Understanding inequities in precision oncology diagnostics

Dutta, Ritika; Vallurupalli, Mounica; McVeigh, Quinn; Huang, Franklin W.; Rebbeck, Timothy R.

doi:10.1038/s43018-023-00568-1

Cited by 6 publications

(3 citation statements)

References 84 publications

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“…However, one potential approach would be to utilize ST on pathology samples where deeper insights are needed from a diagnostic perspective. For example, molecular diagnostics are now being integrated into cancer pathology more frequently to identify targetable pathogenic variants (Dutta et al 2023 ). One potential application could be to determine the tumor’s likelihood of being immune-responsive.…”

Section: Discussion and Future Directionsmentioning

confidence: 99%

Spatial transcriptomics in cancer research and potential clinical impact: a narrative review

Cilento,

Sweeney,

Butler

2024

J Cancer Res Clin Oncol

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Spatial transcriptomics (ST) provides novel insights into the tumor microenvironment (TME). ST allows the quantification and illustration of gene expression profiles in the spatial context of tissues, including both the cancer cells and the microenvironment in which they are found. In cancer research, ST has already provided novel insights into cancer metastasis, prognosis, and immunotherapy responsiveness. The clinical precision oncology application of next-generation sequencing (NGS) and RNA profiling of tumors relies on bulk methods that lack spatial context. The ability to preserve spatial information is now possible, as it allows us to capture tumor heterogeneity and multifocality. In this narrative review, we summarize precision oncology, discuss tumor sequencing in the clinic, and review the available ST research methods, including seqFISH, MERFISH (Vizgen), CosMx SMI (NanoString), Xenium (10x), Visium (10x), Stereo-seq (STOmics), and GeoMx DSP (NanoString). We then review the current ST literature with a focus on solid tumors organized by tumor type. Finally, we conclude by addressing an important question: how will spatial transcriptomics ultimately help patients with cancer?

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Section: Discussion and Future Directionsmentioning

confidence: 99%

Spatial transcriptomics in cancer research and potential clinical impact: a narrative review

Cilento,

Sweeney,

Butler

2024

J Cancer Res Clin Oncol

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“…Also called precision oncology, this specialty involves the molecular profiling of individual tumors to identify targetable alterations and their expressed biomarkers 44. Now considered the standard of care for many types of cancer, precision medicine has led to better outcomes, more durable responses, increased survival time, and application to treatment protocols alongside other modalities 34,45.…”

Section: Recent Advances and Prospectsmentioning

confidence: 99%

Esophageal cancer

Eisner

2024

Jaapa

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Esophageal cancer is a challenging malignancy that often is diagnosed in advanced stages, resulting in a poor prognosis. This article provides a comprehensive review of the two main types of esophageal cancer, esophageal squamous cell carcinoma and esophageal adenocarcinoma, and reviews epidemiology, risk factors, pathogenesis, diagnostic modalities, staging systems, and established and emerging treatments. Recent advancements in treatment for resectable and unresectable esophageal cancer also are explored. These include immunotherapy, targeted therapy, sentinel lymph node mapping, radiogenomics, palliative measures, and screening measures.

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“…Moreover, following amplification and high-throughput sequencing, machine learning algorithms (cluster analysis, neural network, support vector machine, etc.) are increasingly utilized to unveil the overall gene expression state and corresponding structural information in a single cell (Figure 1 The recent advances in NGS technology substantially facilitated the advancement in a variety of biomedical research and application fields [30][31][32][33][34]. As early as 2009, Tang et al performed a single-cell mRNA sequencing experiment for the first time in history [35].…”

Section: Principles and Development Of Scs Technologymentioning

confidence: 99%

Therapeutic implementation of single-cell sequencing for dissecting colorectal cancer immune microenvironment

Li,

Zhou

2024

Preprint

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Colorectal cancer (CRC) is a highly prevalent malignancy in the digestive system around the globe that is characterized by intricate pathogenesis, progression and poor prognosis. Recent studies indicate that tumor immune microenvironment (TIME) is a crucial mediator of tumorigenesis and progression with substantial diagnostic and prognostic value, which is a complex network of malignant cells, immune cells, endothelial cells, extracellular matrix, interstitial components and various molecular factors. Therefore, comprehensive profiling of CRC-associated TIME may substantially contribute to the research on CRC pathology while accelerating pharmaceutical development for effective CRC immunotherapy. However, CRC tissues tend to exhibit high cell heterogeneity, which severely compromises the accuracy of the TIME profiling data acquired through conventional sequencing methods as they are incapable of discriminating different cell populations. Single-cell sequencing (SCS) is a novel sequencing technology capable of comprehensively characterizating individual cells at a high resolution, thereby preserving heterogeneous tissue information and the transcriptional data of rare cell populations. SCS technology-enabled profiling of CRC-associated TIME offers emerging opportunities for elucidating the pathogenesis and progression mechanisms of CRC. This work provides a comprehensive summary on the unique merits and potential breakthroughs of SCS technology in the context of CRC-associated TIME characterization, which may facilitate the development and optimization of intervention strategies for CRC in the clinics.

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Understanding inequities in precision oncology diagnostics

Cited by 6 publications

References 84 publications

Spatial transcriptomics in cancer research and potential clinical impact: a narrative review

Spatial transcriptomics in cancer research and potential clinical impact: a narrative review

Esophageal cancer

Therapeutic implementation of single-cell sequencing for dissecting colorectal cancer immune microenvironment

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