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Bhavani SV, Xiong L, Pius A, Semler M, Qian ET, Verhoef PA, Robichaux C, Coopersmith CM, Churpek MM. Comparison of time series clustering methods for identifying novel subphenotypes of patients with infection. J Am Med Inform Assoc 2023; 30:1158-1166. [PMID: 37043759 PMCID: PMC10198539 DOI: 10.1093/jamia/ocad063] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/06/2023] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
OBJECTIVE Severe infection can lead to organ dysfunction and sepsis. Identifying subphenotypes of infected patients is essential for personalized management. It is unknown how different time series clustering algorithms compare in identifying these subphenotypes. MATERIALS AND METHODS Patients with suspected infection admitted between 2014 and 2019 to 4 hospitals in Emory healthcare were included, split into separate training and validation cohorts. Dynamic time warping (DTW) was applied to vital signs from the first 8 h of hospitalization, and hierarchical clustering (DTW-HC) and partition around medoids (DTW-PAM) were used to cluster patients into subphenotypes. DTW-HC, DTW-PAM, and a previously published group-based trajectory model (GBTM) were evaluated for agreement in subphenotype clusters, trajectory patterns, and subphenotype associations with clinical outcomes and treatment responses. RESULTS There were 12 473 patients in training and 8256 patients in validation cohorts. DTW-HC, DTW-PAM, and GBTM models resulted in 4 consistent vitals trajectory patterns with significant agreement in clustering (71-80% agreement, P < .001): group A was hyperthermic, tachycardic, tachypneic, and hypotensive. Group B was hyperthermic, tachycardic, tachypneic, and hypertensive. Groups C and D had lower temperatures, heart rates, and respiratory rates, with group C normotensive and group D hypotensive. Group A had higher odds ratio of 30-day inpatient mortality (P < .01) and group D had significant mortality benefit from balanced crystalloids compared to saline (P < .01) in all 3 models. DISCUSSION DTW- and GBTM-based clustering algorithms applied to vital signs in infected patients identified consistent subphenotypes with distinct clinical outcomes and treatment responses. CONCLUSION Time series clustering with distinct computational approaches demonstrate similar performance and significant agreement in the resulting subphenotypes.
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Affiliation(s)
- Sivasubramanium V Bhavani
- Department of Medicine, Emory University, Atlanta, Georgia, USA
- Emory Critical Care Center, Atlanta, Georgia, USA
| | - Li Xiong
- Department of Computer Science, Emory University, Atlanta, Georgia, USA
| | - Abish Pius
- Department of Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Matthew Semler
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Edward T Qian
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Philip A Verhoef
- Department of Medicine, University of Hawaii John A. Burns School of Medicine, Honolulu, Hawaii, USA
- Hawaii Permanente Medical Group, Honolulu, Hawaii, USA
| | - Chad Robichaux
- Department of Biomedical Informatics, Emory University, Atlanta, Georgia, USA
| | - Craig M Coopersmith
- Emory Critical Care Center, Atlanta, Georgia, USA
- Department of Surgery, Emory University, Atlanta, Georgia, USA
| | - Matthew M Churpek
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin, USA
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2
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Sahu A, Clemens ZJ, Shinde SN, Sivakumar S, Pius A, Bhatia A, Picciolini S, Carlomagno C, Gualerzi A, Bedoni M, Van Houten B, Lovalekar M, Fitz NF, Lefterov I, Barchowsky A, Koldamova R, Ambrosio F. Regulation of aged skeletal muscle regeneration by circulating extracellular vesicles. Nat Aging 2021; 1:1148-1161. [PMID: 35665306 PMCID: PMC9165723 DOI: 10.1038/s43587-021-00143-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 10/27/2021] [Indexed: 12/21/2022]
Abstract
Heterochronic blood exchange (HBE) has demonstrated that circulating factors restore youthful features to aged tissues. However, the systemic mediators of those rejuvenating effects remain poorly defined. We show here that the beneficial effect of young blood on aged muscle regeneration was diminished when serum was depleted of extracellular vesicles (EVs). Whereas EVs from young animals rejuvenate aged cell bioenergetics and skeletal muscle regeneration, aging shifts EV subpopulation heterogeneity and compromises downstream benefits on recipient cells. Machine learning classifiers revealed that aging shifts the nucleic acid, but not protein, fingerprint of circulating EVs. Alterations in sub-population heterogeneity were accompanied by declines in transcript levels of the pro-longevity protein, α-Klotho, and injection of EVs improved muscle regeneration in a Klotho mRNA-dependent manner. These studies demonstrate that EVs play a key role in the rejuvenating effects of HBE and that Klotho transcripts within EVs phenocopy the effects of young serum on aged skeletal muscle.
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Affiliation(s)
- Amrita Sahu
- Department of Physical Medicine & Rehabilitation, University of Pittsburgh, Pittsburgh, PA
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA
| | - Zachary J. Clemens
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA
| | - Sunita N. Shinde
- Department of Physical Medicine & Rehabilitation, University of Pittsburgh, Pittsburgh, PA
| | - Sruthi Sivakumar
- Department of Physical Medicine & Rehabilitation, University of Pittsburgh, Pittsburgh, PA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA
| | - Abish Pius
- Department of Physical Medicine & Rehabilitation, University of Pittsburgh, Pittsburgh, PA
- Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh PA
| | - Ankit Bhatia
- Robotics Institute, Carnegie Mellon University, Pittsburgh, PA
| | - Silvia Picciolini
- Laboratory of Nanomedicine and Clinical Biophotonics (LABION), IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy
| | - Cristiano Carlomagno
- Laboratory of Nanomedicine and Clinical Biophotonics (LABION), IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy
| | - Alice Gualerzi
- Laboratory of Nanomedicine and Clinical Biophotonics (LABION), IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy
| | - Marzia Bedoni
- Laboratory of Nanomedicine and Clinical Biophotonics (LABION), IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy
| | - Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA
| | - Mita Lovalekar
- Department of Sports Medicine and Nutrition, School of Health and Rehabilitation Sciences, University of Pittsburgh, Pittsburgh PA
| | - Nicholas F. Fitz
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA
| | - Iliya Lefterov
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA
| | - Aaron Barchowsky
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA
| | - Radosveta Koldamova
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA
| | - Fabrisia Ambrosio
- Department of Physical Medicine & Rehabilitation, University of Pittsburgh, Pittsburgh, PA
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA
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3
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Clemens Z, Sivakumar S, Pius A, Sahu A, Shinde S, Mamiya H, Luketich N, Cui J, Dixit P, Hoeck JD, Kreuz S, Franti M, Barchowsky A, Ambrosio F. The biphasic and age-dependent impact of klotho on hallmarks of aging and skeletal muscle function. eLife 2021; 10:e61138. [PMID: 33876724 PMCID: PMC8118657 DOI: 10.7554/elife.61138] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 04/06/2021] [Indexed: 12/15/2022] Open
Abstract
Aging is accompanied by disrupted information flow, resulting from accumulation of molecular mistakes. These mistakes ultimately give rise to debilitating disorders including skeletal muscle wasting, or sarcopenia. To derive a global metric of growing 'disorderliness' of aging muscle, we employed a statistical physics approach to estimate the state parameter, entropy, as a function of genes associated with hallmarks of aging. Escalating network entropy reached an inflection point at old age, while structural and functional alterations progressed into oldest-old age. To probe the potential for restoration of molecular 'order' and reversal of the sarcopenic phenotype, we systemically overexpressed the longevity protein, Klotho, via AAV. Klotho overexpression modulated genes representing all hallmarks of aging in old and oldest-old mice, but pathway enrichment revealed directions of changes were, for many genes, age-dependent. Functional improvements were also age-dependent. Klotho improved strength in old mice, but failed to induce benefits beyond the entropic tipping point.
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Affiliation(s)
- Zachary Clemens
- Department of Physical Medicine & Rehabilitation, University of PittsburghPittsburghUnited States
- Department of Environmental and Occupational Health, University of PittsburghPittsburghUnited States
| | - Sruthi Sivakumar
- Department of Physical Medicine & Rehabilitation, University of PittsburghPittsburghUnited States
- Department of Bioengineering, University of PittsburghPittsburghUnited States
| | - Abish Pius
- Department of Physical Medicine & Rehabilitation, University of PittsburghPittsburghUnited States
- Department of Computational & Systems Biology, School of Medicine, University of PittsburghPittsburghUnited States
| | - Amrita Sahu
- Department of Physical Medicine & Rehabilitation, University of PittsburghPittsburghUnited States
| | - Sunita Shinde
- Department of Physical Medicine & Rehabilitation, University of PittsburghPittsburghUnited States
| | - Hikaru Mamiya
- Department of Bioengineering, University of PittsburghPittsburghUnited States
| | - Nathaniel Luketich
- Department of Bioengineering, University of PittsburghPittsburghUnited States
| | - Jian Cui
- Department of Computational & Systems Biology, School of Medicine, University of PittsburghPittsburghUnited States
| | - Purushottam Dixit
- Department of Physics, University of FloridaGainesvilleUnited States
| | - Joerg D Hoeck
- Department of Research Beyond Borders, Regenerative Medicine, Boehringer Ingelheim Pharmaceuticals, IncRheinGermany
| | - Sebastian Kreuz
- Department of Research Beyond Borders, Regenerative Medicine, Boehringer Ingelheim Pharmaceuticals, IncRheinGermany
| | - Michael Franti
- Department of Research Beyond Borders, Regenerative Medicine, Boehringer Ingelheim Pharmaceuticals, IncRheinGermany
| | - Aaron Barchowsky
- Department of Environmental and Occupational Health, University of PittsburghPittsburghUnited States
| | - Fabrisia Ambrosio
- Department of Physical Medicine & Rehabilitation, University of PittsburghPittsburghUnited States
- Department of Environmental and Occupational Health, University of PittsburghPittsburghUnited States
- Department of Bioengineering, University of PittsburghPittsburghUnited States
- McGowan Institute for Regenerative Medicine, University of PittsburghPittsburghUnited States
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4
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Sachdev U, Ferrari R, Cui X, Pius A, Sahu A, Reynolds M, Liao H, Sun P, Shinde S, Ambrosio F, Shiva S, Loughran P, Scott M. Caspase1/11 signaling affects muscle regeneration and recovery following ischemia, and can be modulated by chloroquine. Mol Med 2020; 26:69. [PMID: 32641037 PMCID: PMC7341481 DOI: 10.1186/s10020-020-00190-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/19/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND We previously showed that the autophagy inhibitor chloroquine (CQ) increases inflammatory cleaved caspase-1 activity in myocytes, and that caspase-1/11 is protective in sterile liver injury. However, the role of caspase-1/11 in the recovery of muscle from ischemia caused by peripheral arterial disease is unknown. We hypothesized that caspase-1/11 mediates recovery in muscle via effects on autophagy and this is modulated by CQ. METHODS C57Bl/6 J (WT) and caspase-1/11 double-knockout (KO) mice underwent femoral artery ligation (a model of hind-limb ischemia) with or without CQ (50 mg/kg IP every 2nd day). CQ effects on autophagosome formation, microtubule associated protein 1A/1B-light chain 3 (LC3), and caspase-1 expression was measured using electron microscopy and immunofluorescence. Laser Doppler perfusion imaging documented perfusion every 7 days. After 21 days, in situ physiologic testing in tibialis anterior muscle assessed peak force contraction, and myocyte size and fibrosis was also measured. Muscle satellite cell (MuSC) oxygen consumption rate (OCR) and extracellular acidification rate was measured. Caspase-1 and glycolytic enzyme expression was detected by Western blot. RESULTS CQ increased autophagosomes, LC3 consolidation, total caspase-1 expression and cleaved caspase-1 in muscle. Perfusion, fibrosis, myofiber regeneration, muscle contraction, MuSC fusion, OCR, ECAR and glycolytic enzyme expression was variably affected by CQ depending on presence of caspase-1/11. CQ decreased perfusion recovery, fibrosis and myofiber size in WT but not caspase-1/11KO mice. CQ diminished peak force in whole muscle, and myocyte fusion in MuSC and these effects were exacerbated in caspase-1/11KO mice. CQ reductions in maximal respiration and ATP production were reduced in caspase-1/11KO mice. Caspase-1/11KO MuSC had significant increases in protein kinase isoforms and aldolase with decreased ECAR. CONCLUSION Caspase-1/11 signaling affects the response to ischemia in muscle and effects are variably modulated by CQ. This may be critically important for disease treated with CQ and its derivatives, including novel viral diseases (e.g. COVID-19) that are expected to affect patients with comorbidities like cardiovascular disease.
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Affiliation(s)
- Ulka Sachdev
- Division of Vascular Surgery; Department of Surgery, University of Pittsburgh Medical Center, Magee Women's Hospital, 200 Lothrop Street, Pittsburgh, PA, 15213, USA.
| | - Ricardo Ferrari
- Division of Vascular Surgery; Department of Surgery, University of Pittsburgh Medical Center, Magee Women's Hospital, 200 Lothrop Street, Pittsburgh, PA, 15213, USA
| | - Xiangdong Cui
- Division of Vascular Surgery; Department of Surgery, University of Pittsburgh Medical Center, Magee Women's Hospital, 200 Lothrop Street, Pittsburgh, PA, 15213, USA
| | - Abish Pius
- McGowan Institute for Regenerative Medicine, University of Pittsburgh Medical Center, Bridgeside Point, Pittsburgh, PA, 15213, USA
| | - Amrita Sahu
- McGowan Institute for Regenerative Medicine, University of Pittsburgh Medical Center, Bridgeside Point, Pittsburgh, PA, 15213, USA
| | - Michael Reynolds
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Medical Center, Biomedical Sciences Towe, Pittsburgh, PA, 15213, USA
| | - Hong Liao
- Division of Vascular Surgery; Department of Surgery, University of Pittsburgh Medical Center, Magee Women's Hospital, 200 Lothrop Street, Pittsburgh, PA, 15213, USA
| | - Ping Sun
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.,Department of Surgery 11/20/2018-11/19/202, Visiting scholar, University of Pittsburgh, Pittsburgh, USA
| | - Sunita Shinde
- McGowan Institute for Regenerative Medicine, University of Pittsburgh Medical Center, Bridgeside Point, Pittsburgh, PA, 15213, USA
| | - Fabrisia Ambrosio
- McGowan Institute for Regenerative Medicine, University of Pittsburgh Medical Center, Bridgeside Point, Pittsburgh, PA, 15213, USA
| | - Sruti Shiva
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Medical Center, Biomedical Sciences Towe, Pittsburgh, PA, 15213, USA
| | - Patricia Loughran
- Center for Biologic Imaging (CBI), University of Pittsburgh Medical Center, Biomedical Sciences Tower, Pittsburgh, PA, 15213, USA
| | - Melanie Scott
- Division of Vascular Surgery; Department of Surgery, University of Pittsburgh Medical Center, Magee Women's Hospital, 200 Lothrop Street, Pittsburgh, PA, 15213, USA
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5
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Cheikhi A, Barchowsky A, Sahu A, Shinde SN, Pius A, Clemens ZJ, Li H, Kennedy CA, Hoeck JD, Franti M, Ambrosio F. Klotho: An Elephant in Aging Research. J Gerontol A Biol Sci Med Sci 2020; 74:1031-1042. [PMID: 30843026 DOI: 10.1093/gerona/glz061] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Indexed: 12/12/2022] Open
Abstract
The year 2017 marked the 20th anniversary of the first publication describing Klotho. This single protein was and is remarkable in that its absence in mice conferred an accelerated aging, or progeroid, phenotype with a dramatically shortened life span. On the other hand, genetic overexpression extended both health span and life span by an impressive 30%. Not only has Klotho deficiency been linked to a number of debilitating age-related illnesses but many subsequent reports have lent credence to the idea that Klotho can compress the period of morbidity and extend the life span of both model organisms and humans. This suggests that Klotho functions as an integrator of organ systems, making it both a promising tool for advancing our understanding of the biology of aging and an intriguing target for interventional studies. In this review, we highlight advances in our understanding of Klotho as well as key challenges that have somewhat limited our view, and thus translational potential, of this potent protein.
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Affiliation(s)
- Amin Cheikhi
- Department of Physical Medicine and Rehabilitation, University of Pittsburgh.,Division of Geriatric Medicine, Department of Medicine, University of Pittsburgh
| | - Aaron Barchowsky
- Department of Environmental and Occupational Health, University of Pittsburgh.,Department of Pharmacology and Chemical Biology, University of Pittsburgh
| | - Amrita Sahu
- Department of Physical Medicine and Rehabilitation, University of Pittsburgh.,Department of Environmental and Occupational Health, University of Pittsburgh
| | - Sunita N Shinde
- Department of Physical Medicine and Rehabilitation, University of Pittsburgh
| | - Abish Pius
- Department of Physical Medicine and Rehabilitation, University of Pittsburgh
| | - Zachary J Clemens
- Department of Physical Medicine and Rehabilitation, University of Pittsburgh
| | - Hua Li
- Department of Biotherapeutics Discovery, Research Division, Boehringer Ingelheim Pharmaceuticals, Inc. Ridgefield, Connecticut
| | - Charles A Kennedy
- Department of Research Beyond Borders, Regenerative Medicine, Boehringer Ingelheim Pharmaceuticals, Inc. Ridgefield, Connecticut
| | - Joerg D Hoeck
- Department of Research Beyond Borders, Regenerative Medicine, Boehringer Ingelheim Pharmaceuticals, Inc. Ridgefield, Connecticut
| | - Michael Franti
- Department of Research Beyond Borders, Regenerative Medicine, Boehringer Ingelheim Pharmaceuticals, Inc. Ridgefield, Connecticut
| | - Fabrisia Ambrosio
- Department of Physical Medicine and Rehabilitation, University of Pittsburgh.,Department of Environmental and Occupational Health, University of Pittsburgh.,Department of Bioengineering, University of Pittsburgh, Pennsylvania.,McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pennsylvania
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Tansir G, Kumar P, Pius A, Sunny S, Soneja M. Pseudo-pseudo Meigs’ syndrome: a rare presentation of systemic lupus erythematosus. Reumatismo 2019; 71:108-112. [DOI: 10.4081/reumatismo.2019.1140] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 09/06/2018] [Indexed: 12/25/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic inflammatory multisystem autoimmune disease. Ascites when associated with pleural effusion and raised CA-125 levels in SLE patient, is known as pseudo-pseudo Meigs’ syndrome (PPMS). This is the case of a 22-year-old lady who presented with complaints of abdominal distension for one month and had a history of spontaneous abortion in the past. Abdominal imaging did not reveal any tumor and after extensive workup a diagnosis of PPMS was made. She was successfully treated with steroids, hydroxychloroquine and cyclophosphamide.
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