Abstract: The present invention provides methods of treating or suppressing Adenoid Cystic Carcinoma (ACC) or inhibiting ACC tumor growth in subjects by administering compositions comprising bisfluoroalkyl-1,4-benzodiazepinone compounds, including compounds of Formula (III) or prodrugs thereof.

Abstract: Methods for preventing or treating subjects having cancer based on the identification of pharmaceutical agents that target cancer stem cells (CSCs) have been identified. These methods include administering to the subject an effective amount of a COX2 inhibitor and an effective amount of a YAP1 inhibitor. In addition, methods of enhancing chemotherapeutic responses in cancer patients have been discovered and are described herein.

Abstract: Methods for preventing or treating subjects having cancer based on the identification of pharmaceutical agents that target cancer stem cells (CSCs) have been identified. These methods include administering to the subject an effective amount of a COX2 inhibitor and an effective amount of a YAP1 inhibitor. In addition, methods of enhancing chemotherapeutic responses in cancer patients have been discovered and are described herein.

Abstract: An experiment has shown that ranpirnase is a microbicide. It is believed that topical application of a topical pharmaceutical composition consisting essentially of a prophylactically effective concentration of an enzymatically-active ribonuclease (e.g. ranpirnase) and a viscous vehicle that does not unacceptably interfere with the enzymatic activity (e.g. K-Y® Brand Jelly) will prophylactically protect an individual from a sexually-transmitted viral infection, particularly HIV. It is also believed that e.g. ranpirnase can be delivered to tissues of an individual who is to be prophylactically protected against viral infections by transfecting ranpirnase DNA into human microbiota and exposing the individual to the thus-modified human microbiota. It is also believed that ranpirnase can be delivered to a woman who is to be prophylactically protected against a sexually-transmitted viral infection by use of an intravaginal ring that has been impregnated with ranpirnase.

Abstract: The present invention provides methods for identifying the susceptibility of a cancer cell or population of cells to treatment with Epidermal Growth Factor (EGF) Tyrosine Kinase Inhibitors (TKIs), such as erlotinib. Methods for the in vitro diagnosis of the susceptibility of a tumor in a subject to treatment with TKIs and monitoring tumor susceptibility during treatment are also provided.

Abstract: In accordance with one or more embodiments, the inventors have conducted the first comprehensive integrated genomic and epigenomic analysis in HNSCC, focusing on identifying genes that have concurrent promoter methylation, mutation and expression downregulation. The intersection of unbiased genome-wide methylation sequencing and methylation array screens uncovered 316 genes, which undergo promoter methylation in HNSCC. Close to 60% concordance was found between concurrent greater promoter methylation and gene downregulation, with PAX1 and PAX5 exhibiting the greatest expression loss. Methods for analyzing tissue samples from a subject for increased risk of poor survival outcomes from HNSCC are provided. Kits for measuring promoter methylation of the genes are also provided.

Abstract: Methods and kits for triaging a human papillomavirus (HPV)-positive woman into colposcopy are disclosed. The methods comprise determining the promoter methylation level of the promoter regions of a group of genes (e.g., viral and host genes) that exhibit increased promoter methylation in women having CIN2+ lesions as compared to women having no intraepithelial lesions or malignancy (NILM).

Abstract: Methods for preventing or treating subjects having cancer based on the identification of pharmaceutical agents that target cancer stem cells (CSCs) have been identified. These methods include administering to the subject an effective amount of a COX2 inhibitor and an effective amount of a YAP1 inhibitor. In addition, methods of enhancing chemotherapeutic responses in cancer patients have been discovered and are described herein.

Abstract: Methods and kits for triaging a human papillomavirus (HPV)-positive woman into colposcopy are disclosed. The methods comprise determining the promoter methylation level of the promoter regions of a group of genes (e.g., viral and host genes) that exhibit increased promoter methylation in women having CIN2+ lesions as compared to women having no intraepithelial lesions or malignancy (NILM).

Abstract: Methods for analyzing the bacterial microbiome of a subject and triaging the subject into treatment for head and neck squamous cell cancer from a saliva or tissue sample are provided. The methods also provide means for differentiation of different cancer patient cohorts from the bacterial microbiome of a subject.

Abstract: Methods for the quantifying HPV Trans Renal DNA (TrDNA) from a urine sample from a subject using a dual sequence-capture approach are disclosed. The presently disclosed methods can be used to predict cancers including, but not limited to, cervical, anal, penile, and oropharyngeal cancers.

Abstract: The present invention provides arrays for gene loci that allow diagnosis of cervical cancer in patients who may be asymptomatic or have inconclusive Pap smears or cytology, and allowing earlier diagnosis and treatment of the subject. The present invention also provides methods of determination of a global promoter DNA methylation in a cervical tissue sample from a subject, using a variety of methods which can detect DNA methylation. Further, the invention provides methods of diagnosis of cervical cancer in a subject, by comparing the global promoter DNA methylation in a cervical tissue sample obtained from a subject to the global promoter DNA methylation of standard controls.

Abstract: The present invention relates to the field of cancer. More specifically, the present invention provides methods and compositions useful in the diagnosis and treatment of head and neck squamous cell carcinoma. As described herein, and particularly in reference to the figures, the present inventors have discovered that OTUs and several microbial communities at different taxonomic levels discriminates HNSCC from normal control samples, HPV+ and HPV? samples and pre- vs. post-surgical treatment samples. Appropriate diagnostic and treatment strategies can be employed based on the identification of the microbiota in patients' saliva.

Abstract: The present invention provides methods for identifying the susceptibility of a cancer cell or population of cells to treatment with Epidermal Growth Factor (EGF) Tyrosine Kinase Inhibitors (TKIs), such as erlotinib. Methods for the in vitro diagnosis of the susceptibility of a tumor in a subject to treatment with TKIs and monitoring tumor susceptibility during treatment are also provided.

Abstract: In accordance with one or more embodiments, the inventors have conducted the first comprehensive integrated genomic and epigenomic analysis in HNSCC, focusing on identifying genes that have concurrent promoter methylation, mutation and expression downregulation. The intersection of unbiased genome-wide methylation sequencing and methylation array screens uncovered 316 genes, which undergo promoter methylation in HNSCC. Close to 60% concordance was found between concurrent greater promoter methylation and gene downregulation, with PAX1 and PAX5 exhibiting the greatest expression loss. Methods for analyzing tissue samples from a subject for increased risk of poor survival outcomes from HNSCC are provided. Kits for measuring promoter methylation of the genes are also provided.

Abstract: Differentially methylated oral squamous cell carcinoma (OSCC) biomarkers, identified in-vitro and validated in well-characterized surgical specimens, have shown poor clinical correlation in cohorts with different risk profiles. To overcome this lack of relevance we used the HumanMethylation27 BeadChip, publicly available methylation and expression array data, and Quantitative Methylation Specific PCR to uncover differential methylation in OSCC clinical samples with heterogeneous risk profiles. A two stage-design consisting of Discovery and Prevalence screens was used to identify differential promoter methylation and deregulated pathways in patients diagnosed with OSCC and head and neck squamous cell carcinoma. This Phase I Biomarker Development Trial identified a panel of differentially methylated genes in normal and OSCC clinical samples from patients with heterogeneous risk profiles. This panel may be useful for early detection and cancer prevention studies.

Abstract: The present invention provides arrays for gene loci that allow diagnosis of cervical cancer in patients who may be asymptomatic or have inconclusive Pap smears or cytology, and allowing earlier diagnosis and treatment of the subject. The present invention also provides methods of determination of a global promoter DNA methylation in a cervical tissue sample from a subject, using a variety of methods which can detect DNA methylation. Further, the invention provides methods of diagnosis of cervical cancer in a subject, by comparing the global promoter DNA methylation in a cervical tissue sample obtained from a subject to the global promoter DNA methylation of standard controls.

Abstract: The present invention provides methods of determination of a global DNA methylation index (GDMI) in a sample from a subject, using a variety of methods which can detect global, genome-wide, and gene-specific DNA methylation to create methylation portraits that can be used for early detection, diagnosis, and clinical management in the personalized medicine space. Further, the invention provides methods of diagnosis of cancer, including gastric cancer and hepatocellular cancer in a subject, by comparing the GDMI in a sample obtained from a subject to the methylation index of standard controls. These methods allow diagnosis of gastric carcinoma and liver cancer in patients who may be asymptomatic or have inconclusive pathology, and allowing earlier treatment of the subject.

Abstract: Pap smears and HPV infection tests do not distinguish between lesions that will progress to an invasive carcinoma and those that will not. We aimed to identify epigenetic biomarkers for diagnosis and progression monitoring of premalignant lesions in cervical cancer. Hypermethylated genes were identified as potential biomarkers after validation by MSP, including GGTLA4 and ZNF516. The methylation frequency for these two genes was higher in tumor: GGTLA4 (100%) and ZNF516 (96%); than in normal samples: GGTLA4 (12%) and ZNF516 (16%). The methylation status of GGTLA4 showed a progression in methylation frequency from normal samples to invasive carcinoma. The immunohistochemical expression was lower in tumor for both: GGTLA4 (50.8%) and ZNF516 (66.2%); than in normal samples: GGTLA4 (71.2%) and ZNF516 (88.1%) (p<0.05). In conclusion, we identified methylation biomarkers for the molecular screening and characterization of cervical cancer.

Abstract: As described in more detail below, the present invention generally features compositions and non-invasive methods useful for the screening, identification, monitoring, or diagnosis of subjects having a neoplasia. The invention further provides highly accurate non-invasive methods for the staging or selection of treatment for a bladder, renal, or prostate cancer in a subject.