Argiris Symeonidis

Aims: Treatment of higher-risk myelodysplastic syndromes (HR-MDS) with azacytidine (AZA) exerts significant effects on the epigenome, primarily through DNA demethylation and reactivation of epigenetically silenced genes. Beyond this established mechanism, molecular AZA-linked effects are increasingly being recognized. Materials and methods: Liquid chromatography combined with mass spectrometry (LC-MS/MS) was employed for the accurate assessment of various RNA and DNA modifications pre- and post-AZA treatment of an HR-MDS cohort (N = 8). Mapping of the AZA treatment-responsive regulatory pathways was performed by miRNA-next generation sequencing (NGS), followed by a multi-layered bioinformatic pipeline, integrating miRNA differential expression, gene set enrichment, and network analyses. The precise number of mitochondrial (mt)DNA copies pre- and post-AZA was evaluated by a digital PCR assay. Results: Cell pathways affected by miRNA differential expression patterns pre- and post-AZA treatment discriminated the clinical phenotypes of Responders against Non-Responders to therapy. Intracellular RNA modifications: N6-methyladenosine (m6A), 5-methylcytidine (m5C), N1-methyladenosine (m1A), 2′-O-methylguanosine (Gm) and adenosine-to-inosine (A → I) editing were evaluated for their potential impact in treatment response. Nuclear DNA/mtDNA methylation profiles and mtDNA copy number reduction manifested the mitochondrial features affected by AZA. Our results suggest that neoplastic HSPCs in HR-MDS Responders to AZA adapt by normalizing glycolytic metabolism and enhancing ribosomal activity. The observed reduction of mtDNA content can be associated with improved survival and suppression of malignant progression. Non-Responders, despite experiencing mtDNA depletion, seem unable to coordinate such metabolic reprogramming and remain disadvantaged to AZA therapy.

The intracellular topography of RNA molecules, encompassing ribonucleotides with biochemical modifications, such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), adenosine to inosine (A → I) editing, and isomerization of uridine to pseudouridine (Ψ), as well as of non-coding RNA molecules, is currently studied within the frame of the epigenome. Circulating RNA molecules in the intracellular space that have incorporated information by carrying specific modifications depend on the balanced activity and correct subcellular installation of their modifying enzymes, the “writers”, “readers” and “erasers”. Modifications are critical for RNA translocation from the nucleus to the cytoplasm, for stability and translation efficiency, and for other, still-uncovered functions. Moreover, trafficking of non-coding RNA molecules depends on membrane transporters capable of recognizing signal sequences and RNA recognition-binding proteins that can facilitate their transport to different intracellular locations, guiding the establishment of interconnection possibilities with different macromolecular networks. The potential of long non-coding RNAs to form multilayer molecular connections, as well as the differential topology of micro-RNAs in cell nuclei, compared to cytoplasm, has been recognized by several studies. The study of the intercellular compartmentalization of these molecules has recently become feasible thanks to technological progress; however, a wealth of information has not yet been produced that would lead to safe conclusions regarding non-coding RNA’s contributions to the early steps of pathogenesis and disease progression in hematological malignancies. Both, the bone marrow, as the main hematopoietic tissue, and the lymphoid tissues are composed of cells with highly reactive potential to signals affecting the epigenome and initiating cascade pathways in response. Independently or in combination with coexistent driver genetic mutations, especially mutations of enzymes involved in epigenomic surveillance, intracellular microenvironmental alterations within the cell nuclear, cytoplasmic, and mitochondrial compartments can lead to disorganization of hematopoietic stem cells’ epigenomes, promoting the generation of hematological malignancies. In this review, we discuss the various intracellular processes that, when disrupted, may result in the ectopic placement of RNA molecules, either inducing specific modifications or non-coding molecules or promoting hematological malignant phenotypes. The crosstalk between mitochondrial and nuclear genomes and the complex regulatory effects of mis-localized RNA molecules are highlighted. This research approach may constitute a field for new, more specifically targeted therapies in hematology based on RNA technology.

The intracellular topography of RNA molecules, encompassing ribonucleotides with biochemical modifications, such as N6-methyladenosine(m6A), 5-methylcytosine (m5C) and isomerization of uridine to pseudouridine (Ψ), as well as of the non-coding RNA molecules, are currently studied within the frame of the epigenome. Circulating RNA molecules in the intracellular space, that have incorporated information by carrying specific modifications, depend on the balanced activity and correct subcellular installation of their modifying enzymes, the “writers”, “readers” and “erasers”. Modifications are critical for RNA translocation from nucleus to cytoplasm, stability and translation efficiency and other, still uncovered functions. Moreover, intracellular movement of non-coding RNA molecules depends on membrane transporters, capable of recognizing signal sequences and RNA recognition-binding proteins, that can facilitate their transport to different intracellular locations, guiding the establishment of interconnection possibilities with different macromolecular networks. The potential of long non-coding RNAs to form multilayer molecular connections, as well as the differential topology of micro-RNAs in cell nucleus over cytoplasm have been recognized by several studies. The study of the intracellular compartmentalization of these molecules has recently become feasible thanks to technological progress, however, a wealth of information has not yet been produced that would lead to safe conclusions, regarding non-coding RNA contribution to the early steps of pathogenesis and disease progression of hematological malignancies. Both the bone marrow, as the main hematopoietic tissue, and the lymphoid tissues are composed of cells with high potential of reaction to signals affecting the epigenome and initiating cascade pathways in response. Independently or in combination with the coexistent driver genetic mutations, especially of enzymes involved in epigenomic surveillance, intracellular microenvironmental alterations within the cell nuclear, cytoplasmic and mitochondrial compartments, can lead to disorganization of hematopoietic stem cells’ epigenome, promoting the generation of hematological malignancies. In this review, we discuss the various intracellular processes that, when disrupted, may result in the ectopic placement of RNA molecules, either inducing specific modifications or non-coding molecules, promoting hematological malignant phenotypes. The crosstalk between mitochondrial and nuclear genomes and the complex regulatory effects of mis-localized RNA molecules is highlighted. This research approach may constitute a field for new, more specifically targeted therapies in hematology, based on the RNA technology.

Biomarkers of bone turnover in serum are suggestive of bone dynamics during treatment in multiple myeloma (MM). We evaluated the role of daratumumab on bone remodeling among patients with relapsed/refractory MM in the prospective, open-label, phase 2 study REBUILD. Daratumumab was administered according to the approved indication. A total of 33 out of 57 enrolled patients completed 4 months of treatment. The median percent change from baseline to 4 months in C-terminal cross-linking telopeptide of type 1 collagen (CTX) (primary endpoint) was 3.9%, with 13 (39.4%) and 11 (33.3%) patients showing at least 20% and 30% reduction in CTX levels, respectively. The median percent decrease from baseline to 4 months in tartrate resistant acid phosphatase 5b (TRACP-5b) levels (co-primary endpoint) was 2.6%, with 10 (30.3%) and 6 (18.2%) patients showing at least 20% and 30% reduction in TRACP-5b levels, respectively. However, the changes in these markers of bone catabolism were not statistically significant. Furthermore, the levels of osteocalcin, bone-specific alkaline phosphatase and procollagen type-I N-pro-peptide (bone formation markers) increased from baseline to 4 months (secondary endpoints) by 18.4%, 92.6% and 10.2%, respectively. Furthermore, the median levels of dickkopf-1 and C-C motif ligand-3 showed a significant decrease at 4 months by 17.5% and 16.0%, respectively. In conclusion, daratumumab improved bone turnover by inducing bone formation and reducing osteoblast inhibition.