Haematopoietic Stem Cell Transplantation Results in Extensive Remodelling of the Clonal T Cell Repertoire in Multiple Sclerosis

Abstract

Autologous haematopoietic stem cell transplantation (AHSCT) is a vital therapeutic option for patients with highly active multiple sclerosis (MS). Rates of remission suggest AHSCT is the most effective form of immunotherapy in controlling the disease. Despite an evolving understanding of the biology of immune reconstitution following AHSCT, the mechanism by which AHSCT enables sustained disease remission beyond the period of lymphopenia remains to be elucidated. Auto-reactive T cells are considered central to MS pathogenesis. Here, we analyse T cell reconstitution for 36 months following AHSCT in a cohort of highly active MS patients. Through longitudinal analysis of sorted naïve and memory T cell clones, we establish that AHSCT induces profound changes in the dominant T cell landscape of both CD4+ and CD8+ memory T cell clones. Lymphopenia induced homeostatic proliferation is followed by clonal attrition; with only 19% of dominant CD4 (p <0.025) and 13% of dominant CD8 (p <0.005) clones from the pre-transplant repertoire detected at 36 months. Recovery of a thymically-derived CD4 naïve T cell repertoire occurs at 12 months and is ongoing at 36 months, however diversity of the naïve populations is not increased from baseline suggesting the principal mechanism of durable remission from MS after AHSCT relates to depletion of putative auto-reactive clones. In a cohort of MS patients expressing the MS risk allele HLA DRB1*15:01, public clones are probed as potential biomarkers of disease. AHSCT appears to induce sustained periods of disease remission with dynamic changes in the clonal T cell repertoire out to 36 months post-transplant.

High titre neutralizing antibodies in response to SARS–CoV–2 infection require RBD–specific CD4 T cells that include proliferative memory cells

“…RNA was extracted from bulk proliferated cultures using RNAeasy micro kit (Qiagen) as per manufacturer’s instructions. TCR high throughput RNA sequencing methods have been previously published in detail ( 44 ). Briefly, reverse transcription of RNA was performed using a modified SmartSeq2 protocol that incorporated a 10bp universal molecular identifiers (UMI) into cDNA molecules.…”

“…Purified PCR products were then barcoded using the Nextera Index kit to enable pooling of multiple samples and sequenced on an Illumina MiSeq at 300bp paired-end reads to a depth of ~0.5 million read pairs per sample. Primer sequences were as previously described ( 44 ).…”

High titre neutralizing antibodies in response to SARS-CoV-2 infection require RBD-specific CD4 T cells that include proliferative memory cells

“…RNA was extracted from bulk proliferated cultures using RNAeasy micro kit (Qiagen) as per manufacturer’s instructions. TCR high throughput RNA sequencing methods have been previously published in detail ( 74 ). Briefly, reverse transcription of RNA was performed using a modified SmartSeq2 protocol that incorporated a 10bp universal molecular identifiers (UMI) into cDNA molecules.…”

“…Purified PCR products were then barcoded using the Nextera Index kit to enable pooling of multiple samples and sequenced on an Illumina MiSeq at 300bp paired-end reads to a depth of ∼0.5 million read pairs per sample. Primer sequences were as previously described ( 74 ).…”

Autologous Hematopoietic Stem Cell Transplantation for Multiple Sclerosis, the Ottawa Protocol

“…Following aHSCT, there is a global and antigen‐specific shift favoring regulatory over pro‐inflammatory lymphocyte phenotypes in the peripheral circulation (Darlington et al., 2018) and an alteration of the T cell repertoire—particularly in the CD4 T cell population. The reconstituted T cell repertoire in blood is composed of novel clonotypes resulting from de novo lymphopoiesis as well as the persistence of some clonotypes present before aHSCT (Massey et al., 2022; Muraro et al., 2005), However, the reconstituted T cell repertoire in the CSF is predominantly composed of novel clonotypes generated from hematopoietic stem cells (HSC) with a smaller population of clonotypes resulting from pre‐transplant memory cells (Harris et al., 2020). These changes representing a “re‐education” of the immune system provide a plausible explanation for the clinical self‐tolerance and protective immune responses that occurs after aHSCT (Cencioni et al., 2021).…”