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Yuan J, Kitchener AC, Lackey LB, Sun T, Jiangzuo Q, Tuohetahong Y, Zhao L, Yang P, Wang G, Huang C, Wang J, Hou W, Liu Y, Chen W, Mi D, Murphy WJ, Li G. The genome of the black-footed cat: Revealing a rich natural history and urgent conservation priorities for small felids. Proc Natl Acad Sci U S A 2024; 121:e2310763120. [PMID: 38165928 PMCID: PMC10786289 DOI: 10.1073/pnas.2310763120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/31/2023] [Indexed: 01/04/2024] Open
Abstract
Habitat degradation and loss of genetic diversity are common threats faced by almost all of today's wild cats. Big cats, such as tigers and lions, are of great concern and have received considerable conservation attention through policies and international actions. However, knowledge of and conservation actions for small wild cats are lagging considerably behind. The black-footed cat, Felis nigripes, one of the smallest felid species, is experiencing increasing threats with a rapid reduction in population size. However, there is a lack of genetic information to assist in developing effective conservation actions. A de novo assembly of a high-quality chromosome-level reference genome of the black-footed cat was made, and comparative genomics and population genomics analyses were carried out. These analyses revealed that the most significant genetic changes in the evolution of the black-footed cat are the rapid evolution of sensory and metabolic-related genes, reflecting genetic adaptations to its characteristic nocturnal hunting and a high metabolic rate. Genomes of the black-footed cat exhibit a high level of inbreeding, especially for signals of recent inbreeding events, which suggest that they may have experienced severe genetic isolation caused by habitat fragmentation. More importantly, inbreeding associated with two deleterious mutated genes may exacerbate the risk of amyloidosis, the dominant disease that causes mortality of about 70% of captive individuals. Our research provides comprehensive documentation of the evolutionary history of the black-footed cat and suggests that there is an urgent need to investigate genomic variations of small felids worldwide to support effective conservation actions.
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Affiliation(s)
- Jiaqing Yuan
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, EdinburghEH1 1JF, United Kingdom
- School of Geosciences, University of Edinburgh, EdinburghEH9 3PX, United Kingdom
| | | | - Ting Sun
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Qigao Jiangzuo
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing100044, China
| | | | - Le Zhao
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
- QinLing-Bashan Mountains Bioresources Comprehensive Development Collaborative Innovation Center, School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong723099, China
| | - Peng Yang
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Guiqiang Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Chen Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Jinhong Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Wenhui Hou
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Wu Chen
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou510070, China
| | - Da Mi
- Xi’an Haorui Genomics Technology Co., Ltd., Xi’an710116, China
- School of Life Science and Technology, Xi’an Jiaotong University, Xi’an710049, China
| | - William J. Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX77843
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou510070, China
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Tzouanas CN, Sherman MS, Shay JE, Rubin AJ, Mead BE, Dao TT, Butzlaff T, Mana MD, Kolb KE, Walesky C, Pepe-Mooney BJ, Smith CJ, Prakadan SM, Ramseier ML, Tong EY, Joung J, Chi F, McMahon-Skates T, Winston CL, Jeong WJ, Aney KJ, Chen E, Nissim S, Zhang F, Deshpande V, Lauer GM, Yilmaz ÖH, Goessling W, Shalek AK. Chronic metabolic stress drives developmental programs and loss of tissue functions in non-transformed liver that mirror tumor states and stratify survival. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569407. [PMID: 38077056 PMCID: PMC10705501 DOI: 10.1101/2023.11.30.569407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Under chronic stress, cells must balance competing demands between cellular survival and tissue function. In metabolic dysfunction-associated steatotic liver disease (MASLD, formerly NAFLD/NASH), hepatocytes cooperate with structural and immune cells to perform crucial metabolic, synthetic, and detoxification functions despite nutrient imbalances. While prior work has emphasized stress-induced drivers of cell death, the dynamic adaptations of surviving cells and their functional repercussions remain unclear. Namely, we do not know which pathways and programs define cellular responses, what regulatory factors mediate (mal)adaptations, and how this aberrant activity connects to tissue-scale dysfunction and long-term disease outcomes. Here, by applying longitudinal single-cell multi -omics to a mouse model of chronic metabolic stress and extending to human cohorts, we show that stress drives survival-linked tradeoffs and metabolic rewiring, manifesting as shifts towards development-associated states in non-transformed hepatocytes with accompanying decreases in their professional functionality. Diet-induced adaptations occur significantly prior to tumorigenesis but parallel tumorigenesis-induced phenotypes and predict worsened human cancer survival. Through the development of a multi -omic computational gene regulatory inference framework and human in vitro and mouse in vivo genetic perturbations, we validate transcriptional (RELB, SOX4) and metabolic (HMGCS2) mediators that co-regulate and couple the balance between developmental state and hepatocyte functional identity programming. Our work defines cellular features of liver adaptation to chronic stress as well as their links to long-term disease outcomes and cancer hallmarks, unifying diverse axes of cellular dysfunction around core causal mechanisms.
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Affiliation(s)
- Constantine N. Tzouanas
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- These authors contributed equally
| | - Marc S. Sherman
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
- These authors contributed equally
| | - Jessica E.S. Shay
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Alcohol Liver Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Gastrointestinal Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- These authors contributed equally
| | - Adam J. Rubin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Benjamin E. Mead
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tyler T. Dao
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Titus Butzlaff
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Miyeko D. Mana
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Kellie E. Kolb
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Chad Walesky
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Brian J. Pepe-Mooney
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Colton J. Smith
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sanjay M. Prakadan
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michelle L. Ramseier
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Evelyn Y. Tong
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Julia Joung
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Science, MA, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, MIT, Cambridge, MA, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Fangtao Chi
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
| | - Thomas McMahon-Skates
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Carolyn L. Winston
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Woo-Jeong Jeong
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Katherine J. Aney
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ethan Chen
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sahar Nissim
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Gastroenterology Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Science, MA, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, MIT, Cambridge, MA, USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Georg M. Lauer
- Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Ömer H. Yilmaz
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
- These senior authors contributed equally
| | - Wolfram Goessling
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Genetics Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA, USA
- These senior authors contributed equally
| | - Alex K. Shalek
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- These senior authors contributed equally
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5
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Teong XT, Liu K, Vincent AD, Bensalem J, Liu B, Hattersley KJ, Zhao L, Feinle-Bisset C, Sargeant TJ, Wittert GA, Hutchison AT, Heilbronn LK. Intermittent fasting plus early time-restricted eating versus calorie restriction and standard care in adults at risk of type 2 diabetes: a randomized controlled trial. Nat Med 2023; 29:963-972. [PMID: 37024596 DOI: 10.1038/s41591-023-02287-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 03/02/2023] [Indexed: 04/08/2023]
Abstract
Intermittent fasting appears an equivalent alternative to calorie restriction (CR) to improve health in humans. However, few trials have considered applying meal timing during the 'fasting' day, which may be a limitation. We developed a novel intermittent fasting plus early time-restricted eating (iTRE) approach. Adults (N = 209, 58 ± 10 years, 34.8 ± 4.7 kg m-2) at increased risk of developing type 2 diabetes were randomized to one of three groups (2:2:1): iTRE (30% energy requirements between 0800 and 1200 hours and followed by a 20-h fasting period on three nonconsecutive days per week, and ad libitum eating on other days); CR (70% of energy requirements daily, without time prescription); or standard care (weight loss booklet). This open-label, parallel group, three-arm randomized controlled trial provided nutritional support to participants in the iTRE and CR arms for 6 months, with an additional 12-month follow-up. The primary outcome was change in glucose area under the curve in response to a mixed-meal tolerance test at month 6 in iTRE versus CR. Glucose tolerance was improved to a greater extent in iTRE compared with CR (-10.10 (95% confidence interval -14.08, -6.11) versus -3.57 (95% confidence interval -7.72, 0.57) mg dl-1 min-1; P = 0.03) at month 6, but these differences were lost at month 18. Adverse events were transient and generally mild. Reports of fatigue were higher in iTRE versus CR and standard care, whereas reports of constipation and headache were higher in iTRE and CR versus standard care. In conclusion, incorporating advice for meal timing with prolonged fasting led to greater improvements in postprandial glucose metabolism in adults at increased risk of developing type 2 diabetes. ClinicalTrials.gov identifier NCT03689608 .
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Affiliation(s)
- Xiao Tong Teong
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Lifelong Health Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Kai Liu
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Lifelong Health Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Andrew D Vincent
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Lifelong Health Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Julien Bensalem
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Lifelong Health Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Bo Liu
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Lifelong Health Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Kathryn J Hattersley
- Lifelong Health Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Lijun Zhao
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Lifelong Health Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | | | - Timothy J Sargeant
- Lifelong Health Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Gary A Wittert
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Lifelong Health Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Amy T Hutchison
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Lifelong Health Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Leonie K Heilbronn
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia.
- Lifelong Health Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.
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