A novel method using formamide for the elution of antibodies from erythrocytes

Ultra High-plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

A deeper understanding of complex biological processes, including tumor development and immune response, requires ultra high-plex, spatial interrogation of multiple "omes". Here we present the development and implementation of a novel spatial proteogenomic (SPG) assay on the GeoMx Digital Spatial Profiler platform with next-generation sequencing readout that enables ultra high-plex digital quantitation of proteins (>100-plex) and RNA (whole transcriptome, >18,000-plex) from a single formalin-fixed paraffin-embedded (FFPE) sample. This study highlighted the high concordance, R > 0.85 and <15% change in sensitivity between the SPG assay and the single-analyte assays on various cell lines and tissues from human and mouse. Furthermore, we demonstrate that the SPG assay was reproducible across multiple users. When used in conjunction with advanced cellular neighborhood segmentation, distinct immune or tumor RNA and protein targets were spatially resolved within individual cell subpopulations in human colorectal cancer and non-small cell lung cancer. We used the SPG assay to interrogate 23 different glioblastoma multiforme (GBM) samples across four pathologies. The study revealed distinct clustering of both RNA and protein based on pathology and anatomic location. The in-depth investigation of giant cell glioblastoma multiforme (gcGBM) revealed distinct protein and RNA expression profiles compared with that of the more common GBM. More importantly, the use of spatial proteogenomics allowed simultaneous interrogation of critical protein posttranslational modifications alongside whole transcriptomic profiles within the same distinct cellular neighborhoods.

Significance

We describe ultra high-plex spatial proteogenomics; profiling whole transcriptome and high-plex proteomics on a single FFPE tissue section with spatial resolution. Investigation of gcGBM versus GBM revealed distinct protein and RNA expression profiles.

Paper-based nuclease protection assay with on-chip sample pretreatment for point-of-need nucleic acid detection

Pathogen detection is crucial for human, animal, and environmental health; crop protection; and biosafety. Current culture-based methods have long turnaround times and lack sensitivity. Nucleic acid amplification tests offer high specificity and sensitivity. However, their cost and complexity remain a significant hurdle to their applications in resource-limited settings. Thus, point-of-need molecular diagnostic platforms that can be used by minimally trained personnel are needed. The nuclease protection assay (NPA) is a nucleic acid hybridization-based technique that does not rely on amplification, can be paired with other methods to improve specificity, and has the potential to be developed into a point-of-need device. In traditional NPAs, hybridization of an anti-sense probe to the target sequence is followed by single-strand nuclease digestion. The double-stranded target-probe hybrids are protected from nuclease digestion, precipitated, and visualized using autoradiography or other methods. We have developed a paper-based nuclease protection assay (PB-NPA) that can be implemented in field settings as the detection approach requires limited equipment and technical expertise. The PB-NPA uses a lateral flow format to capture the labeled target-probe hybrids onto a nitrocellulose membrane modified with an anti-label antibody. A colorimetric enzyme-substrate pair is used for signal visualization, producing a test line. The nuclease digestion of non-target and mismatched DNA provides high specificity while signal amplification with the reporter enzyme-substrate provides high sensitivity. We have also developed an on-chip sample pretreatment step utilizing chitosan-modified paper to eliminate possible interferents from the reaction and preconcentrate nucleic acids, thereby significantly reducing the need for auxiliary equipment. Graphical abstract.

Simultaneous detection of mRNA and protein in single cells using immunofluorescence-combined single-molecule RNA FISH

Although the concept of combining immunofluorescence (IF) with single-molecule RNA fluorescence in situ hybridization (smRNA FISH) seems obvious, the specific materials used during IF and smRNA FISH make it difficult to perform these procedures simultaneously on the same specimen. Even though there are reports where IF and smRNA FISH were combined with success, these were insufficient in terms of signal intensities, staining patterns, and GFP-compatibility, and a detailed exploration of the various factors that influence IF and smRNA FISH outcome has not been published yet. Here, we report a detailed study of conditions and reagents used in classic IF and smRNA FISH that allowed us to establish an easy, robust, and GFP-compatible procedure. Our protocol enables simultaneous detection of mRNA and protein quantity as well as the subcellular distribution of these molecules in single cells by combining an RNase-free modification of the IF technique and the more recent smRNA FISH method. Using this procedure, we have shown the direct interaction of RNase MCPIP1 with IL-6 mRNA. We also demonstrate the use of our protocol in heterogeneous cell population analysis, revealing cell-to-cell differences in mRNA and protein content.

Clinically and/or Serologically Misleading Findings Surrounding Immune Haemolytic Anaemias

Autoimmune haemolytic anaemias (AIHAs) are well-characterized disorders. They can be differentiated from one another and from other non-immune haemolytic anaemias by clinical, laboratory and serological testing. However, several misleading clinical presentations and/or serological findings may result in misinterpretation, delay and/or misdiagnosis. Such failures are avoidable by adequate clinical and serological experience of the responsible physicians and serologists or, at least, by an optimised bidirectional communication. As long as this has not been achieved, unpleasant failures are to be expected. A true diagnosis of AIHA can neither be verified by clinical nor serological findings alone. Thus, a collective clinical and serological picture remains obligatory for fulfilling the criteria of optimal diagnosis and therapy. Ultimately, the majority of pioneer scientific and practical work in this field stems from scientists who were simultaneously involved in both the clinic and serology.

Separation of sensitized and non-sensitized RBCs: sephadex-based cell-affinity adsorbents

INTRODUCTION

In transfusion medicine, antibodies that cause RBCs positive DATs, may interfere with patients' phenotyping. Traditionally, these antibodies were removed using various antibody elution methodologies. However, the elution agents and conditions used have been only partially successful; and no one method is superior. The purpose of this study was to develop a general and efficient method to separate non-sensitized from sensitized RBCs using Sephadex-based cell-affinity adsorbents.

METHODS

First, we coupled Sephadex support with Staphylococcal Protein G (SpG) with or without NHS. Then we simulated clinical conditions by mixing different ratios of sensitized and non-sensitized RBCs in vitro. Sensitized cells were prepared by mixing antibody with corresponding antigen-positive RBCs. Finally, we checked the sensitization status of absorbed RBCs after absorption with modified Sephadex support.

RESULTS

The number of sensitized RBCs bound to Sephadex-based cell-affinity adsorbents is approximately 5×10(8) RBCs/mL support. Activated Sephadex could separate sensitized from non-sensitized RBCs. Conclusion Sephadex-based cell-affinity adsorbents with an NHS spacer arm have bigger capacity for binding RBCs than unmodified Sephadex. The Sephadex-based cell-affinity adsorbents readily separate non-sensitized RBCs from sensitized RBCs, thus providing a new strategy to type the blood for transfused patients.

Potentially antigenic RBC membrane proteins in dogs with primary immune-mediated hemolytic anemia

BACKGROUND

Primary immune-mediated hemolytic anemia (IMHA) is an important cause of morbidity and mortality in dogs. The mechanisms underlying autoimmune reactivity remain poorly understood.

OBJECTIVE

The aim of this study was to identify membrane proteins of RBCs that could be antigenic in dogs with primary IMHA.

METHODS

Antibodies were eluted with xylene from RBCs of 12 dogs with IMHA, 4 dogs with anemia due to causes other than IMHA, and 2 healthy dogs. Pooled RBC membrane proteins were prepared from blood of 17 healthy dogs. The eluted antibodies were then analyzed by immunoblotting for interactions with the pooled membrane proteins and autologous plasma. Bands present in the 12 dogs with IMHA but not in the 6 other dogs were considered potential autoantigens and were identified by liquid chromatography followed by tandem mass spectrometry.

RESULTS

RBC eluates from all 18 dogs had reactivity against band 3 protein. Antibodies to 6 additional proteins were uniquely identified in dogs with IMHA. Reactivity to calpain, complement component 3, and peroxiredoxin 2 was identified in 8, 8, and 4 of the 12 samples, respectively, from dogs with IMHA, but in none of the samples from the 6 dogs without IMHA.

CONCLUSIONS

Detection of universal immune reactivity against band 3 protein probably indicates recognition of senescent RBC. Proteins uniquely recognized by antibodies in dogs with IMHA are involved in oxidative stress and apoptosis (calpain), inflammation (complement), and scavenging of reactive oxygen species (peroxiredoxin 2). It remains to be determined if these proteins are important in initiating autoimmunity or if immunoglobulins targeting these proteins develop during IMHA.