Abstract: Described herein are compositions and methods of using single-cell RNA-sequencing to identify treatment resistance in patients with ovarian cancer. Also, described herein are compositions and methods for treatment targeting resistance in patients with ovarian cancer.

Abstract: The subject matter disclosed herein is generally directed to detecting and modulating novel gene signatures for the treatment and prognosis of cancer. The novel gene signatures predict overall survival in cancer and can be targeted therapeutically.

Abstract: The method of enhancing anti-tumor immunity in a patient by targeting the CD58:CD2 axis uses an administered treatment to target and disrupt CMTM6 regulation of PD-L1 protein, thus enhancing the immune response and cancer immunotherapy in the patient. Targeting and disruption of CMTM6 regulation of the PD-L1 protein may be combined with additional prompting of a PD-1 blockage or adoptive cell transfer (ACT) in the patient. Targeting and disrupting CMTM6 regulation of PD-L1 protein may be initiated by administering an effective amount of antibodies to the patient, which are specific to disrupting CMTM6/PD-L1 protein interaction. Alternatively, to enhance the anti-tumor immunity in the patient, CD2 mediated signaling may be increased in order to stimulate an immune response. As another alternative to using antibodies or a CD58 mimetic, a pharmacological target to boost CD2/CD58 signaling in the patient may be identified and administered to enhance anti-tumor immunity.

Abstract: Methods of targeting CD58 signaling to enhance antitumor immunity and overcome resistance to checkpoint blockade therapy. Gene signatures associated with immune fitness were identified. Markers and therapeutic targets for such immunotherapy resistance.

Abstract: The present invention provides for methods and compositions for treating cancer. Disclosed are novel tumor biomarkers and therapeutic targets. Also disclosed are CAR T cells targeting tumor specific surface proteins. Also disclosed are shared expression programs specific to tumor cells.

Abstract: Described herein are compositions and methods of using single-cell RNA-sequencing to identify treatment resistance in patients with ovarian cancer. Also, described herein are compositions and methods for treatment targeting resistance in patients with ovarian cancer.

Abstract: The subject matter disclosed herein is generally directed to detecting and modulating novel gene signatures for the treatment and prognosis of cancer. The novel gene signatures predict overall survival in cancer and can be targeted therapeutically. Specifically, disclosed is a resistance program identified by a comprehensive single-cell profiling study in melanoma patients, which was validated in two large validation cohorts. Using a large-scale in silico prediction, CDK4/6 inhibitors were identified as a class of drugs that may reverse this resistance program. These predictions were validated in melanoma cell lines, patient-derived co-culture models, and melanoma in vivo models, which show that the combination of abemaciclib and immune checkpoint blockade (ICB) overcome intrinsic drug resistance. The present invention provides for detecting an immunotherapy resistance signature and modulating the signature with CDK4/6 inhibition.

Abstract: The subject matter disclosed herein is generally directed to detecting and modulating novel gene signatures for the treatment and prognosis of cancer. The novel gene signatures predict overall survival in cancer and can be targeted therapeutically.

Abstract: Described herein are compositions and methods of disaggregating a tissue sample into single cells.

Abstract: This invention relates generally to compositions and methods for identifying genes and gene networks that respond to, modulate, control or otherwise influence tumors and tissues, including cells and cell types of the tumors and tissues, and malignant, microenvironmental, or immunologic states of the tumor cells and tissues. The invention also relates to methods of diagnosing, prognosing and/or staging of tumors, tissues and cells, and provides compositions and methods of modulating expression of genes and gene networks of tumors, tissues and cells, as well as methods of identifying, designing and selecting appropriate treatment regimens. The invention also relates to the modulation of complement activity to shift cellular immunity and obtain an effective therapeutic response.