Defining T cell receptor repertoires using nanovial-based binding and functional screening

The ability to selectively bind to antigenic peptides and secrete effector molecules can define rare and low-affinity populations of cells with therapeutic potential in emerging T cell receptor (TCR) immunotherapies. We leverage cavity-containing hydrogel microparticles, called nanovials, each coated with peptide-major histocompatibility complex (pMHC) monomers to isolate antigen-reactive T cells. T cells are captured and activated by pMHCs inducing the secretion of effector molecules including IFN-γ and granzyme B that are accumulated on nanovials, allowing sorting based on both binding and function. The TCRs of sorted cells on nanovials are sequenced, recovering paired αβ-chains using microfluidic emulsion-based single-cell sequencing. By labeling nanovials having different pMHCs with unique oligonucleotide-barcodes and secretions with oligo-barcoded detection antibodies, we could accurately link TCR sequences to specific targets and rank each TCR based on the corresponding cell's secretion level. Using the technique, we identified an expanded repertoire of functional TCRs targeting viral antigens with high specificity and found rare TCRs with activity against cancer-specific splicing-enhanced epitopes.

Temporal evolution reveals bifurcated lineages in aggressive neuroendocrine small cell prostate cancer trans-differentiation

Trans-differentiation from an adenocarcinoma to a small cell neuroendocrine state is associated with therapy resistance in multiple cancer types. To gain insight into the underlying molecular events of the trans-differentiation, we perform a multi-omics time course analysis of a pan-small cell neuroendocrine cancer model (termed PARCB), a forward genetic transformation using human prostate basal cells and identify a shared developmental, arc-like, and entropy-high trajectory among all transformation model replicates. Further mapping with single cell resolution reveals two distinct lineages defined by mutually exclusive expression of ASCL1 or ASCL2. Temporal regulation by groups of transcription factors across developmental stages reveals that cellular reprogramming precedes the induction of neuronal programs. TFAP4 and ASCL1/2 feedback are identified as potential regulators of ASCL1 and ASCL2 expression. Our study provides temporal transcriptional patterns and uncovers pan-tissue parallels between prostate and lung cancers, as well as connections to normal neuroendocrine cell states.

Dual-inhibitory domain iCARs improve the efficiency of the AND-NOT gate CAR T strategy

CAR (chimeric antigen receptor) T cell therapy has shown clinical success in treating hematological malignancies, but its treatment of solid tumors has been limited. One major challenge is on-target, off-tumor toxicity, where CAR T cells also damage normal tissues that express the targeted antigen. To reduce this detrimental side-effect, Boolean-logic gates like AND-NOT gates have utilized an inhibitory CAR (iCAR) to specifically curb CAR T cell activity at selected nonmalignant tissue sites. However, the strategy seems inefficient, requiring high levels of iCAR and its target antigen for inhibition. Using a TROP2-targeting iCAR with a single PD1 inhibitory domain to inhibit a CEACAM5-targeting CAR (CEACAR), we observed that the inefficiency was due to a kinetic delay in iCAR inhibition of cytotoxicity. To improve iCAR efficiency, we modified three features of the iCAR-the avidity, the affinity, and the intracellular signaling domains. Increasing the avidity but not the affinity of the iCAR led to significant reductions in the delay. iCARs containing twelve different inhibitory signaling domains were screened for improved inhibition, and three domains (BTLA, LAIR-1, and SIGLEC-9) each suppressed CAR T function but did not enhance inhibitory kinetics. When inhibitory domains of LAIR-1 or SIGLEC-9 were combined with PD-1 into a single dual-inhibitory domain iCAR (DiCARs) and tested with the CEACAR, inhibition efficiency improved as evidenced by a significant reduction in the inhibitory delay. These data indicate that a delicate balance between CAR and iCAR signaling strength and kinetics must be achieved to regulate AND-NOT gate CAR T cell selectivity.

IRIS: Discovery of cancer immunotherapy targets arising from pre-mRNA alternative splicing

Alternative splicing (AS) is prevalent in cancer, generating an extensive but largely unexplored repertoire of novel immunotherapy targets. We describe Isoform peptides from RNA splicing for Immunotherapy target Screening (IRIS), a computational platform capable of discovering AS-derived tumor antigens (TAs) for T cell receptor (TCR) and chimeric antigen receptor T cell (CAR-T) therapies. IRIS leverages large-scale tumor and normal transcriptome data and incorporates multiple screening approaches to discover AS-derived TAs with tumor-associated or tumor-specific expression. In a proof-of-concept analysis integrating transcriptomics and immunopeptidomics data, we showed that hundreds of IRIS-predicted TCR targets are presented by human leukocyte antigen (HLA) molecules. We applied IRIS to RNA-seq data of neuroendocrine prostate cancer (NEPC). From 2,939 NEPC-associated AS events, IRIS predicted 1,651 epitopes from 808 events as potential TCR targets for two common HLA types (A*02:01 and A*03:01). A more stringent screening test prioritized 48 epitopes from 20 events with "neoantigen-like" NEPC-specific expression. Predicted epitopes are often encoded by microexons of ≤30 nucleotides. To validate the immunogenicity and T cell recognition of IRIS-predicted TCR epitopes, we performed in vitro T cell priming in combination with single-cell TCR sequencing. Seven TCRs transduced into human peripheral blood mononuclear cells (PBMCs) showed high activity against individual IRIS-predicted epitopes, providing strong evidence of isolated TCRs reactive to AS-derived peptides. One selected TCR showed efficient cytotoxicity against target cells expressing the target peptide. Our study illustrates the contribution of AS to the TA repertoire of cancer cells and demonstrates the utility of IRIS for discovering AS-derived TAs and expanding cancer immunotherapies.

Defining T cell receptor repertoires using nanovial-based affinity and functional screening

The ability to selectively bind to antigenic peptides and secrete cytokines can define populations of cells with therapeutic potential in emerging T cell receptor (TCR) immunotherapies. We leverage cavity-containing hydrogel microparticles, called nanovials, each coated with millions of peptide-major histocompatibility complex (pMHC) monomers to isolate antigen-reactive T cells. T cells are captured and activated by pMHCs and secrete cytokines on nanovials, allowing sorting based on both affinity and function. The TCRs of sorted cells on nanovials are sequenced, recovering paired αβ-chains using microfluidic emulsion-based single-cell sequencing. By labeling nanovials having different pMHCs with unique oligonucleotide-barcodes we could link TCR sequence to targets with 100% accuracy. We identified with high specificity an expanded repertoire of functional TCRs targeting viral antigens compared to standard techniques.

Abstract 2438: Determining the role of non-mutated C-Raf kinase in metastatic disease

Many aggressive epithelial cancers do not carry targetable driver mutations (Mendiratta et al. 2021, NCI-MATCH Clinical trial NCT02465060). Commonly altered signaling pathways highlight the propensity for tumors to depend on such pathways for growth and survival where genomic alterations may not be required for pathway activation. The Raf family kinases are crucial mediators of the Ras/Raf/MEK/ERK (MAPK) cascade, which has been shown to be upregulated in a subset of metastatic cancers and are mutated in many epithelial cancers. A recent study suggests non-mutated C-Raf can drive metastasis to the lungs, bone, and various other tissues (Faltermeir et al. 2016). Though the mechanism of C-Raf driven metastasis is likely through MAPK activation, C-Raf has been demonstrated to possess MAPK independent roles that may also contribute to this phenotype. In this study, we explored various C-Raf functions as drivers of metastasis in an intracardiac mouse model system. Using a series of Raf knock-out cell lines and mutants targeting functional residues in C-Raf, we demonstrated that C-Raf dimerization is necessary to drive metastasis. We further showed that the metastasis-promoting activity of C-Raf is dependent on co-expression of its family member, B-Raf, for an accelerated metastatic phenotype. However, overexpression of a kinase-dead C-Raf mutant was still able to produce metastases albeit with lower efficiency, suggesting C-Raf possesses non-kinase dependent functions that also contributed to metastasis. Together, these results point to the importance of Raf non-canonical roles in oncogenic processes that may be unappreciated in metastatic disease.

Citation Format: Lisa H. Ta, Janai R. Carr-Ascher, Weixian Deng, Brandon L. Tsai, Wendy Tran, Donny Gun, Donghui Cheng, Jihui Sha, Yeonjoo Hwang, John W. Phillips, Matthew B. Obusan, Nathanael J. Bangayan, Miyako Noguchi, Zhiyuan Mao, Chia-Chun Chen, Liang Wang, Grigor Varuzhanyan, John D. Gordon, James W. Wohlschlegel, Owen N. Witte. Determining the role of non-mutated C-Raf kinase in metastatic disease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2438.

Potential impact factors on the enhancement of antibiotic resistance in a lake environment

There is considerable concern regarding antibiotic resistance in the water environment due to antibiotic residues from anthropogenic origins. The low antibiotic concentration in the water environment may promote the selection of antibiotic resistance. However, it is unclear how environmental factors affect resistance selection. We investigated the proliferation of quinolone-susceptible faecal bacteria (E. coli) exposed to low norfloxacin concentration (ng/L) at variable temperatures, exposure times, and carbon concentrations, simulating the conditions of the water environment. The induction of antibiotic resistance in thirteen E. coli isolates was more likely to occur at 37 °C. However, resistance also occurred at temperatures as low as 25 °C, provided a longer exposure time of 5 days. These results suggest that antibiotic resistance is more likely to be induced in regions where temperatures may reach 25-37 °C, such as tropical regions.

HLA-A∗02:01 restricted T cell receptors against the highly conserved SARS-CoV-2 polymerase cross-react with human coronaviruses

Cross-reactivity and direct killing of target cells remain underexplored for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-specific CD8⁺ T cells. Isolation of T cell receptors (TCRs) and overexpression in allogeneic cells allows for extensive T cell reactivity profiling. We identify SARS-CoV-2 RNA-dependent RNA polymerase (RdRp/NSP12) as highly conserved, likely due to its critical role in the virus life cycle. We perform single-cell TCRαβ sequencing in human leukocyte antigen (HLA)-A^∗02:01-restricted, RdRp-specific T cells from SARS-CoV-2-unexposed individuals. Human T cells expressing these TCRαβ constructs kill target cell lines engineered to express full-length RdRp. Three TCR constructs recognize homologous epitopes from common cold coronaviruses, indicating CD8⁺ T cells can recognize evolutionarily diverse coronaviruses. Analysis of individual TCR clones may help define vaccine epitopes that can induce long-term immunity against SARS-CoV-2 and other coronaviruses.

Relationships between management factors in dairy production systems and mental health of farm managers in Japan

To facilitate sustainable dairy farming, it is essential to assess and support the mental health of dairy farm workers, which is affected more than that of workers in other industries, as indicated by the relatively few studies to date. In addition, the limited investigations on mental health in dairy workers minimize the opportunities to suggest practical approaches of improvement of their mental health. Therefore, further data acquisition and analysis is required. In the present study, we undertook quantitative surveys on 17 management factors and administered a mental health questionnaire to 81 dairy farm managers (80 male, 1 female) in Hokkaido, northern Japan. The management factors were categorized into 3 groups: production input, production output, and facility indicator; mental health was evaluated based on the Center for Epidemiologic Studies Depression Scale (CES-D). Principal component analysis assigned the factors into 2 groups: intensiveness factors of dairy production systems (PC1: livestock care cost, fat- and protein-corrected milk, stocking density, medical consultation fee per unit time per animal unit, nonfamily wages, fertilizer and pesticide expenses, and net agricultural income ratio) and basic dairy management factors (PC2: net agricultural income ratio, quantity of concentrate feed, and milk quality variable). The depression symptoms of dairy farm managers were not significantly associated with PC1 and milking methods; however, they were significantly negatively associated with PC2, which integrated 3 management factors, including factors related to finances, feeding, and milk quality. According to the findings of the present study, the efforts needed for stable economic farm management, adequate feed supply, and milk quality maintenance may increase the depression levels of dairy farm managers and negatively affect their mental health. These findings could be the basis for future studies on the relationship between the mental health of farm managers and sustainable dairy farm management and production.

The involvement of axillary reverse mapping nodes in patients with clinically node-negative breast cancer

BACKGROUND

Axillary reverse mapping (ARM) was developed to preserve the lymphatic drainage from the upper arm during sentinel lymph-node (SLN) biopsy or axillary lymph-node dissection (ALND). However, the oncological safety of ARM has been controversial because of not infrequent involvement of ARM nodes.

METHODS

Patients with clinically negative nodes (cN0) underwent SLN biopsy and ARM. SLNs were identified using blue dye and radioisotope, and ARM nodes were traced using the fluorescent method. Patients with positive SLN underwent the standard ALND. After surgery, they were followed up for more than 3 years.

RESULTS

A total of 507 patients with cN0 breast cancer were enrolled between May 2009 and November 2017. SLNs were identified in 499 (98%) of 507 patients, and ARM nodes were identified in 159 (31%) patients in the SLN field. The crossover rate of SLN-ARM nodes was 28%. Among 95 patients with positive SLNs, 70 patients underwent conventional ALND. ARM nodes were identified in 65 (93%) of those patients in the ALND field. The mean number of removed ARM nodes was 7.2 (range 0-25) in patients who underwent the standard ALND. Although ARM nodes were involved in 18 of 65 patients, the involved ARM nodes were the same SLNs identified in 14 (78%) patients. Since SLN-ARM nodes should be removed, ARM nodes were involved only in 4 (5.7%) patients after SLN biopsy.

CONCLUSIONS

Except for positive SLN-ARM nodes, the involvement of ARM nodes is infrequent in patients with positive SLN.

Culture independent approach reveals domination of human-oriented microbes in a pharmaceutical manufacturing facility

Strict microbial control is required in pharmaceutical manufacturing facilities, for which environmental microbial monitoring is fundamental. Appropriate microbial control is based on understanding the abundance and community structure of the microbes in the target environment, but most microbes are not culturable by conventional methods. Here, we determined the bacterial abundance and assessed the environmental microbiome in a pharmaceutical manufacturing facility using rRNA gene-targeted quantitative PCR (qPCR) and high-throughput sequencing of rRNA gene fragments. A commercially available microbial particle counter was also used for real-time measurements. In the air of the first gowning room and the passageway of the facility, the microbial particle number determined by both the particle counter and qPCR was ca. 10⁴/m³; the number of microbial particles was about 100 times the number of culturable bacteria. Thus, the measurement of microbes using the particle counter was accurate. In the second gowning room of the facility, managed by a HEPA filter, the number of particles in the air was dependent on human movement, and was below the detection limit around 10 min after movement. Bacteria of the phyla Proteobacteria, Firmicutes, and Actinobacteria were frequently detected in samples from the facility; these bacteria are constituents of the human microbiota. Among fungi, Aspergillus and Cladosporium were detected in the air, and Malassezia was dominant on the walls. Our results provide fundamental data for the evaluation and control of microbes in pharmaceutical and food industry facilities.

Endogenous protein and enzyme fragments induce immunoglobulin E-independent activation of mast cells via a G protein-coupled receptor, MRGPRX2

Mast cells play a central role in inflammatory and allergic reactions by releasing inflammatory mediators through 2 main pathways, immunoglobulin E-dependent and E-independent activation. In the latter pathway, mast cells are activated by a diverse range of basic molecules (collectively known as basic secretagogues) through Mas-related G protein-coupled receptors (MRGPRs). In addition to the known basic secretagogues, here, we discovered several endogenous protein and enzyme fragments (such as chaperonin-10 fragment) that act as bioactive peptides and induce immunoglobulin E-independent mast cell activation via MRGPRX2 (previously known as MrgX2), leading to the degranulation of mast cells. We discuss the possibility that MRGPRX2 responds various as-yet-unidentified endogenous ligands that have specific characteristics, and propose that MRGPRX2 plays an important role in regulating inflammatory responses to endogenous harmful stimuli, such as protein breakdown products released from damaged or dying cells.