Novel Bioinformatics-Based Approach for Proteomic Biomarkers Prediction of Calpain-2 &Caspase-3 Protease Fragmentation: Application to βII-Spectrin Protein

Identifying putative substrates of Calpain-15 in neurodevelopment

Calpain 15 (CAPN15) is an intracellular cysteine protease belonging to the non-classical small optic lobe (SOL) family of calpains, which has an important role in developmental processes. Loss of Capn15 in mice leads to developmental eye anomalies and volumetric changes in the brain. Human individuals with biallelic variants in CAPN15 have developmental delay, neurodevelopmental disorders, as well as congenital malformations, including eye anomalies. However, the substrates of Capn15 are still unidentified. Here, using Capn15 KO P2 mice of both sexes, we have used RNA sequencing (RNA-SEQ), proteomics, and N-terminomics/terminal amino isotopic labelling of substrates (TAILS), to examine putative substrates of Capn15. There were few changes in the transcriptome profile, and we could not verify a protein change in one selected mRNA between Capn15-/- and WT mice, although a putative transcription factor linked to these changes, Pax2, did show a significant increase after the loss of Capn15. TAILS revealed a preference for cleavage at basic residues, and while no hits showed a significant change in cleavage, some were more abundant when Capn15 was removed. These included Doublecortin and Tubb3, and the Doublecortin predicted cleavage was at a lysine residue. Cleavages at lysine residues were enriched in peptides that were lost or reduced when Capn15 was removed, but not in cleavages that were unchanged when Capn15 was removed.

Biomarkers for detection, prognosis and therapeutic assessment of neurological disorders

Neurological disorders have aroused a significant concern among the health scientists globally, as diseases such as Parkinson's, Alzheimer's and dementia lead to disability and people have to live with them throughout the life. Recent evidence suggests that a number of environmental chemicals such as pesticides (paraquat) and metals (lead and aluminum) are also the cause of these diseases and other neurological disorders. Biomarkers can help in detecting the disorder at the preclinical stage, progression of the disease and key metabolomic alterations permitting identification of potential targets for intervention. A number of biomarkers have been proposed for some neurological disorders based on laboratory and clinical studies. In silico approaches have also been used by some investigators. Yet the ideal biomarker, which can help in early detection and follow-up on treatment and identifying the susceptible populations, is not available. An attempt has therefore been made to review the recent advancements of in silico approaches for discovery of biomarkers and their validation. In silico techniques implemented with multi-omics approaches have potential to provide a fast and accurate approach to identify novel biomarkers.

Calpain-2 inhibitor treatment preferentially reduces tumor progression for human colon cancer cells expressing highest levels of this enzyme

Calpain-2 levels are higher in colorectal tumors resistant to chemotherapy and previous work showed calpain-2 inhibitor therapy reduced inflammation-driven colorectal cancer, but direct effects of the inhibitor on colon cancer cells themselves were not demonstrated. In the present study, five human colon cancer cell lines were directly treated with a calpain-2 inhibitor and results showed increased cell death in 4 of 5 cell lines and decreased anchorage-independent growth for all cell five lines. When tested for levels of calpain-2, three cell lines exhibited increasing levels of this enzyme: HCT15 (low), HCC2998 (medium), and HCT116 (significantly higher). This was consistent with gel shift assays showing that calpain-2 inhibitor reduced of NF-κB nuclear translocation most effectively in HCT116 cells. Ability of calpain-2 inhibitor to impede tumor progression in vivo was evaluated using intrarectal transplant of luciferase-expressing cells for these three cell lines. Results showed that calpain-2 inhibitor therapy reduced tumor growth and increased survival only in mice injected with HCT116 cells. These data suggest calpain-2 inhibitor treatment may be most effective on colorectal tumors expressing highest levels of calpain-2.