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Article: Editorial: Cancer evolution: From biological insights to therapeutic opportunities.

Davis, Andrew A / Gerratana, Lorenzo / Mina, Marco

2022 Volume 13, Page(s) 984032

Language	English
Publishing date	2022-08-09
Publishing country	Switzerland
Document type	Editorial
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2022.984032
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Epistasis and evolutionary dependencies in human cancers.

Mina, Marco / Iyer, Arvind / Ciriello, Giovanni

Current opinion in genetics & development

2022 Volume 77, Page(s) 101989

Abstract: Cancer evolution is driven by the concerted action of multiple molecular alterations, which emerge and are selected during tumor progression. An alteration is selected when it provides an advantage to the tumor cell. However, the advantage provided by a ... ...

Abstract	Cancer evolution is driven by the concerted action of multiple molecular alterations, which emerge and are selected during tumor progression. An alteration is selected when it provides an advantage to the tumor cell. However, the advantage provided by a specific alteration depends on the tumor lineage, cell epigenetic state, and presence of additional alterations. In this case, we say that an evolutionary dependency exists between an alteration and what influences its selection. Epistatic interactions between altered genes lead to evolutionary dependencies (EDs), by favoring or vetoing specific combinations of events. Large-scale cancer genomics studies have discovered examples of such dependencies, and showed that they influence tumor progression, disease phenotypes, and therapeutic response. In the past decade, several algorithmic approaches have been proposed to infer EDs from large-scale genomics datasets. These methods adopt diverse strategies to address common challenges and shed new light on cancer evolutionary trajectories. Here, we review these efforts starting from a simple conceptualization of the problem, presenting the tackled and still unmet needs in the field, and discussing the implications of EDs in cancer biology and precision oncology.
MeSH term(s)	Humans ; Epistasis, Genetic ; Neoplasms/genetics ; Precision Medicine ; Genomics/methods ; Phenotype
Language	English
Publishing date	2022-09-29
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1077312-5
ISSN	1879-0380 ; 0959-437X
ISSN (online)	1879-0380
ISSN	0959-437X
DOI	10.1016/j.gde.2022.101989
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Article ; Online: A trait-based approach to both forestry and timber building can synchronize forest harvest and resilience.

Osborne, Peter / Aquilué, Núria / Mina, Marco / Moe, Kiel / Jemtrud, Michael / Messier, Christian

PNAS nexus

2023 Volume 2, Issue 8, Page(s) pgad254

Abstract: Along with forest managers, builders are key change agents of forest ecosystems' structure and composition through the specification and use of wood products. New forest management approaches are being advocated to increase the resilience and ... ...

Abstract	Along with forest managers, builders are key change agents of forest ecosystems' structure and composition through the specification and use of wood products. New forest management approaches are being advocated to increase the resilience and adaptability of forests to climate change and other natural disturbances. Such approaches call for a diversification of our forests based on species' functional traits that will dramatically change the harvested species composition, volume, and output of our forested landscapes. This calls for the wood-building industry to adapt its ways of operating. Accordingly, we expand the evaluation of the ecological resilience of forest ecosystems based on functional diversification to include a trait-based approach to building with wood. This trait-based plant-building framework can illustrate how forecasted forest changes in the coming decades may impact and guide decisions about wood-building practices, policies, and specifications. We apply this approach using a fragmented rural landscape in temperate southeastern Canada. We link seven functional groups based on the ecological traits of tree species in the region to a similar functional grouping of building traits to characterize the push and pull of managing forests and wood buildings together. We relied on a process-based forest landscape model to simulate long-term forest dynamics and timber harvesting to evaluate how various novel management approaches will interact with the changing global environment to affect the forest-building relationships. Our results suggest that adopting a whole system, plant-building approach to forests and wood buildings, is key to enhancing forest ecological and timber construction industry resilience.
Language	English
Publishing date	2023-08-29
Publishing country	England
Document type	Journal Article
ISSN	2752-6542
ISSN (online)	2752-6542
DOI	10.1093/pnasnexus/pgad254
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Thesis ; Online: Forest dynamics, management and ecosystem services

Mina, Marco

the future of European mountain forests in an era of climate change

2016

Keywords	EUROPA ; MOUNTAIN FORESTS (FORESTRY) ; MOUNTAIN FORESTS (PLANT ECOLOGY) ; THEORY OF FOREST GROWTH ; REGISTRATION OF FOREST GROWTH AND STAND STRUCTURE (FORESTRY) ; GLOBAL CHANGE + GLOBAL WARMING (CLIMATOLOGY) ; FOREST BIOLOGY + FOREST ECOLOGY (ECOLOGY) ; GLOBAL CHANGE + KLIMAERWÄRMUNG (KLIMATOLOGIE) ; FORSTMETEOROLOGIE + FORSTKLIMATOLOGIE ; WALDWACHSTUMSLEHRE ; ERFASSUNG VON WALDWACHSTUM UND BESTANDESSTRUKTUR (FORSTWIRTSCHAFT) ; SOZIALFUNKTION UND WOHLFAHRTSFUNKTION DES WALDES ; GEBIRGSWÄLDER (FORSTWIRTSCHAFT) ; GEBIRGSWÄLDER (PFLANZENÖKOLOGIE) ; FOREST CLIMATOLOGY + FOREST METEOROLOGY ; ÖKOSYSTEMDIENSTLEISTUNGEN (UMWELTÖKONOMIE) ; WALDBIOLOGIE + WALDÖKOLOGIE (ÖKOLOGIE) ; EUROPE ; SOCIAL FUNCTION AND WELFARE FUNCTION OF THE FOREST ; ECOSYSTEM SERVICES (ECOLOGICAL ECONOMICS) ; info:eu-repo/classification/ddc/630 ; Agriculture
Language	English
Publisher	ETH Zurich
Publishing country	ch
Document type	Thesis ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Systematic assessment of gene co-regulation within chromatin domains determines differentially active domains across human cancers.

Zufferey, Marie / Liu, Yuanlong / Tavernari, Daniele / Mina, Marco / Ciriello, Giovanni

Genome biology

2021 Volume 22, Issue 1, Page(s) 218

Abstract: Background: Spatial interactions and insulation of chromatin regions are associated with transcriptional regulation. Domains of frequent chromatin contacts are proposed as functional units, favoring and delimiting gene regulatory interactions. However, ... ...

Abstract	Background: Spatial interactions and insulation of chromatin regions are associated with transcriptional regulation. Domains of frequent chromatin contacts are proposed as functional units, favoring and delimiting gene regulatory interactions. However, contrasting evidence supports the association between chromatin domains and transcription. Result: Here, we assess gene co-regulation in chromatin domains across multiple human cancers, which exhibit great transcriptional heterogeneity. Across all datasets, gene co-regulation is observed only within a small yet significant number of chromatin domains. We design an algorithmic approach to identify differentially active domains (DADo) between two conditions and show that these provide complementary information to differentially expressed genes. Domains comprising co-regulated genes are enriched in the less active B sub-compartments and for genes with similar function. Notably, differential activation of chromatin domains is not associated with major changes of domain boundaries, but rather with changes of sub-compartments and intra-domain contacts. Conclusion: Overall, gene co-regulation is observed only in a minority of chromatin domains, whose systematic identification will help unravel the relationship between chromatin structure and transcription.
MeSH term(s)	Algorithms ; Chromatin/chemistry ; Chromatin Assembly and Disassembly ; Datasets as Topic ; Gene Expression Regulation, Neoplastic ; Gene Regulatory Networks ; Genetic Heterogeneity ; Humans ; Neoplasm Proteins/genetics ; Neoplasm Proteins/metabolism ; Neoplasms/genetics ; Neoplasms/metabolism ; Neoplasms/pathology ; Structure-Activity Relationship ; Transcription, Genetic
Chemical Substances	Chromatin ; Neoplasm Proteins
Language	English
Publishing date	2021-08-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-021-02436-6
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Managing for the unexpected: Building resilient forest landscapes to cope with global change.

Mina, Marco / Messier, Christian / Duveneck, Matthew J / Fortin, Marie-Josée / Aquilué, Núria

Global change biology

2022 Volume 28, Issue 14, Page(s) 4323–4341

Abstract: Natural disturbances exacerbated by novel climate regimes are increasing worldwide, threatening the ability of forest ecosystems to mitigate global warming through carbon sequestration and to provide other key ecosystem services. One way to cope with ... ...

Abstract	Natural disturbances exacerbated by novel climate regimes are increasing worldwide, threatening the ability of forest ecosystems to mitigate global warming through carbon sequestration and to provide other key ecosystem services. One way to cope with unknown disturbance events is to promote the ecological resilience of the forest by increasing both functional trait and structural diversity and by fostering functional connectivity of the landscape to ensure a rapid and efficient self-reorganization of the system. We investigated how expected and unexpected variations in climate and biotic disturbances affect ecological resilience and carbon storage in a forested region in southeastern Canada. Using a process-based forest landscape model (LANDIS-II), we simulated ecosystem responses to climate change and insect outbreaks under different forest policy scenarios-including a novel approach based on functional diversification and network analysis-and tested how the potentially most damaging insect pests interact with changes in forest composition and structure due to changing climate and management. We found that climate warming, lengthening the vegetation season, will increase forest productivity and carbon storage, but unexpected impacts of drought and insect outbreaks will drastically reduce such variables. Generalist, non-native insects feeding on hardwood are the most damaging biotic agents for our region, and their monitoring and early detection should be a priority for forest authorities. Higher forest diversity driven by climate-smart management and fostered by climate change that promotes warm-adapted species, might increase disturbance severity. However, alternative forest policy scenarios led to a higher functional and structural diversity as well as functional connectivity-and thus to higher ecological resilience-than conventional management. Our results demonstrate that adopting a landscape-scale perspective by planning interventions strategically in space and adopting a functional trait approach to diversify forests is promising for enhancing ecological resilience under unexpected global change stressors.
MeSH term(s)	Animals ; Carbon ; Climate Change ; Ecosystem ; Forests ; Insecta ; Trees
Chemical Substances	Carbon (7440-44-0)
Language	English
Publishing date	2022-04-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1281439-8
ISSN	1365-2486 ; 1354-1013
ISSN (online)	1365-2486
ISSN	1354-1013
DOI	10.1111/gcb.16197
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Dynamic Emergence of Observed and Hidden Intra-tumor Heterogeneity.

Raynaud, Franck / Mina, Marco / Ciriello, Giovanni

iScience

2019 Volume 21, Page(s) 157–167

Abstract: Intra-tumor heterogeneity is frequently observed in cancer patients, and it is associated with therapeutic resistance and disease relapse. However, its systematic assessment is still limited and often unfeasible. Here, we use a mathematical model of ... ...

Abstract	Intra-tumor heterogeneity is frequently observed in cancer patients, and it is associated with therapeutic resistance and disease relapse. However, its systematic assessment is still limited and often unfeasible. Here, we use a mathematical model of tumor progression to decipher how multiple clones emerge and organize into complex architectures. We found a trade-off between cancer cell alteration and proliferation rates that defines a transition between low and high heterogeneity, the latter characterized by branching tumor phylogenies. We predict the existence of observed and hidden intra-tumor heterogeneity, which challenges the correct estimation of intrinsic tumor complexity. Although the numbers of observed and hidden clones do not always correlate, we demonstrate that population frequencies of observed clones can be used to estimate the extent of hidden heterogeneity in both simulated and human tumors. The characterization of complex clonal architectures is a critical first step toward understanding their organizing principles and predicting their emergence.
Language	English
Publishing date	2019-10-10
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2019.10.018
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Systematic assessment of gene co-regulation within chromatin domains determines differentially active domains across human cancers

Zufferey, Marie / Liu, Yuanlong / Tavernari, Daniele / Minà, Marco / Ciriello, Giovanni

Genome biology. 2021 Dec., v. 22, no. 1 p.218-218

2021

Abstract: BACKGROUND: Spatial interactions and insulation of chromatin regions are associated with transcriptional regulation. Domains of frequent chromatin contacts are proposed as functional units, favoring and delimiting gene regulatory interactions. However, ... ...

Abstract	BACKGROUND: Spatial interactions and insulation of chromatin regions are associated with transcriptional regulation. Domains of frequent chromatin contacts are proposed as functional units, favoring and delimiting gene regulatory interactions. However, contrasting evidence supports the association between chromatin domains and transcription. RESULT: Here, we assess gene co-regulation in chromatin domains across multiple human cancers, which exhibit great transcriptional heterogeneity. Across all datasets, gene co-regulation is observed only within a small yet significant number of chromatin domains. We design an algorithmic approach to identify differentially active domains (DADo) between two conditions and show that these provide complementary information to differentially expressed genes. Domains comprising co-regulated genes are enriched in the less active B sub-compartments and for genes with similar function. Notably, differential activation of chromatin domains is not associated with major changes of domain boundaries, but rather with changes of sub-compartments and intra-domain contacts. CONCLUSION: Overall, gene co-regulation is observed only in a minority of chromatin domains, whose systematic identification will help unravel the relationship between chromatin structure and transcription.
Keywords	algorithms ; chromatin ; data collection ; gene expression regulation ; genes ; humans ; insulating materials ; transcription (genetics)
Language	English
Dates of publication	2021-12
Size	p. 218.
Publishing place	BioMed Central
Document type	Article ; Online
ZDB-ID	2040529-7
ISSN	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-021-02436-6
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Network analysis can guide resilience‐based management in forest landscapes under global change

Minà, Marco / Messier, Christian / Duveneck, Matthew / Fortin, Marie‐Josée / Aquilué, Núria

Ecological applications. 2021 Jan., v. 31, no. 1 p.e2221-

2021

Abstract: Forests are projected to undergo dramatic compositional and structural shifts prompted by global changes, such as climatic changes and intensifying natural disturbance regimes. Future uncertainty makes planning for forest management exceptionally ... ...

Abstract	Forests are projected to undergo dramatic compositional and structural shifts prompted by global changes, such as climatic changes and intensifying natural disturbance regimes. Future uncertainty makes planning for forest management exceptionally difficult, demanding novel approaches to maintain or improve the ability of forest ecosystems to respond and rapidly reorganize after disturbance events. Adopting a landscape perspective in forest management is particularly important in fragmented forest landscapes where both diversity and connectivity play key roles in determining resilience to global change. In this context, network analysis and functional traits combined with ecological dynamic modeling can help evaluate changes in functional response diversity and connectivity within and among forest stands in fragmented landscapes. Here, we coupled ecological dynamic modeling with functional traits analysis and network theory to analyze forested landscapes as an interconnected network of forest patches. We simulated future forest landscape dynamics in a large landscape in southern Quebec, Canada, under a combination of climate, disturbance, and management scenarios. We depicted the landscape as a functional network, assessed changes in future resilience using indicators at multiple spatial scales, and evaluated if current management practices are suitable for maintaining resilience to simulated changes in regimes. Our results show that climate change would promote forest productivity and favor heat‐adapted deciduous species. Changes in natural disturbances will likely have negative impacts on native conifers and will drive changes in forest type composition. Climate change negatively impacted all resilience indicators and triggered losses of functional response diversity and connectivity across the landscape with undesirable consequences on the capacity of these forests to adapt to global change. Also, current management strategies failed to promote resilience at different spatial levels, highlighting the need for a more active and thoughtful approach to forest management under global change. Our study demonstrates the usefulness of combining dynamic landscape‐scale simulation modeling with network analyses to evaluate the possible impacts of climate change as well as human and natural disturbances on forest resilience under global change.
Keywords	climate ; climate change ; forest management ; forest types ; habitat fragmentation ; humans ; landscapes ; network theory ; uncertainty ; Quebec
Language	English
Dates of publication	2021-01
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	NAL-AP-2-clean ; JOURNAL ARTICLE
ZDB-ID	1074505-1
ISSN	1939-5582 ; 1051-0761
ISSN (online)	1939-5582
ISSN	1051-0761
DOI	10.1002/eap.2221
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A simple-to-use management approach to boost adaptive capacity of forests to global uncertainty

Aquilué, Núria / Messier, Christian / Martins, Kyle T. / Dumais-Lalonde, Véronique / Minà, Marco

Forest ecology and management. 2021 Feb. 01, v. 481 p.118692-

2021

Abstract: Given the uncertainty of global environmental changes, forest managers need reliable and science-based tools to support planning decisions. To evaluate the state of forests as well as the outcomes of new management practices aimed at fostering the ... ...

Abstract	Given the uncertainty of global environmental changes, forest managers need reliable and science-based tools to support planning decisions. To evaluate the state of forests as well as the outcomes of new management practices aimed at fostering the adaptive capacity of forest ecosystems, methods and metrics for practitioners should be self-explanatory, based on easily-available data, and straightforward to use. Here, we present and apply the functional network approach, a trait-based approach that scales-up from species functional traits to community-level functional diversity and from stands to landscape-level functional connectivity, to guide sustainable forest management when faced with global change. In the functional network approach, (1) tree and shrub species are clustered into functional groups based on selected functional traits, (2) forest stands become the nodes of the network, and (3) functional traits can be exchanged between nodes according to species dispersal capacity via functional connectivity. We complemented the functional network approach with an assessment of stand-level vulnerability to natural disturbances. This new approach was applied to a mixed temperate forest landscape in south-eastern Canada to test four management scenarios varying in intensity (5–40% of the landscape area) and silvicultural strategy, including planting tree species from rare functional groups or harvesting tree species from predominant functional groups. Managed stands were ranked according to functional diversity and vulnerability to disturbances, and species were considered for planting based on their contribution to functional diversity and level of vulnerability. We found that a species-rich forest may be a functionally poor ecosystem so its adaptive capacity and resilience may be strongly compromised in the face of high global uncertainty. In addition, both functional diversity and connectivity increased with more intense management, and when functionally rare species were planted. By adopting the functional network approach, forest practitioners have a new simple-to-use tool to evaluate landscape-level functional diversity, vulnerability, and functional connectivity. This tool can be used to inform both plans for mitigating natural disturbances and strategies for enhancing overall ecosystem adaptive capacity to future environmental conditions and societal demands.
Keywords	functional diversity ; global change ; landscapes ; rare species ; shrubs ; species dispersal ; sustainable forestry ; temperate forests ; trees ; uncertainty ; Canada ; Functional diversity ; Functional connectivity ; Vulnerability ; Forest management ; Network analysis ; Adaptive capacity
Language	English
Dates of publication	2021-0201
Publishing place	Elsevier B.V.
Document type	Article ; Online
ZDB-ID	751138-3
ISSN	0378-1127
ISSN	0378-1127
DOI	10.1016/j.foreco.2020.118692
Database	NAL-Catalogue (AGRICOLA)

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