Abstract: Stem cell maturation is a fundamental, yet poorly understood aspect of human development. A DNA methylation signature deeply reminiscent of embryonal stem cells was devised to interrogate the evolving character of multiple human tissues. The cell fraction displaying the signature was found to be highly dependent upon developmental stage (fetal vs adult) and in leukocytes, it described a dynamic transition during the first 5 years of life. Significant individual variation in the embryonic signature of leukocytes was evident at birth, in childhood, and throughout adult life. The genes denoting the signature included transcription factors and proteins intimately involved in embryonic development. The DNA methylation signature traces the developmental origin of cells and informs the study of stem cell heterogeneity in humans under homeostatic and pathologic conditions.

Abstract: There are currently no screening tests in routine use for oral and pharyngeal cancer beyond visual inspection and palpation. Described is an improve method of detecting oral and pharyngeal cancer with a saliva sample from a subject. The method includes identifying the presence or absence of a methylation classifier in the saliva the sample. The methylation classifier is determined by the methylation status of a panel of CpG islands in the sample. In an embodiment, the methylation classifier is determined by the methylation status of between 15 and 25 CpG islands, or alternatively, 22 CpG islands. The presence of the methylation classifier indicates a diagnosis of cancer in the subject. In an embodiment, the presence of the methylation classifier is determined with a bisulfite method of determining methylation status of the CpG islands.

Abstract: Methods of diagnosing a carcinoma include comparing the expression of miRNAs in a sample with a control and determining ratios of expression of miRNAs. Methods of treatment include administering a nucleic acid encoding a miR-375 gene product. Methods of optimizing treatment in a subject include determining expression of an miR21-gene product.

Abstract: A method of employing DNA methylation analysis for the diagnosis, prognosis, and prediction of cancer.

Abstract: Disclosed herein are compositions and methods for detecting one or more markers indicative of cancer. In one instance the marker is one or more methylated genes, such as SFRPs. In another instance the marker is an altered protein, such as p53.