. Muscle pO₂ was monitored continuously over the course of experiments to assess the effectiveness of red blood cell preparations at different stages of blood loss and restoration.

RESULTS

Red blood cell morphology, O₂ equilibrium and p50 values of intra-erythrocyte haemoglobin were significantly altered by refrigerated storage for both 7 and 14 days. Transfusion of red blood cells stored for 7 or 14 days demonstrated an equivalently impaired ability to restore hind limb muscle pO₂, consistent with in vitro observations and transfusion with albumin. Red blood cells refrigerated for 1 day demonstrated normal morphology, in vitro oxygenation and in vivo restoration of tissue pO₂.

DISCUSSION

Electron paramagnetic resonance oximetry represents a useful approach to assessing the quality of red blood cells and subsequent transfusion effectiveness.