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4. Cross-tissue omics analysis discovers ten adipose genes encoding secreted proteins in obesity-related non-alcoholic fatty liver disease.

Author

Darci-Maher, Nicholas, Alvarez, Marcus, Arasu, Uma Thanigai, Selvarajan, Ilakya, Lee, Seung Hyuk T, Pan, David Z, Miao, Zong, Das, Sankha Subhra, Kaminska, Dorota, Örd, Tiit, Benhammou, Jihane N, Wabitsch, Martin, Pisegna, Joseph R, Männistö, Ville, Pietiläinen, Kirsi H, Laakso, Markku, Sinsheimer, Janet S, Kaikkonen, Minna U, Pihlajamäki, Jussi, and Pajukanta, Päivi

Subjects
Liver, Humans, Obesity, Genome-Wide Association Study, Non-alcoholic Fatty Liver Disease, Biomarkers, Adipogenesis, Dual-tissue transcriptomics screening, Liver histology, Non-alcoholic fatty liver disease, Serum biomarkers, cis regulatory variants, Chronic Liver Disease and Cirrhosis, Digestive Diseases, Liver Disease, Prevention, Nutrition, Biotechnology, Genetics, Aetiology, 2.1 Biological and endogenous factors, Metabolic and endocrine, Clinical Sciences, Public Health and Health Services
Abstract

BackgroundNon-alcoholic fatty liver disease (NAFLD) is a fast-growing, underdiagnosed, epidemic. We hypothesise that obesity-related inflammation compromises adipose tissue functions, preventing efficient fat storage, and thus driving ectopic fat accumulation into the liver.MethodsTo identify adipose-based mechanisms and potential serum biomarker candidates (SBCs) for NAFLD, we utilise dual-tissue RNA-sequencing (RNA-seq) data in adipose tissue and liver, paired with histology-based NAFLD diagnosis, from the same individuals in a cohort of obese individuals. We first scan for genes that are differentially expressed (DE) for NAFLD in obese individuals' subcutaneous adipose tissue but not in their liver; encode proteins secreted to serum; and show preferential adipose expression. Then the identified genes are filtered to key adipose-origin NAFLD genes by best subset analysis, knockdown experiments during human preadipocyte differentiation, recombinant protein treatment experiments in human liver HepG2 cells, and genetic analysis.FindingsWe discover a set of genes, including 10 SBCs, that may modulate NAFLD pathogenesis by impacting adipose tissue function. Based on best subset analysis, we further follow-up on two SBCs CCDC80 and SOD3 by knockdown in human preadipocytes and subsequent differentiation experiments, which show that they modulate crucial adipogenesis genes, LPL, SREBPF1, and LEP. We also show that treatment of the liver HepG2 cells with the CCDC80 and SOD3 recombinant proteins impacts genes related to steatosis and lipid processing, including PPARA, NFE2L2, and RNF128. Finally, utilizing the adipose NAFLD DE gene cis-regulatory variants associated with serum triglycerides (TGs) in extensive genome-wide association studies (GWASs), we demonstrate a unidirectional effect of serum TGs on NAFLD with Mendelian Randomization (MR) analysis. We also demonstrate that a single SNP regulating one of the SBC genes, rs2845885, produces a significant MR result by itself. This supports the conclusion that genetically regulated adipose expression of the NAFLD DE genes may contribute to NAFLD through changes in serum TG levels.InterpretationOur results from the dual-tissue transcriptomics screening improve the understanding of obesity-related NAFLD by providing a targeted set of 10 adipose tissue-active genes as new serum biomarker candidates for the currently grossly underdiagnosed fatty liver disease.FundingThe work was supported by NIH grants R01HG010505 and R01DK132775. The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. The KOBS study (J. P.) was supported by the Finnish Diabetes Research Foundation, Kuopio University Hospital Project grant (EVO/VTR grants 2005-2019), and the Academy of Finland grant (Contract no. 138006). This study was funded by the European Research Council under the European Union's Horizon 2020 research and innovation program (Grant No. 802825 to M. U. K.). K. H. P. was funded by the Academy of Finland (grant numbers 272376, 266286, 314383, and 335443), the Finnish Medical Foundation, Gyllenberg Foundation, Novo Nordisk Foundation (grant numbers NNF10OC1013354, NNF17OC0027232, and NNF20OC0060547), Finnish Diabetes Research Foundation, Finnish Foundation for Cardiovascular Research, University of Helsinki, and Helsinki University Hospital and Government Research Funds. I. S. was funded by the Instrumentarium Science Foundation. Personal grants to U. T. A. were received from the Matti and Vappu Maukonen Foundation, Ella och Georg Ehrnrooths Stiftelse and the Finnish Foundation for Cardiovascular Research.

Published
2023

5. Variation in human water turnover associated with environmental and lifestyle factors

Author

Yamada, Yosuke, Zhang, Xueying, Henderson, Mary ET, Sagayama, Hiroyuki, Pontzer, Herman, Watanabe, Daiki, Yoshida, Tsukasa, Kimura, Misaka, Ainslie, Philip N, Andersen, Lene F, Anderson, Liam J, Arab, Lenore, Baddou, Issad, Bedu-Addo, Kweku, Blaak, Ellen E, Blanc, Stephane, Bonomi, Alberto G, Bouten, Carlijn VC, Bovet, Pascal, Buchowski, Maciej S, Butte, Nancy F, Camps, Stefan G, Close, Graeme L, Cooper, Jamie A, Cooper, Richard, Das, Sai Krupa, Dugas, Lara R, Eaton, Simon, Ekelund, Ulf, Entringer, Sonja, Forrester, Terrence, Fudge, Barry W, Goris, Annelies H, Gurven, Michael, Halsey, Lewis G, Hambly, Catherine, Hamdouchi, Asmaa El, Hoos, Marije B, Hu, Sumei, Joonas, Noorjehan, Joosen, Annemiek M, Katzmarzyk, Peter, Kempen, Kitty P, Kraus, William E, Kriengsinyos, Wantanee, Kushner, Robert F, Lambert, Estelle V, Leonard, William R, Lessan, Nader, Martin, Corby K, Medin, Anine C, Meijer, Erwin P, Morehen, James C, Morton, James P, Neuhouser, Marian L, Nicklas, Theresa A, Ojiambo, Robert M, Pietiläinen, Kirsi H, Pitsiladis, Yannis P, Plange-Rhule, Jacob, Plasqui, Guy, Prentice, Ross L, Rabinovich, Roberto A, Racette, Susan B, Raichlen, David A, Ravussin, Eric, Redman, Leanne M, Reilly, John J, Reynolds, Rebecca M, Roberts, Susan B, Schuit, Albertine J, Sardinha, Luis B, Silva, Analiza M, Sjödin, Anders M, Stice, Eric, Urlacher, Samuel S, Valenti, Giulio, Van Etten, Ludo M, Van Mil, Edgar A, Wells, Jonathan CK, Wilson, George, Wood, Brian M, Yanovski, Jack A, Murphy-Alford, Alexia J, Loechl, Cornelia U, Luke, Amy H, Rood, Jennifer, Westerterp, Klaas R, Wong, William W, Miyachi, Motohiko, Schoeller, Dale A, Speakman, John R, and Consortium§, International Atomic Energy Agency Doubly Labeled Water Database

Subjects
Prevention, Clean Water and Sanitation, Female, Humans, Pregnancy, Exercise, Humidity, Life Style, Social Class, Water, Infant, Newborn, Infant, Child, Preschool, Child, Adolescent, Young Adult, Adult, Middle Aged, Aged, Aged, 80 and over, Drinking, International Atomic Energy Agency (IAEA) Doubly Labeled Water (DLW) Database Consortium§, General Science & Technology
Abstract

Water is essential for survival, but one in three individuals worldwide (2.2 billion people) lacks access to safe drinking water. Water intake requirements largely reflect water turnover (WT), the water used by the body each day. We investigated the determinants of human WT in 5604 people from the ages of 8 days to 96 years from 23 countries using isotope-tracking (2H) methods. Age, body size, and composition were significantly associated with WT, as were physical activity, athletic status, pregnancy, socioeconomic status, and environmental characteristics (latitude, altitude, air temperature, and humidity). People who lived in countries with a low human development index (HDI) had higher WT than people in high-HDI countries. On the basis of this extensive dataset, we provide equations to predict human WT in relation to anthropometric, economic, and environmental factors.

Published
2022

6. Variability in energy expenditure is much greater in males than females

Author

Halsey, Lewis G, Careau, Vincent, Pontzer, Herman, Ainslie, Philip N, Andersen, Lene F, Anderson, Liam J, Arab, Lenore, Baddou, Issad, Bedu-Addo, Kweku, Blaak, Ellen E, Blanc, Stephane, Bonomi, Alberto G, Bouten, Carlijn VC, Bovet, Pascal, Buchowski, Maciej S, Butte, Nancy F, Camps, Stefan GJA, Close, Graeme L, Cooper, Jamie A, Das, Sai Krupa, Cooper, Richard, Dugas, Lara R, Ekelund, Ulf, Entringer, Sonja, Forrester, Terrence, Fudge, Barry W, Goris, Annelies H, Gurven, Michael, Hambly, Catherine, Hamdouchi, Asmaa El, Hoos, Marije B, Hu, Sumei, Joonas, Noorjehan, Joosen, Annemiek M, Katzmarzyk, Peter, Kempen, Kitty P, Kimura, Misaka, Kraus, William E, Kushner, Robert F, Lambert, Estelle V, Leonard, William R, Lessan, Nader, Martin, Corby K, Medin, Anine C, Meijer, Erwin P, Morehen, James C, Morton, James P, Neuhouser, Marian L, Nicklas, Theresa A, Ojiambo, Robert M, Pietiläinen, Kirsi H, Pitsiladis, Yannis P, Plange-Rhule, Jacob, Plasqui, Guy, Prentice, Ross L, Rabinovich, Roberto A, Racette, Susan B, Raichlen, David A, Ravussin, Eric, Reynolds, Rebecca M, Roberts, Susan B, Schuit, Albertine J, Sjödin, Anders M, Stice, Eric, Urlacher, Samuel S, Valenti, Giulio, Van Etten, Ludo M, Van Mil, Edgar A, Wilson, George, Wood, Brian M, Yanovski, Jack, Yoshida, Tsukasa, Zhang, Xueying, Murphy-Alford, Alexia J, Loechl, Cornelia U, Luke, Amy H, Rood, Jennifer, Sagayama, Hiroyuki, Schoeller, Dale A, Westerterp, Klaas R, Wong, William W, Yamada, Yosuke, and Speakman, John R

Subjects
Obesity, Behavioral and Social Science, Affordable and Clean Energy, Adult, Aged, Aging, Animals, Body Composition, Energy Metabolism, Female, Humans, Male, Mammals, Reproduction, Sex Characteristics, DLW, Energetics, Activity, Trait variability, Biological sex, Evolutionary Biology, Anthropology, Archaeology
Abstract

In mammals, trait variation is often reported to be greater among males than females. However, to date, mainly only morphological traits have been studied. Energy expenditure represents the metabolic costs of multiple physical, physiological, and behavioral traits. Energy expenditure could exhibit particularly high greater male variation through a cumulative effect if those traits mostly exhibit greater male variation, or a lack of greater male variation if many of them do not. Sex differences in energy expenditure variation have been little explored. We analyzed a large database on energy expenditure in adult humans (1494 males and 3108 females) to investigate whether humans have evolved sex differences in the degree of interindividual variation in energy expenditure. We found that, even when statistically comparing males and females of the same age, height, and body composition, there is much more variation in total, activity, and basal energy expenditure among males. However, with aging, variation in total energy expenditure decreases, and because this happens more rapidly in males, the magnitude of greater male variation, though still large, is attenuated in older age groups. Considerably greater male variation in both total and activity energy expenditure could be explained by greater male variation in levels of daily activity. The considerably greater male variation in basal energy expenditure is remarkable and may be explained, at least in part, by greater male variation in the size of energy-demanding organs. If energy expenditure is a trait that is of indirect interest to females when choosing a sexual partner, this would suggest that energy expenditure is under sexual selection. However, we present a novel energetics model demonstrating that it is also possible that females have been under stabilizing selection pressure for an intermediate basal energy expenditure to maximize energy available for reproduction.

Published
2022

7. Human total, basal and activity energy expenditures are independent of ambient environmental temperature

Author

Zhang, Xueying, Yamada, Yosuke, Sagayama, Hiroyuki, Ainslie, Philip N, Blaak, Ellen E, Buchowski, Maciej S, Close, Graeme L, Cooper, Jamie A, Das, Sai Krupa, Dugas, Lara R, Gurven, Michael, Hamdouchi, Asmaa El, Hu, Sumei, Joonas, Noorjehan, Katzmarzyk, Peter, Kraus, William E, Kushner, Robert F, Leonard, William R, Martin, Corby K, Meijer, Erwin P, Neuhouser, Marian L, Ojiambo, Robert M, Pitsiladis, Yannis P, Plasqui, Guy, Prentice, Ross L, Racette, Susan B, Ravussin, Eric, Redman, Leanne M, Reynolds, Rebecca M, Roberts, Susan B, Sardinha, Luis B, Silva, Analiza M, Stice, Eric, Urlacher, Samuel S, Van Mil, Edgar A, Wood, Brian M, Murphy-Alford, Alexia J, Loechl, Cornelia, Luke, Amy H, Rood, Jennifer, Schoeller, Dale A, Westerterp, Klaas R, Wong, William W, Pontzer, Herman, Speakman, John R, consortium, the IAEA DLW database, Andersen, Lene F, Anderson, Liam J, Arab, Lenore, Baddou, Issad, Addo, Bedu, Blanc, Stephane, Bonomi, Alberto, Bouten, Carlijn VC, Bovet, Pascal, Branth, Stefan, De Bruin, Niels C, Butte, Nancy F, Colbert, Lisa H, Camps, Stephan G, Dutman, Alice E, Eaton, Simon D, Ekelund, Ulf, Entringer, Sonja, Ebbeling, Cara, Elmståhl, Sölve, Fogelholm, Mikael, Forrester, Terrence, Fudge, Barry W, Harris, Tamara, Heijligenberg, Rik, Goris, Annelies H, Hambly, Catherine, Hoos, Marije B, Jorgensen, Hans U, Joosen, Annemiek M, Kempen, Kitty P, Kimura, Misaka, Kriengsinyos, Watanee, Lambert, Estelle V, Larsson, Christel L, Lessan, Nader, Ludwig, David S, McCloskey, Margaret, Medin, Anine C, Meijer, Gerwin A, Matsiko, Eric, Melse-Boonstra, Alida, Morehen, James C, Morton, James P, Nicklas, Theresa A, Pannemans, Daphne L, Pietiläinen, Kirsi H, Philippaerts, Renaat M, Rabinovich, Roberto A, Reilly, John J, Rothenberg, Elisabet M, Schuit, Albertine J, Schulz, Sabine, and Sjödin, Anders M

Subjects
Nutrition, IAEA DLW database consortium, Human Physiology, Human activity in medical context, Human metabolism
Abstract

Lower ambient temperature (Ta) requires greater energy expenditure to sustain body temperature. However, effects of Ta on human energetics may be buffered by environmental modification and behavioral compensation. We used the IAEA DLW database for adults in the USA (n = 3213) to determine the effect of Ta (-10 to +30°C) on TEE, basal (BEE) and activity energy expenditure (AEE) and physical activity level (PAL). There were no significant relationships (p > 0.05) between maximum, minimum and average Ta and TEE, BEE, AEE and PAL. After adjustment for fat-free mass, fat mass and age, statistically significant (p

Published
2022

9. Single nucleus RNA-sequencing integrated into risk variant colocalization discovers 17 cell-type-specific abdominal obesity genes for metabolic dysfunction-associated steatotic liver disease

Author

Lee, Seung Hyuk T., Garske, Kristina M., Arasu, Uma Thanigai, Kar, Asha, Miao, Zong, Alvarez, Marcus, Koka, Amogha, Darci-Maher, Nicholas, Benhammou, Jihane N., Pan, David Z., Örd, Tiit, Kaminska, Dorota, Männistö, Ville, Heinonen, Sini, Wabitsch, Martin, Laakso, Markku, Agopian, Vatche G., Pisegna, Joseph R., Pietiläinen, Kirsi H., Pihlajamäki, Jussi, Kaikkonen, Minna U., and Pajukanta, Päivi

Published
2024
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15. Total energy expenditure is repeatable in adults but not associated with short-term changes in body composition

Author

Rimbach, Rebecca, Yamada, Yosuke, Sagayama, Hiroyuki, Ainslie, Philip N, Anderson, Lene F, Anderson, Liam J, Arab, Lenore, Baddou, Issaad, Bedu-Addo, Kweku, Blaak, Ellen E, Blanc, Stephane, Bonomi, Alberto G, Bouten, Carlijn VC, Bovet, Pascal, Buchowski, Maciej S, Butte, Nancy F, Camps, Stefan GJA, Close, Graeme L, Cooper, Jamie A, Das, Sai Krupa, Dugas, Lara R, Ekelund, Ulf, Entringer, Sonja, Forrester, Terrence, Fudge, Barry W, Goris, Annelies H, Gurven, Michael, Hambly, Catherine, El Hamdouchi, Asmaa, Hoos, Marije B, Hu, Sumei, Joonas, Noorjehan, Joosen, Annemiek M, Katzmarzyk, Peter, Kempen, Kitty P, Kimura, Misaka, Kraus, William E, Kushner, Robert F, Lambert, Estelle V, Leonard, William R, Lessan, Nader, Martin, Corby K, Medin, Anine C, Meijer, Erwin P, Morehen, James C, Morton, James P, Neuhouser, Marian L, Nicklas, Theresa A, Ojiambo, Robert M, Pietiläinen, Kirsi H, Pitsiladis, Yannis P, Plange-Rhule, Jacob, Plasqui, Guy, Prentice, Ross L, Rabinovich, Roberto A, Racette, Susan B, Raichlen, David A, Ravussin, Eric, Reynolds, Rebecca M, Roberts, Susan B, Schuit, Albertine J, Sjödin, Anders M, Stice, Eric, Urlacher, Samuel S, Valenti, Giulio, Van Etten, Ludo M, Van Mil, Edgar A, Wells, Jonathan CK, Wilson, George, Wood, Brian M, Yanovski, Jack, Yoshida, Tsukasa, Zhang, Xueying, Murphy-Alford, Alexia J, Loechl, Cornelia U, Luke, Amy H, Rood, Jennifer, Schoeller, Dale A, Westerterp, Klaas R, Wong, William W, Speakman, John R, and Pontzer, Herman

Subjects
Nutrition, Pediatric, Clinical Research, Obesity, Aetiology, 2.1 Biological and endogenous factors, Metabolic and endocrine, Adipose Tissue, Adult, Bayes Theorem, Body Composition, Child, Databases, Factual, Energy Metabolism, Female, Humans, Isotope Labeling, Longitudinal Studies, Male, Middle Aged, Water, Weight Gain, IAEA DLW Database Consortium
Abstract

Low total energy expenditure (TEE, MJ/d) has been a hypothesized risk factor for weight gain, but repeatability of TEE, a critical variable in longitudinal studies of energy balance, is understudied. We examine repeated doubly labeled water (DLW) measurements of TEE in 348 adults and 47 children from the IAEA DLW Database (mean ± SD time interval: 1.9 ± 2.9 y) to assess repeatability of TEE, and to examine if TEE adjusted for age, sex, fat-free mass, and fat mass is associated with changes in weight or body composition. Here, we report that repeatability of TEE is high for adults, but not children. Bivariate Bayesian mixed models show no among or within-individual correlation between body composition (fat mass or percentage) and unadjusted TEE in adults. For adults aged 20-60 y (N = 267; time interval: 7.4 ± 12.2 weeks), increases in adjusted TEE are associated with weight gain but not with changes in body composition; results are similar for subjects with intervals >4 weeks (N = 53; 29.1 ± 12.8 weeks). This suggests low TEE is not a risk factor for, and high TEE is not protective against, weight or body fat gain over the time intervals tested.

Published
2022

16. Total daily energy expenditure has declined over the past three decades due to declining basal expenditure, not reduced activity expenditure

Author

Speakman, John R., de Jong, Jasper M. A., Sinha, Srishti, Westerterp, Klaas R., Yamada, Yosuke, Sagayama, Hiroyuki, Ainslie, Philip N., Anderson, Liam J., Arab, Lenore, Bedu-Addo, Kweku, Blanc, Stephane, Bonomi, Alberto G., Bovet, Pascal, Brage, Soren, Buchowski, Maciej S., Butte, Nancy F., Camps, Stefan G.J.A., Cooper, Jamie A., Cooper, Richard, Das, Sai Krupa, Davies, Peter S. W., Dugas, Lara R., Ekelund, Ulf, Entringer, Sonja, Forrester, Terrence, Fudge, Barry W., Gillingham, Melanie, Ghosh, Santu, Goris, Annelies H., Gurven, Michael, Halsey, Lewis G., Hambly, Catherine, Haisma, Hinke H., Hoffman, Daniel, Hu, Sumei, Joosen, Annemiek M., Kaplan, Jennifer L., Katzmarzyk, Peter, Kraus, William E., Kushner, Robert F., Leonard, William R., Löf, Marie, Martin, Corby K., Matsiko, Eric, Medin, Anine C., Meijer, Erwin P., Neuhouser, Marian L., Nicklas, Theresa A., Ojiambo, Robert M., Pietiläinen, Kirsi H., Plange-Rhule, Jacob, Plasqui, Guy, Prentice, Ross L., Racette, Susan B., Raichlen, David A., Ravussin, Eric, Redman, Leanne M., Roberts, Susan B., Rudolph, Michael C., Sardinha, Luis B., Schuit, Albertine J., Silva, Analiza M., Stice, Eric, Urlacher, Samuel S., Valenti, Giulio, Van Etten, Ludo M., Van Mil, Edgar A., Wood, Brian M., Yanovski, Jack A., Yoshida, Tsukasa, Zhang, Xueying, Murphy-Alford, Alexia J., Loechl, Cornelia U., Kurpad, Anura, Luke, Amy H., Pontzer, Herman, Rodeheffer, Matthew S., Rood, Jennifer, Schoeller, Dale A., and Wong, William W.

Published
2023
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17. Physical activity and fat-free mass during growth and in later life

Author

Westerterp, Klaas R, Yamada, Yosuke, Sagayama, Hiroyuki, Ainslie, Philip N, Andersen, Lene F, Anderson, Liam J, Arab, Lenore, Baddou, Issaad, Bedu-Addo, Kweku, Blaak, Ellen E, Blanc, Stephane, Bonomi, Alberto G, Bouten, Carlijn VC, Bovet, Pascal, Buchowski, Maciej S, Butte, Nancy F, Camps, Stefan GJA, Close, Graeme L, Cooper, Jamie A, Das, Sai K, Cooper, Richard, Dugas, Lara R, Ekelund, Ulf, Entringer, Sonja, Forrester, Terrence, Fudge, Barry W, Goris, Annelies H, Gurven, Michael, Hambly, Catherine, Hamdouchi, Asmaa El, Hoos, Marije B, Hu, Sumei, Joonas, Noorjehan, Joosen, Annemiek M, Katzmarzyk, Peter, Kempen, Kitty P, Kimura, Misaka, Kraus, William E, Kushner, Robert F, Lambert, Estelle V, Leonard, William R, Lessan, Nader, Martin, Corby K, Medin, Anine C, Meijer, Erwin P, Morehen, James C, Morton, James P, Neuhouser, Marian L, Nicklas, Theresa A, Ojiambo, Robert M, Pietiläinen, Kirsi H, Pitsiladis, Yannis P, Plange-Rhule, Jacob, Plasqui, Guy, Prentice, Ross L, Rabinovich, Roberto A, Racette, Susan B, Raichlen, David A, Ravussin, Eric, Reynolds, Rebecca M, Roberts, Susan B, Schuit, Albertine J, Sjödin, Anders M, Stice, Eric, Urlacher, Samuel S, Valenti, Giulio, Van Etten, Ludo M, Van Mil, Edgar A, Wells, Jonathan CK, Wilson, George, Wood, Brian M, Yanovski, Jack, Yoshida, Tsukasa, Zhang, Xueying, Murphy-Alford, Alexia J, Loechl, Cornelia U, Luke, Amy H, Pontzer, Herman, Rood, Jennifer, Schoeller, Dale A, Wong, William W, Speakman, John R, Branth, Stefan, Colbert, Lisa H, De Bruin, Niels C, Dutman, Alice E, Elmståhl, Sölve, Fogelholm, Mikael, Harris, Tamara, Heijligenberg, Rik, Jorgensen, Hans U, Larsson, Christel L, Rothenberg, Elisabet M, McCloskey, Margaret, Meijer, Gerwin A, Pannemans, Daphne L, Schulz, Sabine, Van den Berg-Emons, Rita, Van Gemert, Wim G, and Wilhelmine, W

Subjects
Prevention, Aging, Clinical Research, Nutrition, Adipose Tissue, Adolescent, Adult, Aged, Aged, 80 and over, Body Composition, Child, Child, Preschool, Cross-Sectional Studies, Energy Metabolism, Exercise, Female, Humans, Male, Middle Aged, Young Adult, physical activity level, age, energy expenditure, body composition, doubly labeled water, International Atomic Energy Agency Doubly Labeled Water database group, Engineering, Medical and Health Sciences, Nutrition & Dietetics
Abstract

BackgroundPhysical activity may be a way to increase and maintain fat-free mass (FFM) in later life, similar to the prevention of fractures by increasing peak bone mass.ObjectivesA study is presented of the association between FFM and physical activity in relation to age.MethodsIn a cross-sectional study, FFM was analyzed in relation to physical activity in a large participant group as compiled in the International Atomic Energy Agency Doubly Labeled Water database. The database included 2000 participants, age 3-96 y, with measurements of total energy expenditure (TEE) and resting energy expenditure (REE) to allow calculation of physical activity level (PAL = TEE/REE), and calculation of FFM from isotope dilution.ResultsPAL was a main determinant of body composition at all ages. Models with age, fat mass (FM), and PAL explained 76% and 85% of the variation in FFM in females and males

Published
2021

18. Energy compensation and adiposity in humans

Author

Careau, Vincent, Halsey, Lewis G, Pontzer, Herman, Ainslie, Philip N, Andersen, Lene F, Anderson, Liam J, Arab, Lenore, Baddou, Issad, Bedu-Addo, Kweku, Blaak, Ellen E, Blanc, Stephane, Bonomi, Alberto G, Bouten, Carlijn VC, Buchowski, Maciej S, Butte, Nancy F, Camps, Stefan GJA, Close, Graeme L, Cooper, Jamie A, Das, Sai Krupa, Cooper, Richard, Dugas, Lara R, Eaton, Simon D, Ekelund, Ulf, Entringer, Sonja, Forrester, Terrence, Fudge, Barry W, Goris, Annelies H, Gurven, Michael, Hambly, Catherine, Hamdouchi, Asmaa El, Hoos, Marije B, Hu, Sumei, Joonas, Noorjehan, Joosen, Annemiek M, Katzmarzyk, Peter, Kempen, Kitty P, Kimura, Misaka, Kraus, William E, Kushner, Robert F, Lambert, Estelle V, Leonard, William R, Lessan, Nader, Martin, Corby K, Medin, Anine C, Meijer, Erwin P, Morehen, James C, Morton, James P, Neuhouser, Marian L, Nicklas, Theresa A, Ojiambo, Robert M, Pietiläinen, Kirsi H, Pitsiladis, Yannis P, Plange-Rhule, Jacob, Plasqui, Guy, Prentice, Ross L, Rabinovich, Roberto A, Racette, Susan B, Raichlen, David A, Ravussin, Eric, Reilly, John J, Reynolds, Rebecca M, Roberts, Susan B, Schuit, Albertine J, Sjödin, Anders M, Stice, Eric, Urlacher, Samuel S, Valenti, Giulio, Van Etten, Ludo M, Van Mil, Edgar A, Wells, Jonathan CK, Wilson, George, Wood, Brian M, Yanovski, Jack, Yoshida, Tsukasa, Zhang, Xueying, Murphy-Alford, Alexia J, Loechl, Cornelia U, Luke, Amy H, Rood, Jennifer, Sagayama, Hiroyuki, Schoeller, Dale A, Wong, William W, Yamada, Yosuke, Speakman, John R, and group, the IAEA DLW database

Subjects
Nutrition, Obesity, Clinical Research, Oral and gastrointestinal, Stroke, Metabolic and endocrine, Cancer, Cardiovascular, Affordable and Clean Energy, Adiposity, Energy Intake, Energy Metabolism, Humans, IAEA DLW database group, Homo sapiens, activity, basal metabolic rate, daily energy expenditure, energy compensation, energy management models, exercise, trade-offs, weight loss, Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences, Developmental Biology
Abstract

Understanding the impacts of activity on energy balance is crucial. Increasing levels of activity may bring diminishing returns in energy expenditure because of compensatory responses in non-activity energy expenditures.1-3 This suggestion has profound implications for both the evolution of metabolism and human health. It implies that a long-term increase in activity does not directly translate into an increase in total energy expenditure (TEE) because other components of TEE may decrease in response-energy compensation. We used the largest dataset compiled on adult TEE and basal energy expenditure (BEE) (n = 1,754) of people living normal lives to find that energy compensation by a typical human averages 28% due to reduced BEE; this suggests that only 72% of the extra calories we burn from additional activity translates into extra calories burned that day. Moreover, the degree of energy compensation varied considerably between people of different body compositions. This association between compensation and adiposity could be due to among-individual differences in compensation: people who compensate more may be more likely to accumulate body fat. Alternatively, the process might occur within individuals: as we get fatter, our body might compensate more strongly for the calories burned during activity, making losing fat progressively more difficult. Determining the causality of the relationship between energy compensation and adiposity will be key to improving public health strategies regarding obesity.

Published
2021

19. Daily energy expenditure through the human life course

Author

Pontzer, Herman, Yamada, Yosuke, Sagayama, Hiroyuki, Ainslie, Philip N, Andersen, Lene F, Anderson, Liam J, Arab, Lenore, Baddou, Issaad, Bedu-Addo, Kweku, Blaak, Ellen E, Blanc, Stephane, Bonomi, Alberto G, Bouten, Carlijn VC, Bovet, Pascal, Buchowski, Maciej S, Butte, Nancy F, Camps, Stefan G, Close, Graeme L, Cooper, Jamie A, Cooper, Richard, Das, Sai Krupa, Dugas, Lara R, Ekelund, Ulf, Entringer, Sonja, Forrester, Terrence, Fudge, Barry W, Goris, Annelies H, Gurven, Michael, Hambly, Catherine, Hamdouchi, Asmaa El, Hoos, Marjije B, Hu, Sumei, Joonas, Noorjehan, Joosen, Annemiek M, Katzmarzyk, Peter, Kempen, Kitty P, Kimura, Misaka, Kraus, William E, Kushner, Robert F, Lambert, Estelle V, Leonard, William R, Lessan, Nader, Martin, Corby, Medin, Anine C, Meijer, Erwin P, Morehen, James C, Morton, James P, Neuhouser, Marian L, Nicklas, Teresa A, Ojiambo, Robert M, Pietiläinen, Kirsi H, Pitsiladis, Yannis P, Plange-Rhule, Jacob, Plasqui, Guy, Prentice, Ross L, Rabinovich, Roberto A, Racette, Susan B, Raichlen, David A, Ravussin, Eric, Reynolds, Rebecca M, Roberts, Susan B, Schuit, Albertine J, Sjödin, Anders M, Stice, Eric, Urlacher, Samuel S, Valenti, Giulio, Van Etten, Ludo M, Van Mil, Edgar A, Wells, Jonathan CK, Wilson, George, Wood, Brian M, Yanovski, Jack, Yoshida, Tsukasa, Zhang, Xueying, Murphy-Alford, Alexia J, Loechl, Cornelia, Luke, Amy H, Rood, Jennifer, Schoeller, Dale A, Westerterp, Klaas R, Wong, William W, Speakman, John R, and Consortium§, IAEA DLW Database

Subjects
Aging, Nutrition, Adolescent, Adult, Aged, Aged, 80 and over, Basal Metabolism, Body Composition, Body Weight, Child, Child, Preschool, Energy Metabolism, Exercise, Female, Humans, Infant, Infant, Newborn, Male, Middle Aged, Pregnancy, Young Adult, IAEA DLW Database Consortium, General Science & Technology
Abstract

Total daily energy expenditure ("total expenditure") reflects daily energy needs and is a critical variable in human health and physiology, but its trajectory over the life course is poorly studied. We analyzed a large, diverse database of total expenditure measured by the doubly labeled water method for males and females aged 8 days to 95 years. Total expenditure increased with fat-free mass in a power-law manner, with four distinct life stages. Fat-free mass-adjusted expenditure accelerates rapidly in neonates to ~50% above adult values at ~1 year; declines slowly to adult levels by ~20 years; remains stable in adulthood (20 to 60 years), even during pregnancy; then declines in older adults. These changes shed light on human development and aging and should help shape nutrition and health strategies across the life span.

Published
2021

20. Identification of TBX15 as an adipose master trans regulator of abdominal obesity genes.

Author

Pan, David Z, Miao, Zong, Comenho, Caroline, Rajkumar, Sandhya, Koka, Amogha, Lee, Seung Hyuk T, Alvarez, Marcus, Kaminska, Dorota, Ko, Arthur, Sinsheimer, Janet S, Mohlke, Karen L, Mancuso, Nicholas, Muñoz-Hernandez, Linda Liliana, Herrera-Hernandez, Miguel, Tusié-Luna, Maria Teresa, Aguilar-Salinas, Carlos, Pietiläinen, Kirsi H, Pihlajamäki, Jussi, Laakso, Markku, Garske, Kristina M, and Pajukanta, Päivi

Subjects
Master transcription factor, Polygenic risk score, Trans regulation of genes, Transcriptional regulation of abdominal obesity, Type 2 diabetes, Waist-hip ratio adjusted for body mass index, Genetics, Clinical Sciences
Abstract

BackgroundObesity predisposes individuals to multiple cardiometabolic disorders, including type 2 diabetes (T2D). As body mass index (BMI) cannot reliably differentiate fat from lean mass, the metabolically detrimental abdominal obesity has been estimated using waist-hip ratio (WHR). Waist-hip ratio adjusted for body mass index (WHRadjBMI) in turn is a well-established sex-specific marker for abdominal fat and adiposity, and a predictor of adverse metabolic outcomes, such as T2D. However, the underlying genes and regulatory mechanisms orchestrating the sex differences in obesity and body fat distribution in humans are not well understood.MethodsWe searched for genetic master regulators of WHRadjBMI by employing integrative genomics approaches on human subcutaneous adipose RNA sequencing (RNA-seq) data (n ~ 1400) and WHRadjBMI GWAS data (n ~ 700,000) from the WHRadjBMI GWAS cohorts and the UK Biobank (UKB), using co-expression network, transcriptome-wide association study (TWAS), and polygenic risk score (PRS) approaches. Finally, we functionally verified our genomic results using gene knockdown experiments in a human primary cell type that is critical for adipose tissue function.ResultsHere, we identified an adipose gene co-expression network that contains 35 obesity GWAS genes and explains a significant amount of polygenic risk for abdominal obesity and T2D in the UKB (n = 392,551) in a sex-dependent way. We showed that this network is preserved in the adipose tissue data from the Finnish Kuopio Obesity Study and Mexican Obesity Study. The network is controlled by a novel adipose master transcription factor (TF), TBX15, a WHRadjBMI GWAS gene that regulates the network in trans. Knockdown of TBX15 in human primary preadipocytes resulted in changes in expression of 130 network genes, including the key adipose TFs, PPARG and KLF15, which were significantly impacted (FDR < 0.05), thus functionally verifying the trans regulatory effect of TBX15 on the WHRadjBMI co-expression network.ConclusionsOur study discovers a novel key function for the TBX15 TF in trans regulating an adipose co-expression network of 347 adipose, mitochondrial, and metabolically important genes, including PPARG, KLF15, PPARA, ADIPOQ, and 35 obesity GWAS genes. Thus, based on our converging genomic, transcriptional, and functional evidence, we interpret the role of TBX15 to be a main transcriptional regulator in the adipose tissue and discover its importance in human abdominal obesity.

Published
2021

22. Author Correction: Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk

Author

Shrine, Nick, Izquierdo, Abril G., Chen, Jing, Packer, Richard, Hall, Robert J., Guyatt, Anna L., Batini, Chiara, Thompson, Rebecca J., Pavuluri, Chandan, Malik, Vidhi, Hobbs, Brian D., Moll, Matthew, Kim, Wonji, Tal-Singer, Ruth, Bakke, Per, Fawcett, Katherine A., John, Catherine, Coley, Kayesha, Piga, Noemi Nicole, Pozarickij, Alfred, Lin, Kuang, Millwood, Iona Y., Chen, Zhengming, Li, Liming, Wijnant, Sara R. A., Lahousse, Lies, Brusselle, Guy, Uitterlinden, Andre G., Manichaikul, Ani, Oelsner, Elizabeth C., Rich, Stephen S., Barr, R. Graham, Kerr, Shona M., Vitart, Veronique, Brown, Michael R., Wielscher, Matthias, Imboden, Medea, Jeong, Ayoung, Bartz, Traci M., Gharib, Sina A., Flexeder, Claudia, Karrasch, Stefan, Gieger, Christian, Peters, Annette, Stubbe, Beate, Hu, Xiaowei, Ortega, Victor E., Meyers, Deborah A., Bleecker, Eugene R., Gabriel, Stacey B., Gupta, Namrata, Smith, Albert Vernon, Luan, Jian’an, Zhao, Jing-Hua, Hansen, Ailin F., Langhammer, Arnulf, Willer, Cristen, Bhatta, Laxmi, Porteous, David, Smith, Blair H., Campbell, Archie, Sofer, Tamar, Lee, Jiwon, Daviglus, Martha L., Yu, Bing, Lim, Elise, Xu, Hanfei, O’Connor, George T., Thareja, Gaurav, Albagha, Omar M. E., Suhre, Karsten, Granell, Raquel, Faquih, Tariq O., Hiemstra, Pieter S., Slats, Annelies M., Mullin, Benjamin H., Hui, Jennie, James, Alan, Beilby, John, Patasova, Karina, Hysi, Pirro, Koskela, Jukka T., Wyss, Annah B., Jin, Jianping, Sikdar, Sinjini, Lee, Mikyeong, May-Wilson, Sebastian, Pirastu, Nicola, Kentistou, Katherine A., Joshi, Peter K., Timmers, Paul R. H. J., Williams, Alexander T., Free, Robert C., Wang, Xueyang, Morrison, John L., Gilliland, Frank D., Chen, Zhanghua, Wang, Carol A., Foong, Rachel E., Harris, Sarah E., Taylor, Adele, Redmond, Paul, Cook, James P., Mahajan, Anubha, Lind, Lars, Palviainen, Teemu, Lehtimäki, Terho, Raitakari, Olli T., Kaprio, Jaakko, Rantanen, Taina, Pietiläinen, Kirsi H., Cox, Simon R., Pennell, Craig E., Hall, Graham L., Gauderman, W. James, Brightling, Chris, Wilson, James F., Vasankari, Tuula, Laitinen, Tarja, Salomaa, Veikko, Mook-Kanamori, Dennis O., Timpson, Nicholas J., Zeggini, Eleftheria, Dupuis, Josée, Hayward, Caroline, Brumpton, Ben, Langenberg, Claudia, Weiss, Stefan, Homuth, Georg, Schmidt, Carsten Oliver, Probst-Hensch, Nicole, Jarvelin, Marjo-Riitta, Morrison, Alanna C., Polasek, Ozren, Rudan, Igor, Lee, Joo-Hyeon, Sayers, Ian, Rawlins, Emma L., Dudbridge, Frank, Silverman, Edwin K., Strachan, David P., Walters, Robin G., Morris, Andrew P., London, Stephanie J., Cho, Michael H., Wain, Louise V., Hall, Ian P., and Tobin, Martin D.

Published
2023
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23. Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk

Author

Shrine, Nick, Izquierdo, Abril G., Chen, Jing, Packer, Richard, Hall, Robert J., Guyatt, Anna L., Batini, Chiara, Thompson, Rebecca J., Pavuluri, Chandan, Malik, Vidhi, Hobbs, Brian D., Moll, Matthew, Kim, Wonji, Tal-Singer, Ruth, Bakke, Per, Fawcett, Katherine A., John, Catherine, Coley, Kayesha, Piga, Noemi Nicole, Pozarickij, Alfred, Lin, Kuang, Millwood, Iona Y., Chen, Zhengming, Li, Liming, Wijnant, Sara R. A., Lahousse, Lies, Brusselle, Guy, Uitterlinden, Andre G., Manichaikul, Ani, Oelsner, Elizabeth C., Rich, Stephen S., Barr, R. Graham, Kerr, Shona M., Vitart, Veronique, Brown, Michael R., Wielscher, Matthias, Imboden, Medea, Jeong, Ayoung, Bartz, Traci M., Gharib, Sina A., Flexeder, Claudia, Karrasch, Stefan, Gieger, Christian, Peters, Annette, Stubbe, Beate, Hu, Xiaowei, Ortega, Victor E., Meyers, Deborah A., Bleecker, Eugene R., Gabriel, Stacey B., Gupta, Namrata, Smith, Albert Vernon, Luan, Jian’an, Zhao, Jing-Hua, Hansen, Ailin F., Langhammer, Arnulf, Willer, Cristen, Bhatta, Laxmi, Porteous, David, Smith, Blair H., Campbell, Archie, Sofer, Tamar, Lee, Jiwon, Daviglus, Martha L., Yu, Bing, Lim, Elise, Xu, Hanfei, O’Connor, George T., Thareja, Gaurav, Albagha, Omar M. E., Suhre, Karsten, Granell, Raquel, Faquih, Tariq O., Hiemstra, Pieter S., Slats, Annelies M., Mullin, Benjamin H., Hui, Jennie, James, Alan, Beilby, John, Patasova, Karina, Hysi, Pirro, Koskela, Jukka T., Wyss, Annah B., Jin, Jianping, Sikdar, Sinjini, Lee, Mikyeong, May-Wilson, Sebastian, Pirastu, Nicola, Kentistou, Katherine A., Joshi, Peter K., Timmers, Paul R. H. J., Williams, Alexander T., Free, Robert C., Wang, Xueyang, Morrison, John L., Gilliland, Frank D., Chen, Zhanghua, Wang, Carol A., Foong, Rachel E., Harris, Sarah E., Taylor, Adele, Redmond, Paul, Cook, James P., Mahajan, Anubha, Lind, Lars, Palviainen, Teemu, Lehtimäki, Terho, Raitakari, Olli T., Kaprio, Jaakko, Rantanen, Taina, Pietiläinen, Kirsi H., Cox, Simon R., Pennell, Craig E., Hall, Graham L., Gauderman, W. James, Brightling, Chris, Wilson, James F., Vasankari, Tuula, Laitinen, Tarja, Salomaa, Veikko, Mook-Kanamori, Dennis O., Timpson, Nicholas J., Zeggini, Eleftheria, Dupuis, Josée, Hayward, Caroline, Brumpton, Ben, Langenberg, Claudia, Weiss, Stefan, Homuth, Georg, Schmidt, Carsten Oliver, Probst-Hensch, Nicole, Jarvelin, Marjo-Riitta, Morrison, Alanna C., Polasek, Ozren, Rudan, Igor, Lee, Joo-Hyeon, Sayers, Ian, Rawlins, Emma L., Dudbridge, Frank, Silverman, Edwin K., Strachan, David P., Walters, Robin G., Morris, Andrew P., London, Stephanie J., Cho, Michael H., Wain, Louise V., Hall, Ian P., and Tobin, Martin D.

Published
2023
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25. A standard calculation methodology for human doubly labeled water studies.

Author

Speakman, John R, Yamada, Yosuke, Sagayama, Hiroyuki, Berman, Elena SF, Ainslie, Philip N, Andersen, Lene F, Anderson, Liam J, Arab, Lenore, Baddou, Issaad, Bedu-Addo, Kweku, Blaak, Ellen E, Blanc, Stephane, Bonomi, Alberto G, Bouten, Carlijn VC, Bovet, Pascal, Buchowski, Maciej S, Butte, Nancy F, Camps, Stefan GJA, Close, Graeme L, Cooper, Jamie A, Creasy, Seth A, Das, Sai Krupa, Cooper, Richard, Dugas, Lara R, Ebbeling, Cara B, Ekelund, Ulf, Entringer, Sonja, Forrester, Terrence, Fudge, Barry W, Goris, Annelies H, Gurven, Michael, Hambly, Catherine, El Hamdouchi, Asmaa, Hoos, Marije B, Hu, Sumei, Joonas, Noorjehan, Joosen, Annemiek M, Katzmarzyk, Peter, Kempen, Kitty P, Kimura, Misaka, Kraus, William E, Kushner, Robert F, Lambert, Estelle V, Leonard, William R, Lessan, Nader, Ludwig, David S, Martin, Corby K, Medin, Anine C, Meijer, Erwin P, Morehen, James C, Morton, James P, Neuhouser, Marian L, Nicklas, Theresa A, Ojiambo, Robert M, Pietiläinen, Kirsi H, Pitsiladis, Yannis P, Plange-Rhule, Jacob, Plasqui, Guy, Prentice, Ross L, Rabinovich, Roberto A, Racette, Susan B, Raichlen, David A, Ravussin, Eric, Reynolds, Rebecca M, Roberts, Susan B, Schuit, Albertine J, Sjödin, Anders M, Stice, Eric, Urlacher, Samuel S, Valenti, Giulio, Van Etten, Ludo M, Van Mil, Edgar A, Wells, Jonathan CK, Wilson, George, Wood, Brian M, Yanovski, Jack, Yoshida, Tsukasa, Zhang, Xueying, Murphy-Alford, Alexia J, Loechl, Cornelia U, Melanson, Edward L, Luke, Amy H, Pontzer, Herman, Rood, Jennifer, Schoeller, Dale A, Westerterp, Klaas R, Wong, William W, and IAEA DLW database group

Subjects
IAEA DLW database group, doubly labeled water, free-living, total energy expenditure, validation
Abstract

The doubly labeled water (DLW) method measures total energy expenditure (TEE) in free-living subjects. Several equations are used to convert isotopic data into TEE. Using the International Atomic Energy Agency (IAEA) DLW database (5,756 measurements of adults and children), we show considerable variability is introduced by different equations. The estimated rCO2 is sensitive to the dilution space ratio (DSR) of the two isotopes. Based on performance in validation studies, we propose a new equation based on a new estimate of the mean DSR. The DSR is lower at low body masses (

Published
2021

26. Cold-stimulated brown adipose tissue activation is related to changes in serum metabolites relevant to NAD+ metabolism in humans

Author

U-Din, Mueez, de Mello, Vanessa D., Tuomainen, Marjo, Raiko, Juho, Niemi, Tarja, Fromme, Tobias, Klåvus, Anton, Gautier, Nadine, Haimilahti, Kimmo, Lehtonen, Marko, Kristiansen, Karsten, Newman, John W., Pietiläinen, Kirsi H., Pihlajamäki, Jussi, Amri, Ez-Zoubir, Klingenspor, Martin, Nuutila, Pirjo, Pirinen, Eija, Hanhineva, Kati, and Virtanen, Kirsi A.

Published
2023
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29. Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM.

Author

Alvarez, Marcus, Rahmani, Elior, Jew, Brandon, Garske, Kristina M, Miao, Zong, Benhammou, Jihane N, Ye, Chun Jimmie, Pisegna, Joseph R, Pietiläinen, Kirsi H, Halperin, Eran, and Pajukanta, Päivi

Abstract

Single-nucleus RNA sequencing (snRNA-seq) measures gene expression in individual nuclei instead of cells, allowing for unbiased cell type characterization in solid tissues. We observe that snRNA-seq is commonly subject to contamination by high amounts of ambient RNA, which can lead to biased downstream analyses, such as identification of spurious cell types if overlooked. We present a novel approach to quantify contamination and filter droplets in snRNA-seq experiments, called Debris Identification using Expectation Maximization (DIEM). Our likelihood-based approach models the gene expression distribution of debris and cell types, which are estimated using EM. We evaluated DIEM using three snRNA-seq data sets: (1) human differentiating preadipocytes in vitro, (2) fresh mouse brain tissue, and (3) human frozen adipose tissue (AT) from six individuals. All three data sets showed evidence of extranuclear RNA contamination, and we observed that existing methods fail to account for contaminated droplets and led to spurious cell types. When compared to filtering using these state of the art methods, DIEM better removed droplets containing high levels of extranuclear RNA and led to higher quality clusters. Although DIEM was designed for snRNA-seq, our clustering strategy also successfully filtered single-cell RNA-seq data. To conclude, our novel method DIEM removes debris-contaminated droplets from single-cell-based data fast and effectively, leading to cleaner downstream analysis. Our code is freely available for use at https://github.com/marcalva/diem.

Published
2020

31. Accurate estimation of cell composition in bulk expression through robust integration of single-cell information.

Author

Jew, Brandon, Alvarez, Marcus, Rahmani, Elior, Miao, Zong, Ko, Arthur, Garske, Kristina M, Sul, Jae Hoon, Pietiläinen, Kirsi H, Pajukanta, Päivi, and Halperin, Eran

Abstract

We present Bisque, a tool for estimating cell type proportions in bulk expression. Bisque implements a regression-based approach that utilizes single-cell RNA-seq (scRNA-seq) or single-nucleus RNA-seq (snRNA-seq) data to generate a reference expression profile and learn gene-specific bulk expression transformations to robustly decompose RNA-seq data. These transformations significantly improve decomposition performance compared to existing methods when there is significant technical variation in the generation of the reference profile and observed bulk expression. Importantly, compared to existing methods, our approach is extremely efficient, making it suitable for the analysis of large genomic datasets that are becoming ubiquitous. When applied to subcutaneous adipose and dorsolateral prefrontal cortex expression datasets with both bulk RNA-seq and snRNA-seq data, Bisque replicates previously reported associations between cell type proportions and measured phenotypes across abundant and rare cell types. We further propose an additional mode of operation that merely requires a set of known marker genes.

Published
2020

32. Human total, basal and activity energy expenditures are independent of ambient environmental temperature

Author

Andersen, Lene F., Anderson, Liam J., Arab, Lenore, Baddou, Issad, Addo, Bedu, Blanc, Stephane, Bonomi, Alberto, Bouten, Carlijn V.C., Bovet, Pascal, Branth, Stefan, De Bruin, Niels C., Butte, Nancy F., Colbert, Lisa H., Camps, Stephan G., Dutman, Alice E., Eaton, Simon D., Ekelund, Ulf, Entringer, Sonja, Ebbeling, Cara, Elmståhl, Sölve, Fogelholm, Mikael, Forrester, Terrence, Fudge, Barry W., Harris, Tamara, Heijligenberg, Rik, Goris, Annelies H., Hambly, Catherine, Hoos, Marije B., Jorgensen, Hans U., Joosen, Annemiek M., Kempen, Kitty P., Kimura, Misaka, Kriengsinyos, Watanee, Lambert, Estelle V., Larsson, Christel L., Lessan, Nader, Ludwig, David S., McCloskey, Margaret, Medin, Anine C., Meijer, Gerwin A., Matsiko, Eric, Melse-Boonstra, Alida, Morehen, James C., Morton, James P., Nicklas, Theresa A., Pannemans, Daphne L., Pietiläinen, Kirsi H., Philippaerts, Renaat M., Rabinovich, Roberto A., Reilly, John J., Rothenberg, Elisabet M., Schuit, Albertine J., Schulz, Sabine, Sjödin, Anders M., Subar, Amy, Tanskanen, Minna, Uauy, Ricardo, Valenti, Giulio, Van Etten, Ludo M., Berg-Emons, Rita Van den, Van Gemert, Wim G., Velthuis-te Wierik, Erica J., Verboeket-van de Venne, Wilhelmine W., Verbunt, Jeanine A., Wells, Jonathan C.K., Wilson, George, Zhang, Xueying, Yamada, Yosuke, Sagayama, Hiroyuki, Ainslie, Philip N., Blaak, Ellen E., Buchowski, Maciej S., Close, Graeme L., Cooper, Jamie A., Das, Sai Krupa, Dugas, Lara R., Gurven, Michael, El Hamdouchi, Asmaa, Hu, Sumei, Joonas, Noorjehan, Katzmarzyk, Peter, Kraus, William E., Kushner, Robert F., Leonard, William R., Martin, Corby K., Meijer, Erwin P., Neuhouser, Marian L., Ojiambo, Robert M., Pitsiladis, Yannis P., Plasqui, Guy, Prentice, Ross L., Racette, Susan B., Ravussin, Eric, Redman, Leanne M., Reynolds, Rebecca M., Roberts, Susan B., Sardinha, Luis B., Silva, Analiza M., Stice, Eric, Urlacher, Samuel S., Van Mil, Edgar A., Wood, Brian M., Murphy-Alford, Alexia J., Loechl, Cornelia, Luke, Amy H., Rood, Jennifer, Schoeller, Dale A., Westerterp, Klaas R., Wong, William W., Pontzer, Herman, and Speakman, John R.

Published
2022
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35. The mitochondrial protein Opa1 promotes adipocyte browning that is dependent on urea cycle metabolites

Author

Bean, Camilla, Audano, Matteo, Varanita, Tatiana, Favaretto, Francesca, Medaglia, Marta, Gerdol, Marco, Pernas, Lena, Stasi, Fabio, Giacomello, Marta, Herkenne, Stèphanie, Muniandy, Maheswany, Heinonen, Sini, Cazaly, Emma, Ollikainen, Miina, Milan, Gabriella, Pallavicini, Alberto, Pietiläinen, Kirsi H., Vettor, Roberto, Mitro, Nico, and Scorrano, Luca

Published
2021
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37. Associations of changes in reported and estimated protein and energy intake with changes in insulin resistance, glycated hemoglobin, and BMI during the PREVIEW lifestyle intervention study

Author

Drummen, Mathijs, Adam, Tanja C, Macdonald, Ian A, Jalo, Elli, Larssen, Thomas M, Martinez, J Alfredo, Handjiev-Darlenska, Teodora, Brand-Miller, Jennie, Poppitt, Sally D, Stratton, Gareth, Pietiläinen, Kirsi H, Taylor, Moira A, Navas-Carretero, Santiago, Handjiev, Svetoslav, Muirhead, Roslyn, Silvestre, Marta P, Swindell, Nils, Huttunen-Lenz, Maija, Schlicht, Wolfgang, Lam, Tony, Sundvall, Jouko, Raman, Laura, Feskens, Edith, Tremblay, Angelo, Raben, Anne, and Westerterp-Plantenga, Margriet S

Published
2021
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40. Molecular pathways behind acquired obesity: Adipose tissue and skeletal muscle multiomics in monozygotic twin pairs discordant for BMI

Author

van der Kolk, Birgitta W., Saari, Sina, Lovric, Alen, Arif, Muhammad, Alvarez, Marcus, Ko, Arthur, Miao, Zong, Sahebekhtiari, Navid, Muniandy, Maheswary, Heinonen, Sini, Oghabian, Ali, Jokinen, Riikka, Jukarainen, Sakari, Hakkarainen, Antti, Lundbom, Jesper, Kuula, Juho, Groop, Per-Henrik, Tukiainen, Taru, Lundbom, Nina, Rissanen, Aila, Kaprio, Jaakko, Williams, Evan G., Zamboni, Nicola, Mardinoglu, Adil, Pajukanta, Päivi, and Pietiläinen, Kirsi H.

Published
2021
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43. Roux‐en‐Y versus one‐anastomosis gastric bypass (RYSA study): weight loss, metabolic improvements, and nutrition at 1 year after surgery, a multicenter randomized controlled trial

Author

Heinonen, Sini, primary, Saarinen, Tuure, additional, Meriläinen, Sanna, additional, Sammalkorpi, Henna, additional, Penttilä, Anne K., additional, Koivikko, Minna, additional, Siira, Pertti, additional, Karppinen, Jaro, additional, Säiläkivi, Ulla, additional, Rosengård‐Bärlund, Milla, additional, Koivukangas, Vesa, additional, Pietiläinen, Kirsi H., additional, and Juuti, Anne, additional

Published
2023
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45. RIPK1 gene variants associate with obesity in humans and can be therapeutically silenced to reduce obesity in mice

Author

Karunakaran, Denuja, Turner, Adam W., Duchez, Anne-Claire, Soubeyrand, Sebastien, Rasheed, Adil, Smyth, David, Cook, David P., Nikpay, Majid, Kandiah, Joshua W., Pan, Calvin, Geoffrion, Michele, Lee, Richard, Boytard, Ludovic, Wyatt, Hailey, Nguyen, My-Anh, Lau, Paulina, Laakso, Markku, Ramkhelawon, Bhama, Alvarez, Marcus, Pietiläinen, Kirsi H., Pajukanta, Päivi, Vanderhyden, Barbara C., Liu, Peter, Berger, Scott B., Gough, Peter J., Bertin, John, Harper, Mary-Ellen, Lusis, Aldons J., McPherson, Ruth, and Rayner, Katey J.

Published
2020
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46. Correction to: Identification of TBX15 as an adipose master trans regulator of abdominal obesity genes

Author

Pan, David Z., Miao, Zong, Comenho, Caroline, Rajkumar, Sandhya, Koka, Amogha, Lee, Seung Hyuk T., Alvarez, Marcus, Kaminska, Dorota, Ko, Arthur, Sinsheimer, Janet S., Mohlke, Karen L., Mancuso, Nicholas, Muñoz-Hernandez, Linda Liliana, Herrera-Hernandez, Miguel, Tusié-Luna, Maria Teresa, Aguilar-Salinas, Carlos, Pietiläinen, Kirsi H., Pihlajamäki, Jussi, Laakso, Markku, Garske, Kristina M., and Pajukanta, Päivi

Published
2021
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48. Systemic cross-talk between brain, gut, and peripheral tissues in glucose homeostasis: effects of exercise training (CROSSYS). Exercise training intervention in monozygotic twins discordant for body weight

Author

Heiskanen, Marja A., Honkala, Sanna M., Hentilä, Jaakko, Ojala, Ronja, Lautamäki, Riikka, Koskensalo, Kalle, Lietzén, Martin S., Saunavaara, Virva, Saunavaara, Jani, Helmiö, Mika, Löyttyniemi, Eliisa, Nummenmaa, Lauri, Collado, Maria C., Malm, Tarja, Lahti, Leo, Pietiläinen, Kirsi H., Kaprio, Jaakko, Rinne, Juha O., and Hannukainen, Jarna C.

Published
2021
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