Pleiotropy refers to the phenomenon of a single mutation or gene affecting multiple distinct phenotypic traits and has broad implications in many areas of biology. Due to its central importance, pleiotropy has also been extensively modeled, albeit with virtually no empirical basis. Analyzing phenotypes of large numbers of yeast, nematode, and mouse mutants, we here describe the genomic patterns of pleiotropy. We show that the fraction of traits altered appreciably by the deletion of a gene is minute for most genes and the gene-trait relationship is highly modular. The standardized size of the phenotypic effect of a gene on a trait is approximately normally distributed with variable SDs for different genes, which gives rise to the surprising observation of a larger per-trait effect for genes affecting more traits. This scaling property counteracts the pleiotropy-associated reduction in adaptation rate (i.e., the "cost of complexity") in a nonlinear fashion, resulting in the highest adaptation rate for organisms of intermediate complexity rather than low complexity. Intriguingly, the observed scaling exponent falls in a narrow range that maximizes the optimal complexity. Together, the genome-wide observations of overall low pleiotropy, high modularity, and larger per-trait effects from genes of higher pleiotropy necessitate major revisions of theoretical models of pleiotropy and suggest that pleiotropy has not only allowed but also promoted the evolution of complexity.genetics | adaptation | modularity | yeast | phenotype

Endometrial carcinoma is one of the most common malignancies of the female genital tract, and there is an urgent need for discovery of novel factors for prognostic assessment and therapeutic targets to endometrial carcinoma. Herein a two-dimensional gel electrophoresis and MALDI-Q-TOF MS/MS-based proteomics approach was used to identify differentially expressed proteins in endometrial carcinoma. Of the 99 proteins identified, cyclophilin A was one of the most significantly altered proteins, and its overexpression was confirmed using RT-PCR and Western blot analyses. Immunohistochemistry suggested a link between cyclophilin A expression and poor differentiation and decreased survival (p < 0.01). Knockdown of cyclophilin A expression by RNA interference led to the significant suppression of the cell growth and the induction of apoptosis in endometrial carcinoma HEC-1-B cells in vitro (p < 0.01) and the inhibition of tumor growth in vivo (p < 0.01). These data suggest that cyclophilin A may serve as a novel prognostic factor and possibly an attractive therapeutic target for endometrial carcinoma.

This work demonstrates that a comprehensive strategy of proteomics identification combined with further validation and detailed functional analysis should be adopted in the field of cancer biomarker discovery. A comparative proteomics approach was utilized to identify differentially expressed proteins in 10 oral squamous carcinoma samples paired with their corresponding normal tissues. A total of 52 significantly and consistently altered proteins were identified with eight of these being reported for the first time in oral squamous carcinoma. Of the eight newly implicated proteins, RACK1 was chosen for detailed analysis. RACK1 was demonstrated to be up-regulated in cancer at both the mRNA and protein levels. Immunohistochemical examination showed that the enhanced expression of RACK1 was correlated with the severity of the epithelial dysplasia as well as clinical stage, lymph node involvement, and recurrence, which are known indicators of a relatively poor prognosis in oral squamous carcinoma patients. RNA interference specifically targeted to silence RACK1 could initiate apoptosis of oral squamous carcinoma cells. Taken together, the results indicate that RACK1 is up-regulated in oral squamous carcinoma, not only being closely related to cell proliferation and apoptosis but also linked to clinical invasiveness and metastasis in carcinogenesis. The observations suggest that RACK1 may be a potential biomarker for early diagnosis, prognosis, and monitoring in the therapy of oral squamous carcinoma. Further this comprehensive strategy could be used for identifying other differentially expressed proteins that have potential to be candidate biomarkers of oral squamous carcinoma.

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Post-operative IMRT following narrow-margin hepatectomy may be a favourable therapy for both its safety profile and clinical benefit in patients with HCC located close to the major vessels.

Tertiary lymphoid structures (TLS) are ectopic lymphoid structures in cancers that are largely associated with favourable prognosis. However, the prognostic value of TLSs in oral squamous cell carcinoma (OSCC) is largely unknown, and the association between tumour infiltrating lymphocytes (TILs) and TLSs has been rarely explored in OSCC. In this study, associated markers of TLS, including peripheral node address (PNAd) in high endothelial venules, CD20 in B cells and CD3 in T cells, were examined in 168 OSCC patients, and survival analysis was performed between TLS-positive and TLS-negative cohorts. We detected the presence of TILs by staining CD8+ cytotoxic T cells and CD57+ NK cells as well. TLSs appeared as highly organized structures in 45 (26.8%) cases. TLS-positive patients had a better 5-year overall survival (OS) rate (88.9% vs. 56.1%, P < 0.001) and relapse-free survival (RFS) rate (88.9% vs. 63.4%, P = 0.002). Moreover, the presence of TLS was an independent prognostic factor for both the 5-year OS rate (hazard ratio [HR] = 3.784; 95% confidence interval [CI], 1.498–9.562) and RFS rate (HR = 3.296; 95% CI, 1.279–8.490) in multivariate analysis. Furthermore, a higher density of CD8+ T cells and CD57+ NK cells was found in TLS-positive sections than in TLS-negative counterparts (P < 0.001), and their combination provided a higher predictive accuracy (AUC = 0.730; 95% CI, 0.654–0.805). In conclusion, our results suggest that TLS is an independent positive prognostic factor for OSCC patients. These findings provide a theoretical basis for the future diagnostic and therapeutic value of TLSs in OSCC treatment.

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HER2/ErbB2, an epidermal growth factor receptor-related tyrosine kinase, is overexpressed on the surface of a variety of tumors of epithelial origin, such as breast tumors, ovarian carcinomas, and gastric tumors, and therefore constitutes an ideal therapeutic target (1-3). Among the many advances in the development of HER2-targeted cancer therapy over the past decade (4 -7), antibody-based strategies (e.g. herceptin (trastuzumab) (8 -10), intracellular antibody (11, 12), and fusion proteins for targeted delivery of various classes of therapeutic agents (13-17)) are especially notable. Our previous studies exploited the in vitro and in vivo cytotoxicity of immunotoxins by generating a new class of antigen-specific killer cells (18,19), but this approach may well be limited in its clinical applications because of antigenicity of heterogeneous toxin protein. Hence, our attention turned to human endogenous proteins, especially those acting as executioners during apoptosis, which in principle should be optimal candidates for triggering the death of tumor cells in an intrinsic physiological manner.Granzymes are a family of granular serine proteinases produced by cytotoxic T lymphocytes and natural killer cells, with a triad of key residues, histidine, aspartate, and serine, conserved at the catalytic site (20, 21). One member of the family, granzyme B (GrB), 1 plays an essential role in granule-mediated killing. GrB is originally synthesized as zymogen and activated by removal of the amino-terminal signal peptide and an acidic dipeptide after lymphocyte receptor recognition (21). The active GrB (GrBa) is then released from leukocyte granules by exocytosis, entering target cells to cause extensive proteolysis at specific amino acid residues (22, 23). GrB-mediated apoptosis involves the caspase-dependent pathway, direct nuclear entry, and caspase-independent pathways (24 -28). The potential of GrB therapy to induce multiple apoptotic pathways makes this approach to tumor cell killing especially attractive.In our most recent previous study, chimeric immunocasp-3 protein was shown to have a potent selective antitumor effect both in vitro and in vivo (29). This result led us to another targeted pro-apoptotic fusion protein, designated immunoGrB, which consisted of a single-chain anti-HER2 antibody, e23sFv (30, 31), a Pseudomonas exotoxin A (PE) translocation domain (32-35), and active GrB (GrBa) (21). The recombinant immunoGrB molecule was predicted to bind to tumor cells overexpressing HER2 and be internalized, such that endosomal cleavage would give rise to the active granzyme B domain that would consequently translocate into the cytosol to induce tumor cell death (18,19,29). Here we evaluate the antitumor activity of immunoGrB and immunoGrB-secreting lymphocytes in both in vitro and in vivo models. EXPERIMENTAL PROCEDURESConstruction of Expression Plasmids-The human GrB gene was obtained by reverse-transcription PCR from total RNA derived from healthy human peripheral blood mononuclear cells (PBMCs) following stimulatio...