DPV-001 is an off-the-shelf biologic containing proteins that are overexpressed by adenocarcinoma and squamous cell cancers. It is enriched for short-lived proteins (SLiPs) and defective ribosomal products (DRiPs), containing canonical and non-canonical alternative cancer neoantigens (dark matter, at least 30 microproteins) in spectrin-coated microvesicles targeted to CLEC9A+ conventional dendritic cells (cDC).1 2 Preclinical models demonstrated enhanced antitumor activity when the murine version of DPV-001 was combined with co-stimulatory agonist(s) and delayed PD-1 blockade(d.PD-1), which formed the basis of the current trial.
Methods
Patients were randomized to receive heterologous prime-boost DPV-001 + sequenced d.PD-1 (retifanlimab Q4W) +/- GITR agonist (INCAGN-1949 Q2W). Tumor biopsies were obtained at baseline, week 2 and week 8, with longitudinal blood and serum sampling. Phenotypic and molecular studies were performed.
Results
18 pts have been treated (9 PD-1 refractory & 9 PD-1 naïve). Objective response was observed in 3/9 PD-1 refractory, and in 5/9 PD-1 naïve patients, including two complete responses, one of which continues past 24 months. Responses were observed in HPV+ and HPV- patients and 5 responders had PD-L1 CPS scores of <5. We observed irAE's (G1-3, no G4), at a breadth & frequency greater than would be expected for PD-1 alone, attesting to bioactivity. Tumor biopsy analysis by scRNA-seq identified expanded T cell clones displaying tumor-reactive effector phenotypes which were not detectable at baseline (n=6 pts x 3 biopsy timepoints). In the first patient, TCR reconstruction and functional evaluation of three expanded T cell clones confirmed reactivity against HLA-matched tumors, with one TCR recognizing HNSCC, LUAD, RCC, and melanoma cell lines.
Conclusions
DPV-001 + sequenced d.PD-1 +/- GITR showed promising response rates of 56% (PD-1 naïve) and 33% (PD-1 refractory) in recurrent/metastatic HNSCC pts. Initial functional studies suggests this treatment expanded T cell clones against shared antigens. Ongoing studies are directed at unraveling the nature of the antigens recognized (canonical or dark matter), and whether they persist.
Acknowledgements
Incyte, Murdock Charitable Trust, Providence Portland Medical Foundation, Nancy Lematta, Lynn Loacker, Cindy and Steve Harder, The Chiles Foundation, Robert W. Franz and Elsie Franz Finley
Trial Registration
NCT04470024.
References
Nicoletta Cieri, Catherine J Wu. Splice it up: atypical transcripts to boost leukemia immunotherapy. Immunity 2021;54:608–610 Bernard A Fox, Walter J Urba, Shawn M Jensen, David B Page, Brendan D Curti, Rachel E Sanborn, Rom S Leidner. Cancer's Dark Matter: Lighting the Abyss Unveils Universe of New Therapies. Clin. Can. Res. Clin Cancer Res 2023;29(12):2173–2175.
Ethics Approval
This study was approved by Providence Health System's Ethics Board; approval number 2020000480.
The fast evolving human KIR gene family encodes variable lymphocyte receptors specific for polymorphic HLA class I determinants. Nucleotide sequences for 24 representative human KIR haplotypes were determined. With three previously defined haplotypes, this gave a set of 12 group A and 15 group B haplotypes for assessment of KIR variation. The seven gene-content haplotypes are all combinations of four centromeric and two telomeric motifs. 2DL5, 2DS5 and 2DS3 can be present in centromeric and telomeric locations. With one exception, haplotypes having identical gene content differed in their combinations of KIR alleles. Sequence diversity varied between haplotype groups and between centromeric and telomeric halves of the KIR locus. The most variable A haplotype genes are in the telomeric half, whereas the most variable genes characterizing B haplotypes are in the centromeric half. Of the highly polymorphic genes, only the 3DL3 framework gene exhibits a similar diversity when carried by A and B haplotypes. Phylogenetic analysis and divergence time estimates, point to the centromeric gene-content motifs that distinguish A and B haplotypes having emerged ∼6 million years ago, contemporaneously with the separation of human and chimpanzee ancestors. In contrast, the telomeric motifs that distinguish A and B haplotypes emerged more recently, ∼1.7 million years ago, before the emergence of Homo sapiens. Thus the centromeric and telomeric motifs that typify A and B haplotypes have likely been present throughout human evolution. The results suggest the common ancestor of A and B haplotypes combined a B-like centromeric region with an A-like telomeric region.
Summary: With the advent of modern genomic sequencing technology the ability to obtain new sequence data and to acquire allelic polymorphism data from a broad range of samples has become routine. In this regard, our investigations have started with the most polymorphic of genetic regions fundamental to the immune response in the major histocompatibility complex (MHC). Starting with the completed human MHC genomic sequence, we have developed a resource of methods and information that provide ready access to a large portion of human and nonhuman primate MHCs. This resource consists of a set of primer pairs or amplicons that can be used to isolate about 15% of the 4.0 Mb MHC. Essentially similar studies are now being carried out on a set of immune response loci to broaden the usefulness of the data and tools developed. A panel of 100 genes involved in the immune response have been targeted for single nucleotide polymorphism (SNP) discovery efforts that will analyze 120 Mb of sequence data for the presence of immune‐related SNPs. The SNP data provided from the MHC and from the immune response panel has been adapted for use in studies of evolution, MHC disease associations, and clinical transplantation.
Retrospective characterization of cell-cell relationships in the tumor microenvironment provides significantly better predictive power than PD-L1 expression, tumor mutational burden (TMB), or gene expression profiles. In this small study assessing the safety and possible efficacy of gemcitabine and pembrolizumab in immunotherapy-naive patients with NSCLC who have received prior treatment, we investigated both standard and novel immune parameters on 16 enrolled patients. The combination of gemcitabine and pembrolizumab could be administered safely but did not demonstrate synergism compared with historical controls. Novel findings of this study are that elevated frequencies of Treg cells near CD3 T cells was associated with improved outcome to treatment (p<0.05), and integrating T cell density and T reg-T cell distance correlated (p<0.002) with disease response. We postulate this is indicative of ongoing anti-cancer immune response. Additionally, while prior studies documented that IgG Ab responses to TAA can identify targets of a coordinated T and B cell response and evidence of immune surveillance, this study found that high autoantibody responses, while not statistically significant, trended towards a worse outcome (p=0.06). This suggests to us that tumors may have developed mechanisms to escape the immune response to these TAAs.
Antioxidants have been considered a potential component that can enhance functions of food since these agents have pharmacological activities for multiple chronic disorders such as cancer, diabetes cardiovascular diseases, and age-related diseases. However, due to their low solubility, unstable during processing or storage, and chemical degradation, antioxidants have a limitation on bioavailability when applied in food products. Nanocarriers may assist in delivery of these components without changing good therapeutic properties by their unique physicochemical characteristic, structural characteristics and biological compatibility. Recently, lipid-based and polysaccharides-based nanocarriers have been explored as promising delivery systems of antioxidants by oral route. Positive results obtained across these nano-deliveries could give us new spreading methods for implication of antioxidants in therapeutic functions of foods.
ABSTRACT The innate antiviral factor TRIM5α restricts the replication of some retroviruses through its interaction with the viral capsid protein, leading to abortive infection. While overexpression of human TRIM5α results in modest restriction of human immunodeficiency virus type 1 (HIV-1), this inhibition is insufficient to block productive infection of human cells. We hypothesized that polymorphisms within TRIM5 may result in increased restriction of HIV-1 infection. We sequenced the TRIM5 gene (excluding exon 5) and the 4.8-kb 5′ putative regulatory region in genomic DNA from 110 HIV-1-infected subjects and 96 exposed seronegative persons, along with targeted gene sequencing in a further 30 HIV-1-infected individuals. Forty-eight single nucleotide polymorphisms (SNPs), including 20 with allele frequencies of >1.0%, were identified. Among these were two synonymous and eight nonsynonymous coding polymorphisms. We observed no association between TRIM5 polymorphism in HIV-1-infected subjects and their set-point viral load after acute infection, although one TRIM5 haplotype was weakly associated with more rapid CD4 + T-cell loss. Importantly, a TRIM5 haplotype containing the nonsynonymous SNP R136Q showed increased frequency among HIV-1-infected subjects relative to exposed seronegative persons, with an odds ratio of 5.49 (95% confidence interval = 1.83 to 16.45; P = 0.002). Nonetheless, we observed no effect of individual TRIM5α nonsynonymous mutations on the in vitro HIV-1 susceptibility of CD4 + T cells. Therefore, any effect of TRIM5α polymorphism on HIV-1 infection in primary lymphocytes may depend on combinations of SNPs or on DNA sequences in linkage disequilibrium with the TRIM5α coding sequence.
Neem oil (azadirachtin) is long known as a natural insecticide or medication for humans and animals. This study aimed to formulate an herbal shampoo and understand the efficacy of neem oil in the atopic treatment of companion animals (cats and dogs) of Vietnam. From November 2019 - May 2020, 35kg neem fruits were collected and extracted into essential oil. Four formulas were developed by adding the neem extract in different concentrations (0ml, 5ml, 10ml, 15ml) and endured trial on 40 families having dogs or cats for 2 weeks to evaluate the chemical properties and physical performance of the animals. The four formula surveys on consumers about neem shampoo showed good cleansing and detergency. Significantly, formula 3 (neem oil 10ml; glycerine 40g; bamboo vinegar 5ml; distilled water 150ml; coconut oil 25ml; coco betaine 40ml; vitamin E 4.7mg; pomelo flavor 2g) was selected due to good performance to treat skin diseases, ticks and fleas, and did not irritate people and pets. Further research and development are required to assess its optimal quality and safety.
Abstract Checkpoint inhibitors have been approved for the treatment of solid tumor and hematological malignancies. While significant responses have been observed in a subset of patients, outcomes are variable and there is a need to identify additional predictive biomarkers beyond PD-L1 levels as measured by IHC. Tumor mutation burden (TMB) has been correlated with response to checkpoint inhibitors and is emerging as a key biomarker for predicting checkpoint inhibitor response. So far, the methods used to assess tumor mutation burden have included exome sequencing and multiple laboratory-developed targeted NGS panels (e.g., FoundationOne and MSK-IMPACT). In order to fully determine the value of TMB as a predictive biomarker for immunotherapy, a standardized panel, workflow and data analysis pipeline for TMB assessment are needed. In this study we evaluated the performance of a commercially available targeted NGS panel and workflow for TMB analysis. A set of 30 FFPE tumor samples including colon, renal, gastric, endometrial, and lung tissues was analyzed. DNA and RNA were extracted using the RecoverAll Total Nucleic Acid Isolation Kit. DNA quantity and quality were assessed using Qubit and qPCR, respectively. Samples were analyzed with the ThermoFisher Oncomine™ Mutation Load Research Assay (TML), which evaluates tumor mutation load (mutations/Mb) by interrogating 409 cancer-related genes, spanning ~1.7 megabases of the genome. TMB was measured by counting somatic single-base substitutions per Mb at ≥10% allele frequency in single, non-matched, tumor DNA samples. The impact of DNA quality on the TMB score was evaluated. Deamination errors (i.e. G>A and C>T) in poor quality FFPE samples was found to cause the overestimation of TMB. Therefore, a delta Ct cutoff was established to qualify DNA samples for TMB analysis. 12 of the 30 samples were also analyzed using a comparator NGS panel covering ~1.25 megabases. The correlation of TMB results between the two panels was 0.87. Overall, TMB was lowest in RCC (9-17/Mb) compared to NSCLC and CRC (16-37/Mb). MSI status was determined using the Promega MSI Analysis System v1.2. A correlation was observed between TMB and MSI status in a subset of samples. Reproducibility of the assay was also evaluated. To identify clinically relevant mutations and genetic alteration associated with high mutation burden, the Oncomine Comprehensive assay v3 (OCAv3) was also used to analyze the sample set. Mutations in genes involved in several DNA repair pathways were found to correlate with TMB. This study demonstrated the feasibility of utilizing a commercial targeted NGS panel and data analysis pipeline for TMB evaluation in clinical FFPE tumor samples. Standardization of TMB analysis will enable the clinical validation of TMB as a predictive biomarker for therapy selection. Citation Format: Peng Fang, Zhenyu Yan, Quyen Vu, David Smith, Chad Galderisi, Cynthia S. Spittle, Jin Li. Evaluation of a commercial targeted NGS panel for tumor mutation burden assessment in FFPE tissue [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3614.
'/%3e%3cuse xlink:href='%23a' transform='translate(288.889 -214.211)'/%3e%3cuse xlink:href='%23a' transform='translate(108 342.749)'/%3e%3cuse xlink:href='%23a' transform='translate(469.189 342.749)'/%3e%3c/svg%3e)
'%3e%3ccircle r='20' fill='%23008'/%3e%3ccircle r='17.5' fill='%23fff'/%3e%3ccircle r='3.5' fill='%23008'/%3e%3cg id='d'%3e%3cg id='c'%3e%3cg id='b'%3e%3cg id='a' fill='%23008'%3e%3ccircle r='.875' transform='rotate(7.5 -8.75 133.5)'/%3e%3cpath d='M0 17.5.6 7 0 2l-.6 5L0 17.5z'/%3e%3c/g%3e%3cuse xlink:href='%23a' transform='rotate(15)'/%3e%3c/g%3e%3cuse xlink:href='%23b' transform='rotate(30)'/%3e%3c/g%3e%3cuse xlink:href='%23c' transform='rotate(60)'/%3e%3c/g%3e%3cuse xlink:href='%23d' transform='rotate(120)'/%3e%3cuse xlink:href='%23d' transform='rotate(-120)'/%3e%3c/g%3e%3c/svg%3e)