Abstract: Circulating free RNA (cfRNA) is used for monitoring status and/or treatment response for neural tumors, and especially glioma, glioblastoma, and neuroblastoma. Particularly preferred cfRNAs include those that encode a marker that is specific to a neural tumor, but also markers that are specific to DNA repair status and/or immune status.

Abstract: Cancer is treated using coordinated treatment regimens that uses various compounds and compositions that drive a tumor from the escape phase of cancer immunoediting to the elimination and equilibrium phase of cancer immunoediting.

Abstract: RNA from a biological fluid is stabilized during isolation and/or storage using DNA. In especially preferred aspects, the RNA is cfRNA and/or ctRNA, and the biological fluid is blood.

Abstract: Systems and methods are presented that allow for selection of tumor neoepitopes that are then used to generate a recombinant polytope that is optimized for proper trafficking and processing. In preferred methods, the polytope is encoded in a viral expression system that is used as a therapeutic agent.

Abstract: Cancer is treated using coordinated treatment regimens that uses various compounds and compositions that drive a tumor from the escape phase of cancer immunoediting to the elimination and equilibrium phase of cancer immunoediting.

Abstract: Ex vivo determination of increased tumor immunogenicity of a tumor biopsy is used as a guide to identify immunotherapy of a tumor in a patient. Most preferably, the ex vivo tests will include exposure of biopsy samples to stress conditions to produce pretreated tumor cells that are then assayed with immune competent cells for increased activation or activity. Test conditions include exposure of the biopsy samples to immune stimulatory compositions, antibodies against neoepitopes, and/or modified cells, and an increase of immunogenicity is preferably determined by their exposure to T cells and/or NK cells.

Abstract: Recombinant viruses and viral nucleic acids are contemplated that provide to the infected cell various regulatory molecules that stimulate T-cell and NK-cell activity and that suppress inhibition of T-cell and NK-cell activity. Most preferably, the virus and viral nucleic acid will further include a human cancer-associated sequence, and especially a sequence that encodes a plurality of cancer associated antigens, cancer specific antigens, and/or patient and tumor specific neoantigens. Especially preferred regulatory molecules include CD80 (B7.1), CD86 (B7.2), CD54 (ICAM-1/BB2), CD11 (LFA-1), and an inhibitor of CTLA-4.

Abstract: The present disclosure relates generally to methods for detecting and/or treating cancer by assessing circulating free nucleic acids derived from a bodily fluid sample. In particular, in some embodiments, the disclosed methods involve assessing sequence alteration and/or a fragment-size alteration within microsatellite short tandem repeats which are characteristic to certain cancers and some other health conditions.

Abstract: The present inventive subject matter provides apparatus, systems, and methods in which a diagnostic test is identified, where the diagnostic test is for determining whether a particular treatment is effective for a particular patient based on one or more characteristics of a patient's cells. When a treatment is developed with the potential to treat one or more diseases, the drug can have different effects on different cell lines related to the diseases. A machine learning system is programmed to infer a measurable cell characteristic, out of many different measurable cell characteristics, that has a desirable correlation with the sensitivity data of different cell lines to a treatment. The machine learning system is programmed to then determine, based on the correlation, a threshold level of the cell characteristic the patient should exhibit in order to recommend administering the treatment.

Abstract: In certain embodiments, methods and compositions are provided for generating immune responses against tumor neo-antigens or neo-epitopes. In particular embodiments there may be provided methods for constructing and producing recombinant adenovirus-based vector vaccines containing nucleic acid sequences encoding tumor neo-antigens and neo-epitopes that allow for vaccinations in individuals with preexisting immunity to adenovirus. In additional embodiments, methods and compositions are provided for the treatment of cancer using immunotherapy based on recombinant adenovirus-based vectors combined with engineered natural killer cells. In some embodiments, the methods and compositions further comprises a nucleic acid encoding for an immunological fusion partner.

Abstract: The invention provides a method of validating the therapeutic composition that is prepared for immunotherapy of a tumor or cancer. The method includes, triggering of an immune response to a neoepitope of a subject's tumor by: a) obtaining neoepitope sequence data from the tumor of a subject; b) obtaining immune competent cells; c) using the neoepitope sequence data to generate a neoepitope presentation system; d) triggering an immune response by contacting the immune competent cells with the neoepitope presentation system; and e) quantifying the triggering of the immune response from the contacted immune competent cells.

Abstract: NK cell based cancer immunotherapy, and particularly genetically modified NK92 cell-based immunotherapy is enhanced by expression CXCL12 and/or by suppression or deletion of CXCR4 in the natural killer cells to so reduce aggregation, rejection, and/or fratricide of the natural killer cells. Provided herein are genetically engineered NK (natural killer) cell comprising a recombinant nucleic acid encoding at least a portion of chemokine C—X—C motif ligand 12 (CXCL12), and a transcript for downregulation of chemokine C—X—C motif receptor 4 (CXCR4).

Abstract: Methods and compositions for generating enhanced immune responses using adenovirus vectors that encode for an antigen and calreticulin, which serves as an immunologic adjuvant.

Abstract: Techniques are provided for determining a cell count within a whole slide pathology image. The image is segmented using a global threshold value to define a tissue area. A plurality of patches comprising the tissue area are selected. Stain intensity vectors are determined within the plurality of patches to generate a stain intensity image. The stain intensity image is iteratively segmented to generate a cell mask using a local threshold value that is and gradually reduced after each iteration. A chamfer distance transform is applied to the cell mask to generate a distance map. Cell seeds are determined on the distance map. Cell segments are determined using a watershed transformation, and a whole cell count is calculated for the plurality of patches based on the cell segments. A client device may be configured for real-time cell counting based on the whole cell count.

Abstract: An immune gene expression signature is associated with favorable clinical features in Treg-enriched tumor samples and can be used to predict immunogenicity of a tumor, overall survival, and/or chemosensitivity.

Abstract: cfRNA is used to determine presence or risk of minimal residual disease after treatment of a patient. Most preferably, cfRNA from the patient is analyzed for quantity and/or signatures that are characteristic for the patient's disease.

Abstract: Quantitative levels of ERCC1 cfRNA are used to monitor/predict a clinical response with respect to a disease state of a cancer in a patient subject to treatment with a platinum-based drug. Most typically, the cancer is a NSCLC and the patient is treated with a platinum-based drug. Where treatment also includes immune checkpoint inhibitors, PD-L1 cfRNA may be quantified to further predict treatment outcome.

Abstract: Contemplated cancer therapies use aldoxorubicin as an immunomodulator of a tumor microenvironment to increase therapeutic effects of immune therapeutic compositions.

Abstract: Methods for analyzing omics data and using the omics data to determine prognosis of a cancer, to predict an outcome of a treatment, and/or to determine an effectiveness of a treatment are presented. In preferred methods, blood from a patient having a cancer or suspected to have a cancer is obtained and blood omics data for a plurality of cancer-related, inflammation-related, or DNA repair-related genes are obtained. A cancer score can be calculated based on the omics data, which then can be used to provide a cancer prognosis, a therapeutic recommendation, an effectiveness of a treatment.

Abstract: Cancer immunotherapy is enhanced by co-expression of cancer associated or tumor-specific (neo)epitopes with co-stimulatory molecules and/or other immune activators. Where desired, treatment may be enhanced by administration of a immune checkpoint inhibitor.