Bioinformatics and Raman spectroscopy-based identification of key pathways and genes enabling differentiation between acute myeloid leukemia and T cell acute lymphoblastic leukemia.

Acute myeloid leukemia (AML) and T cell acute lymphoblastic leukemia (T-ALL) are two of the most prevalent hematological malignancies diagnosed among adult leukemia patients, with both being difficult to treat and associated with high rates of recurrence and mortality. In the present study, bioinformatics approaches were used to analyze both of these types of leukemia in an effort to identify characteristic gene expression patterns that were subsequently validated via Raman spectroscopy. For these analyses, four Gene Expression Omnibus datasets (GSE13204, GSE51082, GSE89565, and GSE131184) pertaining to acute leukemia were downloaded, and differentially expressed genes (DEGs) were then identified through comparisons of AML and T-ALL patient samples using the R Bioconductor package. Shared DEGs were then subjected to Gene Ontology (GO) enrichment analyses and were used to establish a protein-protein interaction (PPI) network analysis. In total, 43 and 129 upregulated and downregulated DEGs were respectively identified. Enrichment analyses indicated that these DEGs were closely tied to immune function, collagen synthesis and decomposition, inflammation, the synthesis and decomposition of lipopolysaccharide, and antigen presentation. PPI network module clustering analyses further led to the identification of the top 10 significantly upregulated and downregulated genes associated with disease incidence. These key genes were then validated in patient samples via Raman spectroscopy, ultimately confirming the value of these genes as tools that may aid the differential diagnosis and treatment of AML and T-ALL. Overall, these results thus highlight a range of novel pathways and genes that are linked to the incidence and progression of AML and T-ALL, providing a list of important diagnostic and prognostic molecular markers that have the potential to aid in the clinical diagnosis and treatment of these devastating malignancies.

Application of serum Raman spectroscopy in rapid and early discrimination of aplastic anemia and myelodysplastic syndrome.

BACKGROUND: Raman spectroscopy of hematological diseases has gained attention from various researchers. However, serum analysis of bone marrow failure (BMF), represented by aplastic anemia (AA) and myelodysplastic syndromes (MDS) has not been fully investigated. In this study, we aimed at establishing a simple, non-invasive serum detection method for AA and MDS. METHOD: Serum samples from 35 AA patients (N = 35), MDS patients (N = 25), and control volunteers (N = 23) were systematically analyzed via laser Raman spectroscopy, and orthogonal partial least squares discrimination analysis (OPLS-DA). Then, discrimination models between the BMFs and control were constructed and evaluated using the prediction set. RESULTS: Compared to control volunteers, serum spectral data for BMF patients were specific. The intensities of Raman peaks representing nucleic acids (726, 781, 786, 1078, 1190, 1415 cm-1), proteins (1221 cm-1), phospholipid/cholesterol (1285 cm-1), and ß-carotene (1162 cm-1) significantly decreased, while the intensity of lipids (1437 and 1446 cm-1) significantly increased. Intensities of Raman peaks representing nucleic acids (726 cm-1) and collagen (1344 cm-1) in the AA group were significantly lower than in the control group. Intensities of Raman peaks representing nucleic acids (726 and 786 cm-1), proteins (1003 cm-1), and collagen (1344 cm-1) in the MDS group were significantly lower than those of the control group. The intensity of Raman peaks representing lipids (1437 and 1443 cm-1) in the MDS group was significantly higher than in the control group. Patients with AA and MDS exhibited increased serum triglyceride levels and decreased high-density lipoprotein levels. CONCLUSIONS: The relationship between serological test data for patients and typing of AA and MDS provides essential information for rapid and early identification of BMF. This study shows the potential of Raman spectroscopy for non-invasive detection of different BMF types.

Elucidating the Heterogeneity of Serum Metabolism in Patients with Myelodysplastic Syndrome and Acute Myeloid Leukemia by Raman Spectroscopy.

Myelodysplastic syndrome (MDS) is difficult to diagnose and classify because it has the potential to evolve into acute myeloid leukemia (AML). Raman spectroscopy and orthogonal partial least squares discrimination analysis (OPLS-DA) are used to systematically analyze peripheral blood serum samples from 33 patients with MDS, 25 patients with AML, and 29 control volunteers to gain insight into the heterogeneity of serum metabolism in patients with MDS and AML. AML patients show unique serum spectral data compared to MDS patients with considerably greater peak intensities of collagen (859 and 1345 cm-1) and carbohydrate (920 and 1123 cm-1) compared to MDS patients. Screening and bioinformatics analysis of MDS- and AML-related genes based on the Gene Expression Omnibus (GEO) database shows that 1459 genes are differentially expressed, and the main signaling pathways are related to Th17 cell differentiation, pertussis, and cytokine receptor interaction. Statistical analysis of serological indexes related to glucose and lipid metabolism shows that patients with AML have increased serum triglyceride (TG) levels and decreased total protein levels. This study provides a spectral basis for the relationship between the massive serological data of patients and the typing of MDS and AML and provides important information for the rapid and early identification of MDS and AML.

Elucidating the mitochondrial function of murine lymphocyte subsets and the heterogeneity of the mitophagy pathway inherited from hematopoietic stem cells.

Background: Mitochondria are mainly involved in ATP production to meet the energy demands of cells. Researchers are increasingly recognizing the important role of mitochondria in the differentiation and activation of hematopoietic cells, but research on how mitochondrial metabolism influence different subsets of lymphocyte at different stages of differentiation and activation are yet to be carried out. In this work, the mitochondrial functions of lymphocytes were compared at different differentiation and activation stages and included CD8+ T lymphocytes, CD4+ T lymphocytes, B lymphocytes, NK cells as well as their subsets. For this purpose, a complete set of methods was used to comprehensively analyze mitophagy levels, mitochondrial reactive oxygen species (ROS), mitochondrial membrane potential (MMP) and the mitochondrial mass (MM) of subsets of lymphocytes. It is expected that this will provide a complete set of standards, and drawing the mitochondrial metabolic map of lymphocyte subsets at different stages of differentiation and activation. Results and discussion: Of all lymphocytes, B cells had a relatively high mitochondrial metabolic activity which was evident from the higher levels of mitophagy, ROS, MMP and MM, and this reflected the highly heterogeneous nature of the mitochondrial metabolism in lymphocytes. Among the B cell subsets, pro-B cells had relatively higher levels of MM and MMP, while the mitochondrial metabolism level of mature B cells was relatively low. Similarly, among the subsets of CD4+ T cell, a relatively higher level of mitochondrial metabolism was noted for naive CD4+ T cells. Finally, from the CD8+ T cell subsets, CD8+ Tcm had relatively high levels of MM and MMP but relatively low ones for mitophagy, with effector T cells displaying the opposite characteristics. Meanwhile, the autophagy-related genes of lymphoid hematopoietic cells including hematopoietic stem cells, hematopoietic progenitor cells and lymphocyte subsets were analyzed, which preliminarily showed that these cells were heterogeneous in the selection of mitophagy related Pink1/Park2, BNIP3/NIX and FUNDC1 pathways. The results showed that compared with CD4+ T, CD8+ T and NK cells, B cells were more similar to long-term hematopoietic stem cell (LT-HSC) and short-term hematopoietic stem cell (ST-HSC) in terms of their participation in the Pink1/Park2 pathway, as well as the degree to which the characteristics of autophagy pathway were inherited from HSC. Compared with CLP and B cells, HSC are less involved in BNIP3/NIX pathway. Among the B cell subsets, pro-B cells inherited the least characteristics of HSC in participating in Pink1/Park2 pathway compared with pre-B, immature B and immature B cells. Among CD4+ T cell subsets, nTreg cells inherited the least characteristics of HSC in participating in Pink1/Park2 pathway compared with naive CD4+ T and memory CD4+ T cells. Among the CD8+ T cell subsets, compared with CLP and effector CD8+ T cells, CD8+ Tcm inherit the least characteristics of HSC in participating in Pink1/Park2 pathway. Meanwhile, CLP, naive CD4+ T and effector CD8+ T were more involved in BNIP3/NIX pathway than other lymphoid hematopoietic cells. Conclusion: This study is expected to provide a complete set of methods and basic reference values for future studies on the mitochondrial functions of lymphocyte subsets at different stages of differentiation and activation in physiological state, and also provides a standard and reference for the study of infection and immunity based on mitochondrial metabolism.