Immune functional portraits of head and neck cancer using next generation sequencing

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Background: The addition of biomarkers as companion diagnostics and Next Generation Sequencing (NGS) have dramatically increased therapeutic efficacy and have aided precision medicine development. The unique genomic profile and tumor microenvironment (TME) composition of each patient can be ascertained through NGS. Using TCGA and Geo datasets, we characterized head and neck cancers (HNC) according to the cellular and functional state of their TME and conducted a pilot validation study using prospectively collected HNC tumors. Methods: To stratify the TME of HNC tumors into molecular functional portraits, we analyzed the sequencing data of 1,486 HNC tumor samples and 143 controls (normal, oral leukoplakia) from TCGA and GEO data sets. For the prospective pilot study, resected tissue from oropharyngeal carcinomas independent of HPV status were processed for whole exome (WES) and RNA-seq (n = 6; HPV-positive = 1). Results: To characterize the cellular composition and functional state of HNC tumors and their TMEs, we created 26 separate molecular signatures related to functional processes such as immune checkpoint inhibition, immune infiltration, immunosuppression, and stromal activities represented by angiogenesis and mesenchymal stromal cells. Unsupervised clustering of these signatures delineated tumors into 4 types: immune infiltration with increased stromal signatures (type A), immune infiltration with decreased stromal signatures (type B), no immune infiltration with increased stromal signature (type C), and no immune infiltration and decreased stromal signatures (type D). Most HPV-positive tumors were type B (p = 1e-27) and associated with increased survival compared to the HPV-negative tumors (types C and D; p = 3e-05). Type B HPV-positive tumors had reduced FAT1 and TP53 mutations, whereas type B HPV-negative tumors had increased caspase 8 mutations/loss. In the validation cohort, actionable mutations were found in PI3KCA and TSC2 in types A and B HPV-negative tumors. Moreover, while the HPV-positive tumor was classified as type C, we identified a caspase 8 homozygous deletion and absence of FAT1 and TP53 mutations, supporting the TCGA and GEO analysis. Conclusions: Exome and transcriptome analyses with cellular deconvolution from bulk RNA-seq enrich tumor characterization by including major TME components, providing a comprehensive biomarker profile for precision therapy and clinical decision making. Our prospective analysis identified TME parameters comparable with the large datasets and revealed targetable genomic alterations.

Near-Infrared 1064 nm Laser Modulates Migratory Dendritic Cells To Augment the Immune Response to Intradermal Influenza Vaccine

Brief exposure of skin to near-infrared (NIR) laser light has been shown to augment the immune response to intradermal vaccination and thus act as an immunologic adjuvant. Although evidence indicates that the NIR laser adjuvant has the capacity to activate innate subsets including dendritic cells (DCs) in skin as conventional adjuvants do, the precise immunological mechanism by which the NIR laser adjuvant acts is largely unknown. In this study we sought to identify the cellular target of the NIR laser adjuvant by using an established mouse model of intradermal influenza vaccination and examining the alteration of responses resulting from genetic ablation of specific DC populations. We found that a continuous wave (CW) NIR laser adjuvant broadly modulates migratory DC (migDC) populations, specifically increasing and activating the Lang⁺ and CD11b^-Lang^- subsets in skin, and that the Ab responses augmented by the CW NIR laser are dependent on DC subsets expressing CCR2 and Langerin. In comparison, a pulsed wave NIR laser adjuvant showed limited effects on the migDC subsets. Our vaccination study demonstrated that the efficacy of the CW NIR laser is significantly better than that of the pulsed wave laser, indicating that the CW NIR laser offers a desirable immunostimulatory microenvironment for migDCs. These results demonstrate the unique ability of the NIR laser adjuvant to selectively target specific migDC populations in skin depending on its parameters, and highlight the importance of optimization of laser parameters for desirable immune protection induced by an NIR laser-adjuvanted vaccine.

Abstract 1633: Immunotherapy for malignant mesothelioma that combines a mesothelia-targeted immune-activating protein and CXCL12/CXCR4 blockade

Background and Purpose: There is a significant unmet need for new treatment strategies for malignant mesothelioma (MM). Despite relevant advances in many cancer treatment areas, including improvements in diagnosis, staging, and the clinical course of treated patients, MM remains a highly lethal disease. The purpose of this study is to develop a combination immunotherapy for MM, which involves a fusion protein to target and evoke a cellualr immune response to mesothelin (MSLN) and the blockade of CXCL12/CXCR4 pathway to mobilize cytotoxic effector cells into tumors.

Experimental Procedures: The efficacy of the MSLN targeted immune activating fusion protein (scFv-MtbHsp70), FDA-approved small molecule CXCR4 antagonist AMD3100 (plerixafor), and the combination were evaluated in two syngeneic and orthotopic murine models of MM in immune competent C57BL/6 mice. Mice received 4 intraperitoneal (i.p.) treatments from 7 days post i.p. injection of luciferase-expressing 40L and AE17 cells. Tumor growth was monitored by in vivo imaging of luciferase activity with an IVIS Spectrum. Survival time was calculated as life span from the day of tumor inoculation. In immunological studies, mice were sacrificed 4 weeks after tumor cell inoculation. Immune cells from spleens and tumors were labeled with antibodies against CD3, CD4, CD8, CD25 and Foxp3 antibodies, and examined by flow cytometry. Splenocytes were stimulated with MSLN and assessed for intracellular IFN-γ production by flow cytometry.

Results: In both murine mesothelioma models, the fusion protein scFv-MtbHsp70 alone delayed tumor growth and prolonged mouse survival, which was associated with increased tumor infiltration by CD3+CD8+ T cells. Treatment enhanced the cytotoxic function of tumor-specific CD3+CD8+ T cells by evoking dendritic cell activation as well as antigen presentation and cross presentation. AMD3100 alone reduced the proportion of CD4+CD25+Foxp3+ Treg cells in tumors and decreased PD-1 expression on CD3+CD8+ T cells. The combination of the fusion protein and AMD3100 further significantly slowed tumor growth and enhanced mouse survival while augmenting tumor-specific CD8+ T-cell immune responses and abrogating intratumoral immunosuppression.

Conclusion: Our findings demonstrated for the first time the synergistic effect of combination of MSLN-targeted immune-activating fusion protein scFv-MtbHsp70 and AMD3100 in treatment of MM in mice. This is a new therapeutic strategy which may significantly prolong survival of patients with this disease.

Citation Format: Huabiao Chen, Binghao Li, Yang Zeng, Patrick Reeves, Qiuyan Liu, Ann Sluder, Jeffrey Gelfand, Timothy Brauns, Mark Poznansky. Immunotherapy for malignant mesothelioma that combines a mesothelia-targeted immune-activating protein and CXCL12/CXCR4 blockade [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1633. doi:10.1158/1538-7445.AM2017-1633

Abstract 3649: Combination of mesothelin-targeted immune-activating fusion protein and anti-PD-L1 augments antitumor immunity and prolongs survival in murine model of ovarian cancer

Background and Purpose: Although immunotherapy as an adjuvant to surgery and chemotherapy has been investigated in ovarian cancer (OC) as a means of reducing tumor recurrence and improving survival, there remains a significant unmet need for combinatorial strategies to enhance the antitumor immune response. The purpose of this study was to develop a novel combination immunotherapy for OC, utilizing our novel fusion protein to target and generate a cellular immune response to mesothelin (MSLN) in conjunction with blockade of the PD-1/PD-L1 checkpoint to restore the function of cytotoxic T cells in order to enhance cancer control and prolong survival.

Experimental Procedures: Luciferase-expressing ID8 cells were employed to establish an intraperitoneal ovarian tumor model in immunocompetent C57BL/6 mice. The efficacies of the MSLN-targeted immune-activating fusion protein (VIC-008), αPD-L1, and the combination were evaluated. Mice received 4 intraperitoneal (i.p.) treatments of VIC-008 from day 7 post tumor inoculation weekly, and 6 treatments of αPD-L1 i.p. every other day from 4 weeks post inoculation. Tumor growth was monitored by in vivo imaging of luciferase activity. Survival time was calculated as life span from the day of tumor inoculation. In immunological studies, mice were sacrificed 7 weeks after tumor cell inoculation. Immune cells from lymph nodes, ascites and tumors were stained with antibodies against multiple immune cell markers and profiled by flow cytometry.

Results: VIC-008, αPD-L1 or combination treatment delayed tumor growth. The combination treatment resulted in the greatest prolongation in survival, followed by αPD-L1 treatment and then VIC-008 treatment. Improved survival was associated with increased levels of intratumoral CD3+CD8+ T cells (P<0.0001). The combination treatment also reduced the proportion of CD4+CD25+Foxp3+ Treg cells (P<0.0001) in the lymph nodes. An increased number of CD8+CD27+CD44+ memory T cells (P=0.0134) were observed in ascites in the combination treatment group. CD11b+CD11c+ dendritic cells were enriched in ascites in VIC-008 treatment (P=0.0019) and combination treatment groups (P=0.0010). More CD11c+CD38+ (M1) (P=0.0361) and fewer CD206+CD106+ (M2) (P=0.0285) macrophages were found in the tumors of the combination treatment group.

Conclusion: Our results suggest that, through activating dendritic cells and enhancing antigen presentation and cross-presentation, VIC-008 augments antitumor CD8+ T cell responses and facilitates generation of memory T cells when combined with PD-1/PD-L1 blockade, providing long-term antitumor effects. Our findings demonstrate for the first time a mechanistic rationale for combining VIC-008 and αPD-L1 in treatment of OC in mice, positioning this combination therapy as a potential promising new immunotherapeutic approach for OC.

Citation Format: Yang Zeng, Binghao Li, Qiuyan Liu, Patrick Reeves, Ann Sluder, Jeffrey Gelfand, Timothy Brauns, Mark Poznansky, Huabiao Chen. Combination of mesothelin-targeted immune-activating fusion protein and anti-PD-L1 augments antitumor immunity and prolongs survival in murine model of ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3649. doi:10.1158/1538-7445.AM2017-3649

Cyclosporin derivatives inhibit hepatitis B virus entry without interfering with NTCP transporter activity

BACKGROUND & AIMS

The sodium taurocholate co-transporting polypeptide (NTCP) is the main target of most hepatitis B virus (HBV) specific entry inhibitors. Unfortunately, these agents also block NTCP transport of bile acids into hepatocytes, and thus have the potential to cause adverse effects. We aimed to identify small molecules that inhibit HBV entry while maintaining NTCP transporter function.

METHODS

We characterized a series of cyclosporine (CsA) derivatives for their anti-HBV activity and NTCP binding specificity using HepG2 cells overexpressing NTCP and primary human hepatocytes. The four most potent derivatives were tested for their capacity to prevent HBV entry, but maintain NTCP transporter function. Their antiviral activity against different HBV genotypes was analysed.

RESULTS

We identified several CsA derivatives that inhibited HBV infection with a sub-micromolar IC50. Among them, SCY446 and SCY450 showed low activity against calcineurin (CN) and cyclophilins (CyPs), two major CsA cellular targets. This suggested that instead, these compounds interacted directly with NTCP to inhibit viral attachment to host cells, and have no immunosuppressive function. Importantly, we found that SCY450 and SCY995 did not impair the NTCP-dependent uptake of bile acids, and inhibited multiple HBV genotypes including a clinically relevant nucleoside analog-resistant HBV isolate.

CONCLUSIONS

This is the first example of small molecule selective inhibition of HBV entry with no decrease in NTCP transporter activity. It suggests that the anti-HBV activity can be functionally separated from bile acid transport. These broadly active anti-HBV molecules are potential candidates for developing new drugs with fewer adverse effects.

LAY SUMMARY

In this study, we identified new compounds that selectively inhibited hepatitis B virus (HBV) entry, and did not impair bile acid uptake. Our evidence offers a new strategy for developing anti-HBV drugs with fewer side effects.

Cyclophilin inhibitors reduce phosphorylation of RNA-dependent protein kinase to restore expression of IFN-stimulated genes in HCV-infected cells

BACKGROUND & AIMS

Cyclophilin inhibitors are being developed for treatment of hepatitis C virus (HCV) infection. They are believed to inhibit the HCV replication complex. We investigated whether cyclophilin inhibitors interact with interferon (IFN) signaling in cultured cells infected with HCV.

METHODS

We used immunoblot assays to compare expression of IFN-stimulated genes (ISGs) and of components of IFN signaling in HCV-infected and uninfected cells.

RESULTS

Incubation with IFN alfa induced expression of ISGs in noninfected cells and, to a lesser extent, in HCV-infected cells; addition of the cyclophilin inhibitor SCY-635 restored expression of ISG products in HCV-infected cells. SCY-635 reduced phosphorylation of double-strand RNA-dependent protein kinase (PKR) and its downstream factor eIF2α; the phosphorylated forms of these proteins are negative regulators of ISG translation. Cyclophilin A interacted physically with PKR; this interaction was disrupted by SCY-635. SCY-635 also suppressed PKR-mediated formation of stress granules. Cyclophilin inhibitors were found to inhibit PKR phosphorylation and stress granule formation in HCV-infected and uninfected cells.

CONCLUSIONS

In cultured cells, cyclophilin inhibitors reverse the attenuation of the IFN response by HCV, in addition to their effects on HCV replication complex. Cyclophilin A regulation of PKR has been proposed as a mechanism for observed effects of cyclophilin inhibitors on IFN signaling. We found that cyclophilin inhibitors reduce phosphorylation of PKR and eIF2α during HCV infection to allow for translation of ISG products. Proteins in this pathway might be developed as targets for treatment of HCV infection.

Cyclosporin A and its analogs inhibit hepatitis B virus entry into cultured hepatocytes through targeting a membrane transporter, sodium taurocholate cotransporting polypeptide (NTCP)

Chronic hepatitis B virus (HBV) infection is a major public health problem worldwide. Although nucleos(t)ide analogs inhibiting viral reverse transcriptase are clinically available as anti-HBV agents, emergence of drug-resistant viruses highlights the need for new anti-HBV agents interfering with other targets. Here we report that cyclosporin A (CsA) can inhibit HBV entry into cultured hepatocytes. The anti-HBV effect of CsA was independent of binding to cyclophilin and calcineurin. Rather, blockade of HBV infection correlated with the ability to inhibit the transporter activity of sodium taurocholate cotransporting polypeptide (NTCP). We also found that HBV infection-susceptible cells, differentiated HepaRG cells and primary human hepatocytes expressed NTCP, while nonsusceptible cell lines did not. A series of compounds targeting NTCP could inhibit HBV infection. CsA inhibited the binding between NTCP and large envelope protein in vitro. Evaluation of CsA analogs identified a compound with higher anti-HBV potency, having a median inhibitory concentration <0.2 μM.

CONCLUSION

This study provides a proof of concept for the novel strategy to identify anti-HBV agents by targeting the candidate HBV receptor, NTCP, using CsA as a structural platform.

HCV NS5A and IRF9 compete for CypA binding

BACKGROUND & AIMS

Cyclophilin A (CypA) is vital for HCV replication. Cyp inhibitors successfully decrease viral loads in HCV-infected patients. However, their mechanisms of action remain unknown. Since interferon (IFN) can also suppress HCV replication, we asked whether a link between CypA and the IFN response exists.

METHODS

We used cellular and recombinant pulldown approaches to investigate the possibility of a specific association of CypA with host ligands.

RESULTS

We found for the first time that CypA binds to a major component of the IFN response - the IFN regulatory factor 9 (IRF9). IRF9 is the DNA-binding component of the transcriptional IFN-stimulated gene factor 3 (ISGF3). CypA binds directly to IRF9 via its peptidyl-prolyl isomerase (PPIase) pocket. Cyp inhibitors such as cyclosporine A (CsA) or non-immunosuppressive derivates such as alisporivir and SCY-635, prevent IRF9-CypA complex formation. CypA binds to the C-terminal IRF-association-domain (IAD), but not to the DNA-binding or linker domains of IRF9. Remarkably, CypA associates with the multimeric ISGF3 complex. We also obtained evidence that CypA neutralization enhances IFN-induced transcription. Interestingly, the hepatitis C virus (HCV) non-structural 5A (NS5A) protein, which is known to modulate the IFN response, competes with IRF9 for CypA binding and can prevent the formation of IRF9-CypA complexes.

CONCLUSIONS

This study demonstrates for the first time that CypA binds specifically to a component of the Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway, IRF9. This study also reveals a novel opportunity of HCV to modulate the IFN response via NS5A.

Parasite neuropeptide biology: Seeding rational drug target selection?

The rationale for identifying drug targets within helminth neuromuscular signalling systems is based on the premise that adequate nerve and muscle function is essential for many of the key behavioural determinants of helminth parasitism, including sensory perception/host location, invasion, locomotion/orientation, attachment, feeding and reproduction. This premise is validated by the tendency of current anthelmintics to act on classical neurotransmitter-gated ion channels present on helminth nerve and/or muscle, yielding therapeutic endpoints associated with paralysis and/or death. Supplementary to classical neurotransmitters, helminth nervous systems are peptide-rich and encompass associated biosynthetic and signal transduction components - putative drug targets that remain to be exploited by anthelmintic chemotherapy. At this time, no neuropeptide system-targeting lead compounds have been reported, and given that our basic knowledge of neuropeptide biology in parasitic helminths remains inadequate, the short-term prospects for such drugs remain poor. Here, we review current knowledge of neuropeptide signalling in Nematoda and Platyhelminthes, and highlight a suite of 19 protein families that yield deleterious phenotypes in helminth reverse genetics screens. We suggest that orthologues of some of these peptidergic signalling components represent appealing therapeutic targets in parasitic helminths.

The cyclophilin inhibitor SCY-635 suppresses viral replication and induces endogenous interferons in patients with chronic HCV genotype 1 infection

BACKGROUND & AIMS

SCY-635 is a non-immunosuppressive analog of cyclosporin A that inhibits cyclophilins A and B and hepatitis C virus (HCV) replication in vitro. In a phase 1b multi-dose escalation study, we evaluated the safety, plasma pharmacokinetics, and antiviral activity of 15 days of monotherapy with SCY-635 in adults with chronic genotype 1 HCV infection.

METHODS

Twenty adults with chronic HCV genotype 1 were randomized to SCY-635 oral doses of 100, 200, or 300 mg three times daily for 15 days.

RESULTS

No dose-limiting clinical or laboratory toxicities were identified. On day 15, the mean decline in plasma viremia was 2.24±1.74 log(10) IU/ml with SCY-635 900 mg/d. Individual antiviral responses correlated with host IL28B genotype. Post hoc analyses indicated treatment with SCY-635 increased plasma protein concentrations of interferon α (IFNα), IFNs λ(1) and λ(3), and 2'5' oligoadenylate synthetase 1 (2'5'OAS-1), with the greatest increases in IL28B CC and CT subjects. Changes in plasma concentrations for all markers were coincident with changes in the plasma concentration of SCY-635. Peaks of IFNs α, λ(1), and λ(3) and 2'5'OAS-1 were observed within 2 h after drug administration. In replicon cells, SCY-635 enhanced secretion of type I and type III IFNs and increased the expression of IFN-stimulated genes (ISG).

CONCLUSIONS

These studies establish clinical proof of concept for SCY-635 as a novel antiviral agent and suggest that restoration of the host innate immune response to chronic hepatitis C infection may represent a major mechanism through which cyclophilin inhibitors exert clinical antiviral activity.

Spiroindolines identify the vesicular acetylcholine transporter as a novel target for insecticide action

The efficacy of all major insecticide classes continues to be eroded by the development of resistance mediated, in part, by selection of alleles encoding insecticide insensitive target proteins. The discovery of new insecticide classes acting at novel protein binding sites is therefore important for the continued protection of the food supply from insect predators, and of human and animal health from insect borne disease. Here we describe a novel class of insecticides (Spiroindolines) encompassing molecules that combine excellent activity against major agricultural pest species with low mammalian toxicity. We confidently assign the vesicular acetylcholine transporter as the molecular target of Spiroindolines through the combination of molecular genetics in model organisms with a pharmacological approach in insect tissues. The vesicular acetylcholine transporter can now be added to the list of validated insecticide targets in the acetylcholine signalling pathway and we anticipate that this will lead to the discovery of novel molecules useful in sustaining agriculture. In addition to their potential as insecticides and nematocides, Spiroindolines represent the only other class of chemical ligands for the vesicular acetylcholine transporter since those based on the discovery of vesamicol over 40 years ago, and as such, have potential to provide more selective tools for PET imaging in the diagnosis of neurodegenerative disease. They also provide novel biochemical tools for studies of the function of this protein family.

A new class of anthelmintics effective against drug-resistant nematodes

Anthelmintic resistance in human and animal pathogenic helminths has been spreading in prevalence and severity to a point where multidrug resistance against the three major classes of anthelmintics--the benzimidazoles, imidazothiazoles and macrocyclic lactones--has become a global phenomenon in gastrointestinal nematodes of farm animals. Hence, there is an urgent need for an anthelmintic with a new mode of action. Here we report the discovery of the amino-acetonitrile derivatives (AADs) as a new chemical class of synthetic anthelmintics and describe the development of drug candidates that are efficacious against various species of livestock-pathogenic nematodes. These drug candidates seem to have a novel mode of action involving a unique, nematode-specific clade of acetylcholine receptor subunits. The AADs are well tolerated and of low toxicity to mammals, and overcome existing resistances to the currently available anthelmintics.

Explosive lineage-specific expansion of the orphan nuclear receptor HNF4 in nematodes

The nuclear receptor superfamily expanded in at least two episodes: one early in metazoan evolution, the second within the vertebrate lineage. An exception to this pattern is the genome of the nematode Caenorhabditis elegans, which encodes more than 270 nuclear receptors, most of them highly divergent. We generated 128 cDNA sequences for 76 C. elegans nuclear receptors, confirming that these are active genes. Among these numerous receptors are 13 orthologues of nuclear receptors found in arthropods and/or vertebrates. We show that the supplementary nuclear receptors (supnrs) originated from an explosive burst of duplications of a unique orphan receptor, HNF4. This origin has specific implications for the role of ligand binding in the function and evolution of the nematode supplementary nuclear receptors. Moreover, the supplementary nuclear receptors include a group of very rapidly evolving genes found primarily on chromosome V. We propose a model of lineage-specific duplications from a chromosome on which duplication and substitution rates are highly increased. Our results provide a framework to study nuclear receptors in nematodes, as well as to consider the functional and evolutionary consequences of lineage-specific duplications.

Invertebrate disease models in neurotherapeutic discovery

Models that reproduce many of the cellular and molecular aspects of various human neurodegenerative disorders have been developed in the fruit fly Drosophila melanogaster and the nematode Caenorhabditis elegans. An understanding of the underlying molecular and genetic mechanisms of disease pathogenesis is being gained from studies utilizing the wealth of genetic and molecular tools available for these invertebrate model organisms. This review focuses on recent studies that lay a foundation for utilizing these disease models in drug discovery and for continued genetic dissection of disease mechanisms.

Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila genomes

BACKGROUND

The availability of complete genome sequences enables all the members of a gene family to be identified without limitations imposed by temporal, spatial or quantitative aspects of mRNA expression. Using the nearly completed human genome sequence, we combined in silico and experimental approaches to define the complete human nuclear receptor (NR) set. This information was used to carry out a comparative genomic study of the NR superfamily.

RESULTS

Our analysis of the human genome identified two novel NR sequences. Both these contained stop codons within the coding regions, indicating that both are pseudogenes. One (HNF4 gamma-related) contained no introns and expressed no detectable mRNA, whereas the other (FXR-related) produced mRNA at relatively high levels in testis. If translated, the latter is predicted to encode a short, non-functional protein. Our analysis indicates that there are fewer than 50 functional human NRs, dramatically fewer than in Caenorhabditis elegans and about twice as many as in Drosophila. Using the complete human NR set we made comparisons with the NR sets of C. elegans and Drosophila. Searches for the >200 NRs unique to C. elegans revealed no human homologs. The comparative analysis also revealed a Drosophila member of NR subfamily NR3, confirming an ancient metazoan origin for this subfamily.

CONCLUSIONS

This work provides the basis for new insights into the evolution and functional relationships of NR superfamily members.