The Cytidine Deaminase APOBEC3G Contributes to Cancer Mutagenesis and Clonal Evolution in Bladder Cancer.

Mutagenic processes leave distinct signatures in cancer genomes. The mutational signatures attributed to APOBEC3 cytidine deaminases are pervasive in human cancers. However, data linking individual APOBEC3 proteins to cancer mutagenesis in vivo are limited. Here, we showed that transgenic expression of human APOBEC3G promotes mutagenesis, genomic instability, and kataegis, leading to shorter survival in a murine bladder cancer model. Acting as mutagenic fuel, APOBEC3G increased the clonal diversity of bladder cancer, driving divergent cancer evolution. Characterization of the single-base substitution signature induced by APOBEC3G in vivo established the induction of a mutational signature distinct from those caused by APOBEC3A and APOBEC3B. Analysis of thousands of human cancers revealed the contribution of APOBEC3G to the mutational profiles of multiple cancer types, including bladder cancer. Overall, this study dissects the mutagenic impact of APOBEC3G on the bladder cancer genome, identifying that it contributes to genomic instability, tumor mutational burden, copy-number loss events, and clonal diversity. SIGNIFICANCE: APOBEC3G plays a role in cancer mutagenesis and clonal heterogeneity, which can potentially inform future therapeutic efforts that restrict tumor evolution. See related commentary by Caswell and Swanton, p. 487.

Increased Serine and One-Carbon Pathway Metabolism by PKCλ/ι Deficiency Promotes Neuroendocrine Prostate Cancer.

Increasingly effective therapies targeting the androgen receptor have paradoxically promoted the incidence of neuroendocrine prostate cancer (NEPC), the most lethal subtype of castration-resistant prostate cancer (PCa), for which there is no effective therapy. Here we report that protein kinase C (PKC)λ/ι is downregulated in de novo and during therapy-induced NEPC, which results in the upregulation of serine biosynthesis through an mTORC1/ATF4-driven pathway. This metabolic reprogramming supports cell proliferation and increases intracellular S-adenosyl methionine (SAM) levels to feed epigenetic changes that favor the development of NEPC characteristics. Altogether, we have uncovered a metabolic vulnerability triggered by PKCλ/ι deficiency in NEPC, which offers potentially actionable targets to prevent therapy resistance in PCa.

How Hydrologic Connectivity Regulates Water Quality in River Corridors.

Downstream flow in rivers is repeatedly delayed by hydrologic exchange with off-channel storage zones where biogeochemical processing occurs. We present a dimensionless metric that quantifies river connectivity as the balance between downstream flow and the exchange of water with the bed, banks, and floodplains. The degree of connectivity directly influences downstream water quality - too little connectivity limits the amount of river water exchanged and leads to biogeochemically inactive water storage, while too much connectivity limits the contact time with sediments for reactions to proceed. Using a metric of reaction significance based on river connectivity, we provide evidence that intermediate levels of connectivity, rather than the highest or lowest levels, are the most efficient in removing nitrogen from Northeastern United States' rivers. Intermediate connectivity balances the frequency, residence time, and contact volume with reactive sediments, which can maximize the reactive processing of dissolved contaminants and the protection of downstream water quality. Our simulations suggest denitrification dominantly occurs in riverbed hyporheic zones of streams and small rivers, whereas vertical turbulent mixing in contact with sediments dominates in mid-size to large rivers. The metrics of connectivity and reaction significance presented here can facilitate scientifically based prioritizations of river management strategies to protect the values and functions of river corridors.

Thresholds of lake and reservoir connectivity in river networks control nitrogen removal.

Lakes, reservoirs, and other ponded waters are ubiquitous features of the aquatic landscape, yet their cumulative role in nitrogen removal in large river basins is often unclear. Here we use predictive modeling, together with comprehensive river water quality, land use, and hydrography datasets, to examine and explain the influences of more than 18,000 ponded waters on nitrogen removal through river networks of the Northeastern United States. Thresholds in pond density where ponded waters become important features to regional nitrogen removal are identified and shown to vary according to a ponded waters' relative size, network position, and degree of connectivity to the river network, which suggests worldwide importance of these new metrics. Consideration of the interacting physical and biological factors, along with thresholds in connectivity, reveal where, why, and how much ponded waters function differently than streams in removing nitrogen, what regional water quality outcomes may result, and in what capacity management strategies could most effectively achieve desired nitrogen loading reduction.

Next-Generation Rapid Autopsies Enable Tumor Evolution Tracking and Generation of Preclinical Models.

PURPOSE: Patients with cancer who graciously consent for autopsy represent an invaluable resource for the study of cancer biology. To advance the study of tumor evolution, metastases, and resistance to treatment, we developed a next-generation rapid autopsy program integrated within a broader precision medicine clinical trial that interrogates pre- and postmortem tissue samples for patients of all ages and cancer types. MATERIALS AND METHODS: One hundred twenty-three (22%) of 554 patients who consented to the clinical trial also consented for rapid autopsy. This report comprises the first 15 autopsies, including patients with metastatic carcinoma (n = 10), melanoma (n = 1), and glioma (n = 4). Whole-exome sequencing (WES) was performed on frozen autopsy tumor samples from multiple anatomic sites and on non-neoplastic tissue. RNA sequencing (RNA-Seq) was performed on a subset of frozen samples. Tissue was also used for the development of preclinical models, including tumor organoids and patient-derived xenografts. RESULTS: Three hundred forty-six frozen samples were procured in total. WES was performed on 113 samples and RNA-Seq on 72 samples. Successful cell strain, tumor organoid, and/or patient-derived xenograft development was achieved in four samples, including an inoperable pediatric glioma. WES data were used to assess clonal evolution and molecular heterogeneity of tumors in individual patients. Mutational profiles of primary tumors and metastases yielded candidate mediators of metastatic spread and organotropism including CUL9 and PIGM in metastatic ependymoma and ANKRD52 in metastatic melanoma to the lung. RNA-Seq data identified novel gene fusion candidates. CONCLUSION: A next-generation sequencing-based autopsy program in conjunction with a pre-mortem precision medicine pipeline for diverse tumors affords a valuable window into clonal evolution, metastasis, and alterations underlying treatment. Moreover, such an autopsy program yields robust preclinical models of disease.

Erratum to: Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia.

In the original article, one of the co-authors' (Ken Khong Eng) given name has been published incorrectly. The correct given name should be Ken Khong. The original article has been corrected.

Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia.

There has been a long-standing debate concerning the extent to which the spread of Neolithic ceramics and Malay-Polynesian languages in Island Southeast Asia (ISEA) were coupled to an agriculturally driven demic dispersal out of Taiwan 4000 years ago (4 ka). We previously addressed this question using founder analysis of mitochondrial DNA (mtDNA) control-region sequences to identify major lineage clusters most likely to have dispersed from Taiwan into ISEA, proposing that the dispersal had a relatively minor impact on the extant genetic structure of ISEA, and that the role of agriculture in the expansion of the Austronesian languages was therefore likely to have been correspondingly minor. Here we test these conclusions by sequencing whole mtDNAs from across Taiwan and ISEA, using their higher chronological precision to resolve the overall proportion that participated in the "out-of-Taiwan" mid-Holocene dispersal as opposed to earlier, postglacial expansions in the Early Holocene. We show that, in total, about 20% of mtDNA lineages in the modern ISEA pool result from the "out-of-Taiwan" dispersal, with most of the remainder signifying earlier processes, mainly due to sea-level rises after the Last Glacial Maximum. Notably, we show that every one of these founder clusters previously entered Taiwan from China, 6-7 ka, where rice-farming originated, and remained distinct from the indigenous Taiwanese population until after the subsequent dispersal into ISEA.

Resolving the ancestry of Austronesian-speaking populations.

There are two very different interpretations of the prehistory of Island Southeast Asia (ISEA), with genetic evidence invoked in support of both. The "out-of-Taiwan" model proposes a major Late Holocene expansion of Neolithic Austronesian speakers from Taiwan. An alternative, proposing that Late Glacial/postglacial sea-level rises triggered largely autochthonous dispersals, accounts for some otherwise enigmatic genetic patterns, but fails to explain the Austronesian language dispersal. Combining mitochondrial DNA (mtDNA), Y-chromosome and genome-wide data, we performed the most comprehensive analysis of the region to date, obtaining highly consistent results across all three systems and allowing us to reconcile the models. We infer a primarily common ancestry for Taiwan/ISEA populations established before the Neolithic, but also detected clear signals of two minor Late Holocene migrations, probably representing Neolithic input from both Mainland Southeast Asia and South China, via Taiwan. This latter may therefore have mediated the Austronesian language dispersal, implying small-scale migration and language shift rather than large-scale expansion.

Implications of the minimal clinically important difference for health-related quality-of-life outcomes: a comparison of sample size requirements for an incontinence treatment trial.

BACKGROUND: Sample size calculations for treatment trials that aim to assess health-related quality-of-life (HRQOL) outcomes are often difficult to perform. Researchers must select a target minimal clinically important difference (MCID) in HRQOL for the trial, estimate the effect size of the intervention, and then consider the responsiveness of different HRQOL measures for detecting improvements. Generic preference-based HRQOL measures are usually less sensitive to gains in HRQOL than are disease-specific measures, but are nonetheless recommended to quantify an impact on HRQOL that can be translated into quality-adjusted life-years during cost-effectiveness analyses. Mapping disease-specific measures onto generic measures is a proposed method for yielding more efficient sample size requirements while retaining the ability to generate utility weights for cost-effectiveness analyses. OBJECTIVES: This study sought to test this mapping strategy to calculate and compare the effect on sample size of three different methods. METHODS: Three different methods were used for determining an MCID in HRQOL in patients with incontinence: 1) a global rating of improvement, 2) an incontinence-specific HRQOL instrument, and 3) a generic preference-based HRQOL instrument using mapping coefficients. RESULTS: The sample size required to detect a 20% difference in the MCID for the global rating of improvement was 52 per trial arm, 172 per arm for the incontinence-specific HRQOL outcome, and 500 per arm for the generic preference-based HRQOL outcome. CONCLUSIONS: We caution that treatment trials of conditions for which improvements are not easy to measure on generic HRQOL instruments will still require significantly greater sample size even when mapping functions are used to try to gain efficiency.

Cell-cycle reprogramming for PI3K inhibition overrides a relapse-specific C481S BTK mutation revealed by longitudinal functional genomics in mantle cell lymphoma.

UNLABELLED: Despite the unprecedented clinical activity of the Bruton tyrosine kinase (BTK) inhibitor ibrutinib in mantle cell lymphoma (MCL), acquired resistance is common. By longitudinal integrative whole-exome and whole-transcriptome sequencing and targeted sequencing, we identified the first relapse-specific C481S mutation at the ibrutinib binding site of BTK in MCL cells at progression following a durable response. This mutation enhanced BTK and AKT activation and tissue-specific proliferation of resistant MCL cells driven by CDK4 activation. It was absent, however, in patients with primary resistance or progression following transient response to ibrutinib, suggesting alternative mechanisms of resistance. Through synergistic induction of PIK3IP1 and inhibition of PI3K-AKT activation, prolonged early G1 arrest induced by PD 0332991 (palbociclib) inhibition of CDK4 sensitized resistant lymphoma cells to ibrutinib killing when BTK was unmutated, and to PI3K inhibitors independent of C481S mutation. These data identify a genomic basis for acquired ibrutinib resistance in MCL and suggest a strategy to override both primary and acquired ibrutinib resistance. SIGNIFICANCE: We have discovered the first relapse-specific BTK mutation in patients with MCL with acquired resistance, but not primary resistance, to ibrutinib, and demonstrated a rationale for targeting the proliferative resistant MCL cells by inhibiting CDK4 and the cell cycle in combination with ibrutinib in the presence of BTK(WT) or a PI3K inhibitor independent of BTK mutation. As drug resistance remains a major challenge and CDK4 and PI3K are dysregulated at a high frequency in human cancers, targeting CDK4 in genome-based combination therapy represents a novel approach to lymphoma and cancer therapy. Cancer Discov; 4(9); 1022-35. ©2014 AACR. This article is highlighted in the In This Issue feature, p. 973.

Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas.

BACKGROUND: Molecular mechanisms associated with frequent relapse of diffuse large B-cell lymphoma (DLBCL) are poorly defined. It is especially unclear how primary tumor clonal heterogeneity contributes to relapse. Here, we explore unique features of B-cell lymphomas - VDJ recombination and somatic hypermutation - to address this question. RESULTS: We performed high-throughput sequencing of rearranged VDJ junctions in 14 pairs of matched diagnosis-relapse tumors, among which 7 pairs were further characterized by exome sequencing. We identify two distinctive modes of clonal evolution of DLBCL relapse: an early-divergent mode in which clonally related diagnosis and relapse tumors diverged early and developed in parallel; and a late-divergent mode in which relapse tumors developed directly from diagnosis tumors with minor divergence. By examining mutation patterns in the context of phylogenetic information provided by VDJ junctions, we identified mutations in epigenetic modifiers such as KMT2D as potential early driving events in lymphomagenesis and immune escape alterations as relapse-associated events. CONCLUSIONS: Altogether, our study for the first time provides important evidence that DLBCL relapse may result from multiple, distinct tumor evolutionary mechanisms, providing rationale for therapies for each mechanism. Moreover, this study highlights the urgent need to understand the driving roles of epigenetic modifier mutations in lymphomagenesis, and immune surveillance factor genetic lesions in relapse.

Longitudinal construct validity of the Health Utilities Indices Mark 2 and Mark 3 in hip fracture.

PURPOSE: The objective of this study is to evaluate the longitudinal construct validity of the Health Utilities Index Mark 2 (HUI2) and Health Utilities Index Mark 3 (HUI3) using a convergent/divergent validity approach in patients recovering from hip fracture, with the Functional Independence Measure (FIM) as the comparator. METHODS: A total of 278 patients with a primary diagnosis of hip fracture were interviewed 3-5 days after surgery and then at 1 and 6 months using the HUI2, HUI3 and the FIM and a Likert-type rating of hip pain. A priori hypotheses were formulated. Convergent and divergent correlations between HUI2, HUI3 and FIM change scores for the baseline to 1-month and baseline to 6-month intervals were examined. RESULTS: Overall HUI2 detected continued gain in health-related quality of life between 1 and 6 months after fracture, as the change increased from 0.20 to 0.29 units. The correlation between change in the overall HUI2 score and total FIM score was moderate (r = 0.50) over the 6-month interval, but larger than the observed correlation over the 1-month interval (r = 0.36). The correlation between change in overall HUI3 score and total FIM over the 1-month interval was small (r = 0.32), and the correlation between change in overall HUI3 score and total FIM was moderate (r = 0.37) over the 6-month interval. All hypotheses for the divergent correlations were supported. CONCLUSIONS: Weaker correlations were reported for change over 1 month as compared to change over the 6 months after fracture. Findings supported the longitudinal construct validity of the overall HUI2 and HUI3 for the assessment of recovery following hip fracture, particularly for change over the 6 months following fracture.

A substantial prehistoric European ancestry amongst Ashkenazi maternal lineages.

The origins of Ashkenazi Jews remain highly controversial. Like Judaism, mitochondrial DNA is passed along the maternal line. Its variation in the Ashkenazim is highly distinctive, with four major and numerous minor founders. However, due to their rarity in the general population, these founders have been difficult to trace to a source. Here we show that all four major founders, ~40% of Ashkenazi mtDNA variation, have ancestry in prehistoric Europe, rather than the Near East or Caucasus. Furthermore, most of the remaining minor founders share a similar deep European ancestry. Thus the great majority of Ashkenazi maternal lineages were not brought from the Levant, as commonly supposed, nor recruited in the Caucasus, as sometimes suggested, but assimilated within Europe. These results point to a significant role for the conversion of women in the formation of Ashkenazi communities, and provide the foundation for a detailed reconstruction of Ashkenazi genealogical history.

River flow changes related to land and water management practices across the conterminous United States.

The effects of land and water management practices (LWMP)--such as the construction of dams and roads--on river flows typically have been studied at the scale of single river watersheds or for a single type of LWMP. For the most part, assessments of the relative effects of multiple LWMP within many river watersheds across regional and national scales have been lacking. This study assesses flow alteration--quantified as deviation of several flow metrics from natural conditions--at 4196 gauged rivers affected by a variety of LWMP across the conterminous United States. The most widespread causes of flow changes among the LWMP considered were road density and dams. Agricultural development and wastewater discharges also were associated with flow changes in some regions. Dams generally reduced most attributes of flow, whereas road density, agriculture and wastewater discharges tended to be associated with increased flows compared to their natural condition.

Expenditures on mental health and addictions for Canadian provinces in 2003 and 2004.

OBJECTIVE: To measure total public and private expenditures on mental health in each province. METHOD: Data for expenditures on mental health services were collected in the following categories: physician expenditures (general and psychiatrist fees for service and alternative funding), inpatient hospital (psychiatric and general), outpatient hospital, community mental health, pharmaceuticals, and substance abuse. Data for 2 years, 2003 and 2004, were collected from the Canadian Institute for Health Information (hospital inpatient and fees for service physicians), the individual provinces (pharmaceuticals, alternative physician payments, hospital outpatient, and community), and the Canadian Centre on Substance Abuse. Totals were expressed in terms of per capita and as a percentage of total provincial health spending. RESULTS: Total spending on mental health was $6.6 billion, of which $5.5 billion was from public sources. Nationally, the largest portion of expenditures was for hospitals, followed by community mental health expenses and pharmaceuticals. This varied by province. Public mental health spending was 6% of total public spending on health, while total mental health spending was 5% of total health spending. CONCLUSIONS: Canadian public mental health spending is lower than most developed countries, and a little below the minimum acceptable amount (5%) stated by the European Mental Health Economics Network.

Comparing the health of low income and less well educated groups in the United States and Canada.

BACKGROUND: A limited number of health status and health-related quality of life (HRQL) measures have been used for inter-country comparisons of population health. We compared the health of Canadians and Americans using a preference-based measure. METHODS: The Joint Canada/United States Survey of Health (JCUSH) 2002-03 conducted a comprehensive cross-sectional telephone survey on the health of community-dwelling residents in Canada and the US (n = 8688). A preference-based measure, the Health Utilities Index Mark 3 (HUI3), was included in the JCUSH. Health status was analyzed for the entire population and white population only in both countries. Mean HUI3 overall scores were compared for both countries. A linear regression determinants of health model was estimated to account for differences in health between Canada and the US. Estimation with bootstraps was used to derive variance estimates that account for the survey's complex sampling design of clustering and stratification. RESULTS: Income is associated with health in both countries. In the lowest income quintile, Canadians are healthier than Americans. At lower levels of education, again Canadians are healthier than Americans. Differences in health among subjects in the JCUSH are explained by age, gender, education, income, marital status, and country of residence. CONCLUSION: On average, population health in Canada and the US is similar. However, health disparities between Canadians and Americans exist at lower levels of education and income with Americans worse off. The results highlight the usefulness of continuous preference-based measures of population health such as the HUI3.

A test of prospect theory.

OBJECTIVES: Prospect theory (PT) hypothesizes that people judge states relative to a reference point, usually assumed to be their current health. States better than the reference point are valued on a concave portion of the utility function; worse states are valued on a convex portion. Using prospectively collected utility scores, the objective is to test empirically implications of PT. METHODS: Osteoarthritis (OA) patients undergoing total hip arthroplasty periodically provided standard gamble scores for three OA hypothetical states describing mild, moderate, and severe OA as well as their subjectively defined current state (SDCS). Our hypothesis was that most patients improved between the pre- and postsurgery assessments. According to PT, scores for hypothetical states previously > SDCS but now < SDCS should be lower at the postsurgery assessment. RESULTS: Fourteen patients met the criteria for testing the hypothesis. Predictions were confirmed for 0 patients; there was no change or mixed results for 6 patients (42.9 percent); and scores moved in the direction opposite to that predicted by PT for 8 patients (57.1 percent). CONCLUSIONS: In general, the direction and magnitude of the changes in hypothetical-state scores do not conform to the predictions of PT.

Test-retest reliability of health utilities index scores: evidence from hip fracture.

OBJECTIVES: There is relatively little evidence on the test-retest reliability of utility scores derived from multiattribute measures. The objective was to estimate test-retest reliability for Health Utilities Index Mark 2 (HUI2) and Mark 3 (HUI3) utility scores in patients recovering from hip fracture. METHODS: We enrolled an inception cohort of hip fracture patients within 3 to 5 days of surgery. Baseline assessments included the Functional Independence Measure (FIM), Folstein Mini-Mental State Examinations, and the HUI2 and HUI3 questionnaire. Follow-up assessments at 1, 3, and 6 months also included a global change question. Test-retest reliability was assessed as agreement between 3- and 6-month scores using the intraclass correlation coefficient (ICC). Two approaches were used to classify patients as stable; a third approach based on the generalizability theory was also used. Patients were classified as stable if their FIM overall scores changed by 10 points or fewer and if they classified themselves as having experienced no or only a little change according to their global change question. RESULTS: Complete data at both the 3- and 6-month assessments based on self-report were available for 196 patients; 141 patients with complete data were classified as stable. The ICCs for HUI2 and HUI3 for stable patients were 0.71 and 0.72; the ICCs derived from the generalizability theory were 0.76 and 0.77. CONCLUSIONS: Test-retest reliability for HUI in this cohort was similar to reliability estimates for other preference-based multiattribute and generic health-profile measures--in the acceptable range for making valid group-level comparisons.

A cohort study found the RAND-12 and Health Utilities Index Mark 3 demonstrated construct validity in high-risk primary care patients.

OBJECTIVE: The Short Form 12 (SF-12) is widely used in primary care settings. The RAND-12 Health Status Inventory (HSI) and the Health Utilities Index Mark 3 (HUI3) have not been as widely used in such settings. The objective of this study was to examine the construct validity of the RAND-12 and HUI3 in the context of high-risk primary care patients. STUDY DESIGN AND SETTING: The SF-12, HUI2, and HUI3 were administered to a cohort of high-risk primary care patients. RAND-12 summary scores for physical and mental health were generated. Single-attribute utility scores for each dimension of health status and overall health in HUI3 were computed. A priori hypotheses were specified. RESULTS: In general, the relationships among RAND-12 and HUI3 scores were consistent with construct validity. Twelve of 24 a priori predictions were confirmed. However, predictions about the correlations between the number of medical conditions and the number of medications and the measures of health-related quality of life were, in general, not confirmed. CONCLUSIONS: The RAND-12 and HUI3 seem to be useful among primary care patients with diverse chronic conditions. Further investigation is warranted.