A model to account for the effects of oncogenes, TPA, and retinoic acid on the regulation of genes involved in metastasis

Application of single-cell sequencing to the research of tumor microenvironment

Single-cell sequencing is a technique for detecting and analyzing genomes, transcriptomes, and epigenomes at the single-cell level, which can detect cellular heterogeneity lost in conventional sequencing hybrid samples, and it has revolutionized our understanding of the genetic heterogeneity and complexity of tumor progression. Moreover, the tumor microenvironment (TME) plays a crucial role in the formation, development and response to treatment of tumors. The application of single-cell sequencing has ushered in a new age for the TME analysis, revealing not only the blueprint of the pan-cancer immune microenvironment, but also the heterogeneity and differentiation routes of immune cells, as well as predicting tumor prognosis. Thus, the combination of single-cell sequencing and the TME analysis provides a unique opportunity to unravel the molecular mechanisms underlying tumor development and progression. In this review, we summarize the recent advances in single-cell sequencing and the TME analysis, highlighting their potential applications in cancer research and clinical translation.

SPF: A spatial and functional data analytic approach to cell imaging data

The tumor microenvironment (TME), which characterizes the tumor and its surroundings, plays a critical role in understanding cancer development and progression. Recent advances in imaging techniques enable researchers to study spatial structure of the TME at a single-cell level. Investigating spatial patterns and interactions of cell subtypes within the TME provides useful insights into how cells with different biological purposes behave, which may consequentially impact a subject’s clinical outcomes. We utilize a class of well-known spatial summary statistics, the K-function and its variants, to explore inter-cell dependence as a function of distances between cells. Using techniques from functional data analysis, we introduce an approach to model the association between these summary spatial functions and subject-level outcomes, while controlling for other clinical scalar predictors such as age and disease stage. In particular, we leverage the additive functional Cox regression model (AFCM) to study the nonlinear impact of spatial interaction between tumor and stromal cells on overall survival in patients with non-small cell lung cancer, using multiplex immunohistochemistry (mIHC) data. The applicability of our approach is further validated using a publicly available multiplexed ion beam imaging (MIBI) triple-negative breast cancer dataset.

Investigating spatial patterns and interactions of cells in the tumor microenvironment (TME) provides useful insights into cancer development and progression. In this work, we proposed a novel approach which combined established spatial summary functions with functional data analysis to flexibly model the cell-cell interactions with overall survival at different inter-cell distances, in conjunction with other clinical predictors such as age, disease stage. By applying the proposed framework to multiplex immunohistochemistry (mIHC) data of patients with non-small cell lung cancer (NSCLC), we studied the nonlinear impact of spatial interactions between tumor and stromal cells on overall survival. The applicability of our proposed method is further validated using a publicly available multiplexed ion beam imaging (MIBI) triple-negative breast cancer (TNBC) dataset.

A history of exploring cancer in context

The concept that progression of cancer is regulated by interactions of cancer cells with their microenvironment was postulated by Stephen Paget over a century ago. Contemporary tumour microenvironment (TME) research focuses on the identification of tumour-interacting microenvironmental constituents, such as resident or infiltrating non-tumour cells, soluble factors and extracellular matrix components, and the large variety of mechanisms by which these constituents regulate and shape the malignant phenotype of tumour cells. In this Timeline article, we review the developmental phases of the TME paradigm since its initial description. While illuminating controversies, we discuss the importance of interactions between various microenvironmental components and tumour cells and provide an overview and assessment of therapeutic opportunities and modalities by which the TME can be targeted.

Innovative Therapies against Human Glioblastoma Multiforme

Glioblastoma multiforme is the most invasive and aggressive brain tumor in humans, and despite the latest chemical and radiative therapeutic approaches, it is still scarcely sensitive to these treatments and is generally considered an incurable disease. This paper will focus on the latest approaches to the treatment of this cancer, including the new chemicals such as proautophagic drugs and kinases inhibitors, and differentiating agents. In this field, there have been opening new perspectives as the discovery of possible specific targets such as the EGFRvIII, a truncated form of the EGF receptor. Antibodies against these targets can be used as proapoptotic agents and as possible carriers for chemicals, drugs, radioisotopes, and toxins. In this paper, we review the possible mechanism of action of these therapies, with particular attention to the combined use of toxic substances (for example, immunotoxins) and antiproliferative/differentiating compounds (i.e., ATRA, PPARγ agonists). All these aspects will be discussed in the view of progress clinical trials and of possible new approaches for directed drug formulations.

Fibroblasts transformed by combinations of ras, myc and mutant p53 exhibit increased phosphorylation of histone H1 that is independent of metastatic potential

H1 histones play an important role in regulating higher order structure of chromatin and are potential regulators of gene expression. H1s are phosphorylated, a modification which alters their interaction with DNA. We measured the abundance of three phosphorylated H1 subtypes in mouse fibroblasts transformed by combinations of ras, myc and mutant p53 which differ in metastatic potential. We found that there is an increase in phosphorylation of H1 subtypes in fibroblasts transformed with ras, myc and mutant p53. This increase was found to correlate with cellular transformation but not with induction of the metastatic phenotype.

The H-ras oncogene regulates expression of 70- and 45-kDa cell-surface molecules whose expression correlates with tumor-cell immunogenicity

The effects of the H-ras oncogene on fibroblast cell tumorigenicity and immunogenicity was studied in transfectants of the BALB/c 3T3 clone A31 fibroblastoid cell-line. Cells that were transfected with MC29-LTR-H-ras (98/6) or MC29-LTR-v-myc + H-ras (98/4v) and were inoculated into syngeneic BALB/c mice were tumorigenic in 100% and 60% of animals respectively. By contrast, transfectants containing the pSV2neo plasmid alone (98/1) displayed normal characteristics both in vitro and in vivo. Inoculation of mice with mitomycin-C-treated 98/1 or 98/4v cells induced an effective protective immunity to a challenge of live 98/4v cells, and a partial immunity against 98/6 cells. Mitomycin-C-treated 98/6 cells failed to render immunity against a challenge of either 98/6 or 98/4v cells. To correlate immunogenicity and tumorigenicity of the different cell types with cell-surface-antigen expression, we prepared MAbs against 98/4v cells in syngeneic mice. Immunohistochemical and immunoblot analysis revealed that MAbs 102 and 104 recognized 2 protein band of 70 and 45 kDa respectively, which were expressed predominantly in 98/1 and 98/4v cells. A third immunoreactive protein band of 44 kDa that reacted with MAb 6 was expressed at a similar cell-surface density on all cell types. Cell-differentiation-inducing agents, such as DMSO, retinoic acid or sodium butyrate, were all found to induce 98/6 cell flattening and morphological changes toward a normal phenotype that were followed by up-regulation of the 70- and 45-kDa antigens. The results suggest that regulation of expression of the 70- and 45-kDa molecules is affected by H-ras, and that expression of these cell-surface molecules may be relevant to tumor cell immunogenicity.

Retinoic acid modulates both invasion and plasma membrane ruffling of MCF-7 human mammary carcinoma cells in vitro

The invasiveness of MCF-7 human mammary carcinoma cells was tested in vitro via confronting cultures with embryonic chick heart fragments. Invasive (e.g. MCF-7/6) and non-invasive (e.g. MCF-7/AZ) variants were detected. Automated image analysis of time-lapse video-microscopy recordings showed that the plasma membrane ruffling activity of the invasive MCF-7/6 variant was higher than the ruffling activity of the non-invasive MCF-7/AZ variant. Addition of all-trans-retinoic acid to the culture medium (10(-6) M) inhibited both invasion and ruffling of MCF-7/6 cells, while MCF-7/AZ cells became invasive and acquired an increased ruffling by the same type of treatment. A similar opposite effect on MCF-7 cells was not found after treatment with other ligands of the nuclear steroid/thyroid receptor superfamily. Triiodo-l-thyronine (up to 10(-5) M) and beta-oestradiol (up to 10(-6) M) did not alter the invasiveness of the cells, while dexamethasone (10(-6) M) and the pure anti-oestrogen ICI 164,384 inhibited both invasion and ruffling. Our data show that retinoic acid can modulate invasiveness in opposite directions.

Modulation of clonal progression in B16F1 melanoma cells

We have examined the effects of the microenvironment on the frequency and generation of metastatic variant cells in both parental B16F1 melanoma cells and nascent clones. The metastatic abilities of cultured B16F1 cells were tested after a period of growth in the presence or absence of a second cell population separated from each other by a transwell membrane (0.45 micron pore size). The first population is defined as the 'responder' cells and the second as the 'stimulator' cells. We found that the presence of 10(5) B16F1 stimulator cells during the growth of responder B16F1 cells from approximately 10(4) to approximately 10(6) cells resulted in cells with an increased metastatic phenotype (greater than 8-fold increase in median number of lung tumors relative to untreated B16F1 parental cells). The presence of stimulator cells also increased the metastatic phenotype of nascent clones, which were grown to a population size of less than 10(6) cells, suggesting that the rate of generation of metastatic variants of the responder B16F1 clones was affected by the stimulator cells. Other cell lines, including highly metastatic B16F10 and BL6 melanoma cells, and KHT35-L1 fibrosarcoma cells, were effective stimulator cells when as few as 10(4) cells were added to transwells. In addition, normal immortalized NIH 3T3 cells were effective stimulator cells only at 10(5) cells/transwell. The cell density at which untreated parental B16F1 cells were harvested (3 x 10(3)-3 x 10(5) cells/cm2) did not affect the median number of lung tumors significantly. These results suggest that factors released from both tumor and immortalized normal cells can modulate epigenetic changes in the metastatic phenotype of B16F1 melanoma cells.

The invasive phenotypes

The expression of the invasive (I+ or I-) phenotypes determines cancer metastasis (M+ or M- phenotype). The invasive (I+ or I-) phenotypes can be divided according to time and site of expression into subphenotypes, which can be assessed separately. At various sites along the metastatic pathway the expression of the I phenotypes can be accompanied by the presence of uncontrolled growth (G+ phenotype) or its absence (G- phenotype). Various combinations of the I and G phenotypes determine the behaviour of metazoan or parasitic cells under normal, pathological non-neoplastic and neoplastic conditions. Although the G+I+M+ combination correlates with full malignancy, the sequence of events leading to the acquisition of these phenotypes during tumor development is not clear. Conditional invasion in experimental systems indicates that a tumor may be invasive and metastatic when part of its population temporarily expresses the I+ phenotype. These experiments further stress the importance of the tumor-host ecosystem for the regulation of the I phenotypes. As distinct from some parasites, the invasive morphotype of vertebrate cells cannot be simply identified. Nevertheless, within the tumor-host ecosystem morphological correlates of the activities of invasive cells may be recognized. They reflect one or more of the I+ functions, namely: motility; loss of homotypic cell-cell adhesion; establishment of alternative cell-substrate and heterotypic cell-cell adhesion; breakdown of extracellular matrices. These functions are not exclusive for I+ tumor cells, and neither are the molecular markers investigated so far. Oncogene activation leads mainly to G+ expression, and in this way serves as a signal amplifier for the I and M phenotypes. Attractive candidate molecular markers of I phenotypes are: regulators of hydrolase activities; cell-cell adhesion molecules; cell surface receptors. From data presently available, we hypothesize that invasion depends upon the balance between and I+ and an I- pathway, with both pathways being sensitive to stimulation inhibition.

Nerve growth factor and neuronal cell death

The regulation of neuronal cell death by the neuronotrophic factor, nerve growth factor (NGF), has been described during neural development and following injury to the nervous system. Also, reduced NGF activity has been reported for the aged NGF-responsive neurons of the sympathetic nervous system and cholinergic regions of the central nervous system (CNS) in aged rodents and man. Although there is some knowledge of the molecular structure of the NGF and its receptor, less is known as to the mechanism of action of NGF. Here, a possible role for NGF in the regulation of oxidant--antioxidant balance is discussed as part of a molecular explanation for the known effects of NGF on neuronal survival during development, after injury, and in the aged CNS.

Molecular oncogenetics of metastasis

Metastasis is a complex non-stochastic process that is most likely the result of genetic and epigenetic interactions of a wide variety of genes. The search for a single gene which can encompass such a pleiotropic response as to account for the observed phenotypic characteristics of metastatic tumour populations has been unsuccessful. Particular studies involving gene transfection, subtractive hybridisation and cell fusion are beginning to identify specific genes which contribute to metastasis in some cell types. However, such analyses are complicated by the inherent genetic instability and phenotypic heterogeneity present in tumour populations. A more detailed understanding of the metastatic process may require an abandoning of current generalised approaches to metastasis in favour of concentrating on key components of the metastatic cascade such as adhesion and invasion.

Induction of the metastatic phenotype by transfection of the nuclear oncogene p53: increases in cytoplasmic diacylglycerol levels and reduction in class I major histocompatibility antigen expression are not sufficient to explain the changes in metastatic capacities

Transfection of the oncogene encoding the nuclear protein p53 into a low-metastatic mouse carcinoma cell line resulted in enhanced metastatic capabilities in clones that showed increased p53 protein expression [Pohl J, Goldfinger N, Radler-Pohl A, Rotter V, Schirrmacher V (1988) Mol Cell Biol 8:2078-2081]. This effect seemed neither to be due to increase in cytoplasmic diacylglycerol levels nor to reduced cell-surface expression of class I major histocompatibility antigens.