Single-cell RNAseq Breast Cancer

Study Overview
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Brief Summary
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Molecular characterization of persistent tumor cells remaining after NAC and infiltrating immune cells, for example, M2 macrophages, could strongly contribute to identifying targeted therapeutic approaches for this disease.

Detailed Description
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Triple negative breast cancer (TNBC) represents approximately 15-20% of all breast cancers. Its features are lack of expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (Her2). TNBC exhibits a biologically aggressive behavior and a high inter- and intra-tumor molecular heterogeneity which has recently been highlighted also in single cell RNAseq (scRNAseq) studies. Patients with TNBC often have less positive outcomes then other breast cancer subtypes, due to the absence of specific therapeutic targets. Results of single cell RNA sequencing (scRNAseq) in TNBC before and after treatment with chemotherapy (NAC) were recently reported for a small group of patients. Genetic alterations are also investigated by Whole Exome Sequencing (WES). In addition scRNAseq analysis confirmed the presence of a high percentage of M2 macrophages in TNBC and tumor-adjacent tissue. These macrophages are clinically relevant and able to predict outcome in TNBC. Based on the above evidence, we hypothesize that molecular characterization of persistent tumor cells remaining after NAC and infiltrating immune cells, for example, M2 macrophages, could strongly contribute to identifying targeted therapeutic approaches for this disease. We will conduct a pilot study with a combined retrospective and prospective observational design. Cancer patients diagnosed with histologically proven primary invasive breast cancer with a stage IIA to IIIB and assessed at the molecular level and defined as TNBC, will be eligible to participate to the study. Furthermore, only patients with a tumor >1.5cm in size will be considered, which is the selection criterion for the administration of neoadjuvant therapy.

Official Title
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Study of the Impact of Neoadjuvant Therapy on the Heterogeneity of Triple Negative Breast Cancer Through Single-cell RNA Sequencing (scRNAseq) and Whole-exome Sequencing (WES)

Conditions
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Breast Neoplasms

Intervention / Treatment
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* Other: Single-cell RNA sequencing (scRNAseq), whole-exome sequencing (WES)


Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: Patients with histologically proven primary invasive breast cancer >1.5cm in size, with molecular assessed stage IIA to IIIB defined as TNBC, and who will undergo neoadjuvant chemotherapy and subsequent surgery (and/or have undergone - retrospective part). informed consent (prospective part) Exclusion Criteria: pregnancy, metastatic breast cancer, previous chemotherapy, hormone therapy, radiation therapy, previous other cancers or contralateral breast cancer
Sexes Eligible for Study
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Female

Accepts Healthy Volunteers
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No

Study Plan
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How is the study designed?
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Arms and Interventions

| Intervention/Treatment |
| --- |
|Other: Single-cell RNA sequencing (scRNAseq), whole-exome sequencing (WES)|Combined both retrospective and prospective observational design|

What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Evaluate chemoterapy effect | Decipher, through the execution of scRNAseq profiles, the transcriptional reprogramming that occurs during chemotherapy (NAC) in triple negative breast cancers (TNBC) and provide information of prognostic and/or predictive relevance of response to NAC | 26 months |