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Co-Occurrence of the mcr-1.1 and mcr-3.7 Genes in a Multidrug-Resistan | IDR – Dove Medical Press

Chongtao Du,1,* Yuyang Feng,1,* Guizhen Wang,2 Zhiyuan Zhang,1 Huimin Hu,1 Yu Yu,1 Jiayang Liu,1 Lihao Qiu,1 Hongtao Liu,1 Zhimin Guo,3 Jing Huang,3 Jiazhang Qiu1

1Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun 130062, Peoples Republic of China; 2College of Food Engineering, Jilin Engineering Normal University, Changchun 130052, Peoples Republic of China; 3Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun 130021, Peoples Republic of China

*These authors contributed equally to this work

Correspondence: Jiazhang QiuCollege of Veterinary Medicine, Jilin University, No. 5333 Xian Road, Changchun 130062, Peoples Republic of ChinaEmail qiujz@jlu.edu.cnJing HuangDepartment of Clinical Laboratory, The First Hospital of Jilin University, Changchun 130021, Peoples Republic of ChinaEmail huangj@jlu.edu.cn

Objective: A colistin-resistant Escherichia coli strain isolated from dog feces was characterized in this study.Methods and Results: A multiplex PCR assay was used to detect the presence of colistin-resistant mcr genes; it was found that E. coli QDFD216 co-harbored the mcr-1 and mcr-3 genes. Whole-genome sequencing and further bioinformatics analysis revealed that E. coli QDFD216 belonged to serotype O176:H11, fimH1311 type and ST132. The resistance genes blaCTX-M-14, mdfA, dfrA3, acrA, acrB, tolc, and sul3 were present in the chromosome. The mcr-1.1 and mcr-3.7 genes were located in two plasmids of different incompatibility groups. mcr-1.1 was carried by a IncX4-type plasmid within an typical IS 26-parA-mcr-1.1-pap2 cassette, while mcr-3.7 was encoded by an IncP1-type plasmid with a genetic structure of TnAs2-mcr-3.7-dgkA-IS 26. No additional antibiotic resistance genes were carried by either plasmid.Conclusion: This is the first report of an E. coli isolate co-harboring a mcr-1.1-carrying IncX4 plasmid and a mcr-3.7-carrying IncP1 plasmid. The evolution and mechanism of mcr gene co-existence need further study to assess its impact on public health.

Keywords: colistin resistance, whole-genome sequencing, mcr genes, mcr-1, mcr-3

This work is published and licensed by Dove Medical Press Limited. The full terms of this license are available at https://www.dovepress.com/terms.php and incorporate the Creative Commons Attribution - Non Commercial (unported, v3.0) License.By accessing the work you hereby accept the Terms. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed. For permission for commercial use of this work, please see paragraphs 4.2 and 5 of our Terms.

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FDA officials, experts discuss impact of COVID-19 on cell and gene therapies – Regulatory Focus

While the US Food and Drug Administration (FDA) is still receiving investigational new drug applications (INDs) for cell and gene therapies, officials are concerned about the impact of the COVID-19 pandemic on clinical trials.Its clear that COVID-19 has adversely affected all aspects of development of cell and gene therapies, said Peter Marks, director of FDAs Center for Biologics Evaluation and Research (CBER), said at the Alliance for Regenerative Medicines Meeting on the Mesa. For some of the studies that are ongoing there are some real challenges to overcome in terms of endpoints that may have been missed.The pandemic also has disrupted global harmonization efforts around gene therapies, Marks said.We were on the cusp, in fact, working with global regulators trying to get towards more harmonization of gene therapy programs in different countries, he said. Were trying to keep it moving but its a challenge to do.Marks noted that before COVID-19 he spent about 75% of his time on cell and gene therapies, but the pandemic has forced him to shift priorities. Some things have less policy demands at this point in time. At this point in time its very much reversed and its probably 80% of my time on COVID-related activities.Marks also noted that CBERs Office of Tissues and Advanced Therapies (OTAT) has been struggling to keep up with its workload even before the pandemic. With the influx of applications for cell and gene therapies over the last five years, Marks said the office, Should have doubled in size and its only modestly larger, 15-20% larger in size.Marks said he is not satisfied with the level of dialogue the agency has been able to have with gene therapy developers. Especially early on, we should be able to have this dialogue that really facilitates setting things up well so that our knowledge of the entire fieldwe help leverage that for every sponsor.Weve been so strapped in terms of personnel that its hard to do that, Marks said, noting that COVID-19 has exacerbated things even further. Because the number of gene therapy applications hasnt fallen off dramatically, some of the trials may not be moving as quickly, but the applications keep coming in. Marks said that OTAT has also had to shift priorities during the pandemic and that he hopes the next user fee cycle will bring in the resources necessary to staff up further.Speaking on a separate panel with members of industry, OTAT Director Wilson Bryan echoed Marks sentiment.We were stretched thin before the pandemic, and with the flood of work that came in, it really had an impact, he said. Sometimes folks dont like to admit this, but we all know weve had delayed meetings, weve had to delay review of some applications because of giving priority to the pandemic.However, Bryan said the office is getting its balance and is working to catch up on some of its delayed activities.Bryan expressed some worry about the financial well-being of some of the smaller companies his office works with. Were hearing a lot about their struggles to stay afloat and continue and finish off their development programs and whether or not those development programs are going to be sufficient to meet regulatory standards, he said.One of the challenges, said Timothy Schroeder, CEO of CTI Clinical Trial & Consulting, will be dealing with gaps in data from clinical trials. The question is going to be how do sponsors, how do regulatory authorities and how do companies such as ourselves fill those gaps?On the regulator side, Bryan said his office is working with companies on an individual basis to sort out those issues, which differ from one indication to the next.Bryan added that one positive to come of the pandemic is greater interest in remote outcome assessments in clinical trials. If we have an energy now to develop outcome measures and validate outcome measures that allow us to reliably capture information from patients in remote locations, that will ultimately facilitate development, he said.The pandemic also has significantly disrupted FDAs ability to conduct surveillance and preapproval inspections. While the agency has resumed some domestic inspections and mission-critical foreign inspections, it also is leveraging other sources of information, including inspection reports from other regulators, and requesting documents from applicants and facilities in lieu of on-site inspections where possible. (RELATED: FDA issues pandemic inspections FAQ guidance, Regulatory Focus 19 August 2020).Were considering virtual inspections, particularly for companies where the site has a track record, but if its a site that is brand new with no track record or if its a site with that has a bad track record, were hesitant to do that, Bryan said.Bryan also raised the prospect of FDA inspectors tagging along remotely for an inspection being conducted by other regulators. Is it possible that we could have an inspection by European inspectors and have US regulators going along for a virtual inspection at the same time? We think about those things, I dont know that weve done them yet, Bryan said, adding that he is not sure whether FDA inspectors would be comfortable with the information they would get.Curran Simpson, chief operations and technology officer at REGENXBIO, said he sees promise in virtual audits and believes the level of documentation a site provides can be indicative of its compliance.How often have I walked into a manufacturing facility thats well-run but has terrible documentation? Almost never. I think virtual audits, if you do a risk-based approach and the audit partner has the ability to send documentation in an efficient way and you have experienced people doing this, I think youre going to get the same flavor of an audit very quickly from the level of the documentation, he said.Of course, youll want to accompany that to the extent possible with imaging of the facility, Curran said, To see if those practices are being followed, the overall cleanliness of the facility and the management of material movement If you dont get a good impression from the documentation that youre working through, its probably a bigger issue that you want to escalate.Amy DuRoss, co-founder and CEO of Vineti, an enterprise software company specializing in advanced therapies, expressed some doubts about the current potential for fully remote audits.Certainly our piece of the chain because were enterprise software is readily auditable remotely, but I would say that the overall system and in manufacturing, Im not sure weve evolved as a species yet to adapt our remote techniques to get a full picture I dont think were there yet, she said.

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Identification of Novel Therapeutic Molecular Targets in Inflammatory | CEG – Dove Medical Press

Sachin Mohan,1 3 Shaffer Mok,4 Thomas Judge5

1Department of Gastroenterology and Hepatology, University of Minnesota School of Medicine, St Paul, MN, USA; 2Regions Hospital, Department of Gastroenterology and Hepatology, St Paul, MN, USA; 3Health Partners Digestive Care Center, St Paul, MN, 55130, USA; 4Division of Gastroenterology and Hepatology, University Hospital Digestive Health Institute, Westlake, OH 44145, USA; 5Division of Gastroenterology and Liver Diseases, Cooper University Hospital, Mount Laurel, NJ 08054, USA

Correspondence: Sachin MohanRegions Hospital, Department of Gastroenterology and Hepatology, 435 Phalen Blvd, St Paul, MN 55130, USATel +1 651-254-8680Fax +1 651-254-8656Email sachinmohan01@gmail.com

Purpose: Utilization of genetic databases to identify genes involved in ulcerative colitis (UC), Crohns disease (CD), and their extra-intestinal manifestations.Methods: Protein coding genes involved in ulcerative colitis (3783 genes), Crohns disease (3980 genes), uveitis (1043 genes), arthritis (5583 genes), primary sclerosing cholangitis (PSC) (1313 genes), and pyoderma gangrenosum (119 genes) were categorized using four genetic databases. These include Genecards: The Human Gene Database (www.genecards.org), DisGeNET (https://www.disgenet.org/), The Comparative Toxicogenomics Database (http://ctdbase.org/) and the Universal Protein Resource (https://www.uniprot.org/). NDex, Network Data Exchange (http://www.ndexbio.org/), was then utilized for mapping a unique signal pathway from the identified shared genes involved in the above disease processes.Results: We have detected a unique array of 20 genes with the highest probability of overlay in UC, CD, uveitis, arthritis, pyoderma gangrenosum, and PSC. Figure 1 represents the interactome of these 20 protein coding genes. Of note, unique immune modulators in different disease processes are also noted. Interleukin-25 (IL-25) and monensin-resistant homolog 2 (MON-2) are only noted in UC, CD, pyoderma gangrenosum, and arthritis. Arachidonate 5-lipoxygenase (ALOX5) is involved in UC, CD, and arthritis. SLCO1B3 is exclusively involved with pyoderma gangrenosum, UC, and CD. As expected, TNF involvement is noted in CD, UC, PSC, and arthritis. Table 1 depicts the detailed result.Conclusion: Our work has identified a distinctive set of genes involved in IBD and its associated extra-intestinal disease processes. These genes play crucial roles in mechanisms of immune response, inflammation, and apoptosis and further our understanding of this complex disease process. We postulate that these genes play a critical role at intersecting pathways involved in inflammatory bowel disease, and these novel molecules, their upstream and downstream effectors, are potential targets for future therapeutic agents.

Keywords: inflammatory bowel diseases, IBD, ulcerative colitis, UC, Crohns disease, CD, arthritis, primary sclerosing cholangitis, PSC, uveitis, pyoderma gangrenosum

This work is published and licensed by Dove Medical Press Limited. The full terms of this license are available at https://www.dovepress.com/terms.php and incorporate the Creative Commons Attribution - Non Commercial (unported, v3.0) License.By accessing the work you hereby accept the Terms. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed. For permission for commercial use of this work, please see paragraphs 4.2 and 5 of our Terms.

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Detailed analysis of the competitive landscape in the Global Cell Therapy Manufacturing Market by 2030 – Eurowire

The approval of KYMRIAH, YESCARTA, Alofisel and Zyntelgo has increased the interest of pharma stakeholders in cell therapies; further, owing to the technical challenges in this field, outsourcing manufacturing operations has become a necessity

Roots Analysis has announced the addition of Cell Therapy Manufacturing Market (3rd Edition), 2019 2030 report to its list of offerings.

Owing to various reasons, the demand for cell therapies is anticipated to increase over the coming years. Therefore, both therapy developers and contract service providers may need to strengthen their capabilities and expand available capacity. In this context, automation is expected to be a key enabler within the cell therapy manufacturing and contract services industry.

To order this 500+ page report, which features 160+ figures and 250+ tables, please visit this link

More than 160 organizations claim to be engaged in cell therapy manufacturingThe market landscape is dominated by industry players, representing more than 60% of the total number of stakeholders. Amongst these, over 55 are large or mid-sized firms (having more than 50 employees).

100+ players focused on T-cell and stem cell therapiesMost of these players are focused on manufacturing T-cell therapies, including CART, TCR or TILs. It is worth highlighting that more than 35 organizations claim to have necessary capabilities for the manufacturing of both types of therapies.

Presently, 70+ companies have commercial scale capacityAs majority of the cell therapy products are in clinical trials, the demand is high at this scale. However, it is worth noting that several players (~50%) have already developed commercial scale capacity for cell therapies.

Europe is currently considered a current hub for cell therapy productionMore than 220 manufacturing facilities have been established by various players, worldwide; of these, 35% are in Europe, followed by those based in North America. Other emerging regions include Australia, China, Japan, Singapore, South Korea and Israel.

50+ facility expansions reported between 2015-2019More than 85% of the expansions are related to setting up of new facilities across different regions. Maximum expansion activity was observed in the US and in certain countries within the Asia Pacific regions.

20+ companies offer automated solutions to cell therapy developersPlayers that claim to offer consultancy services related to automation include (in alphabetical order) Berkeley Lights, Cesca Therapeutics, Ferrologix, FluDesign Sonics, GE Healthcare and Terumo BCT. Further, we identified players, namely (in alphabetical order) Fraunhofer Institute for Manufacturing Engineering and Automation IPA, Invetech, KMC Systems, Mayo Clinic Center for Regenerative Medicine and RoosterBio, that offer consultancy solutions related to automation.

Partnership activity has grown at an annualized rate of 16%, between 2014 and 2018More than 200 agreements have been inked in the last 5 years; majority of these were focused on the supply of cell-based therapy products for clinical trials. Other popular types of collaboration models include manufacturing process development agreements (16%), services agreements (12%) and acquisitions (10%).

By 2030, developed geographies will capture over 60% of the market shareAsia Pacific is anticipated to capture the major share (~36%) of the market by 2030. It is also important to highlight that financial resources, technical expertise and established infrastructure is likely to drive cell therapy manufacturing market in Europe, which is estimated to grow at a CAGR of ~26%.

To request a sample copy / brochure of this report, please visit this link

The USD 10+ billion (by 2030) financial opportunity within the cell therapy manufacturing market has been analyzed across the following segments:

The report features inputs from eminent industry stakeholders, according to whom the manufacturing of cell therapies is largely being outsourced due to exorbitant costs associated with the setting-up of in-house expertise. The report includes detailed transcripts of discussions held with the following experts:

The research covers profiles of key players (industry and non-industry) that offer manufacturing services for cell-based therapies, featuring a company overview, information on manufacturing facilities, and recent collaborations.

For additional details, please visithttps://www.rootsanalysis.com/reports/view_document/cell-therapy-manufacturing/285.html or email [emailprotected]

You may also be interested in the following titles:

Contact:Gaurav Chaudhary+1 (415) 800 3415+44 (122) 391 1091[emailprotected]

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IBCN 2020: IBCN 2020: Molecular Correlates of Cisplatin-Based Chemotherapy Response In Muscle-Invasive Blad… – UroToday

(UroToday.com) While cisplatin-based chemotherapy is a mainstay for neoadjuvant and adjuvant treatment of patients with muscle-invasive bladder cancer (MIBC), and none of the reported biomarkers for predicting response have been implemented in the clinic thus far.

Dr. Ann Taber presented data from researchers at the Aarhus University Hospital, Denmark, where they performed comprehensive genomic, transcriptomic, epigenomic, and proteomic analysis of 300 MIBC patients treated with cisplatin-based chemotherapy to identify molecular changes associated with treatment response. Based on mutational signatures, they identified two patient groups: those characterized by mutations in a tri-nucleotide signature 5 context (SBS5) that are related to ERCC2 mutations, and those related to APOBEC mutations.

Expression data identified the basal/squamous gene expression subtype to be associated with poor cisplatin-based treatment response. Immune cell infiltration and high PD-1 protein expression was also significantly associated with treatment response; they identified a unique subset that corresponds to an immune desert, which was associated with poor treatment response (Figure 1).

Figure 1: Association of immune cell infiltration and cisplatin-based treatment response.

The authors then assigned patients to high and low genomic instability groups based on SBS5 mutations, indels, allelic imbalance and BRCA2 mutation status. Patients with high genomic instability had a response rate of 71% versus 49% for patients with low genomic instability (p = 0.007). Through further integration, they identified a group of patients with a very high response rate (80%) characterized by high genomic instability and non-basal/squamous gene expression subtype and a group of patients with a very low response rate (25%) characterized by low genomic instability and basal/squamous gene expression subtype (p<0.001, Figure 2).

Figure 2: Patient subclassification based on genomic instability and basal/squamous gene expression subtype.

The results highlight several molecular correlates of chemotherapy response. These findings are now the basis of a new clinical trial for the treatment of metastatic bladder cancer following radical cystectomy.1

Presented by: Ann Taber, Ph.D., Department of Molecular Medicine (MOMA), Aarhus University Hospital, Denmark.

Written by:Anirban P. Mitra, MD, Ph.D., Urologic Oncology Fellow, The University of Texas MD Anderson Cancer Center, Houston, TX, USA, Twitter: @APMitra, with Ashish M. Kamat, MD, MBBS, President of IBCN and IBCG, Endowed Professor, The University of Texas MD Anderson Cancer Center, Houston, TX, USA, Twitter:@UroDocAsh,at the International Bladder Cancer Network (IBCN) Annual Meeting, #IBCN2020, October 17, 2020.

References:1. Treatment Of Metastatic Bladder Cancer at the Time Of Biochemical reLApse Following Radical Cystectomy (TOMBOLA). ClinicalTrials.gov identifier NCT04138628.

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IBCN 2020: Improving Immune Checkpoint Inhibitor Therapy In Cancer – UroToday

(UroToday.com)Application of immune checkpoint inhibitor (ICI) therapy has seen significant progress in the last few years. Agents targeting programmed cell death protein 1 (PD-1) and its ligand PD-L1 have shown activity in locally advanced and metastatic urothelial carcinoma in the first- and second-line setting.1,2 However, a significant proportion of patients still perform poorly after receiving these therapies as their disease progresses rapidly.

In his keynote presentation at the 2020International Bladder Cancer Network (IBCN) Annual Meeting, Dr. Dan Theodorescu challenged the audience to seek alternative approaches to tackle this problem. He suggested that this may be addressed by either discovery of new therapies, or using novel modalities to enhance the effect of current ICI therapies. His research group has, more recently, focused on the latter approach.

While the idea of combination therapy has been successfully applied for chemotherapeutic regimens, an existing problem is that agnostic drug combinations could result in the need for far too many dual-drug clinical trials that would just not be feasible in the current environment. He, therefore, pointed out that an urgent need, therefore, is to rationally choose drugs that would be potentially optimal combinations with immune checkpoint inhibitors. The underlying goal of his groups current investigations is to identify molecular pathways that allow cancer growth while on ICI, and identify drugs that can target such pathways to enhance ICI response (Figure 1). His group has employed functional genomics to identify such lethal combinations.

Figure 1: Using functional genomics to identify rational combinations with ICI.

He elaborated on the technique for the construction of such functional genomic druggable libraries, wherein gene targets of drugs used in clinical trials for bladder cancer were identified, and five shRNAs per gene were constructed as part of a lentiviral library that were used to infect murine bladder cancer cells. The best performing shRNAs were selected as models for inhibiting the respective pathways and used to test in combination with ICI therapy. Using this approach, and in combination with anti PD-1 therapies, tumors that were resistant to the latter therapy were profiled using next-generation sequencing to identify pathways of ICI escape (Figure 2).

Figure 2: Identifying synthetic lethal combinations with anti PD-1

These investigations identified DDR2 and CCL2 alterations as key escape mechanisms. The DDR2 gene encodes for discoidin domain-containing receptor 2, a receptor tyrosine kinase that can be targeted by dasatinib.3 His group, therefore, proceeded to characterize DDR2 alterations in the context of ICI therapy in bladder cancer.4 Their analysis of published bladder cancer genomic profiling data indicated that patients with high DDR2 were associated with worse survival in four independent cohorts. When bladder cancer cells were transduced with DDR2 shRNAs in vitro, this resulted in appropriate reduction in protein levels (Figure 3). In the presence of anti PID-1, there was a significant reduction in subcutaneous tumor growth in syngeneic mice with bladder tumors that also stably expressed shDDR2, indicating a synergistic response. A similar response was also observed in melanoma and breast cancer in vivo models.

Figure 3: Effect of DDR2 depletion on anti PD-1 response.

RNA from mice bearing shControl and shDDR2-transduced bladder tumors treated with antiPD-1 were analyzed using RNAseq followed by gene set enrichment analysis. This revealed a strong immune response in the shDDR2 tumors treated with anti-PD-1 when compared with controls. Cytometry by time-of-flight analysis of these tumors revealed increased CD8+ T cell infiltration into shDDR2 tumors treated with anti-PD-1, which was not seen in the spleen. These observations suggested a strong T cell presence following the treatment of shDDR2-treated tumors with anti-PD-1.

To further evaluate the efficacy of targeting DDR2, the combination of dasatinib and anti-PD-1 was tested. Whereas therapeutic blockade of PD-1 or DDR2 alone had little or no effect on murine bladder tumors, treatment with the combination of dasatinib and anti-PD-1 showed a significant reduction in tumor burden (Figure 4). Similar results were seen within vivo colon cancer and sarcoma models.

Figure 4: Effect of dasatinib on PD-1 response.

Similar studies of synthetic lethal combinations of anti-PD-1 with CCL2 inhibitors are now underway in Dr. Theodorescus lab. Unpublished data from his group indicates that the combination of CCL2 depletion with anti-PD-1 has a significant effect in metastatic melanoma. The data indicate there may be potential benefits in considering triple-drug combinations that target DDR2, CCL2 and PD-1.

In closing, Dr. Theodorescu highlighted recent developing results from a Phase II trial of sitravatinib, a multi-receptor tyrosine kinase inhibitor in combination with nivolumab that is indicating encouraging clinical activity in checkpoint inhibitor nave, platinum-experienced patients with advanced or metastatic urothelial carcinoma.5 The combination with data generated from his lab and early trial results suggest that there is merit in the addition of targeted therapeutics with ICI for treatment of advanced bladder cancer.

Presented by: Dan Theodorescu, MD, Ph.D., Director of the Cedar-Sinai Cancer Center, Phase ONE Distinguished Endowed Chair in Cancer Research, Professor of the Departments of Surgery, Pathology and Laboratory Medicine, Cedars-Sinai Health System, Los Angeles, CA, USA.

References:1. Powles T, et al. Efficacy and safety of durvalumab in locally advanced or metastatic urothelial carcinoma: Updated results from a phase 1/2 open-label study. JAMA Oncol 2017;3(9):e172411.2. Sharma P, et al. Nivolumab in metastatic urothelial carcinoma after platinum therapy (CheckMate 275): a multicentre, single-arm, phase 2 trial. Lancet Oncol 2017;18(3):312-322.3. Carafoli F, Hohenester E. Collagen recognition and transmembrane signalling by discoidin domain receptors. Biochim Biophys Acta 2013;183:2187-94.4. Tu MM, et al. Targeting DDR2 enhances tumor response to anti-PD-1 immunotherapy. Sci Adv 2019;5(2):eaav2437.5. Msaouel P, et al. 705MO Sitravatinib (sitra) in combination with nivolumab (nivo) demonstrates clinical activity in checkpoint inhibitor (CPI) nave, platinum-experienced patients (pts) with advanced or metastatic urothelial carcinoma (UC). Annals Oncol 2020;31(4):S556.

Written by:Anirban P. Mitra, MD, Ph.D., Urologic Oncology Fellow, The University of Texas MD Anderson Cancer Center, Houston, TX, USA, Twitter: @APMitra, with Ashish M. Kamat, MD, MBBS, President of IBCN and IBCG, Endowed Professor, The University of Texas MD Anderson Cancer Center, Houston, TX, USA, Twitter:@UroDocAsh,at the International Bladder Cancer Network (IBCN) Annual Meeting, #IBCN2020, October 17, 2020.

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