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  1. Article ; Online: Towards Data Driven RT Prescription: Integrating Genomics into RT Clinical Practice.

    Torres-Roca, Javier F / Grass, G Daniel / Scott, Jacob G / Eschrich, Steven A

    Seminars in radiation oncology

    2023  Volume 33, Issue 3, Page(s) 221–231

    Abstract: The genomic era has significantly changed the practice of clinical oncology. The use of genomic-based molecular diagnostics including prognostic genomic signatures and new-generation sequencing has become routine for clinical decisions regarding ... ...

    Abstract The genomic era has significantly changed the practice of clinical oncology. The use of genomic-based molecular diagnostics including prognostic genomic signatures and new-generation sequencing has become routine for clinical decisions regarding cytotoxic chemotherapy, targeted agents and immunotherapy. In contrast, clinical decisions regarding radiation therapy (RT) remain uninformed about the genomic heterogeneity of tumors. In this review, we discuss the clinical opportunity to utilize genomics to optimize RT dose. Although from the technical perspective, RT has been moving towards a data-driven approach, RT prescription dose is still based on a one-size-fits all approach, with most RT dose based on cancer diagnosis and stage. This approach is in direct conflict with the realization that tumors are biologically heterogeneous, and that cancer is not a single disease. Here, we discuss how genomics can be integrated into RT prescription dose, the clinical potential for this approach and how genomic-optimization of RT dose could lead to new understanding of the clinical benefit of RT.
    MeSH term(s) Humans ; Neoplasms/genetics ; Neoplasms/radiotherapy ; Neoplasms/pathology ; Medical Oncology ; Antineoplastic Agents ; Prognosis ; Genomics
    Chemical Substances Antineoplastic Agents
    Language English
    Publishing date 2023-06-16
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1146999-7
    ISSN 1532-9461 ; 1053-4296
    ISSN (online) 1532-9461
    ISSN 1053-4296
    DOI 10.1016/j.semradonc.2023.03.007
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Updates in the use of radiotherapy in the management of primary and locally-advanced penile cancer.

    Patel, Akshar / Naghavi, Arash O / Johnstone, Peter A / Spiess, Philippe E / Grass, G Daniel

    Asian journal of urology

    2022  Volume 9, Issue 4, Page(s) 389–406

    Abstract: Objective: Penile cancer is a rare malignancy in most developed countries, but may represent a significant oncologic challenge in certain African, Asian, and South American regions. Various treatment approaches have been described in penile cancer, ... ...

    Abstract Objective: Penile cancer is a rare malignancy in most developed countries, but may represent a significant oncologic challenge in certain African, Asian, and South American regions. Various treatment approaches have been described in penile cancer, including radiotherapy. This review aimed to provide a synopsis of radiotherapy use in penile cancer management and the associated toxicities. In addition, we aimed to discuss palliative radiation for metastases to the penis and provide a brief overview of how tumor biology may assist with treatment decision-making.
    Methods: Peer-reviewed manuscripts related to the treatment of penile cancer with radiotherapy were evaluated by a PubMed search (1960-2021) in order to assess its role in the definitive and adjuvant settings. Selected manuscripts were also evaluated for descriptions of radiation-related toxicity.
    Results: Though surgical resection of the primary is an excellent option for tumor control, select patients may be treated with organ-sparing radiotherapy by either external beam radiation or brachytherapy. Data from randomized controlled trials comparing radiotherapy and surgery are lacking, and thus management is frequently determined by institutional practice patterns and available expertise. Similarly, this lack of clinical trial data leads to divergence in opinion regarding lymph node management. This is further complicated in that many cited studies evaluating lymph node radiotherapy used non-modern radiotherapy delivery techniques. Groin toxicity from either surgery or radiotherapy remains a challenging problem and further risk assessment is needed to guide intensification with multi-modal therapy. Intrinsic differences in tumor biology, based on human papillomavirus infection, may help aid future prognostic and predictive models in patient risk stratification or treatment approach.
    Conclusion: Penile cancer is a rare disease with limited clinical trial data driving the majority of treatment decisions. As a result, the goal of management is to effectively treat the disease while balancing the importance of quality of life through integrated multidisciplinary discussions. More international collaborations and interrogations of penile cancer biology are needed to better understand this disease and improve patient outcomes.
    Language English
    Publishing date 2022-09-09
    Publishing country Singapore
    Document type Journal Article ; Review
    ZDB-ID 2831144-9
    ISSN 2214-3882
    ISSN 2214-3882
    DOI 10.1016/j.ajur.2022.05.010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: An Analysis of Nectin-4 (

    Grass, G Daniel / Chahoud, Jad / Lopez, Alex / Dhillon, Jasreman / Eschrich, Steven A / Johnstone, Peter A S / Spiess, Philippe E

    European urology open science

    2023  Volume 49, Page(s) 1–5

    Abstract: Penile squamous cell carcinoma (PSCC) remains a worldwide healthcare concern with poor outcomes and inadequate therapeutic options. Molecular characterization continues to describe the intricacies of PSCC biology, which vary by human papillomavirus (HPV) ...

    Abstract Penile squamous cell carcinoma (PSCC) remains a worldwide healthcare concern with poor outcomes and inadequate therapeutic options. Molecular characterization continues to describe the intricacies of PSCC biology, which vary by human papillomavirus (HPV) infection. Despite these advancements in our understanding, utilization of targeted therapies remains limited and underexplored. In this study, we evaluated the transcript and protein expression of Nectin-4 (PVRL4) in PSCC tumors and evaluated whether this is related to tumor features or clinical outcomes. Using two separate PSCC cohorts, we demonstrate that the majority of tumors have active transcription of Nectin-4. We then validated our findings using immunohistochemistry in a tissue microarray representing 57 patients with PSCC. We identified that Nectin-4 was expressed at higher levels in patients with high-risk HPV infection. No significant differences were identified in tumor characteristics or various clinical endpoints when comparing tumors with high and low Nectin-4 expression. This study demonstrates that Nectin-4 is expressed in PSCC and may represent a novel therapeutic target.
    Patient summary: In this study, we evaluated the expression of Nectin-4, a cell surface protein, in tumors from patients with nonmetastatic penile squamous cell carcinoma (PSCC). To our knowledge, this is the first study to describe elevated expression of Nectin-4 in PSCC, which may suggest its utility as a therapeutic target.
    Language English
    Publishing date 2023-01-10
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 3040546-4
    ISSN 2666-1683 ; 2058-4881
    ISSN (online) 2666-1683
    ISSN 2058-4881
    DOI 10.1016/j.euros.2022.12.008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Multi-institutional experience of MR-guided stereotactic body radiation therapy for adrenal gland metastases.

    Mills, Matthew / Kotecha, Rupesh / Herrera, Roberto / Kutuk, Tugce / Fahey, Matthew / Wuthrick, Evan / Grass, G Daniel / Hoffe, Sarah / Frakes, Jessica / Chuong, Michael D / Rosenberg, Stephen A

    Clinical and translational radiation oncology

    2024  Volume 45, Page(s) 100719

    Abstract: Purpose: While dose escalation is associated with improved local control (LC) for adrenal gland metastases (AGMs), the proximity of gastrointestinal (GI) organs-at-risk (OARs) limits the dose that can be safely prescribed via CT-based stereotactic body ... ...

    Abstract Purpose: While dose escalation is associated with improved local control (LC) for adrenal gland metastases (AGMs), the proximity of gastrointestinal (GI) organs-at-risk (OARs) limits the dose that can be safely prescribed via CT-based stereotactic body radiation therapy (SBRT). The advantages of magnetic resonance-guided SBRT (MRgSBRT), including tumor tracking and online plan adaptation, facilitate safe dose escalation.
    Methods: This is a multi-institutional review of 57 consecutive patients who received MRgSBRT on a 0.35-T MR linac to 61 AGMs from 2019 to 2021. The Kaplan-Meier method was used to estimate overall survival (OS), progression-free survival (PFS), and LC, and the Cox proportional hazards model was utilized for univariate analysis (UVA).
    Results: Median follow up from MRgSBRT was 16.4 months (range [R]: 1.1-39 months). Median age was 67 years (R: 28-84 years). Primary histologies included non-small cell lung cancer (N = 38), renal cell carcinoma (N = 6), and melanoma (N = 5), amongst others. The median maximum diameter was 2.7 cm (R: 0.6-7.6 cm), and most AGMs were left-sided (N = 32). The median dose was 50 Gy (R: 30-60 Gy) in 5-10 fractions with a median BED
    Conclusions: We demonstrate that MRgSBRT achieves favorable early LC and no grade 3 + toxicity despite prescribing a median BED
    Language English
    Publishing date 2024-01-05
    Publishing country Ireland
    Document type Journal Article
    ISSN 2405-6308
    ISSN (online) 2405-6308
    DOI 10.1016/j.ctro.2023.100719
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Response to: Noncancer Cells in Tumor Samples May Bias the Predictive Genomically Adjusted Radiation Dose.

    Grass, G Daniel / Scott, Jacob G / Sedor, Geoffrey / Kattan, Michael W / Torres-Roca, Javier F

    Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer

    2021  Volume 16, Issue 6, Page(s) e48–e49

    MeSH term(s) Dose-Response Relationship, Radiation ; Humans ; Lung Neoplasms
    Language English
    Publishing date 2021-05-25
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 2432037-7
    ISSN 1556-1380 ; 1556-0864
    ISSN (online) 1556-1380
    ISSN 1556-0864
    DOI 10.1016/j.jtho.2021.03.020
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Changing Radiotherapy Paradigms in Penile Cancer.

    Johnstone, Peter A S / Spiess, Philippe E / Sedor, Geoff / Grass, G Daniel / Yamoah, Kosj / Scott, Jacob G / Torres-Roca, Javier F

    European urology open science

    2022  Volume 36, Page(s) 47–48

    Abstract: Radiation therapy (RT) has not been prominent in the treatment of penile cancer because of poorly reproducible results when used in the adjuvant setting. A genomic signature has recently been described that assays radiosensitivity of tumors and informs ... ...

    Abstract Radiation therapy (RT) has not been prominent in the treatment of penile cancer because of poorly reproducible results when used in the adjuvant setting. A genomic signature has recently been described that assays radiosensitivity of tumors and informs radiotherapy doses in these cases. Clinical validation in more than 1600 patients demonstrated associations with both overall survival and time to first recurrence. In addition, the signature predicted and quantified the therapeutic benefit of RT for each individual patient. Since penile cancer patients were not part of this analysis, we applied the model to patients with primary and nodal penile cancer tissue and clinical outcomes.
    Language English
    Publishing date 2022-01-04
    Publishing country Netherlands
    Document type Journal Article
    ISSN 2666-1683
    ISSN (online) 2666-1683
    DOI 10.1016/j.euros.2021.12.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: How, with whom and when: an overview of CD147-mediated regulatory networks influencing matrix metalloproteinase activity.

    Grass, G Daniel / Toole, Bryan P

    Bioscience reports

    2015  Volume 36, Issue 1, Page(s) e00283

    Abstract: Matrix metalloproteinases (MMPs) comprise a family of 23 zinc-dependent enzymes involved in various pathologic and physiologic processes. In cancer, MMPs contribute to processes from tumour initiation to establishment of distant metastases. Complex ... ...

    Abstract Matrix metalloproteinases (MMPs) comprise a family of 23 zinc-dependent enzymes involved in various pathologic and physiologic processes. In cancer, MMPs contribute to processes from tumour initiation to establishment of distant metastases. Complex signalling and protein transport networks regulate MMP synthesis, cell surface presentation and release. Earlier attempts to disrupt MMP activity in patients have proven to be intolerable and with underwhelming clinical efficacy; thus targeting ancillary proteins that regulate MMP activity may be a useful therapeutic approach. Extracellular matrix metalloproteinase inducer (EMMPRIN) was originally characterized as a factor present on lung cancer cells, which stimulated collagenase (MMP-1) production in fibroblasts. Subsequent studies demonstrated that EMMPRIN was identical with several other protein factors, including basigin (Bsg), all of which are now commonly termed CD147. CD147 modulates the synthesis and activity of soluble and membrane-bound [membrane-type MMPs (MT-MMPs)] in various contexts via homophilic/heterophilic cell interactions, vesicular shedding or cell-autonomous processes. CD147 also participates in inflammation, nutrient and drug transporter activity, microbial pathology and developmental processes. Despite the hundreds of manuscripts demonstrating CD147-mediated MMP regulation, the molecular underpinnings governing this process have not been fully elucidated. The present review summarizes our present knowledge of the complex regulatory systems influencing CD147 biology and provides a framework to understand how CD147 may influence MMP activity.
    MeSH term(s) Animals ; Basigin/genetics ; Basigin/metabolism ; Cell Communication/physiology ; Collagenases/genetics ; Collagenases/metabolism ; Humans
    Chemical Substances BSG protein, human ; Basigin (136894-56-9) ; Collagenases (EC 3.4.24.-)
    Language English
    Publishing date 2015-11-24
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 764946-0
    ISSN 1573-4935 ; 0144-8463
    ISSN (online) 1573-4935
    ISSN 0144-8463
    DOI 10.1042/BSR20150256
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Comparative Effectiveness of Neoadjuvant Pembrolizumab Versus Cisplatin-based Chemotherapy or Upfront Radical Cystectomy in Patients with Muscle-invasive Urothelial Bladder Cancer.

    Li, Roger / Nocera, Luigi / Rose, Kyle M / Raggi, Daniele / Naidu, Shreyas / Mercinelli, Chiara / Cigliola, Antonio / Tateo, Valentina / Patanè, Damiano / Grass, G Daniel / Gilbert, Scott M / Sexton, Wade J / Bandini, Marco / Moschini, Marco / Briganti, Alberto / Montorsi, Francesco / Spiess, Philippe E / Necchi, Andrea

    European urology oncology

    2024  

    Abstract: Background: Recent progresses in the use of immune checkpoint inhibitor (ICI) have challenged the therapeutic standards in patients with muscle-invasive urothelial bladder carcinoma (MIBC).: Objective: To compare neoadjuvant pembrolizumab followed by ...

    Abstract Background: Recent progresses in the use of immune checkpoint inhibitor (ICI) have challenged the therapeutic standards in patients with muscle-invasive urothelial bladder carcinoma (MIBC).
    Objective: To compare neoadjuvant pembrolizumab followed by radical cystectomy (RC) versus neoadjuvant chemotherapy (NAC) and RC or upfront RC, according to cisplatin eligibility.
    Design, setting, and participants: We conducted two separate analyses for cisplatin-eligible and cisplatin-ineligible cT2-4N0M0 MIBC patients. We used a propensity score adjustment that relied on inverse probability of treatment-weighting (IPTW).
    Intervention: Pembrolizumab within the PURE-01 trial, and NAC and RC or upfront RC from a high-volume tertiary care referral center.
    Outcome measurements and statistical analysis: The primary endpoint in both analyses was event-free survival (EFS), defined as freedom from recurrence, and/or death from any cause indexed from the date of treatment initiation or RC. The secondary endpoints included EFS in propensity score-matched patients, pathologic response rate, and recurrence-free survival (RFS) after RC.
    Results and limitations: A total of 458 patients who underwent RC, with or without NAC, at Moffitt Cancer Center between October 2005 and October 2020, and 146 patients enrolled in PURE-01 were analyzed. In cisplatin-ineligible patients, EFS was superior in those receiving pembrolizumab (p < 0.001). The estimated 3-yr EFS was 77.8% (95% confidence interval [CI]: 63.5-95.2) for pembrolizumab and RC, and 36.1% (95% CI: 28.6-45.5) for upfront RC. EFS remained superior in those receiving neoadjuvant ICI (NICI) following IPTW (p < 0.001). In cisplatin-eligible patients, EFS was superior in those receiving pembrolizumab and RC (p < 0.001). The estimated 3-yr EFS was 86.9% (95% CI: 80.9-93.3) for pembrolizumab and 63.5% (95% CI: 56.5-71.4) for NAC. EFS remained superior in those receiving NICI following IPTW (p < 0.001). Pathologic responses and RFS in pembrolizumab-treated patients were also superior to those in NAC-treated patients. Results are limited by the retrospective nature of the study.
    Conclusions: In the first ever reported comprehensive comparison of outcomes between neoadjuvant ICI and NAC, followed by RC, or upfront RC, we report increased responses and improved oncologic outcomes with neoadjuvant ICI in patients with MIBC.
    Patient summary: We compared the results obtained from the use of pembrolizumab and radical cystectomy with standard-of-care treatments in patients with bladder carcinoma infiltrating the muscle layer. We reported increased response and survival rates possibilities with the use of immunotherapy, anticipating the possibility to set new therapeutic standards in these patients, pending the results of ongoing randomized studies.
    Language English
    Publishing date 2024-01-05
    Publishing country Netherlands
    Document type Journal Article
    ISSN 2588-9311
    ISSN (online) 2588-9311
    DOI 10.1016/j.euo.2023.12.008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Survival Benefits of Adjuvant Chemotherapy for Positive Soft Tissue Surgical Margins Following Radical Cystectomy in Bladder Cancer with Extravesical Extension.

    Murthy, Prithvi B / Naidu, Shreyas / Davaro, Facundo / Spiess, Philippe E / Zemp, Logan / Poch, Michael / Jain, Rohit / Vosoughi, Aram / Grass, G Daniel / Yu, Alice / Sexton, Wade J / Gilbert, Scott M / Li, Roger

    Current oncology (Toronto, Ont.)

    2023  Volume 30, Issue 3, Page(s) 3223–3231

    Abstract: Introduction and objective: Muscle invasive bladder cancer with extravesical extension is an aggressive disease entity that requires multimodal therapy. The benefits of adjuvant chemotherapy (AC) in patients with a positive soft-tissue surgical margin ( ... ...

    Abstract Introduction and objective: Muscle invasive bladder cancer with extravesical extension is an aggressive disease entity that requires multimodal therapy. The benefits of adjuvant chemotherapy (AC) in patients with a positive soft-tissue surgical margin (STSM), however, are relatively unknown due to exclusion of this population in randomized controlled trials of AC. We sought to define survival benefits in this patient population through our institutional bladder cancer database.
    Methods: Retrospective review of all patients undergoing radical cystectomy for urothelial carcinoma of the bladder from 2004-2020 with ≥pT3b disease irrespective of neoadjuvant chemotherapy (NAC) use was conducted. Progression-free survival (PFS) and overall survival (OS) estimates were obtained using the Kaplan-Meier method with log-rank test, and the Cox-proportional hazards model was used to identify predictors of improved PFS and OS. AC was defined by any chemotherapy use within 90 days of cystectomy, regardless of STSM status.
    Results: 476 patients with pT3b disease or worse were identified. Median follow-up was 12.3 months. An amount of 21% of patients were treated with AC. An amount of 24% of patients had positive STSM. Median OS for patients with positive STSM was 8.4 months [95% CI 7-11.5] and 18.3 months [95% CI 15.6-20.8] (
    Conclusions: Administration of adjuvant chemotherapy is of particular benefit in patients with positive STSM following radical cystectomy for gross extravesical disease. Positive STSM may be a representative of "early metastatic" or micrometastatic disease.
    MeSH term(s) Humans ; Urinary Bladder Neoplasms/drug therapy ; Urinary Bladder Neoplasms/surgery ; Carcinoma, Transitional Cell/drug therapy ; Urinary Bladder/pathology ; Cystectomy/adverse effects ; Cystectomy/methods ; Margins of Excision ; Treatment Outcome ; Chemotherapy, Adjuvant
    Language English
    Publishing date 2023-03-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1236972-x
    ISSN 1718-7729 ; 1198-0052
    ISSN (online) 1718-7729
    ISSN 1198-0052
    DOI 10.3390/curroncol30030245
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: DRPPM-PATH-SURVEIOR: Plug-and-Play Survival Analysis of Pathway-level Signatures and Immune Components.

    Obermayer, Alyssa / Chang, Darwin / Nobles, Gabrielle / Teng, Mingxiang / Tan, Aik-Choon / Wang, Xuefeng / Eschrich, Steven / Rodriguez, Paulo / Grass, G Daniel / Meshinchi, Soheil / Tarhini, Ahmad / Chen, Dung-Tsa / Shaw, Timothy

    Research square

    2023  

    Abstract: Pathway-level survival analysis offers the opportunity to examine molecular pathways and immune signatures that influence patient outcomes. However, available survival analysis algorithms are limited in pathway-level function and lack a streamlined ... ...

    Abstract Pathway-level survival analysis offers the opportunity to examine molecular pathways and immune signatures that influence patient outcomes. However, available survival analysis algorithms are limited in pathway-level function and lack a streamlined analytical process. Here we present a comprehensive pathway-level survival analysis suite, DRPPM-PATH-SURVEIOR, which includes a Shiny user interface with extensive features for systematic exploration of pathways and covariates in a Cox proportional-hazard model. Moreover, our framework offers an integrative strategy for performing Hazard Ratio ranked Gene Set Enrichment Analysis (GSEA) and pathway clustering. As an example, we applied our tool in a combined cohort of melanoma patients treated with checkpoint inhibition (ICI) and identified several immune populations and biomarkers predictive of ICI efficacy. We also analyzed gene expression data of pediatric acute myeloid leukemia (AML) and performed an inverse association of drug targets with the patient's clinical endpoint. Our analysis derived several drug targets in high-risk KMT2A-fusion-positive patients, which were then validated in AML cell lines in the Genomics of Drug Sensitivity database. Altogether, the tool offers a comprehensive suite for pathway-level survival analysis and a user interface for exploring drug targets, molecular features, and immune populations at different resolutions.
    Language English
    Publishing date 2023-03-14
    Publishing country United States
    Document type Preprint
    DOI 10.21203/rs.3.rs-2688545/v1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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