Therapeutic resistance to immune checkpoint blockers (ICBs) in melanoma patients is a pressing issue, of which tumor loss of IFN-γ signaling genes is a major underlying mechanism. However, strategies of overcoming this resistance mechanism have been largely elusive. Moreover, given the indispensable role of tumor-infiltrating T cells (TILs) in ICBs, little is known about how tumor-intrinsic loss of IFN-γ signaling (IFNγR1KO) impacts TILs. Here, we report that IFNγR1KO melanomas have reduced infiltration and function of TILs. IFNγR1KO melanomas harbor a network of constitutively active protein tyrosine kinases centered on activated JAK1/2. Mechanistically, JAK1/2 activation is mediated by augmented mTOR. Importantly, JAK1/2 inhibition with Ruxolitinib selectively suppresses the growth of IFNγR1KO but not scrambled control melanomas, depending on T cells and host TNF. Together, our results reveal an important role of tumor-intrinsic IFN-γ signaling in shaping TILs and manifest a targeted therapy to bypass ICB resistance of melanomas defective of IFN-γ signaling.

The development of pathogenic autoantibody producing B cells is normally limited at the early transitional (Tr) stage and a later T-dependent developmental checkpoint. The precise molecular mechanisms underlying defective autoreactive B cell deletion/anergy at each checkpoint have been difficult to define. We utilized a combined single-cell B cell transcriptome and high dimensional flow cytometry analysis approach for a parallel understanding of B-cell developmental checkpoint defects at multiple stages in SLE. We found that while high levels of B-cell endogenous interferon-β (IFNβ) is an important risk factor for autoantibody positive African American (AA) SLE patients, low expression of IL-4R was a risk factor of both AA and European-Americans (EA) patients for development of pathogenic autoantibodies. The molecular signature of autoreactive B cells that escape deletion at the Tr stage include type I IFN stimulated genes (ISGs), including IRF7, ISG15, ISG20, MX1, and STAT1. The molecular signature of autoreactive B cells that escape the second T-dependent checkpoint, include low expression of IL4R and the transcriptional repressor BACH2, and high levels of TBX21, ITGAX, FCRL5 and IFI30. Interestingly, in vitro culture stimulation confirmed that the presence of IL-4 signaling significantly suppressed the development of pathogenic CD21−CD27−IgD−CD11c+T-bet+ double negative 2 (DN2) B cells in SLE. These results suggest that B-cell checkpoint defects can be used to stratify SLE patients according to high type I IFN or low IL-4R and their response signatures. These immune phenotype and transcriptome signatures offer the potential to predict therapy responses to type I IFN blockade or other therapies.

Therapeutic resistance to immune checkpoint blockers (ICBs) is a pressing issue, limiting ICB efficacy to a small proportion of cancer patients. Concerted efforts from our group and others have identified that loss of IFN-γ signaling genes in melanoma is a major mechanism of resistance to ICBs. However, strategies of overcoming this resistance have been largely elusive. Moreover, given the indispensable role of T cells in governing ICBs, little is known about how tumor-intrinsic loss of IFN-γ signaling impacts tumor-infiltrating T cells (TILs). In this study, we report that melanomas with defective IFN-γ signaling (IFNγR1KO) have reduced infiltration and function of TILs. Intriguingly, IFNγR1KO melanoma cells harbor a network of constitutively active protein tyrosine kinases (PTKs) centered on JAK1/2, essential downstream components of the IFN-γ signaling. Additional mechanistic studies reveal that JAK1/2 activation is mediated by augmentation of the mTOR pathway. Importantly, targeting active JAK1/2 with FDA-approved Ruxolitinib (Ruxo) selectively suppresses growth of IFNγR1KO but not scrambled control melanoma, in a T cell and host TNF-dependent manner. Together, our results highlight an important role of tumor-intrinsic IFN-γ signaling in shaping TILs and manifest a therapeutic target that can be leveraged to bypass ICB resistance of melanomas defective of IFN-γ signaling. Citation Format: Hongxing Shen, Fengyuan Huang, Xiangmin Zhang, Oluwagbemiga A. Ojo, Yuebin Li, Hoa Quang Trummell, Joshua C. Anderson, John Fiveash, Markus Bredel, Eddy Yang, Christopher Willey, Zechen Chong, James Bonner, Lewis Z. Shi. Selective suppression of melanoma lacking IFN-γ pathway by JAK inhibition depends on T cells and host TNF signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2864.

While research on human SLE and mouse models of lupus have focused on mechanisms of B cell tolerance loss, these efforts have been complicated by multiple networks of immune regulatory genes, thereby impeding current understanding of the development of autoantibody producing B cells in SLE. We applied an unsupervised single cell RNA-seq (scRNA-seq) approach to determine the network and pathways-associated with the development of plasmablasts (PBs) in SLE. PBs were isolated as CD19+CD21−IgD−CD27hiCD38hi cells from PBMCs of SLE patients (n=3). A high-throughput scRNA-seq was carried out using a droplet-based 10x Chromium approach (~ 2,000 cells per sample). We identified two populations of PBs based on the expression of MKI67 encoding for Ki67, a nuclear protein associated with cellular proliferation. Representative genes elevated in MKI67+ PBs included cell cycle related genes as well as TNFR2. Gene ontology analysis further suggest that TNFR2+ B cells expressed increased levels of genes that are associated with cell cycle G1/S transition, DNA synthesis and elongation, and replication. Flow cytometry analysis identified TNFR2+ B cells as a population of antibody secreting cells expressing higher levels of CD86, CD11c, and CD38 but lower levels of CD20. As both CD86 and CD11c poise B cells to receive T-cell help, our studies suggest that T-cell stimulation enables development of cycling PBs in SLE. The strong association of TNFR2 with cell cycle genes in PBs suggest that blockade of TNFR2 may be a novel strategy to inhibit PB proliferation and differentiation.

Immune checkpoint blockers (ICBs) have brought great promise to patients with advanced melanoma, a tumor type that was claimed largely incurable not long ago. However, therapeutic resistance to ICBs has limited their utility in the clinic. Here, we provide a commentary on recent research endeavors concerning ICB resistance in melanoma patients.