Macrophage morphology correlates with single-cell diversity and prognosis in colorectal liver metastasis

It has long been known that in vitro polarized macrophages differ in morphology. Stemming from a conventional immunohistology observation, we set out to test the hypothesis that morphology of tumor-associated macrophages (TAMs) in colorectal liver metastasis (CLM) represents a correlate of functional diversity with prognostic significance. Density and morphological metrics of TAMs were measured and correlated with clinicopathological variables. While density of TAMs did not correlate with survival of CLM patients, the cell area identified small (S-TAM) and large (L-TAM) macrophages that were associated with 5-yr disease-free survival rates of 27.8% and 0.2%, respectively (P < 0.0001). RNA sequencing of morphologically distinct macrophages identified LXR/RXR as the most enriched pathway in large macrophages, with up-regulation of genes involved in cholesterol metabolism, scavenger receptors, MERTK, and complement. In single-cell analysis of mononuclear phagocytes from CLM tissues, S-TAM and L-TAM signatures were differentially enriched in individual clusters. These results suggest that morphometric characterization can serve as a simple readout of TAM diversity with strong prognostic significance.

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CCL20/TNF/VEGFA Cytokine Secretory Phenotype of Tumor-Associated Macrophages Is a Negative Prognostic Factor in Cutaneous Melanoma

Cancers ◽

10.3390/cancers13163943 ◽

2021 ◽

Vol 13 (16) ◽

pp. 3943

Author(s):

Alba Gutiérrez-Seijo ◽

Elena García-Martínez ◽

Celia Barrio-Alonso ◽

Miriam Pareja-Malagón ◽

Alejandra Acosta-Ocampo ◽

...

Keyword(s):

Cutaneous Melanoma ◽

Large Fraction ◽

Prognostic Significance ◽

Disease Free Survival ◽

Rna Seq ◽

Primary Cutaneous Melanoma ◽

Kaplan Meier ◽

Intracellular Cytokines ◽

Negative Prognostic Factor

TAMs constitute a large fraction of infiltrating immune cells in melanoma tissues, but their significance for clinical outcomes remains unclear. We explored diverse TAM parameters in clinically relevant primary cutaneous melanoma samples, including density, location, size, and polarization marker expression; in addition, because cytokine production is a hallmark of macrophages function, we measured CCL20, TNF, and VEGFA intracellular cytokines by single-cell multiparametric confocal microscopy. The Kaplan–Meier method was used to analyze correlation with melanoma-specific disease-free survival and overall survival. No significant correlations with clinical parameters were observed for TAM density, morphology, or location. Significantly, higher contents of the intracellular cytokines CCL20, TNF, and VEGFA were quantified in TAMs infiltrating metastasizing compared to non-metastasizing skin primary melanomas (p < 0.001). To mechanistically explore cytokine up-regulation, we performed in vitro studies with melanoma-conditioned macrophages, using RNA-seq to explore involved pathways and specific inhibitors. We show that p53 and NF-κB coregulate CCL20, TNF, and VEGFA in melanoma-conditioned macrophages. These results delineate a clinically relevant pro-oncogenic cytokine profile of TAMs with prognostic significance in primary melanomas and point to the combined therapeutic targeting of NF-kB/p53 pathways to control the deviation of TAMs in melanoma.

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Fabrication of high-aspect-ratio microstructures in polymer microfluid chips for in vitro single-cell analysis

Technical Physics ◽

10.1134/s106378421610008x ◽

2016 ◽

Vol 61 (10) ◽

pp. 1566-1571 ◽

Cited By ~ 10

Author(s):

A. S. Bukatin ◽

I. S. Mukhin ◽

E. I. Malyshev ◽

I. V. Kukhtevich ◽

A. A. Evstrapov ◽

...

Keyword(s):

Aspect Ratio ◽

Single Cell ◽

High Aspect Ratio ◽

Single Cell Analysis ◽

Cell Analysis

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Single Cell Analysis Reveals That IL-4 Receptor/Stat6 Signaling Is Not Required for the In Vivo or In Vitro Development of CD4+Lymphocytes with a Th2 Cytokine Profile

The Journal of Immunology ◽

10.4049/jimmunol.164.6.3047 ◽

2000 ◽

Vol 164 (6) ◽

pp. 3047-3055 ◽

Cited By ~ 193

Author(s):

Dragana Jankovic ◽

Marika C. Kullberg ◽

Nancy Noben-Trauth ◽

Patricia Caspar ◽

William E. Paul ◽

...

Keyword(s):

Single Cell ◽

Single Cell Analysis ◽

Cytokine Profile ◽

Cell Analysis ◽

In Vitro Development ◽

Th2 Cytokine ◽

Vitro Development ◽

Cd4 Lymphocytes

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Prognostic significance of early recurrence: a conditional survival analysis in patients with resected colorectal liver metastasis

HPB ◽

10.1111/hpb.12136 ◽

2013 ◽

Vol 15 (10) ◽

pp. 803-813 ◽

Cited By ~ 19

Author(s):

Marcus C.B. Tan ◽

Jean M. Butte ◽

Mithat Gonen ◽

Nancy Kemeny ◽

Yuman Fong ◽

...

Keyword(s):

Survival Analysis ◽

Liver Metastasis ◽

Colorectal Liver Metastasis ◽

Prognostic Significance ◽

Early Recurrence ◽

Conditional Survival

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Single-cell analysis reveals IGF-1 potentiation of inhibition of the TGF-β/Smad pathway of fibrosis in human keratocytes in vitro

Scientific Reports ◽

10.1038/srep34373 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 11

Author(s):

Tomislav Sarenac ◽

Martin Trapecar ◽

Lidija Gradisnik ◽

Marjan Slak Rupnik ◽

Dusica Pahor

Keyword(s):

Single Cell ◽

Single Cell Analysis ◽

Cell Analysis ◽

Smad Pathway ◽

Human Keratocytes

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Single-cell analysis revealed that IL4I1 promoted ovarian cancer progression

Journal of Translational Medicine ◽

10.1186/s12967-021-03123-7 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Hongyu Zhao ◽

Yu Teng ◽

Wende Hao ◽

Jie Li ◽

Zhefeng Li ◽

...

Keyword(s):

Ovarian Cancer ◽

Single Cell ◽

Cancer Progression ◽

Cox Regression ◽

Single Cell Analysis ◽

Cell Types ◽

In Vitro Assays ◽

Migration And Invasion ◽

Dominant Type

Abstract Background Ovarian cancer was one of the leading causes of female deaths. Patients with OC were essentially incurable and portends a poor prognosis, presumably because of profound genetic heterogeneity limiting reproducible prognostic classifications. Methods We comprehensively analyzed an ovarian cancer single-cell RNA sequencing dataset, GSE118828, and identified nine major cell types. Relationship between the clusters was explored with CellPhoneDB. A malignant epithelial cluster was confirmed using pseudotime analysis, CNV and GSVA. Furthermore, we constructed the prediction model (i.e., RiskScore) consisted of 10 prognosis-specific genes from 2397 malignant epithelial genes using the LASSO Cox regression algorithm based on public datasets. Then, the prognostic value of Riskscore was assessed with Kaplan–Meier survival analysis and time-dependent ROC curves. At last, a series of in-vitro assays were conducted to explore the roles of IL4I1, an important gene in Riskscore, in OC progression. Results We found that macrophages possessed the most interaction pairs with other clusters, and M2-like TAMs were the dominant type of macrophages. C0 was identified as the malignant epithelial cluster. Patients with a lower RiskScore had a greater OS (log-rank P < 0.01). In training set, the AUC of RiskScore was 0.666, 0.743 and 0.809 in 1-year, 3-year and 5-year survival, respectively. This was also validated in another two cohorts. Moreover, downregulation of IL4I1 inhibited OC cells proliferation, migration and invasion. Conclusions Our work provide novel insights into our understanding of the heterogeneity among OCs, and would help elucidate the biology of OC and provide clinical guidance in prognosis for OC patients.

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HIV-1 provirus transcription and translation in macrophages differs from pre-integrated cDNA complexes and requires E2F transcriptional programs

10.1101/2021.04.21.440655 ◽

2021 ◽

Author(s):

Albebson L. Lim ◽

Philip Moos ◽

Christopher D. Pond ◽

Erica C. Larson ◽

Laura J. Martins ◽

...

Keyword(s):

Single Cell ◽

Single Cell Analysis ◽

Immunological Response ◽

Virus Production ◽

Cell Analysis ◽

Gene Transcripts ◽

Nuanced Understanding ◽

New Perspective ◽

Hiv 1

AbstractHIV-1 cDNA pre-integration complexes have been shown to persist for weeks in macrophages and to be transcriptionally active. Early and late gene transcripts are produced, along with some viral proteins, yet whole virus is not. While previous work has focused on the transcription and translation of HIV-1 genes; our understanding of cellular milieu that accompanies viral production is incomplete. We have used an in vitro system to model HIV-1 infection of macrophages, and single cell RNA sequencing (scRNA-seq) to compare the transcriptomes of uninfected cells, cells harboring pre-integration HIV-1 complexes (PIC) and those containing integrated provirus and actively making late HIV proteins. These are also compared to control cells, not exposed to virus.Several observations provide new perspective on the effects of HIV-1 transcription from pre-integrated cDNA versus from integrated provirus. First, HIV-1 transcript levels do not necessarily correlate with virus production, cells harboring PIC cDNA have transcript loads comparable to cells transcribing from provirus and making p24, mCherry, and vpu proteins. Second, all HIV-1 transcripts are easily detectable in abundance from PIC cDNA transcription, as is the case with cells transcribing from provirus, although the frequency of PIC cells with detectable gag-pol, tat, env, and nef transcripts is higher than the corresponding frequencies observed for “Provirus cells”. Third, the background transcriptomes of cells harboring pre- integrated HIV-1 cDNA are not otherwise detectably altered from cells not containing any HIV- 1 transcript. Fourth, integration and production of p24, mCherry, and Vpu proteins is accompanied by a switch from transcriptomes characterized by NFkB and AP-1 promoted transcription to a transcriptome characterized by E2F family transcription products. While some of these observations may seem heretical, single cell analysis provides a more nuanced understanding of PIC cDNA transcription and the transcriptomic changes that support HIV-1 protein production from integrated provirus.Author SummarySingle cell analysis is able to distinguish between HIV-1 infected macrophage cells that are transcribing pre-integrated HIV-1 cDNA and those transcribing HIV-1 provirus. Only cells transcribing HIV-1 provirus are making p24, marker mCherry and Vpu proteins, which corresponds with a change in the host cell’s background transcriptome from one expressing viral restriction and immunological response genes to one that is expressing genes associated with cell replication and oxidative phosphorylation.

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Studying human reproductive biology through single-cell analysis and in vitro differentiation of stem cells into germ cell-like cells

Human Reproduction Update ◽

10.1093/humupd/dmaa021 ◽

2020 ◽

Vol 26 (5) ◽

pp. 670-688 ◽

Cited By ~ 1

Author(s):

Lin Li ◽

Risako Yang ◽

Chenghong Yin ◽

Kehkooi Kee

Keyword(s):

Stem Cells ◽

Single Cell ◽

Germ Cells ◽

Regulatory Networks ◽

Single Cell Analysis ◽

Reproductive Development ◽

In Vitro Differentiation ◽

Gene Markers ◽

Human Reproductive

Abstract BACKGROUND Understanding the molecular and cellular mechanisms of human reproductive development has been limited by the scarcity of human samples and ethical constraints. Recently, in vitro differentiation of human pluripotent stem cells into germ cells and single-cell analyses have opened new avenues to directly study human germ cells and identify unique mechanisms in human reproductive development. OBJECTIVE AND RATIONALE The goal of this review is to collate novel findings and insightful discoveries with these new methodologies, aiming at introducing researchers and clinicians to the use of these tools to study human reproductive biology and develop treatments for infertility. SEARCH METHODS PubMed was used to search articles and reviews with the following main keywords: in vitro differentiation, human stem cells, single-cell analysis, spermatogenesis, oogenesis, germ cells and other key terms related to these subjects. The search period included all publications from 2000 until now. OUTCOMES Single-cell analyses of human gonads have identified many important gene markers at different developmental stages and in subpopulations of cells. To validate the functional roles of these gene markers, researchers have used the in vitro differentiation of human pluripotent cells into germ cells and confirmed that some genetic requirements are unique in human germ cells and are not conserved in mouse models. Moreover, transcriptional regulatory networks and the interaction of germ and somatic cells in gonads were elucidated in these studies. WIDER IMPLICATIONS Single-cell analyses allow researchers to identify gene markers and potential regulatory networks using limited clinical samples. On the other hand, in vitro differentiation methods provide clinical researchers with tools to examine these newly identify gene markers and study the causative effects of mutations previously associated with infertility. Combining these two methodologies, researchers can identify gene markers and networks which are essential and unique in human reproductive development, thereby producing more accurate diagnostic tools for assessing reproductive disorders and developing treatments for infertility.

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