RNA sequencing analysis of hepatocellular carcinoma identified oxidative phosphorylation as a major pathologic feature.

Dysregulation of expression of functional genes and pathways plays critical roles in the etiology and progression of hepatocellular carcinoma (HCC). Next generation-based RNA sequencing (RNA-seq) offers unparalleled power to comprehensively characterize HCC at the whole transcriptome level. In this study, 17 fresh-frozen HCC samples with paired non-neoplastic liver tissue from Caucasian patients undergoing liver resection or transplantation were used for RNA-seq analysis. Pairwise differential expression analysis of the RNA-seq data was performed to identify genes, pathways, and functional terms differentially regulated in HCC versus normal tissues. At a false discovery rate (FDR) of 0.10, 13% (n = 4335) of transcripts were up-regulated and 19% (n = 6454) of transcripts were down-regulated in HCC versus non-neoplastic tissue. Eighty-five Kyoto Encyclopedia of Genes and Genomes pathways were differentially regulated (FDR, <0.10), with almost all pathways (n = 83) being up-regulated in HCC versus non-neoplastic tissue. Among the top up-regulated pathways was oxidative phosphorylation (hsa00190; FDR, 1.12E-15), which was confirmed by Database for Annotation, Visualization, and Integrated Discovery (DAVID) gene set enrichment analysis. Consistent with potential oxidative stress due to activated oxidative phosphorylation, DNA damage-related signals (e.g., the up-regulated hsa03420 nucleotide excision repair [FDR, 1.14E-04] and hsa03410 base excision repair [FDR, 2.71E-04] pathways) were observed. Among down-regulated genes (FDR, <0.10), functional terms related to cellular structures (e.g., cell membrane [FDR, 3.05E-21] and cell junction [FDR, 2.41E-07], were highly enriched, suggesting compromised formation of cellular structure in HCC at the transcriptome level. Interestingly, the olfactory transduction (hsa04740; FDR, 1.53E-07) pathway was observed to be down-regulated in HCC versus non-neoplastic tissue, suggesting impaired liver chemosensory functions in HCC. Our findings suggest oxidative phosphorylation and the associated DNA damage may be the major driving pathologic feature in HCC.

Autophagic Markers BECLIN 1 and LC3 are Associated with Prognosis of Multiple Myeloma.

BACKGROUND/AIMS: Autophagy is crucial for the survival and function of plasma cells including protection from toxic misfolded immunoglobulin and proper energy metabolism. Multiple myeloma (MM) is an indolent but eventually fatal neoplasm of plasma cells. Autophagy may play a critical role in the survival of MM cells and their response to chemotherapeutic agents. In this study, we correlated the expression of autophagy-related proteins with the prognosis of MM. METHODS: In this retrospective cohort study, we examined the expression of the autophagic markers BECLIN 1 and microtubule-associated protein light chain 3 (LC3) in 89 cases of MM biopsied from 2001 to 2004 at the Asan Medical Center. The association of the expression scores of these markers with clinical outcomes was assessed. RESULTS: Patients with strong immunoreactivity to BECLIN 1 or LC3 had a significantly better overall survival (OS) than patients with negative to moderate immunoreactivity (p = 0.036 and 0.018, respectively). This was also true for disease-specific survival (DSS; p = 0.051 and 0.043, respectively). In addition, LC3 immunostaining remained an independent factor impacting OS (p = 0.028) and DSS (p = 0.020) after multivariate analysis. CONCLUSIONS: The results of this study suggest that higher immunoreactivity for autophagic markers in MM is associated with superior patient survival.

Expression of CD99 in Multiple Myeloma: A Clinicopathologic and Immunohistochemical Study of 170 Cases.

BACKGROUND: Multiple myeloma (MM) is a heterogeneous and ultimately fatal disease. Risk stratification using prognostic biomarkers is crucial to individualize treatments. We sought to investigate the role of CD99, a transmembrane protein highly expressed in many hematopoietic cells including subpopulations of normal and neoplastic plasma cells, for MM risk stratification. METHODS: CD99 expression was measured in paraffin samples of bone marrow and extramedullary biopsies of 170 patients with MM. Patients were divided into those with high score (moderately and strongly positive) and low score (negative and weakly positive), with all staining being cytoplasmic and/or membranous. RESULTS: High anti-CD99 immunostaining was observed in 72 of 136 (52.9%) bone marrow biopsies and 24 of 87 (27.6%) extramedullary biopsies in MM. High CD99 expression of extramedullary specimens was associated with significantly longer overall survival (OS; p=.016). High CD99 expression of extramedullary specimens was also associated with better prognosis in the nonautologous stem cell transplantation group of MM patients (p=.044). In multivariate analysis, International Staging System stage was an independent prognostic factor, whereas CD99 expression was no longer statistically significant. CONCLUSIONS: Expression of CD99 in extramedullary specimens was correlated with longer OS, suggesting that CD99 may be a helpful immunohistochemical marker for risk stratification.

Sleeping Beauty transposon system harboring HRAS, c-Myc and shp53 induces sarcomatoid carcinomas in mouse skin.

The Sleeping Beauty transposon system is used as a tool for insertional mutagenesis and oncogenesis. However, little is known about the exact histological phenotype of the tumors induced. Thus, we used immunohistochemical markers to enable histological identification of the type of tumor induced by subcutaneous injection of the HRAS, c-Myc and shp53 oncogenes in female C57BL/6 mice. The tumor was removed when it reached 100 mm3 in volume. Subsequently, we used 13 immunohistochemical markers to histologically identify the tumor type. The results suggested that the morphology of the tumor was similar to that of sarcomatoid carcinoma.

Long-term clinical outcome of the surgically resected intraductal papillary neoplasm of the bile duct.

BACKGROUND & AIMS: Intraductal papillary neoplasm of the bile duct (IPNB) is a biliary neoplasm with predominant intraductal papillary growth and various degrees of malignant transformation. Although IPNB has been recently added to the WHO classification, the classification system needs refinements. METHODS: We retrospectively reviewed 93 non-invasive and invasive IPNB cases, surgically resected from 1996 to 2006. To further characterize their biologic behavior, we modified the WHO classification into a 4-tier category system in which non-invasive IPNB cases with complex fused or cribriform papillae were separately designated. Epithelial types such as intestinal, gastric, pancreatobiliary, and oncocytic type were determined by morphology and mucin core protein immunohistochemistry. Resection margins were classified based on their microscopic appearances. The prognostic values of mucinous histology and MUC1 protein expression were also determined. RESULTS: IPNB with complex fused or cribriform papillae showed a worse prognosis than IPNB with simple papillae and one such case showed a metachronous metastasis. In addition, a positive surgical margin including dysplasia was associated with worse outcomes. Among the invasive IPNB cases, MUC1-positive tumors were more aggressive than MUC1-negative tumors. CONCLUSIONS: We propose that non-invasive IPNB with complex fused or cribriform papillae might be better classified as mucosa-confined cholangiocarcinoma rather than IPNB with high grade dysplasia. In addition, aggressive further resection is recommended when a positive surgical margin including dysplasia is reported during intraoperative histopathological evaluation.

Are elastic stain and specialty sign out necessary to evaluate pleural invasion in lung cancers?

The seventh edition of American Joint Committee on Cancer (AJCC) staging system assigns lung cancers with visceral pleural invasion in the tumor size of 3 cm or less than 3 cm as T2 and without pleural invasion as T1. However, it may be difficult to distinguish with certainty between PL0 (no pleural invasion) and PL1 (extends through the elastic layer) on routine hematoxylin and eosin (H&E) stain. In this study, 25 cases of peripherally located lung adenocarcinoma were retrieved from the surgical pathology archives at the Asan Medical Center from May through June 2009. One representative H&E-stained slide was selected from each case and circulated to 31 pathology trainees and board-certified pathologists at Asan Medical Center who evaluated presence or absence of pleural invasion on H&E-stained slides. Elastic stain was used to determine the final status of pleural invasion for each case. The concordance rate of all pathologists with elastic stain results was, overall, 60.5%. The concordance rate of 2 lung specialists was 64%, better than the remaining faculty (54.7%). Fellows' and residents' evaluations were slightly more concordant than those of faculty responses (faculty overall, 56.4%; fellows, 62%; residents, 63.6%), but this difference was not statistically significant (P = .228). Our results confirm that pleural invasion status is difficult to discern with certainty on H&E-stained sections alone. Therefore, we recommend the routine use of elastic stain in evaluation of pleural invasion in all peripherally located lung cancers. Furthermore, our study indicates that subspecialty sign out may be preferable in evaluation of pleural invasion status.