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Resistance to immune-checkpoint blockade remains challenging in patients with non-small cell lung cancer (NSCLC). Tumor-infiltrating leukocyte (TIL) quantity, composition, and activation status profoundly influence responsiveness to cancer immunotherapy. This study examined the immune landscape in the NSCLC tumor microenvironment by analyzing TIL profiles of 281 fresh resected NSCLC tissues. Unsupervised clustering based on numbers and percentages of 30 TIL types classified adenocarcinoma (LUAD) and squamous cell carcinoma (LUSQ) into the cold-, myeloid cell-, and CD8+ T cell-dominant subtypes. These were significantly correlated with patient prognosis; the myeloid cell subtype had worse outcomes than the others. Integrated genomic and transcriptomic analyses, including RNA sequencing, whole-exome sequencing, T cell receptor repertoire, and metabolomics of tumor tissue, revealed that immune reaction-related signaling pathways were inactivated, while the glycolysis and K-ras signaling pathways activated in LUAD and LUSQ myeloid cell-subtypes. Cases with ALK and ROS1 fusion genes were enriched in the LUAD myeloid subtype, and the frequency of TERT copy number variations was higher in LUSQ myeloid subtype than in the others. These classifications of NSCLC based on TIL status may be useful for developing personalized immune therapies for NSCLC.

Polatuzumab vedotin (Pola) is an antibody-drug conjugate that targets the B-cell antigen CD79b and delivers monomethyl auristatin E (MMAE). It is approved in combination with bendamustine and rituximab (Rit) for relapsed/refractory diffuse large B-cell lymphoma (r/r DLBCL). Understanding the molecular basis of Pola combination therapy with Rit, the key component for the treatment of DLBCL, is important to establish the effective treatment strategies against r/r DLBCL. Here, we examined the rationale for the combination of Pola with Rit using Pola-refractory cells. We found that treatment with Pola increased CD20 expression and sensitivity to Rit-induced complement-dependent cytotoxicity (CDC) in several Pola-refractory cells. Pola treatment increased phosphorylation of AKT and ERK and both AKT- and MEK-specific inhibitors attenuated the Pola-induced increase of CD20 and CDC sensitivity, suggesting that these phosphorylation events were required for this combination efficacy. It was revealed that anti-CD79b antibody increased the phosphorylation of AKT but inhibited the phosphorylation of ERK. In contrast, MMAE potentiated phosphorylation of ERK but slightly attenuated the phosphorylation of AKT. Pola also increased CD20 expression on Pola-refractory xenografted tumours and significantly enhanced antitumour activity in combination with Rit. In conclusion, these results could provide a novel rationale for the combination of Pola plus Rit.

Inflammatory factors in the peripheral blood, such as the C-reactive protein level and neutrophil-to-lymphocyte ratio (NLR), are prognostic markers in multiple types of cancer, including non-small cell lung cancer (NSCLC). However, the association between inflammatory factors and prognosis based on histological types has not been adequately reported. In addition, the relationship between these factorsand the immune condition of the tumor microenvironment (TME) is unclear. In this study, we first investigated the relationship between preoperative inflammatory markers and clinical outcomes in 176 patients with NSCLC who underwent surgery. Lung adenocarcinoma (LUAD) showed no significant prognostic marker, whereas for lung squamous cell carcinoma (LUSC), a multivariate analysis showed that a high NLR was significantly associated with postoperative recurrence. In LUSC patients, the median time of postoperative recurrence-free survival in patients with a low NLR was longer than that in patients with a high NLR. We then compared the tumor-infiltrating lymphocyte (TIL) profile with inflammatory markers in peripheral blood and found that the NLR was negatively correlated with the frequencies of T cells and B cells in LUSC tissues. Thus, the NLR is a useful predictive biomarker for postoperative recurrence and may reflect the immune condition of the TME in LUSC.

Identifying a strategy with strong efficacy against non-inflamed tumours is vital in cancer immune therapy. ERY974 is a humanized IgG4 bispecific T cell-redirecting antibody that recognizes glypican-3 and CD3. Here we examine the combination effect of ERY974 and chemotherapy (paclitaxel, cisplatin, and capecitabine) in the treatment of non-inflamed tumours in a xenograft model. ERY974 monotherapy shows a minor antitumour effect on non-inflamed NCI-H446 xenografted tumours, as infiltration of ERY974-redirected T cells is limited to the tumour-stromal boundary. However, combination therapy improves efficacy by promoting T cell infiltration into the tumour centre, and increasing ERY974 distribution in the tumour. ERY974 increases capecitabine-induced cytotoxicity by promoting capecitabine conversion to its active form by inducing thymidine phosphorylase expression in non-inflamed MKN45 tumour through ERY974-induced IFNγ and TNFα in T cells. We show that ERY974 with chemotherapy synergistically and reciprocally increases antitumour efficacy, eradicating non-inflamed tumours.

Cancer care is being revolutionized by immunotherapies such as immune checkpoint inhibitors, engineered T cell transfer, and cell vaccines. The bispecific T cell-redirecting antibody (TRAB) is one such promising immunotherapy, which can redirect T cells to tumor cells by engaging CD3 on a T cell and an antigen on a tumor cell. Because T cells can be redirected to tumor cells regardless of the specificity of T cell receptors, TRAB is considered efficacious for less immunogenic tumors lacking enough neoantigens. Its clinical efficacy has been exemplified by blinatumomab, a bispecific T cell engager targeting CD19 and CD3, which has shown marked clinical responses against hematological malignancies. However, the success of TRAB in solid tumors has been hampered by the lack of a target molecule with sufficient tumor selectivity to avoid "on-target off-tumor" toxicity. Glypican 3 (GPC3) is a highly tumor-specific antigen that is expressed during fetal development but is strictly suppressed in normal adult tissues. We developed ERY974, a whole humanized immunoglobulin G-structured TRAB harboring a common light chain, which bispecifically binds to GPC3 and CD3. Using a mouse model with reconstituted human immune cells, we revealed that ERY974 is highly effective in killing various types of tumors that have GPC3 expression comparable to that in clinical tumors. ERY974 also induced a robust antitumor efficacy even against tumors with nonimmunogenic features, which are difficult to treat by inhibiting immune checkpoints such as PD-1 (programmed cell death protein-1) and CTLA-4 (cytotoxic T lymphocyte-associated protein-4). Immune monitoring revealed that ERY974 converted the poorly inflamed tumor microenvironment to a highly inflamed microenvironment. Toxicology studies in cynomolgus monkeys showed transient cytokine elevation, but this was manageable and reversible. No organ toxicity was evident. These data provide a rationale for clinical testing of ERY974 for the treatment of patients with GPC3-positive solid tumors.

Advances in next-generation sequencing technologies have made possible to identify more efficiently novel fusion proteins in cancer. Among them, fusion kinases are well known as potent oncogenes and promising therapeutic targets for cancer patients. Recently, several FGFR fusion genes, such as FGFR1-TACC1, FGFR2-CCDC6, FGFR3-TACC3, and FGFR3-BAIAP2L1, have been identified in GBM, bladder cancer, and breast cancer as well as other tumor types. In this study, we focused on the FGFR3-BAIAP2L1 (F3-B) gene fusion and investigated its prevalence in clinical samples, tumorigenic activity, mechanism of constitutive activation, and sensitivity to CH5183284/ Debio 1347. We screened cancer tissue panels by RT-PCR for F3-B mRNA and identified F3-B positive specimens in bladder cancer (4.3%: 2/47) and lung cancer (1.2%: 1/83). All these F3-B fusions were confirmed by cDNA sequencing. To expand this study further, we established an FGFR3 break apart FISH assay. In a larger bladder cancer panel, we found 2 additional positive cases (2.2%: 2/89). To investigate the role of F3-B in tumors, we established Rat-2 transfectants with full length F3-B and assessed tumorigenic activity of these cells in in vitro and in vivo settings. Rat-2/F3-B cells acquired sphere forming activity even without FGF1 in vitro, and efficiently formed tumors when subcutaneously inoculated the cells into nude mice. Consistent with these observations, FGFR3 or BAIAP2L1siRNA blocked the proliferation of F3-B positive SW780 cells. Interestingly, the selective FGFR inhibitor, CH5183284/Debio 1347, effectively inhibited the in vivo tumor growth of Rat-2/F3-B and SW780 cells, indicating that F3-B oncogenic activity is depending on FGFR kinase activity. To confirm this, we established Rat-2/F3-B-ΔBAR, which lacks dimerization domain of BAIAP2L1 (BAR domain: Bin-Amphiphysin-Rvs). Phosphorylation of FGFR3 in Rat-2/F3-B-ΔBAR cells was lowered as compared to that in Rat-2/F3-B cells. Furthermore, Rat-2/F3-B-ΔBAR cells exhibited lower spheroid formation activity and slower tumor growth compared with Rat-2/F3-B cells. Taking this information together, the constitutive dimerization though BAR domain is essential for F3-B fusion to exert its potent oncogene activity in tumors. These findings underline the oncogenic potential of FGFR3-BAIAP2L1 gene fusion and warrant further clinical evaluation of the therapeutic potential of CH5183284/Debio 1347 in patients harboring this genetic alteration. Citation Format: Nukinori Akiyama, Yoshito Nakanishi, Toshiyuki Tsukaguchi, Yasuko Satoh, Yasue Nagata, Tsutomu Takahashi, Yukari Nishito, Motoki Ashihara, Nobuya Ishii, Masahiro Aoki. Inhibition of FGFR3-BAIAP2L1 fusion kinase oncogenic potential by CH5183284/Debio 1347, a compound that inhibits FGFR3 kinase activity constitutively activated by BAIAP2L1 BAR domain dimerization. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5252. doi:10.1158/1538-7445.AM2014-5252

Background Bacillus subtilis natto is closely related to the laboratory standard strain B. subtilis Marburg 168, and functions as a starter for the production of the traditional Japanese food "natto" made from soybeans. Although re-sequencing whole genomes of several laboratory domesticated B. subtilis 168 derivatives has already been attempted using short read sequencing data, the assembly of the whole genome sequence of a closely related strain, B. subtilis natto, from very short read data is more challenging, particularly with our aim to assemble one fully connected scaffold from short reads around 35 bp in length. Results We applied a comparative genome assembly method, which combines de novo assembly and reference guided assembly, to one of the B. subtilis natto strains. We successfully assembled 28 scaffolds and managed to avoid substantial fragmentation. Completion of the assembly through long PCR experiments resulted in one connected scaffold for B. subtilis natto. Based on the assembled genome sequence, our orthologous gene analysis between natto BEST195 and Marburg 168 revealed that 82.4% of 4375 predicted genes in BEST195 are one-to-one orthologous to genes in 168, with two genes in-paralog, 3.2% are deleted in 168, 14.3% are inserted in BEST195, and 5.9% of genes present in 168 are deleted in BEST195. The natto genome contains the same alleles in the promoter region of degQ and the coding region of swrAA as the wild strain, RO-FF-1. These are specific for γ-PGA production ability, which is related to natto production. Further, the B. subtilis natto strain completely lacked a polyketide synthesis operon, disrupted the plipastatin production operon, and possesses previously unidentified transposases. Conclusions The determination of the whole genome sequence of Bacillus subtilis natto provided detailed analyses of a set of genes related to natto production, demonstrating the number and locations of insertion sequences that B. subtilis natto harbors but B. subtilis 168 lacks. Multiple genome-level comparisons among five closely related Bacillus species were also carried out. The determined genome sequence of B. subtilis natto and gene annotations are available from the Natto genome browser http://natto-genome.org/.