Impacts of hydrological alteration on ecosystem services changes of a large river-connected lake (Poyang Lake), China.

Large lakes provide various types of ecosystem services (ESs), of which stocks and variations induced by hydrological alterations are largely unquantified. The present study investigates the long-term changes of five key ESs (i.e., flood regulation, water supply, fish production, nutrient retention and biodiversity conservation) in a large river connected lake (Poyang Lake), with special attention to impacts of hydrological alteration induced by the Three Gorges Dam (TGD). Hydrological data series, hydrodynamic model, the nutrient balance, fishery statistics, and wetland winter waterbird survey data from 1980 to 2016 were employed. Results showed that Poyang Lake provide significant ESs, with long-term average flood regulation, water supply and nutrient retention services of 167.7 × 108 m3, 31.53 × 108 m3, and 15.12% of total phosphorus load, respectively. The fish production service ranged from 1.74 × 104t to 7.19 × 104t, with an average value of 3.12 × 104t. All five key ESs exhibited a downward trend since the 2000s, especially for water supply, fish production and nutrient retention services (p < 0.05), which might be largely attributed to the hydrological condition changes induced by TGD operation. Nevertheless, more detailed monitoring data and biophysical models are required to further acknowledge the changes in biodiversity conservation and fish production services and their linkages with the TGD. The present study sheds light on long-term ES changes in large lakes and their possible linkages with human influences through hydropower projects.

Land use change and climate dynamics in the Rift Valley Lake Basin, Ethiopia.

Land use and climate dynamics have a pronounced impact on water resources, biodiversity, land degradation, and productivity at all scales. Thus, in this study, we present the spatio-temporal dynamics of land use change and climate aiming to provide a scientific evidence about gains and losses in major land use categories and associated drivers and significancy and homogeneity of climate change. To this end, Landsat images and historical climate data have been used to determine the dynamics. In addition, population census data and land use policy have been considered to assess the potential drivers of land use change. The spatio-temporal land use dynamics have been evaluated using transition matrix and dynamics index. Likewise, shifts in the climate data were analyzed using change point analysis and three homogenous climate zones have been identified using principal component analysis. The results show that, from 1989 to 2019, the areal percentage of agricultural land increased by 27.5%, settlement by 0.8%, and barren land 0.4% while the natural vegetation, wetland, water body, and grass land decreased by 24.5%, 1.6%, 0.5%, and 2.1%, respectively. The land use dynamics have been stronger in the first decade of the study period. An abrupt shift of climate has occurred in the 1980s. In the last four decades, rainfall shows a not significant decreasing trend. However, a significant increasing trend has been observed for temperature. Rapid population growth, agricultural expansion policy, and climate variability have been identified as the underlying drivers of land use dynamics.

Spatial and temporal assessment of human-water interactions at the Inle Lake, Myanmar: a socio-hydrological DPSIR analysis.

Freshwater resources as a key aspect of socio-economic development, provide a large number of services in human and environmental systems. Nevertheless, human appropriation of these water resources and the modification of landscapes lead to potential threats on water availability and quality from local to global scales. The Inle Lake in Myanmar is an economically, traditionally, and ecologically important freshwater ecosystem that faced severe degradation from the 2000s. In its catchment area, a Driver-Pressure-State-Impact-Response (DPSIR) framework is applied for an assessment period of 30 years from 1990 to 2020. The analysis results are complemented with a socio-hydrological survey, water quality assessment, a land use classification based on ground truth and satellite data, and hydrologic models. The resulting land use changes, - 13% forest, + 13% agriculture, and + 5% urban areas, lead to increased water yield, decreased evapotranspiration, and increased sediment yield. Together with other drivers and pressures such as climate change and anthropogenic pollution, these human activities are major threats for freshwater resources and the ecosystem. However, the existing awareness of the local population for the environmental degradation is obstructed by national and international crises and responses to negative developments can accelerate degradation if they are unplanned and short-term solutions. Our study shows that environmental degradation processes have a complex nature and can only be tackled in a coordinated way with a long-term perspective. DPSIR is a suitable approach to assess human-water dynamics and disentangle the complex interconnectedness of social and environmental systems in freshwater ecosystems, even in data-scarce regions.

Examining characteristics and sampling methods of phosphor dynamics in lowland catchments.

Despite over two decades since the EU Water Framework Directive have passed, achieving the desired water quality in German surface waters remains challenging, regardless of efforts to reduce phosphorus inputs and associated environmental impacts. This study aims at analyzing the characteristics governing the concentrations of four key water quality parameters (total phosphorus, orthophosphate, particulate phosphate, and suspended solids) in two lowland catchments: the 50 km2 catchment of the Kielstau, Germany, and its 7 km2 tributary, the Moorau, which are dominated by agricultural land use. To this end, different sampling methods, particularly high-resolution precipitation event-based sampling and daily mixed samples, are conducted and evaluated, and their effectiveness is compared. The identification of sources and characteristics that affect phosphorus and suspended sediment dynamics, both in general and specifically during heavy precipitation events, is one focus of the study. Over a 15-year period, increasing concentrations of these parameters were observed in daily mixed samples, exhibiting distinct seasonal patterns-higher in summer and lower in winter-consistent with lowland catchment behavior. Particularly during heavy precipitation events, the smaller catchment exhibits a more complex and less predictable response to chemical concentrations compared with the dilution effect observed in the larger catchment. The results underline the complexity of phosphorus dynamics in small catchments and emphasize the importance of event-based sampling for capturing short-term concentration peaks for all four parameters, particularly beneficial regarding measuring suspended solids. While daily mixed samples capture average phosphorus concentrations, event-based sampling is crucial for detecting short-term spikes, providing a more comprehensive understanding of phosphorus dynamics.

A spatio-temporal analysis of environmental fate and transport processes of pesticides and their transformation products in agricultural landscapes dominated by subsurface drainage with SWAT.

Pesticides are detected in surface water and groundwater, endangering the environment. In lowland regions with subsurface drainage systems, drained depressions become hotspots for transport of pesticides and their transformation products (TPs). This study focuses on detailed modelling of the degradation and transport of pesticides with different physico-chemical properties. The objective is to analyse complex hydrological transport processes, to understand the temporal and spatial dynamics of the degradation and transport of pesticides. The ecohydrological model SWAT+ simulates hydrological processes as well as agricultural management and pesticide degradation, and can therefore be used to develop pesticide loss reduction strategies. This study focuses on modelling of three pesticides (pendimethalin, diflufenican, and flufenacet), and two TPs, flufenacet-oxalic acid (FOA) and flufenacet sulfonic acid (FESA). The study area is a 100-hectare farmland in the northern German lowlands of Schleswig-Holstein that is characterized by an spacious drainage network of 6.3 km and managed according to common conventional agricultural practice. SWAT+ modelled streamflow with very good agreement between observed and simulated data during calibration and validation. Regarding pesticides, the model performance for highly mobile substances is better than for non-mobile pesticides. While the transport of the moderately to very mobile substances via tile drains played an important role in both wet and dry conditions, no transport via tile drains was modelled for the highly sorptive and non-mobile pendimethalin. In conclusion, the model can reliably represent the degradation of moderately to very mobile pesticides in small-scale tile drainage-dominated catchments, as well as surface runoff-induced peak loads. However, it has weaknesses in accounting for the subsurface transport of non-mobile substances, which can lead to an underestimation of the subsequent delivery after precipitation events and thus underestimates the total load.

Designing Rigorous and Efficient Clinical Utility Studies for Early Detection Biomarkers.

Before implementing a biomarker in routine clinical care, it must demonstrate clinical utility by leading to clinical actions that positively affect patient-relevant outcomes. Randomly controlled early detection utility trials, especially those targeting mortality endpoint, are challenging due to their high costs and prolonged duration. Special design considerations are required to determine the clinical utility of early detection assays. This commentary reports on discussions among the National Cancer Institute's Early Detection Research Network investigators, outlining the recommended process for carrying out single-organ biomarker-driven clinical utility studies. We present the early detection utility studies in the context of phased biomarker development. We describe aspects of the studies related to the features of biomarker tests, the clinical context of endpoints, the performance criteria for later phase evaluation, and study size. We discuss novel adaptive design approaches for improving the efficiency and practicality of clinical utility trials. We recommend using multiple strategies, including adopting real-world evidence, emulated trials, and mathematical modeling to circumvent the challenges in conducting early detection utility trials.

National Cancer Institute's early detection research network: a model organization for biomarker research.

For many cancers a primary cause of poor survival is that they are detected at a late stage when therapies are less effective. Although screening methods exist to detect some types of cancer at an early stage, there are currently no effective methods to screen for most types of cancer. Biomarkers have the potential to improve detection of early-stage cancers, risk stratification, and prediction of which pre-cancerous lesions are likely to progress and to make screening tests less invasive. Although thousands of research articles on biomarkers for early detection are published every year, few of these biomarkers have been validated and shown to be clinically useful. This reflects both the inherent difficulty in detecting early-stage cancers and a disconnect between the process of discovering biomarkers and their use in the clinic. To overcome this limitation the US National Cancer Institute created the Early Detection Research Network. It is a highly collaborative program that brings together biomarker discoverers, assay developers, and clinicians. It provides an infrastructure that is essential for developing and validating biomarkers and imaging methods for early cancer detection and has successfully completed several multicenter validation studies.

Integrated modeling of global change impacts on land and water resources.

There is a common scientific understanding that global change impact analysis, mitigation, and adaptation require interdisciplinary work. Integrated modeling could help to address the challenges associated with the impacts of global change. Particularly, integrated modeling that takes feedback effects into account will allow for the derivation of climate resilient land use and land management. Here, we call for more of such integrated modeling work focusing on the interdisciplinary subject of water resources and land management. As a proof-of-concept, we tightly couple a hydrologic (SWAT) and a land use model (CLUE-s) and illustrate the benefits of this coupled land and water modeling framework (LaWaCoMo) with a scenario on cropland abandonment induced by water stress. As compared to standalone model runs of SWAT and CLUE-s for the past, LaWaCoMo performs slightly better regarding measured river discharge (PBIAS: +0.8% and +1.5% compared at two gauges) and land use change (figure of merit: +6.4% and +2.3% compared to land use maps at two points in time). We show that LaWaCoMo is suitable for global change impact analysis as it is sensitive to climate and land use inputs as well as to management decisions. Our results shed light on the importance of feedback effects between land use and hydrology to assess impacts of global change on land and water resources accurately and consistently. To facilitate that the developed methodology can serve as a blueprint for integrated modeling of global change impacts, we used two freely available models that belong to the most widely used models in their respective disciplines.

PreCancer Atlas: Present and Future.

Precancer atlases have the potential to revolutionize how we think about the topographic and morphologic structures of precancerous lesions in relation to cellular, molecular, genetic, and pathophysiologic states. This mini review uses the Human Tumor Atlas Network (HTAN), established by the National Cancer Institute (NCI), to illustrate the construction of cellular and molecular three-dimensional atlases of human cancers as they evolve from precancerous lesions to advanced disease. We describe the collaborative nature of the network and the research to determine how and when premalignant lesions progress to invasive cancer, regress or obtain a state of equilibrium. We have attempted to highlight progress made by HTAN in building precancer atlases and discuss possible future directions. It is hoped that the lessons from our experience with HTAN will help other investigators engaged in the construction of precancer atlases to crystallize their thoughts on logistics, rationale, and implementation.

A method for detecting the non-stationarity during high flows under global change.

The sustainability of existing water resources is influenced by extreme streamflow, and climate variability and human activities are generally the major factors controlling these dynamics. However, most of previously proposed methods to determine the effects of these factors have only been developed under the assumption of stationarity. Therefore, to overcome the existing research gap, an innovative method was proposed in this study to analyze and distinguish the effects of climate variability and human activities on extreme streamflow based on the non-stationarity theory. Accordingly, a rainfall-runoff model was developed using long-term hydrological data in the watersheds of Southeast China, which cover >75,000 km2. The model proposed in this study showed an acceptable performance, as indicated by the Nash-Sutcliffe efficiency coefficient (NSE), the Kling-Gupta efficiency (KGE), and percent bias (PBIAS). The NSE, KGE, and |PBIAS| were 0.67-0.75, 0.57-0.74, and 1.22-16.79 during the calibration periods, respectively. And the NSE, KGE, and |PBIAS| were 0.69-0.77, 0.65-0.76, and 0.98-17.51 during the calibration periods, respectively. The trends of the extreme streamflow were analyzed for these watersheds at different time scales. The streamflow extremes at short time scales were found to be more sensitive to changing environment than those at longer time scales. The major factor controlling streamflow extremes at short time scales was human activities and climate change may be the dominant factor influencing streamflow extremes at long time scales. The findings of this study could provide useful insights into water management under global change conditions.

Twenty years of change: Land and water resources in the Chindwin catchment, Myanmar between 1999 and 2019.

Since 2011, Myanmar has undergone a more rapid socio-economic development, which may substantially have affected land use and land cover (LULC) and water resources. This study investigates the changes in land and water resources of the Chindwin River catchment (114,686.9 km2) in Myanmar over a twenty-year timespan from 1999 to 2019. The main aim of this study is to assess LULC change and evaluate its effects on the water balance and the people in the region. To this end, interviews were conducted, LULC classifications based on multi-temporal multi-spectral satellite data and in-situ ground truth data were created, and a hydrologic model was built. The hydrologic model shows a reasonable performance for daily discharge simulation at the catchment outlet (percent bias between -2 and 13.2, Kling-Gupta Efficiency between 0.75 and 0.76, Nash-Sutcliffe Efficiency between 0.57 and 0.61, RMSE-observations standard deviation between 0.63 and 0.66). The LULC changes detected include a decrease in forest area of about 2%, an increase in shrubland area indicating increased degradation of the forest, an increase in mining areas of 0.38%, an overall decrease in agricultural area (2.1%), but also the presence of new agricultural land pointing toward relocation of agricultural areas and an indication of an increase in settlement areas (1.5%). With the help of the hydrologic model, the most significant hydrologic impacts detected were a decrease in evapotranspiration and an increase in water yield which is correlated with the decrease of forest at the sub-catchment scale (R2 = 0.72 and 0.46, respectively). Moreover, an increase of mining areas contributed to the increase in water yield (R2 = 0.62). Interviews confirm that the identified LULC changes deforestation and increased mining activities contribute to major issues, e.g., water pollution, sedimentation, and changes in the river course.

Alpha-fetoprotein, des-gamma carboxyprothrombin, and lectin-bound alpha-fetoprotein in early hepatocellular carcinoma.

BACKGROUND & AIMS: Alpha-fetoprotein (AFP) is widely used as a surveillance test for hepatocellular carcinoma (HCC) among patients with cirrhosis. Des-gamma carboxy-prothrombin (DCP) and lectin-bound AFP (AFP-L3%) are potential surveillance tests for HCC. The aims of this study were to determine performance of DCP and AFP-L3% for the diagnosis of early HCC; whether they complement AFP; and what factors affect DCP, AFP-L3%, or AFP levels. METHODS: We conducted a large phase 2 biomarker case-control study in 7 academic medical centers in the United States. Controls were patients with compensated cirrhosis and cases were patients with HCC. AFP, DCP, and AFP-L3% levels were measured blinded to clinical data in a central reference laboratory. RESULTS: A total of 836 patients were enrolled: 417 (50%) were cirrhosis controls and 419 (50%) were HCC cases, of which 208 (49.6%) had early stage HCC (n = 77 very early, n = 131 early). AFP had the best area under the receiver operating characteristic curve (0.80, 95% confidence interval [CI]: 0.77-0.84), followed by DCP (0.72, 95% CI: 0.68-0.77) and AFP-L3% (0.66, 95% CI: 0.62-0.70) for early stage HCC. The optimal AFP cutoff value was 10.9 ng/mL leading to a sensitivity of 66%. When only those with very early HCC were evaluated, the area under the receiver operating characteristic curve for AFP was 0.78 (95% CI: 0.72-0.85) leading to a sensitivity of 65% at the same cutoff. CONCLUSIONS: AFP was more sensitive than DCP and AFP-L3% for the diagnosis of early and very early stage HCC at a new cutoff of 10.9 ng/mL.

The Early Detection Research Network: A National Infrastructure to Support the Discovery, Development, and Validation of Cancer Biomarkers.

In 2000, the NCI (Rockville, MD) established the Early Detection Research Network (EDRN) to identify, develop, and validate biomarkers to improve the detection of early-stage cancers and risk assessment. This consortium of more than 300 investigators at academic institutions and in the private sector is working collaboratively to bring biomarkers and imaging methods to clinical fruition. Although significant roadblocks have hindered the field of biomarker discovery and validation, the EDRN has helped overcome many of them by setting well-defined strategies and milestones focused on solving defined unmet clinical needs. The EDRN has implemented measures to improve biomarker discovery and validation, such as data sharing, use of common data elements, generating multidisciplinary and multi-institutional collaborations within a cohesive and productive team environment, and putting emphasis on quality control and data replication for all candidate biomarkers for reaching a "go" or "no go" decision. A measure of the success of the EDRN is the number of biomarkers tests or devices approved by the FDA to which EDRN investigators have made significant contributions and the number of biomarkers tests developed by EDRN investigators that are available in Clinical Laboratory Improvement Amendments laboratories.See all articles in this CEBP Focus section, "NCI Early Detection Research Network: Making Cancer Detection Possible."

Anti-HER2 IgY antibody-functionalized single-walled carbon nanotubes for detection and selective destruction of breast cancer cells.

BACKGROUND: Nanocarrier-based antibody targeting is a promising modality in therapeutic and diagnostic oncology. Single-walled carbon nanotubes (SWNTs) exhibit two unique optical properties that can be exploited for these applications, strong Raman signal for cancer cell detection and near-infrared (NIR) absorbance for selective photothermal ablation of tumors. In the present study, we constructed a HER2 IgY-SWNT complex and demonstrated its dual functionality for both detection and selective destruction of cancer cells in an in vitro model consisting of HER2-expressing SK-BR-3 cells and HER2-negative MCF-7 cells. METHODS: The complex was constructed by covalently conjugating carboxylated SWNTs with anti-HER2 chicken IgY antibody, which is more specific and sensitive than mammalian IgGs. Raman signals were recorded on Raman spectrometers with a laser excitation at 785 nm. NIR irradiation was performed using a diode laser system, and cells with or without nanotube treatment were irradiated by 808 nm laser at 5 W/cm2 for 2 min. Cell viability was examined by the calcein AM/ethidium homodimer-1 (EthD-1) staining. RESULTS: Using a Raman optical microscope, we found the Raman signal collected at single-cell level from the complex-treated SK-BR-3 cells was significantly greater than that from various control cells. NIR irradiation selectively destroyed the complex-targeted breast cancer cells without harming receptor-free cells. The cell death was effectuated without the need of internalization of SWNTs by the cancer cells, a finding that has not been reported previously. CONCLUSION: We have demonstrated that the HER2 IgY-SWNT complex specifically targeted HER2-expressing SK-BR-3 cells but not receptor-negative MCF-7 cells. The complex can be potentially used for both detection and selective photothermal ablation of receptor-positive breast cancer cells without the need of internalization by the cells. Thus, the unique intrinsic properties of SWNTs combined with high specificity and sensitivity of IgY antibodies can lead to new strategies for cancer detection and therapy.

Cancer overdiagnosis: a biological challenge and clinical dilemma.

For cancer screening to be successful, it should primarily detect cancers with lethal potential or their precursors early, leading to therapy that reduces mortality and morbidity. Screening programmes have been successful for colon and cervical cancers, where subsequent surgical removal of precursor lesions has resulted in a reduction in cancer incidence and mortality. However, many types of cancer exhibit a range of heterogeneous behaviours and variable likelihoods of progression and death. Consequently, screening for some cancers may have minimal impact on mortality and may do more harm than good. Since the implementation of screening tests for certain cancers (for example, breast and prostate cancers), a spike in incidence of in situ and early-stage cancers has been observed, but a link to reduction in cancer-specific mortality has not been as clear. It is difficult to determine how many of these mortality reductions are due to screening and how many are due to improved treatments of tumours. In cancers with lower incidence but high mortality (for example, pancreatic cancer), screening has focused on high-risk populations, but challenges similar to those for general population screening remain, particularly with regard to finding lesions with difficult-to-characterize malignant potential (for example, intraductal papillary mucinous neoplasms). More sensitive screening methods are detecting smaller and smaller lesions, but this has not been accompanied by a comparable reduction in the incidence of invasive cancers. In this Opinion article, we focus on the contribution of screening in general and high-risk populations to overdiagnosis, the effects of overdiagnosis on patients and emerging strategies to reduce overdiagnosis of indolent cancers through an understanding of tumour heterogeneity, the biology of how cancers evolve and progress, the molecular and cellular features of early neoplasia and the dynamics of the interactions of early lesions with their surrounding tissue microenvironment.

Quantitation of HER2 and telomerase biomarkers in solid tumors with IgY antibodies and nanocrystal detection.

In an effort to improve affinity biomarker validation in fixed patient tissue specimens, we have developed a novel quantum dot-based bioimaging system that utilizes chicken IgY antibody for high sensitivity and specificity relative quantitation of cancer proteins. Monospecific, polyclonal IgYs were generated against human HER2 and telomerase, and analytically validated for specificity by western blot and immunohistochemistry on tumor and normal cells and for relative affinity by layered peptide array (LPA). IgYs bound desired targets in cell lines and fixed tissues and showed greater affinity than commercial mammalian antibodies for both HER2 and telomerase proteins. In tissue microarray experiments, HER2 quantitation with IgY antibody and quantum dot imaging correlated well with chromogenic in situ hybridization (CISH), whereas telomerase quantitation suggested a trend toward correlation with prostate cancer Gleason Grade and differentiation. Although patient numbers were small, these findings demonstrate the feasibility of relative quantitation of cancer biomarkers with IgY and quantum dot fluorophores, and show promise for rigorous clinical validation in large patient cohorts.

Multiple strand displacement amplification of mitochondrial DNA from clinical samples.

BACKGROUND: Whole genome amplification (WGA) methods allow diagnostic laboratories to overcome the common problem of insufficient DNA in patient specimens. Further, body fluid samples useful for cancer early detection are often difficult to amplify with traditional PCR methods. In this first application of WGA on the entire human mitochondrial genome, we compared the accuracy of mitochondrial DNA (mtDNA) sequence analysis after WGA to that performed without genome amplification. We applied the method to a small group of cancer cases and controls and demonstrated that WGA is capable of increasing the yield of starting DNA material with identical genetic sequence. METHODS: DNA was isolated from clinical samples and sent to NIST. Samples were amplified by PCR and those with no visible amplification were re-amplified using the Multiple Displacement Amplificaiton technique of whole genome amplification. All samples were analyzed by mitochip for mitochondrial DNA sequence to compare sequence concordance of the WGA samples with respect to native DNA. Real-Time PCR analysis was conducted to determine the level of WGA amplification for both nuclear and mtDNA. RESULTS: In total, 19 samples were compared and the concordance rate between WGA and native mtDNA sequences was 99.995%. All of the cancer associated mutations in the native mtDNA were detected in the WGA amplified material and heteroplasmies in the native mtDNA were detected with high fidelity in the WGA material. In addition to the native mtDNA sequence present in the sample, 13 new heteroplasmies were detected in the WGA material. CONCLUSION: Genetic screening of mtDNA amplified by WGA is applicable for the detection of cancer associated mutations. Our results show the feasibility of this method for: 1) increasing the amount of DNA available for analysis, 2) recovering the identical mtDNA sequence, 3) accurately detecting mtDNA point mutations associated with cancer.

Facile whole mitochondrial genome resequencing from nipple aspirate fluid using MitoChip v2.0.

BACKGROUND: Mutations in the mitochondrial genome (mtgenome) have been associated with many disorders, including breast cancer. Nipple aspirate fluid (NAF) from symptomatic women could potentially serve as a minimally invasive sample for breast cancer screening by detecting somatic mutations in this biofluid. This study is aimed at 1) demonstrating the feasibility of NAF recovery from symptomatic women, 2) examining the feasibility of sequencing the entire mitochondrial genome from NAF samples, 3) cross validation of the Human mitochondrial resequencing array 2.0 (MCv2), and 4) assessing the somatic mtDNA mutation rate in benign breast diseases as a potential tool for monitoring early somatic mutations associated with breast cancer. METHODS: NAF and blood were obtained from women with symptomatic benign breast conditions, and we successfully assessed the mutation load in the entire mitochondrial genome of 19 of these women. DNA extracts from NAF were sequenced using the mitochondrial resequencing array MCv2 and by capillary electrophoresis (CE) methods as a quality comparison. Sequencing was performed independently at two institutions and the results compared. The germline mtDNA sequence determined using DNA isolated from the patient's blood (control) was compared to the mutations present in cellular mtDNA recovered from patient's NAF. RESULTS: From the cohort of 28 women recruited for this study, NAF was successfully recovered from 23 participants (82%). Twenty two (96%) of the women produced fluids from both breasts. Twenty NAF samples and corresponding blood were chosen for this study. Except for one NAF sample, the whole mtgenome was successfully amplified using a single primer pair, or three pairs of overlapping primers. Comparison of MCv2 data from the two institutions demonstrates 99.200% concordance. Moreover, MCv2 data was 99.999% identical to CE sequencing, indicating that MCv2 is a reliable method to rapidly sequence the entire mtgenome. Four NAF samples contained somatic mutations. CONCLUSION: We have demonstrated that NAF is a suitable material for mtDNA sequence analysis using the rapid and reliable MCv2. Somatic mtDNA mutations present in NAF of women with benign breast diseases could potentially be used as risk factors for progression to breast cancer, but this will require a much larger study with clinical follow up.

Performance of mitochondrial DNA mutations detecting early stage cancer.

BACKGROUND: Mutations in the mitochondrial genome (mtgenome) have been associated with cancer and many other disorders. These mutations can be point mutations or deletions, or admixtures (heteroplasmy). The detection of mtDNA mutations in body fluids using resequencing microarrays, which are more sensitive than other sequencing methods, could provide a strategy to measure mutation loads in remote anatomical sites. METHODS: We determined the mtDNA mutation load in the entire mitochondrial genome of 26 individuals with different early stage cancers (lung, bladder, kidney) and 12 heavy smokers without cancer. MtDNA was sequenced from three matched specimens (blood, tumor and body fluid) from each cancer patient and two matched specimens (blood and sputum) from smokers without cancer. The inherited wildtype sequence in the blood was compared to the sequences present in the tumor and body fluid, detected using the Affymetrix Genechip Human Mitochondrial Resequencing Array 1.0 and supplemented by capillary sequencing for noncoding region. RESULTS: Using this high-throughput method, 75% of the tumors were found to contain mtDNA mutations, higher than in our previous studies, and 36% of the body fluids from these cancer patients contained mtDNA mutations. Most of the mutations detected were heteroplasmic. A statistically significantly higher heteroplasmy rate occurred in tumor specimens when compared to both body fluid of cancer patients and sputum of controls, and in patient blood compared to blood of controls. Only 2 of the 12 sputum specimens from heavy smokers without cancer (17%) contained mtDNA mutations. Although patient mutations were spread throughout the mtDNA genome in the lung, bladder and kidney series, a statistically significant elevation of tRNA and ND complex mutations was detected in tumors. CONCLUSION: Our findings indicate comprehensive mtDNA resequencing can be a high-throughput tool for detecting mutations in clinical samples with potential applications for cancer detection, but it is unclear the biological relevance of these detected mitochondrial mutations. Whether the detection of tumor-specific mtDNA mutations in body fluidsy this method will be useful for diagnosis and monitoring applications requires further investigation.

Mitochondrial genome deletion aids in the identification of false- and true-negative prostate needle core biopsy specimens.

We report the usefulness of a 3.4-kb mitochondrial genome deletion (3.4 mtdelta) for molecular definition of benign, malignant, and proximal to malignant (PTM) prostate needle biopsy specimens. The 3.4 mtdelta was identified through long-extension polymerase chain reaction (PCR) analysis of frozen prostate cancer samples. A quantitative PCR assay was developed to measure the levels of the 3.4 mtdelta in clinical samples. For normalization, amplifications of a nuclear target and total mitochondrial DNA were included. Cycle threshold data from these targets were used to calculate a score for each biopsy sample. In a pilot study of 38 benign, 29 malignant, and 41 PTM biopsy specimens, the difference between benign and malignant core biopsy specimens was well differentiated (P & .0001), with PTM indistinguishable from malignant samples (P = .833). Results of a larger study were identical. In comparison with histopathologic examination for benign and malignant samples, the sensitivity and specificity were 80% and 71%, respectively, and the area under a receiver operating characteristic (ROC) curve was 0.83 for the deletion. In a blinded external validation study, the sensitivity and specificity were 83% and 79%, and the area under the ROC curve was 0.87. The 3.4 mtdelta may be useful in defining malignant, benign, and PTM prostate tissues.