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Shilai Zhang - One of the best experts on this subject based on the ideXlab platform.

  • genotype by environment interactions for performance of perennial rice genotypes oryza sativa l oryza longistaminata relative to annual rice genotypes over regrowth cycles and locations in southern china
    Field Crops Research, 2019
    Co-Authors: Shilai Zhang, Liyu Huang, Jing Zhang, Guangfu Huang, Mao Cheng, Zhili Wang, Yini Zhang, Chunli Wang, Pinfen Zhu, Ke Tao
    Abstract:

    Abstract Genotype by environment (GxE) interactions for performance of 5 perennial rice genotypes (Oryza sativa L./Oryza longistaminata) were examined relative to 1 mutant and 3 annual rice genotypes over 2–6 growth cycles at 7 locations in southern China between 2014 and 2017. Environment main effects accounted for 25.7% of the total sum of squares (SS), with genotype 33.8% and GxE 37.7%. Cluster analysis identified 6 genotype x 6 environment groups, which accounted for 77.9% of the GxE-SS. Principal component axes 1, 2 and 3 accounted for 54.7%, 25.1% and 9.4% of the GxE-SS, respectively, with PCA1 indicating yield potential, PCA2 performance over ratoon cycles, and PCA3 ratoon percentage. Environment groups differed in yield potential, which related to site favourability and whether it was low or high in the ratoon cycle. Genotype groups differed in yield potential and how well they performed in higher ratoon cycles. The medium-maturity (125 days) seasonally-replanted annual rice check BN21 was highest yielding (6.13 t ha−1). Perennial rice PR23 was high yielding and stable (5.25 t ha−1), with earlier maturity (119 days) and strong regrowth (82%). Ratooned annual rice RD23 was high yielding in original crops but poor yielding in ratoon crops, with a low ratoon percentage (16.5%). Similarly, perennial Bt71 and ratooned BN21 were high yielding in original crops and low-cycle ratoons under favourable conditions, but yielded poorly in high-cycle ratoons and less favourable conditions, with moderate regrowth (59.6%). Despite strong regrowth (77.5%), perennials 264 and Bt69 had low yield, as did perennial 139A and mutant TZ, and both these groups were late maturity. A combination of high yield potential, strong regrowth and earlier maturity resulted in higher performance of perennial rice over environments and regrowth cycles, with PR23 outstanding, and able to perform similarly to the seasonally-replanted annual check, BN21, over up to six growth cycles. Ratoon performance and trade-offs need to be examined further.

  • Genotype by environment interactions for performance of perennial rice genotypes (Oryza sativa L./Oryza longistaminata) relative to annual rice genotypes over regrowth cycles and locations in southern China
    Field Crops Research, 2019
    Co-Authors: Shilai Zhang, Liyu Huang, Jing Zhang, Huang Guangfu, Mao Cheng, Zhili Wang, Yini Zhang, Chunli Wang, Pinfen Zhu
    Abstract:

    Abstract Genotype by environment (GxE) interactions for performance of 5 perennial rice genotypes (Oryza sativa L./Oryza longistaminata) were examined relative to 1 mutant and 3 annual rice genotypes over 2–6 growth cycles at 7 locations in southern China between 2014 and 2017. Environment main effects accounted for 25.7% of the total sum of squares (SS), with genotype 33.8% and GxE 37.7%. Cluster analysis identified 6 genotype x 6 environment groups, which accounted for 77.9% of the GxE-SS. Principal component axes 1, 2 and 3 accounted for 54.7%, 25.1% and 9.4% of the GxE-SS, respectively, with PCA1 indicating yield potential, PCA2 performance over ratoon cycles, and PCA3 ratoon percentage. Environment groups differed in yield potential, which related to site favourability and whether it was low or high in the ratoon cycle. Genotype groups differed in yield potential and how well they performed in higher ratoon cycles. The medium-maturity (125 days) seasonally-replanted annual rice check BN21 was highest yielding (6.13 t ha−1). Perennial rice PR23 was high yielding and stable (5.25 t ha−1), with earlier maturity (119 days) and strong regrowth (82%). Ratooned annual rice RD23 was high yielding in original crops but poor yielding in ratoon crops, with a low ratoon percentage (16.5%). Similarly, perennial Bt71 and ratooned BN21 were high yielding in original crops and low-cycle ratoons under favourable conditions, but yielded poorly in high-cycle ratoons and less favourable conditions, with moderate regrowth (59.6%). Despite strong regrowth (77.5%), perennials 264 and Bt69 had low yield, as did perennial 139A and mutant TZ, and both these groups were late maturity. A combination of high yield potential, strong regrowth and earlier maturity resulted in higher performance of perennial rice over environments and regrowth cycles, with PR23 outstanding, and able to perform similarly to the seasonally-replanted annual check, BN21, over up to six growth cycles. Ratoon performance and trade-offs need to be examined further.

  • Performance and survival of perennial rice derivatives (Oryza sativa L./Oryza longistaminata) in Lao PDR
    Experimental Agriculture, 2017
    Co-Authors: Benjamin K. Samson, Shilai Zhang, Dayun Tao, Singtty Voradeth, Sisavanh Xayavong, Thiravong Khammone, Khamsouk Douangboupha, Vorachith Sihathep, Pheng Sengxua, Viengsavanh Phimphachanhvongsod
    Abstract:

    Genotype by environment (G x E) interactions for grain yield were investigated in 13 perennial rice (Oryza sativa L./Oryza longistaminata) derivatives over three sites and 2 years in Lao PDR. Genotype accounted for 29.0% of the total sum of squares, with environment and the G x E interaction responsible for 60.2 and 10.8%, respectively. Cluster analysis identified three environment and six genotype groups, which accounted for 49.7, 98.0 and 42.8% of the E, G and G x E sums of squares, respectively. Principal component axes 1, 2 and 3 accounted for 54.0, 30.6 and 11.7% of the G x E sum of squares, respectively, with PCA1 indicating yield potential, PCA2 timing of cessation of rainfall in the 2011 wet season, and PCA3 environmental stresses affecting regrowth in the 2012 wet season. Genotype groups differed in adaptation to these contrasting conditions. G6 (Line 213, 240 and RD23) was widely adapted to all environments, with G5 (Line 248) being especially adapted to the 2012 environments. G3 and G4 were neutral, though G3 (Line 53) showed some preference for the Na Pok environments. G1 and G2 were poorly adapted everywhere, with the tall and late G1 (Line 11) being especially poor at Na Pok 2011 in a dry finish. While yields were lower in 2012, all derivatives survived the dry season with access to life-saving irrigation. This is promising as the annual rice RD23 was unable to ratoon under these conditions, and had to be re-sown. Importantly, Line 213. 240 and 248 yielded comparably to RD23 from regrowth in 2012. Development of perennial rice should target rainfed and especially upland environments.

  • performance and survival of perennial rice derivatives oryza sativa l oryza longistaminata in lao pdr
    Experimental Agriculture, 2017
    Co-Authors: Benjamin K. Samson, Shilai Zhang, Dayun Tao, Singtty Voradeth, Sisavanh Xayavong, Thiravong Khammone, Khamsouk Douangboupha, Vorachith Sihathep, Pheng Sengxua, Viengsavanh Phimphachanhvongsod
    Abstract:

    Genotype by environment (G x E) interactions for grain yield were investigated in 13 perennial rice (Oryza sativa L./Oryza longistaminata) derivatives over three sites and 2 years in Lao PDR. Genotype accounted for 29.0% of the total sum of squares, with environment and the G x E interaction responsible for 60.2 and 10.8%, respectively. Cluster analysis identified three environment and six genotype groups, which accounted for 49.7, 98.0 and 42.8% of the E, G and G x E sums of squares, respectively. Principal component axes 1, 2 and 3 accounted for 54.0, 30.6 and 11.7% of the G x E sum of squares, respectively, with PCA1 indicating yield potential, PCA2 timing of cessation of rainfall in the 2011 wet season, and PCA3 environmental stresses affecting regrowth in the 2012 wet season. Genotype groups differed in adaptation to these contrasting conditions. G6 (Line 213, 240 and RD23) was widely adapted to all environments, with G5 (Line 248) being especially adapted to the 2012 environments. G3 and G4 were neutral, though G3 (Line 53) showed some preference for the Na Pok environments. G1 and G2 were poorly adapted everywhere, with the tall and late G1 (Line 11) being especially poor at Na Pok 2011 in a dry finish. While yields were lower in 2012, all derivatives survived the dry season with access to life-saving irrigation. This is promising as the annual rice RD23 was unable to ratoon under these conditions, and had to be re-sown. Importantly, Line 213. 240 and 248 yielded comparably to RD23 from regrowth in 2012. Development of perennial rice should target rainfed and especially upland environments.

  • genotype by environment interactions for grain yield of perennial rice derivatives oryza sativa l oryza longistaminata in southern china and laos
    Field Crops Research, 2017
    Co-Authors: Shilai Zhang, Liyu Huang, Benjamin K. Samson, Chundao Yang, Haitao Liu, Feng Yang, Jihua Zhou, Chanthakhone Boualaphanh, Guangfu Huang, Jing Zhang
    Abstract:

    Perennial grains have been proposed to stabilise fragile lands while contributing grain and grazing in mixed farming systems. Genotype by environment (GxE) interactions for grain yield were investigated in 22 perennial rice (Oryza sativa L./Oryza longistaminata) derivatives over four successive growing seasons at three sites in Yunnan in southern China and one site in Lao PDR. The GxE interaction accounted for 25.7% of the total sum of squares, with environment and genotype responsible for 57.4% and 16.9%, respectively. Cluster analysis identified seven environment and six genotype groups, which accounted for 55.6% of the GxE sum of squares. Principal component axes 1, 2 and 3 accounted for 42.3%, 19.1% and 16.5% of the GxE-SS, respectively, with PCA1 indicating yield potential, PCA2 delay in phenology under environmental stress, and PCA3 ratoon percentage. Environment groups differed in mean temperature, whether dry season or wet season, and occurrence of environmental stresses, such as periods of low minimum temperature or periods of rainfall deficit. Genotype groups differed in adaptation to these diverse environments. For genotype groups, G5 (PR23) was highest-yielding and broadly adapted across environments, while G1 (line 188, both 137s, both 139s, both 147s) was low-yielding and poorly adapted. Other genotype groups showed preferential adaptation: G3 (lines 60, 251, 264, Bt69, Bt71) to Simao/Dry Season (E3 and E4), G4 (lines 75, 243, 246, 249, 255) to Menglian/Wet Season (E1 and E2), G2 (line TZ) to Jing Hong 2013 (E7), and G6 (lines 56, 59, 214) to Jing Hong 2102 and Na Pok (E6 and E5). The results imply that regrowth success and maintenance of spikelet fertility over regrowth cycles are important for adaptation of perennial rice, especially to low minimum temperature at higher altitude and rainfall deficit at lower altitude, and future breeding programmes in perennial rice should address these environmental stresses. The high yield and broad adaptation of PR23 (G5) over environments makes it a prime candidate for release to stabilise fragile lands in the humid and subhumid tropics, while contributing grain and forage in mixed-farming systems.

Daphne Hessels - One of the best experts on this subject based on the ideXlab platform.

  • prospective multicentre evaluation of PCA3 and tmprss2 erg gene fusions as diagnostic and prognostic urinary biomarkers for prostate cancer
    European Urology, 2014
    Co-Authors: G H J M Leyten, Daphne Hessels, Sander Jannink, Frank Smit, Hans De Jong, Erik B Cornel, Theo M De Reijke, H Vergunst, Ben C Knipscheer, Inge M Van Oort
    Abstract:

    Abstract Background Prostate cancer antigen 3 ( PCA3 ) and v-ets erythroblastosis virus E26 oncogene homolog ( TMPRSS2-ERG ) gene fusions are promising prostate cancer (PCa) specific biomarkers that can be measured in urine. Objective To evaluate the diagnostic and prognostic value of Progensa PCA3 and TMPRSS2-ERG gene fusions (as individual biomarkers and as a panel) for PCa in a prospective multicentre setting. Design, setting, and participants At six centres, post–digital rectal examination first-catch urine specimens prior to prostate biopsies were prospectively collected from 497 men. We assessed the predictive value of Progensa PCA3 and TMPRSS2-ERG (quantitative nucleic acid amplification assay to detect TMPRSS2-ERG messenger RNA [mRNA]) for PCa, Gleason score, clinical tumour stage, and PCa significance (individually and as a marker panel). This was compared with serum prostate-specific antigen and the European Randomised Study of Screening for Prostate Cancer (ERSPC) risk calculator. In a subgroup ( n =61) we evaluated biomarker association with prostatectomy outcome. Outcome measurements and statistical analysis Univariate and multivariate logistic regression analysis and receiver operating curves were used. Results and limitations Urine samples of 443 men contained sufficient mRNA for marker analysis. PCa was diagnosed in 196 of 443 men. Both PCA3 and TMPRSS2-ERG had significant additional predictive value to the ERSPC risk calculator parameters in multivariate analysis ( p p =0.002). The area under the curve (AUC) increased from 0.799 (ERSPC risk calculator), to 0.833 (ERSPC risk calculator plus PCA3), to 0.842 (ERSPC risk calculator plus PCA3 plus TMPRSS2-ERG) to predict PCa. Sensitivity of PCA3 increased from 68% to 76% when combined with TMPRSS2-ERG. TMPRSS2-ERG added significant predictive value to the ERSPC risk calculator to predict biopsy Gleason score ( p p =0.023), whereas PCA3 did not. Conclusions TMPRSS2-ERG had independent additional predictive value to PCA3 and the ERSPC risk calculator parameters for predicting PCa. TMPRSS2-ERG had prognostic value, whereas PCA3 did not. Implementing the novel urinary biomarker panel PCA3 and TMPRSS2-ERG into clinical practice would lead to a considerable reduction of the number of prostate biopsies.

  • Performance of prostate cancer antigen 3 (PCA3) and prostate-specific antigen in Prescreened men: reproducibility and detection characteristics for prostate cancer patients with high PCA3 scores (≥ 100).
    European urology, 2010
    Co-Authors: Monique J. Roobol, Daphne Hessels, Fritz H. Schröder, Geert L. J. H. Van Leenders, Roderick C.n. Van Den Bergh, Tineke Wolters, Pim J. Van Leeuwen
    Abstract:

    Abstract Background Prostate cancer antigen 3 (PCA3) is considered to be prostate cancer (PCa) specific and highly overexpressed in cancer. Therefore a high PCA3 score should result in a high positive predictive value (PPV) and specificity for a positive biopsy. Objective Our aim was to reevaluate, retest PCA3, and rebiopsy men with an initial PCA3 ≥100 and no PCa detected and compare the results with a random cohort of men with an initial PCA3 Design, setting, and participants We invited men 63–75 yr of age with a PCA3 ≥100 for retesting and a control group with an initial PCA3 Interventions Blood and urine sampling were used to determine prostate-specific antigen (PSA) and PCA3. Prostate biopsies were performed if the PSA was ≥2.5ng/ml and/or the PCA3 score was ≥35. Measurements We correlated the initial and reevaluated PCA3 scores. Our assessment of the PPV after rebiopsy was based on the newly determined PCA3 score. Results and limitations After a mean study period of 19 mo, more cases of PCa were detected in rebiopsied men with initial PCA3 scores ≥100 than in the controls with PCA3 scores Conclusions In spite of our rescreened population, PPV and specificity were comparable with all reported studies of men with PCA3 scores ≥100. These findings do not explain why these PCA3 scores were excessively high in spite of the absence of biopsy-detectable PCa.

  • Performance of the Prostate Cancer Antigen 3 (PCA3) Gene and Prostate-Specific Antigen in Prescreened Men: Exploring the Value of PCA3 for a First-line Diagnostic Test
    European urology, 2010
    Co-Authors: Monique J. Roobol, Fritz H. Schröder, Roderick C.n. Van Den Bergh, Tineke Wolters, Pim J. Van Leeuwen, Geert J L H Van Leenders, Daphne Hessels
    Abstract:

    Abstract Background The performance characteristics of serum prostate-specific antigen (PSA) as a diagnostic test for prostate cancer (PCa) are poor. The performance of the PCa antigen 3 (PCA3) gene as a primary diagnostic is unknown. Objective Assess the value of PCA3 as a first-line diagnostic test. Design, setting and participants Participants included men aged 63–75 who were invited for rescreening in the period from September 2007 to February 2009 within the European Randomised Study of Screening for Prostate Cancer, Rotterdam section. Interventions Lateral sextant biopsies were performed if the serum PSA value was ≥3.0ng/ml and/or the PCA3 score was ≥10. Measurements Measurements included distribution and correlation of PSA value and PCA3 score and their relation to the number of cases and the characteristics of PCa detected. Additional value of PCA3 was included in men with previous negative biopsy and/or PSA Results and limitations In 721 men, all biopsied, 122 PCa cases (16.9%) were detected. Correlation between PSA and PCA3 is poor (Spearman rank correlation: ρ=0.14; p n =19), and 68.2% of biopsies could have been avoided; the respective data for PCA3 ≥35 are 32%, 26.3%, and 51.7%. Performance of PCA3 in men with low PSA (area under the curve [AUC]: 0.63) and/or previous negative biopsy (AUC: 0.68) is unclear but has limited reliability due to small numbers. Conclusions PCA3 as a first-line screening test shows improvement of the performance characteristics and identification of serious disease compared with PSA in this prescreened population.

  • Differential expression of PCA3 and its overlapping PRUNE2 transcript in prostate cancer.
    The Prostate, 2010
    Co-Authors: Maciej Salagierski, Daphne Hessels, Frank Smit, Gerald W. Verhaegh, Sander A. Jannink, Jack A. Schalken
    Abstract:

    BACKGROUND: PCA3 is one of the most prostate cancer (PrCa)-specific markers described so far. Recently, a new genomic structure of PCA3 as well as new flanking and overlapping gene transcripts has been identified. Furthermore, a co-regulation of PCA3 and its overlapping gene PRUNE2(BMCC1) has been suggested. Our aim was to assess the diagnostic performance of a new PCA3 isoform (PCA3-TS4) and to study the interactions between PCA3 and BMCC1 in PrCa. METHODS: We used SYBR Green quantitative (q)PCR with specific primers to compare PCA3 and BMCC1 expression of normal versus tumor tissue of human prostate. PCA3-TS4 plasmid was created to calculate the absolute amounts of PCA3 transcripts. The androgen regulation of PCA3 and BMCC1 expression was studied in LNCaP and 22Rv1 cells stimulated with 5alpha-dihydrotestosterone. RESULTS: We have not found any relevant diagnostic advantage of the PCA3-TS4 isoform over the "classical" PCA3 isoform in our group of PrCa patients. Additionally, PCA3-TS4 appears to be only a minor PCA3 transcript. We were also unable to confirm the hypothesis that BMCC1 isoforms are androgen-induced in vitro. CONCLUSIONS: Despite the presence of the recently identified marginal PCA3 transcripts in human PrCa, the previously described major PCA3 isoform still constitutes the best target for diagnostic purposes. PCA3 and BMCC1 are overlapping genes in reverse orientation that do not appear to be co-regulated.

  • Molecular PCA3 diagnostics on prostatic fluid.
    The Prostate, 2007
    Co-Authors: Martijn P.m.q. Van Gils, Daphne Hessels, Erik B Cornel, Harry G Rittenhouse, Peter F.a. Mulders, W. Pim Peelen, J. Alfred Witjes, Jack A. Schalken
    Abstract:

    BACKGROUND: The PCA3 test on urine can improve specificity in prostate cancer (PCa) diagnosis and could prevent unnecessary prostate biopsies. In this study, we evaluated the PCA3 test on prostatic fluid and compared this with the PCA3 test on urine in a clinical research setting. METHODS: Prostatic fluid and urine samples from 67 men were collected following digital rectal examination (DRE). The sediments were analyzed using the quantitative APTIMA PCA3 test. The results were compared with prostate biopsy results. RESULTS: Using a PCA3 score of 66 as a cut-off value, the test on prostatic fluid had 65% sensitivity for the detection of PCa, 82% specificity and a negative predictive value of 82%. At a cut-off value of 43, the test on urine had 61% sensitivity, 80% specificity and a negative predictive value of 80%. CONCLUSIONS: The PCA3 test can be performed on both urine and prostatic fluid in the diagnosis of PCa with comparable results.

Kim Pettersson - One of the best experts on this subject based on the ideXlab platform.

  • Quantitative real-time RT-PCR assay for PCA3.
    Clinical biochemistry, 2007
    Co-Authors: Riina-minna Väänänen, Maria Rissanen, Otto Kauko, Siina Junnila, Ville Väisänen, Jussi Nurmi, Kalle Alanen, Martti Nurmi, Kim Pettersson
    Abstract:

    To develop a quantitative, internally standardized real-time RT-PCR assay for prostate cancer antigen 3 (PCA3), a non-translated gene found to be prostate-specific and highly overexpressed in cancer, and examine the role of PCA3 in peripheral blood with a small sample cohort. The RT-PCR assay for PCA3 is based on target-specific lanthanide probes. Peripheral blood from 91 prostatic cancer/disorder patients and healthy controls was assayed for PCA3 and prostate-specific antigen (PSA) expression. The dynamic range of the assay reaches over eight orders of magnitude and the limit of quantification is 800 copies per milliliter blood. Peripheral blood from 2/9 patients with metastasized cancers were PCA3 positive, whereas all the other samples were negative. Eight samples were PSA positive. The degree of PCA3 positivity in circulating cells from prostate cancer patients is low compared to that of PSA. In contrast to some previous reports, we found no PCA3 expression in healthy individuals.

  • Quantitative real-time RT-PCR assay for PCA3.
    Clinical Biochemistry, 2007
    Co-Authors: Riina-minna Väänänen, Maria Rissanen, Otto Kauko, Siina Junnila, Ville Väisänen, Jussi Nurmi, Kalle Alanen, Martti Nurmi, Kim Pettersson
    Abstract:

    Abstract Objectives: To develop a quantitative, internally standardized real-time RT-PCR assay for prostate cancer antigen 3 (PCA3), a non-translated gene found to be prostate-specific and highly overexpressed in cancer, and examine the role of PCA3 in peripheral blood with a small sample cohort. Design and methods: The RT-PCR assay for PCA3 is based on target-specific lanthanide probes. Peripheral blood from 91 prostatic cancer/disorder patients and healthy controls was assayed for PCA3 and prostate-specific antigen (PSA) expression. Results: The dynamic range of the assay reaches over eight orders of magnitude and the limit of quantification is 800 copies per milliliter blood. Peripheral blood from 2/9 patients with metastasized cancers were PCA3 positive, whereas all the other samples were negative. Eight samples were PSA positive. Conclusions: The degree of PCA3 positivity in circulating cells from prostate cancer patients is low compared to that of PSA. In contrast to some previous reports, we found no PCA3 expression in healthy individuals.

Scott A Tomlins - One of the best experts on this subject based on the ideXlab platform.

  • evaluation of tissue PCA3 expression in prostate cancer by rna in situ hybridization a correlative study with urine PCA3 and tmprss2 erg
    Modern Pathology, 2014
    Co-Authors: Joshua I Warrick, Scott A Tomlins, Shannon Carskadon, Allison M Young, Javed Siddiqui, John T Wei, Arul M Chinnaiyan, Lakshmi P Kunju, Nallasivam Palanisamy
    Abstract:

    PCA3 is a prostate-specific non-coding RNA, with utility as a urine-based early detection biomarker. Here, we report the evaluation of tissue PCA3 expression by RNA in situ hybridization in a cohort of 41 mapped prostatectomy specimens. We compared tissue PCA3 expression with tissue level ERG expression and matched pre-prostatectomy urine PCA3 and TMPRSS2-ERG levels. Across 136 slides containing 138 foci of prostate cancer, PCA3 was expressed in 55% of cancer foci and 71% of high-grade prostatic intraepithelial neoplasia foci. Overall, the specificity of tissue PCA3 was >90% for prostate cancer and high-grade prostatic intraepithelial neoplasia combined. Tissue PCA3 cancer expression was not significantly associated with urine PCA3 expression. PCA3 and ERG positivity in cancer foci was positively associated (P<0.01). We report the first comprehensive assessment of PCA3 expression in prostatectomy specimens, and find limited correlation between tissue PCA3 and matched urine in prostate cancer.

  • Evaluation of tissue PCA3 expression in prostate cancer by RNA in situ hybridization—a correlative study with urine PCA3 and TMPRSS2-ERG
    Modern pathology : an official journal of the United States and Canadian Academy of Pathology Inc, 2013
    Co-Authors: Joshua I Warrick, Scott A Tomlins, Shannon Carskadon, Allison M Young, Javed Siddiqui, John T Wei, Arul M Chinnaiyan, Lakshmi P Kunju, Nallasivam Palanisamy
    Abstract:

    PCA3 is a prostate-specific non-coding RNA, with utility as a urine-based early detection biomarker. Here, we report the evaluation of tissue PCA3 expression by RNA in situ hybridization in a cohort of 41 mapped prostatectomy specimens. We compared tissue PCA3 expression with tissue level ERG expression and matched pre-prostatectomy urine PCA3 and TMPRSS2-ERG levels. Across 136 slides containing 138 foci of prostate cancer, PCA3 was expressed in 55% of cancer foci and 71% of high-grade prostatic intraepithelial neoplasia foci. Overall, the specificity of tissue PCA3 was >90% for prostate cancer and high-grade prostatic intraepithelial neoplasia combined. Tissue PCA3 cancer expression was not significantly associated with urine PCA3 expression. PCA3 and ERG positivity in cancer foci was positively associated (P

  • Urine PCA3 and TMPRSS2:ERG Using Cancer-specific Markers to Detect Cancer
    European urology, 2012
    Co-Authors: Scott A Tomlins
    Abstract:

    The limitations of serum prostate-specific antigen (PSA) as a prostate cancer (PCa) early detection biomarker are well described, and controversy surrounding its use in the screening setting was highlighted recently. Importantly, PSA is a prostate-specific biomarker rather than a PCaspecific biomarker. The explosion in the knowledge of gene expression changes and driving molecular events in PCa has motivated efforts to identify more PCa-specific biomarkers that may augment or outperform PSA in early detection. Prostate cancer antigen 3 (PCA3) represents a highly PCa-specific biomarker, originally described in 1999 by Bussemakers et al. [1], that has been reported to be overexpressed in >90% of PCa. Subsequent gene expression profiling studies have confirmed that PCA3 is one of the most sensitive and specific PCa biomarkers, similar to alpha-methylacyl-CoA racemase (AMACR; which is used at the tissue level diagnostically). Although PCA3 does not encode a protein, PCA3 transcripts are detectable and quantifiable in urine, and PCA3 has been extensively studied as a urine-based PCa biomarker [2]. Clinical development has focused mainly on an assay based on transcriptionmediated amplification (TMA) (Progensa PCA3 test), which assesses post–digital rectal examination (DRE) whole urine specimens yielding a PCA3 score (urine PCA3 transcripts/ urine PSA transcripts) [3]. Importantly, this assay is CE marked and has been approved by the US Food and Drug Administration for assessing PCa risk in men with a previous negative biopsy. Additionally, the PCA3 test has also shown utility in refining PCa risk in men undergoing initial prostate biopsy (most commonly due to elevated serum PSA) [2].

Jing Zhang - One of the best experts on this subject based on the ideXlab platform.

  • genotype by environment interactions for performance of perennial rice genotypes oryza sativa l oryza longistaminata relative to annual rice genotypes over regrowth cycles and locations in southern china
    Field Crops Research, 2019
    Co-Authors: Shilai Zhang, Liyu Huang, Jing Zhang, Guangfu Huang, Mao Cheng, Zhili Wang, Yini Zhang, Chunli Wang, Pinfen Zhu, Ke Tao
    Abstract:

    Abstract Genotype by environment (GxE) interactions for performance of 5 perennial rice genotypes (Oryza sativa L./Oryza longistaminata) were examined relative to 1 mutant and 3 annual rice genotypes over 2–6 growth cycles at 7 locations in southern China between 2014 and 2017. Environment main effects accounted for 25.7% of the total sum of squares (SS), with genotype 33.8% and GxE 37.7%. Cluster analysis identified 6 genotype x 6 environment groups, which accounted for 77.9% of the GxE-SS. Principal component axes 1, 2 and 3 accounted for 54.7%, 25.1% and 9.4% of the GxE-SS, respectively, with PCA1 indicating yield potential, PCA2 performance over ratoon cycles, and PCA3 ratoon percentage. Environment groups differed in yield potential, which related to site favourability and whether it was low or high in the ratoon cycle. Genotype groups differed in yield potential and how well they performed in higher ratoon cycles. The medium-maturity (125 days) seasonally-replanted annual rice check BN21 was highest yielding (6.13 t ha−1). Perennial rice PR23 was high yielding and stable (5.25 t ha−1), with earlier maturity (119 days) and strong regrowth (82%). Ratooned annual rice RD23 was high yielding in original crops but poor yielding in ratoon crops, with a low ratoon percentage (16.5%). Similarly, perennial Bt71 and ratooned BN21 were high yielding in original crops and low-cycle ratoons under favourable conditions, but yielded poorly in high-cycle ratoons and less favourable conditions, with moderate regrowth (59.6%). Despite strong regrowth (77.5%), perennials 264 and Bt69 had low yield, as did perennial 139A and mutant TZ, and both these groups were late maturity. A combination of high yield potential, strong regrowth and earlier maturity resulted in higher performance of perennial rice over environments and regrowth cycles, with PR23 outstanding, and able to perform similarly to the seasonally-replanted annual check, BN21, over up to six growth cycles. Ratoon performance and trade-offs need to be examined further.

  • Genotype by environment interactions for performance of perennial rice genotypes (Oryza sativa L./Oryza longistaminata) relative to annual rice genotypes over regrowth cycles and locations in southern China
    Field Crops Research, 2019
    Co-Authors: Shilai Zhang, Liyu Huang, Jing Zhang, Huang Guangfu, Mao Cheng, Zhili Wang, Yini Zhang, Chunli Wang, Pinfen Zhu
    Abstract:

    Abstract Genotype by environment (GxE) interactions for performance of 5 perennial rice genotypes (Oryza sativa L./Oryza longistaminata) were examined relative to 1 mutant and 3 annual rice genotypes over 2–6 growth cycles at 7 locations in southern China between 2014 and 2017. Environment main effects accounted for 25.7% of the total sum of squares (SS), with genotype 33.8% and GxE 37.7%. Cluster analysis identified 6 genotype x 6 environment groups, which accounted for 77.9% of the GxE-SS. Principal component axes 1, 2 and 3 accounted for 54.7%, 25.1% and 9.4% of the GxE-SS, respectively, with PCA1 indicating yield potential, PCA2 performance over ratoon cycles, and PCA3 ratoon percentage. Environment groups differed in yield potential, which related to site favourability and whether it was low or high in the ratoon cycle. Genotype groups differed in yield potential and how well they performed in higher ratoon cycles. The medium-maturity (125 days) seasonally-replanted annual rice check BN21 was highest yielding (6.13 t ha−1). Perennial rice PR23 was high yielding and stable (5.25 t ha−1), with earlier maturity (119 days) and strong regrowth (82%). Ratooned annual rice RD23 was high yielding in original crops but poor yielding in ratoon crops, with a low ratoon percentage (16.5%). Similarly, perennial Bt71 and ratooned BN21 were high yielding in original crops and low-cycle ratoons under favourable conditions, but yielded poorly in high-cycle ratoons and less favourable conditions, with moderate regrowth (59.6%). Despite strong regrowth (77.5%), perennials 264 and Bt69 had low yield, as did perennial 139A and mutant TZ, and both these groups were late maturity. A combination of high yield potential, strong regrowth and earlier maturity resulted in higher performance of perennial rice over environments and regrowth cycles, with PR23 outstanding, and able to perform similarly to the seasonally-replanted annual check, BN21, over up to six growth cycles. Ratoon performance and trade-offs need to be examined further.

  • genotype by environment interactions for grain yield of perennial rice derivatives oryza sativa l oryza longistaminata in southern china and laos
    Field Crops Research, 2017
    Co-Authors: Shilai Zhang, Liyu Huang, Benjamin K. Samson, Chundao Yang, Haitao Liu, Feng Yang, Jihua Zhou, Chanthakhone Boualaphanh, Guangfu Huang, Jing Zhang
    Abstract:

    Perennial grains have been proposed to stabilise fragile lands while contributing grain and grazing in mixed farming systems. Genotype by environment (GxE) interactions for grain yield were investigated in 22 perennial rice (Oryza sativa L./Oryza longistaminata) derivatives over four successive growing seasons at three sites in Yunnan in southern China and one site in Lao PDR. The GxE interaction accounted for 25.7% of the total sum of squares, with environment and genotype responsible for 57.4% and 16.9%, respectively. Cluster analysis identified seven environment and six genotype groups, which accounted for 55.6% of the GxE sum of squares. Principal component axes 1, 2 and 3 accounted for 42.3%, 19.1% and 16.5% of the GxE-SS, respectively, with PCA1 indicating yield potential, PCA2 delay in phenology under environmental stress, and PCA3 ratoon percentage. Environment groups differed in mean temperature, whether dry season or wet season, and occurrence of environmental stresses, such as periods of low minimum temperature or periods of rainfall deficit. Genotype groups differed in adaptation to these diverse environments. For genotype groups, G5 (PR23) was highest-yielding and broadly adapted across environments, while G1 (line 188, both 137s, both 139s, both 147s) was low-yielding and poorly adapted. Other genotype groups showed preferential adaptation: G3 (lines 60, 251, 264, Bt69, Bt71) to Simao/Dry Season (E3 and E4), G4 (lines 75, 243, 246, 249, 255) to Menglian/Wet Season (E1 and E2), G2 (line TZ) to Jing Hong 2013 (E7), and G6 (lines 56, 59, 214) to Jing Hong 2102 and Na Pok (E6 and E5). The results imply that regrowth success and maintenance of spikelet fertility over regrowth cycles are important for adaptation of perennial rice, especially to low minimum temperature at higher altitude and rainfall deficit at lower altitude, and future breeding programmes in perennial rice should address these environmental stresses. The high yield and broad adaptation of PR23 (G5) over environments makes it a prime candidate for release to stabilise fragile lands in the humid and subhumid tropics, while contributing grain and forage in mixed-farming systems.