Identification of pan-cancer/testis genes and validation of therapeutic targeting in triple-negative breast cancer: Lin28a-based and Siglece-based vaccination induces antitumor immunity and inhibits metastasis

BACKGROUND

Cancer-testis (CT) genes are targets for tumor antigen-specific immunotherapy given that their expression is normally restricted to the immune-privileged testis in healthy individuals with aberrant expression in tumor tissues. While they represent targetable germ tissue antigens and play important functional roles in tumorigenesis, there is currently no standardized approach for identifying clinically relevant CT genes. Optimized algorithms and validated methods for accurate prediction of reliable CT antigens (CTAs) with high immunogenicity are also lacking.

METHODS

Sequencing data from the Genotype-Tissue Expression (GTEx) and The Genomic Data Commons (GDC) databases was used for the development of a bioinformatic pipeline to identify CT exclusive genes. A CT germness score was calculated based on the number of CT genes expressed within a tumor type and their degree of expression. The impact of tumor germness on clinical outcome was evaluated using healthy GTEx and GDC tumor samples. We then used a triple-negative breast cancer mouse model to develop and test an algorithm that predicts epitope immunogenicity based on the identification of germline sequences with strong major histocompatibility complex class I (MHCI) and MHCII binding affinities. Germline sequences for CT genes were synthesized as long synthetic peptide vaccines and tested in the 4T1 triple-negative model of invasive breast cancer with Poly(I:C) adjuvant. Vaccine immunogenicity was determined by flow cytometric analysis of in vitro and in vivo T-cell responses. Primary tumor growth and lung metastasis was evaluated by histopathology, flow cytometry and colony formation assay.

RESULTS

We developed a new bioinformatic pipeline to reliably identify CT exclusive genes as immunogenic targets for immunotherapy. We identified CT genes that are exclusively expressed within the testis, lack detectable thymic expression, and are significantly expressed in multiple tumor types. High tumor germness correlated with tumor progression but not with tumor mutation burden, supporting CTAs as appealing targets in low mutation burden tumors. Importantly, tumor germness also correlated with markers of antitumor immunity. Vaccination of 4T1 tumor-bearing mice with Siglece and Lin28a antigens resulted in increased T-cell antitumor immunity and reduced primary tumor growth and lung metastases.

CONCLUSION

Our results present a novel strategy for the identification of highly immunogenic CTAs for the development of targeted vaccines that induce antitumor immunity and inhibit metastasis.

Identification of pan-cancer/testis genes and validation of therapeutic targeting in triple-negative breast cancer: Lin28a- and Siglece-based vaccination induces anti-tumor immunity and inhibits metastasis

Background

Cancer-testis (CT) genes are targets for tumor antigen-specific immunotherapy given that their expression is normally restricted to the immune-privileged testis in healthy individuals with aberrant expression in tumor tissues. While they represent targetable germ-tissue antigens and play important functional roles in tumorigenesis, there is currently no standardized approach for identifying clinically relevant CT genes. Optimized algorithms and validated methods for accurate prediction of reliable CT antigens with high immunogenicity are also lacking.

Methods

Sequencing data from the Genotype-Tissue Expression (GTEx) and The Genomic Data Commons (GDC) databases was utilized for the development of a bioinformatic pipeline to identify CT exclusive genes. A CT germness score was calculated based on the number of CT genes expressed within a tumor type and their degree of expression. The impact of tumor germness with clinical outcome was evaluated using healthy GTEx and GDC tumor samples. We then used a triple-negative breast cancer mouse model to develop and test an algorithm that predicts epitope immunogenicity based on the identification of germline sequences with strong MHCI and MHCII binding affinities. Germline sequences for CT genes were synthesized as long synthetic peptide vaccines and tested in the 4T1 triple-negative model of invasive breast cancer with Poly(I:C) adjuvant. Vaccine immunogenicity was determined by flow cytometric analysis of in vitro and in vivo T cell responses. Primary tumor growth and lung metastasis was evaluated by histopathology, flow cytometry and colony formation assay.

Results

We developed a new bioinformatic pipeline to reliably identify CT exclusive genes as immunogenic targets for immunotherapy. We identified CT genes that are exclusively expressed within the testis, lack detectable thymic expression, and are significantly expressed in multiple tumor types. High tumor germness correlated with tumor progression but not with tumor mutation burden, supporting CT antigens as appealing targets in low mutation burden tumors. Importantly, tumor germness also correlated with markers of anti-tumor immunity. Vaccination of 4T1 tumor bearing mice with Siglece and Lin28a antigens resulted in increased T cell anti-tumor immunity and reduced primary tumor growth and lung metastases.

Conclusion

Our results present a novel strategy for the identification of highly immunogenic CT antigens for the development of targeted vaccines that induce anti-tumor immunity and inhibit metastasis.

Inhibition of IRF5 hyperactivation protects from lupus onset and severity

The transcription factor IFN regulatory factor 5 (IRF5) is a central mediator of innate and adaptive immunity. Genetic variations within IRF5 are associated with a risk of systemic lupus erythematosus (SLE), and mice lacking Irf5 are protected from lupus onset and severity, but how IRF5 functions in the context of SLE disease progression remains unclear. Using the NZB/W F1 model of murine lupus, we show that murine IRF5 becomes hyperactivated before clinical onset. In patients with SLE, IRF5 hyperactivation correlated with dsDNA titers. To test whether IRF5 hyperactivation is a targetable function, we developed inhibitors that are cell permeable, nontoxic, and selectively bind to the inactive IRF5 monomer. Preclinical treatment of NZB/W F1 mice with an inhibitor attenuated lupus pathology by reducing serum antinuclear autoantibodies, dsDNA titers, and the number of circulating plasma cells, which alleviated kidney pathology and improved survival. Clinical treatment of MRL/lpr and pristane-induced lupus mice with an inhibitor led to significant reductions in dsDNA levels and improved survival. In ex vivo human studies, the inhibitor blocked SLE serum-induced IRF5 activation and reversed basal IRF5 hyperactivation in SLE immune cells. We believe this study provides the first in vivo clinical support for treating patients with SLE with an IRF5 inhibitor.

Targeting interferon regulatory factor 5 (IRF5) activation with a peptide inhibitor ameliorates clinical lupus in MRL/lpr mice

Systemic lupus erythematosus (SLE) is associated with high levels of inflammatory cytokines as well as increased autoantibodies. Accumulating evidence show that loss and/or inhibition of the transcription factor interferon regulatory factor 5 (Irf5) ameliorates disease severity. Previously, we characterized a peptide inhibitor targeting Irf5 activation in the NZB/W F1 murine model of lupus and showed therapeutic protection when treated before disease onset. Here, we expanded our study to include a clinical treatment arm in the MRL/lpr lupus model after disease onset. 8 week-old MRL/lpr female mice were IP-injected with PBS or inhibitor at a dose of 100ug/mouse/injection on D0, D1, D4, D7 and D14. Proteinuria was monitored weekly; serum auto-antibodies were measured by ANA-HEp-2; anti-dsDNA IgG by ELISA, and kidney pathology was assessed. Blood was collected weekly to examine Irf5 expression and activation in immune cell subsets by imaging flow cytometry. At 8 weeks-old and before treatment, MRL/lpr mice were positive for anti-nuclear antibodies (ANA). At week 17, IgG and IgM staining on HEp-2 cells showed stronger fluorescence intensity in the control group (p=0.0053 for IgG; p<0.0001 for IgM). Serum anti-dsDNA IgG levels were also higher in the control group (782179 ± 337490 U/mL, n=7) as compared to treated (385947 ± 156487 U/mL, n=9). By week 17, 2 out of 9 mice in the control group had died, while all mice in the treated group survived. Proteinuria and body weights remained similar between groups. Data indicate that direct inhibition of murine Irf5 in multiple lupus models (NZB/W F1 and MRL/lpr) ameliorates disease severity. The inhibitor was also well-tolerated supporting the therapeutic utility of IRF5 inhibitors in the clinic.

Inhibition of IRF5 cellular activity with cell-penetrating peptides that target homodimerization

The transcription factor interferon regulatory factor 5 (IRF5) plays essential roles in pathogen-induced immunity downstream of Toll-, nucleotide-binding oligomerization domain-, and retinoic acid-inducible gene I-like receptors and is an autoimmune susceptibility gene. Normally, inactive in the cytoplasm, upon stimulation, IRF5 undergoes posttranslational modification(s), homodimerization, and nuclear translocation, where dimers mediate proinflammatory gene transcription. Here, we report the rational design of cell-penetrating peptides (CPPs) that disrupt IRF5 homodimerization. Biochemical and imaging analysis shows that IRF5-CPPs are cell permeable, noncytotoxic, and directly bind to endogenous IRF5. IRF5-CPPs were selective and afforded cell type- and species-specific inhibition. In plasmacytoid dendritic cells, inhibition of IRF5-mediated interferon-α production corresponded to a dose-dependent reduction in nuclear phosphorylated IRF5 [p(Ser⁴⁶²)IRF5], with no effect on pIRF5 levels. These data support that IRF5-CPPs function downstream of phosphorylation. Together, data support the utility of IRF5-CPPs as novel tools to probe IRF5 activation and function in disease.

Novel role(s) for Irf5 in controlling myelopoiesis and erythropoiesis

Causes of erythropoiesis dysregulation during anemia of inflammation remain largely unknown. Mammalian erythropoiesis can be divided into differentiation of early progenitors and maturation of precursors within anatomic niches called erythroblastic islands (EBI). EBIs consist of a central macrophage surrounded by differentiating erythroblasts and myeloid cells. While recent studies have focused on interactions of the macrophage and surrounding cells, much less is known about the transcription factors that regulate EBI formation and function. Data from scRNAseq revealed that interferon regulatory factor 5 (Irf5) is expressed by the central macrophage within EBIs. At steady state, Irf5−/− mice have decreased numbers of EBIs in the bone marrow (BM) with altered composition - increased CD71 (erythroid marker) and CD11b and Ly6G (myeloid markers). We also found increased numbers of reticulocytes in Irf5−/− BM. We hypothesize that Irf5 has a conserved function in mammalian blood formation by regulating the cellular output of erythroid and myeloid cells. To test this, we induced stress erythropoiesis in wild-type (wt) and Irf5−/− age- and littermate-matched mice by submandibular bleeding. Mice were bled twice (Day 0 and 2) and complete blood counts, erythropoiesis, and EBI formation monitored over recovery (12 days). Using CD44/Ter119 and Forward Scatter as markers of terminal erythropoiesis, we found that erythroid differentiation was significantly delayed in Irf5−/− mice resulting in increased mortality and corresponding to a significant decrease in EBI formation. These data identify Irf5 as a new regulator of the erythroid-myeloid balance within the EBI that results in altered function(s) during anemia of inflammation.

Decubitus ulcers: update on new approaches to treatment

Decubitus ulcers are best treated by eliminating the primary etiology, pressure, while supplementing care with the best available treatment modality. Knowledge of new treatment modalities and appropriate selection will help expedite wound closure. Pressure-relieving devices should not be relied upon to eliminate all pressure from the wound. Pressure relief should be supplemented with choice of appropriate dressings and additional therapy. The use of electrical stimulation, biomaterials, and growth factors may soon become available as additional modalities to expedite closure and facilitate wound repair.