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Bolognini D, Halgren A, Lou RN, Raveane A, Rocha JL, Guarracino A, Soranzo N, Chin J, Garrison E, Sudmant PH. Global diversity, recurrent evolution, and recent selection on amylase structural haplotypes in humans. bioRxiv 2024:2024.02.07.579378. [PMID: 38370750 PMCID: PMC10871346 DOI: 10.1101/2024.02.07.579378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The adoption of agriculture, first documented ~12,000 years ago in the Fertile Crescent, triggered a rapid shift toward starch-rich diets in human populations. Amylase genes facilitate starch digestion and increased salivary amylase copy number has been observed in some modern human populations with high starch intake, though evidence of recent selection is lacking. Here, using 52 long-read diploid assemblies and short read data from ~5,600 contemporary and ancient humans, we resolve the diversity, evolutionary history, and selective impact of structural variation at the amylase locus. We find that both salivary and pancreatic amylase genes have higher copy numbers in populations with agricultural subsistence compared to fishing, hunting, and pastoral groups. We identify 28 distinct amylase structural architectures and demonstrate that identical structures have arisen independently multiple times throughout recent human history. Using a pangenome graph-based approach to infer structural haplotypes across thousands of humans, we identify extensively duplicated haplotypes present at higher frequencies in modern agricultural populations. Leveraging 534 ancient human genomes we find that duplication-containing haplotypes have increased in frequency more than seven-fold over the last 12,000 years providing evidence for recent selection in Eurasians at this locus comparable in magnitude to that at lactase. Together, our study highlights the strong impact of the agricultural revolution on human genomes and the importance of long-read sequencing in identifying signatures of selection at structurally complex loci.
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Affiliation(s)
| | - Alma Halgren
- Department of Integrative Biology, University of California Berkeley, Berkeley, USA
| | - Runyang Nicolas Lou
- Department of Integrative Biology, University of California Berkeley, Berkeley, USA
| | | | - Joana L Rocha
- Department of Integrative Biology, University of California Berkeley, Berkeley, USA
| | - Andrea Guarracino
- Human Technopole, Milan, Italy
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, USA
| | | | - Jason Chin
- Foundation for Biological Data Science, Belmont, CA, USA
| | - Erik Garrison
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, USA
| | - Peter H Sudmant
- Department of Integrative Biology, University of California Berkeley, Berkeley, USA
- Center for Computational Biology, University of California Berkeley, Berkeley, USA
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2
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Abstract
Recent advancements in single-cell technologies have enabled expression quantitative trait locus (eQTL) analysis across many individuals at single-cell resolution. Compared with bulk RNA sequencing, which averages gene expression across cell types and cell states, single-cell assays capture the transcriptional states of individual cells, including fine-grained, transient, and difficult-to-isolate populations at unprecedented scale and resolution. Single-cell eQTL (sc-eQTL) mapping can identify context-dependent eQTLs that vary with cell states, including some that colocalize with disease variants identified in genome-wide association studies. By uncovering the precise contexts in which these eQTLs act, single-cell approaches can unveil previously hidden regulatory effects and pinpoint important cell states underlying molecular mechanisms of disease. Here, we present an overview of recently deployed experimental designs in sc-eQTL studies. In the process, we consider the influence of study design choices such as cohort, cell states, and ex vivo perturbations. We then discuss current methodologies, modeling approaches, and technical challenges as well as future opportunities and applications.
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Affiliation(s)
- Joyce B Kang
- Center for Data Sciences and Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; ,
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA;
| | | | - Aparna Nathan
- Center for Data Sciences and Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; ,
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA;
| | - Nicole Soranzo
- Human Technopole, Milan, Italy; ,
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
- British Heart Foundation Centre of Research Excellence and Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Soumya Raychaudhuri
- Center for Data Sciences and Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; ,
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA;
- Centre for Genetics and Genomics Versus Arthritis, University of Manchester, Manchester, United Kingdom
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3
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Mutti G, Oteo-Garcia G, Caldon M, da Silva MJF, Minhós T, Cowlishaw G, Gottelli D, Huchard E, Carter A, Martinez FI, Raveane A, Capelli C. Assessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes. Sci Rep 2023; 13:13839. [PMID: 37620368 PMCID: PMC10449864 DOI: 10.1038/s41598-023-40931-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 04/03/2023] [Accepted: 08/18/2023] [Indexed: 08/26/2023] Open
Abstract
Y chromosome markers can shed light on male-specific population dynamics but for many species no such markers have been discovered and are available yet, despite the potential for recovering Y-linked loci from available genome sequences. Here, we investigated how effective available bioinformatic tools are in recovering informative Y chromosome microsatellites from whole genome sequence data. In order to do so, we initially explored a large dataset of whole genome sequences comprising individuals at various coverages belonging to different species of baboons (genus: Papio) using Y chromosome references belonging to the same genus and more distantly related species (Macaca mulatta). We then further tested this approach by recovering Y-STRs from available Theropithecus gelada genomes using Papio and Macaca Y chromosome as reference sequences. Identified loci were validated in silico by a) comparing within-species relationships of Y chromosome lineages and b) genotyping male individuals in available pedigrees. Each STR was selected not to extend in its variable region beyond 100 base pairs, so that loci can be developed for PCR-based genotyping of non-invasive DNA samples. In addition to assembling a first set of Papio and Theropithecus Y-specific microsatellite markers, we released TYpeSTeR, an easy-to-use script to identify and genotype Y chromosome STRs using population genomic data which can be modulated according to available male reference genomes and genomic data, making it widely applicable across taxa.
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Affiliation(s)
- Giacomo Mutti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 11/a, 43124, Parma, Italy
- Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Gonzalo Oteo-Garcia
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 11/a, 43124, Parma, Italy
| | - Matteo Caldon
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 11/a, 43124, Parma, Italy
| | - Maria Joana Ferreira da Silva
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Centro de Investigação Em Biodiversidade E Recursos Genéticos, CIBIOInBIO Laboratório AssociadoUniversidade Do Porto, Campus de Vairão, Vairão, Portugal
- ONE ‑ Organisms and Environment Group, School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff, UK
| | - Tânia Minhós
- Centre for Research in Anthropology (CRIA-NOVA FCSH), Av. Forças Armadas, Edifício ISCTE, Sala 2w2, 1649-026, Lisboa, Portugal
- Anthropology Department, School of Social Sciences and Humanities, Universidade Nova de Lisboa (NOVA FCSH), Av. de Berna, 26-C, 1069-061, Lisboa, Portugal
| | - Guy Cowlishaw
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Dada Gottelli
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Elise Huchard
- Institut Des Sciences de L'Evolution, CNRS, Universite de Montpellier, CC 065, 34095, Montpellier 05, France
| | - Alecia Carter
- Department of Anthropology, University College London, 14 Taviton Street, London, WC1H 0BW, UK
| | - Felipe I Martinez
- Escuela de Antropología, Facultad de Ciencias Sociales, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Cristian Capelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 11/a, 43124, Parma, Italy.
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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4
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Capodiferro MR, Chero Osorio AM, Rambaldi Migliore N, Tineo Tineo DH, Raveane A, Xavier C, Bodner M, Simão F, Ongaro L, Montinaro F, Lindo J, Huerta-Sanchez E, Politis G, Barbieri C, Parson W, Gusmão L, Achilli A. The multifaceted genomic history of Ashaninka from Amazonian Peru. Curr Biol 2023; 33:1573-1581.e5. [PMID: 36931272 DOI: 10.1016/j.cub.2023.02.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 09/20/2022] [Revised: 12/14/2022] [Accepted: 02/14/2023] [Indexed: 03/18/2023]
Abstract
Despite its crucial location, the western side of Amazonia between the Andes and the source(s) of the Amazon River is still understudied from a genomic and archaeogenomic point of view, albeit possibly harboring essential information to clarify the complex genetic history of local Indigenous groups and their interactions with nearby regions,1,2,3,4,5,6,7,8 including central America and the Caribbean.9,10,11,12 Focusing on this key region, we analyzed the genome-wide profiles of 51 Ashaninka individuals from Amazonian Peru, observing an unexpected extent of genomic variation. We identified at least two Ashaninka subgroups with distinctive genomic makeups, which were differentially shaped by the degree and timing of external admixtures, especially with the Indigenous groups from the Andes and the Pacific coast. On a continental scale, Ashaninka ancestors probably derived from a south-north migration of Indigenous groups moving into the Amazonian rainforest from a southeastern area with contributions from the Southern Cone and the Atlantic coast. These ancestral populations diversified in the variegated geographic regions of interior South America, on the eastern side of the Andes, differentially interacting with surrounding coastal groups. In this complex scenario, we also revealed strict connections between the ancestors of present-day Ashaninka, who belong to the Arawakan language family,13 and those Indigenous groups that moved further north into the Caribbean, contributing to the early Ceramic (Saladoid) tradition in the islands.14,15.
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Affiliation(s)
- Marco Rosario Capodiferro
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy; Smurfit Institute of Genetics, Trinity College Dublin, D02 CX56 Dublin 2, Ireland.
| | - Ana María Chero Osorio
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Nicola Rambaldi Migliore
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Dean Herman Tineo Tineo
- Laboratorio de Biología Forense, Instituto de Medicina Legal y Ciencias Forenses, Ministerio Público, Lima 15033, Perú
| | | | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4099-002 Porto, Portugal
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Filipa Simão
- Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro 23968-000, Brazil
| | - Linda Ongaro
- Smurfit Institute of Genetics, Trinity College Dublin, D02 CX56 Dublin 2, Ireland
| | - Francesco Montinaro
- Department of Biology-Genetics, University of Bari, 70125 Bari, Italy; Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - John Lindo
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Emilia Huerta-Sanchez
- Smurfit Institute of Genetics, Trinity College Dublin, D02 CX56 Dublin 2, Ireland; Ecology and Evolutionary Biology and Center for Computational and Molecular Biology, Brown University, Providence, RI 02906, USA
| | - Gustavo Politis
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | - Chiara Barbieri
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland; Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; Forensic Science Program, Pennsylvania State University, State College, PA 16801, USA
| | - Leonor Gusmão
- Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro 23968-000, Brazil
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy.
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5
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Cortellino S, Raveane A, Chiodoni C, Delfanti G, Pisati F, Spagnolo V, Visco E, Fragale G, Ferrante F, Magni S, Iannelli F, Zanardi F, Casorati G, Bertolini F, Dellabona P, Colombo MP, Tripodo C, Longo VD. Fasting renders immunotherapy effective against low-immunogenic breast cancer while reducing side effects. Cell Rep 2022; 40:111256. [PMID: 36001966 DOI: 10.1016/j.celrep.2022.111256] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 10/25/2021] [Revised: 05/10/2022] [Accepted: 07/28/2022] [Indexed: 11/26/2022] Open
Abstract
Immunotherapy is improving the prognosis and survival of cancer patients, but despite encouraging outcomes in different cancers, the majority of tumors are resistant to it, and the immunotherapy combinations are often accompanied by severe side effects. Here, we show that a periodic fasting-mimicking diet (FMD) can act on the tumor microenvironment and increase the efficacy of immunotherapy (anti-PD-L1 and anti-OX40) against the poorly immunogenic triple-negative breast tumors (TNBCs) by expanding early exhausted effector T cells, switching the cancer metabolism from glycolytic to respiratory, and reducing collagen deposition. Furthermore, FMD reduces the occurrence of immune-related adverse events (irAEs) by preventing the hyperactivation of the immune response. These results indicate that FMD cycles have the potential to enhance the efficacy of anti-cancer immune responses, expand the portion of tumors sensitive to immunotherapy, and reduce its side effects.
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Affiliation(s)
| | - Alessandro Raveane
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan 20141, Italy
| | - Claudia Chiodoni
- Department of Research, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Gloria Delfanti
- Experimental Immunology Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federica Pisati
- IFOM, FIRC Institute of Molecular Oncology, Milan 20139, Italy
| | | | - Euplio Visco
- IFOM, FIRC Institute of Molecular Oncology, Milan 20139, Italy
| | | | | | - Serena Magni
- IFOM, FIRC Institute of Molecular Oncology, Milan 20139, Italy
| | - Fabio Iannelli
- IFOM, FIRC Institute of Molecular Oncology, Milan 20139, Italy
| | | | - Giulia Casorati
- Experimental Immunology Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesco Bertolini
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan 20141, Italy; Onco-Tech Lab, European Institute of Oncology IRCCS and Politecnico di Milano, Milan, Italy
| | - Paolo Dellabona
- Experimental Immunology Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Mario P Colombo
- Department of Research, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Claudio Tripodo
- IFOM, FIRC Institute of Molecular Oncology, Milan 20139, Italy; University of Palermo School of Medicine, Palermo, Italy
| | - Valter D Longo
- IFOM, FIRC Institute of Molecular Oncology, Milan 20139, Italy; Longevity Institute and Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA.
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6
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Carpen L, Falvo P, Orecchioni S, Mitola G, Hillje R, Mazzara S, Mancuso P, Pileri S, Raveane A, Bertolini F. Abstract 1712: A single-cell RNA atlas of innate and adaptive intratumoral immunity in triple negative breast cancer during chemo- and immunotherapies. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Checkpoint inhibitors (CIs) such as anti-PD-1 and anti PD-L1 have shown combinatorial clinical activity with chemotherapy in triple negative breast cancer (TNBC), but only in a minority of patients and only for a limited period of time. Moreover, it is currently unclear what chemotherapeutic drug is the most appropriate to combine with CIs in TNBC patients. We have investigated at the single cell level the transcriptome and the trajectories of more than 50,000 innate and adaptive intratumoral immune cells in two syngeneic, immune competent, orthotopic murine models of local and metastatic TNBC. Mice injected with 4T1 cells had a predominant lymphoid infiltrate, mice injected with EMT6 cells had a predominant myeloid infiltrate. Mice were treated with CIs and several different types of chemotherapeutics, alone or in combinations. In both models, capecitabine (alone or with CIs) was the less effective drug. Platinum, doxorubicin and taxanes showed synergy with CIs and had superimposable activity. Intermittent, medium dosage cyclophosphamide (CTX) plus vinorelbine and CIs was the most active combinatorial therapy (Falvo et al, Cancer Research 2021). Vinorelbine activated antigen presenting cells and CTX generated new T cell clones including stem cell-like TCF1+ CD8+ T cells. Treatments with most in vivo efficacy were associated to a decrease of regulatory T cells and of gamma delta T cells, which were found to have a pro-tumoral activity in these murine models, likely due to IL-17 expression in the neoplastic microenvironment. An increase of several different clusters of exhausted-like CD8+ T cells was observed in pre-clinical treatments with low efficacy; an opposite trend was found for several clusters of proliferative CD8+ T cells in treatments with high in vivo efficacy. Regarding macrophages, M2-like cells were enriched after treatments with low efficacy, while an opposite behaviour was found in M1-like macrophages. Interestingly, we observed a significant increase of an M1-like cluster with high expression of the Ly6c1/Ly6c2 gene in mice successfully treated with vinorelbine, CTX and CIs. For both cell lines the percentage of plasma B cells increased after in vivo treatments with high efficacy. In particular, the most effective treatment significantly increased the frequency of germinal B cells, which were absent in untreated tumors. These data can lead to new insights on the diagnosis and treatment of TNBC and to possible clinical applications.
Citation Format: Laura Carpen, Paolo Falvo, Stefania Orecchioni, Giulia Mitola, Roman Hillje, Saveria Mazzara, Patrizia Mancuso, Stefano Pileri, Alessandro Raveane, Francesco Bertolini. A single-cell RNA atlas of innate and adaptive intratumoral immunity in triple negative breast cancer during chemo- and immunotherapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1712.
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Affiliation(s)
| | - Paolo Falvo
- 1European Institute of Oncology, Milan, Italy
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7
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Santander C, Molinaro L, Mutti G, Martínez FI, Mathe J, Ferreira da Silva MJ, Caldon M, Oteo-Garcia G, Aldeias V, Archer W, Bamford M, Biro D, Bobe R, Braun DR, Hammond P, Lüdecke T, Pinto MJ, Meira Paulo L, Stalmans M, Regala FT, Bertolini F, Moltke I, Raveane A, Pagani L, Carvalho S, Capelli C. Genomic variation in baboons from central Mozambique unveils complex evolutionary relationships with other Papio species. BMC Ecol Evol 2022; 22:44. [PMID: 35410131 PMCID: PMC8996594 DOI: 10.1186/s12862-022-01999-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/10/2021] [Accepted: 03/28/2022] [Indexed: 11/11/2022] Open
Abstract
Background Gorongosa National Park in Mozambique hosts a large population of baboons, numbering over 200 troops. Gorongosa baboons have been tentatively identified as part of Papio ursinus on the basis of previous limited morphological analysis and a handful of mitochondrial DNA sequences. However, a recent morphological and morphometric analysis of Gorongosa baboons pinpointed the occurrence of several traits intermediate between P. ursinus and P. cynocephalus, leaving open the possibility of past and/or ongoing gene flow in the baboon population of Gorongosa National Park. In order to investigate the evolutionary history of baboons in Gorongosa, we generated high and low coverage whole genome sequence data of Gorongosa baboons and compared it to available Papio genomes. Results We confirmed that P. ursinus is the species closest to Gorongosa baboons. However, the Gorongosa baboon genomes share more derived alleles with P. cynocephalus than P. ursinus does, but no recent gene flow between P. ursinus and P. cynocephalus was detected when available Papio genomes were analyzed. Our results, based on the analysis of autosomal, mitochondrial and Y chromosome data, suggest complex, possibly male-biased, gene flow between Gorongosa baboons and P. cynocephalus, hinting to direct or indirect contributions from baboons belonging to the “northern” Papio clade, and signal the presence of population structure within P. ursinus. Conclusions The analysis of genome data generated from baboon samples collected in central Mozambique highlighted a complex set of evolutionary relationships with other baboons. Our results provided new insights in the population dynamics that have shaped baboon diversity. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01999-7.
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Affiliation(s)
- Cindy Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark. .,Department of Zoology, University of Oxford, Oxford, UK.
| | - Ludovica Molinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Giacomo Mutti
- Department of Biosciences, University of Milan, Milan, Italy.,Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Felipe I Martínez
- Escuela de Antropología, Facultad de Ciencias Sociales, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jacinto Mathe
- School of Anthropology, University of Oxford, Oxford, UK
| | - Maria Joana Ferreira da Silva
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.,ONE - Organisms and Environment Group, School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff, UK
| | - Matteo Caldon
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gonzalo Oteo-Garcia
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Vera Aldeias
- Interdisciplinary Center for Archaeology and Evolution of Human Behavior (ICArEHB), Universidade do Algarve, Faro, Portugal
| | - Will Archer
- Department of Archaeology, National Museum, Bloemfontein, South Africa
| | - Marion Bamford
- Evolutionary Studies Institute, University of the Witwatersrand, Johannesburg, South Africa
| | - Dora Biro
- Department of Zoology, University of Oxford, Oxford, UK
| | - René Bobe
- School of Anthropology, University of Oxford, Oxford, UK.,Gorongosa National Park, Sofala, Mozambique
| | - David R Braun
- Center for the Advanced Study of Human Paleobiology, George Washington University, Washington, USA
| | | | - Tina Lüdecke
- School of Anthropology, University of Oxford, Oxford, UK.,Emmy Noether Group for Hominin Meat Consumption, Max Planck Institute for Chemistry, Mainz, Germany
| | - Maria José Pinto
- AESDA - Associação de Estudos Subterrâneos e Defesa do Ambiente, Lisbon, Portugal
| | - Luis Meira Paulo
- AESDA - Associação de Estudos Subterrâneos e Defesa do Ambiente, Lisbon, Portugal
| | - Marc Stalmans
- Department of Scientific Services, Gorongosa National Park, Chitengo, Sofala Province, Mozambique
| | - Frederico Tátá Regala
- Interdisciplinary Center for Archaeology and Evolution of Human Behavior (ICArEHB), Universidade do Algarve, Faro, Portugal
| | - Francesco Bertolini
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Alessandro Raveane
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Biology, University of Padua, Padua, Italy
| | - Susana Carvalho
- School of Anthropology, University of Oxford, Oxford, UK. .,Gorongosa National Park, Sofala, Mozambique.
| | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford, UK. .,Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
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8
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Pagano A, Gualtieri C, Mutti G, Raveane A, Sincinelli F, Semino O, Balestrazzi A, Macovei A. Identification and Characterization of SOG1 (Suppressor of Gamma-Response 1) Homologues in Plants Using Data Mining Resources and Gene Expression Profiling. Genes (Basel) 2022; 13:genes13040667. [PMID: 35456473 PMCID: PMC9026448 DOI: 10.3390/genes13040667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 03/20/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 12/10/2022] Open
Abstract
SOG1 (Suppressor of the Gamma response 1) is the master-regulator of plant DNA damage response (DDR), a highly coordinated network of DNA damage sensors, transducers, mediators, and effectors, with highly coordinated activities. SOG1 transcription factor belongs to the NAC/NAM protein family, containing the well-conserved NAC domain and five serine-glutamine (SQ) motifs, preferential targets for phosphorylation by ATM and ATR. So far, the information gathered for the SOG1 function comes from studies on the model plant Arabidopsis thaliana. To expand the knowledge on plant-specific DDR, it is opportune to gather information on other SOG1 orthologues. The current study identified plants where multiple SOG1 homologues are present and evaluated their functions by leveraging the information contained in publicly available transcriptomics databases. This analysis revealed the presence of multiple SOG1 sequences in thirteen plant species, and four (Medicago truncatula, Glycine max, Kalankoe fedtschenkoi, Populus trichocarpa) were selected for gene expression data mining based on database availability. Additionally, M. truncatula seeds and seedlings exposed to treatments known to activate DDR pathways were used to evaluate the expression profiles of MtSOG1a and MtSOG1b. The experimental workflow confirmed the data retrieved from transcriptomics datasets, suggesting that the SOG1 homologues have redundant functions in different plant species.
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Carpen L, Falvo P, Orecchioni S, Mitola G, Hillje R, Mazzara S, Mancuso P, Pileri S, Raveane A, Bertolini F. A single-cell transcriptomic landscape of innate and adaptive intratumoral immunity in triple negative breast cancer during chemo- and immunotherapies. Cell Death Dis 2022; 8:106. [PMID: 35260564 PMCID: PMC8904804 DOI: 10.1038/s41420-022-00893-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/03/2022] [Accepted: 02/11/2022] [Indexed: 12/12/2022]
Abstract
Breast cancer (BC) constitutes a major health problem worldwide, making it the most common malignancy in women. Current treatment options for BC depend primarily on histological type, molecular markers, clinical aggressiveness and stage of disease. Immunotherapy, such as αPD-1, have shown combinatorial clinical activity with chemotherapy in triple negative breast cancer (TNBC) delineating some therapeutic combinations as more effective than others. However, a clear overview of the main immune cell populations involved in these treatments has never been provided. Here, an assessment of the immune landscape in the tumor microenvironment (TME) of two TNBC mouse models has been performed using single-cell RNA sequencing technology. Specifically, immune cells were evaluated in untreated conditions and after treatments with chemotherapy or immunotherapy used as single agents or in combination. A decrease of Treg was found in treatments with in vivo efficacy as well as γδ T cells, which have a pro-tumoral activity in mice. Focusing on Cd8 T cells, across all the conditions, a general increase of exhausted-like Cd8 T cells was confirmed in pre-clinical treatments with low efficacy and an opposite trend was found for the proliferative Cd8 T cells. Regarding macrophages, M2-like cells were enriched in treatments with low efficacy while M1-like macrophages followed an opposite trend. For both models, similar proportions of B cells were detected with an increase of proliferative B cells in treatments involving cisplatin in combination with αPD-1. The fine-scale characterization of the immune TME in this work can lead to new insights on the diagnosis and treatment of TNBC.
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Affiliation(s)
- Laura Carpen
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy.,Human Technopole, Milan, Italy
| | - Paolo Falvo
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Stefania Orecchioni
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Giulia Mitola
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | | | - Saveria Mazzara
- Hematopathology Unit, European Institute of Oncology IRCCS, Milan, Italy
| | - Patrizia Mancuso
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Stefano Pileri
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Alessandro Raveane
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy. .,Human Technopole, Milan, Italy.
| | - Francesco Bertolini
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy.
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10
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Aneli S, Saupe T, Montinaro F, Solnik A, Molinaro L, Scaggion C, Carrara N, Raveane A, Kivisild T, Metspalu M, Scheib CL, Pagani L. The genetic origin of Daunians and the Pan-Mediterranean southern Italian Iron Age context. Mol Biol Evol 2022; 39:6509524. [PMID: 35038748 PMCID: PMC8826970 DOI: 10.1093/molbev/msac014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The geographical location and shape of Apulia, a narrow land stretching out in the sea at the South of Italy, made this region a Mediterranean crossroads connecting Western Europe and the Balkans. Such movements culminated at the beginning of the Iron Age with the Iapygian civilization which consisted of three cultures: Peucetians, Messapians, and Daunians. Among them, the Daunians left a peculiar cultural heritage, with one-of-a-kind stelae and pottery, but, despite the extensive archaeological literature, their origin has been lost to time. In order to shed light on this and to provide a genetic picture of Iron Age Southern Italy, we collected and sequenced human remains from three archaeological sites geographically located in Northern Apulia (the area historically inhabited by Daunians) and radiocarbon dated between 1157 and 275 calBCE. We find that Iron Age Apulian samples are still distant from the genetic variability of modern-day Apulians, they show a degree of genetic heterogeneity comparable with the cosmopolitan Republican and Imperial Roman civilization, even though a few kilometers and centuries separate them, and they are well inserted into the Iron Age Pan-Mediterranean genetic landscape. Our study provides for the first time a window on the genetic make-up of pre-Roman Apulia, whose increasing connectivity within the Mediterranean landscape, would have contributed to laying the foundation for modern genetic variability. In this light, the genetic profile of Daunians may be compatible with an at least partial autochthonous origin, with plausible contributions from the Balkan peninsula.
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Affiliation(s)
- Serena Aneli
- Department of Biology, University of Padua, Via Ugo Bassi, 58b, Padova 35121, Italy
| | - Tina Saupe
- Estonian Biocentre,Institute of Genomics,University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Francesco Montinaro
- Department of Biology-Genetics, University of Bari, Via E. Orabona, 4, Bari 70124, Italy
| | - Anu Solnik
- Core Facility,Institute of Genomics,University of Tartu, Riia 23B, Tartu, 51010 Estonia
| | - Ludovica Molinaro
- Estonian Biocentre,Institute of Genomics,University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Cinzia Scaggion
- Department of Geosciences, University of Padua, Via Giovanni Gradenigo, 6, Padova 35131, Italy
| | - Nicola Carrara
- Anthropology Museum,University of Padova,Via Giotto, 1, Padova 35121, Italy
| | - Alessandro Raveane
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Toomas Kivisild
- Estonian Biocentre,Institute of Genomics,University of Tartu, Riia 23B, Tartu 51010, Estonia.,Department of Human Genetics, KU Leuven, Leuven, Herestraat 49, B-3000, Belgium
| | - Mait Metspalu
- Estonian Biocentre,Institute of Genomics,University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Christiana L Scheib
- Estonian Biocentre,Institute of Genomics,University of Tartu, Riia 23B, Tartu 51010, Estonia.,St John's College, Cambridge, CB2 1TP, United Kingdom
| | - Luca Pagani
- Department of Biology, University of Padua, Via Ugo Bassi, 58b, Padova 35121, Italy.,Estonian Biocentre,Institute of Genomics,University of Tartu, Riia 23B, Tartu 51010, Estonia
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11
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Rambaldi Migliore N, Colombo G, Capodiferro MR, Mazzocchi L, Chero Osorio AM, Raveane A, Tribaldos M, Perego UA, Mendizábal T, Montón AG, Lombardo G, Grugni V, Garofalo M, Ferretti L, Cereda C, Gagliardi S, Cooke R, Smith-Guzmán N, Olivieri A, Aram B, Torroni A, Motta J, Semino O, Achilli A. Weaving Mitochondrial DNA and Y-Chromosome Variation in the Panamanian Genetic Canvas. Genes (Basel) 2021; 12:genes12121921. [PMID: 34946870 PMCID: PMC8702192 DOI: 10.3390/genes12121921] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/25/2021] [Accepted: 11/27/2021] [Indexed: 12/14/2022] Open
Abstract
The Isthmus of Panama was a crossroads between North and South America during the continent’s first peopling (and subsequent movements) also playing a pivotal role during European colonization and the African slave trade. Previous analyses of uniparental systems revealed significant sex biases in the genetic history of Panamanians, as testified by the high proportions of Indigenous and sub-Saharan mitochondrial DNAs (mtDNAs) and by the prevalence of Western European/northern African Y chromosomes. Those studies were conducted on the general population without considering any self-reported ethnic affiliations. Here, we compared the mtDNA and Y-chromosome lineages of a new sample collection from 431 individuals (301 males and 130 females) belonging to either the general population, mixed groups, or one of five Indigenous groups currently living in Panama. We found different proportions of paternal and maternal lineages in the Indigenous groups testifying to pre-contact demographic events and genetic inputs (some dated to Pleistocene times) that created genetic structure. Then, while the local mitochondrial gene pool was marginally involved in post-contact admixtures, the Indigenous Y chromosomes were differentially replaced, mostly by lineages of western Eurasian origin. Finally, our new estimates of the sub-Saharan contribution, on a more accurately defined general population, reduce an apparent divergence between genetic and historical data.
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Affiliation(s)
- Nicola Rambaldi Migliore
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Giulia Colombo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Marco Rosario Capodiferro
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Lucia Mazzocchi
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Ana Maria Chero Osorio
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Alessandro Raveane
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Maribel Tribaldos
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (M.T.); (J.M.)
| | - Ugo Alessandro Perego
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Department of Math and Science, Southeastern Community College, West Burlington, IA 52655, USA
| | - Tomás Mendizábal
- Center for Historical, Anthropological and Cultural Research—AIP, Panama City 0816-07812, Panama;
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; (R.C.); (N.S.-G.)
| | - Alejandro García Montón
- Departamento de Geografía, Historia y Filosofía, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.G.M.); (B.A.)
| | - Gianluca Lombardo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Viola Grugni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Maria Garofalo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (C.C.); (S.G.)
| | - Luca Ferretti
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Cristina Cereda
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (C.C.); (S.G.)
| | - Stella Gagliardi
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (C.C.); (S.G.)
| | - Richard Cooke
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; (R.C.); (N.S.-G.)
- Sistema Nacional de Investigadores, Secretaría Nacional de Ciencia y Tecnología, Ciudad del Saber, Clayton 0816-02852, Panama
| | - Nicole Smith-Guzmán
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; (R.C.); (N.S.-G.)
- Sistema Nacional de Investigadores, Secretaría Nacional de Ciencia y Tecnología, Ciudad del Saber, Clayton 0816-02852, Panama
| | - Anna Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Bethany Aram
- Departamento de Geografía, Historia y Filosofía, Universidad Pablo de Olavide, 41013 Seville, Spain; (A.G.M.); (B.A.)
| | - Antonio Torroni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
| | - Jorge Motta
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama; (M.T.); (J.M.)
| | - Ornella Semino
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Correspondence: (O.S.); (A.A.)
| | - Alessandro Achilli
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (N.R.M.); (G.C.); (M.R.C.); (L.M.); (A.M.C.O.); (A.R.); (U.A.P.); (G.L.); (V.G.); (M.G.); (L.F.); (A.O.); (A.T.)
- Correspondence: (O.S.); (A.A.)
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12
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Roma S, Carpen L, Raveane A, Bertolini F. The Dual Role of Innate Lymphoid and Natural Killer Cells in Cancer. from Phenotype to Single-Cell Transcriptomics, Functions and Clinical Uses. Cancers (Basel) 2021; 13:cancers13205042. [PMID: 34680190 PMCID: PMC8533946 DOI: 10.3390/cancers13205042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/30/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Innate lymphoid cells (ILCs), a family of innate immune cells including natural killers (NKs), play a multitude of roles in first-line cancer control, in escape from immunity and in cancer progression. In this review, we summarize preclinical and clinical data on ILCs and NK cells concerning their phenotype, function and clinical applications in cellular therapy trials. We also describe how single-cell transcriptome sequencing has been used and forecast how it will be used to better understand ILC and NK involvement in cancer control and progression as well as their therapeutic potential. Abstract The role of innate lymphoid cells (ILCs), including natural killer (NK) cells, is pivotal in inflammatory modulation and cancer. Natural killer cell activity and count have been demonstrated to be regulated by the expression of activating and inhibitory receptors together with and as a consequence of different stimuli. The great majority of NK cell populations have an anti-tumor activity due to their cytotoxicity, and for this reason have been used for cellular therapies in cancer patients. On the other hand, the recently classified helper ILCs are fundamentally involved in inflammation and they can be either helpful or harmful in cancer development and progression. Tissue niche seems to play an important role in modulating ILC function and conversion, as observed at the transcriptional level. In the past, these cell populations have been classified by the presence of specific cellular receptor markers; more recently, due to the advent of single-cell RNA sequencing (scRNA-seq), it has been possible to also explore them at the transcriptomic level. In this article we review studies on ILC (and NK cell) classification, function and their involvement in cancer. We also summarize the potential application of NK cells in cancer therapy and give an overview of the most recent studies involving ILCs and NKs at scRNA-seq, focusing on cancer. Finally, we provide a resource for those who wish to start single-cell transcriptomic analysis on the context of these innate lymphoid cell populations.
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13
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Ferreira JC, Alshamali F, Montinaro F, Cavadas B, Torroni A, Pereira L, Raveane A, Fernandes V. Projecting Ancient Ancestry in Modern-Day Arabians and Iranians: A Key Role of the Past Exposed Arabo-Persian Gulf on Human Migrations. Genome Biol Evol 2021; 13:6364187. [PMID: 34480555 PMCID: PMC8435661 DOI: 10.1093/gbe/evab194] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
The Arabian Peninsula is strategic for investigations centered on the early structuring of modern humans in the wake of the out-of-Africa migration. Despite its poor climatic conditions for the recovery of ancient human DNA evidence, the availability of both genomic data from neighboring ancient specimens and informative statistical tools allow modeling the ancestry of local modern populations. We applied this approach to a data set of 741,000 variants screened in 291 Arabians and 78 Iranians, and obtained insightful evidence. The west-east axis was a strong forcer of population structure in the Peninsula, and, more importantly, there were clear continuums throughout time linking western Arabia with the Levant, and eastern Arabia with Iran and the Caucasus. Eastern Arabians also displayed the highest levels of the basal Eurasian lineage of all tested modern-day populations, a signal that was maintained even after correcting for a possible bias due to a recent sub-Saharan African input in their genomes. Not surprisingly, eastern Arabians were also the ones with highest similarity with Iberomaurusians, who were, so far, the best proxy for the basal Eurasians amongst the known ancient specimens. The basal Eurasian lineage is the signature of ancient non-Africans who diverged from the common European-eastern Asian pool before 50,000 years ago, prior to the later interbred with Neanderthals. Our results appear to indicate that the exposed basin of the Arabo-Persian Gulf was the possible home of basal Eurasians, a scenario to be further investigated by searching ancient Arabian human specimens.
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Affiliation(s)
- Joana C Ferreira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal.,ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Farida Alshamali
- Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai, United Arab Emirates
| | - Francesco Montinaro
- Department of Biology-Genetics, University of Bari, Italy.,Estonian Biocentre, Institute of Genomics, University of Tartu, Estonia
| | - Bruno Cavadas
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Italy
| | - Luisa Pereira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal
| | - Alessandro Raveane
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Italy.,Laboratory of Haematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Veronica Fernandes
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal
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14
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Falvo P, Orecchioni S, Hillje R, Raveane A, Mitola G, Mancuso P, Camisaschi C, Luzi L, Pelicci P, Bertolini F. Abstract 1653: A single-cell atlas of the effect of chemotherapeutics over intratumoral immune cells reveals that combining an alkylating agent and a vinca alkaloid can activate antigen presenting cells and increase tcf1+ stem-like CD8+ T-cells, thus improving anti-PD-1 efficacy in triple negative breast cancer and lymphoma. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-1653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Checkpoint inhibitors (CIs) instigate anticancer immunity, albeit only in a fraction of patients. Triple negative breast cancer (TNBC) is among the most aggressive and lethal BC types, and currently available therapies have an unsatisfactory clinical impact. The association of CIs with chemotherapy had encouraging results in randomized TNBC trials, but so far there has been no clear evidence of what should be considered the best combinatorial therapy. In B-cell non-Hodgkin's lympoma (NHL), CIs' clinical activity has been so far unsatisfactory. We designed the current study to define what could be considered the most efficient combinatorial regimen of chemotherapy plus CI in TNBC and NHL. We investigated different options including platinum (P), doxorubicin (D), taxol (T), vinorelbine (V), and cyclophosphamide ( C), i.e. the most effective chemotherapy drugs for these diseases. Capecitabine was not considered as found not to be effective in combination with CIs. As TNBC patients have a large intratumoral immune cell heterogeneity, we investigated two immune competent TNBC models: 4T1 with a predominant lymphoid intratumoral infiltrate and EMT6 with a predominant myeloid infiltrate. A C57BL/6 Eμ-myc transgenic NHL model, with a predominant lymphatic dissemination pattern, was also studied. We found that 1) Intermittent, medium-dosage C (C140), was more effective than other combinatorial regimens including the CI anti-PD1 plus low-dose C, or regular-dose T, D, or P. The association of V and anti-PD1 further increased the preclinical efficacy of C140; 2) both CD3+CD4+ and CD3+CD8+ T cells (at variance with other subsets of NK and myeloid cells) were needed to control local and metastatic neoplastic growth in mice treated with C140, V and anti-PD1. 3) The combinatorial therapy including C140, V and anti-PD1 was the most efficient in activating antigen presenting cells (APCs), and the investigation of TCR repertoire indicated that this therapy generated a significantly larger clonal expansion of both CD3+CD4+ and CD3+CD8+ T cells. 4) Single-cell transcriptome analysis of >50,000 intratumoural immune cells showed after C140, V and anti-PD1 therapy a gene signature suggestive of a change resulting from exposure to a mitogen, ligand, or an antigen for which it is specific, as well as APC-to-T-cell adhesion. This transcriptional program also increased intratumoural tcf1+ stem-like CD8+ T-cells and altered the balance between terminally and progenitor exhausted T-cells, favoring the latter. These data support the clinical investigation of this therapy in TNBC and NHL, and we are currently investigating the related transcriptional mechanisms inducing APC activation and T cell rewiring.
Citation Format: Paolo Falvo, Stefania Orecchioni, Roman Hillje, Alessandro Raveane, Giulia Mitola, Patrizia Mancuso, Chiara Camisaschi, Lucilla Luzi, PierGiuseppe Pelicci, Francesco Bertolini. A single-cell atlas of the effect of chemotherapeutics over intratumoral immune cells reveals that combining an alkylating agent and a vinca alkaloid can activate antigen presenting cells and increase tcf1+ stem-like CD8+ T-cells, thus improving anti-PD-1 efficacy in triple negative breast cancer and lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1653.
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Affiliation(s)
- Paolo Falvo
- European Institute of Oncology, Milan, Italy
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Falvo P, Orecchioni S, Roma S, Raveane A, Bertolini F. Drug Repurposing in Oncology, an Attractive Opportunity for Novel Combinatorial Regimens. Curr Med Chem 2021; 28:2114-2136. [PMID: 33109033 DOI: 10.2174/0929867327999200817104912] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/21/2020] [Accepted: 05/26/2020] [Indexed: 11/22/2022]
Abstract
The costs of developing, validating and buying new drugs are dramatically increasing. On the other hand, sobering economies have difficulties in sustaining their healthcare systems, particularly in countries with an elderly population requiring increasing welfare. This conundrum requires immediate action, and a possible option is to study the large, already present arsenal of drugs approved and to use them for innovative therapies. This possibility is particularly interesting in oncology, where the complexity of the cancer genome dictates in most patients a multistep therapeutic approach. In this review, we discuss a) Computational approaches; b) preclinical models; c) currently ongoing or already published clinical trials in the drug repurposing field in oncology; and d) drug repurposing to overcome resistance to previous therapies.
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Affiliation(s)
- Paolo Falvo
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Stefania Orecchioni
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Stefania Roma
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Alessandro Raveane
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Francesco Bertolini
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, 20141 Milan, Italy
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Falvo P, Orecchioni S, Raveane A, Mitola G, Bertolini F. A "two-hit" (chemo)therapy to improve checkpoint inhibition in cancer. Oncoscience 2021; 8:55-57. [PMID: 33997109 PMCID: PMC8115984 DOI: 10.18632/oncoscience.533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/16/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- Paolo Falvo
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan 20141, Italy
- Contributed equally to this work
| | - Stefania Orecchioni
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan 20141, Italy
- Contributed equally to this work
| | - Alessandro Raveane
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan 20141, Italy
- Contributed equally to this work
| | - Giulia Mitola
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan 20141, Italy
| | - Francesco Bertolini
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan 20141, Italy
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Capodiferro MR, Aram B, Raveane A, Rambaldi Migliore N, Colombo G, Ongaro L, Rivera J, Mendizábal T, Hernández-Mora I, Tribaldos M, Perego UA, Li H, Scheib CL, Modi A, Gòmez-Carballa A, Grugni V, Lombardo G, Hellenthal G, Pascale JM, Bertolini F, Grieco GS, Cereda C, Lari M, Caramelli D, Pagani L, Metspalu M, Friedrich R, Knipper C, Olivieri A, Salas A, Cooke R, Montinaro F, Motta J, Torroni A, Martín JG, Semino O, Malhi RS, Achilli A. Archaeogenomic distinctiveness of the Isthmo-Colombian area. Cell 2021; 184:1706-1723.e24. [PMID: 33761327 PMCID: PMC8024902 DOI: 10.1016/j.cell.2021.02.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/20/2020] [Accepted: 02/18/2021] [Indexed: 01/09/2023]
Abstract
The recently enriched genomic history of Indigenous groups in the Americas is still meager concerning continental Central America. Here, we report ten pre-Hispanic (plus two early colonial) genomes and 84 genome-wide profiles from seven groups presently living in Panama. Our analyses reveal that pre-Hispanic demographic events contributed to the extensive genetic structure currently seen in the area, which is also characterized by a distinctive Isthmo-Colombian Indigenous component. This component drives these populations on a specific variability axis and derives from the local admixture of different ancestries of northern North American origin(s). Two of these ancestries were differentially associated to Pleistocene Indigenous groups that also moved into South America, leaving heterogenous genetic footprints. An additional Pleistocene ancestry was brought by a still unsampled population of the Isthmus (UPopI) that remained restricted to the Isthmian area, expanded locally during the early Holocene, and left genomic traces up to the present day.
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Affiliation(s)
| | - Bethany Aram
- Department of Geography, History and Philosophy, the Pablo de Olavide University of Seville, Seville 41013, Spain
| | - Alessandro Raveane
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy; Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan 20141, Italy
| | - Nicola Rambaldi Migliore
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Giulia Colombo
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Linda Ongaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Javier Rivera
- Department of History and Social Sciences, Universidad del Norte, Barranquilla 080001, Colombia
| | - Tomás Mendizábal
- Patronato Panamá Viejo, Panama City 0823-05096, Panama; Coiba Scientific Station (COIBA AIP), City of Knowledge, Clayton 0843-03081, Panama
| | - Iosvany Hernández-Mora
- Department of History and Social Sciences, Universidad del Norte, Barranquilla 080001, Colombia
| | - Maribel Tribaldos
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama
| | - Ugo Alessandro Perego
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Hongjie Li
- Department of Anthropology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
| | - Christiana Lyn Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Alberto Gòmez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain; GenPoB Research Group, Instituto de Investigación Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706 Galicia, Spain
| | - Viola Grugni
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Gianluca Lombardo
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Garrett Hellenthal
- UCL Genetics Institute (UGI), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Juan Miguel Pascale
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama
| | - Francesco Bertolini
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan 20141, Italy
| | | | - Cristina Cereda
- Genomic and Post-Genomic Center, National Neurological Institute C. Mondino, Pavia 27100, Italy
| | - Martina Lari
- Department of Biology, University of Florence, Florence 50122, Italy
| | - David Caramelli
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Department of Biology, University of Padua, Padua 35121, Italy
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Ronny Friedrich
- Curt Engelhorn Center Archaeometry (CEZA), Mannheim 68159, Germany
| | - Corina Knipper
- Curt Engelhorn Center Archaeometry (CEZA), Mannheim 68159, Germany
| | - Anna Olivieri
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain; GenPoB Research Group, Instituto de Investigación Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706 Galicia, Spain
| | - Richard Cooke
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; Sistema Nacional de Investigadores, Secretaría Nacional de Ciencia y Tecnología, Ciudad del Saber, Clayton 0816-02852, Panama
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Department of Biology-Genetics, University of Bari, Bari 70125, Italy
| | - Jorge Motta
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Juan Guillermo Martín
- Department of History and Social Sciences, Universidad del Norte, Barranquilla 080001, Colombia; Coiba Scientific Station (COIBA AIP), City of Knowledge, Clayton 0843-03081, Panama
| | - Ornella Semino
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Ripan Singh Malhi
- Department of Anthropology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy.
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Mutti G, Raveane A, Pagano A, Bertolini F, Semino O, Balestrazzi A, Macovei A. Plant TDP1 (Tyrosyl-DNA Phosphodiesterase 1): A Phylogenetic Perspective and Gene Expression Data Mining. Genes (Basel) 2020; 11:E1465. [PMID: 33297410 PMCID: PMC7762302 DOI: 10.3390/genes11121465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 01/28/2023] Open
Abstract
The TDP1 (tyrosyl-DNA phosphodiesterase 1) enzyme removes the non-specific covalent intermediates between topoisomerase I and DNA, thus playing a crucial role in preventing DNA damage. While mammals possess only one TDP1 gene, in plants two genes (TDP1α and TDP1β) are present constituting a small gene subfamily. These display a different domain structure and appear to perform non-overlapping functions in the maintenance of genome integrity. Namely, the HIRAN domain identified in TDP1β is involved in the interaction with DNA during the recognition of stalled replication forks. The availability of transcriptomic databases in a growing variety of experimental systems provides new opportunities to fill the current gaps of knowledge concerning the evolutionary origin and the specialized roles of TDP1 genes in plants. Whereas a phylogenetic approach has been used to track the evolution of plant TDP1 protein, transcriptomic data from a selection of representative lycophyte, eudicots, and monocots have been implemented to explore the transcriptomic dynamics in different tissues and a variety of biotic and abiotic stress conditions. While the phylogenetic analysis indicates that TDP1α is of non-plant origin and TDP1β is plant-specific originating in ancient vascular plants, the gene expression data mining comparative analysis pinpoints for tissue- and stress-specific responses.
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Affiliation(s)
- Giacomo Mutti
- Department of Biology and Biotechnology ‘L. Spallanzani’, University of Pavia, via Ferrata 9, 27100 Pavia, Italy; (G.M.); (A.P.); (O.S.); (A.B.)
| | - Alessandro Raveane
- Department of Biology and Biotechnology ‘L. Spallanzani’, University of Pavia, via Ferrata 9, 27100 Pavia, Italy; (G.M.); (A.P.); (O.S.); (A.B.)
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, via Ripamonti 435, 20141 Milan, Italy;
| | - Andrea Pagano
- Department of Biology and Biotechnology ‘L. Spallanzani’, University of Pavia, via Ferrata 9, 27100 Pavia, Italy; (G.M.); (A.P.); (O.S.); (A.B.)
| | - Francesco Bertolini
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, via Ripamonti 435, 20141 Milan, Italy;
| | - Ornella Semino
- Department of Biology and Biotechnology ‘L. Spallanzani’, University of Pavia, via Ferrata 9, 27100 Pavia, Italy; (G.M.); (A.P.); (O.S.); (A.B.)
| | - Alma Balestrazzi
- Department of Biology and Biotechnology ‘L. Spallanzani’, University of Pavia, via Ferrata 9, 27100 Pavia, Italy; (G.M.); (A.P.); (O.S.); (A.B.)
| | - Anca Macovei
- Department of Biology and Biotechnology ‘L. Spallanzani’, University of Pavia, via Ferrata 9, 27100 Pavia, Italy; (G.M.); (A.P.); (O.S.); (A.B.)
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Falvo P, Orecchioni S, Hillje R, Raveane A, Mancuso P, Camisaschi C, Luzi L, Pelicci P, Bertolini F. Cyclophosphamide and Vinorelbine Activate Stem-Like CD8 + T Cells and Improve Anti-PD-1 Efficacy in Triple-Negative Breast Cancer. Cancer Res 2020; 81:685-697. [PMID: 33268528 DOI: 10.1158/0008-5472.can-20-1818] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 11/16/2022]
Abstract
Checkpoint inhibitors (CI) instigate anticancer immunity in many neoplastic diseases, albeit only in a fraction of patients. The clinical success of cyclophosphamide (C)-based haploidentical stem-cell transplants indicates that this drug may re-orchestrate the immune system. Using models of triple-negative breast cancer (TNBC) with different intratumoral immune contexture, we demonstrate that a combinatorial therapy of intermittent C, CI, and vinorelbine activates antigen-presenting cells (APC), and abrogates local and metastatic tumor growth by a T-cell-related effect. Single-cell transcriptome analysis of >50,000 intratumoral immune cells after therapy treatment showed a gene signature suggestive of a change resulting from exposure to a mitogen, ligand, or antigen for which it is specific, as well as APC-to-T-cell adhesion. This transcriptional program also increased intratumoral Tcf1+ stem-like CD8+ T cells and altered the balance between terminally and progenitor-exhausted T cells favoring the latter. Overall, our data support the clinical investigation of this therapy in TNBC. SIGNIFICANCE: A combinatorial therapy in mouse models of breast cancer increases checkpoint inhibition by activating antigen-presenting cells, enhancing intratumoral Tcf1+ stem-like CD8+ T cells, and increasing progenitor exhausted CD8+ T cells.
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Affiliation(s)
- Paolo Falvo
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Stefania Orecchioni
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Roman Hillje
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Alessandro Raveane
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Patrizia Mancuso
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Chiara Camisaschi
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Lucilla Luzi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - PierGiuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Francesco Bertolini
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy.
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Mancuso P, Gidaro A, Gregato G, Raveane A, Cremonesi P, Quarna J, Caccia S, Gusso L, Rusconi S, Giacomelli A, Cogliati C, Bertolini F. Circulating endothelial progenitors are increased in COVID-19 patients and correlate with SARS-CoV-2 RNA in severe cases. J Thromb Haemost 2020; 18:2744-2750. [PMID: 32762140 PMCID: PMC7436444 DOI: 10.1111/jth.15044] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [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: 05/13/2020] [Revised: 06/26/2020] [Accepted: 07/31/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND During the course of COVID-19, the disease caused by the new coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), thrombotic phenomena and/or diffuse vascular damage are frequent, and viral elements have been observed within endothelial cells. OBJECTIVES CD146 + circulating endothelial cells (CD146 + CECs) and their progenitors (CEPs) are increased in cardiovascular, thrombotic, infectious, and cancer diseases. The present study was designed to investigate their kinetics in novel coronavirus (COVID-19) patients. METHODS We used a validated flow cytometry procedure to enumerate viable and apoptotic CD146 + CECs and CEPs in COVID-19 patients during the course of the disease and in patients who recovered. RESULTS Viable CEPs per milliliter were significantly increased in COVID-19 patients compared with healthy controls. This increase was observed in patients with mild symptoms and not further augmented in patients with severe symptoms. In patients who recovered, CEPs decreased, but were in a range still significantly higher than normal controls. Regarding mature CD146 + CECs, in COVID-19 patients, their absolute number was similar to those observed in healthy controls, but the viable/apoptotic CD146 + CEC ratio was significantly different. Both mild and severe COVID-19 patients had significantly less apoptotic CD146 + CECs compared with healthy controls. Patients who recovered had significantly less CD146 + CECs per milliliter when compared with controls as well as to mild and severe COVID-19 patients. A positive correlation was found between the copies of SARS-CoV-2 RNA in the cellular fraction and apoptotic CEPs per milliliter in severe COVID-19 patients. CONCLUSIONS CD146 + CECs and CEPs might be investigated as candidate biomarkers of endothelial damage in COVID-19 patients.
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Affiliation(s)
- Patrizia Mancuso
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Antonio Gidaro
- ASST Fatebenefratelli Sacco, Department of Biomedical and Clinical Sciences, "Luigi Sacco" Hospital, University of Milan, Milan, Italy
| | - Giuliana Gregato
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Alessandro Raveane
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Paola Cremonesi
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Jessica Quarna
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Sonia Caccia
- ASST Fatebenefratelli Sacco, Department of Biomedical and Clinical Sciences, "Luigi Sacco" Hospital, University of Milan, Milan, Italy
| | - Luca Gusso
- ASST Fatebenefratelli Sacco, Department of Biomedical and Clinical Sciences, "Luigi Sacco" Hospital, University of Milan, Milan, Italy
| | - Stefano Rusconi
- ASST Fatebenefratelli Sacco, Department of Biomedical and Clinical Sciences, "Luigi Sacco" Hospital, University of Milan, Milan, Italy
| | - Andrea Giacomelli
- ASST Fatebenefratelli Sacco, Department of Biomedical and Clinical Sciences, "Luigi Sacco" Hospital, University of Milan, Milan, Italy
| | - Chiara Cogliati
- ASST Fatebenefratelli Sacco, Department of Biomedical and Clinical Sciences, "Luigi Sacco" Hospital, University of Milan, Milan, Italy
| | - Francesco Bertolini
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
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Falvo P, Orecchioni S, Hillje R, Raveane A, Mancuso P, Camisaschi C, Luzi L, Bertolini F. Abstract 900: Intermittent cyclophosphamide and vinorelbine reshape the immune cell environment, induce T cell clonal replacement and increase the efficacy of PD-1 inhibition in models of triple negative breast cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The clinical success of cyclophosphamide (Cy)-based haploidentical stem cell transplants in hematological malignancies indicates that this drug has the potential to reorchestrate the immune system against cancer cells. Along a similar way, Cy is administered before the infusion of CAR-T cells to improve their clinical efficacy. We have previously found that daily, low/medium-dose Cy (20mg/Kg), in association with vinorelbine (V) was able to improve the preclinical efficacy of checkpoint inhibitors (CIs) anti-PD-1 and anti-PD-L1 in preclinical models of breast cancer and lymphoma (Orecchioni et al, 2018). Randomized clinical trials have recently indicated that the addition of CIs to other chemotherapy drugs such as taxanes (T), doxorubicin (D), or platinum (P) might be beneficial in triple negative breast cancer (TNBC) patients. Thus, we designed the present study in two orthotopic, immunocompetent, local and metastatic models of TNBC (CI-resistant 4T1 and EMT6, moderately responsive to CIs) to investigate whether Cy and V, in different schedules and doses, were more effective than T, D, or P. In vivo studies in local and metastatic models using both 4T1 and EMT6 TNBC cells clearly indicated that intermittent (ie every 6 days), medium-dosage (140 mg/Kg) Cy, was more effective than any other combinatorial regimens including CIs plus daily low/medium-dose Cy, or T, D, or P at their regular dosages. The association of V further increased the preclinical efficacy of intermittent Cy plus CIs, and abrogated tumor growth in both 4T1 and EMT6 models. In vivo studies with neutralizing monoclonal antibodies targeting in separate experiments T, B, NK, and myeloid cells demonstrated that CD3+CD4+, CD3+CD8+ T cells as well as CD11b+ monocyte/macrophage dendritic cells were crucial to abrogate tumor growth in TNBC-bearing mice treated with intermittent Cy, V and CIs. Single-cell transcriptome analysis of more than 60,000 intratumoral immune cells and flow cytometry studies in circulating and intratumoral subsets of immune cells indicated that V promoted the generation and maturation of myeloid APC cells, and that intermittent Cy generated new clones of tumor-infiltrating CD3+CD4+ and CD3+CD8+ TCR alpha beta cells. After treatment with intermittent Cy, V and CIs, intratumoral immune cells showed a unique gene signature of 42 genes (CD3D, Ptprc, CD69, Lat, Lck, CD2, CD28, CD27, and CD3E among others) suggestive of a change in morphology and behavior resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, as well as APC-to-T cell adhesion. Taken together, our data support the hypothesis that APC priming and T cell clonal replacement can significantly improve CI efficacy in vivo in TNBC models. We are further investigating the Cy-related mechanisms inducing intratumoral T-cell clonal replacement and how these T cells cooperate with V-induced APCs.
Citation Format: Paolo Falvo, Stefania Orecchioni, Roman Hillje, Alessandro Raveane, Patrizia Mancuso, Chiara Camisaschi, Lucilla Luzi, Francesco Bertolini. Intermittent cyclophosphamide and vinorelbine reshape the immune cell environment, induce T cell clonal replacement and increase the efficacy of PD-1 inhibition in models of triple negative breast cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 900.
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Affiliation(s)
- Paolo Falvo
- European Institute of Oncology, Milan, Italy
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Modi A, Lancioni H, Cardinali I, Capodiferro MR, Rambaldi Migliore N, Hussein A, Strobl C, Bodner M, Schnaller L, Xavier C, Rizzi E, Bonomi Ponzi L, Vai S, Raveane A, Cavadas B, Semino O, Torroni A, Olivieri A, Lari M, Pereira L, Parson W, Caramelli D, Achilli A. The mitogenome portrait of Umbria in Central Italy as depicted by contemporary inhabitants and pre-Roman remains. Sci Rep 2020; 10:10700. [PMID: 32612271 PMCID: PMC7329865 DOI: 10.1038/s41598-020-67445-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 05/22/2020] [Indexed: 12/19/2022] Open
Abstract
Umbria is located in Central Italy and took the name from its ancient inhabitants, the Umbri, whose origins are still debated. Here, we investigated the mitochondrial DNA (mtDNA) variation of 545 present-day Umbrians (with 198 entire mitogenomes) and 28 pre-Roman individuals (obtaining 19 ancient mtDNAs) excavated from the necropolis of Plestia. We found a rather homogeneous distribution of western Eurasian lineages across the region, with few notable exceptions. Contemporary inhabitants of the eastern part, delimited by the Tiber River and the Apennine Mountains, manifest a peculiar mitochondrial proximity to central-eastern Europeans, mainly due to haplogroups U4 and U5a, and an overrepresentation of J (30%) similar to the pre-Roman remains, also excavated in East Umbria. Local genetic continuities are further attested to by six terminal branches (H1e1, J1c3, J2b1, U2e2a, U8b1b1 and K1a4a) shared between ancient and modern mitogenomes. Eventually, we identified multiple inputs from various population sources that likely shaped the mitochondrial gene pool of ancient Umbri over time, since early Neolithic, including gene flows with central-eastern Europe. This diachronic mtDNA portrait of Umbria fits well with the genome-wide population structure identified on the entire peninsula and with historical sources that list the Umbri among the most ancient Italic populations.
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Affiliation(s)
- Alessandra Modi
- Department of Biology, University of Florence, 50122, Florence, Italy
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123, Perugia, Italy.
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123, Perugia, Italy
| | - Marco R Capodiferro
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Nicola Rambaldi Migliore
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Abir Hussein
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Christina Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Lisa Schnaller
- Institute of Legal Medicine, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Ermanno Rizzi
- Istituto di Tecnologie Biomediche, CNR, Segrate, 20090, Milan, Italy
| | | | - Stefania Vai
- Department of Biology, University of Florence, 50122, Florence, Italy
| | - Alessandro Raveane
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Bruno Cavadas
- IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Porto, Portugal.,i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200-135, Porto, Portugal
| | - Ornella Semino
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy
| | - Martina Lari
- Department of Biology, University of Florence, 50122, Florence, Italy
| | - Luisa Pereira
- IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Porto, Portugal.,i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200-135, Porto, Portugal
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020, Innsbruck, Austria.,Forensic Science Program, The Pennsylvania State University, University Park, PA, 16801, USA
| | - David Caramelli
- Department of Biology, University of Florence, 50122, Florence, Italy
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100, Pavia, Italy.
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23
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Grugni V, Raveane A, Colombo G, Nici C, Crobu F, Ongaro L, Battaglia V, Sanna D, Al-Zahery N, Fiorani O, Lisa A, Ferretti L, Achilli A, Olivieri A, Francalacci P, Piazza A, Torroni A, Semino O. Y-chromosome and Surname Analyses for Reconstructing Past Population Structures: The Sardinian Population as a Test Case. Int J Mol Sci 2019; 20:E5763. [PMID: 31744094 PMCID: PMC6888588 DOI: 10.3390/ijms20225763] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 10/16/2019] [Revised: 11/11/2019] [Accepted: 11/14/2019] [Indexed: 11/17/2022] Open
Abstract
Many anthropological, linguistic, genetic and genomic analyses have been carried out to evaluate the potential impact that evolutionary forces had in shaping the present-day Sardinian gene pool, the main outlier in the genetic landscape of Europe. However, due to the homogenizing effect of internal movements, which have intensified over the past fifty years, only partial information has been obtained about the main demographic events. To overcome this limitation, we analyzed the male-specific region of the Y chromosome in three population samples obtained by reallocating a large number of Sardinian subjects to the place of origin of their monophyletic surnames, which are paternally transmitted through generations in most of the populations, much like the Y chromosome. Three Y-chromosome founding lineages, G2-L91, I2-M26 and R1b-V88, were identified as strongly contributing to the definition of the outlying position of Sardinians in the European genetic context and marking a significant differentiation within the island. The present distribution of these lineages does not always mirror that detected in ancient DNAs. Our results show that the analysis of the Y-chromosome gene pool coupled with a sampling method based on the origin of the family name, is an efficient approach to unravelling past heterogeneity, often hidden by recent movements, in the gene pool of modern populations. Furthermore, the reconstruction and comparison of past genetic isolates represent a starting point to better assess the genetic information deriving from the increasing number of available ancient DNA samples.
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Affiliation(s)
- Viola Grugni
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Alessandro Raveane
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Giulia Colombo
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Carmen Nici
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Francesca Crobu
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), 09042 Monserrato, Italy
| | - Linda Ongaro
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
- Estonian Biocentre, Institute of Genomics, Riia 23, 51010 Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, Riia 23, 51010 Tartu, Estonia
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Daria Sanna
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy
| | - Nadia Al-Zahery
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Ornella Fiorani
- Istituto di Genetica Molecolare “L.L. Cavalli-Sforza”, Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy; (O.F.); (A.L.)
| | - Antonella Lisa
- Istituto di Genetica Molecolare “L.L. Cavalli-Sforza”, Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy; (O.F.); (A.L.)
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Paolo Francalacci
- Dipartimento di Scienza della Vita e dell’Ambiente, Università di Cagliari, 09123 Cagliari, Italy;
| | - Alberto Piazza
- Dipartimento di Scienze Mediche, Scuola di Medicina, Università di Torino, 10124 Torino, Italy;
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
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24
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Ongaro L, Scliar MO, Flores R, Raveane A, Marnetto D, Sarno S, Gnecchi-Ruscone GA, Alarcón-Riquelme ME, Patin E, Wangkumhang P, Hellenthal G, Gonzalez-Santos M, King RJ, Kouvatsi A, Balanovsky O, Balanovska E, Atramentova L, Turdikulova S, Mastana S, Marjanovic D, Mulahasanovic L, Leskovac A, Lima-Costa MF, Pereira AC, Barreto ML, Horta BL, Mabunda N, May CA, Moreno-Estrada A, Achilli A, Olivieri A, Semino O, Tambets K, Kivisild T, Luiselli D, Torroni A, Capelli C, Tarazona-Santos E, Metspalu M, Pagani L, Montinaro F. The Genomic Impact of European Colonization of the Americas. Curr Biol 2019; 29:3974-3986.e4. [PMID: 31735679 DOI: 10.1016/j.cub.2019.09.076] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [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: 07/05/2019] [Revised: 09/06/2019] [Accepted: 09/30/2019] [Indexed: 12/30/2022]
Abstract
The human genetic diversity of the Americas has been affected by several events of gene flow that have continued since the colonial era and the Atlantic slave trade. Moreover, multiple waves of migration followed by local admixture occurred in the last two centuries, the impact of which has been largely unexplored. Here, we compiled a genome-wide dataset of ∼12,000 individuals from twelve American countries and ∼6,000 individuals from worldwide populations and applied haplotype-based methods to investigate how historical movements from outside the New World affected (1) the genetic structure, (2) the admixture profile, (3) the demographic history, and (4) sex-biased gene-flow dynamics of the Americas. We revealed a high degree of complexity underlying the genetic contribution of European and African populations in North and South America, from both geographic and temporal perspectives, identifying previously unreported sources related to Italy, the Middle East, and to specific regions of Africa.
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Affiliation(s)
- Linda Ongaro
- Estonian Biocentre, Institute of Genomics, Riia 23, Tartu 51010, Estonia; Department of Evolutionary Biology, Institute of Molecular and Cell Biology, Riia 23, Tartu 51010, Estonia.
| | - Marilia O Scliar
- Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo, São Paulo, SP 05508-090, Brazil; Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Rodrigo Flores
- Estonian Biocentre, Institute of Genomics, Riia 23, Tartu 51010, Estonia
| | - Alessandro Raveane
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia 27100, Italy
| | - Davide Marnetto
- Estonian Biocentre, Institute of Genomics, Riia 23, Tartu 51010, Estonia
| | - Stefania Sarno
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna 40100, Italy
| | - Guido A Gnecchi-Ruscone
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna 40100, Italy; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Marta E Alarcón-Riquelme
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain
| | - Etienne Patin
- Human Evolutionary Genetics Unit, Pasteur Institute, UMR2000, CNRS, Paris 75015, France
| | - Pongsakorn Wangkumhang
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | | | - Roy J King
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305-5101, USA
| | - Anastasia Kouvatsi
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Oleg Balanovsky
- Vavilov Institute of General Genetics, Ulitsa Gubkina, 3, Moscow 117971, Russia; Research Centre for Medical Genetics, Moskvorech'ye Ulitsa, 1, Moscow 115478, Russia; Biobank of North Eurasia, Kotlyakovskaya Ulitsa, 3 строение 12, Moscow 115201, Russia
| | - Elena Balanovska
- Vavilov Institute of General Genetics, Ulitsa Gubkina, 3, Moscow 117971, Russia; Research Centre for Medical Genetics, Moskvorech'ye Ulitsa, 1, Moscow 115478, Russia; Biobank of North Eurasia, Kotlyakovskaya Ulitsa, 3 строение 12, Moscow 115201, Russia
| | - Lubov Atramentova
- Department of Genetics and Cytology, V.N. Karazin Kharkiv National University, Kharkiv 61022, Ukraine
| | - Shahlo Turdikulova
- Laboratory of Genomics, Institute of Bioorganic Chemistry, Academy of Sciences Republic of Uzbekistan, Tashkent 100047, Uzbekistan
| | - Sarabjit Mastana
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough LE11 3TU, UK
| | - Damir Marjanovic
- Department of Genetics and Bioengineering, Faculty of Engineering and Information Technologies, International Burch University, Sarajevo 71000, Bosnia and Herzegovina; Institute for Anthropological Researches, Zagreb, Croatia
| | | | - Andreja Leskovac
- Vinca Institute of Nuclear Sciences, University of Belgrade, M. Petrovica Alasa 12-14, Belgrade 11001, Serbia
| | - Maria F Lima-Costa
- Instituto de Pesquisa Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, MG 30190-002, Brazil
| | - Alexandre C Pereira
- Instituto do Coração, Universidade de São Paulo, São Paulo, SP 05403-900, Brazil
| | - Mauricio L Barreto
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, BA 0110-040, Brazil; Center of Data and Knowledge Integration for Health (CIDACS), Fundação Oswaldo Cruz (FIOCRUZ), Salvador, BA 41745-715, Brazil
| | - Bernardo L Horta
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, 464, Pelotas, RS 96001-970, Brazil
| | - Nédio Mabunda
- Instituto Nacional de Saúde, Distrito de Marracuene, Estrada Nacional N 1, Província de Maputo, Maputo 1120, Mozambique
| | - Celia A May
- Department of Genetics & Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, Mexico
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia 27100, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia 27100, Italy
| | - Ornella Semino
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia 27100, Italy
| | - Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, Riia 23, Tartu 51010, Estonia
| | - Toomas Kivisild
- Department of Human Genetics, KU Leuven, Herestraat 49 - box 602, Leuven 3000, Belgium
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Ravenna Campus, Ravenna 48100, Italy
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia 27100, Italy
| | | | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, Riia 23, Tartu 51010, Estonia
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, Riia 23, Tartu 51010, Estonia; Department of Biology, University of Padua, Via Ugo Bassi 58B, Padua 35100, Italy
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, Riia 23, Tartu 51010, Estonia; Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK.
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25
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Tamm E, Di Cristofaro J, Mazières S, Pennarun E, Kushniarevich A, Raveane A, Semino O, Chiaroni J, Pereira L, Metspalu M, Montinaro F. Genome-wide analysis of Corsican population reveals a close affinity with Northern and Central Italy. Sci Rep 2019; 9:13581. [PMID: 31537848 PMCID: PMC6753063 DOI: 10.1038/s41598-019-49901-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/31/2019] [Indexed: 01/13/2023] Open
Abstract
Despite being the fourth largest island in the Mediterranean basin, the genetic variation of Corsica has not been explored as exhaustively as Sardinia, which is situated only 11 km South. However, it is likely that the populations of the two islands shared, at least in part, similar demographic histories. Moreover, the relative small size of the Corsica may have caused genetic isolation, which, in turn, might be relevant under medical and translational perspectives. Here we analysed genome wide data of 16 Corsicans, and integrated with newly (33 individuals) and previously generated samples from West Eurasia and North Africa. Allele frequency, haplotype-based, and ancient genome analyses suggest that although Sardinia and Corsica may have witnessed similar isolation and migration events, the latter is genetically closer to populations from continental Europe, such as Northern and Central Italians.
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Affiliation(s)
- Erika Tamm
- Institute of Genomics, University of Tartu, Tartu, Estonia.
| | - Julie Di Cristofaro
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France.,Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | | | - Erwan Pennarun
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Alena Kushniarevich
- Institute of Genomics, University of Tartu, Tartu, Estonia.,Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, 220072, Belarus
| | - Alessandro Raveane
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani" Università di Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani" Università di Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Jacques Chiaroni
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France.,Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | - Luisa Pereira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), 4200-135, Porto, Portugal
| | - Mait Metspalu
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Francesco Montinaro
- Institute of Genomics, University of Tartu, Tartu, Estonia. .,Department of Zoology, University of Oxford, Oxford, UK.
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26
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Perego UA, Bodner M, Raveane A, Woodward SR, Montinaro F, Parson W, Achilli A. Resolving a 150-year-old paternity case in Mormon history using DTC autosomal DNA testing of distant relatives. Forensic Sci Int Genet 2019; 42:1-7. [DOI: 10.1016/j.fsigen.2019.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/31/2019] [Accepted: 05/31/2019] [Indexed: 01/01/2023]
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27
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Raveane A, Aneli S, Montinaro F, Athanasiadis G, Barlera S, Birolo G, Boncoraglio G, Di Blasio AM, Di Gaetano C, Pagani L, Parolo S, Paschou P, Piazza A, Stamatoyannopoulos G, Angius A, Brucato N, Cucca F, Hellenthal G, Mulas A, Peyret-Guzzon M, Zoledziewska M, Baali A, Bycroft C, Cherkaoui M, Chiaroni J, Di Cristofaro J, Dina C, Dugoujon JM, Galan P, Giemza J, Kivisild T, Mazieres S, Melhaoui M, Metspalu M, Myers S, Pereira L, Ricaut FX, Brisighelli F, Cardinali I, Grugni V, Lancioni H, Pascali VL, Torroni A, Semino O, Matullo G, Achilli A, Olivieri A, Capelli C. Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe. Sci Adv 2019; 5:eaaw3492. [PMID: 31517044 PMCID: PMC6726452 DOI: 10.1126/sciadv.aaw3492] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/10/2019] [Accepted: 08/06/2019] [Indexed: 05/10/2023]
Abstract
European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non-steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.
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Affiliation(s)
- A. Raveane
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
- Department of Zoology, University of Oxford, Oxford, UK
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
| | - S. Aneli
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
| | - F. Montinaro
- Department of Zoology, University of Oxford, Oxford, UK
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
| | - G. Athanasiadis
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - S. Barlera
- Department of Cardiovascular Research, Istituto di Ricovero e Cura a Carattere Scientifico–Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - G. Birolo
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - G. Boncoraglio
- Department of Cerebrovascular Diseases, IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
- PhD Program in Neuroscience, University Milano-Bicocca, Monza, Italy
| | - A. M. Di Blasio
- Istituto Auxologico Italiano, IRCCS, Centro di Ricerche e Tecnologie Biomediche, Milano, Italy
| | - C. Di Gaetano
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - L. Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- APE lab, Department of Biology, University of Padua, Padua, Italy
| | - S. Parolo
- Computational Biology Unit, Institute of Molecular Genetics, National Research Council, Pavia, Italy
| | - P. Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - A. Piazza
- Department of Medical Sciences, University of Turin, Turin, Italy
- Academy of Sciences, Turin, Italy
| | - G. Stamatoyannopoulos
- Department of Medicine and Genome Sciences, University of Washington, Seattle, WA, USA
| | - A. Angius
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - N. Brucato
- Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France
| | - F. Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - G. Hellenthal
- University College London Genetics Institute (UGI), University College London, London, UK
| | - A. Mulas
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Lanusei, Italy
| | - M. Peyret-Guzzon
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M. Zoledziewska
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - A. Baali
- Faculté des Sciences Semlalia de Marrakech (FSSM), Université Cadi Ayyad, Marrakech, Morocco
| | - C. Bycroft
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M. Cherkaoui
- Faculté des Sciences Semlalia de Marrakech (FSSM), Université Cadi Ayyad, Marrakech, Morocco
| | - J. Chiaroni
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
- Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | - J. Di Cristofaro
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
- Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | - C. Dina
- l’institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | - J. M. Dugoujon
- Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France
| | - P. Galan
- Equipe de Recherche en Epidémiologie Nutritionnelle (EREN), Centre de Recherche en Epidémiologie et Statistiques, Université Paris 13/Inserm U1153/Inra U1125/ Cnam, COMUE Sorbonne Paris Cité, F-93017 Bobigny, France
| | - J. Giemza
- l’institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | - T. Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Human Genetics, KU Leuven, Herestraat 49, box 604, Leuven 3000, Belgium
| | - S. Mazieres
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
| | - M. Melhaoui
- Faculté des Sciences, Université Mohammed Premier, Oujda, Morocco
| | - M. Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - S. Myers
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - L. Pereira
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP–Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| | - F. X. Ricaut
- Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France
| | - F. Brisighelli
- Section of Legal Medicine, Institute of Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - I. Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - V. Grugni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - H. Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - V. L. Pascali
- Section of Legal Medicine, Institute of Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - A. Torroni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - O. Semino
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - G. Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - A. Achilli
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - A. Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - C. Capelli
- Department of Zoology, University of Oxford, Oxford, UK
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
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Grugni V, Raveane A, Ongaro L, Battaglia V, Trombetta B, Colombo G, Capodiferro MR, Olivieri A, Achilli A, Perego UA, Motta J, Tribaldos M, Woodward SR, Ferretti L, Cruciani F, Torroni A, Semino O. Analysis of the human Y-chromosome haplogroup Q characterizes ancient population movements in Eurasia and the Americas. BMC Biol 2019; 17:3. [PMID: 30674303 PMCID: PMC6345020 DOI: 10.1186/s12915-018-0622-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 10/01/2018] [Accepted: 12/21/2018] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Recent genome studies of modern and ancient samples have proposed that Native Americans derive from a subset of the Eurasian gene pool carried to America by an ancestral Beringian population, from which two well-differentiated components originated and subsequently mixed in different proportion during their spread in the Americas. To assess the timing, places of origin and extent of admixture between these components, we performed an analysis of the Y-chromosome haplogroup Q, which is the only Pan-American haplogroup and accounts for virtually all Native American Y chromosomes in Mesoamerica and South America. RESULTS Our analyses of 1.5 Mb of 152 Y chromosomes, 34 re-sequenced in this work, support a "coastal and inland routes scenario" for the first entrance of modern humans in North America. We show a major phase of male population growth in the Americas after 15 thousand years ago (kya), followed by a period of constant population size from 8 to 3 kya, after which a secondary sign of growth was registered. The estimated dates of the first expansion in Mesoamerica and the Isthmo-Colombian Area, mainly revealed by haplogroup Q-Z780, suggest an entrance in South America prior to 15 kya. During the global constant population size phase, local South American hints of growth were registered by different Q-M848 sub-clades. These expansion events, which started during the Holocene with the improvement of climatic conditions, can be ascribed to multiple cultural changes rather than a steady population growth and a single cohesive culture diffusion as it occurred in Europe. CONCLUSIONS We established and dated a detailed haplogroup Q phylogeny that provides new insights into the geographic distribution of its Eurasian and American branches in modern and ancient samples.
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Affiliation(s)
- Viola Grugni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Alessandro Raveane
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Linda Ongaro
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy.,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Giulia Colombo
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Marco Rosario Capodiferro
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Ugo A Perego
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Jorge Motta
- Secretaría Nacional de Ciencia, Tecnología e Innovación (SENACYT), Panama City, Panama
| | - Maribel Tribaldos
- Department of Health Technology Assessment and Economic Evaluation, Panama City, Panama
| | | | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Via Ferrata, 9, 27100, Pavia, Italy.
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29
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Grugni V, Raveane A, Mattioli F, Battaglia V, Sala C, Toniolo D, Ferretti L, Gardella R, Achilli A, Olivieri A, Torroni A, Passarino G, Semino O. Reconstructing the genetic history of Italians: new insights from a male (Y-chromosome) perspective. Ann Hum Biol 2018; 45:44-56. [PMID: 29382284 DOI: 10.1080/03014460.2017.1409801] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Due to its central and strategic position in Europe and in the Mediterranean Basin, the Italian Peninsula played a pivotal role in the first peopling of the European continent and has been a crossroad of peoples and cultures since then. AIM This study aims to gain more information on the genetic structure of modern Italian populations and to shed light on the migration/expansion events that led to their formation. SUBJECTS AND METHODS High resolution Y-chromosome variation analysis in 817 unrelated males from 10 informative areas of Italy was performed. Haplogroup frequencies and microsatellite haplotypes were used, together with available data from the literature, to evaluate Mediterranean and European inputs and date their arrivals. RESULTS Fifty-three distinct Y-chromosome lineages were identified. Their distribution is in general agreement with geography, southern populations being more differentiated than northern ones. CONCLUSIONS A complex genetic structure reflecting the multifaceted peopling pattern of the Peninsula emerged: southern populations show high similarity with those from the Middle East and Southern Balkans, while those from Northern Italy are close to populations of North-Western Europe and the Northern Balkans. Interestingly, the population of Volterra, an ancient town of Etruscan origin in Tuscany, displays a unique Y-chromosomal genetic structure.
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Affiliation(s)
- Viola Grugni
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Alessandro Raveane
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Francesca Mattioli
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Vincenza Battaglia
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Cinzia Sala
- b Divisione di Genetica e Biologia Cellulare , Istituto Scientifico San Raffaele , Milano , Italy
| | - Daniela Toniolo
- b Divisione di Genetica e Biologia Cellulare , Istituto Scientifico San Raffaele , Milano , Italy
| | - Luca Ferretti
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Rita Gardella
- c Dipartimento di Medicina Molecolare e Traslazionale , Università di Brescia , Brescia , Italy
| | - Alessandro Achilli
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Anna Olivieri
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Antonio Torroni
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
| | - Giuseppe Passarino
- d Dipartimento di Biologia, Ecologia e Scienze della Terra , Università della Calabria , Arcavacata di Rende , Cosenza , Italy
| | - Ornella Semino
- a Dipartimento di Biologia e Biotecnologie "L. Spallanzani" , Università di Pavia , Pavia , Italy
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30
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Balanovsky O, Gurianov V, Zaporozhchenko V, Balaganskaya O, Urasin V, Zhabagin M, Grugni V, Canada R, Al-Zahery N, Raveane A, Wen SQ, Yan S, Wang X, Zalloua P, Marafi A, Koshel S, Semino O, Tyler-Smith C, Balanovska E. Phylogeography of human Y-chromosome haplogroup Q3-L275 from an academic/citizen science collaboration. BMC Evol Biol 2017; 17:18. [PMID: 28251872 PMCID: PMC5333174 DOI: 10.1186/s12862-016-0870-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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] [Indexed: 11/17/2022] Open
Abstract
Background The Y-chromosome haplogroup Q has three major branches: Q1, Q2, and Q3. Q1 is found in both Asia and the Americas where it accounts for about 90% of indigenous Native American Y-chromosomes; Q2 is found in North and Central Asia; but little is known about the third branch, Q3, also named Q1b-L275. Here, we combined the efforts of population geneticists and genetic genealogists to use the potential of full Y-chromosome sequencing for reconstructing haplogroup Q3 phylogeography and suggest possible linkages to events in population history. Results We analyzed 47 fully sequenced Y-chromosomes and reconstructed the haplogroup Q3 phylogenetic tree in detail. Haplogroup Q3-L275, derived from the oldest known split within Eurasian/American haplogroup Q, most likely occurred in West or Central Asia in the Upper Paleolithic period. During the Mesolithic and Neolithic epochs, Q3 remained a minor component of the West Asian Y-chromosome pool and gave rise to five branches (Q3a to Q3e), which spread across West, Central and parts of South Asia. Around 3–4 millennia ago (Bronze Age), the Q3a branch underwent a rapid expansion, splitting into seven branches, some of which entered Europe. One of these branches, Q3a1, was acquired by a population ancestral to Ashkenazi Jews and grew within this population during the 1st millennium AD, reaching up to 5% in present day Ashkenazi. Conclusions This study dataset was generated by a massive Y-chromosome genotyping effort in the genetic genealogy community, and phylogeographic patterns were revealed by a collaboration of population geneticists and genetic genealogists. This positive experience of collaboration between academic and citizen science provides a model for further joint projects. Merging data and skills of academic and citizen science promises to combine, respectively, quality and quantity, generalization and specialization, and achieve a well-balanced and careful interpretation of the paternal-side history of human populations. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0870-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oleg Balanovsky
- Vavilov Institute of General Genetics, Moscow, Russia. .,Research Centre for Medical Genetics, Moscow, Russia.
| | | | - Valery Zaporozhchenko
- Vavilov Institute of General Genetics, Moscow, Russia.,Research Centre for Medical Genetics, Moscow, Russia
| | | | | | - Maxat Zhabagin
- National Laboratory Astana, Nazarbayev University, Astana, Republic of Kazakhstan
| | - Viola Grugni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | | | - Nadia Al-Zahery
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Alessandro Raveane
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Shao-Qing Wen
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Shi Yan
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xianpin Wang
- Department of Criminal Investigation, Xuanwei Public Security Bureau, Xuanwei, China
| | | | | | - Sergey Koshel
- Faculty of Geography, Lomonosov Moscow State University, Moscow, Russia
| | - Ornella Semino
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Elena Balanovska
- Vavilov Institute of General Genetics, Moscow, Russia.,Research Centre for Medical Genetics, Moscow, Russia
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31
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Grugni V, Battaglia V, Perego UA, Raveane A, Lancioni H, Olivieri A, Ferretti L, Woodward SR, Pascale JM, Cooke R, Myres N, Motta J, Torroni A, Achilli A, Semino O. Exploring the Y Chromosomal Ancestry of Modern Panamanians. PLoS One 2015; 10:e0144223. [PMID: 26636572 PMCID: PMC4670172 DOI: 10.1371/journal.pone.0144223] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [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: 03/31/2015] [Accepted: 11/16/2015] [Indexed: 01/07/2023] Open
Abstract
Geologically, Panama belongs to the Central American land-bridge between North and South America crossed by Homo sapiens >14 ka ago. Archaeologically, it belongs to a wider Isthmo-Colombian Area. Today, seven indigenous ethnic groups account for 12.3% of Panama’s population. Five speak Chibchan languages and are characterized by low genetic diversity and a high level of differentiation. In addition, no evidence of differential structuring between maternally and paternally inherited genes has been reported in isthmian Chibchan cultural groups. Recent data have shown that 83% of the Panamanian general population harbour mitochondrial DNAs (mtDNAs) of Native American ancestry. Considering differential male/female mortality at European contact and multiple degrees of geographical and genetic isolation over the subsequent five centuries, the Y-chromosome Native American component is expected to vary across different geographic regions and communities in Panama. To address this issue, we investigated Y-chromosome variation in 408 modern males from the nine provinces of Panama and one indigenous territory (the comarca of Kuna Yala). In contrast to mtDNA data, the Y-chromosome Native American component (haplogroup Q) exceeds 50% only in three populations facing the Caribbean Sea: the comarca of Kuna Yala and Bocas del Toro province where Chibchan languages are spoken by the majority, and the province of Colón where many Kuna and people of mixed indigenous-African-and-European descent live. Elsewhere the Old World component is dominant and mostly represented by western Eurasian haplogroups, which signal the strong male genetic impact of invaders. Sub-Saharan African input accounts for 5.9% of male haplotypes. This reflects the consequences of the colonial Atlantic slave trade and more recent influxes of West Indians of African heritage. Overall, our findings reveal a local evolution of the male Native American ancestral gene pool, and a strong but geographically differentiated unidirectional sex bias in the formation of local modern Panamanian populations.
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Affiliation(s)
- Viola Grugni
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Vincenza Battaglia
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Ugo Alessandro Perego
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Alessandro Raveane
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Luca Ferretti
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Scott R. Woodward
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
| | | | - Richard Cooke
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Natalie Myres
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
- Ancestry, Provo, Utah, United States of America
| | - Jorge Motta
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
| | - Antonio Torroni
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Alessandro Achilli
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Ornella Semino
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
- * E-mail:
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