Replenish the source within: Rescuing tumor-infiltrating lymphocytes by double checkpoint blockade.

We have recently reported that the PD-1 and CTLA4 signaling pathways are active in both effector and regulatory T cells, causing profound immune dysfunctions in the tumor microenvironment. In line with this notion, the dual blockade of PD-1- and CTLA4-conveyed signals may exert robust therapeutic effects. Here, we discuss the mechanisms possibly underlying such a synergic interaction

T-cell and NK-cell infiltration into solid tumors: a key limiting factor for efficacious cancer immunotherapy.

Cancer immunotherapy has great promise, but is limited by diverse mechanisms used by tumors to prevent sustained antitumor immune responses. Tumors disrupt antigen presentation, T/NK-cell activation, and T/NK-cell homing through soluble and cell-surface mediators, the vasculature, and immunosuppressive cells such as myeloid-derived suppressor cells and regulatory T cells. However, many molecular mechanisms preventing the efficacy of antitumor immunity have been identified and can be disrupted by combination immunotherapy. Here, we examine immunosuppressive mechanisms exploited by tumors and provide insights into the therapies under development to overcome them, focusing on lymphocyte traffic

“Statistical Dueling” with Unconventional Weapons: What Courts Should Know about Experts in Employment Discrimination Class Actions

When statistical evidence is offered in a litigation context, the result can be bad law and bad statistics. In recent high profile, high-stakes employment discrimination class actions against large multinationals like UPS, Wal-Mart, and Marriott, plaintiffs have claimed that decentralized and highly discretionary management practices result in systematic gender or racial disparities in pay and promotion. At class certification, plaintiffs have relied in part on statistical analyses of the company’s workforce showing companywide inequality. Defendants have responded with statistical presentations of their own, which frequently demonstrate widely varying outcomes for members of protected groups in different geographic areas of the company. These expert submissions usually suggest either that no problems exist, or that any discrimination is isolated and not attributable to institutional-level bias. In adjudicating between these competing visions, courts must referee what the Second Circuit terms “statistical dueling.” As we show in this paper, sometimes at least one of the parties is dueling with unconventional weapons. Using simulated data, we show why courts should become more critical of statistical expertise purporting to test for subunit differences, particularly when offered at the class certification phase of the case. Under some circumstances, the statistical approach often used to oppose class certification in employment discrimination litigation is guaranteed to support the defendant\u27s position, regardless of the actual facts of the case. Furthermore, some courts have improperly or unwittingly legitimized the use of this approach, even when it is demonstrably non-probative of the issues before the court. Courts need new ways to think about these problems -- approaches that better reflect the relevant legal framework and statistical principles

'Hotspots' of Antigen Presentation Revealed by Human Leukocyte Antigen Ligandomics for Neoantigen Prioritization.

The remarkable clinical efficacy of the immune checkpoint blockade therapies has motivated researchers to discover immunogenic epitopes and exploit them for personalized vaccines. Human leukocyte antigen (HLA)-binding peptides derived from processing and presentation of mutated proteins are one of the leading targets for T-cell recognition of cancer cells. Currently, most studies attempt to identify neoantigens based on predicted affinity to HLA molecules, but the performance of such prediction algorithms is rather poor for rare HLA class I alleles and for HLA class II. Direct identification of neoantigens by mass spectrometry (MS) is becoming feasible; however, it is not yet applicable to most patients and lacks sensitivity. In an attempt to capitalize on existing immunopeptidomics data and extract information that could complement HLA-binding prediction, we first compiled a large HLA class I and class II immunopeptidomics database across dozens of cell types and HLA allotypes and detected hotspots that are subsequences of proteins frequently presented. About 3% of the peptidome was detected in both class I and class II. Based on the gene ontology of their source proteins and the peptide's length, we propose that their processing may partake by the cellular class II presentation machinery. Our database captures the global nature of the in vivo peptidome averaged over many HLA alleles, and therefore, reflects the propensity of peptides to be presented on HLA complexes, which is complementary to the existing neoantigen prediction features such as binding affinity and stability or RNA abundance. We further introduce two immunopeptidomics MS-based features to guide prioritization of neoantigens: the number of peptides matching a protein in our database and the overlap of the predicted wild-type peptide with other peptides in our database. We show as a proof of concept that our immunopeptidomics MS-based features improved neoantigen prioritization by up to 50%. Overall, our work shows that, in addition to providing huge training data to improve the HLA binding prediction, immunopeptidomics also captures other aspects of the natural in vivo presentation that significantly improve prediction of clinically relevant neoantigens

The ovarian cancer oncobiome.

Humans and other mammals are colonized by microbial agents across the kingdom which can represent a unique microbiome pattern. Dysbiosis of the microbiome has been associated with pathology including cancer. We have identified a microbiome signature unique to ovarian cancers, one of the most lethal malignancies of the female reproductive system, primarily because of its asymptomatic nature during the early stages in development. We screened ovarian cancer samples along with matched, and non-matched control samples using our pan-pathogen array (PathoChip), combined with capture-next generation sequencing. The results show a distinct group of viral, bacterial, fungal and parasitic signatures of high significance in ovarian cases. Further analysis shows specific viral integration sites within the host genome of tumor samples, which may contribute to the carcinogenic process. The ovarian cancer microbiome signature provides insights for the development of targeted therapeutics against ovarian cancers

TIE-2 expressing monocytes in human cancers.

Tumor-associated macrophages (TAM) are well known as a key player in the tumor microenvironment, which support cancer progression. More recently, a lineage of monocytes characterized by the expression of the TIE-2/Tek angiopoietin receptor identified a subset of circulating and tumor-associated monocytes endowed with proangiogenic activity. TIE-2 expressing monocytes (TEM) were found both in humans and mice. Here, we review the phenotypes and functions of TEM reported so far in human cancer and their potential use as markers of cancer progression and metastasis. Finally, we discuss the therapeutic approaches currently used or proposed to target TEM

Identifying biological mechanisms for favorable cancer prognosis using non-hypothesis-driven iterative survival analysis.

Survival analyses based on the Kaplan-Meier estimate have been pervasively used to support or validate the relevance of biological mechanisms in cancer research. Recently, with the appearance of gene expression high-throughput technologies, this kind of analysis has been applied to tumor transcriptomics data. In a 'bottom-up' approach, gene-expression profiles that are associated with a deregulated pathway hypothetically involved in cancer progression are first identified and then subsequently correlated with a survival effect, which statistically supports or requires the rejection of such a hypothesis. In this work, we propose a 'top-down' approach, in which the clinical outcome (survival) is the starting point that guides the identification of deregulated biological mechanisms in cancer by a non-hypothesis-driven iterative survival analysis. We show that the application of our novel method to a population of ~2,000 breast cancer patients of the METABRIC consortium allows the identification of several well-known cancer mechanisms, such as ERBB4, HNF3A and TGFB pathways, and the investigation of their paradoxical dual effect. In addition, several novel biological mechanisms are proposed as potentially involved in cancer progression. The proposed exploratory methodology can be considered both alternative and complementary to classical 'bottom-up' approaches for validation of biological hypotheses. We propose that our method may be used to better characterize cancer, and may therefore impact the future design of therapies that are truly molecularly tailored to individual patients. The method, named SURCOMED, was implemented as a web-based tool, which is publicly available at http://surcomed.vital-it.ch. R scripts are also available at http://surcomed.sourceforge.net)

T Cells Bearing a Chimeric Antigen Receptor against Prostate-Specific Membrane Antigen Mediate Vascular Disruption and Result in Tumor Regression.

Aberrant blood vessels enable tumor growth, provide a barrier to immune infiltration, and serve as a source of protumorigenic signals. Targeting tumor blood vessels for destruction, or tumor vascular disruption therapy, can therefore provide significant therapeutic benefit. Here, we describe the ability of chimeric antigen receptor (CAR)-bearing T cells to recognize human prostate-specific membrane antigen (hPSMA) on endothelial targets in vitro as well as in vivo. CAR T cells were generated using the anti-PSMA scFv, J591, and the intracellular signaling domains: CD3ζ, CD28, and/or CD137/4-1BB. We found that all anti-hPSMA CAR T cells recognized and eliminated PSMA(+) endothelial targets in vitro, regardless of the signaling domain. T cells bearing the third-generation anti-hPSMA CAR, P28BBζ, were able to recognize and kill primary human endothelial cells isolated from gynecologic cancers. In addition, the P28BBζ CAR T cells mediated regression of hPSMA-expressing vascular neoplasms in mice. Finally, in murine models of ovarian cancers populated by murine vessels expressing hPSMA, the P28BBζ CAR T cells were able to ablate PSMA(+) vessels, cause secondary depletion of tumor cells, and reduce tumor burden. Taken together, these results provide a strong rationale for the use of CAR T cells as agents of tumor vascular disruption, specifically those targeting PSMA. Cancer Immunol Res; 3(1); 68-84. ©2014 AACR

Bone marrow-derived cells are implicated as a source of lymphatic endothelial progenitors in human breast cancer.

Bone marrow-derived endothelial progenitor cells (EPCs) infiltrate into sites of neovascularization in adult tissues and mature into functional blood endothelial cells (BECs) during a process called vasculogenesis. Human marrow-derived EPCs have recently been reported to display a mixed myeloid and lymphatic endothelial cell (LEC) phenotype during inflammation-induced angiogenesis; however, their role in cancer remains poorly understood. We report the in vitro differentiation of human cord blood CD133(+)CD34(+) progenitors into podoplanin(+) cells expressing both myeloid markers (CD11b, CD14) and the canonical LEC markers vascular endothelium growth factor receptor 3 (VEGFR-3), lymphatic vessel endothelial hyaluronan receptor 1 (LYVE-1), and prospero homeobox 1 (PROX-1). These podoplanin(+) cells displayed sprouting behavior comparable to that of LECs in vitro and a dual hemangiogenic and lymphangiogenic activity in vivo in an endothelial cell sprouting assay and corneal vascularization assay, respectively. Furthermore, these cells expressed vascular endothelium growth factor (VEGF) family members A, -C, and -D. Thus, bone-marrow derived EPCs stimulate hemangiogenesis and lymphangiogenesis through their ability to differentiate into LECs and to produce angiogenic factors. Importantly, plasma from patients with breast cancer induced differentiation of CD34(+) cord blood progenitors into hemangiogenic and lymphangiogenic CD11b(+) myeloid cells, whereas plasma from healthy women did not have this effect. Consistent with these findings, circulating CD11b(+) cells from breast cancer patients, but not from healthy women, displayed a similar dual angiogenic activity. Taken together, our results show that marrow-derived EPCs become hemangiogenic and lymphangiogenic upon exposure to cancer plasma. These newly identified functions of bone-marrow derived EPCs are expected to influence the diagnosis and treatment of breast cancer

High Prevalence of Short Telomeres in ldiopathic Porto-Sinusoidal Vascular Disorder

Les télomères empêchent la destruction de l'ADN codant en jouant le rôle de tampon lorsque les nucléotides terminaux sont naturellement perdus au cours de la mitose. Les mutations des gènes impliqués dans la maintenance des télomères peuvent entraîner un raccourcissement excessif des télomères de manière systémique. Les conséquences sont la sénescence cellulaire et à un dysfonctionnement systémique des organes, un état appelé le syndrome des télomères courts. Mise appart la cirrhose cryptogénique, une des manifestations hépatiques documentées est la maladie porto-sinusoïdal vasculaire (PSVD), dont la pathophysiologie et, dans de nombreux cas, l'étiologie reste inconnue. Bien que des cas de PSVD aient été observés dans le cadre du syndrome de télomères courts, la présence et l'implication des télomères courts dans les cas de PSVD idiopathique n'ont jamais été étudiée. Explorer cette relation est intéressant pour déterminer si les télomères courts sont une caractéristique intrinsèque de la PSVD et évaluer si la longueur est liée à la sévérité de la maladie. Pour les patients, l'implication peut être important, car le syndrome de télomères courts peut être hérité, parfois avec une anticipation génétique. Cette étude monocentrique a porté sur des patients atteints de PSVD définie par des critères histologiques précis et considérée comme idiopathique sur la base de l'exclusion de causes communes. La longueur des télomères dans six sous-populations de leucocytes du sang périphérique a été évaluée par hybridation in situ fluorescente et cytométrie de flux (flowFISH). Les patients ayant des télomères courts ou très courts ont été testés pour des gènes relevant au maintien des télomères. Un total de 22 patients a été inclus. Parmi eux, 16 (73 %) présentaient des télomères courts (ST el, 9/22) ou très courts (VSTel, 7 /22), tandis que six (27 %) avaient une longueur télomérique dans la norme définie par une référence ajustée à l'âge chez les individus sains. Quatorze patients (64 %) présentaient une hypertension portale cliniquement significative. La prévalence de télomères courts était significativement plus élevée chez les hommes (p = 0,005) et chez les patients présentant une pneumopathie interstitielle (p < 0,001), une insuffisance rénale chronique (p < 0,001) et une macrocytose érythrocytaire (p = 0,007). La présence d'une hypertension portale (p = 0,021), une hypoalbuminémie (p < 0,001), une thrombocytopénie (p = 0,007) et une hyperbilirubinémie (p = 0,053) étaient également associés à des télomères plus courts. Des variants dans des gènes connus pour être liés au syndrome de télomères courts ont été identifiés chez quatre patients avec VSTel et un avec Sîel. Les télomères courts étaient présents à un taux très élevé chez les patients atteints de PSVD idiopathique, ce qui renforce l'hypothèse que la biologie des télomères pourrait jouer un rôle dans la pathogenèse de la maladie vasculaire du foie. Par conséquent, les cliniciens devraient envisager de mesurer les télomères dans le cadre du processus de diagnostic de tout patient présentant une PSVD idiopathique