T Cell Receptor Repertoire Sequencing

T-cell Recovery After Autologous Hematopoietic Stem Cell Transplantation in Autoimmune Diseases

Over the last three decades, autologous hematopoietic stem cell transplantation (AHSCT) has emerged as a significant therapeutic strategy for patients with various refractory autoimmune diseases. Globally, more than 3000 AHSCT procedures have been performed for severe autoimmune diseases. The rationale behind this treatment is abrogation of autoreactivity; renovation of the immune system from the infused hematopoietic stem cells and establishment of a balanced, long-lasting, and self-tolerant immune system. Thymic rebound is a central event in the mechanisms of action of transplantation, promoting the generation of a new repertoire of T cells and reinstating self-tolerance. Here, we critically review the immunological mechanisms of AHSCT in various autoimmune disease settings, with a central focus on thymic rejuvenation. We understand that elucidating the mechanisms of action of the transplant and conducting immunological monitoring studies are crucial for comprehending the risks, benefits, and long-term efficacy of the treatment, thereby promoting functional improvements in patients with autoimmune diseases refractory to conventional treatment.

A Framework to Predict the Molecular Classification and Prognosis of Breast Cancer Patients and Characterize the Landscape of Immune Cell Infiltration

It is known that all current cancer therapies can only benefit a limited proportion of patients; thus, molecular classification and prognosis evaluation are critical for correctly classifying breast cancer patients and selecting the best treatment strategy. These processes usually involve the disclosure of molecular information like mutation, expression, and immune microenvironment of a breast cancer patient, which are not been fully studied until now. Therefore, there is an urgent clinical need to identify potential markers to enhance molecular classification, precision prognosis, and therapy stratification for breast cancer patients. In this study, we explored the gene expression profiles of 1,721 breast cancer patients through CIBERSORT and ESTIMATE algorithms; then, we obtained a comprehensive intratumoral immune landscape. The immune cell infiltration (ICI) patterns of breast cancer were classified into 3 separate subtypes according to the infiltration levels of 22 immune cells. The differentially expressed genes between these subtypes were further identified, and ICI scores were calculated to assess the immune landscape of BRCA patients. Importantly, we demonstrated that ICI scores correlate with patients' survival, tumor mutation burden, neoantigens, and sensitivity to specific drugs. Based on these ICI scores, we were able to predict the prognosis of patients and their response to immunotherapy. Together, these findings provide a realistic scenario to stratify breast cancer patients for precision medicine.

Identification and Characterization of Antigen-Specific CD8+ T Cells Using Surface-Trapped TNF-α and Single-Cell Sequencing

CD8+ T cells are key mediators of antiviral and antitumor immunity. The isolation and study of Ag-specific CD8+ T cells, as well as mapping of their MHC restriction, has practical importance to the study of disease and the development of therapeutics. Unfortunately, most experimental approaches are cumbersome, owing to the highly variable and donor-specific nature of MHC-bound peptide/TCR interactions. Here we present a novel system for rapid identification and characterization of Ag-specific CD8+ T cells, particularly well suited for samples with limited primary cells. Cells are stimulated ex vivo with Ag of interest, followed by live cell sorting based on surface-trapped TNF-α. We take advantage of major advances in single-cell sequencing to generate full-length sequence data from the paired TCR α- and β-chains from these Ag-specific cells. The paired TCR chains are cloned into retroviral vectors and used to transduce donor CD8+ T cells. These TCR transductants provide a virtually unlimited experimental reagent, which can be used for further characterization, such as minimal epitope mapping or identification of MHC restriction, without depleting primary cells. We validated this system using CMV-specific CD8+ T cells from rhesus macaques, characterizing an immunodominant Mamu-A1*002:01-restricted epitope. We further demonstrated the utility of this system by mapping a novel HLA-A*68:02-restricted HIV Gag epitope from an HIV-infected donor. Collectively, these data validate a new strategy to rapidly identify novel Ags and characterize Ag-specific CD8+ T cells, with applications ranging from the study of infectious disease to immunotherapeutics and precision medicine.

Is Global Microbial Biodiversity Increasing, Decreasing, or Staying the Same?

Animal and plant biodiversity is decreasing. In contrast, the global direction and the pace of change in microbial, including viral, biodiversity is unknown. Important niches for microbial diversity occur in highly specific associations with plants and animals, and these niches are lost as hosts become extinct. The taxonomic diversity of human gut bacteria is reported to be decreasing. On the other hand, SARS-CoV-2 variation is increasing. Where microbes are concerned, Darwin’s “tangled bank” of interdependent organisms may be composed mostly of other microbes. There is the likelihood that as some classes of microbes become extinct, others evolve and diversify. A better handle on all processes that affect microbial biodiversity and their net balance is needed. Lack of insight into the dynamics of evolution of microbial biodiversity is arguably the single most profound and consequential unknown with regard to human knowledge of the biosphere. If some or all parts of microbial diversity are relentlessly increasing, then survey approaches may be too slow to ever catch up. New approaches, including single-molecule or single-cell sequencing in populations, as well as focused attention on modulators and vectors of vertical and horizontal evolution may offer more direct insights into some aspects of the pace of microbial evolution.