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Article ; Online: Isolation of Mitochondria from Mouse Tissues for Functional Analysis.

Acín-Pérez, Rebeca / Montales, Katrina P / Nguyen, Kaitlyn B / Brownstein, Alexandra J / Stiles, Linsey / Divakaruni, Ajit S

Methods in molecular biology (Clifton, N.J.)

2023 Volume 2675, Page(s) 77–96

Abstract: Methods for isolating mitochondria from different rodent tissues have been established for decades. Although the general principles for crude mitochondrial preparations are largely shared across tissues - tissue disruption followed by differential ... ...

Abstract	Methods for isolating mitochondria from different rodent tissues have been established for decades. Although the general principles for crude mitochondrial preparations are largely shared across tissues - tissue disruption followed by differential centrifugation - critical differences exist for isolation from different tissues to optimize mitochondrial yield and function. This protocol offers a unified resource for preparations of isolated mitochondria from mouse liver, kidney, heart, brain, skeletal muscle, and brown and white adipose tissue suitable for functional analysis.
MeSH term(s)	Mice ; Animals ; Mitochondria ; Adipose Tissue, White/metabolism ; Muscle, Skeletal/metabolism ; Mitochondria, Muscle/metabolism
Language	English
Publishing date	2023-05-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-3247-5_7
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Mitochondria isolated from lipid droplets of white adipose tissue reveal functional differences based on lipid droplet size.

Brownstein, Alexandra J / Veliova, Michaela / Acin-Perez, Rebeca / Villalobos, Frankie / Petcherski, Anton / Tombolato, Alberto / Liesa, Marc / Shirihai, Orian S

Life science alliance

2023 Volume 7, Issue 2

Abstract: Recent studies in brown adipose tissue (BAT) described a unique subpopulation of mitochondria bound to lipid droplets (LDs), which were termed PeriDroplet Mitochondria (PDM). PDM can be isolated from BAT by differential centrifugation and salt washes. ... ...

Abstract	Recent studies in brown adipose tissue (BAT) described a unique subpopulation of mitochondria bound to lipid droplets (LDs), which were termed PeriDroplet Mitochondria (PDM). PDM can be isolated from BAT by differential centrifugation and salt washes. Contrary to BAT, this approach has so far not led to the successful isolation of PDM from white adipose tissue (WAT). Here, we developed a method to isolate PDM from WAT with high yield and purity by an optimized proteolytic treatment that preserves the respiratory function of mitochondria. Using this approach, we show that, contrary to BAT, WAT PDM have lower respiratory and ATP synthesis capacities compared with WAT cytoplasmic mitochondria (CM). Furthermore, by isolating PDM from LDs of different sizes, we found a negative correlation between LD size and the respiratory capacity of their PDM in WAT. Thus, our new isolation method reveals tissue-specific characteristics of PDM and establishes the existence of heterogeneity in PDM function determined by LD size.
MeSH term(s)	Lipid Droplets/metabolism ; Energy Metabolism ; Adipose Tissue, White/metabolism ; Adipose Tissue, Brown/metabolism ; Mitochondria/metabolism
Language	English
Publishing date	2023-12-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2575-1077
ISSN (online)	2575-1077
DOI	10.26508/lsa.202301934
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Article: Analyzing electron transport chain supercomplexes.

Acín-Pérez, Rebeca / Hernansanz-Agustín, Pablo / Enríquez, José Antonio

Methods in cell biology

2020 Volume 155, Page(s) 181–197

Abstract: This review focuses on three independent and complementary approaches to obtain information on the combined function of respiratory complexes when present in different structural situations, either as individual complexes or when superassembled with ... ...

Abstract	This review focuses on three independent and complementary approaches to obtain information on the combined function of respiratory complexes when present in different structural situations, either as individual complexes or when superassembled with other complexes. We review the utility of in-gel activity after blue native electrophoresis, integrated oxygen consumption of supercomplexes containing complex IV, and spectrophotometric activity measurements.
MeSH term(s)	Cytological Techniques/methods ; Electron Transport ; Electron Transport Chain Complex Proteins/metabolism ; Electrophoresis, Polyacrylamide Gel ; Oxygen Consumption
Chemical Substances	Electron Transport Chain Complex Proteins
Language	English
Publishing date	2020-02-27
Publishing country	United States
Document type	Journal Article
ISSN	0091-679X
ISSN	0091-679X
DOI	10.1016/bs.mcb.2019.12.002
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Article: Utilization of Human Samples for Assessment of Mitochondrial Bioenergetics: Gold Standards, Limitations, and Future Perspectives.

Acin-Perez, Rebeca / Benincá, Cristiane / Shabane, Byourak / Shirihai, Orian S / Stiles, Linsey

Life (Basel, Switzerland)

2021 Volume 11, Issue 9

Abstract: Mitochondrial bioenergetic function is a central component of cellular metabolism in health and disease. Mitochondrial oxidative phosphorylation is critical for maintaining energetic homeostasis, and impairment of mitochondrial function underlies the ... ...

Abstract	Mitochondrial bioenergetic function is a central component of cellular metabolism in health and disease. Mitochondrial oxidative phosphorylation is critical for maintaining energetic homeostasis, and impairment of mitochondrial function underlies the development and progression of metabolic diseases and aging. However, measurement of mitochondrial bioenergetic function can be challenging in human samples due to limitations in the size of the collected sample. Furthermore, the collection of samples from human cohorts is often spread over multiple days and locations, which makes immediate sample processing and bioenergetics analysis challenging. Therefore, sample selection and choice of tests should be carefully considered. Basic research, clinical trials, and mitochondrial disease diagnosis rely primarily on skeletal muscle samples. However, obtaining skeletal muscle biopsies requires an appropriate clinical setting and specialized personnel, making skeletal muscle a less suitable tissue for certain research studies. Circulating white blood cells and platelets offer a promising primary tissue alternative to biopsies for the study of mitochondrial bioenergetics. Recent advances in frozen respirometry protocols combined with the utilization of minimally invasive and non-invasive samples may provide promise for future mitochondrial research studies in humans. Here we review the human samples commonly used for the measurement of mitochondrial bioenergetics with a focus on the advantages and limitations of each sample.
Language	English
Publishing date	2021-09-10
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2662250-6
ISSN	2075-1729
ISSN	2075-1729
DOI	10.3390/life11090949
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Article ; Online: ATP-consuming futile cycles as energy dissipating mechanisms to counteract obesity.

Brownstein, Alexandra J / Veliova, Michaela / Acin-Perez, Rebeca / Liesa, Marc / Shirihai, Orian S

Reviews in endocrine & metabolic disorders

2021 Volume 23, Issue 1, Page(s) 121–131

Abstract: Obesity results from an imbalance in energy homeostasis, whereby excessive energy intake exceeds caloric expenditure. Energy can be dissipated out of an organism by producing heat (thermogenesis), explaining the long-standing interest in exploiting ... ...

Abstract	Obesity results from an imbalance in energy homeostasis, whereby excessive energy intake exceeds caloric expenditure. Energy can be dissipated out of an organism by producing heat (thermogenesis), explaining the long-standing interest in exploiting thermogenic processes to counteract obesity. Mitochondrial uncoupling is a process that expends energy by oxidizing nutrients to produce heat, instead of ATP synthesis. Energy can also be dissipated through mechanisms that do not involve mitochondrial uncoupling. Such mechanisms include futile cycles described as metabolic reactions that consume ATP to produce a product from a substrate but then converting the product back into the original substrate, releasing the energy as heat. Energy dissipation driven by cellular ATP demand can be regulated by adjusting the speed and number of futile cycles. Energy consuming futile cycles that are reviewed here are lipolysis/fatty acid re-esterification cycle, creatine/phosphocreatine cycle, and the SERCA-mediated calcium import and export cycle. Their reliance on ATP emphasizes that mitochondrial oxidative function coupled to ATP synthesis, and not just uncoupling, can play a role in thermogenic energy dissipation. Here, we review ATP consuming futile cycles, the evidence for their function in humans, and their potential employment as a strategy to dissipate energy and counteract obesity.
MeSH term(s)	Adenosine Triphosphate/metabolism ; Adipose Tissue, Brown/metabolism ; Energy Metabolism ; Humans ; Obesity/metabolism ; Substrate Cycling ; Thermogenesis
Chemical Substances	Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2021-11-06
Publishing country	Germany
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	2185718-0
ISSN	1573-2606 ; 1389-9155
ISSN (online)	1573-2606
ISSN	1389-9155
DOI	10.1007/s11154-021-09690-w
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Article ; Online: How Mitochondrial Metabolism Contributes to Macrophage Phenotype and Functions.

Benmoussa, Khaddouj / Garaude, Johan / Acín-Pérez, Rebeca

Journal of molecular biology

2018 Volume 430, Issue 21, Page(s) 3906–3921

Abstract: Metabolic reprogramming of cells from the innate immune system is one of the most noteworthy topics in immunological research nowadays. Upon infection or tissue damage, innate immune cells, such as macrophages, mobilize various immune and metabolic ... ...

Abstract	Metabolic reprogramming of cells from the innate immune system is one of the most noteworthy topics in immunological research nowadays. Upon infection or tissue damage, innate immune cells, such as macrophages, mobilize various immune and metabolic signals to mount a response best suited to eradicate the threat. Current data indicate that both the immune and metabolic responses are closely interconnected. On account of its peculiar position in regulating both of these processes, the mitochondrion has emerged as a critical organelle that orchestrates the coordinated metabolic and immune adaptations in macrophages. Significant effort is now underway to understand how metabolic features of differentiated macrophages regulate their immune specificities with the eventual goal to manipulate cellular metabolism to control immunity. In this review, we highlight some of the recent work that place cellular and mitochondrial metabolism in a central position in the macrophage differentiation program.
MeSH term(s)	Animals ; Biomarkers ; Energy Metabolism ; Host-Pathogen Interactions/immunology ; Humans ; Immune System/cytology ; Immune System/immunology ; Immune System/metabolism ; Immunity, Innate ; Macrophage Activation/immunology ; Macrophages/immunology ; Macrophages/metabolism ; Mitochondria/metabolism ; Oxidation-Reduction ; Phenotype ; Signal Transduction
Chemical Substances	Biomarkers
Language	English
Publishing date	2018-07-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2018.07.003
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Article: How Mitochondrial Metabolism Contributes to Macrophage Phenotype and Functions

Benmoussa, Khaddouj / Garaude, Johan / Acín-Pérez, Rebeca

Journal of molecular biology. 2018 Oct. 19, v. 430, no. 21

2018

Abstract	Metabolic reprogramming of cells from the innate immune system is one of the most noteworthy topics in immunological research nowadays. Upon infection or tissue damage, innate immune cells, such as macrophages, mobilize various immune and metabolic signals to mount a response best suited to eradicate the threat. Current data indicate that both the immune and metabolic responses are closely interconnected. On account of its peculiar position in regulating both of these processes, the mitochondrion has emerged as a critical organelle that orchestrates the coordinated metabolic and immune adaptations in macrophages. Significant effort is now underway to understand how metabolic features of differentiated macrophages regulate their immune specificities with the eventual goal to manipulate cellular metabolism to control immunity. In this review, we highlight some of the recent work that place cellular and mitochondrial metabolism in a central position in the macrophage differentiation program.
Keywords	biochemical pathways ; innate immunity ; macrophages ; metabolism ; mitochondria ; phenotype
Language	English
Dates of publication	2018-1019
Size	p. 3906-3921.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2018.07.003
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A novel approach to measure complex V ATP hydrolysis in frozen cell lysates and tissue homogenates.

Fernandez-Del-Rio, Lucia / Benincá, Cristiane / Villalobos, Frankie / Shu, Cynthia / Stiles, Linsey / Liesa, Marc / Divakaruni, Ajit S / Acin-Perez, Rebeca / Shirihai, Orian S

Life science alliance

2023 Volume 6, Issue 4

Abstract: Mitochondrial depolarization can initiate reversal activity of ATP synthase, depleting ATP by its hydrolysis. We have recently shown that increased ATP hydrolysis contributes to ATP depletion leading to a maladaptation in mitochondrial disorders, where ... ...

Abstract	Mitochondrial depolarization can initiate reversal activity of ATP synthase, depleting ATP by its hydrolysis. We have recently shown that increased ATP hydrolysis contributes to ATP depletion leading to a maladaptation in mitochondrial disorders, where maximal hydrolytic capacity per CV content is increasing. However, despite its importance, ATP hydrolysis is not a commonly studied parameter because of the limitations of the currently available methods. Methods that measure CV hydrolytic activity indirectly require the isolation of mitochondria and involve the introduction of detergents, preventing their utilization in clinical studies or any high-throughput analyses. Here, we describe a novel approach to assess maximal ATP hydrolytic capacity and maximal respiratory capacity in a single assay in cell lysates, PBMCs, and tissue homogenates that were previously frozen. The methodology described here has the potential to be used in clinical samples to determine adaptive and maladaptive adjustments of CV function in diseases, with the added benefit of being able to use frozen samples in a high-throughput manner and to explore ATP hydrolysis as a drug target for disease treatment.
MeSH term(s)	Hydrolysis ; Adenosine Triphosphate ; Mitochondrial Proton-Translocating ATPases/metabolism ; Mitochondria/metabolism
Chemical Substances	oligomycin sensitivity-conferring protein (EC 7.1.2.2) ; Adenosine Triphosphate (8L70Q75FXE) ; Mitochondrial Proton-Translocating ATPases (EC 3.6.3.-)
Language	English
Publishing date	2023-03-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ISSN	2575-1077
ISSN (online)	2575-1077
DOI	10.26508/lsa.202201628
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Article ; Online: Mitochondrial Health in Aging and Age-Related Metabolic Disease.

Sebastián, David / Acín-Pérez, Rebeca / Morino, Katsutaro

Oxidative medicine and cellular longevity

2016 Volume 2016, Page(s) 5831538

MeSH term(s)	Aging/metabolism ; Antioxidants/metabolism ; Energy Metabolism ; Health ; Humans ; Metabolic Diseases/metabolism ; Mitochondria/metabolism ; Nerve Degeneration/metabolism ; Nerve Degeneration/pathology
Chemical Substances	Antioxidants
Language	English
Publishing date	2016
Publishing country	United States
Document type	Editorial ; Introductory Journal Article
ISSN	1942-0994
ISSN (online)	1942-0994
DOI	10.1155/2016/5831538
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Article: Impaired AMPK Control of Alveolar Epithelial Cell Metabolism Promotes Pulmonary Fibrosis.

bioRxiv : the preprint server for biology

2024

Abstract: Alveolar epithelial type II (AT2) cell dysfunction is implicated in the pathogenesis of familial and sporadic idiopathic pulmonary fibrosis (IPF). We previously described that expression of an AT2 cell exclusive disease-associated protein isoform (SP- ... ...

Abstract	Alveolar epithelial type II (AT2) cell dysfunction is implicated in the pathogenesis of familial and sporadic idiopathic pulmonary fibrosis (IPF). We previously described that expression of an AT2 cell exclusive disease-associated protein isoform (SP-CI73T) in murine and patient-specific induced pluripotent stem cell (iPSC)-derived AT2 cells leads to a block in late macroautophagy and promotes time-dependent mitochondrial impairments; however, how a metabolically dysfunctional AT2 cell results in fibrosis remains elusive. Here using murine and human iPSC-derived AT2 cell models expressing SP-CI73T, we characterize the molecular mechanisms governing alterations in AT2 cell metabolism that lead to increased glycolysis, decreased mitochondrial biogenesis, disrupted fatty acid oxidation, accumulation of impaired mitochondria, and diminished AT2 cell progenitor capacity manifesting as reduced AT2 self-renewal and accumulation of transitional epithelial cells. We identify deficient AMP-kinase signaling as a key upstream signaling hub driving disease in these dysfunctional AT2 cells and augment this pathway to restore alveolar epithelial metabolic function, thus successfully alleviating lung fibrosis in vivo.
Language	English
Publishing date	2024-03-28
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.03.26.586649
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