Deterministic evolution and stringent selection during preneoplasia

The earliest events during human tumour initiation, although poorly characterized, may hold clues to malignancy detection and prevention1. Here we model occult preneoplasia by biallelic inactivation of TP53, a common early event in gastric cancer, in human gastric organoids. Causal relationships between this initiating genetic lesion and resulting phenotypes were established using experimental evolution in multiple clonally derived cultures over 2 years. TP53 loss elicited progressive aneuploidy, including copy number alterations and structural variants prevalent in gastric cancers, with evident preferred orders. Longitudinal single-cell sequencing of TP53-deficient gastric organoids similarly indicates progression towards malignant transcriptional programmes. Moreover, high-throughput lineage tracing with expressed cellular barcodes demonstrates reproducible dynamics whereby initially rare subclones with shared transcriptional programmes repeatedly attain clonal dominance. This powerful platform for experimental evolution exposes stringent selection, clonal interference and a marked degree of phenotypic convergence in premalignant epithelial organoids. These data imply predictability in the earliest stages of tumorigenesis and show evolutionary constraints and barriers to malignant transformation, with implications for earlier detection and interception of aggressive, genome-instable tumours

Proceedings of the 3rd Biennial Conference of the Society for Implementation Research Collaboration (SIRC) 2015: advancing efficient methodologies through community partnerships and team science

It is well documented that the majority of adults, children and families in need of evidence-based behavioral health interventionsi do not receive them [1, 2] and that few robust empirically supported methods for implementing evidence-based practices (EBPs) exist. The Society for Implementation Research Collaboration (SIRC) represents a burgeoning effort to advance the innovation and rigor of implementation research and is uniquely focused on bringing together researchers and stakeholders committed to evaluating the implementation of complex evidence-based behavioral health interventions. Through its diverse activities and membership, SIRC aims to foster the promise of implementation research to better serve the behavioral health needs of the population by identifying rigorous, relevant, and efficient strategies that successfully transfer scientific evidence to clinical knowledge for use in real world settings [3]. SIRC began as a National Institute of Mental Health (NIMH)-funded conference series in 2010 (previously titled the “Seattle Implementation Research Conference”; $150,000 USD for 3 conferences in 2011, 2013, and 2015) with the recognition that there were multiple researchers and stakeholdersi working in parallel on innovative implementation science projects in behavioral health, but that formal channels for communicating and collaborating with one another were relatively unavailable. There was a significant need for a forum within which implementation researchers and stakeholders could learn from one another, refine approaches to science and practice, and develop an implementation research agenda using common measures, methods, and research principles to improve both the frequency and quality with which behavioral health treatment implementation is evaluated. SIRC’s membership growth is a testament to this identified need with more than 1000 members from 2011 to the present.ii SIRC’s primary objectives are to: (1) foster communication and collaboration across diverse groups, including implementation researchers, intermediariesi, as well as community stakeholders (SIRC uses the term “EBP champions” for these groups) – and to do so across multiple career levels (e.g., students, early career faculty, established investigators); and (2) enhance and disseminate rigorous measures and methodologies for implementing EBPs and evaluating EBP implementation efforts. These objectives are well aligned with Glasgow and colleagues’ [4] five core tenets deemed critical for advancing implementation science: collaboration, efficiency and speed, rigor and relevance, improved capacity, and cumulative knowledge. SIRC advances these objectives and tenets through in-person conferences, which bring together multidisciplinary implementation researchers and those implementing evidence-based behavioral health interventions in the community to share their work and create professional connections and collaborations

The genetic history of the Southern Arc: a bridge between West Asia and Europe

By sequencing 727 ancient individuals from the Southern Arc (Anatolia and its neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic period and Bronze Age (about 5000 to 1000 BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southward into the Balkans and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra–West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe

"For the greater good" 99.8 % free and the expendable 0.2%: Freedom Fighters and the COVID-19 pandemic

83 p. : color illustration

Functional competence and cognition in individuals with amnestic mild cognitive impairment

OBJECTIVE The objective of this study is to characterize functional competence (measure of assistance needed for independence) on Performance Assessment of Self-Care Skills (PASS) Cognitively Mediated Instrumental Activities of Daily Living (C-IADL), in individuals with amnestic mild cognitive impairment (aMCI). It aims to determine: (1) the association of functional competence on PASS C-IADL tasks with neurocognitive test performance in aMCI, (2) its ability to discriminate individuals with aMCI from healthy control (HC) individuals, and (3) its added value in discriminating aMCI from HC individuals when combined with neurocognitive test performance. DESIGN Cross-sectional secondary analysis of baseline data from a cohort of individuals enrolled in a clinical trial (NCT02386670). SETTING Five university-affiliated outpatient clinics in Toronto, Canada. PARTICIPANTS aMCI (N = 137) and HC (N = 51) participants, all aged 60 years or older. METHODS We assessed the relationship between functional competence on three C-IADL PASS tasks (shopping, bill paying, and checkbook balancing) and neurocognitive tests in 137 participants with aMCI using multiple linear regressions. Additionally, we constructed receiver operating characteristic curves to assess the role of PASS functional competence in discriminating between 137 aMCI and 51 HC participants. RESULTS Functional competence on PASS was significantly associated with tests of verbal memory, information processing speed, and executive function. It demonstrated 79% accuracy in discriminating aMCI from HC participants. Combining functional competence on PASS with individual neurocognitive tests significantly increased the discriminant accuracy of individual tests, and neurocognitive test scores combined with functional competence on PASS had the highest discriminant accuracy (94%). CONCLUSION Functional competence on PASS is predicted by the underlying cognitive deficits and possibly captures additional element of effort that could improve the diagnostic accuracy of aMCI when combined with neurocognitive tests. Thus, PASS appears to be a promising tool for assessment of functional competence in aMCI in clinical or research settings

Functional Competence and Cognition in Individuals With Amnestic Mild Cognitive Impairment

OBJECTIVE The objective of this study is to characterize functional competence (measure of assistance needed for independence) on Performance Assessment of Self-Care Skills (PASS) Cognitively Mediated Instrumental Activities of Daily Living (C-IADL), in individuals with amnestic mild cognitive impairment (aMCI). It aims to determine: (1) the association of functional competence on PASS C-IADL tasks with neurocognitive test performance in aMCI, (2) its ability to discriminate individuals with aMCI from healthy control (HC) individuals, and (3) its added value in discriminating aMCI from HC individuals when combined with neurocognitive test performance. DESIGN Cross-sectional secondary analysis of baseline data from a cohort of individuals enrolled in a clinical trial (NCT02386670). SETTING Five university-affiliated outpatient clinics in Toronto, Canada. PARTICIPANTS aMCI (N = 137) and HC (N = 51) participants, all aged 60 years or older. METHODS We assessed the relationship between functional competence on three C-IADL PASS tasks (shopping, bill paying, and checkbook balancing) and neurocognitive tests in 137 participants with aMCI using multiple linear regressions. Additionally, we constructed receiver operating characteristic curves to assess the role of PASS functional competence in discriminating between 137 aMCI and 51 HC participants. RESULTS Functional competence on PASS was significantly associated with tests of verbal memory, information processing speed, and executive function. It demonstrated 79% accuracy in discriminating aMCI from HC participants. Combining functional competence on PASS with individual neurocognitive tests significantly increased the discriminant accuracy of individual tests, and neurocognitive test scores combined with functional competence on PASS had the highest discriminant accuracy (94%). CONCLUSION Functional competence on PASS is predicted by the underlying cognitive deficits and possibly captures additional element of effort that could improve the diagnostic accuracy of aMCI when combined with neurocognitive tests. Thus, PASS appears to be a promising tool for assessment of functional competence in aMCI in clinical or research settings

Deterministic evolution and stringent selection during preneoplasia.

Acknowledgements: We thank Z. Hu, S. Tilk, L. Attardi and A. Bhatt for helpful discussions, the Stanford University Hospital Tissue Procurement Shared Resource facility for specimen procurement and the Stanford Functional Genomics Core for assistance with sequencing. This work was supported by the US Department of Health & Human Services National Institutes of Health Director’s Pioneer Award (no. DP1-CA238296) to C.C. and a National Cancer Institute Cancer Target Discovery and Development Center (no. U01-CA217851) to C.J.K. and C.C. K. Karlsson was supported in part by a Swedish Research Council (Ventenskapsradet) International postdoctoral grant (no. 2018-00454).The earliest events during human tumour initiation, although poorly characterized, may hold clues to malignancy detection and prevention1. Here we model occult preneoplasia by biallelic inactivation of TP53, a common early event in gastric cancer, in human gastric organoids. Causal relationships between this initiating genetic lesion and resulting phenotypes were established using experimental evolution in multiple clonally derived cultures over 2 years. TP53 loss elicited progressive aneuploidy, including copy number alterations and structural variants prevalent in gastric cancers, with evident preferred orders. Longitudinal single-cell sequencing of TP53-deficient gastric organoids similarly indicates progression towards malignant transcriptional programmes. Moreover, high-throughput lineage tracing with expressed cellular barcodes demonstrates reproducible dynamics whereby initially rare subclones with shared transcriptional programmes repeatedly attain clonal dominance. This powerful platform for experimental evolution exposes stringent selection, clonal interference and a marked degree of phenotypic convergence in premalignant epithelial organoids. These data imply predictability in the earliest stages of tumorigenesis and show evolutionary constraints and barriers to malignant transformation, with implications for earlier detection and interception of aggressive, genome-instable tumours