Mathematical modeling of intratumoral immunotherapy yields strategies to improve the treatment outcomes

Intratumoral injection of immunotherapy aims to maximize its activity within the tumor. However, cytokines are cleared via tumor vessels and escape from the tumor periphery into the host-tissue, reducing efficacy and causing toxicity. Thus, understanding the determinants of the tumor and immune response to intratumoral immunotherapy should lead to better treatment outcomes. In this study, we developed a mechanistic mathematical model to determine the efficacy of intratumorally-injected conjugated-cytokines, accounting for properties of the tumor microenvironment and the conjugated-cytokines. The model explicitly incorporates i) the tumor vascular density and permeability and the tumor hydraulic conductivity, ii) conjugated-cytokines size and binding affinity as well as their clearance via the blood vessels and the surrounding tissue, and iii) immune cells-cancer cells interactions. Model simulations show how the properties of the tumor and of the conjugated-cytokines determine treatment outcomes and how selection of proper parameters can optimize therapy. A high tumor tissue hydraulic permeability allows for the uniform distribution of the cytokines into the tumor, whereas uniform tumor perfusion is required for sufficient access and activation of immune cells. The permeability of the tumor vessels affects the blood clearance of the cytokines and optimal values depend on the size of the conjugates. A size >5 nm in radius was found to be optimal, whereas the binding of conjugates should be high enough to prevent clearance from the tumor into the surrounding tissue. In conclusion, development of strategies to improve vessel perfusion and tissue hydraulic conductivity by reprogramming the microenvironment along with optimal design of conjugated-cytokines can enhance intratumoral immunotherapy.

Cytoplasmic-delivery of polyinosine-polycytidylic acid inhibits pancreatic cancer progression increasing survival by activating Stat1-CCL2-mediated immunity

BACKGROUND

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer without effective therapies and with poor prognosis, causing 7% of all cancer-related fatalities in the USA. Considering the lack of effective therapies for this aggressive cancer, there is an urgent need to define newer and more effective therapeutic strategies. Polyinosine-polycytidylic acid (pIC) is a synthetic double-stranded RNA (dsRNA) which directly activates dendritic cells and natural killer cells inhibiting tumor growth. When pIC is delivered into the cytoplasm using polyethyleneimine (PEI), pIC-PEI, programmed-cell death is induced in PDAC. Transfection of [pIC]PEI into PDAC cells inhibits growth, promotes toxic autophagy and also induces apoptosis in vitro and in vivo in animal models.

METHODS

The KPC transgenic mouse model that recapitulates PDAC development in patients was used to interrogate the role of an intact immune system in vivo in PDAC in response to [pIC]PEI. Antitumor efficacy and survival were monitored endpoints. Comprehensive analysis of the tumor microenvironment (TME) and immune cells, cytokines and chemokines in the spleen, and macrophage polarization were analyzed.

RESULTS

Cytosolic delivery of [pIC]PEI induces apoptosis and provokes strong antitumor immunity in vivo in immune competent mice with PDAC. The mechanism underlying the immune stimulatory properties of [pIC]PEI involves Stat1 activation resulting in CCL2 and MMP13 stimulation thereby provoking macrophage polarization. [pIC]PEI induces apoptosis via the AKT-XIAP pathway, as well as macrophage differentiation and T-cell activation via the IFNγ-Stat1-CCL2 signaling pathways in PDAC. In transgenic tumor mouse models, [pIC]PEI promotes robust and profound antitumor activity implying that stimulating the immune system contributes to biological activity. The [pIC]PEI anti-PDAC effects are enhanced when used in combination with a standard of care (SOC) treatment, that is, gemcitabine.

CONCLUSIONS

In summary, [pIC]PEI treatment is non-toxic toward normal pancreatic cells while displaying strong cytotoxic and potent immune activating activities in PDAC, making it an attractive therapeutic when used alone or in conjunction with SOC therapeutic agents, potentially providing a safe and effective treatment protocol with translational potential for the effective therapy of PDAC.

Seryl-tRNA synthetase promotes translational readthrough by mRNA binding and involvement of the selenocysteine incorporation machinery

Translational readthrough of UGA stop codons by selenocysteine-specific tRNA (tRNASec) enables the synthesis of selenoproteins. Seryl-tRNA synthetase (SerRS) charges tRNASec with serine, which is modified into selenocysteine and delivered to the ribosome by a designated elongation factor (eEFSec in eukaryotes). Here we found that components of the human selenocysteine incorporation machinery (SerRS, tRNASec, and eEFSec) also increased translational readthrough of non-selenocysteine genes, including VEGFA, to create C-terminally extended isoforms. SerRS recognizes target mRNAs through a stem-loop structure that resembles the variable loop of its cognate tRNAs. This function of SerRS depends on both its enzymatic activity and a vertebrate-specific domain. Through eCLIP-seq, we identified additional SerRS-interacting mRNAs as potential readthrough genes. Moreover, SerRS overexpression was sufficient to reverse premature termination caused by a pathogenic nonsense mutation. Our findings expand the repertoire of selenoprotein biosynthesis machinery and suggest an avenue for therapeutic targeting of nonsense mutations using endogenous factors.

vWCluster: Vector-valued optimal transport for network based clustering using multi-omics data in breast cancer

In this paper, we present a network-based clustering method, called vector Wasserstein clustering (vWCluster), based on the vector-valued Wasserstein distance derived from optimal mass transport (OMT) theory. This approach allows for the natural integration of multi-layer representations of data in a given network from which one derives clusters via a hierarchical clustering approach. In this study, we applied the methodology to multi-omics data from the two largest breast cancer studies. The resultant clusters showed significantly different survival rates in Kaplan-Meier analysis in both datasets. CIBERSORT scores were compared among the identified clusters. Out of the 22 CIBERSORT immune cell types, 9 were commonly significantly different in both datasets, suggesting the difference of tumor immune microenvironment in the clusters. vWCluster can aggregate multi-omics data represented as a vectorial form in a network with multiple layers, taking into account the concordant effect of heterogeneous data, and further identify subgroups of tumors in terms of mortality.

Single-cell transcriptome analysis of tumor and stromal compartments of pancreatic ductal adenocarcinoma primary tumors and metastatic lesions

BACKGROUND

Solid tumors such as pancreatic ductal adenocarcinoma (PDAC) comprise not just tumor cells but also a microenvironment with which the tumor cells constantly interact. Detailed characterization of the cellular composition of the tumor microenvironment is critical to the understanding of the disease and treatment of the patient. Single-cell transcriptomics has been used to study the cellular composition of different solid tumor types including PDAC. However, almost all of those studies used primary tumor tissues.

METHODS

In this study, we employed a single-cell RNA sequencing technology to profile the transcriptomes of individual cells from dissociated primary tumors or metastatic biopsies obtained from patients with PDAC. Unsupervised clustering analysis as well as a new supervised classification algorithm, SuperCT, was used to identify the different cell types within the tumor tissues. The expression signatures of the different cell types were then compared between primary tumors and metastatic biopsies. The expressions of the cell type-specific signature genes were also correlated with patient survival using public datasets.

RESULTS

Our single-cell RNA sequencing analysis revealed distinct cell types in primary and metastatic PDAC tissues including tumor cells, endothelial cells, cancer-associated fibroblasts (CAFs), and immune cells. The cancer cells showed high inter-patient heterogeneity, whereas the stromal cells were more homogenous across patients. Immune infiltration varies significantly from patient to patient with majority of the immune cells being macrophages and exhausted lymphocytes. We found that the tumor cellular composition was an important factor in defining the PDAC subtypes. Furthermore, the expression levels of cell type-specific markers for EMT+ cancer cells, activated CAFs, and endothelial cells significantly associated with patient survival.

CONCLUSIONS

Taken together, our work identifies significant heterogeneity in cellular compositions of PDAC tumors and between primary tumors and metastatic lesions. Furthermore, the cellular composition was an important factor in defining PDAC subtypes and significantly correlated with patient outcome. These findings provide valuable insights on the PDAC microenvironment and could potentially inform the management of PDAC patients.

Extracellular vesicles in human semen modulate antigen-presenting cell function and decrease downstream antiviral T cell responses

Human semen contains trillions of extracellular vesicles (SEV) similar in size to sexually transmitted viruses and loaded with potentially bioactive miRNAs, proteins and lipids. SEV were shown to inhibit HIV and Zika virus infectivity, but whether SEV are able also to affect subsequent immune responses is unknown. We found that SEV efficiently bound to and entered antigen-presenting cells (APC) and thus we set out to further dissect the impact of SEV on APC function and the impact on downstream T cell responses. In an APC–T cell co-culture system, SEV exposure to APC alone markedly reduced antigen-specific cytokine production, degranulation and cytotoxicity by antigen-specific memory CD8+ T cells. In contrast, inhibition of CD4+ T cell responses required both APC and T cell exposure to SEV. Surprisingly, SEV did not alter MHC or co-stimulatory receptor expression on APCs, but caused APCs to upregulate indoleamine 2,3 deoxygenase, an enzyme known to indirectly inhibit T cells. Thus, SEV reduce the ability of APCs to activate T cells. We propose here that these immune-inhibitory properties of SEV may be intended to prevent immune responses against semen-derived antigens, but can be hi-jacked by genitally acquired viral infections to compromise adaptive cellular immunity.

The relationship between sitting height, sitting height to height ratio with blood pressure among Polokwane private school children aged 6-13 years

BACKGROUND

It is notable that sitting height (SH) correlates with blood pressure (BP) in children and adolescents of developed countries. However, little is known about the relationships between SH and SH to height ratio (SH/H) with BP in South African children from middle and upper socio-economic groups. The purpose of this study was to compare SH and SH/H of private school attending children in the Polokwane area with National Health and Nutrition Examination Survey III (NHANES III) reference population and to determine the relationship between SH, SH/H with BP among private school attending children.

METHODS

A total of 1665 children (846 boys and 819 girls) aged between 6 and 13 years attending three private schools in Polokwane, underwent anthropometric and BP measurements using standard procedures. Linear regression was used to determine the relationship between height, SH, SH/H with BP among these children.

RESULTS

Polokwane private school attending boys from age 7 to 13 years displayed a lower mean SH compared to the NHANES III whereas NHANHES III girls from age 10 to 13 years had a higher mean SH compared to those in private school. In the simple regression analysis, SH was positively associated with SBP (β =1.318; 95% CI = 1.217-1.418) and DBP (β = 0.641; 95% Cl = 0.555-0.727). The findings remains statistically significant only for SH with both SBP (β = 1.025; 95% Cl = 0.844-1.201) and DBP (β = 0.585; 95% Cl 0.434-0.736) after adjusting for age, gender and BMI among these children.

CONCLUSION

In South African children, SH and SH/H were lower compared to the NHANES III children. There was a significant positive association between DBP and SBP together with the components of height among Polokwane private school children.

Inhibition of ROCK1 kinase modulates both tumor cells and stromal fibroblasts in pancreatic cancer

ROCK, or Rho-associated coiled coil-containing protein kinase, is a member of the AGC kinase family and has been shown to play a role in cell migration, ECM synthesis, stress-fiber assembly, and cell contraction. Increased ROCK expression has been reported in multiple pathological conditions, including cancer. Here, we report increased expression of ROCK 1 in pancreatic tumor epithelial cells as well as in cancer associated fibroblasts (CAF). In our analysis, 62% of tumor samples exhibited ≥2+ in staining intensity by IHC analysis, versus 40% of adjacent normal tissue samples (P<0.0001). Thus, we hypothesized that ROCKs may play a significant role in pancreatic cancer progression, and may serve as a suitable target for treatment. We report a low frequency (4/34) amplification of the ROCK1 gene locus at chromosome 18q11.1 in pancreatic ductal adenocarcinoma (PDAC) patient tissue samples by aCGH analysis. Inhibition of ROCK kinase activity by a small molecule inhibitor (fasudil) resulted in moderate (IC50s of 6-71 μM) inhibition of PDAC cell proliferation, migration, and activation of co-cultured stellate cells. In the KPC mouse model for pancreatic cancer, fasudil decreased tumor collagen deposition. This translated to an enhanced overall survival of the mice and an increase in gemcitabine uptake. Though fasudil may target both the tumor epithelial cells and the CAFs, our findings are consistent with the hypothesis that inhibition of tumor stroma enhances drug penetration and efficacy in PDAC. Overall, our data suggests that ROCK1 may serve as a potential therapeutic target to enhance current treatment regimens for pancreatic cancer.