The upregulation of CD74, a chaperone involved in MHC-II antigen processing, has been mostly interpreted as indicative of antigen presentation in multiple brain disorders. However, CD74 expression has also been described in cancer cells across multiple tumor types and in the tumor microenvironment, notably in glioma. In this study, we found that the presence of CD74+ microglia/macrophages, which was induced by increased levels of interferon γ in brains affected by metastases, did not relate to its canonical pathway. Instead, the alternative function of CD74 as a cytokine receptor was pivotal. Proliferating cancer cells produced high levels of the ligand migration inhibitory factor (MIF) that bound the CD74 receptor and induced its translocation to the nucleus where it activated an NF-κB-dependent program that promoted metastatic progression. In patients, a CD74 signature was associated with more aggressive progression of brain metastatic disease, although it had no clinical correlation with the matched primary tumor. Interestingly, a pan-disease noncanonical and clinically relevant signature derived from the CD74+ myeloid population was identified that occurred in additional brain disorders, including Alzheimer's disease and multiple sclerosis. The brain-penetrant drug ibudilast, which prevents the binding of MIF to CD74, decreased brain metastasis in experimental models in vivo and in patient-derived organotypic cultures ex vivo in a primary tumor-agnostic manner. These findings suggest that MIF/CD74-induced reprogramming of myeloid cells in brain disorders is a vulnerability that could be exploited therapeutically against brain metastases and possibly other brain disorders. SIGNIFICANCE:A reprogrammable subset of CD74+ microglia/macrophages is a shared population with translational relevance across neurologic diseases that drives pathology in brain metastases. See related commentary by Lee and Kang, p. 3103.

Supplementary File S7. Combinations of immune markers used for flow cytometry analysis.

Differentially expressed genes in CD74+ CCR2+ cells vs CD74+ CCR2- cells

List of the human 37- gene signature derived from the bulk RNA-seq of CD74+ microglia/macrophages

Supplementary Fig. S3. Comparison of genetic results (mutations in loci of interest, TMB, and HRD) obtained through WES profiling between non-responders and responders.

GDSC-derived therapeutic candidates for non-responder patients based on the 11-gene responder signature

Supplementary Table S2. Representativeness of the study participants.

List of deregulated genes in the CD74+ microglia (disease associated microglia, reactive microglia)/macrophages (reactive macrophages) vs CD74- microglia (homeostatic microglia)/macrophages (homeostatic macrophages) in brain metastasis, Alzheimer disease and multiple sclerosis

Supplementary File S3. Genetic variants detected through WES profiling in TURBT and cystectomy samples.

Rank signaling regulates mammary gland development and epithelial differentiation. While Rank is expressed in both basal and luminal cells, its basal-specific role is unclear. Here, using inducible basal-specific Rank expression and lineage tracing, we show that Rank signaling regulates basal cell identity in postnatal mammary glands. Increased basal Rank activity disrupts basal and luminal identities, causing aberrant luminal-like differentiation, lactation defects, and premalignant lesions composed of hybrid basal-derived cells that progress to basal and luminal adenocarcinomas. Conversely, Rank loss reduces tumor formation and also impairs cell identity. Mechanistically, proteomic, transcriptomic, and chromatin analyses reveal that Rank activation drives epigenetic remodeling, leading to basal identity loss and tumor initiation. A basal Rank gene signature correlates with ductal carcinoma in situ recurrence, as well as poor outcomes in luminal breast cancers. Thus, basal Rank-driven lineage infidelity promotes pre-invasive lesions and transition to invasive breast cancer in females.

Supplementary Table S3. Clinical data related to neoadjuvant treatment with Olaparib.

Supplementary Table S1. Panel of antibodies used in flow cytometry studies.

CD74+ microglia/macrophages are enriched in protumoral markers

Cancer cells are the main source of MIF and CD74 expression is induced in the brain tumor microenvironment

Supplementary File S6. Differentially expressed genes and functional categories enriched according to RNASeq data in the comparison between cystectomies vs. TURBT.

TIMP1 mediates brain metastasis in a CD8+ T cell-dependent manner. Supplementary Figure 5 shows additional data corresponding to Figure 4.

Overall survival according to TIMP1 in the CSF. Overall survival of brain metastasis patients with different primary tumors according to their levels of TIMP1 in the cerebrospinal fluid (CSF). The table contains information corresponding to Supplementary Figure 9B.

TIMP1 is a downstream target of STAT3 in brain metastasis-associated astrocytes. Supplementary Figure 3 shows additional data corresponding to Figure 3.

TIMP1 levels from ELISA applied to CSF from patient samples. Levels of TIMP1 in the blood or in the cerebrospinal fluid (CSF) of non-cancer patients and brain metastasis patients from different primary tumors. Immune Cluster is shown for patients in Figure 7N. The table contains information corresponding to Figure 7L, 7N and Supplementary Figure 9A,C-D.

TIMP1 through CD63 alters relevant properties of CD8+ T cells. Supplementary Figure 6 shows additional data corresponding to Figure 6.