WFRF:(Nakajima M.)
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The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force
- Wang, QBS (author)
- Edahiro, R (author)
- Namkoong, H (author)
- show more...
- Hasegawa, T (author)
- Shirai, Y (author)
- Sonehara, K (author)
- Tanaka, H (author)
- Lee, H (author)
- Saiki, R (author)
- Hyugaji, T (author)
- Shimizu, E (author)
- Katayama, K (author)
- Kanai, M (author)
- Naito, T (author)
- Sasa, N (author)
- Yamamoto, K (author)
- Kato, Y (author)
- Morita, T (author)
- Takahashi, K (author)
- Harada, N (author)
- Naito, T (author)
- Hiki, M (author)
- Matsushita, Y (author)
- Takagi, H (author)
- Ichikawa, M (author)
- Nakamura, A (author)
- Harada, S (author)
- Sandhu, Y (author)
- Kabata, H (author)
- Masaki, K (author)
- Kamata, H (author)
- Ikemura, S (author)
- Chubachi, S (author)
- Okamori, S (author)
- Terai, H (author)
- Morita, A (author)
- Asakura, T (author)
- Sasaki, J (author)
- Morisaki, H (author)
- Uwamino, Y (author)
- Nanki, K (author)
- Uchida, S (author)
- Uno, S (author)
- Nishimura, T (author)
- Ishiguro, T (author)
- Isono, T (author)
- Shibata, S (author)
- Matsui, Y (author)
- Hosoda, C (author)
- Takano, K (author)
- Nishida, T (author)
- Kobayashi, Y (author)
- Takaku, Y (author)
- Takayanagi, N (author)
- Ueda, S (author)
- Tada, A (author)
- Miyawaki, M (author)
- Yamamoto, M (author)
- Yoshida, E (author)
- Hayashi, R (author)
- Nagasaka, T (author)
- Arai, S (author)
- Kaneko, Y (author)
- Sasaki, K (author)
- Tagaya, E (author)
- Kawana, M (author)
- Arimura, K (author)
- Takahashi, K (author)
- Anzai, T (author)
- Ito, S (author)
- Endo, A (author)
- Uchimura, Y (author)
- Miyazaki, Y (author)
- Honda, T (author)
- Tateishi, T (author)
- Tohda, S (author)
- Ichimura, N (author)
- Sonobe, K (author)
- Sassa, CT (author)
- Nakajima, J (author)
- Nakano, Y (author)
- Nakajima, Y (author)
- Anan, R (author)
- Arai, R (author)
- Kurihara, Y (author)
- Harada, Y (author)
- Nishio, K (author)
- Ueda, T (author)
- Azuma, M (author)
- Saito, R (author)
- Sado, T (author)
- Miyazaki, Y (author)
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- Nagasaki, T (author)
- Yasui, Y (author)
- Hasegawa, Y (author)
- Mutoh, Y (author)
- Kimura, T (author)
- Sato, T (author)
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- Noguchi, Y (author)
- Yamano, Y (author)
- Sasano, H (author)
- Ota, S (author)
- Nakamori, Y (author)
- Yoshiya, K (author)
- Saito, F (author)
- Yoshihara, T (author)
- Wada, D (author)
- Iwamura, H (author)
- Kanayama, S (author)
- Maruyama, S (author)
- Yoshiyama, T (author)
- Ohta, K (author)
- Kokuto, H (author)
- Ogata, H (author)
- Tanaka, Y (author)
- Arakawa, K (author)
- Shimoda, M (author)
- Osawa, T (author)
- Tateno, H (author)
- Hase, I (author)
- Yoshida, S (author)
- Suzuki, S (author)
- Kawada, M (author)
- Horinouchi, H (author)
- Saito, F (author)
- Mitamura, K (author)
- Hagihara, M (author)
- Ochi, J (author)
- Uchida, T (author)
- Baba, R (author)
- Arai, D (author)
- Ogura, T (author)
- Takahashi, H (author)
- Hagiwara, S (author)
- Nagao, G (author)
- Konishi, S (author)
- Nakachi, I (author)
- Murakami, K (author)
- Yamada, M (author)
- Sugiura, H (author)
- Sano, H (author)
- Matsumoto, S (author)
- Kimura, N (author)
- Ono, Y (author)
- Baba, H (author)
- Suzuki, Y (author)
- Nakayama, S (author)
- Masuzawa, K (author)
- Namba, S (author)
- Shiroyama, T (author)
- Noda, Y (author)
- Niitsu, T (author)
- Adachi, Y (author)
- Enomoto, T (author)
- Amiya, S (author)
- Hara, R (author)
- Yamaguchi, Y (author)
- Murakami, T (author)
- Kuge, T (author)
- Matsumoto, K (author)
- Yamamoto, Y (author)
- Yamamoto, M (author)
- Yoneda, M (author)
- Tomono, K (author)
- Kato, K (author)
- Hirata, H (author)
- Takeda, Y (author)
- Koh, H (author)
- Manabe, T (author)
- Funatsu, Y (author)
- Ito, F (author)
- Fukui, T (author)
- Shinozuka, K (author)
- Kohashi, S (author)
- Miyazaki, M (author)
- Shoko, T (author)
- Kojima, M (author)
- Adachi, T (author)
- Ishikawa, M (author)
- Takahashi, K (author)
- Inoue, T (author)
- Hirano, T (author)
- Kobayashi, K (author)
- Takaoka, H (author)
- Watanabe, K (author)
- Miyazawa, N (author)
- Kimura, Y (author)
- Sado, R (author)
- Sugimoto, H (author)
- Kamiya, A (author)
- Kuwahara, N (author)
- Fujiwara, A (author)
- Matsunaga, T (author)
- Sato, Y (author)
- Okada, T (author)
- Hirai, Y (author)
- Kawashima, H (author)
- Narita, A (author)
- Niwa, K (author)
- Sekikawa, Y (author)
- Nishi, K (author)
- Nishitsuji, M (author)
- Tani, M (author)
- Suzuki, J (author)
- Nakatsumi, H (author)
- Ogura, T (author)
- Kitamura, H (author)
- Hagiwara, E (author)
- Murohashi, K (author)
- Okabayashi, H (author)
- Mochimaru, T (author)
- Nukaga, S (author)
- Satomi, R (author)
- Oyamada, Y (author)
- Mori, N (author)
- Baba, T (author)
- Fukui, Y (author)
- Odate, M (author)
- Mashimo, S (author)
- Makino, Y (author)
- Yagi, K (author)
- Hashiguchi, M (author)
- Kagyo, J (author)
- Shiomi, T (author)
- Fuke, S (author)
- Saito, H (author)
- Tsuchida, T (author)
- Fujitani, S (author)
- Takita, M (author)
- Morikawa, D (author)
- Yoshida, T (author)
- Izumo, T (author)
- Inomata, M (author)
- Kuse, N (author)
- Awano, N (author)
- Tone, M (author)
- Ito, A (author)
- Nakamura, Y (author)
- Hoshino, K (author)
- Maruyama, J (author)
- Ishikura, H (author)
- Takata, T (author)
- Odani, T (author)
- Amishima, M (author)
- Hattori, T (author)
- Shichinohe, Y (author)
- Kagaya, T (author)
- Kita, T (author)
- Ohta, K (author)
- Sakagami, S (author)
- Koshida, K (author)
- Hayashi, K (author)
- Shimizu, T (author)
- Kozu, Y (author)
- Hiranuma, H (author)
- Gon, Y (author)
- Izumi, N (author)
- Nagata, K (author)
- Ueda, K (author)
- Taki, R (author)
- Hanada, S (author)
- Kawamura, K (author)
- Ichikado, K (author)
- Nishiyama, K (author)
- Muranaka, H (author)
- Nakamura, K (author)
- Hashimoto, N (author)
- Wakahara, K (author)
- Koji, S (author)
- Omote, N (author)
- Ando, A (author)
- Kodama, N (author)
- Kaneyama, Y (author)
- Maeda, S (author)
- Kuraki, T (author)
- Matsumoto, T (author)
- Yokote, K (author)
- Nakada, TA (author)
- Abe, R (author)
- Oshima, T (author)
- Shimada, T (author)
- Harada, M (author)
- Takahashi, T (author)
- Ono, H (author)
- Sakurai, T (author)
- Shibusawa, T (author)
- Kimizuka, Y (author)
- Kawana, A (author)
- Sano, T (author)
- Watanabe, C (author)
- Suematsu, R (author)
- Sageshima, H (author)
- Yoshifuji, A (author)
- Ito, K (author)
- Takahashi, S (author)
- Ishioka, K (author)
- Nakamura, M (author)
- Masuda, M (author)
- Wakabayashi, A (author)
- Watanabe, H (author)
- Ueda, S (author)
- Nishikawa, M (author)
- Chihara, Y (author)
- Takeuchi, M (author)
- Onoi, K (author)
- Shinozuka, J (author)
- Sueyoshi, A (author)
- Nagasaki, Y (author)
- Okamoto, M (author)
- Ishihara, S (author)
- Shimo, M (author)
- Tokunaga, Y (author)
- Kusaka, Y (author)
- Ohba, T (author)
- Isogai, S (author)
- Ogawa, A (author)
- Inoue, T (author)
- Fukuyama, S (author)
- Eriguchi, Y (author)
- Yonekawa, A (author)
- Kan-o, K (author)
- Matsumoto, K (author)
- Kanaoka, K (author)
- Ihara, S (author)
- Komuta, K (author)
- Inoue, Y (author)
- Chiba, S (author)
- Yamagata, K (author)
- Hiramatsu, Y (author)
- Kai, H (author)
- Asano, K (author)
- Oguma, T (author)
- Ito, Y (author)
- Hashimoto, S (author)
- Yamasaki, M (author)
- Kasamatsu, Y (author)
- Komase, Y (author)
- Hida, N (author)
- Tsuburai, T (author)
- Oyama, B (author)
- Takada, M (author)
- Kanda, H (author)
- Kitagawa, Y (author)
- Fukuta, T (author)
- Miyake, T (author)
- Yoshida, S (author)
- Ogura, S (author)
- Abe, S (author)
- Kono, Y (author)
- Togashi, Y (author)
- Takoi, H (author)
- Kikuchi, R (author)
- Ogawa, S (author)
- Ogata, T (author)
- Ishihara, S (author)
- Kanehiro, A (author)
- Ozaki, S (author)
- Fuchimoto, Y (author)
- Wada, S (author)
- Fujimoto, N (author)
- Nishiyama, K (author)
- Terashima, M (author)
- Beppu, S (author)
- Yoshida, K (author)
- Narumoto, O (author)
- Nagai, H (author)
- Ooshima, N (author)
- Motegi, M (author)
- Umeda, A (author)
- Miyagawa, K (author)
- Shimada, H (author)
- Endo, M (author)
- Ohira, Y (author)
- Watanabe, M (author)
- Inoue, S (author)
- Igarashi, A (author)
- Sato, M (author)
- Sagara, H (author)
- Tanaka, A (author)
- Ohta, S (author)
- Kimura, T (author)
- Shibata, Y (author)
- Tanino, Y (author)
- Nikaido, T (author)
- Minemura, H (author)
- Sato, Y (author)
- Yamada, Y (author)
- Hashino, T (author)
- Shinoki, M (author)
- Iwagoe, H (author)
- Takahashi, H (author)
- Fujii, K (author)
- Kishi, H (author)
- Kanai, M (author)
- Imamura, T (author)
- Yamashita, T (author)
- Yatomi, M (author)
- Maeno, T (author)
- Hayashi, S (author)
- Takahashi, M (author)
- Kuramochi, M (author)
- Kamimaki, I (author)
- Tominaga, Y (author)
- Ishii, T (author)
- Utsugi, M (author)
- Ono, A (author)
- Tanaka, T (author)
- Kashiwada, T (author)
- Fujita, K (author)
- Saito, Y (author)
- Seike, M (author)
- Watanabe, H (author)
- Matsuse, H (author)
- Kodaka, N (author)
- Nakano, C (author)
- Oshio, T (author)
- Hirouchi, T (author)
- Makino, S (author)
- Egi, M (author)
- Omae, Y (author)
- Nannya, Y (author)
- Ueno, T (author)
- Takano, T (author)
- Katayama, K (author)
- Ai, M (author)
- Kumanogoh, A (author)
- Sato, T (author)
- Hasegawa, N (author)
- Tokunaga, K (author)
- Ishii, M (author)
- Koike, R (author)
- Kitagawa, Y (author)
- Kimura, A (author)
- Imoto, S (author)
- Miyano, S (author)
- Ogawa, S (author)
- Kanai, T (author)
- Fukunaga, K (author)
- Okada, Y (author)
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- 2022-08-22
- 2022
- English.
- In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1, s. 4830-
- Journal article (peer-reviewed)
Abstract
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- Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection.
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- ref (subject category)
- art (subject category)
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- Wang, QBS
- Edahiro, R
- Namkoong, H
- Hasegawa, T
- Shirai, Y
- Sonehara, K
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- Tanaka, H
- Lee, H
- Saiki, R
- Hyugaji, T
- Shimizu, E
- Katayama, K
- Kanai, M
- Naito, T
- Sasa, N
- Yamamoto, K
- Kato, Y
- Morita, T
- Takahashi, K
- Harada, N
- Hiki, M
- Matsushita, Y
- Takagi, H
- Ichikawa, M
- Nakamura, A
- Harada, S
- Sandhu, Y
- Kabata, H
- Masaki, K
- Kamata, H
- Ikemura, S
- Chubachi, S
- Okamori, S
- Terai, H
- Morita, A
- Asakura, T
- Sasaki, J
- Morisaki, H
- Uwamino, Y
- Nanki, K
- Uchida, S
- Uno, S
- Nishimura, T
- Ishiguro, T
- Isono, T
- Shibata, S
- Matsui, Y
- Hosoda, C
- Takano, K
- Nishida, T
- Kobayashi, Y
- Takaku, Y
- Takayanagi, N
- Ueda, S
- Tada, A
- Miyawaki, M
- Yamamoto, M
- Yoshida, E
- Hayashi, R
- Nagasaka, T
- Arai, S
- Kaneko, Y
- Sasaki, K
- Tagaya, E
- Kawana, M
- Arimura, K
- Anzai, T
- Ito, S
- Endo, A
- Uchimura, Y
- Miyazaki, Y
- Honda, T
- Tateishi, T
- Tohda, S
- Ichimura, N
- Sonobe, K
- Sassa, CT
- Nakajima, J
- Nakano, Y
- Nakajima, Y
- Anan, R
- Arai, R
- Kurihara, Y
- Harada, Y
- Nishio, K
- Ueda, T
- Azuma, M
- Saito, R
- Sado, T
- Sato, R
- Haruta, Y
- Nagasaki, T
- Yasui, Y
- Hasegawa, Y
- Mutoh, Y
- Kimura, T
- Sato, T
- Takei, R
- Hagimoto, S
- Noguchi, Y
- Yamano, Y
- Sasano, H
- Ota, S
- Nakamori, Y
- Yoshiya, K
- Saito, F
- Yoshihara, T
- Wada, D
- Iwamura, H
- Kanayama, S
- Maruyama, S
- Yoshiyama, T
- Ohta, K
- Kokuto, H
- Ogata, H
- Tanaka, Y
- Arakawa, K
- Shimoda, M
- Osawa, T
- Tateno, H
- Hase, I
- Yoshida, S
- Suzuki, S
- Kawada, M
- Horinouchi, H
- Mitamura, K
- Hagihara, M
- Ochi, J
- Uchida, T
- Baba, R
- Arai, D
- Ogura, T
- Takahashi, H
- Hagiwara, S
- Nagao, G
- Konishi, S
- Nakachi, I
- Murakami, K
- Yamada, M
- Sugiura, H
- Sano, H
- Matsumoto, S
- Kimura, N
- Ono, Y
- Baba, H
- Suzuki, Y
- Nakayama, S
- Masuzawa, K
- Namba, S
- Shiroyama, T
- Noda, Y
- Niitsu, T
- Adachi, Y
- Enomoto, T
- Amiya, S
- Hara, R
- Yamaguchi, Y
- Murakami, T
- Kuge, T
- Matsumoto, K
- Yamamoto, Y
- Yoneda, M
- Tomono, K
- Kato, K
- Hirata, H
- Takeda, Y
- Koh, H
- Manabe, T
- Funatsu, Y
- Ito, F
- Fukui, T
- Shinozuka, K
- Kohashi, S
- Miyazaki, M
- Shoko, T
- Kojima, M
- Adachi, T
- Ishikawa, M
- Inoue, T
- Hirano, T
- Kobayashi, K
- Takaoka, H
- Watanabe, K
- Miyazawa, N
- Kimura, Y
- Sado, R
- Sugimoto, H
- Kamiya, A
- Kuwahara, N
- Fujiwara, A
- Matsunaga, T
- Sato, Y
- Okada, T
- Hirai, Y
- Kawashima, H
- Narita, A
- Niwa, K
- Sekikawa, Y
- Nishi, K
- Nishitsuji, M
- Tani, M
- Suzuki, J
- Nakatsumi, H
- Kitamura, H
- Hagiwara, E
- Murohashi, K
- Okabayashi, H
- Mochimaru, T
- Nukaga, S
- Satomi, R
- Oyamada, Y
- Mori, N
- Baba, T
- Fukui, Y
- Odate, M
- Mashimo, S
- Makino, Y
- Yagi, K
- Hashiguchi, M
- Kagyo, J
- Shiomi, T
- Fuke, S
- Saito, H
- Tsuchida, T
- Fujitani, S
- Takita, M
- Morikawa, D
- Yoshida, T
- Izumo, T
- Inomata, M
- Kuse, N
- Awano, N
- Tone, M
- Ito, A
- Nakamura, Y
- Hoshino, K
- Maruyama, J
- Ishikura, H
- Takata, T
- Odani, T
- Amishima, M
- Hattori, T
- Shichinohe, Y
- Kagaya, T
- Kita, T
- Sakagami, S
- Koshida, K
- Hayashi, K
- Shimizu, T
- Kozu, Y
- Hiranuma, H
- Gon, Y
- Izumi, N
- Nagata, K
- Ueda, K
- Taki, R
- Hanada, S
- Kawamura, K
- Ichikado, K
- Nishiyama, K
- Muranaka, H
- Nakamura, K
- Hashimoto, N
- Wakahara, K
- Koji, S
- Omote, N
- Ando, A
- Kodama, N
- Kaneyama, Y
- Maeda, S
- Kuraki, T
- Matsumoto, T
- Yokote, K
- Nakada, TA
- Abe, R
- Oshima, T
- Shimada, T
- Harada, M
- Takahashi, T
- Ono, H
- Sakurai, T
- Shibusawa, T
- Kimizuka, Y
- Kawana, A
- Sano, T
- Watanabe, C
- Suematsu, R
- Sageshima, H
- Yoshifuji, A
- Ito, K
- Takahashi, S
- Ishioka, K
- Nakamura, M
- Masuda, M
- Wakabayashi, A
- Watanabe, H
- Nishikawa, M
- Chihara, Y
- Takeuchi, M
- Onoi, K
- Shinozuka, J
- Sueyoshi, A
- Nagasaki, Y
- Okamoto, M
- Ishihara, S
- Shimo, M
- Tokunaga, Y
- Kusaka, Y
- Ohba, T
- Isogai, S
- Ogawa, A
- Fukuyama, S
- Eriguchi, Y
- Yonekawa, A
- Kan-o, K
- Kanaoka, K
- Ihara, S
- Komuta, K
- Inoue, Y
- Chiba, S
- Yamagata, K
- Hiramatsu, Y
- Kai, H
- Asano, K
- Oguma, T
- Ito, Y
- Hashimoto, S
- Yamasaki, M
- Kasamatsu, Y
- Komase, Y
- Hida, N
- Tsuburai, T
- Oyama, B
- Takada, M
- Kanda, H
- Kitagawa, Y
- Fukuta, T
- Miyake, T
- Ogura, S
- Abe, S
- Kono, Y
- Togashi, Y
- Takoi, H
- Kikuchi, R
- Ogawa, S
- Ogata, T
- Kanehiro, A
- Ozaki, S
- Fuchimoto, Y
- Wada, S
- Fujimoto, N
- Terashima, M
- Beppu, S
- Yoshida, K
- Narumoto, O
- Nagai, H
- Ooshima, N
- Motegi, M
- Umeda, A
- Miyagawa, K
- Shimada, H
- Endo, M
- Ohira, Y
- Watanabe, M
- Inoue, S
- Igarashi, A
- Sato, M
- Sagara, H
- Tanaka, A
- Ohta, S
- Shibata, Y
- Tanino, Y
- Nikaido, T
- Minemura, H
- Yamada, Y
- Hashino, T
- Shinoki, M
- Iwagoe, H
- Fujii, K
- Kishi, H
- Imamura, T
- Yamashita, T
- Yatomi, M
- Maeno, T
- Hayashi, S
- Takahashi, M
- Kuramochi, M
- Kamimaki, I
- Tominaga, Y
- Ishii, T
- Utsugi, M
- Ono, A
- Tanaka, T
- Kashiwada, T
- Fujita, K
- Saito, Y
- Seike, M
- Matsuse, H
- Kodaka, N
- Nakano, C
- Oshio, T
- Hirouchi, T
- Makino, S
- Egi, M
- Omae, Y
- Nannya, Y
- Ueno, T
- Takano, T
- Ai, M
- Kumanogoh, A
- Hasegawa, N
- Tokunaga, K
- Ishii, M
- Koike, R
- Kimura, A
- Imoto, S
- Miyano, S
- Kanai, T
- Fukunaga, K
- Okada, Y
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