VHIO’s UNIQUE CaixaResearch platform will allow the single-cell analysis of the different cells that make up a tumour to develop new therapies

“la Caixa” Foundation has subsidized a new transversal platform for next generation single-cell sequencing: UNderstanding cancer through sIngle cell seQUEncing: the UNIQUE CaixaResearch platform, which will be integrated into the core technology platforms of the Vall d’Hebron Institute of Oncology (VHIO), which forms part of the Vall d’Hebron Campus.

A single tumour can have millions of cells from very different tumour populations and types. That is why single cell analysis is necessary to study tumour heterogeneity, identify different cell subpopulations and the role they play, and discover new tumour biomarkers for tumours that until now were considered well characterized, better understand the response to treatment or investigate tumours evolution over time, their different stages and how they have responded to different treatments.

Tumour heterogeneity is a major obstacle that limits the efficacy of targeted therapies and compromises treatment outcomes. “Current approaches to mass sequencing of samples give us a general overview of the tumour. However, the truth is that tumours contain cells of different properties and malignant potential that constantly change with the evolution of the tumour or its response to treatment”, explained Dr Marcos Malumbres, ICREA professor, director of the Systems Oncology Programme and head of VHIO’s Cell Cycle and Cancer Group, which uses this technology to develop and test novel therapeutic strategies with a view to translating them into clinical practice.

The implementation of the UNIQUE CaixaResearch platform will allow VHIO researchers to address new scientific questions in order to better understand the complexity of tumours and find new therapeutic solutions and biomarkers that improve the care of cancer patients.

Single-cell technology makes it possible to dissect gene expression programmes in tumour tissue and peripheral blood samples and characterise expression patterns on a cell-by-cell basis. In other words, it tells us which genes are, or are not, expressed in each cell. “We went from having a blurred overview of the behaviour of thousands of cells to having thousands of complete pictures of individual cells,” said Dr Malumbres.

State-of-the-art devices

“Single-cell sequencing allows us to detect and characterise rare stem cell populations present in the tumour microenvironment that are responsible for therapy resistance and tumour relapse, latent tumour cells that cause metastasis, circulating tumour cells of low abundance and immune cells that may have functional relevance and clinical significance”, explained Dr Elena Serrano, coordinator of the VHIO’s High Technology Unit.

To meet these objectives, the UNIQUE-CaixaImpulse platform has three state-of-the-art devices that are integrated into the VHIO’s core transversal technology platforms. For example, it has a Parsotix machine which is capable of isolating circulating tumour cells by liquid biopsy and a Chromium X machine (10x Genomics) that separates tissue and circulating tumour cells one-by-one and prepares them for individual sequencing.

It also has a Leica DMi8 microscope equipped with Thunder technology and a CytAssist device (10x Genomics) that makes it possible to identify, based on solid tumour samples, the location of each of the tumour’s cells by knowing the genes expressed by each one. “To summarise,” concluded Dr Elena Serrano, “we obtain information about which genes a particular tumour cell does or does not express and what place it occupies within the tumour environment. This is known as spatial transcriptomics”.

The UNIQUE CaixaResearch platform will generate an enormous amount of data. The VHIO’s Bioinformatics Unit, led by Dr Lara Nonell, will therefore play a vital role in processing and interpreting this data in the name of cancer research. The integration of data obtained from the UNIQUE CaixaResearch platform with that from other available technologies, as well as integration with clinical data, will be key in identifying response biomarkers.

Several VHIO research groups are already conducting single-cell sequencing research projects with external collaborators. With the implementation of this new platform, they’ll be able to conduct their research in house as part of the translational research model.

The medium-term goal is to implement this technology in the clinical setting and facilitate the translation of research into new treatments from which patients can benefit.

In the Cell Cycle and Cancer laboratory led by Dr Marcos Malumbres, this technology is already being used to study cell-to-cell expression patterns in circulating tumour cells in hormone receptor-positive advanced breast cancer with a view to understanding why these tumours become resistant to conventional therapies.

The Antitumour Therapies Modelling Group led by ICREA Professor Dr Laura Soucek, a pioneer in Myc protein inhibition as a potential treatment for different cancer types, also uses single-cell sequencing to “identify immune cell populations in the tumour microenvironment of non-small cell lung cancer and melanoma and observe the impact of Myc protein inhibition on tumour immune suppression with the aim of finding new ways to reactivate the immune system against the tumour”.

“Our group has conducted extensive research on brain metastasis,” said Dr Joan Seoane, ICREA professor and head of VHIO’s Gene Expression Group. “The UNIQUE platform will allow us to identify which genes are expressed by cells in melanoma brain metastasis and non-small cell lung cancer samples of patients undergoing treatment, as well as the characteristics of immune cells surrounding the tumour. This will allow us to identify biomarkers that could serve as new therapeutic targets or predict how patients will respond to treatment.”

Dr Alena Gros, head of the Cancer Immunotherapy and Immunology Group, works on several projects that use single-cell sequencing to analyse T-cell receptors (TCRs) and differentially expressed genes of tumour infiltrating lymphocytes (TILs) and circulating lymphocytes that contribute to tumour and neoantigen recognition. “Our goal is to harness the potential of this technology in order to detect, monitor and exploit the anti-tumour T response in cancer patients”.

The new platform will also enable the implementation of spatial transcriptomics projects that will tell us which genes are expressed in different areas of the tumour and its microenvironment. For example, the Prostate Cancer Translational Research Group, led by Dr Joaquin Mateo, will use this technology to study biopsies before, during and after hormonal treatment for late-stage prostate cancer in order to gain a better understanding of how tumour heterogeneity in the way in which it adapts to treatment is relevant to designing new treatment strategies.