The Extended Polydimensional Immunome Characterization (EPIC) web-based reference and discovery tool for cytometry data

Yeo, Joo Guan; Wasser, Martin; Kumar, Pavanish; Pan, Lu; Poh, Su Li; Ally, Fauziah; Arkachaisri, Thaschawee; Lim, Amanda Jin Mei; Leong, Jing Yao; Lai, Liyun; Yeo, Kee Thai; Lee, Elene Seck Choon; Chua, Camillus; Larbi, Anis; Nyunt, Ma Shwe Zin; Ng, Tze Pin; Chiesa, Sabrina; Gattorno, Marco; Martini, Alberto; Paleja, Bhairav; Dutertre, Charles–Antoine; Chen, Jinmiao; Yaung, Katherine Nay; Tang, Swee Ping; Ng, S. K.; Yung, Chee Fu; Tan, Angela Yun June; Lee, S.Y.; Ginhoux, Florent; Albani, Salvatore

doi:10.1038/s41587-020-0532-1

Cited by 27 publications

(31 citation statements)

References 11 publications

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“…We employed Phenograph clustering 18 and our in-house CyTOF analytics pipeline 19 on the data generated from all tumour sectors and identified 30 immune cell clusters (Fig. 1b).…”

Section: Resultsmentioning

confidence: 99%

Intratumoural immune heterogeneity as a hallmark of tumour evolution and progression in hepatocellular carcinoma

Nguyen

Phua

et al. 2021

Nat Commun

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The clinical relevance of immune landscape intratumoural heterogeneity (immune-ITH) and its role in tumour evolution remain largely unexplored. Here, we uncover significant spatial and phenotypic immune-ITH from multiple tumour sectors and decipher its relationship with tumour evolution and disease progression in hepatocellular carcinomas (HCC). Immune-ITH is associated with tumour transcriptomic-ITH, mutational burden and distinct immune microenvironments. Tumours with low immune-ITH experience higher immunoselective pressure and escape via loss of heterozygosity in human leukocyte antigens and immunoediting. Instead, the tumours with high immune-ITH evolve to a more immunosuppressive/exhausted microenvironment. This gradient of immune pressure along with immune-ITH represents a hallmark of tumour evolution, which is closely linked to the transcriptome-immune networks contributing to disease progression and immune inactivation. Remarkably, high immune-ITH and its transcriptomic signature are predictive for worse clinical outcome in HCC patients. This in-depth investigation of ITH provides evidence on tumour-immune co-evolution along HCC progression.

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“…We employed Phenograph clustering 18 and our in-house CyTOF analytics pipeline 19 on the data generated from all tumour sectors and identified 30 immune cell clusters (Fig. 1b).…”

Section: Resultsmentioning

confidence: 99%

Intratumoural immune heterogeneity as a hallmark of tumour evolution and progression in hepatocellular carcinoma

Nguyen

Phua

et al. 2021

Nat Commun

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“…The cells in all groups, except the PMA/ionomycin stimulation group, were processed using the standardized EPIC staining protocol as described previously ( 22 ). In brief, PBMCs were washed once with cell staining buffer (CSB) (phosphate buffered saline [PBS] with 4% FCS, 2 mM EDTA, 0.05% sodium azide) and centrifuged at 524 × g for 6 min at 4°C.…”

Section: Methodsmentioning

confidence: 99%

“…To mitigate the effect of batch variations between mass cytometry runs, we applied batch-wise scaling as a pre-processing step before clustering as described previously ( 22 ). Batch-wise scaling involves standard scaling grouped by batches instead of applying to all data.…”

Section: Methodsmentioning

confidence: 99%

“…In this study, we aimed to gain a comprehensive understanding of the convalescent COVID-19 immune architecture. For this purpose, we analyzed the COVID-19 immune response in peripheral blood mononuclear cells (PBMCs) using an adaptation of a standardized mass cytometry protocol based on the Extended Polydimensional Immunome Characterization (EPIC) platform ( Supplemental Tables 1 , 2 ) ( 22 ). We characterized the immunological profiles of 19 convalescent COVID-19 patients whose infections were confirmed by nasal swab SARS-CoV-2 polymerase chain reaction (PCR) ( Supplemental Table 3 ).…”

Section: Introductionmentioning

confidence: 99%

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A Virus-Specific Immune Rheostat in the Immunome of Patients Recovering From Mild COVID-19

Yeo

Leong

et al. 2021

Front. Immunol.

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An accurate depiction of the convalescent COVID-19 immunome will help delineate the immunological milieu crucial for disease resolution and protection. Using mass cytometry, we characterized the immune architecture in patients recovering from mild COVID-19. We identified a virus-specific immune rheostat composed of an effector T (Teff) cell recall response that is balanced by the enrichment of a highly specialized regulatory T (Treg) cell subset. Both components were reactive against a peptide pool covering the receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein. We also observed expansion of IFNγ+ memory CD4+ T cells and virus-specific follicular helper T (TFH) cells. Overall, these findings pinpoint critical immune effector and regulatory mechanisms essential for a potent, yet harmless resolution of COVID-19 infection.

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“…We first profiled T cells from fetal lung, skin, gut, thymus, liver, mesenteric lymph nodes (mLN), and blood by using state-of-theart CyTOF approach as recently described (Yeo et al, 2020) (antibody list in the Key resources table). Fetal spleens were not sufficiently large enough to use for both T cell analysis and bacterial DNA sequencing; hence, they were excluded from T cell profiling.…”

Section: T Cell Pool During the 2 Nd Trimester Of Human Fetal Development Is Diverse And Competentmentioning

confidence: 99%

Microbial exposure during early human development primes fetal immune cells

Mishra

Lai

Leong

et al. 2021

Cell

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The Extended Polydimensional Immunome Characterization (EPIC) web-based reference and discovery tool for cytometry data

Cited by 27 publications

References 11 publications

Intratumoural immune heterogeneity as a hallmark of tumour evolution and progression in hepatocellular carcinoma

Intratumoural immune heterogeneity as a hallmark of tumour evolution and progression in hepatocellular carcinoma

A Virus-Specific Immune Rheostat in the Immunome of Patients Recovering From Mild COVID-19

Microbial exposure during early human development primes fetal immune cells

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