Single-cell protein-mRNA correlation analysis enabled by multiplexed dual-analyte co-detection

Gong, Haibiao; Wang, Xiaohui; Liu, Benjamin; Boutet, Stéphane C.; Holcomb, Ilona N.; Dakshinamoorthy, Gajalakshmi; Ooi, Aik T.; Sanada, Chad; Sun, Gang; Ramakrishnan, Ramesh

doi:10.1038/s41598-017-03057-5

Cited by 26 publications

(22 citation statements)

References 26 publications

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“…To support the results obtained at the protein level, we quantified respective mRNA expression levels in unstimulated single CD56 bright NK cells from peripheral blood and liver, using the Fluidigm technology. Although mRNA levels do not necessarily correspond to protein levels, we still observed a significant difference in PLZF mRNA expression between CD56 bright pbNK and ihNK cells, with more cells carrying PLZF mRNA in liver (Fig. A).…”

Section: Resultsmentioning

confidence: 77%

The Transcription Factor Promyelocytic Leukemia Zinc Finger Protein Is Associated With Expression of Liver‐Homing Receptors on Human Blood CD56bright Natural Killer Cells

et al. 2020

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The transcription factor promyelocytic leukemia zinc finger protein (PLZF) is involved in the development of natural killer (NK) cells and innate lymphoid cells, including liver‐resident NK cells in mice. In human NK cells, the role of PLZF in liver residency is still unknown. Expression of PLZF in matched human peripheral blood‐ and liver‐derived NK cells and the association of PLZF expression with surface molecules and transcription factors relevant for tissue residency were investigated using multiparameter flow cytometry and assessing single‐cell messenger RNA (mRNA) levels. Intrahepatic cluster of differentiation (CD)56bright NK cells expressed significantly higher levels of PLZF than peripheral blood CD56bright NK cells, which were predominantly PLZFlo. Expression of PLZF was highest within C‐X‐C motif chemokine receptor 6 (CXCR6)+CD69+ liver‐resident NK cells among intrahepatic CD56bright NK cell populations. Association of PLZF with liver‐residency markers was also reflected at mRNA levels. A small PLZFhiCD56bright NK cell population was identified in peripheral blood that also expressed the liver‐residency markers CXCR6 and CD69 and shared functional characteristics with liver‐resident NK cells. Conclusion: PLZF is implicated as part of a transcriptional network that promotes liver residency of human NK cells. Expression of liver‐homing markers on peripheral blood PLZFhiCD56bright NK cells identifies an intermediate population potentially contributing to the maintenance of liver‐resident NK cells.

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Section: Resultsmentioning

confidence: 77%

The Transcription Factor Promyelocytic Leukemia Zinc Finger Protein Is Associated With Expression of Liver‐Homing Receptors on Human Blood CD56bright Natural Killer Cells

et al. 2020

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“…We have demonstrated here that protein expression profiling by CyTOF can reveal striking intertumoral and intratumoral heterogeneity at single cell resolution, which is currently prohibitively expensive using single cell sequencing approaches in a study of this scale. Furthermore, paired single cell protein‐transcriptome studies have demonstrated that protein and mRNA levels correlate in many, but not all instances , and thus high‐parameter measurement of protein expression levels provides a critical layer of functional information not captured by transcriptomic approaches. The current study demonstrates the success of high dimensional single cell protein analysis in segregating normal from malignant B cells in an unsupervised manner, and in revealing elements of phenotypic diversity that are not prominently displayed by transcriptomic approaches.…”

Section: Discussionmentioning

confidence: 99%

Single Cell Phenotypic Profiling of 27 DLBCL Cases Reveals Marked Intertumoral and Intratumoral Heterogeneity

et al. 2019

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Diffuse large B‐cell lymphoma (DLBCL) is the most common histologic subtype of non‐Hodgkin lymphoma and is notorious for its clinical heterogeneity. Patient outcomes can be predicted by cell‐of‐origin (COO) classification, demonstrating that the underlying transcriptional signature of malignant B‐cells informs biological behavior in the context of standard combination chemotherapy regimens. In the current study, we used mass cytometry (CyTOF) to examine tumor phenotypes at the protein level with single cell resolution in a collection of 27 diagnostic DLBCL biopsy specimens from treatment naïve patients. We found that malignant B‐cells from each patient occupied unique regions in 37‐dimensional phenotypic space with no apparent clustering of samples into discrete subtypes. Interestingly, variable MHC class II expression was found to be the greatest contributor to phenotypic diversity. Within individual tumors, a subset of cases showed multiple phenotypic subpopulations, and in one case, we were able to demonstrate direct correspondence between protein‐level phenotypic subsets and DNA mutation‐defined subclones. In summary, CyTOF analysis can resolve both intertumoral and intratumoral heterogeneity among primary samples and reveals that each case of DLBCL is unique and may be comprised of multiple, genetically distinct subclones. © 2019 International Society for Advancement of Cytometry

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“…The authors identified a transcriptional program associated with neural crest stem cells in the minimal residual melanoma cells driven by the nuclear receptor RXRG and showed that targeting RXR signaling synergizes with targeted therapy to delay time to disease progression. Recently developed single-cell proteomics methods allow for multiplexed protein detection from single cells and analyzing functional protein expression simultaneously with gene expression [143, 144]. However, single-cell analyses lack in their ability to recapitulate the effects of cell-cell and cell-matrix interactions, as the tumor has to be dissociated prior to conducting these experiments.…”

Section: Previous Limitations and Novel Methods For Linking Intratumomentioning

confidence: 99%

Emerging insights of tumor heterogeneity and drug resistance mechanisms in lung cancer targeted therapy

2019

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The biggest hurdle to targeted cancer therapy is the inevitable emergence of drug resistance. Tumor cells employ different mechanisms to resist the targeting agent. Most commonly in EGFR-mutant non-small cell lung cancer, secondary resistance mutations on the target kinase domain emerge to diminish the binding affinity of first- and second-generation inhibitors. Other alternative resistance mechanisms include activating complementary bypass pathways and phenotypic transformation. Sequential monotherapies promise to temporarily address the problem of acquired drug resistance, but evidently are limited by the tumor cells’ ability to adapt and evolve new resistance mechanisms to persist in the drug environment. Recent studies have nominated a model of drug resistance and tumor progression under targeted therapy as a result of a small subpopulation of cells being able to endure the drug (minimal residual disease cells) and eventually develop further mutations that allow them to regrow and become the dominant population in the therapy-resistant tumor. This subpopulation of cells appears to have developed through a subclonal event, resulting in driver mutations different from the driver mutation that is tumor-initiating in the most common ancestor. As such, an understanding of intratumoral heterogeneity—the driving force behind minimal residual disease—is vital for the identification of resistance drivers that results from branching evolution. Currently available methods allow for a more comprehensive and holistic analysis of tumor heterogeneity in that issues associated with spatial and temporal heterogeneity can now be properly addressed. This review provides some background regarding intratumoral heterogeneity and how it leads to incomplete molecular response to targeted therapies, and proposes the use of single-cell methods, sequential liquid biopsy, and multiregion sequencing to discover the link between intratumoral heterogeneity and early adaptive drug resistance. In summary, minimal residual disease as a result of intratumoral heterogeneity is the earliest form of acquired drug resistance. Emerging technologies such as liquid biopsy and single-cell methods allow for studying targetable drivers of minimal residual disease and contribute to preemptive combinatorial targeting of both drivers of the tumor and its minimal residual disease cells.

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Single-cell protein-mRNA correlation analysis enabled by multiplexed dual-analyte co-detection

Cited by 26 publications

References 26 publications

The Transcription Factor Promyelocytic Leukemia Zinc Finger Protein Is Associated With Expression of Liver‐Homing Receptors on Human Blood CD56bright Natural Killer Cells

The Transcription Factor Promyelocytic Leukemia Zinc Finger Protein Is Associated With Expression of Liver‐Homing Receptors on Human Blood CD56bright Natural Killer Cells

Single Cell Phenotypic Profiling of 27 DLBCL Cases Reveals Marked Intertumoral and Intratumoral Heterogeneity

Emerging insights of tumor heterogeneity and drug resistance mechanisms in lung cancer targeted therapy

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