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Jiménez, Rafael E.

https://orcid.org/0000-0003-2348-0214

Mayo Clinic

Mayo Clinic

Citations 48

Proteomic and Clinicopathologic Assessment of Penile Amyloidosis: A Single Institutional Review of 12 Cases
Gilani, Sarwat, Dasari, Surendra , Theis, Jason D. , Dao, Linda N. , Cubilla, Antonio L. , Hernandez, Loren P. Herrera , Jiménez, Rafael E. , Cheville, John C. , Howard, Matthew T., Guo, Ruifeng , Gupta, Sounak , Gilani, Sarwat I, Herrera Hernandez, Loren P, Guo, Ruifeng , Tekin, Burak , Rech, Karen L. , Dispenzieri, Angela , McPhail, Ellen Darcy , Erickson, Lori A

American Journal of Clinical Pathology | May 19, 2023 | Volume: 160 | Issue: 3 | Pages: 303-313

10.1093/ajcp/aqad054 Get It

Abstract Objectives There is a paucity of data on penile amyloidosis. We aimed to assess the frequency of different amyloid types in surgical specimens from the penis involved by amyloidosis and correlate relevant clinicopathologic parameters with proteomic findings. Methods Since 2008, our reference laboratory has performed liquid chromatography/tandem mass spectrometry (LC-MS/MS) for amyloid typing. The institutional pathology archive and reference laboratory database were queried to retrospectively identify all penile surgical pathology specimens with LC-MS/MS results between January 1, 2008, and November 23, 2022. Archived H&E-stained and Congo red–stained sections were re-reviewed. Results Twelve cases of penile amyloidosis were identified, which represented 0.35% (n = 3,456) of penile surgical specimens. AL-type amyloid was most frequent (n = 7), followed by keratin-type amyloid (n = 3) and ATTR (transthyretin)–type amyloid (n = 2). AL-type amyloid cases often showed diffuse dermal/lamina propria deposition, whereas all keratin-type amyloid cases were localized to the superficial dermis. Two cases with keratin-type amyloid had concomitant cutaneous findings (penile intraepithelial neoplasia and condyloma). Conclusions This series, the largest to date, demonstrates that penile amyloidosis has a heterogeneous proteomic landscape. To the best of our knowledge, this is the first study describing ATTR (transthyretin)–type penile amyloid.
Homologous recombination repair (HRR) mutation concordance between liquid biopsy (LB) and tumor tissue by NGS in a real-world prostate cancer (PC) database.
Jiménez, Rafael E. , Stoppler, Melissa C. , Chao, Calvin Y., Shen, John P , Wang, Liang , Khaki, Ali Raza , Mauer, Elizabeth , Chao, Calvin Y. , Kohli, Manish

Journal of Clinical Oncology | March 14, 2023 | Volume: 41 | Issue: 6_suppl | Pages: 260-260

10.1200/jco.2023.41.6_suppl.260 Get It

260 Background: NGS to identify HRR mutations (mut) is indicated in advanced prostate cancer (aPC); samples for testing may be tissue or plasma. In a large real-world (RW) database, we determined concordance between plasma ctDNA and primary tumor tissue (PT) and/or metastatic tissue (MT) for BRCA1, BRCA2, and ATM mut in PC patients (pts) who received both LB and tissue NGS any time during standard of care (SOC) management. The study objective was to assess the utility of LB to detect actionable mut in these HRR genes and demonstrate the utility of combined LB and tissue testing. Methods: We examined de-identified data from pts who had NGS using both Tempus xF (105 genes-LB) and Tempus xT (648 genes-tissue) during SOC for aPC. Analyses included 1) PT and LB and 2) MT and LB. The results from the pts’ earliest PT or MT and earliest LB were used for paired analyses. The prevalence of a pathogenic/likely pathogenic germline and/or somatic mut in BRCA1, BRCA2, or ATM was reported as N (%), 95% CI. The sensitivity of the LB to identify observed HRR mut in tissue was also reported as N (%), 95% CI. Concordance between pairs was evaluated by Cohen’s kappa statistic with 95% CI. Results: HRR results are show for 1074 PC pts who had NGS performed on PT and LB and 451 PC pts with NGS on both MT and LB. In the PT and LB analysis, HRR mut were found in 6.2% (95% CI: 4.9%-7.9%) of LB and 8.8% (95% CI: 7.2%-11%) of PT. The sensitivity of LB to detect HRR mut in the PT was 53% (95% CI: 43%-64%). Cohen’s kappa statistic was 0.59, 95% CI=0.50-0.68, between PT and LB. In the MT and LB analysis, HRR mut were found in 10% (95% CI 7.8%-14%) of LB and 10% (7.6%-13%) of MT. The sensitivity of LB to detect HRR mut in the MT was 70% (95% CI: 54%-82%). Cohen’s kappa statistic was 0.65, 95% CI=0.54-0.77, between MT and LB. Conclusions: In this large RW dataset, plasma ctDNA-based analysis of BRCA1, BRCA2, and ATM mut showed greater concordance between LB and MT than LB and PT, and may be used as an initial tool for HRR mut detection. When LB results are negative, further exploration with tissue-based testing may identify HRR mut to guide clinical decisions. [Table: see text]
Single patch super-resolution of histopathology whole slide images: a comparative study
Afshari, Mehdi, Yasir, Saba , Keeney, Gary L., Jiménez, Rafael E. , García, Joaquín J. , Tizhoosh, Hamid R , Tizhoosh, Hamid R.

Journal of Medical Imaging | January 31, 2023 | Volume: 10 | Issue: 01 | Pages: No page available

10.1117/1.jmi.10.1.017501 Get It

SETDB1 Modulates Degradation of Phosphorylated RB and Anticancer Efficacy of CDK4/6 Inhibitors
Huang, Zhenlin , Li, Xiang , Tang, Bo , Li, Hao , Zhang, Jianong , Sun, Rui , Ma, Jian , Pan, Yunqian , Yan, Binyuan , Zhou, Yingke , Ding, Donglin , Yan, Yuqian , Jiménez, Rafael E. , Orme, Jacob J. , Yang, Jinjian , Jia, Zhankui , Sun, Rui , Jimenez, Raphael E , Jin, Xin , Yang, Jinjian , Huang, Rui , Jia, Zhankui , Zhou, Yingke , Yan, Binyuan , Ding, Donglin , Jin, Xin , Huang, Haojie

Cancer Research | January 13, 2023 | Volume: 83 | Issue: 6 | Pages: 875-889

10.1158/0008-5472.can-22-0264 Get It

Abstract Retinoblastoma (RB) protein can exert tumor suppressor functions even when it becomes phosphorylated. It is thus essential to understand how phosphorylated RB (p-RB) expression and function are regulated. Here, we demonstrated that RING finger domain protein TRIM28 bound and promoted ubiquitination and degradation of CDK4/6-phosphorylated RB protein. SETDB1, a known TRIM28 binding partner, protected p-RB from degradation through the binding of methylated RB by its Tudor domain independent of its methyltransferase activity. SETDB1 was found to be frequently overexpressed due to gene amplification and positively correlated with p-RB in prostate cancer patient specimens. Inhibition of SETDB1 expression using a gene-specific antisense oligonucleotide (ASO) reduced tumor growth but accelerated RB protein degradation, limiting the therapeutic efficacy. However, coadministration of the CDK4/6 inhibitor palbociclib blocked ASO-induced RB degradation and resulted in a much greater cancer-inhibitory effect than each inhibitor alone both in vitro and in vivo. This study identified CDK4/6-dependent, TRIM28-mediated proteasomal degradation as a mechanism of RB inactivation and reveals SETDB1 as a key inhibitor of this process. Our findings suggest that combined targeting of SETDB1 and CDK4/6 represents a viable approach for the treatment of cancers with SETDB1 gene amplification or overexpression. Significance: The identification of a role for TRIM28 and SETDB1 in regulating CDK4/6-phosphorylated RB stability uncovers a combination strategy using CDK4/6 and SETDB1 inhibition to decrease RB degradation and inhibit cancer growth.
Molecular and Immunophenotypic Correlates of Metastatic Epithelioid Angiomyolipoma Include Alterations of TP53 , RB1 , and ATRX
McCarthy, Michael R., Nichols, Paige , Sharma, Vidit , Stanton, Melissa, Halling, Kevin C. , Lohse, Christine M. , Herrera-Hernandez, Loren , Thompson, R. Houston, Leibovich, Bradley C. , Jiménez, Rafael E. , Boorjian, Stephen A. , Cheville, John C. , Gupta, Sounak , Nichols, Paige E, Stanton, Melissa L, Reynolds, Jordan , Pitel, Beth A.

Archives of Pathology & Laboratory Medicine | October 29, 2022 | Volume: 147 | Issue: 7 | Pages: 817-825

10.5858/arpa.2022-0127-oa Get It

Context.— Epithelioid angiomyolipomas (eAMLs) are rare tumors of the kidney that occur in patients with tuberous sclerosis complex or in a sporadic setting; a subset of these tumors exhibit metastatic behavior. Objective.— To analyze molecular profiling data to identify pathogenic alterations in rare cases of metastatic eAML, and to identify immunohistochemistry (IHC)-based surrogate markers. Design.— Molecular profiling data from the American Association for Cancer Research GENIE registry was accessed for 23 patients with angiomyolipomas, and 9 of 16 patients with eAMLs in our institutional registry were evaluated with next-generation sequencing. IHC was performed to screen for alterations of P53, RB, and ATRX for all 16 institutional cases. Results.— Combined alterations of 5 tumor-suppressor genes (TP53, ATRX, RB1, APC, and NF1) were identified using next-generation sequencing in 7 of 8 (88%) patients with metastatic disease compared to a single patient with nonmetastatic disease (RB1 variant of uncertain significance; 1 of 24, 4%). No cases with abnormal IHC results were identified in 11 patients with nonmetastatic disease compared to 3 of 5 patients with metastatic disease. Conclusions.— Our results show that the majority of metastatic eAMLs have mutations of 5 tumor-suppressor genes (TP53, ATRX, RB1, APC, and NF1), while these are rare in patients with nonmetastatic disease. Furthermore, IHC for P53, RB, and ATRX may serve as a screen for a subset of these alterations in resource-limited settings. These findings, if validated in larger data sets, have the potential to predict metastatic behavior in eAMLs.
Granulomatosis with polyangiitis presenting as obstructive uropathy and vasculitic myopathy
Kimbrough, Bradly A. , Naddaf, Elie , Warrington, Kenneth J. , Jiménez, Rafael E. , Naddaf, Elie , Warrington, Kenneth J , Koster, Matthew J.

Rheumatology | September 2, 2022 | Volume: 62 | Issue: 4 | Pages: e136-e137

10.1093/rheumatology/keac506 Get It

“A monument to suffering and to patience” : The harrowing journey of Nabby Adams through breast cancer
Jiménez, Rafael E.

Journal of Medical Biography | April 29, 2022 | Volume: 31 | Issue: 2 | Pages: 133-142

10.1177/09677720221097792 Get It

In 1813, Abigail “Nabby” Adams, the daughter of the second president of the United States, John Adams (1797–1801), passed away from metastatic breast cancer. Her ordeal began in 1810, at age 44, when she discovered a lump in her right breast She consulted with Dr Benjamin Rush, one of the most prominent physicians of the time and a signer of the Declaration of Independence, which resulted in a recommendation for an immediate mastectomy. The surgery was performed at her parent's home in Quincy, Massachusetts, by Dr John Warren. The crude and painful nature of the surgical procedure was highly traumatic to Ms. Adams and her family. After a few months, she returned to her home in rural New York. Within a few months she began feeling generalized pain. When it was evident that her symptoms were the result of disseminated breast cancer, she returned to her parents’ house, where she died on August 15, a mere 22 months after her surgery. Ms. Adams’ suffering through the stark treatment was the result of a unique historical period, when the medical community had just recently dismissed Galen's paradigms, but still lacked a basic knowledge of the disease's nature or the ability to administer painless, safe surgical treatment.
Assessment of Risk of Hereditary Predisposition in Patients With Melanoma and/or Mesothelioma and Renal Neoplasia
Gupta, Sounak , Lohse, Christine M. , Shen, Wei , Knight, Shannon M. , Halling, Kevin C. , Herrera-Hernandez, Loren , Boorjian, Stephen A. , Thompson, R. Houston, Leibovich, Bradley C. , Jiménez, Rafael E. , Cheville, John C. , Shen, Wei , Erickson, Lori A. , Pitel, Beth A.

JAMA Network Open | November 12, 2021 | Volume: 4 | Issue: 11 | Pages: e2132615

10.1001/jamanetworkopen.2021.32615 Get It

Fumarate Hydratase ( FH ) c.1431_1433dupAAA (p.Lys477dup) variant is not associated with FH protein deficiency and increased 2SC in two separate patients with renal neoplasia
Gupta, Sounak , Shen, Wei , Jiménez, Rafael E. , Cheville, John C. , Shen, Wei

Human Mutation | August 2, 2021 | Volume: 42 | Issue: 10 | Pages: 1362-1364

10.1002/humu.24268 Get It

MAP3K7-IKK Inflammatory Signaling Modulates AR Protein Degradation and Prostate Cancer Progression
Huang, Zhenlin , Tang, Bo , Yang, Yinhui , Yang, Zhaogang , Shi, Lei , Bai, Yang , Yan, Binyuan , Karnes, R. Jeffrey , Jiménez, Rafael E. , Wang, Liguo , Wei, Qiang , Yang, Jinjian , Xu, Wanhai , Jia, Zhankui , Jimenez, Rafael, Wang, Liguo , Huang, Rui , Yan, Binyuan , Zhang, Jun , Huang, Haojie

Cancer Research | June 22, 2021 | Volume: 81 | Issue: 17 | Pages: 4471-4484

10.1158/0008-5472.can-20-4194 Get It

Abstract Androgen receptor (AR) is a major survival factor for prostate cancer. Inflammation is implicated in many cancer types, including prostate cancer. Activation of MAP3K7 (also termed TAK1) and downstream IκB kinase β (IKKβ) by proinflammatory cytokines such as TNFα stimulates NF-κB survival pathways. Paradoxically, MAP3K7 is often deleted in human prostate cancer. Here, we demonstrate that AR protein expression is lower in inflammatory tumor areas compared with non-inflammatory tissues in patients with prostate cancer. Map3k7 knockout increased AR protein levels and activity in the mouse prostate, and MAP3K7 and AR protein levels were inversely correlated in prostate cancer patient specimens. TNFα treatment increased AR protein ubiquitination and proteasomal degradation. Mechanistically, activation of IKKβ by TNFα induced phosphorylation and TRCP1/2 E3 ligase–mediated polyubiquitination and degradation of AR protein. TNFα suppressed prostate cancer proliferation, which could be rescued by blockade of AR degradation. These findings reveal a previously unrecognized tumor suppressive function of the inflammation-activated MAP3K7–IKKβ axis in degrading AR protein. Moreover, they suggest that aberrant elevation of AR protein could be a prognostic biomarker and therapeutic target for MAP3K7-deficient prostate cancer. Significance: This study identifies that MAP3K7–IKKβ signaling plays a tumor-suppressive role in prostate cancer by degrading AR, revealing potential prognostic and therapeutic strategies for MAP3K7-deficient tumors.