Biology subjects

Rubinstein, M. P.

Publications and source records attributed to Rubinstein, M. P..

5 recordsLinked to original sources

bioRxiv2024

A workflow for targeted proteomics assay development using a versatile linear ion trap

Advances in proteomics and mass spectrometry have enabled the study of limited cell populations, such as single-cell proteomics, where high-mass accuracy instruments are typically required. While triple quadrupoles offer fast and sensitive nominal resolution measurements, these instruments are effectively limited to targeted proteomics. Linear ion traps (LITs) offer a versatile, cost-effective alternative capable of both targeted and global proteomics. We demonstrate a workflow using a newly released, hybrid quadrupole-LIT instrument for developing targeted proteomics assays from global data-independent acquisition (DIA) measurements without needing high-mass accuracy. Gas-phase fraction-based DIA enables rapid target library generation in the same background chemical matrix as each quantitative injection. Using a new software tool embedded within EncyclopeDIA for scheduling parallel reaction monitoring assays, we show consistent quantification across three orders of magnitude of input material. Using this approach, we demonstrate measuring peptide quantitative linearity down to 25x dilution in a background of only a 1 ng proteome without requiring stable isotope labeled standards. At 1 ng total protein on column, we found clear consistency between immune cell populations measured using flow cytometry and immune markers measured using LIT-based proteomics. We believe hybrid quadrupole-LIT instruments represent an economic solution to democratizing mass spectrometry in a wide variety of laboratory settings.

biochemistry↗

bioRxiv2021

Discovering tumor-reactive T-cell receptors through single-cell sequencing of tumor-infiltrating lymphocytes

We evaluated the utility of single-cell sequencing of tumor-infiltrating lymphocytes (TIL) for tumor-reactive T-cell receptor (TCR) discovery. Using the MC38 cell line as our tumor model in mice, we show that expression of exogenous TCRs via mRNA electroporation in human T cells provides an easy and quick path to validating tumor-specific candidate TCRs. We detail the identification and validation of four novel MC38-reactive mouse TCRs with varying levels of reactivity to the target cells. Validating our process, one of the MC38 TCRs is specific against a previously reported neoantigen (ASMTNMELM in the Adpgk gene). Consideration of these methodologies may aid in the development of rapid TCR-based therapies for the treatment of cancer and human disease. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=197 SRC="FIGDIR/small/470597v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@792d44org.highwire.dtl.DTLVardef@18af6aforg.highwire.dtl.DTLVardef@498c2aorg.highwire.dtl.DTLVardef@9127e8_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2021

B cells imprint adoptively transferred CD8+ T cells with enhanced tumor immunity

Here we report a novel strategy to reverse the tolerant state of adoptively transferred CD8+ T cells against melanoma through ex vivo expansion with the TLR9 agonist CpG. T cells generated in the presence of CpG display potent anti-tumor efficacy without in vivo co-administration of high dose IL-2 or vaccination, which are classically required for effective treatment of solid tumors using adoptive cell therapies. CD8+ T cells adopt a unique proteomic signature and are characterized by an IL-2RhighICOShighCD39low phenotype after CpG-mediated expansion. Surprisingly, we found that the presence of B cells, in the culture, was essential for imprinting CD8+ T cells with this phenotype and moreover purified B cells were sufficient to mediate the CpG-associated changes in T cells. These findings reveal a vital role for B cells in the generation of effective antitumor CD8+ T cells and have immediate implications for profoundly improving immunotherapy for patients. SUMMARY STATEMENTThe TLR9 agonist CpG allows B cells to license adoptively transferred CD8+ T cells with potent tumor immunity. These licensed T cells have a unique proteomic signature, are marked by low CD39 and high ICOS and IL-2R expression, and engraft robustly in vivo.

immunology↗

bioRxiv2021

Modeling ex vivo tumor-infiltrating lymphocyte expansion from established solid malignancies

Adoptive transfer of tumor-infiltrating lymphocytes (TIL) elicits the regression of metastatic malignancies, yet a low proportion of patients achieve complete durable responses. The high incidence of relapse in these patients highlights the need to better understand mechanisms of tumor escape from T cell control. While melanoma has provided the foundation for developing TIL therapy, much less is known about TIL efficacy and relapse in other malignancies. We sought to investigate TIL characteristics in mouse tumors which have not been studied in this setting. Here, we expanded murine TIL ex vivo in IL-2 from fragments of multiple tumor models, including oral cavity cancer models of varying immunogenicity. Additionally, TIL was expanded from pmel-1 mice bearing B16 melanoma, yielding an enriched population of tumor-infiltrating TCR transgenic T cells. Murine TILs are similar to human TIL in that they express high levels of inhibitory receptors (PD-1, Tim-3, etc.) and can be expanded ex vivo in IL-2 extensively. Of clinical relevance, we draw parallels between murine and patient TIL, evaluating relationships between PD-1, Lag-3, and Tim-3 on TILs from a cohort of oral cavity cancer patients. This platform can be used by labs even in the absence of clinical specimens or clean cell facilities and will be important to more broadly understand TIL phenotypes across many different malignancies.

immunology↗

bioRxiv2020

Identification of human CD4+ T cell populations with distinct antitumor activity

How naturally arising human CD4+ T helper subsets impact tumor immunity is unknown. We reported that human CD4+CD26high T cells elicit potent immunity against solid tumor malignancies. As CD26high T cells secrete type-17 cytokines and have been categorized as Th17 cells, we posited these helper populations would possess similar molecular properties. Herein, we reveal that CD26high T cells are epigenetically and transcriptionally distinct from Th17 cells. Of clinical significance, CD26high T cells engineered with a chimeric antigen receptor (CAR) ablated large human tumors to a greater extent than enriched Th17, Th1, or Th2 cells. Moreover, CD26high T cells mediated curative responses in mice, even when redirected with a suboptimal CAR and without the aid of CD8+ CAR T cells. CD26high T cells co-secreted effector cytokines at heightened levels and robustly persisted. Collectively, our work reveals the potential of human CD4+ T cell populations to improve durability of solid tumor therapies.

immunology↗