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Lotan Y, Agarwal P, Black P, Dickstein R, Kamat AM, Lee B, Narayan VM, Porten S, Psutka SP, Smith AK, Svatek RS, Williams SB, Woldu S. Standardization of the evaluation and surveillance of patients with BCG unresponsive high grade non-muscle invasive bladder cancer clinical trials. Urol Oncol 2024; 42:223-228. [PMID: 38307803 DOI: 10.1016/j.urolonc.2024.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/07/2024] [Accepted: 01/17/2024] [Indexed: 02/04/2024]
Abstract
There are multiple ongoing and planned clinical trials that are evaluating novel therapies to treat patients with BCG-unresponsive high grade nonmuscle invasive bladder cancer (NMIBC). Importantly, there is considerable variation in surveillance strategies between these clinical trials, specifically with regards to the use of advanced imaging, enhanced cystoscopy, and mandatory biopsies, which could impact landmark efficacy assessments of investigational agents. To present guideline recommendations for the standardization of cystoscopic evaluation, surveillance, and efficacy assessments for patients with BCG-unresponsive NMIBC participating in clinical trials. On September 29, 2023 at the annual meeting of the International Bladder Cancer Network, a breakout session was convened, during which representatives from various disciplines discussed potential guidance statements with opportunity for discussion and comment. A set of statements regarding use of white light and enhanced cystoscopy were developed to help guide a pragmatic approach to surveillance and efficacy assessments of patients in clinical trials. The use of "for cause" and "mandatory" biopsies was also addressed. A standard approach to evaluation of patients within the context of clinical trials is necessary to accurately assess the efficacy of novel agents, especially within single arm trials that lack an appropriate comparator. Additionally, the utilization and timing of mandatory biopsies is critical, as these biopsies may impact both disease evaluations and the determination of duration of response.
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Lotan Y, Daneshmand S, Shore N, Black P, Scarpato KR, Patel A, Lough T, Shoskes DA, Raman JD. Reply by Authors. J Urol 2024; 212:50-51. [PMID: 38728316 DOI: 10.1097/ju.0000000000004028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 04/28/2024] [Indexed: 05/12/2024]
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Lotan Y, Daneshmand S, Shore N, Black P, Scarpato KR, Patel A, Lough T, Shoskes DA, Raman JD. A Multicenter Prospective Randomized Controlled Trial Comparing Cxbladder Triage to Cystoscopy in Patients With Microhematuria: The Safe Testing of Risk for Asymptomatic Microhematuria Trial. J Urol 2024; 212:41-51. [PMID: 38700731 DOI: 10.1097/ju.0000000000003991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/12/2024] [Indexed: 05/05/2024]
Abstract
PURPOSE AUA guidelines for patients with microhematuria (≥3 red blood cells [RBC]/high-power field [hpf]) include cystoscopy for most over age 40 due to risk of urothelial cancer (UC). Cxbladder Triage (CxbT) is a urinary genomic test with UC negative predictive value of 99%. In this prospective randomized controlled trial, we compared cystoscopy use in a standard of care (SOC) arm vs a marker-based approach. MATERIALS AND METHODS All patients with hematuria provided urine for a CxbT. Those categorized as lower risk (LR), defined as 3 to 29 RBC/hpf and minimal smoking history (<10 pack-years) were randomized between the test group provided with the CxbT result vs the SOC control group. Negative CxbT patients were offered omission of cystoscopy with surveillance. "Not lower risk" (NLR) patients (>30 RBC/hpf or >10 pack-year smoking history) had a CxbT but otherwise SOC. Patient decision and outcomes were recorded. RESULTS Of 390 eligible patients, 255 were NLR and 135 were LR randomized to CxbT informed decision or SOC. The median age was 62 years (range 18-94) and 54% were male. Overall, 63% of CxbT tests were negative. For NLR patients, 82% had cystoscopy. In the LR control group, cystoscopy was performed in 67% of SOC and 27% in the test group (relative risk 0.41 [95% CI 0.27-0.61]). Compared to cystoscopy, CxbT had 90% sensitivity, 56% specificity, and 99% negative predictive value for UC. CONCLUSIONS In this prospective randomized controlled trial, use of CxbT in patients with LR hematuria resulted in 59% reduction of cystoscopy use. This clinical utility of CxbT can reduce the burden of unnecessary cystoscopies.
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Buddhdev P, Tebby J, Black P, Harding D, Kendall J, Shah H. Improving Theatre Productivity by Digitising Surgical Equipment Repairs. Cureus 2024; 16:e61802. [PMID: 38975507 PMCID: PMC11227270 DOI: 10.7759/cureus.61802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2024] [Indexed: 07/09/2024] Open
Abstract
Introduction A few cancelled surgeries are due to surgical equipment issues representing a significant burden to both patients and National Health Service (NHS) hospitals on waiting lists. Despite this, there remain very few strategies designed to tackle these avoidable cancellations, especially in combination with digitisation. Our aim was to demonstrate improved efficiency through a pilot study in collaboration with Broomfield Hospital (Broomfield, United Kingdom), MediShout Ltd (London, United Kingdom), and B. Braun Medical Ltd (Sheffield, United Kingdom) with the digitalisation of the equipment repair pathway. Methods MediShout digitised two distinct repair pathways: ad-hoc repairs and maintenance equipment services (MES). Pre- and post-digitisation outcome measures were collected including the number of process steps, staff contribution time, non-staff continuation time, turnaround time, cancelled surgeries, planned preventative maintenance compliance, and staff satisfaction. The number of steps, staff contribution time, and non-staff contribution time were calculated using cognitive task analyses and time-motion studies, respectively. Turnaround time and cancellation data were taken from existing hospital data sets and staff satisfaction was measured through two staff surveys. Results Digitising the ad-hoc repair pathway reduced the number of steps by 18 (118 to 100) and saved 74 minutes of total staff time (Broomfield Hospital and B. Braun) per repair, resulting in annual efficiency savings of £21,721.48. Digitising the MES repair pathway reduced the number of steps by 13 (74 to 61) and saved 56 minutes of total staff time per repair, resulting in annual efficiency savings of £3469.44. Turnaround time for the repaired kit decreased by 14 days and 29 days for the digital ad-hoc and digital MES pathways, respectively. Elective operations cancelled due to equipment issues decreased by 44%, from 1.5 operations/month pre-pilot to 0.83 operations/month post-pilot. Planned preventative maintenance compliance across the MES pathway increased by 67% (33% to 100%). Staff satisfaction with the repair pathway improved from 12% to 96%. Conclusion This pilot study showcases the numerous benefits that can be achieved through digitisation and offers an innovative case study to approach avoidable cancellations due to equipment failure.
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To MNN, Fooladgar F, Wilson P, Harmanani M, Gilany M, Sojoudi S, Jamzad A, Chang S, Black P, Mousavi P, Abolmaesumi P. LensePro: label noise-tolerant prototype-based network for improving cancer detection in prostate ultrasound with limited annotations. Int J Comput Assist Radiol Surg 2024; 19:1121-1128. [PMID: 38598142 DOI: 10.1007/s11548-024-03104-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 04/11/2024]
Abstract
PURPOSE The standard of care for prostate cancer (PCa) diagnosis is the histopathological analysis of tissue samples obtained via transrectal ultrasound (TRUS) guided biopsy. Models built with deep neural networks (DNNs) hold the potential for direct PCa detection from TRUS, which allows targeted biopsy and subsequently enhances outcomes. Yet, there are ongoing challenges with training robust models, stemming from issues such as noisy labels, out-of-distribution (OOD) data, and limited labeled data. METHODS This study presents LensePro, a unified method that not only excels in label efficiency but also demonstrates robustness against label noise and OOD data. LensePro comprises two key stages: first, self-supervised learning to extract high-quality feature representations from abundant unlabeled TRUS data and, second, label noise-tolerant prototype-based learning to classify the extracted features. RESULTS Using data from 124 patients who underwent systematic prostate biopsy, LensePro achieves an AUROC, sensitivity, and specificity of 77.9%, 85.9%, and 57.5%, respectively, for detecting PCa in ultrasound. Our model shows it is effective for detecting OOD data in test time, critical for clinical deployment. Ablation studies demonstrate that each component of our method improves PCa detection by addressing one of the three challenges, reinforcing the benefits of a unified approach. CONCLUSION Through comprehensive experiments, LensePro demonstrates its state-of-the-art performance for TRUS-based PCa detection. Although further research is necessary to confirm its clinical applicability, LensePro marks a notable advancement in enhancing automated computer-aided systems for detecting prostate cancer in ultrasound.
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MacDonald A, Bao L, Mehrnoush V, Ismail A, Di Matteo L, Zakaria A, Elmansy H, Black P, Kotb A. Does intravesical Bacillus Calmette-Guérin for bladder cancer protect from COVID-19? Arch Ital Urol Androl 2024; 96:12449. [PMID: 38722143 DOI: 10.4081/aiua.2024.12449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 03/28/2024] [Indexed: 06/28/2024] Open
Abstract
INTRODUCTION The study aimed to correlate the history of intravesical BCG as well as infantile BCG immunization with the incidence and severity of COVID-19 infection. METHODS Retrospective data collection of patients with high-risk non muscle invasive bladder cancer (NMIBC) from two Canadian centers. Data collection included a history of BCG instillation, infantile immunization, and the development of COVID-19 infection. Admission and/ or mortality because of COVID-19 was reported. RESULTS We could include data from 348 patients: including 188 and 160 patients from Ontario and British Columbia respectively. COVID-19 affected 15% of these patients. Intravesical BCG was used in 44% of these patients. Intravesical BCG and/or infantile BCG immunization did not correlate with the incidence of COVID-19 infection. CONCLUSIONS Previous intravesical BCG and/ or a history of infantile BCG vaccination were not more/ less frequent in patients who had COVID-19 infection.
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Kim S, St-Laurent MP, Black P. Biomarker challenges in the pursuit of personalized neoadjuvant chemotherapy for muscle-invasive bladder cancer: conclusions from SWOG S1314. Transl Androl Urol 2024; 13:458-462. [PMID: 38590957 PMCID: PMC10999026 DOI: 10.21037/tau-23-620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/08/2024] [Indexed: 04/10/2024] Open
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Helisaz H, Belanger E, Black P, Bacca M, Chiao M. Quantifying the Impact of Cancer on the Viscoelastic Properties of the Prostate Gland using a Quasi-Linear Viscoelastic Model. Acta Biomater 2024; 173:184-198. [PMID: 37939817 DOI: 10.1016/j.actbio.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/27/2023] [Accepted: 11/01/2023] [Indexed: 11/10/2023]
Abstract
Pathological disorders can alter the mechanical properties of biological tissues, and studying such changes can help to better understand the disease progression. The prostate gland is no exception, as previous studies have shown that cancer can affect its mechanical properties. However, most of these studies have focused on the elastic properties of the tissue and have overlooked the impact of cancer on its viscous response. To address this gap, we used a quasi-linear viscoelastic model to investigate the impact of cancer on both the elastic and viscous characteristics of the prostate gland. By comparing the viscoelastic properties of segments influenced by cancer and those unaffected by cancer in 49 fresh prostates, removed within two hours after prostatectomy surgery, we were able to determine the influence of cancer grade and tumor volume on the tissue. Our findings suggest that tumor volume significantly affects both the elastic modulus and viscosity of the prostate (p-value less than 2%). Specifically, we showed that cancer increases Young's modulus and shear relaxation modulus by 20%. These results have implications for using mechanical properties of the prostate as a potential biomarker for cancer. However, developing an in vivo apparatus to measure these properties remains a challenge that needs to be addressed in future research. STATEMENT OF SIGNIFICANCE: This study is the first to explore how cancer impacts the mechanical properties of prostate tissues using a quasi-linear viscoelastic model. We examined 49 fresh prostate samples collected immediately after surgery and correlated their properties with cancer presence identified in pathology reports. Our results demonstrate a 20% change in the viscoelastic properties of the prostate due to cancer. We initially validated our approach using tissue-mimicking phantoms and then applied it to differentiate between cancerous and normal prostate tissues. These findings offer potential for early cancer detection by assessing these properties. However, conducting these tests in vivo remains a challenge for future research.
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Chrisochoides N, Liu Y, Drakopoulos F, Kot A, Foteinos P, Tsolakis C, Billias E, Clatz O, Ayache N, Fedorov A, Golby A, Black P, Kikinis R. Comparison of physics-based deformable registration methods for image-guided neurosurgery. Front Digit Health 2023; 5:1283726. [PMID: 38144260 PMCID: PMC10740151 DOI: 10.3389/fdgth.2023.1283726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 11/02/2023] [Indexed: 12/26/2023] Open
Abstract
This paper compares three finite element-based methods used in a physics-based non-rigid registration approach and reports on the progress made over the last 15 years. Large brain shifts caused by brain tumor removal affect registration accuracy by creating point and element outliers. A combination of approximation- and geometry-based point and element outlier rejection improves the rigid registration error by 2.5 mm and meets the real-time constraints (4 min). In addition, the paper raises several questions and presents two open problems for the robust estimation and improvement of registration error in the presence of outliers due to sparse, noisy, and incomplete data. It concludes with preliminary results on leveraging Quantum Computing, a promising new technology for computationally intensive problems like Feature Detection and Block Matching in addition to finite element solver; all three account for 75% of computing time in deformable registration.
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Black P, Britton A, Davis E, Dusan F, Gang R, Garner MG, Hamilton SA, Petrey A, Schipp M, Weerasinghe G, Wilks C. Dr Mike Nunn 9 February 1953-19 May 2023. Aust Vet J 2023; 101:460-461. [PMID: 37918954 DOI: 10.1111/avj.13285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2023] [Indexed: 11/04/2023]
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Lu AT, Fei Z, Haghani A, Robeck TR, Zoller JA, Li CZ, Lowe R, Yan Q, Zhang J, Vu H, Ablaeva J, Acosta-Rodriguez VA, Adams DM, Almunia J, Aloysius A, Ardehali R, Arneson A, Baker CS, Banks G, Belov K, Bennett NC, Black P, Blumstein DT, Bors EK, Breeze CE, Brooke RT, Brown JL, Carter GG, Caulton A, Cavin JM, Chakrabarti L, Chatzistamou I, Chen H, Cheng K, Chiavellini P, Choi OW, Clarke SM, Cooper LN, Cossette ML, Day J, DeYoung J, DiRocco S, Dold C, Ehmke EE, Emmons CK, Emmrich S, Erbay E, Erlacher-Reid C, Faulkes CG, Ferguson SH, Finno CJ, Flower JE, Gaillard JM, Garde E, Gerber L, Gladyshev VN, Gorbunova V, Goya RG, Grant MJ, Green CB, Hales EN, Hanson MB, Hart DW, Haulena M, Herrick K, Hogan AN, Hogg CJ, Hore TA, Huang T, Izpisua Belmonte JC, Jasinska AJ, Jones G, Jourdain E, Kashpur O, Katcher H, Katsumata E, Kaza V, Kiaris H, Kobor MS, Kordowitzki P, Koski WR, Krützen M, Kwon SB, Larison B, Lee SG, Lehmann M, Lemaitre JF, Levine AJ, Li C, Li X, Lim AR, Lin DTS, Lindemann DM, Little TJ, Macoretta N, Maddox D, Matkin CO, Mattison JA, McClure M, Mergl J, Meudt JJ, Montano GA, Mozhui K, Munshi-South J, Naderi A, Nagy M, Narayan P, Nathanielsz PW, Nguyen NB, Niehrs C, O'Brien JK, O'Tierney Ginn P, Odom DT, Ophir AG, Osborn S, Ostrander EA, Parsons KM, Paul KC, Pellegrini M, Peters KJ, Pedersen AB, Petersen JL, Pietersen DW, Pinho GM, Plassais J, Poganik JR, Prado NA, Reddy P, Rey B, Ritz BR, Robbins J, Rodriguez M, Russell J, Rydkina E, Sailer LL, Salmon AB, Sanghavi A, Schachtschneider KM, Schmitt D, Schmitt T, Schomacher L, Schook LB, Sears KE, Seifert AW, Seluanov A, Shafer ABA, Shanmuganayagam D, Shindyapina AV, Simmons M, Singh K, Sinha I, Slone J, Snell RG, Soltanmaohammadi E, Spangler ML, Spriggs MC, Staggs L, Stedman N, Steinman KJ, Stewart DT, Sugrue VJ, Szladovits B, Takahashi JS, Takasugi M, Teeling EC, Thompson MJ, Van Bonn B, Vernes SC, Villar D, Vinters HV, Wallingford MC, Wang N, Wayne RK, Wilkinson GS, Williams CK, Williams RW, Yang XW, Yao M, Young BG, Zhang B, Zhang Z, Zhao P, Zhao Y, Zhou W, Zimmermann J, Ernst J, Raj K, Horvath S. Author Correction: Universal DNA methylation age across mammalian tissues. NATURE AGING 2023; 3:1462. [PMID: 37674040 PMCID: PMC10645586 DOI: 10.1038/s43587-023-00499-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
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Chrisochoides N, Fedorov A, Liu Y, Kot A, Foteinos P, Drakopoulos F, Tsolakis C, Billias E, Clatz O, Ayache N, Golby A, Black P, Kikinis R. Real-Time Dynamic Data Driven Deformable Registration for Image-Guided Neurosurgery: Computational Aspects. ARXIV 2023:arXiv:2309.03336v1. [PMID: 37731651 PMCID: PMC10508827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Current neurosurgical procedures utilize medical images of various modalities to enable the precise location of tumors and critical brain structures to plan accurate brain tumor resection. The difficulty of using preoperative images during the surgery is caused by the intra-operative deformation of the brain tissue (brain shift), which introduces discrepancies concerning the preoperative configuration. Intra-operative imaging allows tracking such deformations but cannot fully substitute for the quality of the pre-operative data. Dynamic Data Driven Deformable Non-Rigid Registration (D4NRR) is a complex and time-consuming image processing operation that allows the dynamic adjustment of the pre-operative image data to account for intra-operative brain shift during the surgery. This paper summarizes the computational aspects of a specific adaptive numerical approximation method and its variations for registering brain MRIs. It outlines its evolution over the last 15 years and identifies new directions for the computational aspects of the technique.
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Lu AT, Fei Z, Haghani A, Robeck TR, Zoller JA, Li CZ, Lowe R, Yan Q, Zhang J, Vu H, Ablaeva J, Acosta-Rodriguez VA, Adams DM, Almunia J, Aloysius A, Ardehali R, Arneson A, Baker CS, Banks G, Belov K, Bennett NC, Black P, Blumstein DT, Bors EK, Breeze CE, Brooke RT, Brown JL, Carter GG, Caulton A, Cavin JM, Chakrabarti L, Chatzistamou I, Chen H, Cheng K, Chiavellini P, Choi OW, Clarke SM, Cooper LN, Cossette ML, Day J, DeYoung J, DiRocco S, Dold C, Ehmke EE, Emmons CK, Emmrich S, Erbay E, Erlacher-Reid C, Faulkes CG, Ferguson SH, Finno CJ, Flower JE, Gaillard JM, Garde E, Gerber L, Gladyshev VN, Gorbunova V, Goya RG, Grant MJ, Green CB, Hales EN, Hanson MB, Hart DW, Haulena M, Herrick K, Hogan AN, Hogg CJ, Hore TA, Huang T, Izpisua Belmonte JC, Jasinska AJ, Jones G, Jourdain E, Kashpur O, Katcher H, Katsumata E, Kaza V, Kiaris H, Kobor MS, Kordowitzki P, Koski WR, Krützen M, Kwon SB, Larison B, Lee SG, Lehmann M, Lemaitre JF, Levine AJ, Li C, Li X, Lim AR, Lin DTS, Lindemann DM, Little TJ, Macoretta N, Maddox D, Matkin CO, Mattison JA, McClure M, Mergl J, Meudt JJ, Montano GA, Mozhui K, Munshi-South J, Naderi A, Nagy M, Narayan P, Nathanielsz PW, Nguyen NB, Niehrs C, O'Brien JK, O'Tierney Ginn P, Odom DT, Ophir AG, Osborn S, Ostrander EA, Parsons KM, Paul KC, Pellegrini M, Peters KJ, Pedersen AB, Petersen JL, Pietersen DW, Pinho GM, Plassais J, Poganik JR, Prado NA, Reddy P, Rey B, Ritz BR, Robbins J, Rodriguez M, Russell J, Rydkina E, Sailer LL, Salmon AB, Sanghavi A, Schachtschneider KM, Schmitt D, Schmitt T, Schomacher L, Schook LB, Sears KE, Seifert AW, Seluanov A, Shafer ABA, Shanmuganayagam D, Shindyapina AV, Simmons M, Singh K, Sinha I, Slone J, Snell RG, Soltanmaohammadi E, Spangler ML, Spriggs MC, Staggs L, Stedman N, Steinman KJ, Stewart DT, Sugrue VJ, Szladovits B, Takahashi JS, Takasugi M, Teeling EC, Thompson MJ, Van Bonn B, Vernes SC, Villar D, Vinters HV, Wallingford MC, Wang N, Wayne RK, Wilkinson GS, Williams CK, Williams RW, Yang XW, Yao M, Young BG, Zhang B, Zhang Z, Zhao P, Zhao Y, Zhou W, Zimmermann J, Ernst J, Raj K, Horvath S. Universal DNA methylation age across mammalian tissues. NATURE AGING 2023; 3:1144-1166. [PMID: 37563227 PMCID: PMC10501909 DOI: 10.1038/s43587-023-00462-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 06/21/2023] [Indexed: 08/12/2023]
Abstract
Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.
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Haghani A, Li CZ, Robeck TR, Zhang J, Lu AT, Ablaeva J, Acosta-Rodríguez VA, Adams DM, Alagaili AN, Almunia J, Aloysius A, Amor NM, Ardehali R, Arneson A, Baker CS, Banks G, Belov K, Bennett NC, Black P, Blumstein DT, Bors EK, Breeze CE, Brooke RT, Brown JL, Carter G, Caulton A, Cavin JM, Chakrabarti L, Chatzistamou I, Chavez AS, Chen H, Cheng K, Chiavellini P, Choi OW, Clarke S, Cook JA, Cooper LN, Cossette ML, Day J, DeYoung J, Dirocco S, Dold C, Dunnum JL, Ehmke EE, Emmons CK, Emmrich S, Erbay E, Erlacher-Reid C, Faulkes CG, Fei Z, Ferguson SH, Finno CJ, Flower JE, Gaillard JM, Garde E, Gerber L, Gladyshev VN, Goya RG, Grant MJ, Green CB, Hanson MB, Hart DW, Haulena M, Herrick K, Hogan AN, Hogg CJ, Hore TA, Huang T, Belmonte JCI, Jasinska AJ, Jones G, Jourdain E, Kashpur O, Katcher H, Katsumata E, Kaza V, Kiaris H, Kobor MS, Kordowitzki P, Koski WR, Krützen M, Kwon SB, Larison B, Lee SG, Lehmann M, Lemaître JF, Levine AJ, Li X, Li C, Lim AR, Lin DTS, Lindemann DM, Liphardt SW, Little TJ, Macoretta N, Maddox D, Matkin CO, Mattison JA, McClure M, Mergl J, Meudt JJ, Montano GA, Mozhui K, Munshi-South J, Murphy WJ, Naderi A, Nagy M, Narayan P, Nathanielsz PW, Nguyen NB, Niehrs C, Nyamsuren B, O’Brien JK, Ginn PO, Odom DT, Ophir AG, Osborn S, Ostrander EA, Parsons KM, Paul KC, Pedersen AB, Pellegrini M, Peters KJ, Petersen JL, Pietersen DW, Pinho GM, Plassais J, Poganik JR, Prado NA, Reddy P, Rey B, Ritz BR, Robbins J, Rodriguez M, Russell J, Rydkina E, Sailer LL, Salmon AB, Sanghavi A, Schachtschneider KM, Schmitt D, Schmitt T, Schomacher L, Schook LB, Sears KE, Seifert AW, Shafer AB, Shindyapina AV, Simmons M, Singh K, Sinha I, Slone J, Snell RG, Soltanmohammadi E, Spangler ML, Spriggs M, Staggs L, Stedman N, Steinman KJ, Stewart DT, Sugrue VJ, Szladovits B, Takahashi JS, Takasugi M, Teeling EC, Thompson MJ, Van Bonn B, Vernes SC, Villar D, Vinters HV, Vu H, Wallingford MC, Wang N, Wilkinson GS, Williams RW, Yan Q, Yao M, Young BG, Zhang B, Zhang Z, Zhao Y, Zhao P, Zhou W, Zoller JA, Ernst J, Seluanov A, Gorbunova V, Yang XW, Raj K, Horvath S. DNA methylation networks underlying mammalian traits. Science 2023; 381:eabq5693. [PMID: 37561875 PMCID: PMC11180965 DOI: 10.1126/science.abq5693] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/21/2023] [Indexed: 08/12/2023]
Abstract
Using DNA methylation profiles (n = 15,456) from 348 mammalian species, we constructed phyloepigenetic trees that bear marked similarities to traditional phylogenetic ones. Using unsupervised clustering across all samples, we identified 55 distinct cytosine modules, of which 30 are related to traits such as maximum life span, adult weight, age, sex, and human mortality risk. Maximum life span is associated with methylation levels in HOXL subclass homeobox genes and developmental processes and is potentially regulated by pluripotency transcription factors. The methylation state of some modules responds to perturbations such as caloric restriction, ablation of growth hormone receptors, consumption of high-fat diets, and expression of Yamanaka factors. This study reveals an intertwined evolution of the genome and epigenome that mediates the biological characteristics and traits of different mammalian species.
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Daneshmand S, Cary C, Masterson T, Einhorn L, Adra N, Boorjian SA, Kollmannsberger C, Schuckman A, So A, Black P, Bagrodia A, Skinner E, Alemozaffar M, Brand T, Eggener S, Pierorazio P, Stratton K, Nappi L, Nichols C, Luo C, Li M, Hu B. Surgery in Early Metastatic Seminoma: A Phase II Trial of Retroperitoneal Lymph Node Dissection for Testicular Seminoma With Limited Retroperitoneal Lymphadenopathy. J Clin Oncol 2023; 41:3009-3018. [PMID: 36913642 DOI: 10.1200/jco.22.00624] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 01/31/2023] [Indexed: 03/15/2023] Open
Abstract
PURPOSE The long-term toxicities of chemotherapy and radiotherapy can represent a significant burden to testicular cancer survivors. Retroperitoneal lymph node dissection (RPLND) is an established treatment for testicular germ cell tumors with minimal late morbidity although little data exist on its efficacy in early metastatic seminoma. Surgery in early metastatic seminoma is a prospective phase II single-arm, multi-institutional trial of RPLND as first-line treatment for testicular seminoma with clinically low-volume retroperitoneal lymphadenopathy. PATIENTS AND METHODS Twelve sites in the United States and Canada prospectively enrolled adult patients with testicular seminoma and isolated retroperitoneal lymphadenopathy (1-3 cm). Open RPLND was performed by certified surgeons with a primary end point of 2-year recurrence-free survival (RFS). Complication rates, pathologic up/downstaging, recurrence patterns, adjuvant therapies, and treatment-free survival were assessed. RESULTS A total of 55 patients were enrolled, with a median (IQR) largest clinical lymph node size of 1.6 cm (1.3-1.9). RPLND pathology demonstrated a median (IQR) largest lymph node size of 2.3 cm (0.9-3.5); nine patients (16%) were pN0, 12 (22%) pN1, 31 (56%) pN2, and 3 (5%) pN3. One patient received adjuvant chemotherapy. With a median (IQR) follow-up of 33 months (12.0-61.6), 12 patients experienced recurrence, with a 2-year RFS of 81% and a recurrence rate of 22%. Of the patients who experienced recurrence, 10 were treated with chemotherapy and two underwent additional surgery. At last follow-up, all patients who experienced a recurrence were disease-free and the 2-year overall survival was 100%. Four patients (7%) experienced short-term complications, and four patients experienced long-term complications including incisional hernia (1) and anejaculation (3). CONCLUSION RPLND is a treatment option for testicular seminoma with clinically low-volume retroperitoneal lymphadenopathy and is associated with low long-term morbidity.
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Lotan Y, Raman JD, Konety B, Daneshmand S, Schroeck F, Shariat SF, Black P, de Lange M, Asroff S, Goldfischer E, Efros M, Chong KT, Huang E, Chua HL, Wu QH, Yeow S, Lau W, Yong J, Eng M. Urinary Analysis of FGFR3 and TERT Gene Mutations Enhances Performance of Cxbladder Tests and Improves Patient Risk Stratification. J Urol 2023; 209:762-772. [PMID: 36583640 DOI: 10.1097/ju.0000000000003126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE Cxbladder tests are urinary biomarker tests for detection of urothelial carcinoma. We developed enhanced Cxbladder tests that incorporate DNA analysis of 6 single nucleotide polymorphisms for the FGFR3 and TERT genes, in addition to the current 5 mRNA biomarkers and clinical risk factors. MATERIALS AND METHODS Two multicenter, prospective studies were undertaken in: (1) U.S. patients with gross hematuria aged ≥18 years and (2) Singaporean patients with gross hematuria or microhematuria aged >21 years. All patients provided a midstream urine sample and underwent cystoscopy. Samples were retrospectively analyzed using enhanced Cxbladder-Triage (risk stratifies patients), enhanced Cxbladder-Detect (risk stratifies patients and detects positive patients), and the combination enhanced Cxbladder-Triage × Cxbladder-Detect. RESULTS In the pooled cohort (N=804; gross hematuria: n=484, microhematuria: n=320), enhanced Cxbladder-Detect had a sensitivity of 97% (95% CI 89%-100%), specificity of 90% (95% CI 88%-92%), and negative predictive value of 99.7% (95% CI 99%-100%) for detection of urothelial carcinoma. Overall, 83% of patients were enhanced Cxbladder-Detect-negative (ie, needed no further work-up). Of 133 enhanced Cxbladder-Detect-positive patients, 59 had a confirmed tumor, of which 19 were low-grade noninvasive papillary carcinoma or papillary urothelial neoplasm of low malignant potential. In total, 40 tumors were high-grade Ta, T1-T4, Tis, including concomitant carcinoma in situ. Of the 74 patients with normal cystoscopy, 41 were positive by single nucleotide polymorphism analysis. Enhanced Cxbladder-Triage and enhanced Cxbladder-Detect had significantly better specificity than the first-generation Cxbladder tests (P < .001). CONCLUSIONS This study in ethnically diverse patients with hematuria showed the analytical validity of the enhanced Cxbladder tests.
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Heidenreich A, Ladi Seyedian S, Alsyouf M, Hu B, Cary C, Masterson T, Einhorn L, Adra N, Boorjian S, Schuckman A, Bagrodia A, Kollmannsberger C, So A, Black P, Skinner E, Alemozaffar M, Brand T, Eggener S, Pierorazio P, Pierorazio K, Nappi L, Nichols C, Daneshmand S. Surgical and oncologic outcomes of surgery in early metastatic seminoma: Multi-institutional retrospective study. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00795-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Klotz L, Chin J, Black P, Finelli A, Anidjar M, Kebabdjian M, Mittman N, Seung S. Multi-parametric MRI-targeted biopsy compared to systematic TRUS biopsy for biopsy-naïve men at risk for prostate cancer: 2 year follow up data and economic analysis. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00217-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Contreras-Sanz A, Reike M, Negri G, Oo H, Spencer Miko S, Nielsen K, Roberts M, Scurll J, Ikeda K, Wang G, Seiler R, Morin G, Black P. Proteomic profiling of muscle invasive bladder cancer treated with neoadjuvant chemotherapy. EUR UROL SUPPL 2023. [DOI: 10.1016/s2666-1683(23)00035-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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Nikkola J, Black P. Predictive Biomarkers of Response to Neoadjuvant Therapy in Muscle Invasive Bladder Cancer. Methods Mol Biol 2023; 2684:229-247. [PMID: 37410238 DOI: 10.1007/978-1-0716-3291-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Neoadjuvant cisplatin-based chemotherapy is recommended prior to surgical removal of the bladder for patients with non-metastatic muscle invasive bladder cancer. Despite a survival benefit, approximately half of patients do not respond to chemotherapy and are exposed potentially unnecessarily to substantial toxicity and delay in surgery. Therefore, biomarkers to identify likely responders before initiating chemotherapy would be a helpful clinical tool. Furthermore, biomarkers may be able to identify patients who do not need subsequent surgery after clinical complete response to chemotherapy. To date, there are no clinically approved predictive biomarkers of response to neoadjuvant therapy. Recent advances in the molecular characterization of bladder cancer have shown the potential role for DNA damage repair (DDR) gene alterations and molecular subtypes to guide therapy, but these need validation from prospective clinical trials. This chapter reviews candidate predictive biomarkers of response to neoadjuvant therapy in muscle invasive bladder cancer.
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Fooladgar F, Nguyen Nhat to M, Javadi G, Sojoudi S, Eshumani W, Chang S, Black P, Mousavi P, Abolmaesumi P. Semi-supervised learning from coarse histopathology labels. COMPUTER METHODS IN BIOMECHANICS AND BIOMEDICAL ENGINEERING: IMAGING & VISUALIZATION 2022. [DOI: 10.1080/21681163.2022.2154275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Bénard F, Harsini S, Wilson D, Zukotynski K, Abikhzer G, Turcotte E, Cossette M, Metser U, Romsa J, Martin M, Mar C, Saad F, Soucy JP, Eigl BJ, Black P, Krauze A, Burrell S, Nichol A, Tardif JC. Intra-individual comparison of 18F-sodium fluoride PET-CT and 99mTc bone scintigraphy with SPECT in patients with prostate cancer or breast cancer at high risk for skeletal metastases (MITNEC-A1): a multicentre, phase 3 trial. Lancet Oncol 2022; 23:1499-1507. [PMID: 36343655 DOI: 10.1016/s1470-2045(22)00642-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/03/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Detection of skeletal metastases in patients with prostate cancer or breast cancer remains a major clinical challenge. We aimed to compare the diagnostic performance of 99mTc-methylene diphosphonate (99mTc-MDP) single-photon emission CT (SPECT) and 18F-sodium fluoride (18F-NaF) PET-CT for the detection of osseous metastases in patients with high-risk prostate or breast cancer. METHODS MITNEC-A1 was a prospective, multicentre, single-cohort, phase 3 trial conducted in ten hospitals across Canada. Patients aged 18 years or older with breast or prostate cancer with a WHO performance status of 0-2 and with high risk or clinical suspicion for bone metastasis, but without previously documented bone involvement, were eligible. 18F-NaF PET-CT and 99mTc-MDP SPECT were done within 14 days of each other for each participant. Two independent reviewers interpreted each modality without knowledge of other imaging findings. The primary endpoint was the overall accuracy of 99mTc-MDP SPECT and 18F-NaF PET-CT scans for the detection of bone metastases in the per-protocol population. A combination of histopathological, clinical, and imaging follow-up for up to 24 months was used as the reference standard to assess the imaging results. Safety was assessed in all enrolled participants. This study is registered with ClinicalTrials.gov, NCT01930812, and is complete. FINDINGS Between July 11, 2014, and March 3, 2017, 290 patients were screened, 288 of whom were enrolled (64 participants with breast cancer and 224 with prostate cancer). 261 participants underwent both 18F-NaF PET-CT and 99mTc-MDP SPECT and completed the required follow-up for statistical analysis. Median follow-up was 735 days (IQR 727-750). Based on the reference methods used, 109 (42%) of 261 patients had bone metastases. In the patient-based analysis, 18F-NaF PET-CT was more accurate than 99mTc-MDP SPECT (84·3% [95% CI 79·9-88·7] vs 77·4% [72·3-82·5], difference 6·9% [95% CI 1·3-12·5]; p=0·016). No adverse events were reported for the 288 patients recruited. INTERPRETATION 18F-NaF has the potential to displace 99mTc-MDP as the bone imaging radiopharmaceutical of choice in patients with high-risk prostate or breast cancer. FUNDING Canadian Institutes of Health Research.
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Marcq G, Afferi L, Neuzillet Y, Nykopp T, Voskuilen CS, Furrer MA, Kassouf W, Aziz A, Bajeot AS, Alvarez-Maestro M, Black P, Roupret M, Noon AP, Seiler R, Hendricksen K, Roumiguie M, Pang KH, Laine-Caroff P, Xylinas E, Ploussard G, Moschini M, Sargos P. Oncological Outcomes for Patients Harboring Positive Surgical Margins Following Radical Cystectomy for Muscle-Invasive Bladder Cancer: A Retrospective Multicentric Study on Behalf of the YAU Urothelial Group. Cancers (Basel) 2022; 14:cancers14235740. [PMID: 36497222 PMCID: PMC9739538 DOI: 10.3390/cancers14235740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Introduction: Adjuvant therapy has no defined role for patients with positive surgical margins (PSMs) following radical cystectomy (RC) for muscle-invasive bladder cancer (MIBC). The aim of our study was to describe loco-regional recurrence-free survival (LRFS), metastatic-free survival (MFS), recurrence-free survival (RFS), cancer-specific survival (CSS) and overall survival (OS) and identify predictors of each endpoint in patients with PSMs following RC for MIBC. Methods: A collaborative retrospective cohort study was conducted on 394 patients with PSMs who underwent RC for MIBC between January 2000 and December 2018 at 10 tertiary referral centers. Patients receiving perioperative radiotherapy were excluded from the study. Kaplan−Meier curves were used to estimate patient survival. Cox regression analysis was used to identify predictors of survival. Results: Median age at surgery was 70 years (IQR 62−76) with 129 (33%) and 204 (52%) patients had pT3 and pT4 tumors, respectively. Nodal metastasis (pN+) was identified in 148 (38%). Soft tissue PSMs were found in 283 (72%) patients, urethral PSMs in 65 (16.5%), and ureteral PSMs were found in 73 (18.5%). The median follow-up time was 44 months (95% CI 32−60). Median LRFS, MRFS, RFS, CSS, and OS were 14 (95% CI 11−17), 12 (95% CI 10−16), 10 (95% CI 8−12), 23 (95% CI 18−33), and 16 months (95% CI 12−19), respectively. On multivariable Cox regression analysis, the pT3−4 stage, pN+ stage, and multifocal PSMs were independent predictors of LRFS, MRFS, RFS, and OS. Adjuvant chemotherapy improved all oncological outcomes studied (p < 0.05). The number of lymph nodes removed was independently associated with better LRFS, MRFS, and RFS. Advanced age at diagnosis was independently associated with worse OS. Conclusion: Patients with PSMs following RC have poor outcomes since half of them will recur within a year and will die of their disease. Among all PSMs types, patients with multifocal PSMs harbor the worst prognosis. We observed a benefit of adjuvant chemotherapy, but clinical trials evaluating innovative adjuvant strategies for these patients remain an unmet need.
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McGlinchey L, Barr O, Black P. Healthcare professionals knowledge of inherited cardiac arrhythmias ica their views towards and confidence in caring for a person with an ica in a surgical environment. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Inherited Cardiac Arrhythmias (ICA) are potentially life-threatening conditions which may be induced by several factors during the perioperative period. Safety and quality of care of patients may be affected by insufficient knowledge, or confidence by healthcare professionals in surgical areas.
Purpose
To determine the knowledge of ICAs by healthcare professionals, their views towards and confidence in caring for a person with an ICA in a surgical environment.
Methods
In Phase One, a twenty-four item questionnaire was distributed to registered nurses and midwives, surgeons and anaesthestists within surgical areas of seventeen hospitals of the Republic of Ireland and Northern Ireland.
Results
Completed questionnaires were returned from 154 participants in Phase 1 involving all four professions of the participant cohort. This comprised of one hundred and seventeen nurses, seven midwives, ten surgeons and nineteen anaesthetists. Sudden Adult/Arrhythmic Death syndrome (SADs) was heard of by 91% of participants, and 54% have heard of ICA. The majority of participants were not at all confident or only slightly confident (48% and 32%) in caring for patients with an ICA. Eighty-four percent were not aware (61.7%) or not sure if they were aware (22.7%) of the drugs to avoid in ICA conditions such as Long QT and Brugada syndrome. Those aware (11%) of drugs to avoid were seven anaethetists, two midwives and eight nurses. Of the ten surgeons, none were aware of the drugs to avoid. When all participants were asked how relevant is knowledge of ICA to your current role 5.8% said it was not at all relevant, 29.2% said it was slightly relevant, 31.8% moderately relevant and 28.6% extremely relevant. Ninety-five percent (95%) of participants would like further education about these conditions delivered mainly by online sessions and face to face workshop methods.
Conclusions
There is limited knowledge of and confidence in caring for people with Inherited Cardiac Arrhythmias in surgical areas of the hospitals surveyed. Education is required in relation to awareness and identification of people with these conditions, signs and symptoms, unmasking and triggering a cardiac event and what medications need to be avoided. Patients may not be aware they have an Inherited Cardiac Arrhythmia, so healthcare professionals' awareness is crucial with the ability to recognise and respond appropriately to a possible cardiac event. There is a need to address these gaps as these have potential serious implications for people with an ICA during their perioperative journey.
Funding Acknowledgement
Type of funding sources: Other. Main funding source(s): The Cormac Trust
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Park A, Stewart J, Morisak P, Gustafson S, Meihls S, Black P, Ameel K, Asfour F. 110 Inadequacy of targeted hearing screening for children with cystic fibrosis. J Cyst Fibros 2022. [DOI: 10.1016/s1569-1993(22)00801-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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