Oxford Nanopore technology used to uncover insights into complex immune system genes, paving the way for future antibody therapies

In a new preprint, teams at Oxford Nanopore and Mount Sinai describe a method of nanopore full-length, single-cell transcriptome sequencing that was used to explore multiple features of the immune system’s reactive antibody response, showing future potential for antibody therapies to support immunotherapy.

Oxford Nanopore sequencing technology has been used to explore and assemble the notoriously complex immune system repertoire, creating a new method to replicate specific human antibodies using a combination of whole genome and single-cell sequencing. These findings could support the future development of immunotherapies that would help a range of patients who are immunosuppressed, for example, and need support fighting infections by recognising – and calling other immune cells to destroy – pathogens such as viruses, bacteria or toxins.

The immune system is a complex network of cells, tissues and organs that collaborate to defend the body against infection and foreign invaders. The adaptive immune system provides a specific, targeted response to pathogens by developing a memory of past exposures stored by immune cells, known as B cells, that secrete antibodies. These antibodies then bind to and signal for other immune cells to destroy these invaders more rapidly and robustly.

In a new preprint publication, a team led by scientists from Oxford Nanopore and the Icahn School of Medicine at Mount Sinai outline a method using Oxford Nanopore long read sequencing and single-cell antibody sequencing to assemble complex immune genes from blood samples, characterising antibody diversity at the DNA and RNA level in the same individual. Single-cell RNA from B cells was prepared using a 10x Genomics kit and sequenced using Oxford Nanopore long reads, enabling the team to generate and validate individual antibody consensus sequences.

Unlike short-read approaches, which miss novel transcripts and isoforms, long-read sequencing was able to produce reads that spanned entire transcripts in single cells, removing the need for isoform reconstruction. This method unravelled the genetic components of the isoforms, which had previously been impossible to achieve using short-read methods only.

Finally, the team was able to use the sequence of the specific antiviral antibodies to produce functional antibody clones against viral antigens. These results show the potential of nanopore sequencing to detect specific antibodies in individuals who have successfully cleared infection – information that can then be used to produce the antibodies needed by others suffering from similar infections.

In this new study, the team used Oxford Nanopore’s PromethION device in combination with 10x Genomics Chromium Next GEM Single Cell 3’ Reagent kits v3.1.

Access the preprint in full here.