Gene expression profiling of human plasma cell differentiation and classification of multiple myeloma based on similarities to distinct stages of late-stage B-cell development

To identify genes linked to normal plasma cell (PC) differentiation and to classify multiple myeloma (MM) with respect to the expression patterns of these genes, we analyzed global mRNA expression in CD19-enriched B cells (BCs) from 7 tonsils, CD138-enriched PCs from 11 tonsils, 31 normal bone marrow samples, and 74 MM bone marrow samples using microarrays interrogating 6800 genes. Hierarchical clustering analyses with 3288 genes clearly segregated the 4 cell types, and chi-square and Wilcoxin rank sum tests (P <.0005) identified 359 and 500 previously defined and novel genes that distinguish tonsil BCs from tonsil PCs (early differentiation genes [EDGs]), and tonsil PCs from bone marrow PCs (late differentiation genes [LDGs]), respectively. MM as a whole was found to have dramatically variable expression of EDGs and LDGs, and one-way analysis of variance (ANOVA) was used to identify the most variable EDGs (vEDGs) and LDGs (v1LDG and v2LDG). Hierarchical cluster analysis with these genes revealed that previously defined MM gene expression subgroups (MM1-MM4) could be linked to one of the 3 normal cell types. Clustering with 30 vEDGs revealed that 13 of 18 MM4 cases clustered with tonsil BCs (P =.000 05), whereas 14 of 15 MM3 cases clustered with tonsil PCs when using 50 v1LDG (P =.000 008), and 14 of 20 MM2 cases clustered with bone marrow PCs when using 50 v2LDG (P =.000 09). MM1 showed no significant linkage with normal cell types studied. Thus, genes whose expression is linked to distinct transitions in late-stage B-cell differentiation can be used to classify MM.     

Gene expression profiles of different clinical stages of colorectal carcinoma: toward a molecular genetic understanding of tumor progression

Background and aims Colorectal cancer is one of the leading causes of cancer deaths in the Western world. A better understanding of the development and progression of colorectal carcinoma is needed to define novel targets and strategies for treatment.Patients/methods Gene expression profiles were determined for primary tumors of 10 locally restricted (T3N0M0), 8 lymphatically metastasized (T3N+M0), 7 systemically metastasized (T3N+M1) colorectal carcinomas, and 6 specimens of normal colorectal tissue by histology-guided oligonucleotide microarray analysis.Results A total of 1,995 genes were differently regulated in primary tumors of colorectal carcinoma compared with normal colorectal tissue. Besides common features of dedifferentiation and different expression of genes involved in cell division, cell adhesion, angiogenesis, signal transduction and metabolism we observed a deregulation of genes with an as yet unclear function. We identified 126 genes that were subsequently up- and 204 genes down-regulated during tumor progression. Furthermore, we found a cluster of five genes exclusively up-regulated in primary tumors of systemically metastasized colorectal carcinomas. A comparison of locally restricted (T3N0M0) and systemically metastasized (T3N+M1) primary tumors showed 50 deregulated genes with a massive down-regulation of immune-modulatory genes in primary tumors of systemically metastasized carcinomas. Primary tumors of lymphatically (T3N+M0) and systemically metastasized (T3N+M1) carcinomas differed in the expression of 19 genes.Conclusion These results provide an additional step toward the identification of crucial genes for the progression of colorectal cancer and the identification of novel treatment targets or strategies.     

Gene expression profiling of diffuse large B-cell lymphoma supervised by CD21 expression

This study investigated the gene expression profiles of 40 cases of diffuse large B-cell lymphoma (DLBCL) according to CD21 expression, a favourable prognostic factor in DLBCL. Signature genes were analysed by Gene Ontology Tree Machine, and genes concerned with the immune system and related categories were significantly upregulated in CD21⁻ DLBCLs. Of 40 DLBCLs, four were germinal centre B cell-like (GCB) and 36 non-GCB. Of the 36 non-GCB DLBCLs, 14 CD21⁺ DLBCLs showed significantly better overall survival than the 22 CD21⁻ DLBCLs ( P  =   0·036). Hierarchical cluster analysis of signature genes related to CD21 was applied to previously published data sets, resulting in two groups for each data set, CD21⁺ type DLBCLs and CD21⁻ type DLBCLs. Survival of CD21⁺ type DLBCLs was significantly better than that of CD21^– type ( P  =   0·006 and P  =   0·004, respectively). In both data sets, CD21⁺ type DLBCLs predominantly included GCB DLBCLs compared with CD21⁻ type. The top classifier gene of CD21 expression was IGHM, and the five of nine Gene Ontology categories significant in CD21^– DLBCLs included IGHM . Immunohistochemical analysis of 216 DLBCLs confirmed that overall survival of surface (s) IgM⁺ DLBCLs was significantly poorer than that of sIgM^- DLBCLs ( P  =   0·013).     

Relationship between CD45 antigen expression and putative stages of differentiation in B-cell malignancies.

The cell-surface antigen CD45 is a complex family of high-molecular-weight glycoproteins expressed on all lymphohematopoietic cells, but not in the same molecular isoform. This antigen complex is known to exhibit protein tyrosine phosphatase (PTPase) activity and appears to have a role in regulation of cell differentiation. In that CD45 expression parallels stages of differentiation in normal bone marrow B cells, it was of interest to evaluate this process in malignant B cells. Monoclonal antibodies (MoAbs) were used to investigate the quantitative expression of CD45 and CD45RA on the B cells of lymphoid leukemias. Employing standardized flow cytometric methods, it was found that the fluorescence intensity (FI) of immunostained malignant B cells, as a reflection of the antigen content, demonstrated correlations with the putative stage of cell differentiation for malignancies at the earlier stages, but at the later stages, a progressive loss of CD45 was observed. Since this antigen family has been found to display PTPase activity, further investigation of CD45 alterations in malignancies may provide insight into potential regulatory disturbances.     

Numerical simulation of two consecutive nasal respiratory cycles: toward a better understanding of nasal physiology

Background

Computational fluid dynamic (CFD) simulations have greatly improved the understanding of nasal physiology. We postulate that simulating the entire and repeated respiratory nasal cycles, within the whole sinonasal cavities, is mandatory to gather more accurate observations and better understand airflow patterns.

Methods

A 3‐dimensional (3D) sinonasal model was constructed from a healthy adult computed tomography (CT) scan which discretized in 6.6 million cells (mean volume, 0.008 mm³). CFD simulations were performed with ANSYS©FluentTMv16.0.0 software with transient and turbulent airflow (k‐ω model). Two respiratory cycles (8 seconds) were simulated to assess pressure, velocity, wall shear stress, and particle residence time.

Results

The pressure gradients within the sinus cavities varied according to their place of connection to the main passage. Alternations in pressure gradients induced a slight pumping phenomenon close to the ostia but no movement of air was observed within the sinus cavities. Strong movements were observed within the inferior meatus during expiration contrary to the inspiration, as in the olfactory cleft at the same time. Particle residence time was longer during expiration than inspiration due to nasal valve resistance, as if the expiratory phase was preparing the next inspiratory phase. Throughout expiration, some particles remained in contact with the lower turbinates. The posterior part of the olfactory cleft was gradually filled with particles that did not leave the nose at the next respiratory cycle. This pattern increased as the respiratory cycle was repeated.

Conclusion

CFD is more efficient and reliable when the entire respiratory cycle is simulated and repeated to avoid losing information.

     

Gene expression profiling of the response of esophageal carcinoma cells to cisplatin

SUMMARY.  Cisplatin is the most common chemotherapeutic agent used in esophageal cancer. However, sensitivity to cisplatin varies greatly between patients. It is important to identify the gene(s) that are related to the sensitivity to cisplatin in esophageal cancer patients. The IC50 for cisplatin was measured for 15 esophageal cancer cell lines (TE1–5, TE8–15, KYSE140, and KYSE150). RNA was extracted from each of these cell lines and a normal esophageal epithelial cell line, namely, Het1A, and gene expression profiles were analyzed using an oligonucleotide microarray consisting of 34 594 genes. TE4 was highly resistant and TE12, 14, and 15 were sensitive to cisplatin. Thirty-seven genes were differentially expressed in the cisplatin-resistant esophageal cancer cell line. Our investigation provides a list of candidate genes that may be associated with resistance to cisplatin in esophageal cancer cells, which may serve as a basis for additional functional studies.