Jorge D Mena

All Publications

• Zinc-enriched Pathological Biominerals in the Human Kidney Encode their Anatomical Microenvironments. Acta biomaterialia Srirangapatanam, S., Greenfield, B., Mena, J., Farzannekou, D., Yang, G., Kang, M., Ustriyana, P., Webb, S., Tzou, D., Ho, S. P. 2026

  Abstract

  The fundamental mechanisms underlying kidney stone formation remain elusive despite extensive research, limiting prevention strategies and contributing to high recurrence rates. Traditionally understood to arise through systemic urine supersaturation and conceptualized as monolithic concretions, kidney stones exhibit marked structural and compositional heterogeneity across distinct renal microenvironments. We hypothesized that these heterogeneous biominerals preserve physicochemical signatures of their anatomical origin and spatial organization of zinc (Zn) reflects microenvironment-specific mineralization processes. Using multiscale correlative microspectroscopy workflow, we characterized three morphologically distinct biominerals from three anatomically distinct renal niches. Papillary plaques and mineralized papillary stems exhibited strong compositional similarity, whereas collecting system stones were predominantly Ca- and P-rich inorganic mineral. Spatial gradients in zinc, calcium, phosphorus, and organic matrix components distinguished papillary mineralization from collecting system stone maturation. Zinc, traditionally a trace element, emerged as a spatially organized constituent with region-dependent abundance. Zn was enriched in papillary interstitium, and cellular substructures, where it colocalized with phosphorus and formed discrete high-density domains. Conserved spherical micro- and nanoparticles composed primarily of calcium and phosphorus, with variable organic content, were present across all biomineral types, indicating shared nucleation units. Based on these findings, we hypothesize a hierarchical mineralization model in which Zn-associated domains are spatially associated with calcium phosphate and calcium oxalate deposits. The coexistence of intratubular and interstitial mineral features reconciles classical free- and fixed-particle theories, indicating that heterogeneous stone formation arises through complementary mechanisms. Collectively, the observed anatomy-specific biominerals encode the physicochemical environments and highlight the importance of targeting localized microenvironments for improved therapeutic interventions. STATEMENT OF SIGNIFICANCE: Traditionally, kidney stones are viewed as uniform masses formed by mineral supersaturation in urine. This study challenges that paradigm by demonstrating that stones are complex, anatomy-specific biominerals that encode signatures of their chemical microenvironments and formation pathways within their structure. Using high-resolution, correlative imaging, we identify zinc as a spatially organized component of early mineralization rather than a passive trace byproduct, revealing previously unrecognized mechanisms of stone initiation. These findings shift the focus from purely physicochemical precipitation to microenvironment-driven formation and highlight mineral-tissue interactions as key targets for earlier detection, prevention, and therapeutic intervention in recurrent stone formation.

  View details for DOI 10.1016/j.actbio.2026.07.042

  View details for PubMedID 42501772

• Endoscopically visible Randall's plaques are an independent predictor of future stone events UROLITHIASIS Meyer, N., Lee, J., Liu, V., Pepic, L., Pearce, R., Li, K., Shee, K., Mena, J., Ahn, J., Bayne, D., Stoller, M., Chi, T., Sui, W., Yang, H. 2026; 54 (1): 46

  Abstract

  Randall’s plaques have been long thought to be precursors for kidney stone formation, but how their presence impacts future stone recurrence is not known. The aim of this study was to determine whether patients with endoscopically visible plaques were more likely to have subsequent stone events compared to those without. The presence of Randall’s plaque in adult patients was prospectively assessed during endoscopic cases as part of the Registry for Stones of the Kidney and Ureter (ReSKU). In each case, the visible Randall’s plaque burden was scored by the attending surgeon as “none,” “minimal,” or “many.” Data regarding stone composition, 24-hour urine tests, and subsequent stone events on follow up were collected. Stone events were defined as patient-reported stone passage or any primary operation for kidney stones; second-look or staged operations were not counted as separate stone events. We identified 673 subjects with a Randall’s plaque assessment, of which 78 had “none,” 306 had “minimal,” and 289 had “many.” Despite having no significant differences in initial stone burden, subjects with visible Randall’s plaque (“minimal” or “many”) had a higher relative risk of stone recurrences after surgery compared to those without (RRR 1.711 (1.121–2.611), p = 0.01). Interestingly, no significant differences in 24-hour urine analytes were observed. Subjects with visible plaque were more likely to have calcium-based stones (84% vs. 58%, p < 0.001). The presence of endoscopically visible Randall’s plaque is associated with an increased risk of stone recurrence independent of urine composition.

  View details for DOI 10.1007/s00240-025-01896-w

  View details for Web of Science ID 001679499200001

  View details for PubMedID 41632113

  View details for PubMedCentralID 2925677

• The relationship between frailty, incontinence severity, and treatment decisions for men with post-prostatectomy stress urinary incontinence: a mixed methods analysis TRANSLATIONAL ANDROLOGY AND UROLOGY Jones, C. P., Shaw, N. M., Mena, J., Breyer, B. N., Walter, L. C., Baussan, C., Quanstrom, K., Allen, I., Dohan, D., Hampson, L. A. 2023; 12 (5): 840-848

  Abstract

  Frailty is common among urology patients in general as well as among men seeking evaluation for stress urinary incontinence (SUI), with 6.1% of men undergoing artificial urinary sphincter placement considered frail. It is unclear if and how patient views on frailty and incontinence severity impact decision-making with regards to SUI treatment.We undertook a mixed methods analysis to evaluate the intersection of frailty, incontinence severity, and treatment decision-making is presented. To do so, we utilized a previously published cohort of men undergoing evaluation for SUI at the University of California, San Francisco between 2015 and 2020, selecting those who had evaluation with timed up and go test (TUGT), objective measures of incontinence, and patient-reported outcome measures (PROMs). A subset of these participants had additionally undergone semi-structured interviews, and these interviews were re-examined to thematically code them with a focus on the impact of frailty and incontinence severity on SUI treatment decision-making.Among the original cohort of 130 patients, 72 had an objective measure of frailty and were included in our analysis; 18 of these individuals had corresponding qualitative interviews. Common themes identified included (I) impact of incontinence severity on decision-making; (II) the interaction between frailty and incontinence; (III) the impact of comorbidity on treatment decision-making; and (IV) age as a construct of frailty and impact on surgical choice and/or recovery. Direct quotations regarding each theme provides insight into patients' views and drivers of SUI treatment decision-making.The impact of frailty on treatment decision-making for patients with SUI is complex. This mixed methods study highlights the variety of patient views on frailty with regards to surgical intervention for male SUI. Urologists should make a concerted effort to personalize patient counseling for SUI management and take time to understand each patient's perspective in order to individualize SUI treatment decision-making. More research is needed to help identify factors that influence decision-making for frail male patients with SUI.

  View details for DOI 10.21037/tau-22-839

  View details for Web of Science ID 000967014300001

  View details for PubMedID 37305619

  View details for PubMedCentralID PMC10251103

• Progressive, Subacute Penile Swelling After Recent Trauma UROLOGY Ahamed, F., Balakrishnan, A. S., Mena, J., Breyer, B. N., Shaw, N. M. 2022; 165: E1-E3

  View details for DOI 10.1016/j.urology.2022.04.011

  View details for Web of Science ID 000852855700001

  View details for PubMedID 35469805

• Nedosiran Dramatically Reduces Serum Oxalate in Dialysis-Dependent Primary Hyperoxaluria 1: A Compassionate Use Case Report UROLOGY Shee, K., Ahn, J., Hamouche, F., Mena, J., Chi, T., Stoller, M. L. 2021; 156: E147-E149

  Abstract

  Primary hyperoxaluria 1 (PH1) is a devastating condition involving recurrent urolithiasis, early end-stage renal disease and multisystemic deposition of calcium oxalate crystals. Treatment options for PH1 are limited, inevitably requiring transplantation, usually combined kidney and liver transplant. Here we report successful compassionate use of Nedosiran, an RNA interference targeting lactate dehydrogenase, in an index patient. Monthly Nedosiran injections led to dramatically decreased plasma oxalate levels, decreased frequency of weekly hemodialysis sessions from 6 to 3, and deferral of combined kidney and liver transplant. Nedosiran represents a novel and impactful potential therapeutic for PH1 patients with end-stage renal disease.

  View details for DOI 10.1016/j.urology.2021.03.014

  View details for Web of Science ID 000759725500016

  View details for PubMedID 33774044

• Structural and chemical heterogeneities of primary hyperoxaluria kidney stones from pediatric patients JOURNAL OF PEDIATRIC UROLOGY Du, Y., Roger, V., Mena, J., Kang, M., Stoller, M. L., Ho, S. P. 2021; 17 (2): 214.e1-214.e11

  Abstract

  Calcium oxalate stones are the most common type among stone-forming patients and in some cases result from predisposed genetic conditions. In this work, we examined the differences in structure and chemical composition between oxalate stones from patients from three groups: 1) pediatric patients that were genetically predisposed (primary hyperoxaluria) to form stones (PPH); 2) control pediatric patients that did not have such genetic predisposition (PN-PH); 3) adult patients that formed oxalate stones without the genetic predisposition (A-CaOx). A variety of instrumental analyses were conducted to identify physicochemical properties of stones characteristic of predisposed pediatric (PPH), pediatric hyperoxaluria (PN-PH), and adult (A-CaOx) patient populations.Genetic variants of 16 stone-forming patients were determined using whole-exome gene sequencing. Components of stones from PPH (n = 6), PN-PH (n = 5), and A-CaOx (n = 5) groups were identified using Fourier transform infrared (FTIR) spectroscopy. Stone morphology and density were evaluated using high resolution X-ray computed tomography (micro-XCT). Stone microstructure and elemental composition were mapped with scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) spectroscopy, respectively.Calcium oxalate bipyramidal crystals were found on stones from all groups. Stones from PPH patients with PH types I and II were composed of calcium oxalate monohydrate (COM) with relatively uniform mineral density (1224 ± 277 mg/cc) and distinct smooth surfaces. By contrast, micro-spherical calcium phosphate particles were found only on PN-PH stones, which also showed a broader range of mineral densities (1266 ± 342 mg/cc). Stones from the PN-PH group also contained phosphorus (P), which was absent in NP-PH stones. A-CaOx stones were of significantly lower mineral density (645 ± 237 mg/cc) than pediatric stones and were more heterogeneous in their elemental composition.Unique structural and compositional characteristics were identified in stones from pediatric patients with primary hyperoxaluria. These include the absence of phosphorus, a narrower mineral density distribution, and a uniform elemental composition compared to stones from pediatric patients without the genetic predisposition. Thus, characterization of stones at the macro- and micro-scales in combination with genetic testing of patients can provide insights and accurate diagnosis to develop a treatment plan for effective patient care.

  View details for DOI 10.1016/j.jpurol.2020.11.023

  View details for Web of Science ID 000642604700029

  View details for PubMedID 33495102

  View details for PubMedCentralID PMC8709938

• Structure and elemental composition of Ceftriaxone induced pediatric nephrolithiasis UROLITHIASIS Du, Y., Kang, M., Mena, J., Stoller, M. L., Ho, S. P., Li, J. 2021; 49 (4): 309-320

  Abstract

  Ceftriaxone is a widely used antibiotic because to its broad-spectrum gram-negative coverage, safety, and biological half life (5-9 h) permit dose once-daily administration. It is specifically used in pediatric patients in developing countries. Ceftriaxone forms insoluble sludge/stone when combined with calcium in the urinary system. In this study, Ceftriaxone induced sludge/stones from pediatric patients were collected to identify its microstructure and composition to gather insights into the mechanism of Ceftriaxone induced sludge/stone formation. The results illustrated that Ceftriaxone induced stones formed rapidly following antibiotic administration. Ceftriaxone calcium salt crystals could easily be broken with minimal intervention. However, Ceftriaxone combined with calcium phosphate formed an insoluble stone aggregate.

  View details for DOI 10.1007/s00240-020-01231-5

  View details for Web of Science ID 000618124000002

  View details for PubMedID 33587147

  View details for PubMedCentralID 4391782

• Ectopic biomineralization in kidney stone formers compared to non-stone formers TRANSLATIONAL ANDROLOGY AND UROLOGY Fernandez, A. M., Sherer, B. A., Gansky, S. A., Mena, J. D., Srirangapatanam, S., Wiener, S., Chi, T., Ho, S. P., Stoller, M. L. 2020; 9 (5): 2129-+

  Abstract

  Kidney stone formers (SFs) are at increased risk of stroke, myocardial infarction, and atherosclerosis of the carotid and coronary arteries. These cardiovascular and urologic pathologies can result from ectopic biomineral deposition. The objectives of this study are: (I) to evaluate risk factors for ectopic biomineralization, and (II) to characterize the overall burden of ectopic minerals in known SFs compared to non-stone formers (NSFs) matched for these risk factors.Presence and quantity of biominerals at eight anatomic locations (abdominal aorta, common iliac arteries, pelvic veins, prostate or uterus, mesentery, pancreas, and spleen) were determined in a case control study by retrospective analysis of clinical non-contrast computed tomography scans obtained from 190 SFs and 190 gender- and age-matched NSFs (renal transplant donors). Predictors of biomineralization were determined using negative binomial regression. A subgroup of 140 SFs and 140 NSFs were matched for risk factors for systemic biomineralization, and mineralization was compared between these matched SFs and NSFs using ordinal logistic regression.Hypertension, hyperlipidemia, diabetes mellitus, and smoking were more common amongst SFs. Risk factors for increased systemic biomineralization included history of nephrolithiasis, male gender, older age, and history of hyperlipidemia. When controlling for these comorbidities, SFs had significantly increased biomineralization systemically and at the abdominal aorta, iliac arteries, prostate, mesentery, pancreas, and spleen compared to NSFs.The current study provides evidence that SFs are at increased risk of biomineralization systemically, independent of common risk factors of atherosclerosis.

  View details for DOI 10.21037/tau-19-927

  View details for Web of Science ID 000583714800025

  View details for PubMedID 33209676

  View details for PubMedCentralID PMC7658123

• Use of GoFundMe® to crowdfund complementary and alternative medicine treatments for cancer JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY Song, S., Cohen, A. J., Lui, H., Mmonu, N. A., Brody, H., Patino, G., Liaw, A., Butler, C., Fergus, K. B., Mena, J., Lee, A., Weiser, J., Johnson, K., Breyer, B. N. 2020; 146 (7): 1857-1865

  Abstract

  Complementary and alternative medicine (CAM) use is common amongst cancer patients. However, there is growing concern about its safety and efficacy. Online crowdfunding campaigns represent a unique avenue to understand the cancer patient's perspective for using CAM or declining conventional cancer therapy (CCT).Five hundred GoFundMe campaigns from 2012 to 2019 detailing financial need for cancer treatment were randomly selected and reviewed for endorsement of CAM use, reasons for using CAM, and reasons for declining CCT. Descriptive statistics were used to compare patient and campaign characteristics between 250 CAM users and 250 non-CAM users.Compared to non-CAM users, CAM users were more likely to be female (70% vs. 54%, p < 0.01), to report more stage IV cancer (54% vs. 12%, p < 0.01), and to have a history of delayed, missed, or misdiagnosis (10% vs. 4%, p < 0.01). Reasons for using CAM include endorsing curative/therapeutic effects 212 (85%), pain/stress reduction 137 (55%), and dissatisfaction with current or past medical treatment options 105 (42%). 87 (35%) CAM users that declined CCT reported that they wanted to try to fight off cancer using CAM first 57 (61%), that CCT was too "toxic" to the body 39 (42%), and cancer was already too advanced, so that CCT would be futile or too aggressive 25 (27%).Cancer patients on GoFundMe using CAM highly value quality of life, comfort, and autonomy. Physicians should educate themselves on CAM to set realistic expectations and provide comprehensive counseling of the risks and benefits of CAM usage to patients who choose to use CAM to either augment or completely replace CCT.

  View details for DOI 10.1007/s00432-020-03191-0

  View details for Web of Science ID 000521912000001

  View details for PubMedID 32219517

  View details for PubMedCentralID PMC11804722

• A rare presentation of hepatolithiasis in an adolescent patient: A case report INTERNATIONAL JOURNAL OF SURGERY CASE REPORTS Freise, J., Mena, J., Wen, K., Stoller, M., Ho, S., Corvera, C. 2020; 72: 343-345

  Abstract

  Hepatolithiasis (intrahepatic stones) is rare in adolescent patients and requires complex management strategies to prevent recurrent infections and progression to hepatic fibrosis. Surgical management is often required. In cases of unclear etiology, further work-up is indicated to provide insight into future management. In this report we describe an extensive stone analysis.A 20-year-old Caucasian female presented with known hepatolithiasis and multiple prior recurrent bouts of abdominal pain requiring hospitalization. Magnetic resonance cholangiopancreatography (MRCP) demonstrated an abnormal left-sided hepatic biliary ductal system dilatation. She was treated surgically with a formal left hepatectomy and preservation of the caudate lobe. The right ductal system had no stones or evidence of inflammation, and her bile and stones cultures were negative for organism growth. An extensive analysis demonstrated stone composition primarily of cholesterol.Adolescent presentations of hepatolithiasis are rare and considerations in the differential diagnosis include primary sclerosing cholangitis, bile acid transporter defects, and other known genetic diseases. This case is unique because only the left half of the intrahepatic ductal system had evidence of stone disease and the bile was sterile. A detailed stone analysis demonstrating cholesterol supersaturation provides additional context though the etiology remains unclear in this case and will require lifelong follow-up.Early-onset hepatolithiasis is rare and requires expert management, and in some cases definitive surgical management with life-long follow-up. Extensive stone analysis and genetic testing can be performed to help identify disease etiology in unique cases.

  View details for DOI 10.1016/j.ijscr.2020.06.017

  View details for Web of Science ID 000548926300001

  View details for PubMedID 32563817

  View details for PubMedCentralID PMC7306511

• Perspectives From Authors and Editors in the Biomedical Disciplines on Predatory Journals: Survey Study JOURNAL OF MEDICAL INTERNET RESEARCH Cohen, A. J., Patino, G., Kamal, P., Ndoye, M., Tresh, A., Mena, J., Butler, C., Washington, S., Breyer, B. N. 2019; 21 (8): e13769

  Abstract

  Predatory journals fail to fulfill the tenets of biomedical publication: peer review, circulation, and access in perpetuity. Despite increasing attention in the lay and scientific press, no studies have directly assessed the perceptions of the authors or editors involved.Our objective was to understand the motivation of authors in sending their work to potentially predatory journals. Moreover, we aimed to understand the perspective of journal editors at journals cited as potentially predatory.Potential online predatory journals were randomly selected among 350 publishers and their 2204 biomedical journals. Author and editor email information was valid for 2227 total potential participants. A survey for authors and editors was created in an iterative fashion and distributed. Surveys assessed attitudes and knowledge about predatory publishing. Narrative comments were invited.A total of 249 complete survey responses were analyzed. A total of 40% of editors (17/43) surveyed were not aware that they were listed as an editor for the particular journal in question. A total of 21.8% of authors (45/206) confirmed a lack of peer review. Whereas 77% (33/43) of all surveyed editors were at least somewhat familiar with predatory journals, only 33.0% of authors (68/206) were somewhat familiar with them (P<.001). Only 26.2% of authors (54/206) were aware of Beall's list of predatory journals versus 49% (21/43) of editors (P<.001). A total of 30.1% of authors (62/206) believed their publication was published in a predatory journal. After defining predatory publishing, 87.9% of authors (181/206) surveyed would not publish in the same journal in the future.Authors publishing in suspected predatory journals are alarmingly uninformed in terms of predatory journal quality and practices. Editors' increased familiarity with predatory publishing did little to prevent their unwitting listing as editors. Some suspected predatory journals did provide services akin to open access publication. Education, research mentorship, and a realignment of research incentives may decrease the impact of predatory publishing.

  View details for DOI 10.2196/13769

  View details for Web of Science ID 000483306700001

  View details for PubMedID 31471960

  View details for PubMedCentralID PMC6743260

• Computational Fluid Dynamic Modeling of Urethral Strictures JOURNAL OF UROLOGY Cohen, A. J., Baradaran, N., Mena, J., Krsmanovich, D., Breyer, B. N. 2019; 202 (2): 347-352

  Abstract

  Computational fluid dynamics have paradigm shifting potential in understanding the physiological flow of fluids in the human body. This translational branch of engineering has already made an important clinical impact on the study of cardiovascular disease. We evaluated the feasibility and applicability of computational fluid dynamics to model urine flow.We prepared a computational fluid dynamics model using an idealized male genitourinary system. We created 16 hypothetical urethral stricture scenarios as a test bed. Standard parameters of urine such as pressure, temperature and viscosity were applied as well as typical assumptions germane to fluid dynamic modeling. We used ABAQUS/CAE 6.14 (Dassault Systèmes®) with a direct unsymmetrical solver with standard (FC3D8) 3D brick 8Node elements for model generation.The average flow rate in urethral stricture disease as measured by our model was 5.97 ml per second (IQR 2.2-10.9). The model predicted a flow rate of 2.88 ml per second for a single 5Fr stricture in the mid bulbar urethra when assuming all other variables constant. The model demonstrated that increasing stricture diameter and bladder pressure strongly impacted urine flow while stricture location and length, and the sequence of multiple strictures had a weaker impact.We successfully created a computational fluid dynamics model of an idealized male urethra with varied types of urethral strictures. The resultant flow rates were consistent with the literature. The accuracy of modeling increasing bladder pressure should be improved by future iterations. This technology has vast research and clinical potential.

  View details for DOI 10.1097/JU.0000000000000187

  View details for Web of Science ID 000475859600042

  View details for PubMedID 30810463

• The landscape of urological retractions: the prevalence of reported research misconduct BJU INTERNATIONAL Mena, J. D., Ndoye, M., Cohen, A. J., Kamal, P., Breyer, B. N. 2019; 124 (1): 174-179

  Abstract

  To evaluate the landscape of retractions of literature and to determine the prevalence of research misconduct in the field of urology.Three databases (PUBMED, Embase, Retraction Watch) were queried for all retracted studies on urological topics in both urological and non-urological journals from April 1999 to March 2018. Two reviewers screened the records and determined the final list of articles to be included in the analysis.A total of 138 articles met the inclusion criteria. Over 80% of retractions occurred after 2009. Retractions originated from 76 different journals (13 urological journals) and 28 countries. The most common reasons for retraction were plagiarism (28%), fake peer review (20%), error (20%), and falsification of data (13%). Misconduct accounted for two-thirds of the retractions (n = 93). A large watermark, indicating retraction of the article, was present in 75% of the manuscripts. Articles were cited a total of 4454 times, 38% of citations happened after retraction. The majority of retracted articles related to urological oncology (70%). The highest number of retractions for an individual author was five. Rates of retraction among popular urological journals since 2010 have increased but remain a small proportion of all publications: BJUI, 0.189%; World Journal of Urology, 0.132%; European Urology, 0.058%; Urology, 0.047%; and Journal of Urology, 0.024%.Retractions of urological literature, similarly to retractions of other biomedical literature, have been rising over the last decade. The majority of these retractions stem from research misconduct. Despite retractions, flawed articles continued to be cited.

  View details for DOI 10.1111/bju.14706

  View details for Web of Science ID 000471830900026

  View details for PubMedID 30748082

• Altruistic donation to improve survey responses: a global randomized trial BMC RESEARCH NOTES Cohen, A. J., Washington, S., Butler, C., Kamal, P., Patino, G., Tresh, A., Mena, J., Ndoye, M., Breyer, B. N. 2019; 12: 113

  Abstract

  Web-based platforms have revolutionized the ability for researchers to perform global survey research. Methods to incentivize participation have been singularly focused on European and North American participants with varied results. With an ever increasing proportion of biomedical research being performed in non-western countries, assessment of novel methods to improve global survey response is timely and necessary. To that end, we created a three-arm nested randomized control trial (RCT) within a prospective cohort study to assess the impact of incentives on survey responsiveness in a global audience of biomedical researchers.Email invitations were sent to authors and editors involved in online publishing totaling 2426 participants from 111 countries. Overall we observed a 13.0% response rate: 13.3% for the control group, 14.4% for a group entered to win a gift card, and 11.1% for a group whose participation lead to donation to charity (p = 0.17). Year of publication nor country impacted response rate. Within subgroups, editors were significantly less likely to respond to the survey as compared to authors (6.5% vs. 18.9%; p-value < 0.01). With power to detect a 4.8% difference among groups, we could not detect an impact of incentives on global survey response.

  View details for DOI 10.1186/s13104-019-4146-y

  View details for Web of Science ID 000459924900006

  View details for PubMedID 30819217

  View details for PubMedCentralID PMC6396474