ALS blood expression profiling identifies new biomarkers, patient subgroups, and evidence for neutrophilia and hypoxia

Abstract

Background Amyotrophic lateral sclerosis (ALS) is a debilitating disease with few treatment options. Progress towards new therapies requires validated disease biomarkers, but there is no consensus on which fluid-based measures are most informative. Methods This study analyzed microarray data derived from blood samples of patients with ALS ( n = 396), ALS mimic diseases ( n = 75), and healthy controls ( n = 645). Goals were to provide in-depth analysis of differentially expressed genes (DEGs), characterize patient-to-patient heterogeneity, and identify candidate biomarkers. Results We identified 752 ALS-increased and 764 ALS-decreased DEGs (FDR < 0.10 with > 10% expression change). Gene expression shifts in ALS blood broadly resembled acute high altitude stress responses. ALS-increased DEGs had high exosome expression, were neutrophil-specific, associated with translation, and overlapped significantly with genes near ALS susceptibility loci (e.g., IFRD1 , TBK1 , CREB5 ). ALS-decreased DEGs, in contrast, had low exosome expression, were erythroid lineage-specific, and associated with anemia and blood disorders. Genes encoding neurofilament proteins ( NEFH , NEFL ) had poor diagnostic accuracy (50–53%). However, support vector machines distinguished ALS patients from ALS mimics and controls with 87% accuracy (sensitivity: 86%, specificity: 87%). Expression profiles were heterogeneous among patients and we identified two subgroups: (i) patients with higher expression of IL6R and myeloid lineage-specific genes and (ii) patients with higher expression of IL23A and lymphoid-specific genes. The gene encoding copper chaperone for superoxide dismutase ( CCS ) was most strongly associated with survival (HR = 0.77; P = 1.84e−05) and other survival-associated genes were linked to mitochondrial respiration. We identify a 61 gene signature that significantly improves survival prediction when added to Cox proportional hazard models with baseline clinical data (i.e., age at onset, site of onset and sex). Predicted median survival differed 2-fold between patients with favorable and risk-associated gene expression signatures. Conclusions Peripheral blood analysis informs our understanding of ALS disease mechanisms and genetic association signals. Our findings are consistent with low-grade neutrophilia and hypoxia as ALS phenotypes, with heterogeneity among patients partly driven by differences in myeloid and lymphoid cell abundance. Biomarkers identified in this study require further validation but may provide new tools for research and clinical practice. Electronic supplementary material The online version of...

The Peripheral Immune System and Amyotrophic Lateral Sclerosis

“…The ratio of neutrophils to monocytes was also shown to be increased (53), as was the total number of granulocytes (54). A micro-array study further confirmed evidence for mild neutrophilia in ALS patients (55). In the SOD1 G93A transgenic mouse ALS model, circulating neutrophils are increased (73), and neutrophils and mast cells are present along peripheral motor axons, with masitinib treatment leading to reduction of axonal damage (56).…”

“…In the peripheral blood monocytes of ALS patients there is also dysregulation of hypoxia pathways (153). A gene expression study found evidence of hypoxia related genes in peripheral blood of ALS patients (55). In an animal model of ALS, hypoxia aggravates the loss of motor neurons (154).…”

“…A study of gene expression indicated that patients can be grouped into patients with higher expression of IL-6R and myeloid lineage-specific genes, and patients with higher expression of IL-23A and lymphoid-specific genes (55). The results from a clinical trial of Toclizumab also led the authors to note that Toclizumab reduced IL-6 and other cytokines in cells from some ALS patients (i.e., an "inflammatory group") but not others (89).…”

Controlling technical variation amongst 6693 patient microarrays of the randomized MINDACT trial

“…The resulting dataset is representative of an early stage breast cancer population and is now available (unadjusted and adjusted) together with patient characteristics and clinical outcomes for future translational research by submitting proposals to the EORTC for access to the gene expression data as well as the clinical and patient data (https://www.eortc.org/data-sharing/), and if granted can be used for analysis and discovery science 31,32 , datamining or creating new signatures of clinically relevant questions 33 .…”

Klotho Pathways, Myelination Disorders, Neurodegenerative Diseases, and Epigenetic Drugs

“…58,[224][225][226][227] Unfortunately, patients with ALS, at present, have limited therapeutic options (Table 2). 96,173,228 Moreover, given the rapid and terminal progression of the disease postdiagnosis, there is a pressing need to develop new therapies and/or based on mechanism of action repurposing drugs already approved for other diseases. 176,180 Recruiting ALS subjects into traditional clinical trials is challenging because of the low number of cases in the population.…”