The long and winding road to biomarkers for immunotherapy: a retrospective analysis of samples from patients with triple-negative breast cancer treated with pembrolizumab.

BACKGROUND: Immune checkpoint blockade (ICB) in combination with chemotherapy improves outcome of patients with triple-negative breast cancer (TNBC) in metastatic and early settings. The identification of predictive biomarkers able to guide treatment decisions is challenging and currently limited to programmed death-ligand 1 (PD-L1) expression and high tumor mutational burden (TMB) in the advanced setting, with several limitations. MATERIALS AND METHODS: We carried out a retrospective analysis of clinical-pathological and molecular characteristics of tumor samples from 11 patients with advanced TNBC treated with single-agent pembrolizumab participating in two early-phase clinical trials: KEYNOTE-012 and KEYNOTE-086. Clinical, imaging, pathological [i.e. tumor-infiltrating lymphocytes (TILs), PD-L1 status], RNA sequencing, and whole-exome sequencing data were analyzed. We compared our results with publicly available transcriptomic data from TNBC cohorts from TCGA and METABRIC. RESULTS: Response to pembrolizumab was heterogeneous: two patients experienced exceptional long-lasting responses, six rapid progressions, and three relatively slower disease progression. Neither PD-L1 nor stromal TILs were significantly associated with response to treatment. Increased TMB values were observed in tumor samples from exceptional responders compared to the rest of the cohort (P = 3.4 × 10-4). Tumors from exceptional responders were enriched in adaptive and innate immune cell signatures. Expression of regulatory T-cell markers (FOXP3, CCR4, CCR8, TIGIT) was mainly observed in tumors from responders except for glycoprotein-A repetitions predominant (GARP), which was overexpressed in tumors from rapid progressors. GARP RNA expression in primary breast tumors from the public dataset was significantly associated with a worse prognosis. CONCLUSIONS: The wide spectrum of clinical responses to ICB supports that TNBC is a heterogeneous disease. Tumors with high TMB respond better to ICB. However, the optimal cut-off of 10 mutations (mut)/megabase (Mb) may not reflect the complexity of all tumor subtypes, despite its approval as a tumor-agnostic biomarker. Further studies are required to better elucidate the relevance of the tumor microenvironment and its components as potential predictive biomarkers in the context of ICB.

Leveraging big data of immune checkpoint blockade response identifies novel potential targets.

BACKGROUND: The development of immune checkpoint blockade (ICB) has changed the way we treat various cancers. While ICB produces durable survival benefits in a number of malignancies, a large proportion of treated patients do not derive clinical benefit. Recent clinical profiling studies have shed light on molecular features and mechanisms that modulate response to ICB. Nevertheless, none of these identified molecular features were investigated in large enough cohorts to be of clinical value. MATERIALS AND METHODS: Literature review was carried out to identify relevant studies including clinical dataset of patients treated with ICB [anti-programmed cell death protein 1 (PD-1)/programmed death-ligand 1 (PD-L1), anti-cytotoxic T-lymphocyte antigen 4 (CTLA-4) or the combination] and available sequencing data. Tumor mutational burden (TMB) and 37 previously reported gene expression (GE) signatures were computed with respect to the original publication. Biomarker association with ICB response (IR) and survival (progression-free survival/overall survival) was investigated separately within each study and combined together for meta-analysis. RESULTS: We carried out a comparative meta-analysis of genomic and transcriptomic biomarkers of IRs in over 3600 patients across 12 tumor types and implemented an open-source web application (predictIO.ca) for exploration. TMB and 21/37 gene signatures were predictive of IRs across tumor types. We next developed a de novo GE signature (PredictIO) from our pan-cancer analysis and demonstrated its superior predictive value over other biomarkers. To identify novel targets, we computed the T-cell dysfunction score for each gene within PredictIO and their ability to predict dual PD-1/CTLA-4 blockade in mice. Two genes, F2RL1 (encoding protease-activated receptor-2) and RBFOX2 (encoding RNA-binding motif protein 9), were concurrently associated with worse ICB clinical outcomes, T-cell dysfunction in ICB-naive patients and resistance to dual PD-1/CTLA-4 blockade in preclinical models. CONCLUSION: Our study highlights the potential of large-scale meta-analyses in identifying novel biomarkers and potential therapeutic targets for cancer immunotherapy.

A network approach to developing immuno-oncology combinations in Canada.

Immune checkpoint inhibitors have revolutionized care for many cancer indications, with considerable effort now being focused on increasing the rate, depth, and duration of patient response. One strategy is to combine immune strategies (for example, ctla-4 and PD-1/L1-directed agents) to harness additive or synergistic efficacy while minimizing toxicity. Despite encouraging results with such combinations in multiple tumour types, numerous clinical challenges remain, including a lack of biomarkers that reliably predict outcome, the emergence of therapeutic resistance, and optimal management of immune-related toxicities. Furthermore, the selection of ideal combinations from the myriad of immune, systemic, and locoregional therapies has yet to be determined. A longitudinal network-based approach could offer advantages in addressing those critical questions, including long-term follow-up of patients beyond individual trials. The molecular cancer registry Personalize My Treatment, managed by the Networks of Centres of Excellence nonprofit organization Exactis Innovation, is uniquely positioned to accelerate Canadian immuno-oncology (io) research efforts throughout its national network of cancer sites. To gain deeper insight into how a pan-Canadian network could advance research in io combinations, Exactis invited preeminent clinical and scientific advisors from across Canada to a roundtable event in November 2017. The present white paper captures the expert advice provided: leverage longitudinal patient data collection; facilitate network collaboration and assay harmonization; synergize with existing initiatives, networks, and biobanks; and develop an io combination trial based on Canadian discoveries.

Immuno-oncology-101: overview of major concepts and translational perspectives.

Cancer immunotherapy is demonstrating impressive clinical benefit in different malignancies and clinical oncologists are increasingly turning their attention to immune-oncology. It is now well recognized that innate and adaptive immune cells infiltrating tumors are associated with clinical outcomes and responses to treatments, and can be harnessed to patients' benefit. Considerable advances have also been made in understanding how cancers escape from immune attack. Targeting of immunological escape processes regulated by the expression of immune checkpoint receptors and ligands and the down-modulation of tumor antigen presentation is the basis of immuno-oncology treatments. Despite recent achievements, there remain a number of unresolved issues in order to successfully implement cancer immunotherapy in many cancers. Importantly, clinical biomarkers are still needed for better optimization of emerging combination immunotherapies and better treatment tailoring. In this review, we summarize the function of innate and adaptive immune cells in anti-tumor immunity and the general mechanisms exploited by tumor cells to escape and inhibit immune responses as well as therapeutic strategies developed to overcome these mechanisms and discuss emerging biomarkers in immuno-oncology.

Clinical significance of CD73 in triple-negative breast cancer: multiplex analysis of a phase III clinical trial.

Background: CD73 is an ecto-enzyme that promotes tumor immune escape through the production of immunosuppressive extracellular adenosine in the tumor microenvironment. Several CD73 inhibitors and adenosine receptor antagonists are being evaluated in phase I clinical trials. Patients and methods: Full-face sections from formalin-fixed paraffin-embedded primary breast tumors from 122 samples of triple-negative breast cancer (TNBC) from the BIG 02-98 adjuvant phase III clinical trial were included in our analysis. Using multiplex immunofluorescence and image analysis, we assessed CD73 protein expression on tumor cells, tumor-infiltrating leukocytes and stromal cells. We investigated the associations between CD73 protein expression with disease-free survival (DFS), overall survival (OS) and the extent of tumor immune infiltration. Results: Our results demonstrated that high levels of CD73 expression on epithelial tumor cells were significantly associated with reduced DFS, OS and negatively correlated with tumor immune infiltration (Spearman's R= -0.50, P < 0.0001). Patients with high levels of CD73 and low levels of tumor-infiltrating leukocytes had the worse clinical outcome. Conclusions: Taken together, our study provides further support that CD73 expression is associated with a poor prognosis and reduced anti-tumor immunity in human TNBC and that targeting CD73 could be a promising strategy to reprogram the tumor microenvironment in this BC subtype.

The protein tyrosine phosphatase DEP-1/PTPRJ promotes breast cancer cell invasion and metastasis.

DEP-1/PTPRJ is a receptor-like protein tyrosine phosphatase mainly known for its antiproliferative and tumor-suppressive functions. Many identified substrates are growth factor receptors, and DEP-1 is deleted and/or mutated in human cancers including that of the breast. However, DEP-1 was also identified as a promoter of Src activation and proinvasive functions in the endothelium, suggesting it could perhaps mediate breast cancer invasiveness that is likewise driven by Src family kinases. We show here that DEP-1 expression was greater in highly invasive breast cancer cells (MDA-MB-231, Hs578T, BT-549) than in the less invasive or untransformed cell lines tested (MCF-7, T47D, SK-BR3 and MCF10A). DEP-1 silencing experiments in invasive cells demonstrated that moderately expressed and catalytically active DEP-1 was required, in collaboration with basal epidermal growth factor receptor activity, for Src activation and the phosphorylation of its substrate Cortactin, and for their colocalization at the cell's leading edge. This correlated with an increased number of cell protrusions, and an enhanced capacity of the cells to migrate and invade. Similarly, moderate overexpression of DEP-1 in the low-invasive cells resulted in the promotion of their invasiveness in an Src-dependent manner. Consistent with these data, the expression of endogenous DEP-1 was elevated in a bone metastatic cell line derived from MDA-MB-231 cells, and promoted increased Src Y418 and Cortactin Y421 phosphorylation, as well as pro-MMP9 secretion and Matrigel invasion. Importantly, the silencing of DEP-1 in MDA-MB-231 cells greatly decreased their ability to metastasize, despite having no effect on tumor growth or angiogenesis. Hence, we found that moderate expression of DEP-1 was associated with the increased relapse and decreased survival of breast cancer patients. These results therefore identify a new and unsuspected role for DEP-1 as a mediator of an invasive cell program implicating Src activation and the promotion of breast cancer progression.

Mechanisms of immune modulation by mesenchymal stromal cells and clinical translation.

Cell therapy with mesenchymal stromal cells (MSCs) is the focus of intensive investigation. Several clinical trials, including large-scale placebo-controlled phase III clinical trials, are currently underway evaluating the therapeutic potential of autologous and allogeneic MSCs for treatment of catastrophic inflammatory diseases, including steroid-refractory graft-versus-host disease (GvHD), multiple sclerosis (MS) and Crohn's disease. MSCs are also being investigated as carriers of anti-cancer biotherapeutics. We here review recent developments in our understanding of the immunosuppressive properties of MSCs. We firstly discuss the effects of ex vivo culture conditions on the phenotype and functions of MSCs. Secondly, we summarize the immune functions suppressed by MSCs with a focus on T cell, B cell, natural killer cell and dendritic cell functions. Thirdly, we discuss newly identified pathways responsible for the immunosuppressive activity of MSCs, including the expression of heme-oxygenase (HO)-1, the secretion of galectins, CCL2 antagonism, T regulatory cell (Treg) cross-talk and production of TNF-α stimulated gene/protein-6 (TSG-6). Finally, we review the literature on the molecular pathways governing MSC homing and discuss recent clinical data on the use of MSCs for treatment of GvHD, MS and Crohn's disease.

Extracellular adenosine triphosphate and adenosine in cancer.

Adenosine triphosphate (ATP) is actively released in the extracellular environment in response to tissue damage and cellular stress. Through the activation of P2X and P2Y receptors, extracellular ATP enhances tissue repair, promotes the recruitment of immune phagocytes and dendritic cells, and acts as a co-activator of NLR family, pyrin domain-containing 3 (NLRP3) inflammasomes. The conversion of extracellular ATP to adenosine, in contrast, essentially through the enzymatic activity of the ecto-nucleotidases CD39 and CD73, acts as a negative-feedback mechanism to prevent excessive immune responses. Here we review the effects of extracellular ATP and adenosine on tumorigenesis. First, we summarize the functions of extracellular ATP and adenosine in the context of tumor immunity. Second, we present an overview of the immunosuppressive and pro-angiogenic effects of extracellular adenosine. Third, we present experimental evidence that extracellular ATP and adenosine receptors are expressed by tumor cells and enhance tumor growth. Finally, we discuss recent studies, including our own work, which suggest that therapeutic approaches that promote ATP-mediated activation of inflammasomes, or inhibit the accumulation of tumor-derived extracellular adenosine, may constitute effective new means to induce anticancer activity.

Immune plasticity of bone marrow-derived mesenchymal stromal cells.

Isolated from simple bone marrow aspirates, mesenchymal stromal cells (MSCs) can be easily expanded ex vivo and differentiated into various cell lineages. Because they are present in humans of all ages, are harvested in the absence of prior mobilization and preserve their plasticity following gene modification, MSCs are particularly attractive for cell-based medicine. One of the most fascinating properties of ex vivo expanded MSCs is their ability to suppress ongoing immune responses, both in vitro and in vivo. Although not fully understood, the immunosuppressive properties of MSCs have been reported to affect the function of a broad range of immune cells, including T cells, antigen-presenting cells, natural killer cells and B cells. Whereas successful harnessing of these immunosuppressive properties might one day open the door to the development of new cell-based strategies for the control of graft-versus-host and other autoimmune diseases, recent studies suggest that the immune-modulating properties of MSCs are far more complex than first thought. Reminiscent of the dichotomy of function of dendritic cells (DCs), which can act as potent activators or potent suppressors of immune responses, new studies including our own work has shown that MSCs in fact possess the dual ability to suppress or activate immune responses. In this review, we summarize the different biological properties of MSCs and discuss the current literature on the complex mechanism of immune modulation mediated by ex vivo expanded MSCs.

Targeting death-inducing receptors in cancer therapy.

Deregulated cell death pathways may lead to the development of cancer, and induction of tumor cell apoptosis is the basis of many cancer therapies. Knowledge accumulated concerning the molecular mechanisms of apoptotic cell death has aided the development of new therapeutic strategies to treat cancer. Signals through death receptors of the tumor necrosis factor (TNF) superfamily have been well elucidated, and death receptors are now one of the most attractive therapeutic targets in cancer. In particular, DR5 and DR4, death receptors of TNF-related apoptosis-inducing ligand (TRAIL or Apo2L), are interesting targets of antibody-based therapy, since TRAIL may also bind decoy receptors that may prevent TRAIL-mediated apoptosis, whereas TRAIL ligand itself selectively induces apoptosis in cancer cells. Here, we review the potential therapeutic utility of agonistic antibodies against DR5 and DR4 and discuss the possible extension of this single-antibody-based strategy when combined with additional modalities that either synergizes to cause enhanced apoptosis or further engage the cellular immune response. Rational design of antibody-based therapies combining the induction of tumor cell apoptosis and activation of tumor-specific adaptive immunity enables promotion of distinct steps of the antitumor immune response, thereby enhancing tumor-specific lymphocytes that can eradicate TRAIL/DR5-resistant mutating, large established and heterogeneous tumors in a manner that does not require the definition of individual tumor-specific antigens.

Immune regulation by mesenchymal stem cells: two sides to the coin.

Mesenchymal stem cells (MSCs) constitute a rare population of adult stem cells that can be isolated from a simple bone marrow aspirate in the absence of prior mobilization. For this reason, MSCs are particularly attractive for cell-based medicine. Ex-vivo-expanded MSCs isolated from different species, including human MSCs, have been shown to suppress the activity of a broad range of immune cells, including T cells, antigen-presenting cells, natural killer (NK) cells and B cells. New studies have further shown that MSCs interact with NK cells, express NK cell receptor ligands, express Toll-like receptors (TLRs), respond to TLR ligands and act as antigen-presenting cells upon interferon-gamma stimulation. Taken together, these studies suggest that MSCs may constitute a previously unrecognized player of the immune system with dichotomy of function reminiscent of other antigen-presenting cells. An important question that remains unanswered is whether resident MSCs actually play a role in endogenous immune responses? I here review the mechanisms of MSC-mediated immune regulation and discuss the major roles of resident MSCs in health and disease.

Genetic and structural analysis of the Bacteroides conjugative transposon CTn341.

The genetic structure and functional organization of a Bacteroides conjugative transposon (CTn), CTn341, were determined. CTn341 was originally isolated from a tetracycline-resistant clinical isolate of Bacteroides vulgatus. The element was 51,993 bp long, which included a 5-bp coupling sequence that linked the transposon ends in the circular form. There were 46 genes, and the corresponding gene products fell into three major functional groups: DNA metabolism, regulation and antibiotic resistance, and conjugation. The G + C content and codon usage observed in the functional groups suggested that the groups belong to different genetic lineages, indicating that CTn341 is a composite, modular element. Mutational analysis of genes representing the different functional groups provided evidence for the gene assignments and showed that the basic conjugation and excision genes are conserved among Bacteroides spp. A group IIA1 intron, designated B.f.I1, was found to be inserted into the bmhA methylase gene. Reverse transcriptase PCR analysis of CTn341 RNA showed that B.fr.I1 was functional and was spliced out of the bmhA gene. Six related CTn-like elements were found in the genome sequences of Bacteroides fragilis NCTC9343 and Bacteroides thetaiotaomicron VPI5482. The putative elements were similar to CTn341 primarily in the tra and mob regions and in the exc gene, and several appeared to contain intron elements. Our data provide the first reported sequence for a complete Bacteroides CTn, and they should be of considerable benefit to further functional and genetic analyses of antibiotic resistance elements and genome evolution in Bacteroides.

Pseudotyped retrovectors for tumor-specific delivery of toxic suicide genes.

Tumor-targeted gene transfer of the suicide gene, herpes simplex virus thymidine kinase (HSV-TK) is an extremely powerful biopharmaceutical approach for the treatment of cancer. However, no substantive clinical benefit has been reported since this concept was first developed more than a decade ago. This review summarizes the current status of human clinical trials employing viral-vector based delivery of HSV-TK as well as novel means being developed by which killing of tumor cells could be enhanced. In particular, we discuss of the use of VSV-G pseudotyped retrovectors in successfully achieving high tumor-restricted gene transfer efficiency in preclinical studies and the challenges still to be overcome to bring cancer gene therapy safely to the clinic.

Clinical experience with the Palmaz-Schatz coronary stent. Initial results of a multicenter study.

Stenting of native coronary arteries with a balloon-expandable stent was attempted in 226 patients after elective angioplasty. Delivery of the device was successful in 213 (94%) of the patients. Of these, 39 received aspirin and dipyridamole only (group 1) and 174 received aspirin, dipyridamole, and warfarin for 1-3 months (group 2). There was no abrupt closure (less than or equal to 1 day) or perioperative death in either group. In-hospital or perioperative complications in group 1 compared with group 2 were as follows: subacute closure (1-14 days), seven (18%) patients versus one (0.6%) patient, respectively, p less than 0.0001; myocardial infarction, five (13%) patients versus one (0.6%) patient, respectively; condition requiring urgent bypass surgery, one (2.5%) patient versus no patients, respectively. Thus, the incidence of major complications such as death, myocardial infarction, or a condition requiring urgent bypass surgery was 15% in group 1 and 0.6% in group 2. Clinical follow-up revealed that 92% of the patients were asymptomatic at 3 months after stenting compared with 6% before stenting (p less than 0.0001). Of the 13 patients who were symptomatic, nine underwent cardiac catheterization and, ultimately, successful elective coronary angioplasty or bypass surgery. We conclude that a high delivery success rate can be expected with this device and that clinical thrombosis is less frequent in anticoagulated patients than in nonanticoagulated patients. Furthermore, in this selected patient population, coronary stenting results in a low incidence of in-hospital and perioperative complications. Clinical success, defined by absence of symptoms, appears to be sustained at 3 months.

Functional cardiac imaging in coronary disease: increased sensitivity of first-pass radionuclide angiography utilizing sequential regional left ventricular early diastolic filling rate images.

In 127 patients, 113 with greater than or equal to 50% coronary artery stenosis (CAD), 14 with normal coronaries, cardiac catheterization and first-pass radionuclide angiography (RNA) utilizing left ventricular (LV) regional ejection fraction, first half systolic LV regional mean transit time and ejection rate images were performed. Additionally, the incremental value of a new technique, sequential regional LV filling rate images focusing on the first third of diastole, was established. Diastolic imaging improved RNA sensitivity from 88% (100/113) to 96% (109/113). Single vessel disease sensitivity increased from 77% (23/30) to 90% (27/30), whereas multivessel disease RNA positivity changed from 93% (77/83) to 99% (82/83). LAD system (LAD/D) sensitivity improved by 24% to 94% (79/84); RCA system (RCA/PDA) sensitivity increased 17% to 84% (59/70); circumflex system (CFX/OM) sensitivity was 83% (67/81), an improvement of 5%. Specificity was well maintained despite the increased sensitivity, as 86% (12/14) of patients with normal coronaries were normal by RNA. Furthermore, in the 113 CAD patients, 81% (84/104) of the vessels with insignificant or no stenosis were normal by RNA. We conclude sequential regional LV diastolic filling images substantially increase RNA sensitivity for CAD, while specificity is satisfactorily maintained.

Perilymphatic pressure in the cat. Description of a new method for study of inner ear hydrodynamics.

Continuous recordings of the perilymphatic (Pp), cerebrospinal fluid (PCSF), central venous (PCV) and arterial (PA) pressures have been performed on anesthetized cats. The perilymphatic space was reached by an extraural approach that leaves the ear canal and middle ear intact. A conical canal was drilled into the temporal bone down to the vestibule. The position of the canal was later confirmed histologically. A small, threaded, metallic cannula was screwed into the bone. For pressure measurements Millar microtip transducers were used, thus giving minimum measurement volume displacement. The mean PP and PCSF were found to be equal, whereas the maximum pressure during expiration was significantly higher in the CSF. not affected by the given anesthetics. Ligation of the external jugular veins had a minor and temporary effect on the PP and PCSF. The method is considered to be suitable for studies on the inner ear hydrodynamics as well as for audiophysiological measurements with an intact middle ear transmission system.

A compact infrasound and pressure waveform generator for use with small cavities.

The described apparatus is a small portable sound and pressure-step generator capable of producting pressure levels of over 150 dB into cavities of maximum volume 30 cm3. The form of the pressure waveform is an exact replica of the electrical input waveform independent of leakage and flexibility in the cavity. Complex sound waveforms can be easily produced with the aid of a function generator.

Pressure-regulating mechanisms in the inner ear.

The perilymphatic pressure was studied in relation to pressure step variations in the external ear canal and in the middle ear. The transfer of pressure via the ossicular chain reached its limiting value at quite low pressures. When pressure steps were applied directly to the middle ear, there was almost a direct transfer of pressure for positive changes. Nonlinearities were shown between positive and negative pressure steps. The pressure-regulating ability of the inner ear was illustrated by means of calculating the time constants of the pressure transfer curves.

Electronic analysis of foetal breathing movements: a practical application of phase-lock-loop principles.

Measurement of foetal breathing movements is becoming more common as a means of monitoring processes occurring in the human foetus. Conventional time-period analysis of breathing movements is prone to error owing to their complexity, and it is laborious to decipher any frequency pattern. The described apparatus has been designed to give an on-line visual indication of the instantaneous frequency of foetal breathing movements when measured by a time-distance recorder connected to an echoscope. It is affected insignificantly by spurious signals, and can be build cheaply with easily-available components. Practical trials suggest that frequency analysis by this device can be of value for examining episodes of continuous breathing movements in the foetus.