Application of Single-Cell Multi-Omics in Dissecting Cancer Cell Plasticity and Tumor Heterogeneity

Tumor heterogeneity, a hallmark of cancer, impairs the efficacy of cancer therapy and drives tumor progression. Exploring inter- and intra-tumoral heterogeneity not only provides insights into tumor development and progression, but also guides the design of personalized therapies. Previously, high-throughput sequencing techniques have been used to investigate the heterogeneity of tumor ecosystems. However, they could not provide a high-resolution landscape of cellular components in tumor ecosystem. Recently, advance in single-cell technologies has provided an unprecedented resolution to uncover the intra-tumoral heterogeneity by profiling the transcriptomes, genomes, proteomes and epigenomes of the cellular components and also their spatial distribution, which greatly accelerated the process of basic and translational cancer research. Importantly, it has been demonstrated that some cancer cells are able to transit between different states in order to adapt to the changing tumor microenvironment, which led to increased cellular plasticity and tumor heterogeneity. Understanding the molecular mechanisms driving cancer cell plasticity is critical for developing precision therapies. In this review, we summarize the recent progress in dissecting the cancer cell plasticity and tumor heterogeneity by use of single-cell multi-omics techniques.

Download Full-text

An Intricate Connection between Alternative Splicing and Phenotypic Plasticity in Development and Cancer

Cells ◽

10.3390/cells9010034 ◽

2019 ◽

Vol 9 (1) ◽

pp. 34 ◽

Cited By ~ 4

Author(s):

Giuseppe Biamonti ◽

Lucia Infantino ◽

Daniela Gaglio ◽

Angela Amato

Keyword(s):

Alternative Splicing ◽

Cancer Cells ◽

Cancer Cell ◽

Tumor Heterogeneity ◽

Molecular Mechanisms ◽

High Throughput Sequencing ◽

Dependent Manner ◽

Cellular Plasticity ◽

Cell Plasticity ◽

Cellular Mechanisms

During tumor progression, hypoxia, nutrient deprivation or changes in the extracellular environment (i.e., induced by anti-cancer drugs) elicit adaptive responses in cancer cells. Cellular plasticity increases the chance that tumor cells may survive in a challenging microenvironment, acquire new mechanisms of resistance to conventional drugs, and spread to distant sites. Re-activation of stem pathways appears as a significant cause of cellular plasticity because it promotes the acquisition of stem-like properties through a profound phenotypic reprogramming of cancer cells. In addition, it is a major contributor to tumor heterogeneity, depending on the coexistence of phenotypically distinct subpopulations in the same tumor bulk. Several cellular mechanisms may drive this fundamental change, in particular, high-throughput sequencing technologies revealed a key role for alternative splicing (AS). Effectively, AS is one of the most important pre-mRNA processes that increases the diversity of transcriptome and proteome in a tissue- and development-dependent manner. Moreover, defective AS has been associated with several human diseases. However, its role in cancer cell plasticity and tumor heterogeneity remains unclear. Therefore, unravelling the intricate relationship between AS and the maintenance of a stem-like phenotype may explain molecular mechanisms underlying cancer cell plasticity and improve cancer diagnosis and treatment.

Download Full-text

Single-Cell Transcriptomic Analysis Revealed a Critical Role of SPP1/CD44-Mediated Crosstalk Between Macrophages and Cancer Cells in Glioma

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.779319 ◽

2021 ◽

Vol 9 ◽

Author(s):

Cong He ◽

Luoyan Sheng ◽

Deshen Pan ◽

Shuai Jiang ◽

Li Ding ◽

...

Keyword(s):

Single Cell ◽

Tumor Heterogeneity ◽

Molecular Mechanisms ◽

Critical Role ◽

Cell Communication ◽

High Grade Glioma ◽

Sequencing Analysis ◽

High Grade ◽

Cellular Components

High-grade glioma is one of the most lethal human cancers characterized by extensive tumor heterogeneity. In order to identify cellular and molecular mechanisms that drive tumor heterogeneity of this lethal disease, we performed single-cell RNA sequencing analysis of one high-grade glioma. Accordingly, we analyzed the individual cellular components in the ecosystem of this tumor. We found that tumor-associated macrophages are predominant in the immune microenvironment. Furthermore, we identified five distinct subpopulations of tumor cells, including one cycling, two OPC/NPC-like and two MES-like cell subpopulations. Moreover, we revealed the evolutionary transition from the cycling to OPC/NPC-like and MES-like cells by trajectory analysis. Importantly, we found that SPP1/CD44 interaction plays a critical role in macrophage-mediated activation of MES-like cells by exploring the cell-cell communication among all cellular components in the tumor ecosystem. Finally, we showed that high expression levels of both SPP1 and CD44 correlate with an increased infiltration of macrophages and poor prognosis of glioma patients. Taken together, this study provided a single-cell atlas of one high-grade glioma and revealed a critical role of macrophage-mediated SPP1/CD44 signaling in glioma progression, indicating that the SPP1/CD44 axis is a potential target for glioma treatment.

Download Full-text

Impact of the Tumor Microenvironment on Tumor Heterogeneity and Consequences for Cancer Cell Plasticity and Stemness

Cancers ◽

10.3390/cancers12123716 ◽

2020 ◽

Vol 12 (12) ◽

pp. 3716

Author(s):

Ralf Hass ◽

Juliane von der Ohe ◽

Hendrik Ungefroren

Keyword(s):

Tumor Microenvironment ◽

Cancer Cell ◽

Tumor Heterogeneity ◽

Cancer Therapies ◽

Epigenetic Alterations ◽

Cell Plasticity ◽

Cellular Phenotypes ◽

Therapy Success ◽

Physical And Chemical

Tumor heterogeneity is considered the major cause of treatment failure in current cancer therapies. This feature of solid tumors is not only the result of clonal outgrowth of cells with genetic mutations, but also of epigenetic alterations induced by physical and chemical signals from the tumor microenvironment (TME). Besides fibroblasts, endothelial and immune cells, mesenchymal stroma/stem-like cells (MSCs) and tumor-associated macrophages (TAMs) intimately crosstalk with cancer cells and can exhibit both anti- and pro-tumorigenic effects. MSCs can alter cancer cellular phenotypes to increase cancer cell plasticity, eventually resulting in the generation of cancer stem cells (CSCs). The shift between different phenotypic states (phenotype switching) of CSCs is controlled via both genetic programs, such as epithelial-mesenchymal transdifferentiation or retrodifferentiation, and epigenetic alterations triggered by signals from the TME, like hypoxia, spatial heterogeneity or stromal cell-derived chemokines. Finally, we highlight the role of spontaneous cancer cell fusion with various types of stromal cells. i.e., MSCs in shaping CSC plasticity. A better understanding of cell plasticity and phenotype shifting in CSCs is a prerequisite for exploiting this phenomenon to reduce tumor heterogeneity, thereby improving the chance for therapy success.

Download Full-text

Tumorigenic Cell Reprogramming and Cancer Plasticity: Interplay between Signaling, Microenvironment, and Epigenetics

Stem Cells International ◽

10.1155/2018/4598195 ◽

2018 ◽

Vol 2018 ◽

pp. 1-16 ◽

Cited By ~ 22

Author(s):

Vittoria Poli ◽

Luca Fagnocchi ◽

Alessio Zippo

Keyword(s):

Cancer Cell ◽

Tumor Heterogeneity ◽

Critical Role ◽

Cell Reprogramming ◽

Tumor Initiation ◽

Cell Of Origin ◽

Cell Plasticity ◽

New Developments ◽

Dynamic Mechanisms ◽

Tumor Maintenance

Accumulating evidences indicate that many tumors rely on subpopulations of cancer stem cells (CSCs) with the ability to propagate malignant clones indefinitely and to produce an overt cancer. Of importance, CSCs seem to be more resistant to the conventional cytotoxic treatments, driving tumor growth and contributing to relapse. CSCs can originate from normal committed cells which undergo tumor-reprogramming processes and reacquire a stem cell-like phenotype. Increasing evidences also show how tumor homeostasis and progression strongly rely on the capacity of nontumorigenic cancer cells to dedifferentiate to CSCs. Both tumor microenvironment and epigenetic reprogramming drive such dynamic mechanisms, favoring cancer cell plasticity and tumor heterogeneity. Here, we report new developments which led to an advancement in the CSC field, elucidating the concepts of cancer cell of origin and CSC plasticity in solid tumor initiation and maintenance. We further discuss the main signaling pathways which, under the influence of extrinsic environmental factors, play a critical role in the formation and maintenance of CSCs. Moreover, we propose a review of the main epigenetic mechanisms whose deregulation can favor the onset of CSC features both in tumor initiation and tumor maintenance. Finally, we provide an update of the main strategies that could be applied to target CSCs and cancer cell plasticity.

Download Full-text

Detecting Interactive Gene Groups for Single-Cell RNA-Seq Data Based on Co-Expression Network Analysis and Subgraph Learning

Cells ◽

10.3390/cells9091938 ◽

2020 ◽

Vol 9 (9) ◽

pp. 1938 ◽

Cited By ~ 1

Author(s):

Xiucai Ye ◽

Weihang Zhang ◽

Yasunori Futamura ◽

Tetsuya Sakurai

Keyword(s):

Network Analysis ◽

Single Cell ◽

Tumor Heterogeneity ◽

High Throughput Sequencing ◽

Enrichment Analysis ◽

Functional Enrichment ◽

Cell Subpopulation ◽

Rna Seq ◽

Cancer Subtypes ◽

Learning Framework

High-throughput sequencing technologies have enabled the generation of single-cell RNA-seq (scRNA-seq) data, which explore both genetic heterogeneity and phenotypic variation between cells. Some methods have been proposed to detect the related genes causing cell-to-cell variability for understanding tumor heterogeneity. However, most existing methods detect the related genes separately, without considering gene interactions. In this paper, we proposed a novel learning framework to detect the interactive gene groups for scRNA-seq data based on co-expression network analysis and subgraph learning. We first utilized spectral clustering to identify the subpopulations of cells. For each cell subpopulation, the differentially expressed genes were then selected to construct a gene co-expression network. Finally, the interactive gene groups were detected by learning the dense subgraphs embedded in the gene co-expression networks. We applied the proposed learning framework on a real cancer scRNA-seq dataset to detect interactive gene groups of different cancer subtypes. Systematic gene ontology enrichment analysis was performed to examine the detected genes groups by summarizing the key biological processes and pathways. Our analysis shows that different subtypes exhibit distinct gene co-expression networks and interactive gene groups with different functional enrichment. The interactive genes are expected to yield important references for understanding tumor heterogeneity.

Download Full-text

Time to Move to the Single-Cell Level: Applications of Single-Cell Multi-Omics to Hematological Malignancies and Waldenström’s Macroglobulinemia—A Particularly Heterogeneous Lymphoma

Cancers ◽

10.3390/cancers13071541 ◽

2021 ◽

Vol 13 (7) ◽

pp. 1541

Author(s):

Ramón García-Sanz ◽

Cristina Jiménez

Keyword(s):

Single Cell ◽

Tumor Heterogeneity ◽

Tumor Development ◽

Therapy Resistance ◽

Single Cell Level ◽

Waldenström’S Macroglobulinemia ◽

Cell Level ◽

Waldenstrom's Macroglobulinemia ◽

Waldenstrom’S Macroglobulinemia ◽

Waldenström's Macroglobulinemia

Single-cell sequencing techniques have become a powerful tool for characterizing intra-tumor heterogeneity, which has been reflected in the increasing number of studies carried out and reported. We have rigorously reviewed and compiled the information about these techniques inasmuch as they are relative to the area of hematology to provide a practical view of their potential applications. Studies show how single-cell multi-omics can overcome the limitations of bulk sequencing and be applied at all stages of tumor development, giving insights into the origin and pathogenesis of the tumors, the clonal architecture and evolution, or the mechanisms of therapy resistance. Information at the single-cell level may help resolve questions related to intra-tumor heterogeneity that have not been previously explained by other techniques. With that in mind, we review the existing knowledge about a heterogeneous lymphoma called Waldenström’s macroglobulinemia and discuss how single-cell studies may help elucidate the underlying causes of this heterogeneity.

Download Full-text

Effects of poor sleep on the immune cell landscape as assessed by single-cell analysis

Communications Biology ◽

10.1038/s42003-021-02859-8 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Xiuxing Liu ◽

Binyao Chen ◽

Zhaohao Huang ◽

Runping Duan ◽

He Li ◽

...

Keyword(s):

Single Cell ◽

Regulatory Networks ◽

Molecular Mechanisms ◽

Immune Cell ◽

Single Cell Analysis ◽

Tumor Development ◽

Public Health Issue ◽

Poor Sleep ◽

Transcriptional Regulatory Networks ◽

Transcriptional Regulatory

AbstractPoor sleep has become an important public health issue. With loss of sleep durations, poor sleep has been linked to the increased risks for diseases. Here we employed mass cytometry and single-cell RNA sequencing to obtain a comprehensive human immune cells landscape in the context of poor sleep, which was analyzed in the context of subset composition, gene signatures, enriched pathways, transcriptional regulatory networks, and intercellular interactions. Participants subjected to staying up had increased T and plasma cell frequency, along with upregulated autoimmune-related markers and pathways in CD4+ T and B cells. Additionally, staying up reduced the differentiation and immune activity of cytotoxic cells, indicative of a predisposition to infection and tumor development. Finally, staying up influenced myeloid subsets distribution and induced inflammation development and cellular senescence. These findings could potentially give high-dimensional and advanced insights for understanding the cellular and molecular mechanisms of pathologic conditions related to poor sleep.

Download Full-text

Spontaneous fusion of MSC with breast cancer cells can generate tumor dormancy

10.21203/rs.3.rs-321562/v1 ◽

2021 ◽

Author(s):

Catharina Melzer ◽

Juliane von der Ohe ◽

Tianjiao Luo ◽

Ralf Hass

Keyword(s):

Breast Cancer ◽

Cancer Cells ◽

Cell Fusion ◽

Cancer Cell ◽

Tumor Heterogeneity ◽

Breast Cancer Cells ◽

Tumor Development ◽

Cell Populations ◽

Hybrid Cells

Abstract Background: A variety of different tumors including breast cancer cells can closely interact with mesenchymal stroma/stem-like cells (MSC) in the tumor microenvironment eventually resulting in cell fusion and formation of new hybrid cancer cell populations displaying altered properties. Methods: Lentiviral-transduced MDA-MB-231 cherry breast cancer cells and MSC GFP were co-cultured and a resulting hybrid cancer cell population (MDA-MSC-hyb5) was isolated. Characterization was performed for marker expression and short tandem repeat (STR) fragment analysis compared to the parental cells. Moreover, in vivo tumor development and metastatic capacity of MDA-MSC-hyb5 was studied and unique properties were analyzed by RNA microarray expression analyses compared to other breast cancer hybrid populations. Potential chemotherapeutic sensitivity was carried out in tumor explant cultures of MDA-MSC-hyb5 cells. Results: Direct cellular interactions of MDA-MB-231 cherry breast cancer cells with human MSC GFP in a co-culture model resulted in spontaneous cell fusion by generation of MDA-MSC-hyb5 cherry GFP breast cancer hybrid cells. Proliferative capacity of MDA-MSC-hyb5 cells was about 1.8-fold enhanced when compared to the parental MDA-MB-231 cherry breast cancer cells. In contrast to a spontaneous MDA-MB-231 cherry -induced tumor development in vivo within 18.8 days MDA-MSC-hyb5 cells initially remained quiescent in a dormancy-like state. At distinct time points up to about a half year later after injection NODscid mice started to develop MDA-MSC-hyb5 cell-induced tumors. Following tumor initiation, formation of metastases in various different organs occurred rapidly within about 10.5 days. Changes in gene expression levels were evaluated by RNA-microarray analysis and revealed certain increase in dormancy-associated transcripts in MDA-MSC-hyb5. Chemotherapeutic responsiveness of MDA-MSC-hyb5 cells was partially enhanced as compared to MDA-MB-231 cells, however, some resistance e.g. for taxol was detectable in cancer hybrid cells. Moreover, drug response partially changed during tumor development of MDA-MSC-hyb5 cells suggesting unstable in vivo phenotypes of MDA-hyb5 cells with increased tumor heterogeneity. Conclusions: The spontaneous formation of cancer hybrid cell populations like MDA-MSC-hyb5 by cell fusion contributes to tumorigenic diversification by acquisition of new properties such as altered chemotherapeutic responsiveness. The unique tumor dormancy of MDA-MSC-hyb5 cells not observed in other breast cancer hybrid cells so far markedly increases tumor heterogeneity.

Download Full-text

Modeling non-genetic dynamics of cancer cell states measured by single-cell analysis: Uncovering bifurcations that explain why treatment either kills a cancer cell or makes it resistant

10.1101/574848 ◽

2019 ◽

Author(s):

S. Huang

Keyword(s):

Dynamical System ◽

Single Cell ◽

Cancer Cell ◽

Single Cell Analysis ◽

Cell Plasticity ◽

System A ◽

Critical Transitions ◽

Stable Attractor ◽

Statistical Ensembles ◽

Tumor Cell Plasticity

AbstractSingle-cell transcriptomics offers a new vista on non-genetic tumor cell plasticity, a neglected aspect of cancer. The gene expression state of each cell is governed by the gene regulatory network which represents a high-dimensional non-linear dynamical system that generates multiple stable attractor states and undergoes destabilizing bifurcations, manifest as critical transitions. Modeling clonal cell population as statistical ensembles of the same dynamical system, a index IC is derived for detecting destabilization towards critical transitions in single-cell molecular profiles. Therapy-induced bifurcation explains why treatment backfires: a drug-treated cell is imposed the binary choice to either apoptose or become a cancer-stem cell.

Download Full-text

The Role of Macrophages in Cancer Development and Therapy

Cancers ◽

10.3390/cancers13081946 ◽

2021 ◽

Vol 13 (8) ◽

pp. 1946

Author(s):

Ewa Cendrowicz ◽

Zuzanna Sas ◽

Edwin Bremer ◽

Tomasz P. Rygiel

Keyword(s):

Cancer Cell ◽

Strong Association ◽

Tumor Development ◽

Therapeutic Approaches ◽

Cell Recruitment ◽

Patient Prognosis ◽

And Function ◽

Cellular Components ◽

Activation Status

Macrophages are critical mediators of tissue homeostasis and influence various aspects of immunity. Tumor-associated macrophages are one of the main cellular components of the tumor microenvironment. Depending on their activation status, macrophages can exert a dual influence on tumorigenesis by either antagonizing the cytotoxic activity of immune cells or, less frequently, by enhancing antitumor responses. In most situations, TAMs suppress T cell recruitment and function or regulate other aspects of tumor immunity. The importance of TAMs targeting in cancer therapy is derived from the strong association between the high infiltration of TAMs in the tumor tissue with poor patient prognosis. Several macrophage-targeting approaches in anticancer therapy are developed, including TAM depletion, inhibition of new TAM differentiation, or re-education of TAM activation for cancer cell phagocytosis. In this review, we will describe the role of TAMs in tumor development, including such aspects as protumorigenic inflammation, immune suppression, neoangiogenesis, and enhancement of tissue invasion and distant metastasis. Furthermore, we will discuss therapeutic approaches that aim to deplete TAMs or, on the contrary, re-educate TAMs for cancer cell phagocytosis and antitumor immunity.

Download Full-text