Histone deacetylases (HDACs) are key mediators of gene expression and, thus, major regulators of cell function. As such, HDACs play a role in orchestrating tumor biology, and the use of small inhibitors targeting theses proteins is attractive for the field of cancer therapy. Indeed, several HDAC inhibitors have received FDA-approval for the treatment of malignancies, while a myriad of these compounds continue to be evaluated in clinical trials. Besides their direct impact on tumor growth, HDAC inhibitors have been shown to increase immunogenicity of cancer cells, facilitating generation of a productive immune response against tumors. Immunotherapeutic approaches take advantage of the intrinsic ability of the immune system to manifest an anti-tumor response. Mechanisms of immune escape are often developed by cancer cells, neutralizing activity of the immune system. For example, upregulation of the PD1 ligands PDL1 and PDL2 by tumor cells negatively regulates the anti-tumor functions of PD1-expressing infiltrating T-cells. Importantly, strategies targeting this inhibitory axis have shown outstanding clinical benefit for the treatment of solid and hematological malignancies. The mechanisms by which HDAC inhibitors modulate tumor and immune cells biology were explored herein. Initially, treatment of melanoma cells with pan- and class I-selective HDAC inhibitors resulted in upregulation of PDL1 and PDL2 molecules. These effects were observed in mouse and human cell lines, as well as in tumor cells resected from metastatic melanoma patients. This upregulation was robust and sustained, lasting at least 96 hours in vitro, and validated in vivo using a B16F10 syngeneic mouse model. Enhanced expression of PDL1 mediated by HDAC inhibitors was found to result from enhanced histone acetylation at the PDL1 gene promoter region. Combination therapy of HDAC inhibition and PD1 blockade was explored in the tumor setting, leading to synergistic effects in terms of reducing melanoma progression and increasing survival of B16F10 melanoma-bearing mice. These data provide a clinical rationale for combination therapy of epigenetic modifiers (e.g. HDAC inhibitors) and PD1 blockade as means to augment cancer immunotherapy, improving patient outcomes. As a second pillar of this research, the impacts of HDAC-selective inhibition were explored on immune cell biology, since the broad nature of pan-HDAC inhibitors was shown to be detrimental to T-cells in vitro and in vivo. Based on screening assay results, novel implications of treating melanoma patient T-cells ex vivo with the HDAC6-selective inhibitor ACY1215 were investigated. Treatment with this compound was unique among pan- and isotype-selective HDAC inhibitors in modulating T-cell cytokine production and showing minimal impact of T-cell viability. ACY1215 tempered Th2 cytokine production (i.e. IL-4, IL-6 and IL-10), and maintained Th1 effector cytokines (e.g. IFNγ and IL-2). Furthermore, ACY1215 increased expression of surface markers, including CD69 activation marker and ICOS co-stimulatory molecule. In addition, ACY1215 treatment enhanced accumulation of central memory T-cells during ex vivo expansion of tumor infiltrating T-cells harvested from resected tumors of metastatic melanoma patients. Importantly, ACY1215-mediated inhibition improved tumor-killing capacity of T-cells. These results highlight an unexplored ability of selective HDAC inhibitor ACY1215 to augment T-cell expansion during protocols of adoptive cell therapy. While the discoveries presented here warrant further investigation of cellular and molecular mechanisms associated with ACY1215-treated T-cells, the clinic implications are clear and rapidly translatable.

Peripheral T-cell non-Hodgkin lymphoma (PTCL) are heterogeneous, rare, and aggressive diseases mostly incurable with current cell cycle therapies. Aurora kinases (AKs) are key regulators of mitosis that drive PTCL proliferation. Alisertib (AK inhibitor) has a response rate similar to 30% in relapsed and refractory PTCL (SWOG1108). Since PTCL are derived from CD4(+)/CD8(+) cells, we hypothesized that Program Death Ligand-1 (PDL1) expression is essential for uncontrolled proliferation. Combination of alisertib with PI3K alpha (MLN1117) or pan-PI3K inhibition (PF-04691502) or vincristine (VCR) was highly synergistic in PTCL cells. Expression of PD-L1 relative to PD-1 is high in PTCL biopsies (similar to 9-fold higher) and cell lines. Combination of alisertib with pan-PI3K inhibition or VCR significantly reduced PD-L1, NF-kappa B expression and inhibited phosphorylation of AKT, ERK1/2 and AK with enhanced apoptosis. In a SCID PTCL xenograft mouse model, alisertib displayed high synergism with MLN1117. In a syngeneic PTCL mouse xenograft model alisertib demonstrated tumor growth inhibition (TGI) similar to 30%, whilst anti-PD-L1 therapy alone was ineffective. Alisertib + anti-PD-L1 resulted in TGI > 90% indicative of a synthetic lethal interaction. PF-04691502 + alisertib + anti-PD-L1 + VCR resulted in TGI 100%. Overall, mice tolerated the treatments well. Co-targeting AK, PI3K and PD-L1 is a rational and novel therapeutic strategy for PTCL.

Les macrophages associés aux tumeurs (TAM) sont des cellules immunorégulatrices qui s’accumulent massivement dans le microenvironnement (ME) tumoral. Chez les patients atteints de cancer de l’ovaire (CO) ou de mésothéliome pleural malin (MPM), leur densité est associé à un mauvais pronostic. Le projet est porté sur la caractérisation des mécanismes impliqués dans leur recrutement et leur polarisation. L’éctonucléotidase CD39 hydrolyse l’ATP enadénosine extracellulaire, présentant des propriétés immunosuppressives. Nous avons montré que les TAMCD14+CD163+ isolés de CO et les M générés in vitro en présence de M-CSF, expriment un niveau élevé de CD39membranaire comparativement aux M immunostimulants. L’inhibition de CD39 diminue les fonctions immunorégulatrices des M CD163+CD39+high (i.e. IL-10 etPD-L1). Nous avons identifié la cytokine IL-27, sécrétée parles neutrophiles infiltrants la tumeur, comme rhéostat de l’expression de CD39. En conséquence, neutraliser l’IL-27pendant la différenciation des M en présence de M-CSF diminue l’expression de CD39 et PD-L1 ainsi que la sécrétiond’IL-10 par ces M . Parallèlement, nous avons montré que les effusions pleurales du MPM induisent la migration des monocytes via CCL2, polarisent les monocytes en MCD163+ et protègent des cellules tumorales de l’effet des agents cytotoxiques. L’ensemble de ces résultats suggère que le ciblage du recrutement (CCL2) et des molécules impliquées dans la polarisation des TAM (ligands du MCSFR,IL-27, CD39) représentent de nouvelles pistes thérapeutiques dans le traitement de certaines tumeurs solides. / Tumor-associated macrophages (TAM) are immunosuppressive cells that can massively accumulate in the tumor microenvironment (ME). In patients with ovarian cancer (OC) and malignant pleural mesothelioma (MPM), their density is correlated with poor prognosis. Targeting mediators that control the recruitment or the polarization of immunoregulatory macrophages (M ) represents therapeutic challenge to overcome tumor-associated immunosuppression. The ectonucleotidase CD39 hydrolyzes ATP into extracellular adenosine that exhibits potent immunosuppressive properties. We report here thatCD14+CD163+ TAM isolated from OC patients and Mgenerated in vitro with M-CSF, express high levels of the membrane ectonucleotidase CD39 compared to classically activated M . CD39 blockade diminished some of the immunosuppressive functions ofCD163+CD39hugh, such as IL-10 secretion. We identified the cytokine IL-27, secreted by tumorin-filtrating neutrophils, located close to infiltratingCD163+ M , as a major rheostat of CD39 expression and consequently, on the acquisition of immunoregulatory properties by macrophages. Accordingly, the depletion of IL-27 down-regulatedCD39, PD-L1 expression as well as IL-10 secretion byM-CSF-M . In parallel, we showed that pleural effusion of MPM induced monocytes migration via CCL2, the polarization of monocytes into CD163+ and induced protection to tumor cell death after chemotherapeutic treatments. Collectively, these data suggest that targeting the recruitment (CCL2) or molecules that maintain the immunosuppressive phenotype of TAM(CD39, drived by IL-27 and M-CSFR ligands) could give substantial benefit to the treatment of some solid tumors.

abstract: Immunotherapy has received great attention recently, as it has become a powerful tool in fighting certain types of cancer. Immunotherapeutic drugs strengthen the immune system's natural ability to identify and eradicate cancer cells. This work focuses on immune checkpoint inhibitor and oncolytic virus therapies. Immune checkpoint inhibitors act as blocking mechanisms against the binding partner proteins, enabling T-cell activation and stimulation of the immune response. Oncolytic virus therapy utilizes genetically engineered viruses that kill cancer cells upon lysing. To elucidate the interactions between a growing tumor and the employed drugs, mathematical modeling has proven instrumental. This dissertation introduces and analyzes three different ordinary differential equation models to investigate tumor immunotherapy dynamics. The first model considers a monotherapy employing the immune checkpoint inhibitor anti-PD-1. The dynamics both with and without anti-PD-1 are studied, and mathematical analysis is performed in the case when no anti-PD-1 is administrated. Simulations are carried out to explore the effects of continuous treatment versus intermittent treatment. The outcome of the simulations does not demonstrate elimination of the tumor, suggesting the need for a combination type of treatment. An extension of the aforementioned model is deployed to investigate the pairing of an immune checkpoint inhibitor anti-PD-L1 with an immunostimulant NHS-muIL12. Additionally, a generic drug-free model is developed to explore the dynamics of both exponential and logistic tumor growth functions. Experimental data are used for model fitting and parameter estimation in the monotherapy cases. The model is utilized to predict the outcome of combination therapy, and reveals a synergistic effect: Compared to the monotherapy case, only one-third of the dosage can successfully control the tumor in the combination case. Finally, the treatment impact of oncolytic virus therapy in a previously developed and fit model is explored. To determine if one can trust the predictive abilities of the model, a practical identifiability analysis is performed. Particularly, the profile likelihood curves demonstrate practical unidentifiability, when all parameters are simultaneously fit. This observation poses concerns about the predictive abilities of the model. Further investigation showed that if half of the model parameters can be measured through biological experimentation, practical identifiability is achieved. / Dissertation/Thesis / Doctoral Dissertation Applied Mathematics 2020

BACKGROUND: Soft tissue sarcomas (STSs) are a diverse group of cancers that originate from mesenchymal tissue and are estimated to result in 13,130 new cases and 5,350 deaths this year. These neoplasms are hard to detect, which results in physicians struggling to treat late-stage STSs with a limited number of ineffective treatments. Currently, surgical excision is the primary treatment with radiation therapy administered when possible. However, even with optimal margins, the rate of recurrence is high, and the overall survival is low. There is a desperate need for new, more effective treatments. Immune checkpoint blockade (ICB) has recently had widespread success in treating melanoma, and in recent trials, SARC028 and Alliance A091401, have shown demonstrated activity of ICBs in STS in the neoadjuvant setting. Two histological subtypes of STS showed more promise than others: dedifferentiated liposarcoma (DDLPS) and undifferentiated pleomorphic sarcoma (UPS). Another issue plaguing the field of STS is that there is no universal indicator of response. The percentage of hyalinization found within the tumor was recently identified as a better marker of response than radiographic imaging or percent viable tumor. METHODS: This study was an investigator-initiated, single-center, randomized, open-label, phase II study (NCT03307616), in which 23 patients with either DDLPS of the retroperitoneum (RP) or UPS of the extremity/trunk (ET) were separated by disease into Cohort 1 and 2, respectively. Subjects in each cohort were randomized into two neoadjuvant treatment arms per cohort. Arm A (n=7) of Cohort 1 received nivolumab (anti-PD-1) monotherapy, while Arm B (n=7) of Cohort 1 received nivolumab and ipilimumab (anti-CTLA-4) combination therapy. Arm C (n=5) of Cohort 2 received nivolumab monotherapy and radiation therapy, whereas Arm D (n=4) of Cohort 2 received nivolumab/ipilimumab combination therapy and radiation therapy. A tumor biopsy was obtained before treatment, and another sample was taken during the primary treatment of surgical excision. These samples were processed and analyzed by a pathologist who determined the percentage of viable tumor, hyalinization, and necrosis in each sample. Radiographic imaging was also taken throughout to make RECIST 1.1 response determinations. RESULTS: The average treatment response (1 - % viable tumor) for Cohort 1 was 25 ± 23 and there was no difference between Arm A and Arm B, p=0.48. The average treatment response in Cohort 2 was higher at 85 ± 27, but there was also no significant difference between the arms, p = 0.46. The mean percent hyalinization for Cohort 1 was 13 ± 13%, and for Cohort 2 was 69 ± 35%. Again, there was no significant difference between the arms in the Cohort 1 or 2, p = 0.45 and p = 0.54, respectively. Lastly, the mean % necrosis in Cohort 1 was 13 ± 13 %, and in Cohort 2 was 17 ± 24%, and neither had significantly different results in the arms, p = 0.60 and p = 0.92. The RECIST 1.1 results were independent of the arms of the study, and the radiographic response (percent image change) did not correlate to any metric of histologic response. Those who received Ipilimumab had higher rates of adverse events. CONCLUSION: There is significant evidence that ICBs elicited a response in RP DDLPS and ET UPS, and the response of ET UPS was profound. However, there was no apparent benefit from the combination therapy compared to the monotherapy in either cohort. The higher response in ET UPS may be due to the additional radiation therapy or to the nature of UPS itself. Finally, radiographic imaging does not show the response which is apparent at the histological level, so treatment regimens and future experiments should no longer rely on radiographic imaging as a marker for response. / 2021-06-07T00:00:00Z

Pancreatic ductal adenocarcinoma (PDAC) is a highly fatal cancer, accounting for 3.2% of new cancer cases yearly but nearly 8% of all yearly cancer mortalities. Over the past twenty years, our understanding of cancer biology has greatly improved which has resulted in vastly improved prognoses for many cancers. However, the prognosis of pancreatic ductal adenocarcinoma has not improved despite the advance in cancer treatments. This is especially apparent with cancer immunotherapies, a newer therapeutic strategy that utilizes the innate defense mechanism of the body to target malignancies. Immune checkpoint inhibitors are a type of cancer immunotherapy that act by inhibiting the PD-1/PD-L1 and CTLA-4 immune checkpoint pathways and allowing T lymphocytes to proliferate and generate an antitumor response. They have greatly improved the prognosis for many types of malignancies, but clinical studies show that immune checkpoint inhibition has had a limited effect on the prognosis of PDAC. Recent studies have demonstrated that the immune microenvironment of PDAC is highly immunosuppressive, which is a probable factor in limiting the therapeutic efficacy of immune checkpoint inhibitors. Myeloid derived suppressor cells (MDSCs) are a main component of the immune microenvironment in PDAC. They are immature cells of myeloid origin that express CD11b+Gr-1+ on their surface, making them phenotypically distinct from mature dendritic cells. Their infiltration of the PDAC microenvironment early on in the course of the disease is promoted in a large part by the cytokine GM-CSF. MDSCs are believed to contribute to the limited efficacy of immune checkpoint inhibitor therapy both directly and indirectly. Indirect mechanisms are mediated by promoting the activity of other immunosuppressive cells in the PDAC microenvironment such as tumor associated macrophages and regulatory T lymphocytes. MDSCs induce the transformation of naïve CD4+ T lymphocytes into protumorigenic regulatory T lymphocytes. They also promote the polarization of macrophages to the tumor associated macrophage phenotype (IL-10high IL-12low) by secreting IL-10, which decreases IL-12 synthesis by macrophages present in the tumor microenvironment. On top of mediating immunosuppression through other cell types, MDSCs directly mediate immunosuppression by decreasing the amounts of amino acids necessary for anti-tumor immunity in the tumor microenvironment and disrupting the activity of antigen presenting cells and the signaling needed to initiate a cytotoxic T lymphocyte response. The decreased amount of arginine limits the ability of T cells to proliferate, resulting in a weaker cytotoxic response. These mechanisms limit the antitumor response against pancreatic ductal adenocarcinoma, resulting in the decreased response to immune checkpoint inhibitor therapy observed in clinical trials. Future attempts to strengthen the anti-tumor immune response must be combinatorial therapies that incorporate therapeutic strategies that seek to alleviate MDSC-mediated immunosuppression of T lymphocytes from the tumor microenvironment in addition to the more widely available immune checkpoint inhibitor therapy. Such therapeutics are currently being studied in murine models and have shown promising preliminary results but have yet to have been examined in clinical trials. These therapies are an ideal avenue to explore in a search for more effective therapy for this highly lethal disease.

Programmed death-ligand 1 (PD-L1) is a type 1 transmembrane protein that has been reported to play a vital role in mediating suppressed immunity. The interaction between PD-L1 and PD-1 delivers a negative signal that reduces the proliferation of these T cells and induces apoptosis at the same time. Antibodies that can block the Programmed death-ligand 1 (PD-L1) on tumor cells have been shown to alleviate cancer-induced immunosuppression. While antibodies have a great potential in various therapeutic uses, many drawbacks such as the high cost of production, huge molecular size, and poor permeability impose restrictions on the extensive use of full-length antibodies. These limitations have necessitated research for finding alternatives to antibodies, such as peptides, that have lower molecular weight and similar properties as antibodies but do not have the lengthy and complicated approach of producing antibodies. In this study, a novel approach based on molecular interactions of the PD1-PD-L1 complex was developed to design peptides against PD-L1 using Knob-Socket model as basis. Three generations of peptides, α-helix, over-packed and salt bridge function peptides, were designed. All designed peptides were docked in the Molecular Operating Environment (MOE) and the AutoDock Vina software for the docking energy and the detail interaction information. Synthesis and characterization of selected peptides were performed after simulation studies. Surface Plasmon Resonance (SPR) studies showed that α-helix and over-packed peptides can’t bind to the PD-L1 protein with no response on sensorgrams, while peptides with salt bridge function had a higher binding response than those two generations of peptides. In confocal microscopic studies, PD-L1 positive breast cancer cell line MDA-MB-231 was used to determine the binding specificity of the salt bridge function peptides to PD-L1 in vitro, while another breast cancer cell line (MCF-7, without PD-L1) was used as a control. After incubation with peptides, significant fluorescence intensities were detected on the MDA-MB-231 cells, while only background fluorescence was observed on MCF-7 cells. In conclusion, this study demonstrated that peptides against PD-L1 designed using the Knob-Socket model and molecular interaction between PD-L1-PD1 complex showed feasibility to bind specifically with PD-L1 receptors.

No description available.

Immunotherapy has emerged as one of the four “standard” cancer therapies, alongside surgery, chemotherapy, and radiotherapy. Immune checkpoint inhibitor (ICI) therapy is an immunotherapy that blocks inhibitory immune checkpoint interactions, allowing T cells and other immune cells to kill tumor cells. In the tumor microenvironment, there is often overexpression of immune checkpoint proteins, whose binding interaction with cytotoxic T cells and other immune cells results in the dampening of the antitumor response. Programmed cell death protein 1 (PD-1) and T-lymphocyte-associated protein 4 (CTLA-4) are the two most targeted immune checkpoint proteins. Antibodies against PD-1 and CTLA-4, as well as other checkpoint proteins, are approved for clinical use as well as in clinical trials. While ICIs have changed the treatment landscape for many cancers, particularly those with significant immunogenicity, only 20-40% of patients respond to ICI therapy. Many factors are behind the lack of response and resistance, and significant efforts are aimed at improving the response to ICI therapy. One major area is modulating the gut microbiome, as it is well-established that microbial dysbiosis is associated with various human diseases. The concept is that by modulating the microbiome, we might be able to return it to a composition more similar to that seen in healthy individuals or provide microorganisms beneficial to clinical response. In the case of ICI therapy, it is proposed that there is a connection between certain microbial species and the immune system via metabolites and other signaling effects. The microbiome can be manipulated through many methods, including fecal microbiota transplantation (FMT), transferring bacterial isolates or consortia, probiotics, antibiotics, and soluble dietary fiber. For clinical insights, it is important to consider how the pre-treatment microbiome of patients may affect their response to ICI therapy, as well as how their microbiomes can be manipulated to enhance their response. Initial clinical trials have been promising, but this is an emerging field with additional work to be done. Particularly, a better understanding of the microorganisms involved in the response to ICI therapy and the mechanism by which they communicate with the immune system is essential. Future studies will need to be much larger to reduce noise between studies and to allow for emerging computational techniques to be applied.

Blockering av NKG2A receptorn på NK - och CD8+ T celler med en anti-NKG2A antikropp, medför en aktivering av cytolytisk aktivitet, och är en lovande immunkontrollpunkt i immunterapi mot cancer. Nyligen har en TCR-liknande antikropp, EXX1, som binder till liganden för NKG2A receptorn, Qa-1b - en icke-klassisk MHC klass Ib molekyl i möss -studerats i tumör modeller in vitro. Resultat påvisar att den TCR-liknande antikroppen endast binder till Qa-1b om denna presenterar Qdm peptiden på sin yta, som erhålls från ledarsekvensen hos klassika MHC klass Ia H-2D. Detta väcker frågor kring strukturella faktorer som möjliggör antigenpresentation på Qa-1b och de exakta molekylära parametrarna som ger upphov till antikroppens specificitet. Syftet med denna studie var att bestämma och jämföra kristallstrukturerna för Qa-1b med Qdm (AMAPRTLLL) samt peptid 001 (AQAERTPEL). Den tunga peptidkedjan hos Qa-1b och beta-2-mikroglobulin producerades rekombinant i E.coli, återveckades med respektive peptid, renades med kromatografimetoder och slutligen kristalliserades genom ångdiffusionsmetoden med hängande droppar. Värmestabilitet hos MHC/peptid undersöktes med nano differential scanning fluorimetry, där Qa-1b /001 uppvisade bättre stabilitet. Kristaller för Qa-1b /Qdm och Qa-1b /001 kunde erhållas med 8% PEG4000, 10mM NiCl2, 0.1M natriumacetat vid pH 5.7, respektive 10% PEG4000, 10 mM NiCl2 och 0.1 M natriumacetat vid pH 6.0. Strukturen för Qa-1b /001 kunde bestämmas vid 2.43 Å med molekylär ersättning. Med anledning av negativt laddade sidogrupper i peptid 001 som har en ytlig konformation i bindningsfickan, kan avsaknaden av bindning till EXX1 förklaras av en skillnad i elektrostatiska interaktioner mellan Qdm och peptid 001. Ytterligare strukturella karakteriseringar av Qa-1b komplexen med antikroppen är av fortsatt stort intresse. / Blocking of the NKG2A receptor expressed on NK cells and CD8+ T cells with an anti-NKG2A antibody for elicitation of cytolytic activity, is a promising immune checkpoint in cancer immunotherapy. EXX1, a novel TCR-like antibody with specificity for the NKG2A ligand, Qa-1b - a murine non-classical MHC class Ib ortholog of HLA-E - has been assessed in tumor models in vitro. The antibody only engages with Qa-1b when it presents the dominant peptide Qdm, derived from the leader sequence of the classical MHC class Ia H-2D. This raises questions about the structural features of antigen presentation by Qa-1b, and the molecular parameters driving the specificity of the TCR-like antibody. The purpose of this study is to determine and compare the crystal structures of Qa-1b in complex with Qdm (AMAPRTLLL) and peptide 001 (AQAERTPEL). The Qa-1b heavy chain and mouse beta-2 microglobulin were recombinantly expressed in E.coli, refolded in the presence of respective peptide, purified using size exclusion chromatography and crystallized with the hanging drop vapor diffusion method. Thermal stability of the MHC/peptide complexes was assessed with nano differential scanning fluorimetry, implying a higher stability of Qa-1b/001. Crystals of the Qa-1b/Qdm and Qa-1b/001 were obtained with 8% PEG4000, 10 mM NiCl2, 0.1 M sodium acetate at pH 5.7, and 10% PEG4000, 10mM NiCl2 and 0.1 M sodium acetate at pH 6.0, respectively. The structure of Qa-1b/001 was resolved by molecular replacement at 2.43 Å, and the presence of negatively charged side chains that protrude from the binding groove, may imply that differences in electrostatic interactions between Qdm and 001 will determine antibody-binding. Further structural characterizations, of Qa-1b complexes with bound EXX1 are of great interest.