Periodic Reporting for period 1 - SelfOrg (Addressing the role of self-organization in tumor heterogeneity and plasticity)
Periodo di rendicontazione: 2025-04-01 al 2027-03-31
Colorectal cancer (CRC) remains a major health challenge, with a survival rate of 15% in stage IV cases due to therapy resistance and tumor relapse. A key barrier to effective treatment is the high degree of intratumor heterogeneity and plasticity. These features enable the coexistence of diverse cancer cell populations within a tumor, each of them specialized in key functions such as proliferation, invasion or resistance to treatment. Additionally, phenotypic plasticity grants these cancer cells flexibility to dynamically tune their phenotype, to the extent that a single surviving cell can regenerate a full heterogeneous tumor. Despite their crucial role in CRC pathology, the biological mechanisms driving tumor heterogeneity and plasticity remain poorly understood.
Current research suggests that tumor plasticity is driven by microenvironmental cues, where external signals induce specific cell states within localized tumor niches. However, my preliminary data reveal that cancer cells also possess an intrinsic ability to self-organize and establish heterogeneity even in the absence of external signals. SelfOrg will tackle the unexplored contribution of self-organization to tumor heterogeneity and plasticity. To do so, I will combine quantitative measurements in bioengineered human organoids with physiologically relevant mouse tumor models to dissect the intrinsic mechanochemical signals regulating tumor heterogeneity. The project is divided in three main aims:
- Aim 1: To quantitatively characterize the self-organization of colon organoids representing different stages of tumor progression.
- Aim 2: To identify the molecular mechanisms driving tumor self-organization and their role in vivo.
- Aim 3: To quantify the heterogeneity in self-organization of a PDO biobank and to assess its correlation with tumor clinicopathological features.
Overall, SelfOrg will dissect how intrinsic mechanochemical interactions among epithelial cells drive the formation of a homeostatic tissue and how this program deteriorates during tumor progression. Through a quantitative biology framework, we will systematically quantify, classify, and mechanistically understand the self-organization programs that pattern human tumors, uncover how they interact with the microenvironment, and assess their predictive value for patient outcomes. Ultimately, EvoSelf will establish self-organization as a fundamental principle of tumor biology
Current research suggests that tumor plasticity is driven by microenvironmental cues, where external signals induce specific cell states within localized tumor niches. However, my preliminary data reveal that cancer cells also possess an intrinsic ability to self-organize and establish heterogeneity even in the absence of external signals. SelfOrg will tackle the unexplored contribution of self-organization to tumor heterogeneity and plasticity. To do so, I will combine quantitative measurements in bioengineered human organoids with physiologically relevant mouse tumor models to dissect the intrinsic mechanochemical signals regulating tumor heterogeneity. The project is divided in three main aims:
- Aim 1: To quantitatively characterize the self-organization of colon organoids representing different stages of tumor progression.
- Aim 2: To identify the molecular mechanisms driving tumor self-organization and their role in vivo.
- Aim 3: To quantify the heterogeneity in self-organization of a PDO biobank and to assess its correlation with tumor clinicopathological features.
Overall, SelfOrg will dissect how intrinsic mechanochemical interactions among epithelial cells drive the formation of a homeostatic tissue and how this program deteriorates during tumor progression. Through a quantitative biology framework, we will systematically quantify, classify, and mechanistically understand the self-organization programs that pattern human tumors, uncover how they interact with the microenvironment, and assess their predictive value for patient outcomes. Ultimately, EvoSelf will establish self-organization as a fundamental principle of tumor biology
Tumor phenotypic heterogeneity and plasticity drive growth, metastasis, and relapse, posing major challenges to effective therapy. These properties are mainly attributed to genetic alterations and extrinsic cues from the tumor microenvironment. However, in my previous postdoc, I produced preliminary data pointing towards self-organized mechanisms as intrinsic coordinators of tumor heterogeneity. Beyond this proof of principle, how self-organization coordinates tumor heterogeneity and plasticity remained largely unexplored. SelfOrg was designed to fill this gap and uncover the contribution of self-organization to tumor heterogeneity during colorectal cancer progression.
During the six months of duration of SelfOrg, I have advanced three research lines that tackle this question from different angles:
1. I worked on the preliminary data presented in SelfOrg on mouse tumor organoids. I analysed in vitro and in vivo experiments, and I wrote a manuscript with the main findings. This manuscript is currently under review and has been posted as a preprint in bioRxiv:
Pérez-González C*†, Bruckner D*, Di-Luoffo M, Richon S, Goswami R, Baghdadi M, Piastra-Facon F, Felsenthal N, Fumagalli A, Bouras R, van der Net M, Gloerich M, Salvatore G, Guck J, van Rheenen J, Guillermet-Guibert J, Hannezo E, Vignjevic DM. Self-organization of tumor heterogeneity and plasticity. bioRxiv 2025.10.09.681487 (2025)
2. The results in mouse organoids mentioned above constitute a proof of concept of tumor self-organization. SelfOrg will explore this concept in human colorectal tumors. I have been working on optimizing the culture of human colon organoid as monolayers on soft substrates compatible with force measurements. Furthermore, I designed CRISPR-Cas9 strategies to generate live-reporters of different cell state markers. Due to the early termination of the phellowship, most initial aims were not yet achieved.
3. I have been working on obtaining a patient-derived organoid (PDO) cohort of colorectal cancer in collaboration with the group of Prof. Alberto Muñoz (CSIC-UAM). In the upcoming weeks we will receive 20 organoid lines to study the intertumor heterogeneity in self-organization.
During the six months of duration of SelfOrg, I have advanced three research lines that tackle this question from different angles:
1. I worked on the preliminary data presented in SelfOrg on mouse tumor organoids. I analysed in vitro and in vivo experiments, and I wrote a manuscript with the main findings. This manuscript is currently under review and has been posted as a preprint in bioRxiv:
Pérez-González C*†, Bruckner D*, Di-Luoffo M, Richon S, Goswami R, Baghdadi M, Piastra-Facon F, Felsenthal N, Fumagalli A, Bouras R, van der Net M, Gloerich M, Salvatore G, Guck J, van Rheenen J, Guillermet-Guibert J, Hannezo E, Vignjevic DM. Self-organization of tumor heterogeneity and plasticity. bioRxiv 2025.10.09.681487 (2025)
2. The results in mouse organoids mentioned above constitute a proof of concept of tumor self-organization. SelfOrg will explore this concept in human colorectal tumors. I have been working on optimizing the culture of human colon organoid as monolayers on soft substrates compatible with force measurements. Furthermore, I designed CRISPR-Cas9 strategies to generate live-reporters of different cell state markers. Due to the early termination of the phellowship, most initial aims were not yet achieved.
3. I have been working on obtaining a patient-derived organoid (PDO) cohort of colorectal cancer in collaboration with the group of Prof. Alberto Muñoz (CSIC-UAM). In the upcoming weeks we will receive 20 organoid lines to study the intertumor heterogeneity in self-organization.
Further research that I am currently performing will advance our understanding on tumor self-organization. I expect to produce, at least, one publication on the topic of SelfOrg in the upcoming years. In the long term, these findings may improve current cancer treatments. These objectives were not yet achieved due to the early termination of the fellowship, but I am still advancing the project of SelfOrg under a different funding.