Precision Oncology at a Crossroads: How Organoid Platforms Are Reshaping the Field

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The manuscript provides a comprehensive overview of 3D modeling platforms for head and neck, lung, and hematological malignancies. The authors included sections on new approaches using AI-driven analysis and multi-omics integration, as well as the discussion of recent 2025 studies utilizing organoids for rare variant discovery. These elements add significant value to the piece. However, the overall impact is currently hindered by an outdated narrative tone that frames organoids as a newly emerging tool, a premise that ignores over 15 years of established methodology. To improve the impact of this review the authors should address the points below:

1. Introduction

The authors repeatedly frame organoids as a "newly emerging" tool. I suggest the authors recontextualize the novelty to focus instead on recent sophisticated iterations (e.g., vascularization, multi-lineage assembloids, or high-throughput integration) rather than the platform itself.

The authors list several drawbacks for Patient-Derived Xenografts (PDX), however, many of these issues (establishment times, costs, limited scalability, no immune system), which restricts their use in some research areas (e.g. immunotherapy) are equally prevalent in organoid cultures. Acknowledging shared limitations will provide a useful guide for researchers choosing between these models.

The discussion on co-culture implies it is a unique advantage of organoid systems. It is important to acknowledge that co-culture techniques are routinely and successfully performed in 2D and Transwell platforms. The authors can indicate the specific advantages 3D organoid platforms offer over these established 2D co-culture models (e.g. 3D spatial organization or mechanical signaling).

2. Organoid Technologies in Cancer Research

The authors completely omit organoid integration with animal models.

It is nearly impossible to transition a drug candidate to clinical trials without in vivo data and the manuscript should discuss the importance of organoid xenografts/orthotopic organoid transplants into murine models. Organoids alone can’t account for whole-body dynamics that are traditionally managed in rodent models, such as systemic factors (drug absorption, distribution, metabolism, excretion) as well as multi organ toxicity. If the authors are proposing that organoids could bypass rodent models entirely, they should provide a robust justification or discuss the emerging new systems as a potential alternative.

 

3. Organoid Models in Head and Neck Cancers

The authors list the failures of current multidisciplinary treatments a justification for organoid platforms. An in vitro model can assist in drug selection but does not address the physical or systemic complications of treatment regimens mentioned. Please clarify the specific translational value here.

163- The assertion that HNSCC treatment follows a "one-size-fits-all" approach is factually incorrect and disregards current standards in medical practice, which includes different targeted therapies. This part must be updated to reflect current precision oncology practices.

180-182- The tone here suggests organoids are a brand-new discovery. Given their use in HNC research for years, the authors should focus on unsolved challenges there.

197- The authors cite organoid establishment rates in some cases are as low as <30%. This contradicts their earlier argument that organoids solve the efficiency and quantity issues of PDX models. If the success rate is this low, the authors must address how this platform remains representative.

The authors should address the downsides of organoid culture too, specifically culture-induced drift and the phenotypic/genotypic divergence that occurs between the organoid and the primary tissue over time.

4. Organoid-Based Precision Medicine in Lung Cancer

The authors cite "ethical concerns" as a limitation for PDX models but fail to specify what these are or how they differ from the ethical considerations of organoid research (e.g., patient consent for genomic data, commercialization of patient-derived materials).

430: Identifying sampling bias in biopsy-derived PDOs is a critical point. However, the authors should go beyond identifying the problem and propose strategies to mitigate it. This could include discussing multi-region sampling, the integration of spatial transcriptomics, or the use of "organoid-on-a-chip" systems to better represent intra-tumoral heterogeneity.

The inclusion of Air-Liquid Interface (ALI) culture techniques is a strong addition.

5. Organoids in Hematological Malignancies

The authors correctly identify that many lymphoid organoids rely on reaggregation, leading to "morphologically unstable constructs." It would be useful to discuss in more detail the current new solutions to this such as microfluidics, BM-on-a-Chip and 3D Bioprinting. These approaches allow for the precise, computer-aided deposition of stromal cells and bioinks to create stable, spatial architectures that mimic the bone marrow niche far better than simple reaggregation, while microfluidic platforms are an important model for recruitment of leukemic cells and their interaction with the vasculature in real-time.

Author Response

We sincerely thank the reviewers for their thoughtful and constructive comments on our manuscript. We greatly appreciate the reviewers’ insightful suggestions, which helped us improve the scientific balance, clarity, and overall quality of the manuscript. In response to the comments, we carefully revised the manuscript throughout and addressed the major concerns raised by the reviewers. Detailed responses are provided below. Additionally, we have included a graphical abstract (GA) in the revised submission.

 

Reviewer 1

1. Comment: The manuscript overemphasizes organoids as newly emerging platforms and does not sufficiently discuss recent technological refinements.

Response: We appreciate this valuable comment. In response, we revised the Introduction to place greater emphasis on recent technological advancements in sophisticated PDO-based systems, including vascularized organoids, multi-lineage assembloids, and high-throughput drug screening platforms, rather than describing organoids themselves as newly emerging tools.

Revision: The demand for experimental systems that precisely represent individual tumor characteristics has driven recent advancements in sophisticated patient-derived organoid (PDO)-based platforms, including vascularized organoids, multi-lineage assembloids, and high-throughput drug screening systems.

 

2. Comment: The manuscript discusses several limitations of PDX models without adequately acknowledging that organoid systems also share important limitations.

Response: We thank the reviewer for this important observation. We revised the manuscript to clarify that PDO and PDX models share several limitations, including variable establishment efficiency and incomplete immune microenvironment representation. We further emphasized that these models should be regarded as complementary rather than mutually exclusive translational platforms.

Revision: Importantly, several of these limitations, including high cost, variable establishment efficiency, and incomplete immune microenvironment representation, are also shared by organoid culture systems. Therefore, PDX and organoid models should be considered complementary rather than mutually exclusive platforms in translational cancer research

 

3. Comment: The manuscript implies that co-culture systems are unique advantages of organoid models.

Response: We appreciate this clarification. We revised the relevant section to acknowledge that co-culture systems have long been implemented in conventional 2D and Transwell platforms while emphasizing the specific advantages provided by 3D organoid-based systems.

Revision: Although co-culture systems have long been successfully implemented in conventional 2D and Transwell platforms, recent 3D organoid-based approaches provide additional advantages by enabling spatially organized multicellular interactions, extracellular matrix-dependent signaling, and more physiologically relevant mechanical microenvironments

 

4. Comment: The manuscript should discuss the continued importance of in vivo models and organoid xenograft systems.

Response: We thank the reviewer for this insightful suggestion. We expanded the discussion regarding the limitations of organoid systems and incorporated additional discussion regarding organoid xenograft and orthotopic transplantation approaches to improve translational relevance and preclinical predictability.

Revision: Despite these advantages, organoid systems alone cannot fully recapitulate the systemic physiological dynamics traditionally evaluated using in vivo animal models, including drug absorption, distribution, metabolism, excretion (ADME), and multi-organ toxicity. Accordingly, increasing efforts have focused on integrating organoid technologies with in vivo validation strategies, including patient-derived organoid xenografts and orthotopic transplantation models, to improve translational relevance and preclinical predictability.

 

5. Comment: The discussion of biopsy-derived PDOs identifies sampling bias but does not discuss strategies to mitigate this limitation.

Response: We appreciate this helpful suggestion. In response, we added discussion regarding recently proposed approaches to mitigate intra-tumoral heterogeneity and sampling bias, including multi-region tumor sampling, spatial transcriptomic profiling, and organoid-on-a-chip approaches.

Revision: To mitigate these limitations, recent approaches have explored multi-region tumor sampling, integration of spatial transcriptomic profiling, and organoid-on-a-chip platforms designed to better preserve intra-tumoral heterogeneity and microenvironmental complexity

Reviewer 2 Report

Comments and Suggestions for Authors

Summary
This manuscript ‘Precision Oncology at a Crossroads: How Organoid Platforms Are Reshaping the Field’ reviewed patient-derived 21 organoid (PDO) technologies as functional platforms that complement molecular profiling by directly investigating patient-specific sensitivity, resistance, and microenvironment dependent vulnerability. It is an important and timely topic and reframes organoids 35 as functional stratification platforms supporting a conceptual shift from genotype-guided to response-driven precision oncology.However, the structure of this review is not ideal, and reads more like a descriptive overview than a systematic critical review. Therefore, I would recommend accept with a major revision.

Comments:

1. PDX: define it in ‘Introduction’ part. The authors defined it in the ‘4.2. Development of Lung Cancer Organoids’.
2. Too many repeats, for example, the authors already compared the advantages and disadvantages of PDX and PDX in the introduction part, they repeated it in the ‘4.2. Development of Lung Cancer Organoids’ again.
3. ‘2. Organoid Technologies in Cancer Research’ part, the content is smore about “applications and significance” than “technologies.”. I would expect contents like:
4. Types of organoid systems:Patient-derived organoids (PDOs), Air–liquid interface (ALI), Co-culture systems (immune/stromal), and Organoid-on-chip / microfluidicsb.
5. Technical components: ECM (e.g., Matrigel vs synthetic matrices), Media composition (Wnt, R-spondin, Noggin, etc.), culture methods (embedding vs suspension)
6. Engineering advances: CRISPR editing in organoids, High-throughput screening platforms, Automation / imaging systems
7. The review of ‘3. Organoid Models in Head and Neck Cancers’ is detailed and mechanistically rich, whereas the sections on lung cancer and hematological malignancies appear comparatively less developed or less directly connected to clinical workflows. I would recommend balancing the depth across these three sections or state the reasons why the authors focused on one disease.
8. There are some over statement. For example: ‘In recent years, organoid plat- 118 forms have moved beyond their original role as experimental disease models and have 119 emerged as decision-support tools that functionally complement genomics-centered pre- 120 cision oncology for various cancer types, including lung, gastric, and ovarian cancers’------most organoids work is still preclinical, retrospective correlation, and early feasibility studies; ‘supporting a conceptual shift from genotype-guided to response-driven precision oncology’----- The proposed “conceptual shift” from genotype-guided to response-driven precision oncology is an interesting perspective but may be a little bit overstated----- genomics-based approaches remain the primary clinical standard.

Please double check the review thoroughly to avoid overstatement.

Author Response

We sincerely thank the reviewers for their thoughtful and constructive comments on our manuscript. We greatly appreciate the reviewers’ insightful suggestions, which helped us improve the scientific balance, clarity, and overall quality of the manuscript. In response to the comments, we carefully revised the manuscript throughout and addressed the major concerns raised by the reviewers. Detailed responses are provided below. Additionally, we have included a graphical abstract (GA) in the revised submission.

 

Reviewer 2

1. Comment: PDX models should be defined in the Introduction section.

Response: We thank the reviewer for this suggestion and revised the Introduction accordingly.

Revision: Patient-derived xenograft (PDX) models, in which patient tumor tissues are implanted into immunodeficient mice, preserve the histological and genetic characteristics of the parental tumors relatively well…

 

2. Comment: Several statements appear overstated, particularly regarding organoids as “decision-support tools” and the proposed transition from genotype-guided to response-driven precision oncology.

Response: We appreciate this important comment. To provide a more balanced and clinically realistic perspective, we revised several statements throughout the manuscript to reduce potential overstatement and to emphasize the complementary role of organoid-based functional profiling alongside genomics-guided precision oncology approaches.

Revision: are increasingly being explored as functional platforms that may complement genomics-centered precision oncology.

Revision: supporting the integration of functional response profiling alongside genomics-guided precision oncology approaches.

 

3. Comment: Section 2 focuses more on applications than technologies.

Response: We thank the reviewer for this valuable suggestion. In response, we revised Section 2 to better reflect technological and engineering aspects of organoid systems by incorporating descriptions of diverse organoid culture systems and platform technologies.

Revision: Organoid technologies encompass diverse culture systems and engineering strategies, including patient-derived organoids (PDOs), air–liquid interface (ALI) systems, co-culture platforms, and organoid-on-a-chip approaches

 

4. Comment: The HNC section is more detailed than the lung cancer and hematological malignancy sections.

Response: We appreciate this thoughtful observation. We added a statement clarifying the rationale for focusing on these three cancer types and emphasizing their distinct translational and biological contexts relevant to PDO-based functional profiling.

Revision: “Head and neck cancer, lung cancer, and hematological malignancies were selected because they represent distinct clinical and biological contexts in which PDO-based functional profiling has shown translational relevance, including radiosensitivity prediction, targeted therapy selection, and microenvironment-dependent therapeutic responses.”

Reviewer 3 Report

Comments and Suggestions for Authors

Lee, Kim, and colleagues conducted a review on the use of patient-derived organoid (PDO) technologies as functional stratification platforms that complement molecular profiling towards response-driven precision oncology. The writing is excellent and the references are adequate. However, there are several issues that would need to be addressed to improve the quality of the manuscript. 

• This review mainly focuses on three types of cancer: head and neck cancer, lung cancer, and haematological malignancies. The rationale for focusing on these three types of cancer rather than others should be explained more clearly.
• It is recommended that the generation of patient-derived organoids from rare but aggressive tumours, such as ovarian carcinosarcoma and uveal melanoma, is mentioned.
• Studies comparing the preservation of genomic alterations, such as mutations and chromosomal aberrations, in PDOs with their original tumour should be emphasised.

Author Response

We sincerely thank the reviewers for their thoughtful and constructive comments on our manuscript. We greatly appreciate the reviewers’ insightful suggestions, which helped us improve the scientific balance, clarity, and overall quality of the manuscript. In response to the comments, we carefully revised the manuscript throughout and addressed the major concerns raised by the reviewers. Detailed responses are provided below. Additionally, we have included a graphical abstract (GA) in the revised submission.

 

Reviewer 3

1. Comment: The rationale for focusing on head and neck cancer, lung cancer, and hematological malignancies should be explained more clearly.

Response: We thank the reviewer for this helpful suggestion. We added an explanatory statement in the Introduction clarifying the rationale for selecting these three disease contexts.

Revision: “Head and neck cancer, lung cancer, and hematological malignancies were selected because they represent distinct clinical and biological contexts in which PDO-based functional profiling has shown translational relevance, including radiosensitivity prediction, targeted therapy selection, and microenvironment-dependent therapeutic responses.”

 

2. Comment: The manuscript should mention PDO generation from rare but aggressive tumors such as ovarian carcinosarcoma and uveal melanoma.

Response: We appreciate this valuable suggestion. We expanded the discussion in Section 6.2 to include examples of rare but aggressive malignancies in which PDO technologies are being explored.

Revision: Beyond the cancer types discussed in this review, PDO technologies are also being explored in rare but aggressive malignancies, including ovarian carcinosarcoma and uveal melanoma, highlighting the expanding applicability of organoid-based precision oncology approaches.

 

3. Comment: Studies demonstrating preservation of genomic alterations in PDOs relative to the original parental tumors should be emphasized.

Response: We thank the reviewer for this important comment. We strengthened the discussion regarding genomic concordance between PDOs and parental tumors, including the preservation of major genomic and molecular features.

Revision: Multiple studies have shown that PDOs preserve key genomic alterations, including driver mutations, copy number alterations, chromosomal aberrations, and transcriptomic features, with substantial concordance to the original parental tumors.

 

We sincerely appreciate the reviewers’ thoughtful comments and suggestions, which significantly improved the quality and balance of the manuscript.

Round 2

Reviewer 3 Report

Comments and Suggestions for Authors

The authors addressed the concerns raised by this reviewer. While more citations would be desirable to support the new statements, the manuscript is suitable for publication.