bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unraveling T cell exhaustion in the immune microenvironment of osteosarcoma via single-cell RNA transcriptome
Authors: Cheng Debin , Zhang Zhao , Liu Dong , Mi Zhenzhou , Tao Weidong , Fu Jun , Fan Hongbin 
Published: January 2024

Abstract
Osteosarcoma (OS) represents a profoundly invasive malignancy of the skeletal system. T cell exhaustion (Tex) is known to facilitate immunosuppression and tumor progression, but its role in OS remains unclear. In this study, single-cell RNA sequencing data was employed to identify exhausted T cells within the tumor immune microenvironment (TIME) of OS. We found that exhausted T cells exhibited substantial infiltration in OS samples. Pseudotime trajectory analysis revealed a progressive increase in the expression of various Tex marker genes, including PDCD1, CTLA4, LAG3, ENTPD1, and HAVCR2 in OS. GSVA showed that apoptosis, fatty acid metabolism, xenobiotic metabolism, and the interferon pathway were significantly activated in exhausted T cells in OS. Subsequently, a prognostic model was constructed using two Tex-specific genes, MYC and FCGR2B, which exhibited exceptional prognostic accuracy in two independent cohorts. Drug sensitivity analysis revealed that OS patients with a low Tex risk were responsive to Dasatinib and Pazopanib. Finally, immunohistochemistry verified that MYC and FCGR2B were significantly upregulated in OS tissues compared with adjacent tissues. This study investigates the role of Tex within the TIME of OS, and offers novel insights into the mechanisms underlying disease progression as well as the potential treatment strategies for OS.

Graphic Abstract
Personalized neoantigen vaccine enhances the therapeutic efficacy of bevacizumab and anti-PD-1 antibody in advanced non-small cell lung cancer
Authors: Lin Xiuhua , Tang Shichuan , Guo Yutong , Tang Ruijing , Li Zhenli , Pan Xinting , Chen Geng , Qiu Liman , Dong Xiuqing , Zhang Ling , Liu Xiaolong , Cai Zhixiong , Xie Baosong 
Published: January 2024

AbstractClinically, a considerable number of non-small cell lung cancer (NSCLC) patients are unable to receive or resist chemotherapy, and the efficacy of non-chemotherapy treatment strategies based on anti-angiogenic agents combined with immune checkpoint blockade is still unsatisfactory. Neoantigen vaccine, based on personalized tumor DNA mutations, could elicit tumor specific T cell infiltration into the tumor site, exerting potent anti-tumor efficacy. Here, we evaluated the feasibility and safety of a new antitumor strategy by adding neoantigen vaccine to the regimen of bevacizumab and anti-PD-1 antibody. Firstly, 7 novel immunogenic neoantigen peptides were identified and developed for neoantigen vaccine (LLCvac), which can elicit strong antitumor immune response in vivo. Then, in orthotopic lung cancer model, LLCvac further combining with bevacizumab and anti-PD-1 antibody exerted a stronger antitumor effect, exhibiting significant decrease of tumor volume without obvious toxicity. Furthermore, tumor immune microenvironment assessment also showed that the proportion of neoantigen-specific T cells in blood could be induced dramatically by the combined therapy. And a large amount of neoantigen-specific Ki67-positive CD8+ T cells were found in tumor tissues, which infiltrated tumor tissues effectively to kill tumor cells expressing identified neoantigens. Overall, these results suggested that this combined therapy could safely induce robust antitumor efficacy, serving as an effective chemotherapy-free strategy for NSCLC treatment.
New CEACAM-targeting 2A3 single-domain antibody-based chimeric antigen receptor T-cells produce anticancer effects in vitro and in vivo
Authors: Jancewicz Iga , Śmiech Magdalena , Winiarska Magdalena , Zagozdzon Radoslaw , Wisniewski Pawel 
Published: January 2024

AbstractRecently, a breakthrough immunotherapeutic strategy of chimeric antigen receptor (CAR) T-cells has been introduced to hematooncology. However, to apply this novel treatment in solid cancers, one must identify suitable molecular targets in the tumors of choice. CEACAM family proteins are involved in the progression of a range of malignancies, including pancreatic and breast cancers, and pose attractive targets for anticancer therapies. In this work, we used a new CEACAM-targeted 2A3 single-domain antibody-based chimeric antigen receptor T-cells to evaluate their antitumor properties in vitro and in animal models. Originally, 2A3 antibody was reported to target CEACAM6 molecule; however, our in vitro co-incubation experiments showed activation and high cytotoxicity of 2A3-CAR T-cells against CEACAM5 and/or CEACAM6 high human cell lines, suggesting cross-reactivity of this antibody. Moreover, 2A3-CAR T-cells tested in vivo in the BxPC-3 xenograft model demonstrated high efficacy against pancreatic cancer xenografts in both early and late intervention treatment regimens. Our results for the first time show an enhanced targeting toward CEACAM5 and CEACAM6 molecules by the new 2A3 sdAb-based CAR T-cells. The results strongly support the further development of 2A3-CAR T-cells as a potential treatment strategy against CEACAM5/6-overexpressing cancers.
An analysis pipeline for understanding 6-thioguanine effects on a mouse tumour genome
Authors: Yankilevich Patricio , Nazerai Loulieta , Willis Shona Caroline , Schmiegelow Kjeld , De Zio Daniela , Nielsen Morten 
Published: January 2024

AbstractMouse tumour models are extensively used as a pre-clinical research tool in the field of oncology, playing an important role in anticancer drugs discovery. Accordingly, in cancer genomics research, the demand for next-generation sequencing (NGS) is increasing, and consequently, the need for data analysis pipelines is likewise growing. Most NGS data analysis solutions to date do not support mouse data or require highly specific configuration for their use. Here, we present a genome analysis pipeline for mouse tumour NGS data including the whole-genome sequence (WGS) data analysis flow for somatic variant discovery, and the RNA-seq data flow for differential expression, functional analysis and neoantigen prediction. The pipeline is based on standards and best practices and integrates mouse genome references and annotations. In a recent study, the pipeline was applied to demonstrate the efficacy of low dose 6-thioguanine (6TG) treatment on low-mutation melanoma in a pre-clinical mouse model. Here, we further this study and describe in detail the pipeline and the results obtained in terms of tumour mutational burden (TMB) and number of predicted neoantigens, and correlate these with 6TG effects on tumour volume. Our pipeline was expanded to include a neoantigen analysis, resulting in neopeptide prediction and MHC class I antigen presentation evaluation. We observed that the number of predicted neoepitopes were more accurate indicators of tumour immune control than TMB. In conclusion, this study demonstrates the usability of the proposed pipeline, and suggests it could be an essential robust genome analysis platform for future mouse genomic analysis.
Characterization of T cell receptor repertoire in penile cancer
Authors: Zhang Junying , Wang Yapeng , Huang Yiqiang , Tan Xintao , Xu Jing , Yan Qian , Tan Jiao , Zhang Yao , Zhang Jun , Ma Qiang , Zhu Hailin , Ye Jin , Zhu Zhaojing , Lan Weihua 
Published: January 2024

AbstractTumor-infiltrating lymphocytes (TILs) play a key role in regulating the host immune response and shaping tumor microenvironment. It has been previously shown that T cell infiltration in penile tumors was associated with clinical outcomes. However, few studies have reported the T cell receptor (TCR) repertoire in patients with penile cancer. In the present study, we evaluated the TCR repertoires in tumor and adjacent normal tissues from 22 patients with penile squamous cell carcinoma (PSCC). Analysis of the T cell receptor beta-variable (TRBV) and joining (TRBJ) genes usage and analysis of complementarity determining region 3 (CDR3) length distribution did not show significant differences between tumor and matched normal tissues. Moreover, analysis of the median Jaccard index indicated a limited overlap of TCR repertoire between these groups. Compared with normal tissues, a significantly lower diversity and higher clonality of TCR repertoire was observed in tumor samples, which was associated with clinical characteristics. Further analysis of transcriptional profiles demonstrated that tumor samples with high clonality showed increased expression of genes associated with CD8 + T cells. In addition, we analyzed the TCR repertoire of CD4 + T cells and CD8 + T cells isolated from tumor tissues. We identified that expanded clonotypes were predominantly in the CD8 + T cell compartment, which presented with an exhausted phenotype. Overall, we comprehensively compared TCR repertoire between penile tumor and normal tissues and demonstrated the presence of distinct T cell immune microenvironments in patients with PSCC.
The complex role of IL-10 in malignant ascites: a review
Authors: Huang Yue , Zou Kangni , Jiang Heng , Li Zhengyu 
Published: January 2024

AbstractThe emergence of malignant ascites (MA) indicates poor prognoses in patients with ovarian, gastrointestinal, breast, and pancreatic cancer. Interleukin-10 (IL-10) is a pleiotropic cytokine with immunoregulatory effects in tumor microenvironment. The level of IL-10 in MA varied across cancer types and patients, influencing cancer progression and outcomes. Originating from various immune and cancer cells, IL-10 contributes to complex signaling pathways in MA. Systemic IL-10 administration, although the evidence of its efficacy on MA is limited, still emerges as a promising therapeutic strategy because it can increase CD8+ T cells cytotoxicity and invigorate exhausted CD8+ tumor infiltration lymphocytes (TILs) directly. IL-10 signaling blockade also demonstrates great potential when combined with other immunotherapies in MA treatment. We reviewed the levels, origins, and functions of IL-10 in malignant ascites and overviewed the current IL-10 signaling targeting therapies, aiming to provide insights for MA treatment.
Presence of Epstein–Barr virus (EBV) antigens detected by sensitive methods has no influence on local immune environment in diffuse large B cell lymphoma
Authors: Mangiaterra T. , Alonso-Alonso R. , Rabinovich A. , De Dios Soler M. , Galluzzo L. , Soria M. , Colli S. , De Matteo E. , Rodriguez Pinilla S. M. , Chabay P. 
Published: January 2024

AbstractEBV+ diffuse large B cell lymphoma (DLBCL) not otherwise specified (NOS) is a new entity confirmed by the World Health Organization (WHO) in 2017. In this new entity, the virus may contribute to a tolerogenic microenvironment. Traces of the virus have been described in DLBCL with more sensitive methods, in cases that were originally diagnosed as negative. The aim of this study was to analyze the expression of immune response genes in the tumor microenvironment to disclose the role of the virus and its traces in DLBCL. In 48 DLBCL cases, the expression of immune response genes and the presence of molecules that induce tolerance, such as TIM3, LAG3 and PDL1 by immunohistochemistry (IHC), were studied. To broaden the study of the microenvironment, tumor-associated macrophages (TMAs) were also explored. No significant differences were observed in the expression of immune response genes in the EBV+ DLBCL and those cases that were EBV− DLBCL but that exhibited viral traces, assessed by ViewRNA assay. Only the EBV+ DLBCL cases displayed a significantly higher increase in the expression of CD8 and cytotoxic T cells detected by gene expression analysis, and of PDL1 in tumor cells and in the expression of CD68 in the tumor microenvironment detected by IHC, not observed in those cases with viral traces. The increase in CD8 and cytotoxic T cells, PDL1 and CD68 markers only in EBV+ DLBCL may indicate that traces of viral infection might not have influence in immune response markers.
A CAR-T response prediction model for r/r B-NHL patients based on a T cell subset nomogram
Authors: Zhang Xiaomei , Sun Rui , Zhang Meng , Zhao Yifan , Cao Xinping , Guo Ruiting , Zhang Yi , Liu Xingzhong , Lyu Cuicui , Zhao Mingfeng 
Published: January 2024

Abstract
Background
Chimeric antigen receptor (CAR) T cells for refractory or relapsed (r/r) B cell no-Hodgkin lymphoma (NHL) patients have shown promising clinical effectiveness. However, the factors impacting the clinical response of CAR-T therapy have not been fully elucidated. We here investigate the independent influencing factors of the efficacy of CD19 CAR-T cell infusion in the treatment of r/r B-NHL and to establish an early prediction model.

Methods
A total of 43 r/r B-NHL patients were enrolled in this retrospective study. The patients’ general data were recorded, and the primary endpoint is the patients’ treatment response. The independent factors of complete remission (CR) and partial remission (PR) were investigated by univariate and binary logistic regression analysis, and the prediction model of the probability of CR was constructed according to the determined independent factors. Receiver operating characteristic (ROC) and calibration plot were used to assess the discrimination and calibration of the established model. Furthermore, we collected 15 participators to validate the model.

Results
Univariate analysis and binary logistic regression analysis of 43 patients showed that the ratio of central memory T cell (Tcm) and naïve T cell (Tn) in cytotoxic T cells (Tc) was an independent risk factor for response to CD19 CAR-T cell therapy in r/r B-NHL. On this basis, the area under the curve (AUC) of Tcm in the Tc and Tn in the Tc nomogram model was 0.914 (95%CI 0.832–0.996), the sensitivity was 83%, and the specificity was 74.2%, which had excellent predictive value. We did not found the difference of the progression-free survival (PFS).

Conclusions
The ratio of Tcm and Tn in Tc was found to be able to predict the treatment response of CD19 CAR-T cells in r/r B-NHL. We have established a nomogram model for the assessment of the CD19 CAR-T therapy response presented high specificity and sensitivity.
First evaluation of stiff-in-soft host–inclusion systems: experimental synthesis of zircon inclusions in quartz crystals
Authors: Gonzalez Joseph P. , Thomas Jay B. , Mazzucchelli Mattia L. , Angel Ross J. , Alvaro Matteo 
Published: January 2024

AbstractQuartz crystals with zircon inclusions were synthesized using a piston-cylinder apparatus to experimentally evaluate the use of inclusions in “soft” host minerals for elastic thermobarometry. Synthesized zircon inclusion strains and, therefore, pressures (Pinc) were measured using Raman spectroscopy and then compared with the expected inclusion strains and pressures calculated from elastic models. Measured inclusion strains and inclusion pressures are systematically more tensile than the expected values and, thus, re-calculated entrapment pressures are overestimated. These discrepancies are not caused by analytical biases or assumptions in the elastic models and strain calculations. Analysis shows that inclusion strain discrepancies progressively decrease with decreasing experimental temperature in the α-quartz field. This behavior is consistent with inelastic deformation of the host–inclusion pairs induced by the development of large differential stresses during experimental cooling. Therefore, inclusion strains are more reliable for inclusions trapped at lower temperature conditions in the α-quartz field where there is less inelastic deformation of the host–inclusion systems. On the other hand, entrapment isomekes of zircon inclusions entrapped in the β-quartz stability field plot along the α–β quartz phase boundary, suggesting that the inclusion strains were mechanically reset at the phase boundary during experimental cooling and decompression. Therefore, inclusions contained in soft host minerals can be used for elastic thermobarometry and inclusions contained in β-quartz may provide constraints on the P–T at which the host–inclusion system crossed the phase boundary during exhumation.
ChatGPT fails challenging the recent ESCMID brain abscess guideline
Authors: Dyckhoff-Shen Susanne , Koedel Uwe , Brouwer Matthijs C. , Bodilsen Jacob , Klein Matthias 
Published: January 2024

Abstract
Background
With artificial intelligence (AI) on the rise, it remains unclear if AI is able to professionally evaluate medical research and give scientifically valid recommendations.

Aim
This study aimed to assess the accuracy of ChatGPT’s responses to ten key questions on brain abscess diagnostics and treatment in comparison to the guideline recently published by the European Society for Clinical Microbiology and Infectious Diseases (ESCMID).

Methods
All ten PECO (Population, Exposure, Comparator, Outcome) questions which had been developed during the guideline process were presented directly to ChatGPT. Next, ChatGPT was additionally fed with data from studies selected for each PECO question by the ESCMID committee. AI’s responses were subsequently compared with the recommendations of the ESCMID guideline.

Results
For 17 out of 20 challenges, ChatGPT was able to give recommendations on the management of patients with brain abscess, including grade of evidence and strength of recommendation. Without data prompting, 70% of questions were answered very similar to the guideline recommendation. In the answers that differed from the guideline recommendations, no patient hazard was present. Data input slightly improved the clarity of ChatGPT’s recommendations, but, however, led to less correct answers including two recommendations that directly contradicted the guideline, being associated with the possibility of a hazard to the patient.

Conclusion
ChatGPT seems to be able to rapidly gather information on brain abscesses and give recommendations on key questions about their management in most cases. Nevertheless, single responses could possibly harm the patients. Thus, the expertise of an expert committee remains inevitable.
Histamine H2-receptor antagonism improves conduit artery endothelial function and reduces plasma aldosterone level without lowering arterial blood pressure in angiotensin II–hypertensive mice
Authors: Assersen Kasper B. , Jensen Boye L. , Enggaard Camilla , Vanhoutte Paul M. , Hansen Pernille B. L. 
Published: January 2024

AbstractAldosterone through the mineralocorticoid receptor MR has detrimental effects on cardiovascular disease. It reduces the bioavailability of nitric oxide and impairs endothelium-dependent vasodilatation. In resistance arteries, aldosterone impairs the sensitivity of vascular smooth muscle cells to nitric oxide by promoting the local secretion of histamine which activates H2 receptors. The present experiments tested in vivo and ex vivo the hypothesis that systemic H2-receptor antagonism reduces arterial blood pressure and improves vasodilatation in angiotensin II–induced chronic hypertension. Hypertension was induced by intravenous infusion of angiotensin II (60 ng kg−1 min−1) in conscious, unrestrained mice infused concomitantly with the H2-receptor antagonist ranitidine (27.8 µg kg−1 min−1) or vehicle for 24 days. Heart rate and arterial blood pressure were recorded by indwelling arterial catheter. Resistance (mesenteric) and conductance (aortae) arteries were harvested for perfusion myography and isometric tension recordings by wire myography, respectively. Plasma was analyzed for aldosterone concentration. ANGII infusion resulted in elevated arterial blood pressure and while in vivo treatment with ranitidine reduced plasma aldosterone concentration, it did not reduce blood pressure. Ranitidine improved ex vivo endothelial function (acetylcholine 10−9 to 10−6 mol L−1) in mesenteric resistance arteries. This was abolished by ex vivo treatment with aldosterone (10−9 mol L−1, 1 h). In aortic segments, in vivo ranitidine treatment impaired relaxation. Activation of histamine H2 receptors promotes aldosterone secretion, does not affect arterial blood pressure, and protects endothelial function in conduit arteries but promotes endothelial dysfunction in resistance arteries during angiotensin II–mediated hypertension. Aldosterone contributes little to angiotensin II–induced hypertension in mice.
Long COVID in pediatrics—epidemiology, diagnosis, and management
Authors: Toepfner Nicole , Brinkmann Folke , Augustin Silvia , Stojanov Silvia , Behrends Uta 
Published: January 2024

AbstractThis review summarizes current knowledge on post-acute sequelae of COVID-19 (PASC) and post-COVID-19 condition (PCC) in children and adolescents. A literature review was performed to synthesize information from clinical studies, expert opinions, and guidelines. PASC also termed Long COVID — at any age comprise a plethora of unspecific symptoms present later than 4 weeks after confirmed or probable infection with severe respiratory syndrome corona virus type 2 (SARS-CoV-2), without another medical explanation. PCC in children and adolescents was defined by the WHO as PASC occurring within 3 months of acute coronavirus disease 2019 (COVID-19), lasting at least 2 months, and limiting daily activities. Pediatric PASC mostly manifest after mild courses of COVID-19 and in the majority of cases remit after few months. However, symptoms can last for more than 1 year and may result in significant disability. Frequent symptoms include fatigue, exertion intolerance, and anxiety. Some patients present with postural tachycardia syndrome (PoTS), and a small number of cases fulfill the clinical criteria of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). To date, no diagnostic marker has been established, and differential diagnostics remains challenging. Therapeutic approaches include appropriate self-management as well as the palliation of symptoms by non-pharmaceutical and pharmaceutical strategies. Conclusion: PASC in pediatrics present with heterogenous severity and duration. A stepped, interdisciplinary, and individualized approach is essential for appropriate clinical management. Current health care structures have to be adapted, and research was extended to meet the medical and psychosocial needs of young people with PASC or similar conditions.

What is Known:• Post-acute sequelae of coronavirus 2019 (COVID-19) (PASC) — also termed Long COVID — in children and adolescents can lead to activity limitation and reduced quality of life.• PASC belongs to a large group of similar post-acute infection syndromes (PAIS). Specific biomarkers and causal treatment options are not yet available.

What is New:• In February 2023, a case definition for post COVID-19 condition (PCC) in children and adolescents was provided by the World Health Organization (WHO), indicating PASC with duration of at least 2 months and limitation of daily activities. PCC can present as myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS).• Interdisciplinary collaborations are necessary and have been established worldwide to offer harmonized, multimodal approaches to diagnosis and management of PASC/PCC in children and adolescents.