Human genome sequencing was started to solve four letter algorithm of the genome to understand the complex nature of human metabolism. However, after completion of Human Genome Project many scientists realized that sequence information alone was not sufficient to solve the biochemical mechanism of the organism through classical approaches. Non-coding parts of the genome produce small conserved ribonucleic acids, miRNAs to control cellular and physiological processes [1, 2]. This breakthrough discovery directed researches to examine role of miRNA in cancer since miRNAs are involved in the development, cell differentiation, and regulation of cell cycle [3]. The first paper of the special issue provides general information of miRNA in cancer research. This thematic issue presents two computational approaches for miRNA identification and their role in cancer. The first one comes from Dr. Wang and his presented work predicts cancer-related miRNAs by using expression profiles in tumor tissues. The work relies on R-squared method to investigate miRNA-mRNA regulatory relationship between miRNAs and mRNAs from different tissues and predicts miRNAs associated with colon, prostate, pancreatic, lung, breast, bladder, and kidney cancer. The second paper by Allmer et al. examines miRNA-gene regulatory networks and their implications in cancer. Their work provides complex network of expression regulation and miRNAs' role in personalized medicine. miRNAs regulate tumor progression and metastasis by interacting with target genes in the cells. Exosomal shuttle small RNAs mediate cell to cell communication and regulate cancer metastasis. The regulation via heterotypic signals in the microenvironment was explained by Dr. Liang and Dr. Yu groups. The rest of the issue highlights the roles of miRNAs on multiple myeloma, non-small cell lung cancer, urological malignancies, myeloid leukemia, and laryngeal squamous cell carcinoma. Proliferation of bone marrow of malignant plasma cells leads multiple myeloma and this accounts for ten percent of the hematological tumors. miRNAs biology in multiple myeloma and miRNA study methods was discussed by Dr. Cho's group along with translational therapeutics. Dr. Papavassiliou highlights recent literature on miRNA-colerectal cancer. miRNA in colorectal cancer regulates tumor specific markers and these markers have oncogenic and tumor suppressive functions as other types of cancer. The paper overviews miRNA biomarkers extracted from plasma and fecal samples and also explain novel therapeutic applications by miRNA delivery and inhibition. Lung cancer is the leading cause of cancer deaths and non-small cell lung cancer shows poor prognosis and recurrence. Drug resistance limits current treatments and miRNA based gene therapy provides an alternative and attractive method for cancer inhibition since dysregulation of specific miRNAs involved in cancer cell resistance. Therefore, Dr. Giovannetti group explains current efforts in developing miRNA mimickers or antagomiRs for drug resistance mechanism. Dr. El...

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Pseudogenes are ubiquitous and abundant in genomes. Pseudogenes were once called “genomic fossils” and treated as “junk DNA” several years. Nevertheless, it has been recognized that some pseudogenes play essential roles in gene regulation of their parent genes, and many pseudogenes are transcribed into RNA. Pseudogene transcripts may also form small interfering RNA or decrease cellular miRNA concentration. Thus, pseudogenes regulate tumor suppressors and oncogenes. Their essential functions draw the attention of our research group in my current work on heat shock protein 90: a chaperone of oncogenes. The paper reviews our current knowledge on pseudogenes and evaluates preliminary results of the chaperone data. Current efforts to understand pseudogenes interactions help to understand the functions of a genome.

Heat shock proteins (Hsps) protect protein substrates against conformational damage to promote the function of the proteins, prevent aggregation and prevent formation of toxic inclusion bodies. Protein aggregates and fibrils have been associated with neurodegenerative diseases and with inclusion bodies. High-level expression of recombinant protein for biotechnological purposes often leads to insoluble inclusion bodies. Therefore, misfolded proteins must be properly folded or must be degraded through heat shock protein action. This function protects cells against cytotoxic outcomes. In addition to their cytoprotective roles, Hsps are involved in other functions since Hsps exist in all types of cells and tissues. Therefore, several diseases are associated with alterations of these biochemical functions. This first review of the theme issue will discuss general properties of Hsps concisely along with their potential use in pharmaceutical and biotechnological applications.

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Hsp70's are highly conserved essential protein chaperones that assist protein folding and prevent protein aggregation. They have modular structures consisting of ATPase, substrate-binding, and C-terminal domains. Substrate binding and release is regulated by ATP hydrolysis and nucleotide exchange, which in turn are regulated by cochaperones. Eukaryotes have constitutive (Hsc70) and stress-inducible (iHsp70) isoforms, but their functions have not been systematically compared. Using a yeast system to evaluate heterologous Hsp70's we find that primate Hsc70 supported growth but iHsp70 did not. Plant Hsc70 and iHsp70 counterparts behaved similarly, implying evolutionary conservation of this distinction. Swapping yeast and primate Hsp70 domains showed that (i) the Hsc70-iHsp70 distinction resided in the ATPase domain, (ii) substrate-binding domains of Hsp70's within and across species functioned similarly regarding growth, (iii) C-terminal domain function was important for growth, and (iv) Hsp70 functions important for cell growth and prion propagation were separable. Enzymatic analysis uncovered a correlation between substrate affinity and prion phenotype and showed that ATPase and protein-folding activities were generally similar. Our data support a view that intrinsic activities of Hsp70 isoforms are comparable, and functional differences in vivo lie mainly in complex interactions of Hsp70 with cochaperones.

Cysteine cathepsins are lysosomal enzymes belonging to the papain family. Their expression is misregulated in a wide variety of tumors, and ample data prove their involvement in cancer progression, angiogenesis, metastasis, and in the occurrence of drug resistance. However, while their overexpression is usually associated with highly aggressive tumor phenotypes, their mechanistic role in cancer progression is still to be determined to develop new therapeutic strategies. In this review, we highlight the literature related to the role of the cysteine cathepsins in cancer biology, with particular emphasis on their input into tumor biology.

MiRNAs are a family of small, endogenous, and evolutionarily conserved non-coding ribonucleic acids that have been involved in the regulation of several essential, cellular, and functional processes. MicroRNAs are known to play key roles in all types of cancer and function as oncogenes (oncomirs) or tumour-suppressors in up-regulation or down-regulation processes respectively. MiRNAs have potential power to be examined as prognostic and diagnostic biomarkers. Modulating miRNAs, based on two major approaches (miRNA mimics and miRNA antagonists), is used for clinical development of therapeutic miRNAs. This review emphasizes the latest discovery in the field of miRNA research involved in cancer, biomarkers, and therapeutics.