The author successfully demonstrated the VDJ sequence space transcriptomics technology and showcased its advantages in the study of human cancer tissues and B cell maturation mechanisms. Through this research, for the first time, we are able to spatially trace the lineage evolution of B cell clones within human tissues," commented a reviewer on a paper published in Science.
This study, for the first time, is able to simultaneously and with high throughput obtain the clonal spatial information of T cells and B cells in the immune system, revealing their diversity in different human tissues.
A collaborative team from the Karolinska Institute in Sweden and the Royal Institute of Technology in Sweden introduced spatial transcriptomics, and researchers developed a more comprehensive understanding and study of VDJ sequences in space transcriptomics, named Spatial VDJ (spatial transcriptomics for variable, diversity and joining sequences).
Based on this technology, they have mapped the full-length T cell receptor (T-cell Receptor, TCR) and B cell receptor (B-cell Receptor, BCR) sequence maps in human tissues.
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Recently, the relevant paper was published in Science, titled "Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics" [1].The article is translated into English as follows:
Dr. Camilla Engblom, now an Assistant Professor at the Molecular Medicine Center of Karolinska Institutet, Dr. Kim Thrane from the Royal Institute of Technology, and doctoral student Lin Qirong are the co-first authors.
Researcher Jeff Mold from Karolinska Institutet serves as the corresponding author, Professor Joakim Lundeberg from the Royal Institute of Technology, and Professor Jonas Frisén from Karolinska Institutet are the senior authors.
Take a "snapshot" of the first time for clonal evolution
T cells and B cells in the immune system are very important components of the acquired immune response, and they will recognize antigens in a specific clonal form.During the developmental process, each T cell and B cell has the potential to acquire a unique antigen receptor through the rearrangement of variable (V), diversity (D), and joining (J) region sequences (VDJ sequences).
The sequence of the antigen receptor determines the complexity and specificity of antigen-antibody recognition. Cells that possess the same antigen receptor sequence, especially within the CDR3 segment of the VDJ sequence, are referred to as a clonal population (clone).
As the human body develops, T and B cell populations form billions of clones. These clones are widely distributed within numerous tissues of the human body and are directly or indirectly involved in the maintenance of homeostasis, inflammatory responses, and tumor immunity.
Therefore, not only the clonal information of the two but also their spatial positioning plays an important role in helping people understand the development of immune diseases and cancer.
So, how can we simultaneously obtain the clonal information and spatial information of T cells and B cells?Prior to this, single-cell RNA sequencing (scRNA-seq) could measure the VDJ sequences of TCR and BCR, and understand the diversity of immune receptors at the single-cell level.
However, due to the lack of spatial information in single-cell sequencing, it may lead to a series of problems, including the loss of cell interactions and the loss of spatial gene expression patterns.
In 2016, Professor Friesén and Professor Lundeberg jointly developed Spatial Transcriptomics (Spatial GEX).
This is a technique that combines tissue spatial information with gene expression data, and by combining tissue sections and transcriptome sequencing, it can locate gene expression on the spatial scale of the tissue.
They published the first paper on obtaining spatial location information through sequencing in Science, and the related technology was acquired by the American biotechnology company 10x Genomics in 2018, and the Visium Spatial Gene Expression Solution was commercialized [2].The technology allows researchers to conduct spatial transcriptomics analysis on tissue sections, providing a more comprehensive understanding of the spatial organization of cell types and gene expression. It is reported that the journal Nature Methods has also rated this method as the "Method of the Year 2020".
However, while conventional spatial transcriptomics technology can effectively preserve spatial information, due to limitations in library construction, VDJ sequences cannot be retained in the sequencing library, making it difficult to obtain clonal information.
In this study, the research team developed the Spatial VDJ technology based on the Visium spatial transcriptomics platform. They also developed two versions: long-read (LR) Spatial VDJ and short-read (SR) Spatial VDJ.
The former utilizes long-read sequencing (third-generation sequencing) technology to construct libraries with positional information of T and B cell receptor sequences.
To facilitate the widespread adoption of this technology among more researchers, the team improved experimental operations, enabling the common short-read sequencing (second-generation sequencing) technology to also obtain spatial barcodes and clonal sequence information simultaneously.Researchers in the tonsil tissue, through the analysis of long-read Spatial VDJ sequencing results, identified a total of 62,533 unique TCR and BCR clones.
The biggest advantage of Spatial VDJ is its simplicity and ease of use. Specifically, it can directly hybridize and capture from the already obtained cDNA library, enrich the sequences of T and B cell receptors for sequencing, without the need to re-slice the samples from scratch, which greatly simplifies the operation process.
Compared with non-enriched Spatial GEX libraries, hybrid capture significantly increases the number of TCR and BCR sequences and retains the positional information of both sequences.
Spatial VDJ technology can not only obtain clone information but also be used to comprehensively understand the highly dynamic maturation process of B cells.
In fact, after re-activation, B cells will proliferate massively and select B cells with specific clones and higher affinity.In this study, we used the human tonsil as an experimental carrier to obtain a large number of T and B cell receptor sequences, demonstrating the method's good enrichment capability and application potential, said Lin Qirong.
Spatial VDJ is the first technology that can display the dynamics of clonal evolution in tissue/space.
For example, researchers observed the evolution of a single clonal family in two different germinal centers, which is difficult to intuitively observe in studies relying on single-cell sequencing.
"Thanks to the longer sequencing length, we can make more refined distinctions of clonal lineages and restore their spatial distribution, as if we took a snapshot of the clonal evolution process," said Lin Qirong.Has Potential for Application in Basic Biology/Medicine and Clinical Settings
In this study, researchers have verified the feasibility and reproducibility of the Spatial VDJ method, and demonstrated its potential for application in basic biology/medicine and clinical settings.
In terms of the development of basic biological theories, Spatial VDJ provides more research directions and possibilities. For example, exploring the developmental dynamics of immune cells, the spatial relationships between immune and non-immune cells, and their potential interactions.
Specifically, Spatial VDJ can be involved in the maturation process of B cells, the recruitment process of T cells and B cells to local tissues, participation in immune processes, and whether the immune responses involving different clones have clonal specificity.
In the clinical aspect, the Spatial VDJ technology can also be used to evaluate and optimize immunotherapy strategies. By analyzing the VDJ rearrangement patterns and spatial distribution of immune cells in tissues, combined with spatial transcriptome information to assess the targeting of immunotherapy, it provides guidance for the individualization and targeted treatment of immunotherapy.At the same time, people can locate T cell and B cell clones in space, and further determine their positional relationships within the tumor.
That is to say, researchers or clinicians can directly see individual immune cell clones related to the tumor, and analyze whether they are at the edge of the tumor or within the tumor, to assist in the formulation of tumor immunotherapy plans, or to explore the mechanisms of tumor immune escape and the potential of immunotherapy.
On the other hand, people can find potential antigens through the sequence of antibodies, to assist in the treatment of autoimmune diseases.
In addition, Spatial VDJ can also be used to study and optimize the positioning and distribution of immune cells in the field of tissue engineering and regenerative medicine, which is helpful to improve the immune adaptability and functionality of tissue engineering constructs.
It is understood that in the next stage of research, researchers plan to continue to explore biological issues in the direction of immunology, more in-depth and extensive, based on the value of biology and clinical.For instance, confirming the specific distribution of immune cells in tumors, the interrelationship between the clonal diversity of immune cells and tumor heterogeneity, and the developmental dynamics of B cells in different tissues and organs, etc.
The team hopes that through in-depth exploration and research, they can help the clinic solve the current problems in tumor immunity.
At the same time, from the perspective of basic biological research, it is necessary to reveal the related mechanisms, explore the developmental dynamics of immune cells, the spatial interrelationships between immune and non-immune cells, and their potential interactions.
The breakthrough progress of this study is not only due to the long-term technical accumulation of the research group, but also inseparable from the open, inclusive, and friendly scientific research atmosphere within and between groups.
In reality, everyone's time and ability are limited, and it is difficult for a person to "fight alone" to solve all the problems in scientific research. Although the cooperation team comes from different universities and research groups, it is an inseparable whole in the process of cooperation."Each member of the collaboration leverages their professional knowledge and expertise to actively address problems. Inevitably, we engage in intense discussions, but ultimately, we reach a scientific consensus and proceed with the research topic. This has been my deepest insight from this study," Lin Qirong concluded.
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