Immunostimulatory bacteria for converting macrophages into a phenotype amenable to treatment, and companion diagnostic for identifying subjects for treatment

An immunostimulatory bacterium that is a Salmonella strain;

• wherein:
• the phenotype comprises YS1646Δasd/ΔFLG/ΔpagP/ΔansB/ΔcsgD/F-ΔpurI, or YS1646Δasd/ΔFLG/ΔpagP/ΔansB/ΔcsgD/F-ΔpurI/ΔthyA, or ΔpurI/ΔmsbB/Δasd/ΔFLG/ΔpagP/ΔansB/ΔcsgD;
• YS1646 is ΔpurI/ΔmsbB;
• and
• F-ΔpurI is a full deletion of the purI coding region.

A method for identifying subjects likely to or predicted to respond to treatment with a therapeutic that comprises a delivery vehicle containing non-integrating nucleic acid encoding one or more immunostimulatory proteins, the method comprising detecting proliferating macrophages or detecting particular markers in a tumor or body fluid sample, wherein:

• response to treatment and/or proliferating macrophages is/are identified by a combination of markers selected from among markers detectable by immunohistochemistry (IHC) and genetic markers for a particular tumor type;
• and
• the combinations of markers detectable by IHC and genetic markers for tumor types are selected from:
• SPP1+ and NRF2 pathway alterations in a tumor biopsy or body fluid sample from a subject with a squamous carcinoma(s);
• SPP1+ and TP53 mutations in breast cancer (BRCA);
• SPP1+ and PI3K mutations in prostate cancer (PRAD);
• SPP1+ and BRAF mutations in skin cutaneous melanoma (SKCM);
• C1QC+ and HIPPO pathway mutations;
• C1QC+ in uterine corpus endometrial cancer (UCEC);
• C1QC+ and KMT2A mutations in bladder cancer (BLCA);
• and
• C1QC+ and TP53 pathway mutations in breast cancer (BRCA).

A method of identifying therapeutics that convert macrophages to an M1/M2 phenotype, comprising:

• a) preparing one or more candidate therapeutics that comprise a delivery vehicle and nucleic acid encoding immunostimulatory proteins, wherein one of the immunostimulatory proteins induces an anti-viral or anti-cancer immune response, and the other induces type I IFN, and the delivery vehicle is TLR2 or TLR4, or TLR2 and TLR4 or 5, or TLR2/4/5 attenuated, whereby the therapeutic does not inhibit type I IFN in macrophages when introduced into or that infect the macrophages;
• b) introducing the candidate therapeutic(s) into proliferating macrophages;
• c) determining the phenotype of the resulting macrophages;
• and
• d) selecting a candidate therapeutic(s) if the resulting macrophages have a M1/M2 hybrid phenotype.

A method of increasing the therapeutic effect of an immunostimulatory bacterium in a subject, comprising:

• pre-treating the subject with anti-PD-1 antibody or other PD-1 antagonist to suppress PD-1 expression on macrophages in the tumor of the subject to thereby promote their phagocytic capacity;
• administering the immunostimulatory bacterium, wherein the bacterium encodes one or more immunostimulatory protein(s);
• and
• then, after a sufficient time so that the nucleic acid encoding the payload(s) is delivered to the macrophages, treating with an anti-PD-L1 agent.

An anti-cancer treatment protocol, comprising:

• a) pre-treating a subject to be treated with the delivery vehicle with an agent that suppresses PD-1 expression on macrophages to thereby promote the phagocytic capacity of the macrophage, wherein:
• the delivery vehicle comprises nucleic acid encoding an anti-cancer product;
• and
• the delivery vehicle targets or can be phagocytosed by phagocytic macrophages;
• and
• then administering the delivery vehicle;
• or
• b) pre-treating a subject to be treated with the delivery vehicle with an anti-PD-1 agent, whereby PD-1 expression on the macrophages is suppressed to thereby promote phagocytic capacity of the macrophages, wherein the delivery vehicle comprises nucleic acid encoding an anti-cancer product and is a vehicle that targets or can be phagocytosed by phagocytic macrophages;
• and
• then administering the delivery vehicle.