1
|
Delli Paoli G, van de Laarschot D, Friesema ECH, Verkaik R, Giacco A, Senese R, Arp PP, Jhamai PM, Pagnotta SM, Broer L, Uitterlinden AG, Lanni A, Zillikens MC, de Lange P. Short-Term, Combined Fasting and Exercise Improves Body Composition in Healthy Males. Int J Sport Nutr Exerc Metab 2020; 30:386-395. [PMID: 32998111 DOI: 10.1123/ijsnem.2020-0058] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 01/12/2023]
Abstract
Fasting enhances the beneficial metabolic outcomes of exercise; however, it is unknown whether body composition is favorably modified on the short term. A baseline-follow-up study was carried out to assess the effect of an established protocol involving short-term combined exercise with fasting on body composition. One hundred seven recreationally exercising males underwent a 10-day intervention across 15 fitness centers in the Netherlands involving a 3-day gradual decrease of food intake, a 3-day period with extremely low caloric intake, and a gradual 4-day increase to initial caloric intake, with daily 30-min submaximal cycling. Using dual-energy X-ray absorptiometry analysis, all subjects substantially lost total body mass (-3.9 ± 1.9 kg; p < .001) and fat mass (-3.3 ± 1.3 kg; p < .001). Average lean mass was lost (-0.6 ± 1.5 kg; p < .001), but lean mass as a percentage of total body mass was not reduced. The authors observed a loss of -3.9 ± 1.9% android fat over total fat mass (p < .001), a loss of -2.2 ± 1.9% gynoid over total fat mass (p < .001), and reduced android/gynoid ratios (-0.05 ± 0.1; p < .001). Analyzing 15 preselected single-nucleotide polymorphisms in 13 metabolism-related genes revealed trending associations for thyroid state-related single-nucleotide polymorphisms rs225014 (deiodinase 2) and rs35767 (insulin-like growth factor1), and rs1053049 (PPARD). In conclusion, a short period of combined fasting and exercise leads to a substantial loss of body and fat mass without a loss of lean mass as a percentage of total mass.
Collapse
Affiliation(s)
- Giuseppe Delli Paoli
- Università degli Studi della Campania "Luigi Vanvitelli"
- European Consortium for Lifestyle, Exercise, Adaptation, and Nutrition (EULEAN)
| | - Denise van de Laarschot
- European Consortium for Lifestyle, Exercise, Adaptation, and Nutrition (EULEAN)
- Erasmus University Medical Center
| | - Edith C H Friesema
- European Consortium for Lifestyle, Exercise, Adaptation, and Nutrition (EULEAN)
- Erasmus University Medical Center
| | - Remco Verkaik
- European Consortium for Lifestyle, Exercise, Adaptation, and Nutrition (EULEAN)
- European Nutraceutical Services
| | - Antonia Giacco
- European Consortium for Lifestyle, Exercise, Adaptation, and Nutrition (EULEAN)
- Università degli Studi del Sannio
| | - Rosalba Senese
- Università degli Studi della Campania "Luigi Vanvitelli"
- European Consortium for Lifestyle, Exercise, Adaptation, and Nutrition (EULEAN)
| | | | | | | | | | - André G Uitterlinden
- European Consortium for Lifestyle, Exercise, Adaptation, and Nutrition (EULEAN)
- Erasmus University Medical Center
| | - Antonia Lanni
- Università degli Studi della Campania "Luigi Vanvitelli"
- European Consortium for Lifestyle, Exercise, Adaptation, and Nutrition (EULEAN)
| | - M Carola Zillikens
- European Consortium for Lifestyle, Exercise, Adaptation, and Nutrition (EULEAN)
- Erasmus University Medical Center
| | - Pieter de Lange
- Università degli Studi della Campania "Luigi Vanvitelli"
- European Consortium for Lifestyle, Exercise, Adaptation, and Nutrition (EULEAN)
| |
Collapse
|
2
|
Caruso FP, Garofano L, D'Angelo F, Yu K, Tang F, Yuan J, Zhang J, Cerulo L, Pagnotta SM, Bedognetti D, Sims PA, Suvà M, Su XD, Lasorella A, Iavarone A, Ceccarelli M. A map of tumor-host interactions in glioma at single-cell resolution. Gigascience 2020; 9:giaa109. [PMID: 33155039 PMCID: PMC7645027 DOI: 10.1093/gigascience/giaa109] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 03/30/2020] [Revised: 08/08/2020] [Accepted: 09/17/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Single-cell RNA sequencing is the reference technique for characterizing the heterogeneity of the tumor microenvironment. The composition of the various cell types making up the microenvironment can significantly affect the way in which the immune system activates cancer rejection mechanisms. Understanding the cross-talk signals between immune cells and cancer cells is of fundamental importance for the identification of immuno-oncology therapeutic targets. RESULTS We present a novel method, single-cell Tumor-Host Interaction tool (scTHI), to identify significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data. We apply our approach to uncover the ligand-receptor interactions in glioma using 6 publicly available human glioma datasets encompassing 57,060 gene expression profiles from 71 patients. By leveraging this large-scale collection we show that unexpected cross-talk partners are highly conserved across different datasets in the majority of the tumor samples. This suggests that shared cross-talk mechanisms exist in glioma. CONCLUSIONS Our results provide a complete map of the active tumor-host interaction pairs in glioma that can be therapeutically exploited to reduce the immunosuppressive action of the microenvironment in brain tumor.
Collapse
Affiliation(s)
- Francesca Pia Caruso
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples “Federico II”, Via Claudio 21, 80128 Naples, Italy
- Bioinformatics Lab, BIOGEM, Via Camporeale, 83031 Ariano Irpino, Italy
| | - Luciano Garofano
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples “Federico II”, Via Claudio 21, 80128 Naples, Italy
- Institute for Cancer Genetics, Columbia University, 1130 St Nicholas Ave, New York, NY 10032, USA
| | - Fulvio D'Angelo
- Bioinformatics Lab, BIOGEM, Via Camporeale, 83031 Ariano Irpino, Italy
- Institute for Cancer Genetics, Columbia University, 1130 St Nicholas Ave, New York, NY 10032, USA
| | - Kai Yu
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, 5 Yiheyuan Rd, Haidian District, 100871 Beijing, China
| | - Fuchou Tang
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, 5 Yiheyuan Rd, Haidian District, 100871 Beijing, China
| | - Jinzhou Yuan
- Department of Science and Technologies, Università degli Studi del Sannio, Via de Sanctis, 82100 Benevento, Italy
- Cancer Program, Sidra Medicine, Al Luqta Street, Zone 52, Education City, 26999, Doha Qatar
| | - Jing Zhang
- Institute for Cancer Genetics, Columbia University, 1130 St Nicholas Ave, New York, NY 10032, USA
| | - Luigi Cerulo
- Bioinformatics Lab, BIOGEM, Via Camporeale, 83031 Ariano Irpino, Italy
- Department of Science and Technologies, Università degli Studi del Sannio, Via de Sanctis, 82100 Benevento, Italy
| | - Stefano M Pagnotta
- Department of Science and Technologies, Università degli Studi del Sannio, Via de Sanctis, 82100 Benevento, Italy
| | - Davide Bedognetti
- Cancer Program, Sidra Medicine, Al Luqta Street, Zone 52, Education City, 26999, Doha Qatar
- Department of Internal Medicine and Medical Specialties (Di.M.I.), University of Genoa, Viale Benedetto XV 10, 16132 Genoa, Italy
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, 1130 St Nicholas Ave, New York , NY 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, 1130 St Nicholas Ave, New York, NY 10032, USA
| | - Mario Suvà
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, 55 Fruit St, Boston, MA 02114, USA
- Broad Institute of Harvard and MIT, 415 Main St, Cambridge, MA 02142, USA
| | - Xiao-Dong Su
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, 5 Yiheyuan Rd, Haidian District, 100871 Beijing, China
| | - Anna Lasorella
- Institute for Cancer Genetics, Columbia University, 1130 St Nicholas Ave, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, 1130 St Nicholas Ave, New York , NY 10032 USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University, 1130 St Nicholas Ave, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, 1130 St Nicholas Ave, New York , NY 10032 USA
- Department of Neurology, Columbia University Medical Center, 1130 St Nicholas Ave, New York, NY 10032, USA
| | - Michele Ceccarelli
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples “Federico II”, Via Claudio 21, 80128 Naples, Italy
- Bioinformatics Lab, BIOGEM, Via Camporeale, 83031 Ariano Irpino, Italy
| |
Collapse
|
3
|
Agnihotri S, Jalali S, Wilson MR, Danesh A, Li M, Klironomos G, Krieger JR, Mansouri A, Khan O, Mamatjan Y, Landon-Brace N, Tung T, Dowar M, Li T, Bruce JP, Burrell KE, Tonge PD, Alamsahebpour A, Krischek B, Agarwalla PK, Bi WL, Dunn IF, Beroukhim R, Fehlings MG, Bril V, Pagnotta SM, Iavarone A, Pugh TJ, Aldape KD, Zadeh G. The genomic landscape of schwannoma. Nat Genet 2016; 48:1339-1348. [PMID: 27723760 DOI: 10.1038/ng.3688] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 09/02/2016] [Indexed: 12/13/2022]
Abstract
Schwannomas are common peripheral nerve sheath tumors that can cause debilitating morbidities. We performed an integrative analysis to determine genomic aberrations common to sporadic schwannomas. Exome sequence analysis with validation by targeted DNA sequencing of 125 samples uncovered, in addition to expected NF2 disruption, recurrent mutations in ARID1A, ARID1B and DDR1. RNA sequencing identified a recurrent in-frame SH3PXD2A-HTRA1 fusion in 12/125 (10%) cases, and genomic analysis demonstrated the mechanism as resulting from a balanced 19-Mb chromosomal inversion on chromosome 10q. The fusion was associated with male gender predominance, occurring in one out of every six men with schwannoma. Methylation profiling identified distinct molecular subgroups of schwannomas that were associated with anatomical location. Expression of the SH3PXD2A-HTRA1 fusion resulted in elevated phosphorylated ERK, increased proliferation, increased invasion and in vivo tumorigenesis. Targeting of the MEK-ERK pathway was effective in fusion-positive Schwann cells, suggesting a possible therapeutic approach for this subset of tumors.
Collapse
MESH Headings
- Adaptor Proteins, Vesicular Transport/genetics
- Animals
- Cell Line, Tumor
- DNA Methylation
- DNA Mutational Analysis
- DNA, Neoplasm
- Ear Neoplasms/genetics
- Exome
- Female
- Gene Fusion
- Genome, Human
- High-Temperature Requirement A Serine Peptidase 1
- Humans
- Male
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Mutation
- Neurilemmoma/genetics
- RNA, Neoplasm
- Sequence Analysis, DNA
- Sequence Analysis, RNA
- Serine Endopeptidases/genetics
- Spinal Neoplasms/genetics
- Vestibule, Labyrinth
Collapse
Affiliation(s)
- Sameer Agnihotri
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shahrzad Jalali
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mark R Wilson
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Arnavaz Danesh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mira Li
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - George Klironomos
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jonathan R Krieger
- SPARC Biocentre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Alireza Mansouri
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Osaama Khan
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yasin Mamatjan
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Natalie Landon-Brace
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Takyee Tung
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mark Dowar
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Tiantian Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jeffrey P Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Kelly E Burrell
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Peter D Tonge
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Amir Alamsahebpour
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Boris Krischek
- Department of Neurosurgery, University Hospital of Cologne, Cologne Germany
| | - Pankaj Kumar Agarwalla
- Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Neurosurgery, Massachusetts General Hospital, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Wenya Linda Bi
- Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Ian F Dunn
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Rameen Beroukhim
- Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Michael G Fehlings
- Department of Neurosurgery, University Health Network, Toronto, Ontario, Canada
| | - Vera Bril
- Department of Medicine (Neurology), and the Elizabeth Raab Neurofibromatosis Program, University of Toronto, Toronto, Ontario, Canada
| | - Stefano M Pagnotta
- Department of Science and Technology, Università degli Studi del Sannio, Benevento, Italy
- Department of Pathology and Cell Biology and Neurology, Columbia University, New York, New York, USA
| | - Antonio Iavarone
- Department of Pathology and Cell Biology and Neurology, Columbia University, New York, New York, USA
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Kenneth D Aldape
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Pathology, Maryland Anderson Cancer Center, Houston, Texas, USA
- Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, Ontario, Canada
| | - Gelareh Zadeh
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Neurosurgery, University Health Network, Toronto, Ontario, Canada
| |
Collapse
|
4
|
Colaprico A, Silva TC, Olsen C, Garofano L, Cava C, Garolini D, Sabedot TS, Malta TM, Pagnotta SM, Castiglioni I, Ceccarelli M, Bontempi G, Noushmehr H. TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data. Nucleic Acids Res 2016; 44:e71. [PMID: 26704973 PMCID: PMC4856967 DOI: 10.1093/nar/gkv1507] [Citation(s) in RCA: 1956] [Impact Index Per Article: 244.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/06/2015] [Accepted: 12/10/2015] [Indexed: 12/18/2022] Open
Abstract
The Cancer Genome Atlas (TCGA) research network has made public a large collection of clinical and molecular phenotypes of more than 10 000 tumor patients across 33 different tumor types. Using this cohort, TCGA has published over 20 marker papers detailing the genomic and epigenomic alterations associated with these tumor types. Although many important discoveries have been made by TCGA's research network, opportunities still exist to implement novel methods, thereby elucidating new biological pathways and diagnostic markers. However, mining the TCGA data presents several bioinformatics challenges, such as data retrieval and integration with clinical data and other molecular data types (e.g. RNA and DNA methylation). We developed an R/Bioconductor package called TCGAbiolinks to address these challenges and offer bioinformatics solutions by using a guided workflow to allow users to query, download and perform integrative analyses of TCGA data. We combined methods from computer science and statistics into the pipeline and incorporated methodologies developed in previous TCGA marker studies and in our own group. Using four different TCGA tumor types (Kidney, Brain, Breast and Colon) as examples, we provide case studies to illustrate examples of reproducibility, integrative analysis and utilization of different Bioconductor packages to advance and accelerate novel discoveries.
Collapse
Affiliation(s)
- Antonio Colaprico
- Interuniversity Institute of Bioinformatics in Brussels (IB), Brussels, Belgium Machine Learning Group (MLG), Department d'Informatique, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Tiago C Silva
- Department of Genetics Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, São Paulo, Brazil
| | - Catharina Olsen
- Interuniversity Institute of Bioinformatics in Brussels (IB), Brussels, Belgium Machine Learning Group (MLG), Department d'Informatique, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Luciano Garofano
- Department of Science and Technology, University of Sannio, Benevento, Italy Unlimited Software srl, Naples, Italy
| | - Claudia Cava
- Institute of Molecular Bioimaging and Physiology of the National Research Council (IBFM-CNR), Milan, Italy
| | - Davide Garolini
- Physics for Complex Systems, Department of Physics, University of Turin, Italy
| | - Thais S Sabedot
- Department of Genetics Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, São Paulo, Brazil
| | - Tathiane M Malta
- Department of Genetics Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, São Paulo, Brazil
| | - Stefano M Pagnotta
- Department of Science and Technology, University of Sannio, Benevento, Italy Bioinformatics Laboratory, BIOGEM, Ariano Irpino, Avellino, Italy
| | - Isabella Castiglioni
- Institute of Molecular Bioimaging and Physiology of the National Research Council (IBFM-CNR), Milan, Italy
| | | | - Gianluca Bontempi
- Interuniversity Institute of Bioinformatics in Brussels (IB), Brussels, Belgium Machine Learning Group (MLG), Department d'Informatique, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Houtan Noushmehr
- Department of Genetics Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil Center for Integrative Systems Biology - CISBi, NAP/USP, Ribeirão Preto, São Paulo, Brazil
| |
Collapse
|
5
|
Barthel FP, Ceccarelli M, Malta TM, Sabedot TS, Salama SR, Pagnotta SM, Murray BA, Morozova O, Newton Y, Brat DJ, Cherniack AD, Zhang H, Poisson L, Cooper L, Rabadan R, Laird PW, Gutmann DH, Noushmehr H, Iavarone A, Verhaak RG. GENO-06A PAN-GLIOMA CHARACTERIZATION OF GENOMIC, EPIGENOMIC AND TRANSCRIPTOMIC ACTIVITIES REVEALS NOVEL RELATIONSHIPS BETWEEN HISTOLOGICAL SUBTYPES AND MOLECULAR SIGNATURES. Neuro Oncol 2015. [DOI: 10.1093/neuonc/nov215.06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|