Asian diversity in human immune cells

Kian Hong Kock; Le Min Tan; Kyung Yeon Han; Yoshinari Ando; Damita Jevapatarakul; Ankita Chatterjee; Quy Xiao Xuan Lin; Eliora Violain Buyamin; Radhika Sonthalia; Deepa Rajagopalan; Yoshihiko Tomofuji; Shvetha Sankaran; Mi So Park; Mai Abe; Juthamard Chantaraamporn; Seiko Furukawa; Supratim Ghosh; Gyo Inoue; Miki Kojima; Tsukasa Kouno; Jinyeong Lim; Keiko Myouzen; Sarintip Nguantad; Jin Mi Oh; Nirmala Arul Rayan; Sumanta Sarkar; Akari Suzuki; Narita Thungsatianpun; Prasanna Nori Venkatesh; Jonathan Moody; Masahiro Nakano; Ziyue Chen; Chi Tian; Yuntian Zhang; Yihan Tong; Crystal T.Y. Tan; Anteneh Mehari Tizazu; Marie Loh; You Yi Hwang; Roger C. Ho; Anis Larbi; Tze Pin Ng; Hong Hee Won; Fred A. Wright; Alexandra Chloé Villani; Jong Eun Park; Murim Choi; Boxiang Liu; Arindam Maitra; Manop Pithukpakorn; Bhoom Suktitipat; Kazuyoshi Ishigaki; Yukinori Okada; Kazuhiko Yamamoto; Piero Carninci; John C. Chambers; Chung Chau Hon; Ponpan Matangkasombut; Varodom Charoensawan; Partha P. Majumder; Jay W. Shin; Woong Yang Park; Shyam Prabhakar

doi:10.1016/j.cell.2025.02.017

Asian diversity in human immune cells

Kian Hong Kock, Le Min Tan, Kyung Yeon Han, Yoshinari Ando, Damita Jevapatarakul, Ankita Chatterjee, Quy Xiao Xuan Lin, Eliora Violain Buyamin, Radhika Sonthalia, Deepa Rajagopalan, Yoshihiko Tomofuji, Shvetha Sankaran, Mi So Park, Mai Abe, Juthamard Chantaraamporn, Seiko Furukawa, Supratim Ghosh, Gyo Inoue, Miki Kojima, Tsukasa KounoJinyeong Lim, Keiko Myouzen, Sarintip Nguantad, Jin Mi Oh, Nirmala Arul Rayan, Sumanta Sarkar, Akari Suzuki, Narita Thungsatianpun, Prasanna Nori Venkatesh, Jonathan Moody, Masahiro Nakano, Ziyue Chen, Chi Tian, Yuntian Zhang, Yihan Tong, Crystal T.Y. Tan, Anteneh Mehari Tizazu, Marie Loh, You Yi Hwang, Roger C. Ho, Anis Larbi, Tze Pin Ng, Hong Hee Won, Fred A. Wright, Alexandra Chloé Villani, Jong Eun Park, Murim Choi, Boxiang Liu, Arindam Maitra, Manop Pithukpakorn, Bhoom Suktitipat, Kazuyoshi Ishigaki, Yukinori Okada, Kazuhiko Yamamoto, Piero Carninci, John C. Chambers, Chung Chau Hon, Ponpan Matangkasombut, Varodom Charoensawan, Partha P. Majumder, Jay W. Shin, Woong Yang Park, Shyam Prabhakar

Research output: Contribution to journal › Article › peer-review

Abstract

The relationships of human diversity with biomedical phenotypes are pervasive yet remain understudied, particularly in a single-cell genomics context. Here, we present the Asian Immune Diversity Atlas (AIDA), a multi-national single-cell RNA sequencing (scRNA-seq) healthy reference atlas of human immune cells. AIDA comprises 1,265,624 circulating immune cells from 619 donors, spanning 7 population groups across 5 Asian countries, and 6 controls. Though population groups are frequently compared at the continental level, we found that sub-continental diversity, age, and sex pervasively impacted cellular and molecular properties of immune cells. These included differential abundance of cell neighborhoods as well as cell populations and genes relevant to disease risk, pathogenesis, and diagnostics. We discovered functional genetic variants influencing cell-type-specific gene expression, which were under-represented in non-Asian populations, and helped contextualize disease-associated variants. AIDA enables analyses of multi-ancestry disease datasets and facilitates the development of precision medicine efforts in Asia and beyond.

Original language	English
Pages (from-to)	2288-2306.e24
Journal	Cell
Volume	188
Issue number	8
DOIs	https://doi.org/10.1016/j.cell.2025.02.017
Publication status	Published - 17 Apr 2025

Keywords

eQTL
genetic diversity
genetics
genomics
healthy baseline
human diversity
immune cells
precision medicine
single-cell RNA sequencing
sub-continental diversity

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10.1016/j.cell.2025.02.017

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Kock, K. H., Tan, L. M., Han, K. Y., Ando, Y., Jevapatarakul, D., Chatterjee, A., Lin, Q. X. X., Buyamin, E. V., Sonthalia, R., Rajagopalan, D., Tomofuji, Y., Sankaran, S., Park, M. S., Abe, M., Chantaraamporn, J., Furukawa, S., Ghosh, S., Inoue, G., Kojima, M., ... Prabhakar, S. (2025). Asian diversity in human immune cells. Cell, 188(8), 2288-2306.e24. https://doi.org/10.1016/j.cell.2025.02.017

@article{03655b00f3564f71ad3dc0808d21bbd4,

title = "Asian diversity in human immune cells",

abstract = "The relationships of human diversity with biomedical phenotypes are pervasive yet remain understudied, particularly in a single-cell genomics context. Here, we present the Asian Immune Diversity Atlas (AIDA), a multi-national single-cell RNA sequencing (scRNA-seq) healthy reference atlas of human immune cells. AIDA comprises 1,265,624 circulating immune cells from 619 donors, spanning 7 population groups across 5 Asian countries, and 6 controls. Though population groups are frequently compared at the continental level, we found that sub-continental diversity, age, and sex pervasively impacted cellular and molecular properties of immune cells. These included differential abundance of cell neighborhoods as well as cell populations and genes relevant to disease risk, pathogenesis, and diagnostics. We discovered functional genetic variants influencing cell-type-specific gene expression, which were under-represented in non-Asian populations, and helped contextualize disease-associated variants. AIDA enables analyses of multi-ancestry disease datasets and facilitates the development of precision medicine efforts in Asia and beyond.",

keywords = "eQTL, genetic diversity, genetics, genomics, healthy baseline, human diversity, immune cells, precision medicine, single-cell RNA sequencing, sub-continental diversity",

author = "Kock, {Kian Hong} and Tan, {Le Min} and Han, {Kyung Yeon} and Yoshinari Ando and Damita Jevapatarakul and Ankita Chatterjee and Lin, {Quy Xiao Xuan} and Buyamin, {Eliora Violain} and Radhika Sonthalia and Deepa Rajagopalan and Yoshihiko Tomofuji and Shvetha Sankaran and Park, {Mi So} and Mai Abe and Juthamard Chantaraamporn and Seiko Furukawa and Supratim Ghosh and Gyo Inoue and Miki Kojima and Tsukasa Kouno and Jinyeong Lim and Keiko Myouzen and Sarintip Nguantad and Oh, {Jin Mi} and Rayan, {Nirmala Arul} and Sumanta Sarkar and Akari Suzuki and Narita Thungsatianpun and Venkatesh, {Prasanna Nori} and Jonathan Moody and Masahiro Nakano and Ziyue Chen and Chi Tian and Yuntian Zhang and Yihan Tong and Tan, {Crystal T.Y.} and Tizazu, {Anteneh Mehari} and Marie Loh and Hwang, {You Yi} and Ho, {Roger C.} and Anis Larbi and Ng, {Tze Pin} and Won, {Hong Hee} and Wright, {Fred A.} and Villani, {Alexandra Chlo{\'e}} and Park, {Jong Eun} and Murim Choi and Boxiang Liu and Arindam Maitra and Manop Pithukpakorn and Bhoom Suktitipat and Kazuyoshi Ishigaki and Yukinori Okada and Kazuhiko Yamamoto and Piero Carninci and Chambers, {John C.} and Hon, {Chung Chau} and Ponpan Matangkasombut and Varodom Charoensawan and Majumder, {Partha P.} and Shin, {Jay W.} and Park, {Woong Yang} and Shyam Prabhakar",

note = "Publisher Copyright: {\textcopyright} 2025 The Authors",

year = "2025",

month = apr,

day = "17",

doi = "10.1016/j.cell.2025.02.017",

language = "English",

volume = "188",

pages = "2288--2306.e24",

journal = "Cell",

issn = "0092-8674",

publisher = "Elsevier B.V.",

number = "8",

}

Kock, KH, Tan, LM, Han, KY, Ando, Y, Jevapatarakul, D, Chatterjee, A, Lin, QXX, Buyamin, EV, Sonthalia, R, Rajagopalan, D, Tomofuji, Y, Sankaran, S, Park, MS, Abe, M, Chantaraamporn, J, Furukawa, S, Ghosh, S, Inoue, G, Kojima, M, Kouno, T, Lim, J, Myouzen, K, Nguantad, S, Oh, JM, Rayan, NA, Sarkar, S, Suzuki, A, Thungsatianpun, N, Venkatesh, PN, Moody, J, Nakano, M, Chen, Z, Tian, C, Zhang, Y, Tong, Y, Tan, CTY, Tizazu, AM, Loh, M, Hwang, YY, Ho, RC, Larbi, A, Ng, TP, Won, HH, Wright, FA, Villani, AC, Park, JE, Choi, M, Liu, B, Maitra, A, Pithukpakorn, M , Suktitipat, B, Ishigaki, K, Okada, Y, Yamamoto, K, Carninci, P, Chambers, JC, Hon, CC, Matangkasombut, P , Charoensawan, V, Majumder, PP, Shin, JW, Park, WY & Prabhakar, S 2025, 'Asian diversity in human immune cells', Cell, vol. 188, no. 8, pp. 2288-2306.e24. https://doi.org/10.1016/j.cell.2025.02.017

TY - JOUR

T1 - Asian diversity in human immune cells

AU - Kock, Kian Hong

AU - Tan, Le Min

AU - Han, Kyung Yeon

AU - Ando, Yoshinari

AU - Jevapatarakul, Damita

AU - Chatterjee, Ankita

AU - Lin, Quy Xiao Xuan

AU - Buyamin, Eliora Violain

AU - Sonthalia, Radhika

AU - Rajagopalan, Deepa

AU - Tomofuji, Yoshihiko

AU - Sankaran, Shvetha

AU - Park, Mi So

AU - Abe, Mai

AU - Chantaraamporn, Juthamard

AU - Furukawa, Seiko

AU - Ghosh, Supratim

AU - Inoue, Gyo

AU - Kojima, Miki

AU - Kouno, Tsukasa

AU - Lim, Jinyeong

AU - Myouzen, Keiko

AU - Nguantad, Sarintip

AU - Oh, Jin Mi

AU - Rayan, Nirmala Arul

AU - Sarkar, Sumanta

AU - Suzuki, Akari

AU - Thungsatianpun, Narita

AU - Venkatesh, Prasanna Nori

AU - Moody, Jonathan

AU - Nakano, Masahiro

AU - Chen, Ziyue

AU - Tian, Chi

AU - Zhang, Yuntian

AU - Tong, Yihan

AU - Tan, Crystal T.Y.

AU - Tizazu, Anteneh Mehari

AU - Loh, Marie

AU - Hwang, You Yi

AU - Ho, Roger C.

AU - Larbi, Anis

AU - Ng, Tze Pin

AU - Won, Hong Hee

AU - Wright, Fred A.

AU - Villani, Alexandra Chloé

AU - Park, Jong Eun

AU - Choi, Murim

AU - Liu, Boxiang

AU - Maitra, Arindam

AU - Pithukpakorn, Manop

AU - Suktitipat, Bhoom

AU - Ishigaki, Kazuyoshi

AU - Okada, Yukinori

AU - Yamamoto, Kazuhiko

AU - Carninci, Piero

AU - Chambers, John C.

AU - Hon, Chung Chau

AU - Matangkasombut, Ponpan

AU - Charoensawan, Varodom

AU - Majumder, Partha P.

AU - Shin, Jay W.

AU - Park, Woong Yang

AU - Prabhakar, Shyam

PY - 2025/4/17

Y1 - 2025/4/17

N2 - The relationships of human diversity with biomedical phenotypes are pervasive yet remain understudied, particularly in a single-cell genomics context. Here, we present the Asian Immune Diversity Atlas (AIDA), a multi-national single-cell RNA sequencing (scRNA-seq) healthy reference atlas of human immune cells. AIDA comprises 1,265,624 circulating immune cells from 619 donors, spanning 7 population groups across 5 Asian countries, and 6 controls. Though population groups are frequently compared at the continental level, we found that sub-continental diversity, age, and sex pervasively impacted cellular and molecular properties of immune cells. These included differential abundance of cell neighborhoods as well as cell populations and genes relevant to disease risk, pathogenesis, and diagnostics. We discovered functional genetic variants influencing cell-type-specific gene expression, which were under-represented in non-Asian populations, and helped contextualize disease-associated variants. AIDA enables analyses of multi-ancestry disease datasets and facilitates the development of precision medicine efforts in Asia and beyond.

AB - The relationships of human diversity with biomedical phenotypes are pervasive yet remain understudied, particularly in a single-cell genomics context. Here, we present the Asian Immune Diversity Atlas (AIDA), a multi-national single-cell RNA sequencing (scRNA-seq) healthy reference atlas of human immune cells. AIDA comprises 1,265,624 circulating immune cells from 619 donors, spanning 7 population groups across 5 Asian countries, and 6 controls. Though population groups are frequently compared at the continental level, we found that sub-continental diversity, age, and sex pervasively impacted cellular and molecular properties of immune cells. These included differential abundance of cell neighborhoods as well as cell populations and genes relevant to disease risk, pathogenesis, and diagnostics. We discovered functional genetic variants influencing cell-type-specific gene expression, which were under-represented in non-Asian populations, and helped contextualize disease-associated variants. AIDA enables analyses of multi-ancestry disease datasets and facilitates the development of precision medicine efforts in Asia and beyond.

KW - eQTL

KW - genetic diversity

KW - genetics

KW - genomics

KW - healthy baseline

KW - human diversity

KW - immune cells

KW - precision medicine

KW - single-cell RNA sequencing

KW - sub-continental diversity

UR - http://www.scopus.com/inward/record.url?scp=105000483474&partnerID=8YFLogxK

U2 - 10.1016/j.cell.2025.02.017

DO - 10.1016/j.cell.2025.02.017

M3 - Article

AN - SCOPUS:105000483474

SN - 0092-8674

VL - 188

SP - 2288-2306.e24

JO - Cell

JF - Cell

IS - 8

ER -

Asian diversity in human immune cells

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Keywords

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