Abstract While immune checkpoint therapies have revolutionized cancer treatment, their efficacy remains limited in colorectal cancer (CRC) and other malignancies. Tumors employ diverse strategies to evade immune-mediated destruction, hindering the success of immunotherapies. We introduce iOTarg, a robust high-throughput screening platform designed to uncover resistance pathways against T cell-mediated tumor killing within the tumor microenvironment. Focusing on CRC, we utilized iOTarg to dissect evasion mechanisms against antigen-specific T cell (TC) killing. In a representative CRC cell line co-culture system (SW480, HCT116 or COLO-678) with various TC sources, we gained key insights of tumor resistance towards killing. Survivin-specific TCs induce strong tumor lysis while tumor-infiltrating lymphocyte 412 (TIL412) represent a weaker basal killing representative of the situation in the tumor. Knockout of β₂-microglobulin abrogated TC-mediated killing, while c-FLIP knockout significantly enhanced tumor lysis. Intriguingly, PD-L1 blockade had no impact on TC activation or killing, underlining its lack of efficacy in CRC. Screening over 6000 druggable genes revealed several critical candidates, including anti-apoptotic BIRC family members (BIRC2, 3), apoptosis regulators (Bcl-xL, XIAP), TNF signaling regulators (TRAF2, MAP3K7), and genes recently described as sensitization mediators (B3GNT3, CHMP4B). Caspase-8 knockout prevented TC-mediated killing of CRC cells, confirming its crucial role in immune-mediated tumor cell clearance. Further validation in secondary screenings reinforced a subset of genes as strong regulators of tumor cell killing, uncovering an array of CRC resistance mechanisms. Our findings present a pioneering platform delineating resistance mechanisms against T cell-mediated colorectal tumor killing. We identify established and novel targets, offering prospects for novel therapeutics and expanding immune oncology treatment options. This platform holds promise for developing first-in-class therapies targeting the tumor microenvironment, potentially transforming CRC treatment paradigms. Citation Format: Tillmann Michels, Valentina Volpin, Carmen Amerhauser, Claudia Tschulik, Leonie Majunke, Aleksandra Weglarz, Kilian Baritz, Kritika Sudan, Szilvia Bak-Kiss, Alina Huth, Carolin Strobl, Adriana Turqueti-Neves, Nisit Khandelwal. iOTarg screening platform reveals novel mechanisms of colorectal cancer evasion from antigen-specific tumor cell killing by T cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB080.

Tumor-associated macrophages (TAMs) are important players to maintain immunosuppression within the tumor microenvironment (TME) and attenuate the function of effector immune cells to promote tumor survival. High density of TAMs is well-recognized as a feature of tumor progression and poor prognostic factor across various tumor types. Therefore, therapeutic strategies to dampen TAMs’ suppressive potential in TME and reprogram them towards a pro-inflammatory phenotype are being increasingly appreciated as being paramount for an effective immunotherapy. Nevertheless, the key mediators of TAM-induced immunosuppression remain largely unknown, identification of which can lead to the development of novel immunotherapeutic strategies aimed at re-educating the immunosuppressive TAMs to an anti-tumor phenotype. To systematically interrogate the genes responsible for the immune-suppressive phenotype of TAMs, we developed a functional, high-throughput genetic screening platform (iOTarg™) based on human primary monocyte-derived M2-like macrophages. Using CRISPR, we knocked out a proprietary library of well-expressed and druggable genes (1400 genes) in two independent donor-derived M2-like macrophages and cocultured them with activated autologous effector T cells (TCs). We achieved nearly complete knockout (KO) efficacy over a range of control genes. Functional impact of individual KO on macrophage viability and phenotype, as well as on TC activity, was measured using multiparametric assay readouts. Initial hits were reconfirmed in three additional donors in a secondary screen that integrated an additional tumor lysis readout. As expected, knockout of CSF1R, which is essential for macrophage maintenance, resulted in a dramatic loss of macrophage cell viability, whereas KO of established TAM markers, TREM2 and Clever-1, induced a change in macrophage phenotype. Furthermore, KO of immune-inhibitory receptor LILRB2 reduced the M2-like phenotype and restored TC activity. Inhibition of M2 activation of macrophages and subsequent increase in TC activation culminated in strong tumor cell killing for a subset of genes, highlighting an untapped repertoire of novel TAM-associated immune-checkpoint targets. Taken together, we report for the first time a highly sophisticated target discovery platform that addresses the functional role of any TAM-expressed gene in regulating macrophage viability, phenotype, T cell activity and even its gross impact on tumor cell lysis, all done in a high-throughput format employing CRISPR-edited primary human immune cells and multi-parametric functional immunological assays. As a result, we could confirm well-known targets in clinical testing, as well as identify additional novel targets that could lead to first-in-class, TME-based therapeutics and expansion of treatment options in immune oncology. Citation Format: Kritika Sudan, Tillmann Michels, Carmen Amerhauser, Claudia Tschulik, Leonie Majunke, Lucille Albert, Valentina Volpin, Adriana Turqueti-Neves, Ronny Milde, Nisit Khandelwal. A function-based high-throughput discovery platform, myeloid iOTarg, identifies novel immune checkpoints of the tumor microenvironment [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 3471.

Background Cancer immunotherapeutic strategies showed unprecedented results in the clinic. However, many patients do not respond to immuno-oncological treatments due to the occurrence of a plethora of immunological obstacles, including tumor intrinsic mechanisms of resistance to cytotoxic T-cell (TC) attack. Thus, a deeper understanding of these mechanisms is needed to develop successful immunotherapies. Methods To identify novel genes that protect tumor cells from effective TC-mediated cytotoxicity, we performed a genetic screening in pancreatic cancer cells challenged with tumor-infiltrating lymphocytes and antigen-specific TCs. Results The screening revealed 108 potential genes that protected tumor cells from TC attack. Among them, salt-inducible kinase 3 (SIK3) was one of the strongest hits identified in the screening. Both genetic and pharmacological inhibitions of SIK3 in tumor cells dramatically increased TC-mediated cytotoxicity in several in vitro coculture models, using different sources of tumor and TCs. Consistently, adoptive TC transfer of TILs led to tumor growth inhibition of SIK3-depleted cancer cells in vivo. Mechanistic analysis revealed that SIK3 rendered tumor cells susceptible to tumor necrosis factor (TNF) secreted by tumor-activated TCs. SIK3 promoted nuclear factor kappa B (NF- κB) nuclear translocation and inhibited caspase-8 and caspase-9 after TNF stimulation. Chromatin accessibility and transcriptome analyses showed that SIK3 knockdown profoundly impaired the expression of prosurvival genes under the TNF–NF- κB axis. TNF stimulation led to SIK3-dependent phosphorylation of the NF-κB upstream regulators inhibitory-κB kinase and NF-kappa-B inhibitor alpha on the one side, and to inhibition of histone deacetylase 4 on the other side, thus sustaining NF-κB activation and nuclear stabilization. A SIK3-dependent gene signature of TNF-mediated NF-κB activation was found in a majority of pancreatic cancers where it correlated with increased cytotoxic TC activity and poor prognosis. Conclusion Our data reveal an abundant molecular mechanism that protects tumor cells from cytotoxic TC attack and demonstrate that pharmacological inhibition of this pathway is feasible.

Post-translational modifications of DNA and histones can improve the intrinsic antitumor capacity of the immune system. Using the iOTarg screening platform, salt-inducible kinase 3 (SIK3) was identified as a novel epigenetic modulator in cancer therapy. SIK3, a serine/threonine kinase of the AMP-activated protein kinase family, is known for regulating the NF-κB driven gene landscape through phosphorylation of class IIa histone deacetylases (HDACs) and CREB-regulated transcriptional coactivators causing the tumor to evade death receptor-mediated killing. Moreover, salt inducible kinases were recently described to regulate cell cycle checkpoints and thereby promote cancer cell proliferation. We demonstrate that SIK3 knockdown abates downstream pro-survival signaling and induces cell death in a distinct panel of tumor cell lines. OMX-0407, an orally available, single-digit nanomolar inhibitor of SIK3 was shown to effectively reduce TNF-induced HDAC4 phosphorylation and downstream NF-κB activity in a dose-dependent manner, thereby enhancing apoptosis in murine and human tumor cell lines. OMX-0407 dose-dependent suppression of intratumoral NF-κB activity was shown in vivo in an MC38 NF-κB-luc reporter cell line. Using OMX-0407 monotherapy, this translated to significant tumor growth inhibition as well as prolonged survival in the highly immune infiltrated syngeneic murine colorectal carcinoma model MC38. Besides its direct inhibitory effects on cancer cells, OMX-0407 repolarizes the tumor microenvironment (TME) by strongly decreasing regulatory T cells (T-regs) and M2-polarized macrophages in the tumor bed, while not affecting the peripheral T cell compartment. Thus, exposure to OMX-0407 leads to a distinct pro-inflammatory TME, characterized by an expansion of activated cytotoxic T lymphocytes (CTL) and an increased CTL-to-T-reg ratio. Using an immune-excluded tumor phenotype as seen in the breast cancer mouse model EMT6, we demonstrated that OMX-0407 and anti-PD-1 act synergistically by combining the sensitization towards cell death with a reduction in immunosuppressive TME and an increase in cytotoxic T cell activity, despite having only minimal anti-tumor efficacy as monotherapy. Thereby, partial or complete tumor remission in 60% of the animals and extension of overall survival were achieved. In summary, OMX-0407, a first-in-class oral SIK3 inhibitor, demonstrates potent monotherapy efficacy in a pro-inflammatory tumor setting by reshaping the immune compartment and accelerating tumor cell death. The ability of OMX-0407 to remodel an immunosuppressed TME in a generally cold tumor setting, harbors great clinical potential for OMX-0407 combination therapy with anti-PD-1/PD-L1 immune checkpoint blockade, specifically in patients with high unmet medical need who are resistant to current immune checkpoint inhibitor monotherapy. Citation Format: Christina Hartl, Ilona-Petra Maser, Tillmann Michels, Ronny Milde, Vanessa Klein, Philipp Beckhove, Nisit Khandelwal, Hannes Loferer, Stefan Bissinger. OMX-0407, a highly potent SIK3 inhibitor, sensitizes tumor cells to cell death and eradicates tumors in combination with PD-1 inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3708.

Background: The cGAS-cGAMP-STING pathway plays a crucial role in both tumor and immune cells to promote anti-tumor immunity. Preclinically, synthetic STING agonists have shown promise, but have not demonstrated robust clinical efficacy potentially due to detrimental effects on immune cells which may compromise anti-tumor efficacy. ENPP1, an ectonucleotide pyrophosphatase/phosphodiesterase that catalyzes the hydrolysis of the endogenous STING agonist 2′,3′-cGAMP, is a negative regulator of STING activation and its inhibition represents an alternative way to stimulate the STING pathway that would potentially spare the immune damaging effects associated with hyperactivation of STING.

Background Interference with post-translational modifications such as methylation and acetylation of DNA and histones may enhance the intrinsic anti-tumor capacity of the immune system. Using the iOTarg genetic screening platform, salt-inducible kinase 3 (SIK3) was recently identified as a novel immune checkpoint that controls T cell-mediated apoptosis in tumor cells. SIK3, a serine/threonine kinase of the AMPK family, regulates pro-survival gene expression in tumor cells through epigenetic modulation of the NF κB-driven gene landscape via histone deacetylase 4 (HDAC4), causing the tumor to evade T cell-mediated killing. Methods In turn, SIK3 knockout or knockdown abates downstream pro-survival signaling and sensitizes a panel of murine and human tumor cells to death receptor-mediated apoptosis.OMX-0407, an orally available, single-digit nanomolar inhibitor of SIK3 was shown to effectively reduce TNF-induced HDAC4 phosphorylation and downstream NF-κB activity in a dose-dependent manner, thereby enhancing caspase-mediated apoptosis in murine and human tumor cell lines. Decreased intratumoral NF-κB activity was demonstrated in vivo with an MC38 NF κB-luc reporter cell line. Results Inhibition of the pro-tumorigenic NF-κB pathway using OMX-0407 monotherapy translated into significant tumor growth inhibition (TGI) as well as prolonged survival in the highly infiltrated syngeneic murine colorectal carcinoma model MC38 (76% TGI). Moreover, OMX-0407 repolarized the tumor microenvironment (TME) by strongly reducing the number of regulatory T cells (T-regs) and M2-polarized macrophages in the tumor bed, while not affecting the peripheral T cell compartment. Thereby, exposure to OMX-0407 achieved a pronounced pro-inflammatory TME, characterized by a rise in activated cytotoxic T lymphocytes (CTL) and an increased CTL-to-T-reg ratio.Using the breast cancer mouse model EMT6, which represents an immune-excluded, cold tumor phenotype, we demonstrated that despite the minimal anti-tumor efficacy of OMX-0407 and anti-PD-1 monotherapy, respectively, upon combination treatment, both therapies synergize by combining apoptosis sensitization with a reduction in immunosuppressive TME and an increase in cytotoxic T cell activity. Combination treatment resulted in partial and complete tumor remissions in 60% of the animals, along with a significant prolongation of overall survival. Conclusions In summary, OMX-0407, a first-in-class oral SIK3 inhibitor, demonstrates potent monotherapy efficacy in a pro-inflammatory tumor setting by reshaping the immune compartment and sensitizing tumor cells to death receptor-mediated apoptosis. The ability of OMX-0407 to remodel an immunosuppressed TME in a generally cold tumor setting, harbors great clinical potential for OMX-0407 combination therapy with anti-PD-1/PD-L1 immune checkpoint blockade, specifically in patients with high unmet medical need who are resistant to current immune checkpoint inhibitor monotherapy.

Regulatory CD4 + T cells (Treg) prevent tumor clearance by conventional T cells (Tconv) comprising a major obstacle of cancer immune-surveillance. Hitherto, the mechanisms of Treg repertoire formation in human cancers remain largely unclear. Here, we analyze Treg clonal origin in breast cancer patients using T-Cell Receptor and single-cell transcriptome sequencing. While Treg in peripheral blood and breast tumors are clonally distinct, Tconv clones, including tumor-antigen reactive effectors (Teff), are detected in both compartments. Tumor-infiltrating CD4 + cells accumulate into distinct transcriptome clusters, including early activated Tconv, uncommitted Teff, Th1 Teff, suppressive Treg and pro-tumorigenic Treg. Trajectory analysis suggests early activated Tconv differentiation either into Th1 Teff or into suppressive and pro-tumorigenic Treg. Importantly, Tconv, activated Tconv and Treg share highly-expanded clones contributing up to 65% of intratumoral Treg. Here we show that Treg in human breast cancer may considerably stem from antigen-experienced Tconv converting into secondary induced Treg through intratumoral activation.

Abstract SIK3 is an intracellular serine/threonine kinase belonging to the AMPK superfamily. We recently discovered a novel role of SIK3 in conferring TNF resistance to tumor cells. Resistance to TNF is an emerging mode of immune evasion in multiple solid tumors. In fact, while treating a broad panel of tumor cell lines with TNF we observed that almost 70% were either resistant or even proliferative in response to TNF. SIK3 knockout using CRISPR re-sensitized human PANC-1 and murine MC38 tumor cells to TNF-mediated death. Intratumoral SIK3 induces TNF resistance by retaining HDAC4 in the cytoplasm thus keeping the chromatin open and potentiating the TNF-driven pro-tumorigenic activity of NF-κB. To translate these findings into the clinic, we have developed a potent (low nM range) inhibitor of SIK3, OMX-0370. Firstly, OMX-0370 exhibits dose-dependent inhibition of HDAC4 phosphorylation and nuclear NF-κB activity in response to TNF, thereby effectively neutralizing the SIK3-HDAC4-NF-κB axis. Consequently, treatment of human as well as murine tumor cells with OMX-0370 induces significant TNF-mediated apoptosis while sparing non-TNF treated cells. In mouse DMPK studies, OMX-0370 was found to be orally bioavailable with a favorable pharmacokinetic profile and was well tolerated at 100 mg/kg twice daily dosing in wild type C57BL/6 mice. Having shown a potent and favorable biochemical, functional as well as pharmacokinetic profile of the molecule, we next investigated the ability of OMX-0370 to inhibit the growth of established tumors in multiple syngeneic tumor models, including MC38, EMT6 and RENCA. Notably, OMX-0370 showed significant tumor growth inhibition as a single agent, which was found to be even superior to anti-PD-1 antibody treatment in RENCA and EMT-6 models. Immune profiling showed enhanced activation of intratumoral T cells, improved ratio of CTLs to Tregs and depletion of tumor-associated M2 macrophages, while no effect on peripheral leukocyte counts was observed. To monitor target engagement and pharmacodynamics of OMX-0370 in vivo, we developed a reporter MC38 cell line expressing luciferase under a NF-κB promotor. Using this reporter cell line, we could show that OMX-0370 inhibits TNF-induced NF-κB activation in a dose-dependent manner. Encouraged by the strong single-agent activity of OMX-0370 in solid tumor models, we have developed follow-on variants that exhibit higher potency as well as improved exposure in vivo. In summary, we here report that OMX-0370, a first-in-class inhibitor of SIK3 kinase, is an active immunotherapeutic drug in vivo which effectively abolishes the TNF-driven NF-κB activity in tumors and re-sensitize them to TNF-induced apoptosis. OMX-0370 and its follow-on improved variants address the high unmet medical need of effective immunotherapeutic agents that neutralize clinically relevant and key orthogonal immune evasion axes in solid tumors as a monotherapy regimen. Citation Format: Tillmann Michels, Stefan Bissinger, Peter Sennhenn, Hannes Loferer, Catarina Martins Freire, Olivia Reidell, Sebastian Meier-Ewert, Apollon Papadimitriou, Philipp Beckhove, Nisit Khandelwal. A first-in-class SIK3 inhibitor, OMX-0370, effectively inhibits tumor growth in syngeneic tumor models, as single agent, by abolishing tumor resistance to immune-derived TNF [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6698.

Abstract The success of cancer immunotherapy is limited by resistance to immune checkpoint blockade. We therefore conducted a genetic screen to identify genes that mediated resistance against CTLs in anti–PD-L1 treatment–refractory human tumors. Using PD-L1–positive multiple myeloma cells cocultured with tumor-reactive bone marrow–infiltrating CTL as a model, we identified calcium/calmodulin-dependent protein kinase 1D (CAMK1D) as a key modulator of tumor-intrinsic immune resistance. CAMK1D was coexpressed with PD-L1 in anti–PD-L1/PD-1 treatment–refractory cancer types and correlated with poor prognosis in these tumors. CAMK1D was activated by CTL through Fas-receptor stimulation, which led to CAMK1D binding to and phosphorylating caspase-3, -6, and -7, inhibiting their activation and function. Consistently, CAMK1D mediated immune resistance of murine colorectal cancer cells in vivo. The pharmacologic inhibition of CAMK1D, on the other hand, restored the sensitivity toward Fas-ligand treatment in multiple myeloma and uveal melanoma cells in vitro. Thus, rapid inhibition of the terminal apoptotic cascade by CAMK1D expressed in anti–PD-L1–refractory tumors via T-cell recognition may have contributed to tumor immune resistance.

Background: Multiple myeloma (MM) is a B-cell malignancy, characterized by the accumulation of plasma cell clones in the bone marrow. Despite tremendous progresses in cancer immunotherapy, a plethora of tumor patients is still refractory to current immunotherapeutic strategies. Several studies showed that by taking advantage of different immune-checkpoint molecules tumor cells can either dampen immune cell functionality or promote tumor cell resistance towards immune attack. Despite the encouraging results achieved by blocking CTLA-4 and the PD-1/PD-L1 axis in the treatment of various solid tumors and Hodgkin's lymphoma, targeting these checkpoints did not induce objective responses in Phase I/II trials in MM patients. Therefore, the identification of novel immune-checkpoints and defining the subsequent molecular mechanisms of inhibition is essential for further improvement.

Clinical trials with immune-checkpoint blockade antibodies have bolstered the importance of immune therapy as the standard of care for cancer patients, but it has also simultaneously highlighted the heterogeneity in patient responses to such treatment. These heterogeneities can be explained to a certain extent by the lack of tumor-specific expression of the targeted immune checkpoint molecules. But in many cases it can also be conceived that tumors either develop resistance to a targeted immune-checkpoint node by circumventing it or more than one player is involved in a concerted action to subvert the T cell response. In either scenario, we lack a holistic understanding of the putative genes in the tumor genome that could functionally suppress the immune response. To bridge this gap, we employed a high-throughput RNAi-mediated knockdown of upto 2800 genes (~50% associated with surface molecules) in MCF7 (breast), M579-A2 (melanoma) and PANC-1 (pancreatic) tumor cell lines and co-cultured them with either antigen-specific T cell clones or respective patient-derived and tumor-specific infiltrating lymphocytes (TILs) to assess the impact on anti-tumor immunity using a luciferase-based readout. Primary hit-list was further subjected to a secondary screen based on multi-cytokine profiling of the T cells. Our investigation revealed a few salient caveats of tumor-mediated immune suppression. Firstly, we discovered a family of orphan receptors, which were never attributed to the immune system before, to actively suppress the T cells in a manner comparable to the currently defined immune-checkpoint molecules, such as PD-L1. Secondly, the trans-versatility of these novel molecules across the tumor types was highly limited, with only 3-14 common molecules being involved in two or more tumor types. This leads us to our third observation that there exists a complex organ-specific orchestration of peripheral immune tolerance, which needs to be taken into account when devising immune-checkpoint blockade therapies. Amongst the key immunosuppressive candidate genes, CCR9 was validated to directly subvert T cell responses in melanoma, breast and pancreatic cancer in the in vitro and in vivo tumor models. Additionally we have verified TiMi1, an orphan G-protein coupled receptor, to mediate strong immunosuppression in melanoma and pancreatic cancer against the respective TILs. Knockdown of both CCR9 and TiMi1, either via siRNAs or shRNAs, in tumor cells significantly increased Th1 cytokine secretion by TILs along with elevated tumor lysis in vitro and in vivo xenotransplanted mouse models. Moreover, they both induce a highly immunosuppressive genetic signature in the encountering TILs. While TiMi1 appeared to modulate calcium-dependent signaling, CCR9 regulated STAT signaling in T cells leading to an immunosuppressed phenotype. Overall, these candidates represent attractive targets for cancer immunotherapy either through function blocking antibodies or small molecules. In conclusion, we here report an effective genetic screen strategy in multiple tumor types that has the potential to uncover novel modifiers of anti-tumor immunity. Extensively validated candidates from these screens are attractive targets for cancer immunotherapy that will allow us to further expand our limited arsenal of immune-checkpoint inhibitors, with the overall goal of increasing patient responses to such treatments. Citation Format: Nisit Khandelwal, Tillmann Michels, Marco Breinig, Antonio Sorrentino, Isabel Poschke, Rienk Offringa, Michal Lotem, Michael Boutros, Philipp Beckhove. Genetic knockdown screens across tumor types unravel a diverse tumor “immune-modulatome” landscape. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr A070.

Abstract BACKGROUND: Being one of the most treatment-resistant cancer types, pancreatic ductal adenocarcinoma (PDAC) is characterized by its ability to escape immune surveillance by developing many immunological obstacles. These include a plethora of mechanisms that either dampen immune cell functionality, or foster tumor cell resistance towards immune attack. Immunotherapeutic strategies, such as immune checkpoint blockade, have proven clinical success in many cancer entities, but showed little clinical benefit in PDAC patients, emphasizing the need to identify more key players that could radically improve immunotherapy. AIM: We aim to systematically identify the whole arsenal of tumor-associated immune modulators by performing a high-throughput RNAi screen and subsequently validate novel therapeutic targets, whose blockade could potentially enhance anti-tumor immune response in PDAC patients. METHODS: We generated a luciferase-expressing PANC-1 cell line and knocked down 2514 genes using a siRNA library. Our library includes G-protein coupled receptors, protein kinases and 1117 surface proteins. We co-cultured HLA-A201+ matched tumor infiltrating lymphocytes (TILs) derived from a PDAC patient with the transfected tumor cells. We then measured the remaining luciferase intensity of the tumor cells as an estimation of TIL-mediated cytotoxicity. In order to exclude genes whose knock-down affected cell viability per se, we cultivated tumor cells with the siRNA library in the absence of TILs. RESULTS: We identified 155 candidate genes whose knock-down enhances TIL-mediated killing more efficiently than PD-L1 down-regulation. 35% of these genes are surface molecules and are most likely to directly mediate tumor immune evasion. Beside novel undescribed genes, our list contains well characterized immune modulators, supporting the reliability of our approach. Of note 13 of our hits were also found in a related melanoma screen and might play a role in the regulation of immune surveillance of different tumor entities. Among our candidates, 4 hits were chosen for further validation. We confirmed the expression of our selected candidates in several tumor cell lines and assessed the siRNA on-target effect using several non-overlapping siRNA sequences targeting the same hit. Transfection of PANC-1 with different siRNA sequences showed knock-down of the target gene as assessed via qPCR. Additionally we observed increased T-cell mediated killing as measured via luciferase-based killing assay and Chromium release assay. CONCLUSION: We set up a robust and systematic method to unravel novel key players of pancreatic cancer immune surveillance. Further functional validation of our candidate genes will prove their potential to be used as relevant therapeutic targets in the clinic. Citation Format: Antonio Sorrentino, Ayse Nur Menevse, Tillmann Michels, Nisit Khandelwal, Marco Breinig, Isabel Poschke, Valentina Volpin, Sabrina Wagner, Rienk Offringa, Michael Boutros, Philipp Beckhove. RNAi discovery platform to identify novel genes that prevent immune surveillance in pancreatic ductal adenocarcinoma (PDAC). [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2339.

Abstract Immunotherapeutic treatment of melanoma achieved major progress in recent years leading for the first time to improved survival. However, since melanoma cells employ various suppressive mechanisms in order to evade recognition and destruction by immune effector cells many patients still do not benefit from immunotherapy. These mechanisms are far more diverse than reflected by currently used immune modulatory drugs. In this study, we established and utilized a novel high throughput RNAi screening to identify new immune checkpoint molecules in melanoma using antigen-specific patient-derived tumor infiltrating lymphocytes (TILs) in conjunction with primary HLA-matched melanoma cells. Using this approach, we screened a siRNA library targeting more than 1200 surface receptors and kinases to explore novel targets for immunotherapy. Briefly, HLA-A2 and luciferase positive M579-A2-luc melanoma cells were reversely transfected with the siRNA library and then co-cultured with MART1- and gp100-specific TILs to validate the TIL-mediated tumor lysis. Local regression models (LOESS) were applied to generate a hit list of 48 candidates that negatively regulated CTL cytotoxicity. Interestingly, four candidates of a related breast cancer screen were among the top hits. To streamline the discovery process for large scale molecule libraries, we established a secondary screen assaying multiple T cell activation markers, including effector cytokines. One of the strongest candidates from our primary and secondary screening is TiMi1 (name altered), a cell surface receptor belonging to the class of GPCRs. We found that knock-down of TiMi1 increased TIL-mediated killing of M579-A2-luc without affecting their viability. TiMi1 knock-down increased TIL activity measured by production of type 1-associated cytokines (e.g. IFN γ and TNF-α), reduced TC apoptosis and increased markers associated with raised activity and cytotoxicity (4-1BB and CD107a). We were able to verify the immune checkpoint function of TiMi1 in melanoma patients using an autologous set of melanoma cells and TILs. Phosphoplex analysis in T cells revealed an involvement of the transcription factor CREB in the mode of action of TiMi1. Preliminary experiments suggest that TiMi1 inhibits anti-tumor immune responses in pancreatic (PDAC) and colorectal (CRC) cancers as well. In summary, we established a novel antigen-specific screening approach for immune checkpoints expressed in melanoma and were able to identify TiMi1 as a promising candidate. Moreover, TiMi1 inhibits T cell responses in melanoma, PDAC and CRC and might be an interesting target for immunotherapy. Our novel high-throughput screening offers a systematic platform to uncover the “immune-modulatome” of cancer and subsequently discover novel targets for immunotherapy. Since the presented work is considered for patent protection, some gene targets are masked in the presented study. Citation Format: Tillmann Michels, Christina A. Hartl, Nisit Khandelwal, Marco Breinig, Antonio Sorrentino, Christina Mäder, Ludmila Umansky, Isabel Poschke, Rienk Offringa, Michael Boutros, Galit Eisenberg, Michal Lotem, Philipp Beckhove. TiMi1 is a novel immune-checkpoint in solid tumors identified via a tumor-infiltrating lymphocyte (TIL)-based RNAi screening. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 254. doi:10.1158/1538-7445.AM2015-254

Abstract BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) accounts for 95% of pancreatic cancers and constitutes the fourth leading cause of cancer related death worldwide. In contrast to other malignancies, PDAC is highly resistant to chemotherapy and radiotherapy. Additionally, few immunotherapies are currently available because this malignancy was thought to be poorly immunogenic. Recent studies have shown that infiltration of immune cells in biopsies of PDAC patients correlates with improved clinical outcome. Nevertheless, tumor cells can elude the immune system through several inhibitory mechanisms including the expression of immune checkpoints. These are a plethora of molecules that can either boost or dampen the T-cell receptor (TCR) signaling. Some of these molecules, such as PD-L1, have been successfully used as therapeutic targets of novel anticancer drugs. AIM: We hypothesize that many immune checkpoint molecules on tumor cells remain undiscovered and we performed a high-throughput RNAi screen to unravel the whole arsenal of immune modulators. METHODS: We generated a luciferase-expressing PANC-1 cell line and knocked down 2514 genes using a siRNA library. Our library included G-protein coupled receptors, protein kinases and 1117 surface proteins. We co-cultured HLA-A201+ matched tumor infiltrating lymphocytes (TILs) derived from a PDAC patient with the transfected tumor cells. We then measured the remaining luciferase intensity of the tumor cells as an estimation of TIL-mediated cytotoxicity. In order to exclude genes whose knock-down affected cell viability per se, we cultivated tumor cells with the siRNA library in the absence of TILs. Data were analyzed with the cellHTS2 R package. RESULTS: Our screen revealed 155 candidate genes whose knock-down enhances TIL-mediated killing more efficiently than PD-L1 down-regulation. 35% of these genes are surface molecules and are most likely to directly mediate tumor immune evasion. Beside novel undescribed immune checkpoints, our list contains well characterized immune modulators, supporting the reliability of our approach. Of note 13 of our hits were also found in a related melanoma screen and might play a role in the regulation of immune surveillance of many solid tumors. Among our candidates, TONI1 was one of the most prominent hits. So far, we confirmed the role of TONI1 in inhibiting TIL-mediated killing both in chromium release and luciferase based kill assays. Additionally we detected increased T-cell activity upon TONI1 down-regulation, as measured with interferon-γ ELISPOT and TNF-α ELISA. Since the presented work is considered for patent protection, some gene targets are masked. CONCLUSION: We set up a robust and systematic method to identify novel immune checkpoints for pancreatic cancer. Further functional validation of our candidate genes will prove their use as therapeutic targets. Citation Format: Antonio Sorrentino, Tillmann Michels, Ayse Nur Menevse, Nisit Khandelwal, Marco Breinig, Isabel Poschke, Rienk Offringa, Michael Boutros, Philipp Beckhove. Identification of novel immune checkpoints as potential therapeutic targets in pancreatic ductal adenocarcinoma (PDAC) using RNAi screening. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 245. doi:10.1158/1538-7445.AM2015-245

The success of T cell-based cancer immunotherapy is limited by tumor's resistance against killing by cytotoxic T lymphocytes (CTLs). Tumor-immune resistance is mediated by cell surface ligands that engage immune-inhibitory receptors on T cells. These ligands represent potent targets for therapeutic inhibition. So far, only few immune-suppressive ligands have been identified. We here describe a rapid high-throughput siRNA-based screening approach that allows a comprehensive identification of ligands on human cancer cells that inhibit CTL-mediated tumor cell killing. We exemplarily demonstrate that CCR9, which is expressed in many cancers, exerts strong immune-regulatory effects on T cell responses in multiple tumors. Unlike PDL1, which inhibits TCR signaling, CCR9 regulates STAT signaling in T cells, resulting in reduced T-helper-1 cytokine secretion and reduced cytotoxic capacity. Moreover, inhibition of CCR9 expression on tumor cells facilitated immunotherapy of human tumors by tumor-specific T cells in vivo. Taken together, this method allows a rapid and comprehensive determination of immune-modulatory genes in human tumors which, as an entity, represent the 'immune modulatome' of cancer.

V. Shurin, Michael R. Shurin and Viktor UmanskyLudmila Umansky, Philipp Beckhove, Masashi Kato, GalinaAlexandra Sevko, Tillmann Michels, Melissa Vrohlings,http://www.jimmunol.org/content/190/5/2464doi: 10.4049/jimmunol.1202781January 2013;J Immunol€2013; 190:2464-2471; Prepublished online 28MaterialSupplementary1.DC1.htmlhttp://www.jimmunol.org/content/suppl/2013/01/28/jimmunol.120278Referenceshttp://www.jimmunol.org/content/190/5/2464.full#ref-list-1This article cites 39 articles, 13 of which you can access for free at: Subscriptionshttp://jimmunol.org/subscriptionsInformation about subscribing to The Journal of Immunology is online at: Permissionshttp://www.aai.org/ji/copyright.htmlSubmit copyright permission requests at: Email Alertshttp://jimmunol.org/cgi/alerts/etocReceive free email-alerts when new articles cite this article. Sign up at:

The antitumor effects of paclitaxel are generally attributed to the suppression of microtubule dynamics resulting in defects in cell division. New data demonstrated that in ultralow noncytotoxic concentrations, paclitaxel modulated in immune cells in vitro the activity of small Rho GTPases, the key regulators of intracellular actin dynamics. However, the immunomodulatory properties of paclitaxel in vivo have not been evaluated. In this study, using the ret transgenic murine melanoma model, which mimics human cutaneous melanoma, we tested effects of ultralow noncytotoxic dose paclitaxel on functions of myeloid-derived suppressor cells (MDSCs), chronic inflammatory mediators, and T cell activities in the tumor microenvironment in vivo. Administration of paclitaxel significantly decreased accumulation and immunosuppressive activities of tumor-infiltrating MDSCs without alterations of the bone marrow hematopoiesis. This was associated with the inhibition of p38 MAPK activity, TNF-α and production, and S100A9 expression in MDSCs. The production of mediators of chronic inflammation in the tumor milieu also was diminished. Importantly, reduced tumor burden and increased animal survival upon paclitaxel application was mediated by the restoration of CD8 T cell effector functions. We suggest that the ability of paclitaxel in a noncytotoxic dose to block the immunosuppressive potential of MDSCs in vivo represents a new therapeutic strategy to downregulate immunosuppression and chronic inflammation in the tumor microenvironment for enhancing the efficacy of concomitant anticancer therapies.