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Introduction: CAR T cell immunotherapy represents a major breakthrough in treatment of hematological tumors. Its manufacture is based on the ex vivo manipulation of human lymphocytes, which are later reinfused to the patient. New methodologies for the generation of CAR T cells are needed, with a focus on reducing the ex vivo manipulation period as well as preventing adverse effects. Here, we produced CAR T cells using DNA-loaded Lipid Nanoparticles (LNPs), assessing the expression anti-CD19 CAR as well as activation of effector cells and specific killing of tumor cells. Methods: To assess the transfection efficiency of LNPs, Jurkat cells were transfected with an LNP encapsulating a pDNA for a second-generation CAR targeting CD19 (LNP-CAR). Activation of transfected Jurkat cells was evaluated by coplating CAR expressing cells with Raji cells for 24 hours at a 1:1 ratio or at different ratios and measuring the expression levels of CD69 in CAR+ cells. Primary human T-cells isolated from healthy donors were transfected with the optimized LNP and coplated with Raji cells to evaluate specific killing by flow cytometry. Results: A peak of CAR+ cells was observed 3 days after transfection, which diminished overtime, indicating the transient expression of CAR in these cells. A screening of LNP-CAR using Jurkat as a model identified an optimized formulation for the transfection of T-cells (LNP-9-CAR). We observed, by evaluating the expression of CD69 in CAR+ cells, that the activation of Jurkat cells transfected with LNP-9-CAR was dependent on the effector-to-target ratio. Primary T lymphocytes transfected with our optimized LNP-9-CAR were effective in killing CD19+ Raji cells also in a ratio-dependent manner. Conclusion: We developed an LNP platform for the delivery of pDNA to produce anti-CD19 CAR T cells ex vivo. This transfection method showed low toxicity to transfected cells even when compared to standard methods. Primary CAR T cells produced using LNP-9-CAR were activated and induced specific killing of CD19+ tumor cells. As a non-viral delivery method, LNPs open an alternative to produce CAR T-cells in less time than viral vectors, thus reducing the associated costs and improving the effectiveness of the adoptive cells. This method can also be applied using other CAR constructs, opening possibilities for the personalized treatment of different tumors, as well as to treat autoimmune diseases and other B-cell related illnesses.

Colorectal carcinoma (CRC) is a common cause of mortality 1 , but a comprehensive description of its genomic landscape is lacking 2-9 . Here we perform whole-genome sequencing of 2,023 CRC samples from participants in the UK 100,000 Genomes Project, thereby providing a highly detailed somatic mutational landscape of this cancer. Integrated analyses identify more than 250 putative CRC driver genes, many not previously implicated in CRC or other cancers, including several recurrent changes outside the coding genome. We extend the molecular pathways involved in CRC development, define four new common subgroups of microsatellite-stable CRC based on genomic features and show that these groups have independent prognostic associations. We also characterize several rare molecular CRC subgroups, some with potential clinical relevance, including cancers with both microsatellite and chromosomal instability. We demonstrate a spectrum of mutational profiles across the colorectum, which reflect aetiological differences. These include the role of Escherichia coli pks+ colibactin in rectal cancers 10 and the importance of the SBS93 signature 11-13 , which suggests that diet or smoking is a risk factor. Immune-escape driver mutations 14 are near-ubiquitous in hypermutant tumours and occur in about half of microsatellite-stable CRCs, often in the form of HLA copy number changes. Many driver mutations are actionable, including those associated with rare subgroups (for example, BRCA1 and IDH1), highlighting the role of whole-genome sequencing in optimizing patient care., (© 2024. The Author(s).)

The sparsity of mutations observed across tumours hinders our ability to study mutation rate variability at nucleotide resolution. To circumvent this, here we investigated the propensity of mutational processes to form mutational hotspots as a readout of their mutation rate variability at single base resolution. Mutational signatures 1 and 17 have the highest hotspot propensity (5-78 times higher than other processes). After accounting for trinucleotide mutational probabilities, sequence composition and mutational heterogeneity at 10 Kbp, most (94-95%) signature 17 hotspots remain unexplained, suggesting a significant role of local genomic features. For signature 1, the inclusion of genome-wide distribution of methylated CpG sites into models can explain most (80-100%) of the hotspot propensity. There is an increased hotspot propensity of signature 1 in normal tissues and de novo germline mutations. We demonstrate that hotspot propensity is a useful readout to assess the accuracy of mutation rate models at nucleotide resolution. This new approach and the findings derived from it open up new avenues for a range of somatic and germline studies investigating and modelling mutagenesis., (© 2023. The Author(s).)

We report an autosomal recessive, multi-organ tumor predisposition syndrome, caused by bi-allelic loss-of-function germline variants in the base excision repair (BER) gene MBD4. We identified five individuals with bi-allelic MBD4 variants within four families and these individuals had a personal and/or family history of adenomatous colorectal polyposis, acute myeloid leukemia, and uveal melanoma. MBD4 encodes a glycosylase involved in repair of G:T mismatches resulting from deamination of 5'-methylcytosine. The colorectal adenomas from MBD4-deficient individuals showed a mutator phenotype attributable to mutational signature SBS1, consistent with the function of MBD4. MBD4-deficient polyps harbored somatic mutations in similar driver genes to sporadic colorectal tumors, although AMER1 mutations were more common and KRAS mutations less frequent. Our findings expand the role of BER deficiencies in tumor predisposition. Inclusion of MBD4 in genetic testing for polyposis and multi-tumor phenotypes is warranted to improve disease management., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)

Neoantigens are now recognized drivers of the antitumor immune response. Recurrent neoantigens, shared among groups of patients, have thus become increasingly coveted therapeutic targets. Here, we report on the data-driven identification of a robustly presented, immunogenic neoantigen that is derived from the combination of HLA-A*01:01 and RAS.Q61K. Analysis of large patient cohorts indicated that this combination applies to 3% of patients with melanoma. Using HLA peptidomics, we were able to demonstrate robust endogenous presentation of the neoantigen in 10 tumor samples. We detected specific reactivity to the mutated peptide within tumor-infiltrating lymphocytes (TILs) from 2 unrelated patients, thus confirming its natural immunogenicity. We further investigated the neoantigen-specific clones and their T cell receptors (TCRs) via a combination of TCR sequencing, TCR overexpression, functional assays, and single-cell transcriptomics. Our analysis revealed a diverse repertoire of neoantigen-specific clones with both intra- and interpatient TCR similarities. Moreover, 1 dominant clone proved to cross-react with the highly prevalent RAS.Q61R variant. Transcriptome analysis revealed a high association of TCR clones with specific T cell phenotypes in response to cognate melanoma, with neoantigen-specific cells showing an activated and dysfunctional phenotype. Identification of recurrent neoantigens and their reactive TCRs can promote "off-the-shelf" precision immunotherapies, alleviating limitations of personalized treatments.

Ovarian cancer (OC) represents the most common and lethal gynecologic malignancy, due to its increased incidence and mortality rate. It is usually diagnosed in advanced stages and, even though surgery and platinum-based treatments are initially efficient, recurrences emerge in over 70% of cases. Although there are multiple options of chemotherapy drugs from which to choose, little is known regarding the best strategy for prolonged survival. Thus, this study aimed to assess the effect that most frequently used chemotherapeutic regimens have upon time-to-treatment-failure (TTF) from the first line and beyond, considering clinical and biological factors which influence the treatment outcome of platinum-resistant recurrent OC. We retrospectively analyzed data from 78 patients diagnosed with platinum-resistant OC, who underwent chemotherapy-based treatment with or without anti-angiogenic therapy at OncoHelp Oncology Center, Romania (January 2016-February 2021). Our study identified positive predictive factors for TTF related to histology (serous carcinoma subtype), anthropometry (age over 60 for patients treated with topotecan with or without bevacizumab), renal function (creatinine levels between 0.65 and 1 mg/dL for patients treated with regimens containing bevacizumab and pegylated liposomal doxorubicin) and treatment choice (bevacizumab in combination with pegylated liposomal doxorubicin or topotecan used from the first line and beyond).

The glycolytic modulator TP53-Inducible Glycolysis and Apoptosis Regulator (TIGAR) is overexpressed in several types of cancer and has a role in metabolic rewiring during tumor development. However, little is known about the role of this enzyme in proliferative tissues under physiological conditions. In the current work, we analysed the role of TIGAR in primary human lymphocytes stimulated with the mitotic agent Concanavalin A (ConA). We found that TIGAR expression was induced in stimulated lymphocytes through the PI3K/AKT pathway, since Akti-1/2 and LY294002 inhibitors prevented the upregulation of TIGAR in response to ConA. In addition, suppression of TIGAR expression by siRNA decreased the levels of the proliferative marker PCNA and increased cellular ROS levels. In this model, TIGAR was found to support the activity of glucose 6-phosphate dehydrogenase (G6PDH), the first enzyme of the pentose phosphate pathway (PPP), since the inhibition of TIGAR reduced G6PDH activity and increased autophagy. In conclusion, we demonstrate here that TIGAR is upregulated in stimulated human lymphocytes through the PI3K/AKT signaling pathway, which contributes to the redirection of the carbon flux to the PPP.

Cancers arise through the acquisition of oncogenic mutations and grow by clonal expansion 1,2 . Here we reveal that most mutagenic DNA lesions are not resolved into a mutated DNA base pair within a single cell cycle. Instead, DNA lesions segregate, unrepaired, into daughter cells for multiple cell generations, resulting in the chromosome-scale phasing of subsequent mutations. We characterize this process in mutagen-induced mouse liver tumours and show that DNA replication across persisting lesions can produce multiple alternative alleles in successive cell divisions, thereby generating both multiallelic and combinatorial genetic diversity. The phasing of lesions enables accurate measurement of strand-biased repair processes, quantification of oncogenic selection and fine mapping of sister-chromatid-exchange events. Finally, we demonstrate that lesion segregation is a unifying property of exogenous mutagens, including UV light and chemotherapy agents in human cells and tumours, which has profound implications for the evolution and adaptation of cancer genomes.

Red light-sensitized squaraine ( SQ ) dyes were developed and incorporated into dye-sensitized catalysts (DSCs) with the formula of SQ /TiO 2 /Cat, and their efficacies were evaluated in terms of performance on either water or carbon dioxide reduction. Pt nanoparticles or fac -[Re(4,4'-bis-(diethoxyphosphorylmethyl)-2,2'-bipyridine)(CO) 3 Cl] were used as each catalytic center within the DSC frame of SQ /TiO 2 /Pt (Type I) or SQ /TiO 2 /Re(I) (Type II). In order to convey the potential utility of SQ in low energy sensitization, the following catalytic reductions were carried out under selective lower energy irradiation (>500 nm). Type I and II showed different catalytic performances, primarily due to the choice of solvent for each catalytic condition: hydrogenation was carried out in H 2 O, but CO 2 reduction in dimethylformamide (DMF), and SQ was more stable in aqueous acid conditions for hydrogen generation than CO 2 reduction in DMF. A suspension of Type I in 3 mL water containing 0.1 M ascorbic acid (pH = 2.66) resulted in efficient photocatalytic hydrogen evolution, producing 37 μmol of H 2 for 4 h. However, in photocatalysis of Type II ( SQ /TiO 2 /Re(I)) in 3 mL DMF containing 0.1 M 1,3-dimethyl-2-phenyl-1,3-dihydrobenzimidazole, the TiO 2 -bound SQ dyes were not capable of working as a low energy sensitizer because SQ was susceptible to dye decomposition in nucleophilic DMF conditions, resulting in DSC deactivation for the CO 2 reduction. Even with the limitation of solvent, the DSC conditions for the utility of SQ have been established: the anchoring group effect of SQ with either phosphonic acid or carboxylic acid onto the TiO 2 surface; energy alignment of SQ with the flat band potentials ( E fb ) of TiO 2 semiconductors and the reduction power of electron donors; and the wavelength range of the light source used, particularly when >500 nm., Competing Interests: The authors declare no competing financial interest.

Prostate cancer subtypes are poorly defined and functional validation of drivers of ETS rearrangement-negative prostate cancer has not been conducted. Here, we identified an ETS(-) subtype of aggressive prostate cancer (ERG(-)MAP3K7(del)CHD1(del)) and used a novel developmental model and a cell line xenograft model to show that cosuppression of MAP3K7 and CHD1 expression promotes aggressive disease. Analyses of publicly available prostate cancer datasets revealed that MAP3K7 and CHD1 were significantly codeleted in 10% to 20% of localized tumors and combined loss correlated with poor disease-free survival. To evaluate the functional impact of dual MAP3K7-CHD1 loss, we suppressed Map3k7 and/or Chd1 expression in mouse prostate epithelial progenitor/stem cells (PrP/SC) and performed tissue recombination experiments in vivo. Dual shMap3k7-shChd1 PrP/SC recombinants displayed massive glandular atypia with regions of prostatic intraepithelial neoplasia and carcinoma apparent. Combined Map3k7-Chd1 suppression greatly disrupted normal prostatic lineage differentiation; dual recombinants displayed significant androgen receptor loss, increased neuroendocrine differentiation, and increased neural differentiation. Clinical samples with dual MAP3K7-CHD1 loss also displayed neuroendocrine and neural characteristics. In addition, dual Map3k7-Chd1 suppression promoted E-cadherin loss and mucin production in recombinants. MAP3K7 and CHD1 protein loss also correlated with Gleason grade and E-cadherin loss in clinical samples. To further validate the phenotype observed in the PrP/SC model, we suppressed MAP3K7 and/or CHD1 expression in LNCaP prostate cancer cells. Dual shMAP3K7-shCHD1 LNCaP xenografts displayed increased tumor growth and decreased survival compared with shControl, shMAP3K7, and shCHD1 xenografts. Collectively, these data identify coordinate loss of MAP3K7 and CHD1 as a unique driver of aggressive prostate cancer development., (©2015 American Association for Cancer Research.)

The direct coupling reactions of 1,8-naphthalimide compounds efficiently occurred at 130 or 170 degrees C without the intervention of the leuco form dyes in the presence of base complex reagent, t-BuOK/1,5-diazabicyclo[4.3.0]non-5-ene (DBN), to give the corresponding perylene dyes in good yields with > 95% purities. A possible mechanistic speculation for these oxidative coupling reactions is briefly discussed.

The oxidation reactions of hydroquinones, 2-naphthols, or 2,6-di-tert-butylphenol efficiently occurred by catalysis with alumina-supported copper(II) sulfate to give the corresponding benzoquinones, 1,1'-bi-2-naphthols, and 4,4'-diphenoquinone, respectively, in good yields. The synthetic potentiality of the catalytic reactions was demonstrated by easy isolation of the final products using only filtration and solvent evaporation as well as by application to large-scale syntheses of the benzoquinones and binaphthols. The catalysis with alumina-supported copper(II) sulfate was also applied to the oxidative intramolecular coupling of 5,5'-diacenaphthene to the corresponding perylene compound.