Single-cell sequencing and its applications in head and neck cancer

Qi, Zongtai; Barrett, Thomas F.; Parikh, Anuraag S.; Tirosh, Itay; Puram, Sidharth V.

doi:10.1016/j.oraloncology.2019.104441

Cited by 70 publications

(73 citation statements)

References 115 publications

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“…Single-cell genomics of clinical tumor specimens obtained as part of routine disease management or through research biopsies should help guide new discoveries and better deployment of therapies 26,27 , as initial studies have shown in the context of gliomas 6,17 , melanoma 3,28 , head and neck squamous cell carcinoma 4,29 and other malignancies 30-34 . However, this requires adaptation of laboratory protocols, initially developed in research settings and requiring very rapid handling of fresh tissue, into the context of clinical sample acquisition and processing.…”

Section: Discussionmentioning

confidence: 99%

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

Slyper

Porter

Ashenberg

et al. 2020

Nat Med

463

295

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umors encompass complex cellular ecosystems of malignant and non-malignant cells, whose diversity and interactions affect cancer progression and drug response and resistance. Recent advances in single-cell genomics, especially single-cell RNA-Seq (scRNA-Seq), have transformed our ability to analyze tumors, revealing cell types, states, genetic diversity and interactions in the complex tumor ecosystem 1-6. Single-cell analysis of tumors is rapidly expanding, including the launch of a Human Tumor Atlas Network (HTAPP) as part of the Cancer Moonshot 7. Successful scRNA-Seq of clinical tumor specimens poses several challenges. First, it requires quick dissociation tailored to the tumor type, and involves enzymatic digestion, which can lead to loss of sensitive cells or changes in gene expression. Moreover, obtaining fresh tissue is time-sensitive and requires tight coordination

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Section: Discussionmentioning

confidence: 99%

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

Slyper

Porter

Ashenberg

et al. 2020

Nat Med

463

295

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“…This lack of association may be related to more complex mechanisms of CXCL14-related tumor suppression or MHC class I regulation in human tumors, but they may also reflect the well known technical limitations of scRNA-seq, including alterations in gene expression due to tumor dissociation and cell sorting, as well as bias in genes detected. 19 Our murine models of OSCC demonstrate the tumor suppressive effect of malignant cell-specific CXCL14; we anticipate that further work with manipulation of stromal and, specifically, fibroblast-derived CXCL14 would be useful in better defining this context dependence in HNSCC to determine if head and neck cancers mimic the findings from breast oncology. We believe our data validating inverse association of tumor size and direct association of TIL with malignant cell-specific CXCL14 expression may have implications for targeted therapies in OSCC and head and neck cancer, in general.…”

Section: Discussionmentioning

confidence: 85%

“…Importantly, we demonstrate that the tumor suppressive effect An important aspect of our work is the use of human tumor samples to further define the role of CXCL14 in the HNSCC ecosystem. By taking advantage of single cell RNA-seq to overcome the challenges of cellular and expression-based heterogeneity, [19][20][21] our data suggest that the effects of CXCL14 in OSCC may specifically depend on the cell type secreting this chemokine, with only malignant cell-specific CXCL14 being associated with increased TIL in patient samples in our cohort (figure 7). Notably, this compartment-specific effect has been previously suggested in breast cancer: Sjöberg et al 3 used RNAscope to demonstrate that epithelial CXCL14 was associated with decreased proliferation, while stromal CXCL14 was associated with shorter recurrence free and cancer-specific survival.…”

Section: Discussionmentioning

confidence: 89%

Section: Discussionmentioning

confidence: 99%

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Malignant cell-specific CXCL14 promotes tumor lymphocyte infiltration in oral cavity squamous cell carcinoma

Parikh

Shin

Faquin

et al. 2020

J Immunother Cancer

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ObjectivesTo explore lymphocyte infiltration as a potential mechanism behind CXCL14-mediated tumor growth suppression in oral cavity squamous cell carcinoma (OSCC).MethodsWe analyzed single cell RNA-sequencing (scRNA-seq) data from OSCC to identify expression changes among malignant cells in lymph nodes (LN) versus primary tumors. CXCL14 expression in murine OSCC cell lines was quantified using qRT-PCR. Short hairpin RNA knockdown of CXCL14 was performed in mouse oral cavity (MOC)1 cells, and CXCL14 overexpression was performed in MOC2 cells. Cells in each condition were injected into C57BL/6 mice with and without T cell depletion, and tumor volume was measured. At 30 days, tumors were dissociated and analyzed by flow cytometry for CD45+CD3+ T cells. CXCL14 expression was correlated with gene expression signatures of tumor infiltrating lymphocytes (TIL) in scRNA-seq data, as well as TCGA tumors.ResultsscRNA-seq revealed CXCL14 as the most significantly downregulated gene among malignant cells in LNs relative to primary tumor, supporting a role in preventing invasion and/or metastasis. In a murine immunocompetent model, CXCL14 expression was higher in indolent MOC1 cells than in more aggressive MOC2 cells. Tumor growth in vivo was significantly increased by CXCL14 knockdown in MOC1 cells relative to control, with a corresponding decrease in TIL. In MOC2 cells, tumor growth was significantly reduced by CXCL14 overexpression relative to control and TIL were increased. Both effects were lost with T cell depletion. In a human tumor scRNA-seq cohort, we found that only malignant cell CXCL14, but not non-malignant cell or fibroblast CXCL14, was associated with TIL. Bulk CXCL14 from the TCGA cohort had no association with TIL.ConclusionsHigher CXCL14 expression by tumor cells is associated with reduced tumor growth and increased TIL, supporting immune-mediated suppression of tumor growth in OSCC. Given that CXCL14 is downregulated in LN metastases compared with primary tumors, our data raise the possibility that CXCL14-mediated immune infiltration may discourage invasion and metastasis. In human scRNA-seq data, only malignant cell-specific CXCL14 was associated with TIL, suggesting a critical context-dependent effect of CXCL14 expression.

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“…Single-cell RNA sequencing (scRNA-Seq) technique, which provides an avenue to understand gene regulation networks, metastasis and the complexity of intratumoral cell-to-cell heterogeneity at the single-cell level, has diverse applications on bioinformatics, stem cell differentiation, organ development, whole-tissue subtyping and tumor biology [17,18,19] . It captures cellular differences underlying tumor biology at a higher resolution than regular bulk RNA-seq and has revolutionized studies of cancer mechanisms and personalized medicine [ 20 ] . For better understanding the potential infection risk in oral cavity, we explored whether the ACE2 and FURIN were expressed and their expressing cells composition and proportion in different oral tissues based on the public scRNA-seq profiles from GEO public databases.…”

Section: Introductionmentioning

confidence: 99%

Significant expression of FURIN and ACE2 on oral epithelial cells may facilitate the efficiency of SARS-CoV-2 entry

Zhong

Lin

Gao

et al. 2020

Preprint

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Background:Leading to a sustained epidemic spread with >2,000,000 confirmed human infections, including >100,000 deaths, COVID-19 was caused by SARS-CoV-2 and resulted in acute respiratory distress syndrome (ARDS) and sepsis, which brought more challenges to the patient's treatment. The S-glycoprotein, which recognized as the key factor for the entry of SARS-CoV-2 into the cell, contains two functional domains: an ACE2 receptor binding domain and a second domain necessary for fusion of the coronavirus and cell membranes. FURIN activity, exposes the binding and fusion domains, is essential for the zoonotic transmission of SARS-CoV-2. Moreover, it has been reported that ACE2 is likely to be the receptor for SARS-CoV-2. In addition, FURIN enzyme and ACE2 receptor were expressed in airway epithelia, cardiac tissue, and enteric canals, which considered as the potential target organ of the virus.However, report about the expression of FURIN and ACE2 in oral tissues was limited. Methods:In order to investigate the potential infective channel of new coronavirus in oral cavity, we analyze the expression of ACE2 and FURIN that mediate the new coronavirus entry into host cells in oral mucosa using the public single-cell sequence datasets. Furthermore, immunohistochemical staining experiment was performed to confirm the expression of ACE2 and FURIN in the protein level. Results:The bioinformatics results indicated the differential expression of ACE2 and FURIN on epithelial cells of different oral mucosal tissues and the proportion of FURIN-positive cells was obviously higher than that of ACE2-positive cells. IHC experiments revealed that both the ACE2-positive and FURIN-positive cells in the target tissues were mainly positioned in the epithelial layers, partly expressed in fibroblasts, which further confirm the bioinformatics results.Conclusions: Based on these findings, we speculated that SARS-CoV-2 could effectively invade oral mucosal cells though two possible routes: binding to the ACE2 receptor and fusion with cell membrane activated by FURIN protease. Our results indicated that oral mucosa tissues are susceptible to SARS-CoV-2, which provides valuable information for virus-prevention strategy in clinical care as well as daily life.

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Single-cell sequencing and its applications in head and neck cancer

Cited by 70 publications

References 115 publications

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

Malignant cell-specific CXCL14 promotes tumor lymphocyte infiltration in oral cavity squamous cell carcinoma

Significant expression of FURIN and ACE2 on oral epithelial cells may facilitate the efficiency of SARS-CoV-2 entry

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