TIGIT/CD155 axis mediates resistance to immunotherapy in patients with melanoma with the inflamed tumor microenvironment

Background Patients with cancer benefit from treatment with immune checkpoint inhibitors (ICIs), and those with an inflamed tumor microenvironment (TME) and/or high tumor mutation burden (TMB), particularly, tend to respond to ICIs; however, some patients fail, whereas others acquire resistance after initial response despite the inflamed TME and/or high TMB. We assessed the detailed biological mechanisms of resistance to ICIs such as programmed death 1 and/or cytotoxic T-lymphocyte-associated protein 4 blockade therapies using clinical samples. Methods We established four pairs of autologous tumor cell lines and tumor-infiltrating lymphocytes (TILs) from patients with melanoma treated with ICIs. These tumor cell lines and TILs were subjected to comprehensive analyses and in vitro functional assays. We assessed tumor volume and TILs in vivo mouse models to validate identified mechanism. Furthermore, we analyzed additional clinical samples from another large melanoma cohort. Results Two patients were super-responders, and the others acquired resistance: the first patient had a non-inflamed TME and acquired resistance due to the loss of the beta-2 microglobulin gene, and the other acquired resistance despite having inflamed TME and extremely high TMB which are reportedly predictive biomarkers. Tumor cell line and paired TIL analyses showed high CD155, TIGIT ligand, and TIGIT expression in the tumor cell line and tumor-infiltrating T cells, respectively. TIGIT blockade or CD155-deletion activated T cells in a functional assay using an autologous cell line and paired TILs from this patient. CD155 expression increased in surviving tumor cells after coculturing with TILs from a responder, which suppressed TIGIT+ T-cell activation. Consistently, TIGIT blockade or CD155-deletion could aid in overcoming resistance to ICIs in vivo mouse models. In clinical samples, CD155 was related to resistance to ICIs in patients with melanoma with an inflamed TME, including both primary and acquired resistance. Conclusions The TIGIT/CD155 axis mediates resistance to ICIs in patients with melanoma with an inflamed TME, promoting the development of TIGIT blockade therapies in such patients with cancer

Evolutionary histories of breast cancer and related clones

乳がん発生の進化の歴史を解明 --ゲノム解析による発がんメカニズムの探索--. 京都大学プレスリリース. 2023-07-28.Tracking the ol' mutation trail: Unraveling the long history of breast cancer formation. 京都大学プレスリリース. 2023-08-31.Recent studies have documented frequent evolution of clones carrying common cancer mutations in apparently normal tissues, which are implicated in cancer development1, 2, 3. However, our knowledge is still missing with regard to what additional driver events take place in what order, before one or more of these clones in normal tissues ultimately evolve to cancer. Here, using phylogenetic analyses of multiple microdissected samples from both cancer and non-cancer lesions, we show unique evolutionary histories of breast cancers harbouring der(1;16), a common driver alteration found in roughly 20% of breast cancers. The approximate timing of early evolutionary events was estimated from the mutation rate measured in normal epithelial cells. In der(1;16)(+) cancers, the derivative chromosome was acquired from early puberty to late adolescence, followed by the emergence of a common ancestor by the patient’s early 30s, from which both cancer and non-cancer clones evolved. Replacing the pre-existing mammary epithelium in the following years, these clones occupied a large area within the premenopausal breast tissues by the time of cancer diagnosis. Evolution of multiple independent cancer founders from the non-cancer ancestors was common, contributing to intratumour heterogeneity. The number of driver events did not correlate with histology, suggesting the role of local microenvironments and/or epigenetic driver events. A similar evolutionary pattern was also observed in another case evolving from an AKT1-mutated founder. Taken together, our findings provide new insight into how breast cancer evolves

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

Two Pathways in Scandium Ion-Coupled Electron Transfer of Superoxide Ion

Superoxide ion (O2•–) forms a stable 1:1 complex with scandium hexamethylphosphoric triamide complex [Sc(HMPA)33+], which can be detected by ESR spectroscopy in solution at ambient temperature. We report kinetics and mechanism of electron-transfer reactions from the O2•––Sc(HMPA)33+ complex to a series of electron acceptors: p-benzoquinone derivatives such as p-benzoquinone and coenzyme Q10. Electron transfer from the O2•––Sc(HMPA)33+ complex to a series of p-benzoquinone derivatives occurs, accompanied by binding of Sc(HMPA)33+ to the corresponding semiquinone radical anion complex to produce the semiquinone radical anion-Sc(HMPA)33+ complexes. The 1:1 and 1:2 complexes between semiquinone radical anions and Sc(HMPA)33+ depending on the type of semiquinone radical anions were detected by ESR measurements. This is defined as Sc(HMPA)33+-coupled electron transfer. There are two reaction pathways in the Sc(HMPA)33+-coupled electron transfer. One is a stepwise pathway in which the binding of Sc(HMPA)33+ to semiquinone radical anions occurs after the electron transfer, when the rate of electron transfer remains constant with the change in concentration of Sc(HMPA)33+. The other is a concerted pathway in which electron transfer and the binding of Sc(HMPA)33+ occurs in a concerted manner, when the rates of electron transfer exhibit first-order and second-order dependence on concentration of Sc(HMPA)33+ depending the number of Sc(HMPA)33+ (one and two) bound to semiquinone radical anions. The contribution of two pathways is changed depending on substituents on p-benzoquinone derivatives. The present study provides the first example to clarify the kinetics and mechanism of metal ion-coupled electron-transfer reactions of superoxide ion.The 2010 International Chemical Congress of Pacific Basin Societies (PACIFICHEM 2010

Photoinduced DNA Cleavage with 5-Hydroxytryptamine and Aromatic Amino Acid

UV irradiation is the most frequent cause of DNA abnormality produced by reactive oxygen species (ROS). Photochemistry of aromatic amino acids has widely been studied with regard to generation of ROS such as singlet oxygen (1O2) and superoxide (O2•–). In general, there are two main processes responsible for photosensitized reactions (scheme 1): (1) the chromophore is excited by light to a triplet state, and undergoes a direct electron or hydrogen exchange with a substrate, creating a free radical (Type I process); (2) energy transfer from the excited chromophore directly to oxygen, resulting in generation of 1O2 (Type II process). However, DNA damage by ROS generated by photoirradiation of aromatic amino acid or neurotransmitter with oxygen has yet to be reported. We report the effects of ROS produced by UV-B photoirradiation of a neurotransmitter, serotonin (5-hydroxytryptamine: 5-HT) and aromatic amino acids, tryptophan (Trp) and tyrosine (Tyr), with oxygen on DNA cleavage. UV-B photoirradiation of a neurotransmitter (5-HT) and aromatic amino acids (tryptophan and tyrosine) with oxygen results in DNA cleavage by generation of superoxide as demonstrated by agarose gel electrophoresis with pBR322 DNA. The reactive species for DNA cleavage is superoxide which was detected by ESR. The formation of O2•– upon photoexcitation of 5-HT with O2 by use of a mercury lamp is confirmed by the ESR spectrum measured at 77 K, where the anisotropic signals at g| = 2.080 and g^ = 2.002 are well assigned to O2•–. We also investigated electron-transfer dynamics of the formation of superoxide anion in electron transfer from the triplet excited state of neurotransmitter or aromatic amino acid to O2 by laser flash photolysis.The 2010 International Chemical Congress of Pacific Basin Societies (PACIFICHEM 2010

Electron Transfer from Stable Superoxide Complex to electron Acceptors as Benzoquinone Derivatives

Superoxide ion (O2•–) is important as the product of the one-electron reduction of dioxygen, which occurs widely in nature. O2•– forms a stable 1:1 complex with scandium hexamethylphosphoric triamide [Sc(HMPA)33+], which can be detected by ESR in solution at ambient temperature. We report the kinetics and mechanism of electron-transfer reactions from the O2•––Sc(HMPA)33+ complex to a series of electron acceptors: p-benzoquinone derivatives, such as p-benzoquinone and coenzyme Q10. Electron transfer from the O2•––Sc(HMPA)33+ complex top-benzoquinone derivatives occurred, accompanied by binding of Sc(HMPA)33+ to the corresponding semiquinone radical anion complex to produce the semiquinone radical anion-Sc(HMPA)33+ complexes. There are two reaction pathways, in the Sc(HMPA)33+-coupled electron transfer. One is a stepwise pathway, in which the binding of Sc(HMPA)33+ to semiquinone radical anions occurs after the electron transfer. The other is a concerted pathway in which electron transfer and the binding of Sc(HMPA)33+ occurs in a concerted manner.SFRBM/SFRRI 201