The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support

Irmisch, Anja; Bonilla, Ximena; Chevrier, Stéphane; Lehmann, Kjong-Van; Singer, Franziska; Toussaint, Nora C.; Esposito, Cinzia; Mena, Julien; Milani, Emanuela S.; Casanova, Ruben; Stekhoven, Daniel J.; Wegmann, Rebekka; Jacob, Francis; Sobottka, Bettina; Goetze, Sandra; Kuipers, Jack; Castillo, Jacobo Sarabia del; Prummer, Michael; Tuncel, Mustafa A.; Menzel, Ulrike; Jacobs, Andrea; Engler, Stefanie; Sivapatham, Sujana; Frei, Anja; Gut, Gabriele; Ficek, Joanna; Miglino, Nicola; Ak, Melike; Alquaddoomi, Faisal; Albinus, Jonas; Alborelli, Ilaria; Andani, Sonali; Attinger, Per-Olof; Baumhoer, Daniel; Beck‐Schimmer, Beatrice; Bernasconi, Lara; Bertolini, Anne; Chicherova, Natalia; D’Costa, Maya; Danenberg, Esther; Davidson, Natalie J.; Drăgan, M; Erkens, Martin; Eschbach, Katja; Fedier, André; Ferreira, Pedro; Frey, Bruno S.; Grob, Linda; Günther, Detlef; Haberecker, Martina; Haeuptle, Pirmin; Herter, Sylvia; Holtackers, René; Huesser, Tamara; Jaeger, Tim M.; Jahn, Katharina; James, Alva Rani; Jermann, Philip; Kahles, André; Kahraman, Abdullah; Kuebler, Werner; Kunze, Christian P.; Kurzeder, Christian; Lugert, Sebastian; Maass, G.; Markolin, Philipp; Metzler, Julian M.; Muenst, Simone; Murri, Rita; Ng, Charlotte K.Y.; Nicolet, Stefan; Nowak, Marta; Pedrioli, Patrick G. A.; Piscuoglio, Salvatore; Ritter, Mathilde; Rommel, Christian; Rosano-González, María Lourdes; Santacroce, Natascha; Schlenker, Ramona; Schwalie, Petra; Schwan, Severin; Schär, Tobias; Senti, Gabriela; Sreedharan, Vipin T.; Stark, Stefan G.; Thomas, Tinu M.; Toševski, Vinko; Tusup, Marina; Drogen, Audrey van; Vetter, Marcus; Vlajnic, Tatjana; Weber, Sandra; Weber, Walter; Weller, Michael; Wendt, Fabian; Wey, Norbert; Wildschut, Mattheus H.E.; Yu, Shuqing; Ziegler, Johanna; Zimmermann, Marc; Zoche, Martin; Zuend, Gregor; Aebersold, Rudolf; Bacac, Marina; Beerenwinkel, Niko; Beisel, Christian; Bodenmiller, Bernd; Dummer, Reinhard; Heinzelmann‐Schwarz, Viola; Koelzer, Viktor H.; Manz, Markus G.; Moch, Holger; Pelkmans, Lucas; Snijder, Berend; Theocharides, Alexandre; Tolnay, Markus; Wicki, Andreas; Wollscheid, Bernd; Rätsch, Gunnar; Levesque, Mitchell P.

doi:10.1016/j.ccell.2021.01.004

Cited by 98 publications

(53 citation statements)

References 15 publications

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“…With all foreseeable challenges, this venture would be imperative to transform bladder cancer management and necessitate very close collaboration among physicians, basic researchers and translational scientists. Recently launched large-scale initiatives, including the Human Tumor Atlas Network (HTAN) and the Tumor Profiler (TuPro) study, are poised to accelerate the standardization of key protocols, best-practice guidelines, quality control solutions, metadata schemata, and analytic pipelines ( 128 , 129 ). These projects may lead to refined diagnostics in precision oncology and pave the way for the translation of single-cell profiling into clinical decision-making.…”

Section: Outstanding Questions and Future Prospectsmentioning

confidence: 99%

Immunotherapy in the Treatment of Urothelial Bladder Cancer: Insights From Single-Cell Analysis

Zang

Yang

et al. 2021

Front. Oncol.

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Urothelial bladder cancer (UBC) is a global challenge of public health with limited therapeutic options. Although the emergence of cancer immunotherapy, most notably immune checkpoint inhibitors, represents a major breakthrough in the past decade, many patients still suffer from unsatisfactory clinical outcome. A thorough understanding of the fundamental cellular and molecular mechanisms responsible for antitumor immunity may lead to optimized treatment guidelines and new immunotherapeutic strategies. With technological developments and protocol refinements, single-cell approaches have become powerful tools that provide unprecedented insights into the kaleidoscopic tumor microenvironment and intricate cell-cell communications. In this review, we summarize recent applications of single-cell analysis in characterizing the UBC multicellular ecosystem, and discuss how to leverage the high-resolution information for more effective immune-based therapies.

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Section: Outstanding Questions and Future Prospectsmentioning

confidence: 99%

Immunotherapy in the Treatment of Urothelial Bladder Cancer: Insights From Single-Cell Analysis

Zang

Yang

et al. 2021

Front. Oncol.

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“…The heterogeneities of the tumor microenvironment and strikingly different clinical outcomes in tumor patients require comprehensive molecular profiling to guide the personalized therapies. Multiple initiatives have been founded to identify tumor-specific biomarkers to facilitate better clinical decisions using integrative single-cell omics data analyses ( 73 , 113 , 114 ).…”

Section: Application Of Single-cell Omics In Tumor Immunologymentioning

confidence: 99%

Applications of Single-Cell Omics in Tumor Immunology

Liu

Zhang

et al. 2021

Front. Immunol.

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The tumor microenvironment (TME) is an ecosystem that contains various cell types, including cancer cells, immune cells, stromal cells, and many others. In the TME, cancer cells aggressively proliferate, evolve, transmigrate to the circulation system and other organs, and frequently communicate with adjacent immune cells to suppress local tumor immunity. It is essential to delineate this ecosystem’s complex cellular compositions and their dynamic intercellular interactions to understand cancer biology and tumor immunology and to benefit tumor immunotherapy. But technically, this is extremely challenging due to the high complexities of the TME. The rapid developments of single-cell techniques provide us powerful means to systemically profile the multiple omics status of the TME at a single-cell resolution, shedding light on the pathogenic mechanisms of cancers and dysfunctions of tumor immunity in an unprecedently resolution. Furthermore, more advanced techniques have been developed to simultaneously characterize multi-omics and even spatial information at the single-cell level, helping us reveal the phenotypes and functionalities of disease-specific cell populations more comprehensively. Meanwhile, the connections between single-cell data and clinical characteristics are also intensively interrogated to achieve better clinical diagnosis and prognosis. In this review, we summarize recent progress in single-cell techniques, discuss their technical advantages, limitations, and applications, particularly in tumor biology and immunology, aiming to promote the research of cancer pathogenesis, clinically relevant cancer diagnosis, prognosis, and immunotherapy design with the help of single-cell techniques.

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“…Regarding the development of novel, high‐performing treatment decision‐making tools, the Tumour Profiler Study [ 48 ] assessed a novel strategy aimed at accelerating diagnostics in parallel with advancing cancer science. This observational study applied and integrated various molecular profiling technologies to create novel opportunities for personalized medicine.…”

Section: Infrastructure For Clinical and Prevention Trialsmentioning

confidence: 99%

The Porto European Cancer Research Summit 2021

et al. 2021

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Key stakeholders from the cancer research continuum met in May 2021 at the European Cancer Research Summit in Porto to discuss priorities and specific action points required for the successful implementation of the European Cancer Mission and Europe's Beating Cancer Plan (EBCP). Speakers presented a unified view about the need to establish high‐quality, networked infrastructures to decrease cancer incidence, increase the cure rate, improve patient's survival and quality of life, and deal with research and care inequalities across the European Union (EU). These infrastructures, featuring Comprehensive Cancer Centres (CCCs) as key components, will integrate care, prevention and research across the entire cancer continuum to support the development of personalized/precision cancer medicine in Europe. The three pillars of the recommended European infrastructures – namely translational research, clinical/prevention trials and outcomes research – were pondered at length. Speakers addressing the future needs of translational research focused on the prospects of multiomics assisted preclinical research, progress in Molecular and Digital Pathology, immunotherapy, liquid biopsy and science data. The clinical/prevention trial session presented the requirements for next‐generation, multicentric trials entailing unified strategies for patient stratification, imaging, and biospecimen acquisition and storage. The third session highlighted the need for establishing outcomes research infrastructures to cover primary prevention, early detection, clinical effectiveness of innovations, health‐related quality‐of‐life assessment, survivorship research and health economics. An important outcome of the Summit was the presentation of the Porto Declaration, which called for a collective and committed action throughout Europe to develop the cancer research infrastructures indispensable for fostering innovation and decreasing inequalities within and between member states. Moreover, the Summit guidelines will assist decision making in the context of a unique EU‐wide cancer initiative that, if expertly implemented, will decrease the cancer death toll and improve the quality of life of those confronted with cancer, and this is carried out at an affordable cost.

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The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support

Cited by 98 publications

References 15 publications

Immunotherapy in the Treatment of Urothelial Bladder Cancer: Insights From Single-Cell Analysis

Immunotherapy in the Treatment of Urothelial Bladder Cancer: Insights From Single-Cell Analysis

Applications of Single-Cell Omics in Tumor Immunology

The Porto European Cancer Research Summit 2021

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