Kris B. Prado

All Publications

• Development of robust artificial neural networks for prediction of 5-year survival in bladder cancer. Urologic oncology Bhambhvani, H. P., Zamora, A., Shkolyar, E., Prado, K., Greenberg, D. R., Kasman, A. M., Liao, J., Shah, S., Srinivas, S., Skinner, E. C., Shah, J. B. 2020

  Abstract

  PURPOSE: When exploring survival outcomes for patients with bladder cancer, most studies rely on conventional statistical methods such as proportional hazards models. Given the successful application of machine learning to handle big data in many disciplines outside of medicine, we sought to determine if machine learning could be used to improve our ability to predict survival in bladder cancer patients. We compare the performance of artificial neural networks (ANN), a type of machine learning algorithm, with that of multivariable Cox proportional hazards (CPH) models in the prediction of 5-year disease-specific survival (DSS) and overall survival (OS) in patients with bladder cancer.SUBJECTS AND METHODS: The National Cancer Institute's Surveillance, Epidemiology, and End Results (SEER) 18 program database was queried to identify adult patients with bladder cancer diagnosed between 1995 and 2010, yielding 161,227 patients who met our inclusion criteria. ANNs were trained and tested on an 80/20 split of the dataset. Multivariable CPH models were developed in parallel. Variables used for prediction included age, sex, race, grade, SEER stage, tumor size, lymph node involvement, degree of extension, and surgery received. The primary outcomes were 5-year DSS and 5-year OS. Receiver operating characteristic curve analysis was conducted, and ANN models were tested for calibration.RESULTS: The area under the curve for the ANN models was 0.81 for the OS model and 0.80 for the DSS model. Area under the curve for the CPH models was 0.70 for OS and 0.81 for DSS. The ANN OS model achieved a calibration slope of 1.03 and a calibration intercept of -0.04, while the ANN DSS model achieved a calibration slope of 0.99 and a calibration intercept of -0.04.CONCLUSIONS: Machine learning algorithms can improve our ability to predict bladder cancer prognosis. Compared to CPH models, ANNs predicted OS more accurately and DSS with similar accuracy. Given the inherent limitations of administrative datasets, machine learning may allow for optimal interpretation of the complex data they contain.

  View details for DOI 10.1016/j.urolonc.2020.05.009

  View details for PubMedID 32593506

• MANAGEMENT OF VARIANT HISTOLOGY IN NON-MUSCLE INVASIVE BLADDER CANCER Prado, K., Greenberg, D., Zhang, C., Sun, A., Skinner, E. LIPPINCOTT WILLIAMS & WILKINS. 2020: E263

  View details for Web of Science ID 000527010301488

• Implementation of a Reduced Opioid Utilization Protocol for Radical Cystectomy BLADDER CANCER Greenberg, D. R., Kee, J. R., Stevenson, K., Van Zyl, E., Dugala, A., Prado, K., Gill, H. S., Skinner, E. C., Shah, J. B. 2020; 6 (1): 33?42

  View details for DOI 10.3233/BLC-190243

  View details for Web of Science ID 000523301600004

• IMPLEMENTATION OF A REDUCED OPIOID UTILIZATION PROTOCOL FOR RADICAL CYSTECTOMY Greenberg, D., Kee, J., Stevenson, K., Van Zyl, E., Dugala, A., Prado, K., Gill, H., Skinner, E., Shah, J. LIPPINCOTT WILLIAMS & WILKINS. 2019: E1196?E1197

  View details for Web of Science ID 000473345204010

• Giant renal angiomyolipoma in a solitary kidney CANADIAN JOURNAL OF UROLOGY Sohlberg, E., Sun, A., Massoudi, R., Prado, K., Skinner, E. 2018; 25 (6): 9614?16

  View details for Web of Science ID 000454188000010

• Sequencing of cancer cell subpopulations identifies micrometastases in a bladder cancer patient ONCOTARGET Prado, K., Zhang, K. X., Pellegrini, M., Chin, A. I. 2017; 8 (28): 45619?25

  Abstract

  Pathologic staging of bladder cancer patients remains a challenge. Standard-of-care histology exhibits limited sensitivity in detection of micrometastases, which can increase risk of cancer progression and delay potential adjuvant therapies. Here, we sought to develop a proof of concept novel molecular approach to improve detection of cancer micrometastasis.We combined fluorescence activated cell sorting and next-generation sequencing and performed whole-exome sequencing of total cancer cells and cancer cell subpopulations in multiple tumor specimens and regional lymph nodes in a single patient with muscle-invasive urothelial carcinoma of the bladder following radical cystectomy.Mean allele frequency analysis demonstrated a significant correlation between primary tumor cancer cells and cancer cells isolated from the lymph nodes, confirming lymph node disease despite negative pathologic staging. RNA-sequencing revealed intratumoral heterogeneity as well as enrichment for immune system and lipid metabolism gene sets in the micrometastatic cancer cell subpopulations.Our analysis illustrates how next-generation sequencing of cancer cell subpopulations may be utilized to enrich for cancer cell markers and enhance detection of bladder cancer micrometastases to improve pathologic staging and provide insight into cancer cell biology.

  View details for PubMedID 28487492

• Is Targeted Biopsy Applicable to Patients on Active Surveillance? EUROPEAN UROLOGY Prado, K., Reiter, R. E. 2017; 71 (2): 181?82

  View details for PubMedID 27292867

• How nerve-sparing technique has been applied to radiotherapy ASIAN JOURNAL OF ANDROLOGY Prado, K., Chin, A. I. 2016; 18 (6): 898?99

  View details for PubMedID 27453071

  View details for PubMedCentralID PMC5109883

• Biased Expression of the FOXP3 Delta 3 Isoform in Aggressive Bladder Cancer Mediates Differentiation and Cisplatin Chemotherapy Resistance CLINICAL CANCER RESEARCH Zhang, H., Prado, K., Zhang, K. X., Peek, E. M., Lee, J., Wang, X., Huang, J., Li, G., Pellegrini, M., Chin, A. I. 2016; 22 (21): 5349?61

  Abstract

  The transcriptional regulation mediating cancer cell differentiation into distinct molecular subtypes and modulating sensitivity to existing treatments is an enticing therapeutic target. Our objective was to characterize the ability of the forkhead/winged transcription factor FOXP3 to modulate the differentiation of bladder cancer.Expression of FOXP3 was analyzed by immunohistochemistry in a tumor microarray of 587 samples and overall survival in a subset of 187 patients following radical cystectomy. Functional assays were performed in SW780 and HT1376 cell lines in vitro and in vivo and gene expression profiling performed by RNA-Seq. Validation was undertaken using gene expression profiles of 131 patients from The Cancer Genome Atlas (TCGA) consortium in bladder cancer.FOXP3 expression correlates with bladder cancer stage and inversely with overall survival, with biased expression of the FOXP3?3 isoform. Functional assays of FOXP3?3 demonstrated resistance to chemotherapy in vitro, whereas subcutaneous xenografts overexpressing FOXP3?3 developed larger and more poorly differentiated bladder cancers. RNA expression profiling revealed a unique FOXP3?3 gene signature supporting a role in chemotherapy resistance. Accordingly, knockdown of Foxp3 by siRNA in HT1376 cells conferred sensitivity to cisplatin- and gemcitabine-induced cytotoxicity. Validation in TCGA dataset demonstrated increased expression of FOXP3 in subtypes II to IV and skewing of molecular subtypes based on FOXP3?3-specific gene expression.(i) Biased expression of the FOXP3?3 isoform in bladder cancer inversely correlates with overall survival, (ii) FOXP3?3 induces a unique gene program that mediates cancer differentiation, and (iii) FOXP3?3 may augment chemotherapy resistance. Clin Cancer Res; 22(21); 5349-61. ©2016 AACR.

  View details for PubMedID 27189164

• Economics of Robotic Surgery Does It Make Sense and for Whom? UROLOGIC CLINICS OF NORTH AMERICA Williams, S. B., Prado, K., Hu, J. C. 2014; 41 (4): 591-+

  Abstract

  The authors performed a literature review to identify cost-effectiveness research as it pertains to robotic surgery. There is increased utilization of robotic surgery in urology with limited comparative effectiveness research demonstrating superiority over conventional, less costly treatment options. Further research into identifying determinants for optimal utilization of robotics and newer technology is needed.

  View details for PubMedID 25306170

• Allosteric Inhibition of the IRE1 alpha RNase Preserves Cell Viability and Function during Endoplasmic Reticulum Stress CELL Ghosh, R., Wang, L., Wang, E. S., Perera, B. K., Igbaria, A., Morita, S., Prado, K., Thamsen, M., Caswell, D., Macias, H., Weiberth, K. F., Gliedt, M. J., Alavi, M. V., Hari, S. B., Mitra, A. K., Bhhatarai, B., Schuerer, S. C., Snapp, E. L., Gould, D. B., German, M. S., Backes, B. J., Maly, D. J., Oakes, S. A., Papa, F. R. 2014; 158 (3): 534?48

  Abstract

  Depending on endoplasmic reticulum (ER) stress levels, the ER transmembrane multidomain protein IRE1? promotes either adaptation or apoptosis. Unfolded ER proteins cause IRE1? lumenal domain homo-oligomerization, inducing trans autophosphorylation that further drives homo-oligomerization of its cytosolic kinase/endoribonuclease (RNase) domains to activate mRNA splicing of adaptive XBP1 transcription factor. However, under high/chronic ER stress, IRE1? surpasses an oligomerization threshold that expands RNase substrate repertoire to many ER-localized mRNAs, leading to apoptosis. To modulate these effects, we developed ATP-competitive IRE1? Kinase-Inhibiting RNase Attenuators-KIRAs-that allosterically inhibit IRE1?'s RNase by breaking oligomers. One optimized KIRA, KIRA6, inhibits IRE1? in vivo and promotes cell survival under ER stress. Intravitreally, KIRA6 preserves photoreceptor functional viability in rat models of ER stress-induced retinal degeneration. Systemically, KIRA6 preserves pancreatic ? cells, increases insulin, and reduces hyperglycemia in Akita diabetic mice. Thus, IRE1? powerfully controls cell fate but can itself be controlled with small molecules to reduce cell degeneration.

  View details for PubMedID 25018104

  View details for PubMedCentralID PMC4244221

• Early and Late Abdominal Bleeding After Roux-en-Y Gastric Bypass: Sources and Tailored Therapeutic Strategies OBESITY SURGERY Rabl, C., Peeva, S., Prado, K., James, A. W., Rogers, S. J., Posselt, A., Campos, G. M. 2011; 21 (4): 413?20

  Abstract

  Bleeding is a potentially serious complication after Roux-en-Y gastric bypass (RYGB). Preventive measures and therapeutic strategies have not been adequately defined. We reviewed data on 742 consecutive patients treated at the University of California San Francisco to identify cases of early and late bleeding (less or greater than 30 days after surgery) after RYGB. Bleeding was defined as symptoms or signs of bleeding, associated with blood transfusion. We recorded patient characteristics, details of the operative technique, diagnostic approach, therapeutic strategies, and outcomes. Twenty-six patients (3.5%) had postoperative bleeding, which mostly occurred in the first 30 days postoperatively (N=19). Hematocrit decreased significantly from preoperative values (-5.2 ± 3.1 without bleeding vs. -14.8 ± 4.7 with, p<0.01). Type 2 diabetes was more prevalent in patients who had bleeding (58% vs. 32%, p=0.03). No other patient characteristics or details of the operative technique were associated with different rates of bleeding. Therapeutic intervention other than transfusion was needed for seven patients with early bleeding (36.8%) and for all patients with late bleeding. Four patients with early bleeding required reoperation. Early bleeding source was intraluminal in four patients, intraperitoneal in five, and self-limited and of unknown location in ten. Late bleeding occurred on average at 62.6 months (range, 5 to 300 months) after index surgery, five patients required reoperation, and the source was always intraluminal. Bleeding after RYGB may be from various anatomic sites; details of the operative technique were not associated with different rates of bleeding, and therapy should be tailored to suspected location of bleeding.

  View details for DOI 10.1007/s11695-011-0354-9

  View details for Web of Science ID 000288457600001

  View details for PubMedID 21240659

• Creating an Effective and Efficient Publicly Sponsored Health Care Delivery System JOURNAL OF HEALTH CARE FOR THE POOR AND UNDERSERVED Zweifler, J., Prado, K., Metchnikoff, C. 2011; 22 (1): 311?19

  Abstract

  An effective and efficient publicly sponsored health care delivery system can increase access to care, improve health care outcomes, and reduce spending. A publicly sponsored health care delivery system can be created by integrating services that are already federally subsidized: community health centers (CHCs), public and safety-net hospitals, and residency training programs. The Patient Protection and Affordable Care Act includes measures that support primary care generally and CHCs in particular. A publicly sponsored health care delivery system combining primary care based in CHCs with safety-net hospitals and the specialists that serve them could also benefit from incentives in the Patient Protection and Affordable Care Act for the creation of accountable care organizations, and reimbursement based on quality and cost control.

  View details for PubMedID 21317524

• Improved Glycemic Control with Colesevelam Treatment in Patients with Type 2 Diabetes Is Not Directly Associated with Changes in Bile Acid Metabolism HEPATOLOGY Brufau, G., Stellaard, F., Prado, K., Bloks, V. W., Jonkers, E., Boverhof, R., Kuipers, F., Murphy, E. J. 2010; 52 (4): 1455?64

  Abstract

  Bile acids (BAs) are essential for fat absorption and appear to modulate glucose and energy metabolism. Colesevelam, a BA sequestrant, improves glycemic control in type 2 diabetes mellitus (T2DM). We aimed to characterize the alterations in BA metabolism associated with T2DM and colesevelam treatment and to establish whether metabolic consequences of T2DM and colesevelam are related to changes in BA metabolism. Male subjects with T2DM (n = 16) and controls (n = 12) were matched for age and body mass index. BA pool sizes and synthesis/input rates were determined before and after 2 and 8 weeks of colesevelam treatment. T2DM subjects had higher cholic acid (CA) synthesis rate, higher deoxycholic acid (DCA) input rate, and enlarged DCA pool size. Colesevelam resulted in a preferential increase in CA synthesis in both groups. CA pool size was increased whereas chenodeoxycholic acid and DCA pool sizes were decreased upon treatment. Fasting and postprandial fibroblast growth factor 19 (FGF19) levels did not differ between controls and diabetics, but were decreased by treatment in both groups. Colesevelam treatment reduced hemoglobin A1C by 0.7% (P < 0.01) in diabetics. Yet, no relationships between BA kinetic parameters and changes in glucose metabolism were found in T2DM or with colesevelam treatment.Our results reveal significant changes in BA metabolism in T2DM, particularly affecting CA and DCA. Colesevelam treatment reduced FGF19 signaling associated with increased BA synthesis, particularly of CA, and resulted in a more hydrophilic BA pool without altering total BA pool size. However, these changes could not be related to the improved glycemic control in T2DM.

  View details for DOI 10.1002/hep.23831

  View details for Web of Science ID 000282613000032

  View details for PubMedID 20725912

• Plasma bile acids are not associated with energy metabolism in humans NUTRITION & METABOLISM Brufau, G., Bahr, M. J., Staels, B., Claudel, T., Ockenga, J., Boker, K. W., Murphy, E. J., Prado, K., Stellaard, F., Manns, M. P., Kuipers, F., Tietge, U. F. 2010; 7: 73

  Abstract

  Bile acids (BA) have recently been shown to increase energy expenditure in mice, but this concept has not been tested in humans. Therefore, we investigated the relationship between plasma BA levels and energy expenditure in humans. Type 2 diabetic (T2DM) patients (n = 12) and gender, age and BMI-matched healthy controls (n = 12) were studied before and after 8 weeks of treatment with a BA sequestrant. In addition, patients with liver cirrhosis (n = 46) were investigated, since these display elevated plasma BA together with increased energy expenditure. This group was compared to gender-, age- and BMI-matched healthy controls (n = 20). Fasting plasma levels of total BA and individual BA species as well as resting energy expenditure were determined. In response to treatment with the BA sequestrant, plasma deoxycholic acid (DCA) levels decreased in controls (-60%, p < 0.05) and T2DM (-32%, p < 0.05), while chenodeoxycholic acid (CDCA) decreased in controls only (-33%, p < 0.05). Energy expenditure did not differ between T2DM and controls at baseline and, in contrast to plasma BA levels, was unaffected by treatment with the BA sequestrant. Total BA as well as individual BA species did not correlate with energy expenditure at any time throughout the study. Patients with cirrhosis displayed on average an increase in energy expenditure of 18% compared to values predicted by the Harris-Benedict equation, and plasma levels of total BA (up to 12-fold) and individual BA (up to 20-fold) were increased over a wide range. However, neither total nor individual plasma BA levels correlated with energy expenditure. In addition, energy expenditure was identical in patients with a cholestatic versus a non-cholestatic origin of liver disease while plasma total BA levels differed four-fold between the groups. In conclusion, in the various (patho)physiological conditions studied, plasma BA levels were not associated with changes in energy expenditure. Therefore, our data do not support an important role of circulating BA in the control of human energy metabolism.

  View details for PubMedID 20815878

• Benzothiadiazole- and pyrrole-based polymers bearing thermally cleavable solubilizing groups as precursors for low bandgap polymers CHEMICAL COMMUNICATIONS Edder, C., Armstrong, P. B., Prado, K. B., Frechet, J. M. 2006: 1965?67

  Abstract

  We report the design, synthesis and characterization of new benzothiadiazole- and pyrrole-based copolymers whose solubility and bandgap drastically change after thermal treatment of their thin films.

  View details for PubMedID 16767251