Comparing neoantigen cancer vaccines and immune checkpoint therapy unveils an effective vaccine and anti-TREM2 macrophage-targeting dual therapy.

The goal of therapeutic cancer vaccines and immune checkpoint therapy (ICT) is to promote T cells with anti-tumor capabilities. Here, we compared mutant neoantigen (neoAg) peptide-based vaccines with ICT in preclinical models. NeoAg vaccines induce the most robust expansion of proliferating and stem-like PD-1+TCF-1+ neoAg-specific CD8 T cells in tumors. Anti-CTLA-4 and/or anti-PD-1 ICT promotes intratumoral TCF-1- neoAg-specific CD8 T cells, although their phenotype depends in part on the specific ICT used. Anti-CTLA-4 also prompts substantial changes to CD4 T cells, including induction of ICOS+Bhlhe40+ T helper 1 (Th1)-like cells. Although neoAg vaccines or ICTs expand iNOS+ macrophages, neoAg vaccines maintain CX3CR1+CD206+ macrophages expressing the TREM2 receptor, unlike ICT, which suppresses them. TREM2 blockade enhances neoAg vaccine efficacy and is associated with fewer CX3CR1+CD206+ macrophages and induction of neoAg-specific CD8 T cells. Our findings highlight different mechanisms underlying neoAg vaccines and different forms of ICT and identify combinatorial therapies to enhance neoAg vaccine efficacy.

Resuscitative endovascular balloon occlusion of the aorta provides better survival outcomes for noncompressible blunt torso bleeding below the diaphragm compared to resuscitative thoracotomy.

BACKGROUND: Resuscitative endovascular balloon occlusion of the aorta (REBOA) serves as a bridging intervention for subsequent definitive haemorrhagic control. This study compared the clinical outcomes of REBOA and resuscitative thoracotomy (RT) in patients with bleeding below the diaphragm. MATERIALS AND METHODS: This retrospective cohort study included adult trauma patients who presented to the Trauma Quality Improvement Program between 2020 and 2021 and who underwent either REBOA or RT in the emergency department (ED). Patients with severe head and chest injuries, characterised by an Abbreviated Injury Scale (AIS) score greater than 3, were excluded. The clinical data of patients treated with REBOA and those treated with RT were compared, and multivariable logistic regression (MLR) was employed to identify prognostic factors associated with mortality. RESULTS: A total of 346 patients were enrolled: 138 (39.9 %) received REBOA, and 208 (60.1 %) received RT at the ED. Patients in the RT group underwent ED cardiopulmonary resuscitation (CPR) more frequently (58.2 % vs. 23.2 %; p < 0.001) and had a higher mortality rate (87.0 % vs. 45.7 %; p < 0.001). Patients who died had lower Glasgow Coma Scale scores (6 [4.5] vs. 11 [4.9]; p < 0.001), underwent more ED CPR (58.6 % vs. 9.8 %; p < 0.001), and received RT more frequently (74.2 % vs. 26.5 %, p < 0.001). The MLR revealed that the major prognostic factors for mortality were systolic blood pressure (odds ratio [OR] 0.988, 95 % confidence interval [CI] 0.978-0.998; p = 0.014), ED CPR (OR 11.111, 95 % CI 4.667-26.452; p < 0.001), abdominal injuries with an AIS score ≥ 4 (OR 4.694, 95 % CI 1.921-11.467; p = 0.001) and RT (OR 5.693, 95 % CI 2.690-12.050; p < 0.001). CONCLUSIONS: In cases of blunt trauma, prompt identification of the bleeding source is crucial. For patients with bleeding below the diaphragm, REBOA led to higher survival rates than did RT. However, it is important to consider the limitations of the database and the necessary exclusions from our analysis.

Stem cell activity-coupled suppression of endogenous retrovirus governs adult tissue regeneration.

Mammalian retrotransposons constitute 40% of the genome. During tissue regeneration, adult stem cells coordinately repress retrotransposons and activate lineage genes, but how this coordination is controlled is poorly understood. Here, we observed that dynamic expression of histone methyltransferase SETDB1 (a retrotransposon repressor) closely mirrors stem cell activities in murine skin. SETDB1 ablation leads to the reactivation of endogenous retroviruses (ERVs, a type of retrotransposon) and the assembly of viral-like particles, resulting in hair loss and stem cell exhaustion that is reversible by antiviral drugs. Mechanistically, at least two molecularly and spatially distinct pathways are responsible: antiviral defense mediated by hair follicle stem cells and progenitors and antiviral-independent response due to replication stress in transient amplifying cells. ERV reactivation is promoted by DNA demethylase ten-eleven translocation (TET)-mediated hydroxymethylation and recapitulated by ablating cell fate transcription factors. Together, we demonstrated ERV silencing is coupled with stem cell activity and essential for adult hair regeneration.

Enhanced soluble expression and characterization of human N-acetylglucosaminyltransferase IVa in Escherichia coli.

N-Glycosylation is one of the most important posttranslational modifications of proteins. Nearly the entire surface of cells and almost all secreted proteins in humans are modified with complex-type N-glycans, whose functions are affected by the number of N-glycan branches. N-Acetylglucosaminyltransferase-IVa (GnT-IVa) is a Golgi glycosyltransferase that transfers a GlcNAc to the α-1,3 mannose arm of the biantennary N-glycan GlcNAc2Man3GlcNAc2 to form a ß-1,4 GlcNAc branched structure. The soluble expression of mammalian glycosyltransferases in heterologous hosts is often challenging. In the present study, human GnT-IVa (HsGnT-IVa) was cloned as an N-terminal truncated form that was fused with solubility-enhancing tags or signal peptides and overexpressed in Escherichia coli (E. coli). Our results showed that recombinant HsGnT-IVa could be overexpressed in its highest soluble and active form when the first 87 amino acids were removed and was fused with maltose-binding protein (MBP). By optimizing the induction conditions, the expression level of the recombinant protein was increased to yield approximately 540 mg per liter of culture after affinity purification. The purified enzyme exhibited appropriate glycosyltransferase activity, and the Km value of the acceptor substrate was calculated as 1.1 mM. Characterization of the enzyme revealed that it reached its maximum activity with 5 mM Mn2+ at 37 °C in MES/NaOH (pH 7.0). In addition, the effects of key amino acids in the catalytic and lectin domains on enzyme activity were measured. This work offers an efficient approach for the large-scale production of bioactive HsGnT-IVa, which can be used for in vitro synthesis and functional studies of multiantennary complex-type N-glycans.

Targeting the Epidermal Growth Factor Receptor Pathway in Chemotherapy-Resistant Triple-Negative Breast Cancer: A Phase II Study.

PURPOSE: Epidermal growth factor receptor (EGFR) pathway activation causes chemotherapy resistance, and inhibition of the EGFR pathway sensitizes triple-negative breast cancer (TNBC) cells to chemotherapy in preclinical models. Given the high prevalence of EGFR overexpression in TNBC, we conducted a single-arm phase II study of panitumumab (anti-EGFR monoclonal antibody), carboplatin, and paclitaxel as the second phase of neoadjuvant therapy (NAT) in patients with doxorubicin and cyclophosphamide (AC)-resistant TNBC (NCT02593175). PATIENTS AND METHODS: Patients with early-stage, AC-resistant TNBC, defined as disease progression or ≤80% reduction in tumor volume after four cycles of AC, were eligible for this study and received panitumumab (2.5 mg/kg i.v., every week × 13), paclitaxel (80 mg/m2 i.v. every week × 12), and carboplatin (AUC = 4 i.v., every 3 weeks × 4) as the second phase of NAT. A two-stage Gehan-type design was used to detect an improvement in the pathological complete response (pCR)/residual cancer burden class I (RCB-I) rate from 5% to 20%. Whole-exome sequencing was performed on diagnostic tumor biospecimens, where available. RESULTS: From November 3, 2016, through August 23, 2021, 43 patients with AC-resistant TNBC were enrolled. The combined pCR/RCB-I rate was 30.2%. The most common treatment-related adverse events were neutropenia (72%) and anemia (61%), with 7 (16%), 16 (37%), and 8 (19%) patients experiencing grade 4 neutropenia, grade 3 neutropenia, and grade 3 anemia, respectively. No new safety signals were observed. CONCLUSIONS: This study met its primary endpoint (pCR/RCB-I = 30.2% vs. 5% in historical controls), suggesting that panitumumab should be evaluated as a component of NAT in patients with chemotherapy-resistant TNBC in a larger, randomized clinical trial. SIGNIFICANCE: The epidermal growth factor receptor (EGFR) pathway has been implicated as a driver of chemotherapy resistance in triple-negative breast cancer (TNBC). Here, we evaluate the combination of panitumumab, carboplatin, and paclitaxel as the second phase of neoadjuvant therapy (NAT) in patients with AC-resistant TNBC. This study met its primary efficacy endpoint, and molecular alterations in EGFR pathway genes did not seem to influence response to the study regimen.

Temporal recording of mammalian development and precancer.

Temporal ordering of cellular events offers fundamental insights into biological phenomena. Although this is traditionally achieved through continuous direct observations1,2, an alternative solution leverages irreversible genetic changes, such as naturally occurring mutations, to create indelible marks that enables retrospective temporal ordering3-5. Using a multipurpose, single-cell CRISPR platform, we developed a molecular clock approach to record the timing of cellular events and clonality in vivo, with incorporation of cell state and lineage information. Using this approach, we uncovered precise timing of tissue-specific cell expansion during mouse embryonic development, unconventional developmental relationships between cell types and new epithelial progenitor states by their unique genetic histories. Analysis of mouse adenomas, coupled to multiomic and single-cell profiling of human precancers, with clonal analysis of 418 human polyps, demonstrated the occurrence of polyclonal initiation in 15-30% of colonic precancers, showing their origins from multiple normal founders. Our study presents a multimodal framework that lays the foundation for in vivo recording, integrating synthetic or natural indelible genetic changes with single-cell analyses, to explore the origins and timing of development and tumorigenesis in mammalian systems.

BATF is a major driver of NK cell epigenetic reprogramming and dysfunction in AML.

Myelodysplastic syndrome and acute myeloid leukemia (AML) belong to a continuous disease spectrum of myeloid malignancies with poor prognosis in the relapsed/refractory setting necessitating novel therapies. Natural killer (NK) cells from patients with myeloid malignancies display global dysfunction with impaired killing capacity, altered metabolism, and an exhausted phenotype at the single-cell transcriptomic and proteomic levels. In this study, we identified that this dysfunction was mediated through a cross-talk between NK cells and myeloid blasts necessitating cell-cell contact. NK cell dysfunction could be prevented by targeting the αvß-integrin/TGF-ß/SMAD pathway but, once established, was persistent because of profound epigenetic reprogramming. We identified BATF as a core transcription factor and the main mediator of this NK cell dysfunction in AML. Mechanistically, we found that BATF was directly regulated and induced by SMAD2/3 and, in turn, bound to key genes related to NK cell exhaustion, such as HAVCR2, LAG3, TIGIT, and CTLA4. BATF deletion enhanced NK cell function against AML in vitro and in vivo. Collectively, our findings reveal a previously unidentified mechanism of NK immune evasion in AML manifested by epigenetic rewiring and inactivation of NK cells by myeloid blasts. This work highlights the importance of using healthy allogeneic NK cells as an adoptive cell therapy to treat patients with myeloid malignancies combined with strategies aimed at preventing the dysfunction by targeting the TGF-ß pathway or BATF.

A Deep Learning Method for Human Sleeping Pose Estimation with Millimeter Wave Radar.

Recognizing sleep posture is crucial for the monitoring of people with sleeping disorders. Existing contact-based systems might interfere with sleeping, while camera-based systems may raise privacy concerns. In contrast, radar-based sensors offer a promising solution with high penetration ability and the capability to detect vital bio-signals. This study propose a deep learning method for human sleep pose recognition from signals acquired from single-antenna Frequency-Modulated Continuous Wave (FMCW) radar device. To capture both frequency features and sequential features, we introduce ResTCN, an effective architecture combining Residual blocks and Temporal Convolution Network (TCN) to recognize different sleeping postures, from augmented statistical motion features of the radar time series. We rigorously evaluated our method with an experimentally acquired data set which contains sleeping radar sequences from 16 volunteers. We report a classification accuracy of 82.74% on average, which outperforms the state-of-the-art methods.

Somatic mutation phasing and haplotype extension using linked-reads in multiple myeloma.

Somatic mutation phasing informs our understanding of cancer-related events, like driver mutations. We generated linked-read whole genome sequencing data for 23 samples across disease stages from 14 multiple myeloma (MM) patients and systematically assigned somatic mutations to haplotypes using linked-reads. Here, we report the reconstructed cancer haplotypes and phase blocks from several MM samples and show how phase block length can be extended by integrating samples from the same individual. We also uncover phasing information in genes frequently mutated in MM, including DIS3, HIST1H1E, KRAS, NRAS, and TP53, phasing 79.4% of 20,705 high-confidence somatic mutations. In some cases, this enabled us to interpret clonal evolution models at higher resolution using pairs of phased somatic mutations. For example, our analysis of one patient suggested that two NRAS hotspot mutations occurred on the same haplotype but were independent events in different subclones. Given sufficient tumor purity and data quality, our framework illustrates how haplotype-aware analysis of somatic mutations in cancer can be beneficial for some cancer cases.

Irisin-Encapsulated Mitochondria-Targeted Biomimetic Nanotherapeutics for Alleviating Acute Kidney Injury.

Acute kidney injury (AKI) is the sudden decrease in renal function that can be attributed to dysregulated reactive oxygen species (ROS) production and impaired mitochondrial function. Irisin, a type I membrane protein secreted by skeletal muscles in response to physical activity, has been reported to alleviate kidney damage through regulation of mitochondrial biogenesis and oxidative metabolism. In this study, a macrophage membrane-coated metal-organic framework (MCM@MOF) is developed as a nanocarrier for encapsulating irisin to overcome the inherent characteristics of irisin, including a short circulation time, limited kidney-targeting ability, and low membrane permeability. The engineered irisin-mediated biomimetic nanotherapeutics have extended circulation time and enhanced targeting capability toward injured kidneys due to the preservation of macrophage membrane proteins. The irisin-encapsulated biomimetic nanotherapeutics effectively mitigate acute ischemia-reperfusion injury by protecting mitochondrial function and modulating SOD2 levels in renal tubular epithelial cells. The present study provides novel insights to advance the development of irisin as a potential therapeutic approach for AKI.

VCAT: an integrated variant function annotation tools.

The development of sequencing technology has promoted discovery of variants in the human genome. Identifying functions of these variants is important for us to link genotype to phenotype, and to diagnose diseases. However, it usually requires researchers to visit multiple databases. Here, we presented a one-stop webserver for variant function annotation tools (VCAT, https://biomed.nscc-gz.cn/zhaolab/VCAT/ ) that is the first one connecting variant to functions via the epigenome, protein, drug and RNA. VCAT is also the first one to make all annotations visualized in interactive charts or molecular structures. VCAT allows users to upload data in VCF format, and download results via a URL. Moreover, VCAT has annotated a huge number (1,262,041,068) of variants collected from dbSNP, 1000 Genomes projects, gnomAD, ICGC, TCGA, and HPRC Pangenome project. For these variants, users are able to searcher their functions, related diseases and drugs from VCAT. In summary, VCAT provides a one-stop webserver to explore the potential functions of human genomic variants including their relationship with diseases and drugs.

Interleukin-21 engineering enhances NK cell activity against glioblastoma via CEBPD.

Glioblastoma (GBM) is an aggressive brain cancer with limited therapeutic options. Natural killer (NK) cells are innate immune cells with strong anti-tumor activity and may offer a promising treatment strategy for GBM. We compared the anti-GBM activity of NK cells engineered to express interleukin (IL)-15 or IL-21. Using multiple in vivo models, IL-21 NK cells were superior to IL-15 NK cells both in terms of safety and long-term anti-tumor activity, with locoregionally administered IL-15 NK cells proving toxic and ineffective at tumor control. IL-21 NK cells displayed a unique chromatin accessibility signature, with CCAAT/enhancer-binding proteins (C/EBP), especially CEBPD, serving as key transcription factors regulating their enhanced function. Deletion of CEBPD resulted in loss of IL-21 NK cell potency while its overexpression increased NK cell long-term cytotoxicity and metabolic fitness. These results suggest that IL-21, through C/EBP transcription factors, drives epigenetic reprogramming of NK cells, enhancing their anti-tumor efficacy against GBM.

Multifunctional Wearable Electronic Based on Fabric Modified by PPy/NiCoAl-LDH for Energy Storage, Electromagnetic Interference Shielding, and Photothermal Conversion.

With the rapid advancement of electronic technology, traditional textiles are challenged to keep up with the demands of wearable electronics. It is anticipated that multifunctional textile-based electronics incorporating energy storage, electromagnetic interference (EMI) shielding, and photothermal conversion are expected to alleviate this problem. Herein, a multifunctional cotton fabric with hierarchical array structure (PPy/NiCoAl-LDH/Cotton) is fabricated by the introduction of NiCoAl-layered double hydroxide (NiCoAl-LDH) nanosheet arrays on cotton fibers, followed by polymerization and growth of continuous dense polypyrrole (PPy) conductive layers. The multifunctional cotton fabric shows a high specific areal capacitance of 754.72 mF cm-2 at 5 mA cm-2 and maintains a long cycling life (80.95% retention after 1000 cycles). The symmetrical supercapacitor assembled with this fabric achieves an energy density of 20.83 µWh cm-2 and a power density of 0.23 mWcm-2. Moreover, the excellent electromagnetic interference shielding (38.83 dB), photothermal conversion (70.2 °C at 1000 mW cm-2), flexibility and durability are also possess by the multifunctional cotton fabric. Such a multifunctional cotton fabric has great potential for using in new energy, smart electronics, and thermal management applications.

Gene Expression Profiles Perturbed by Injury to the Mouse Intervertebral Disc.

OBJECTIVES: Back pain subsequent to intervertebral disc (IVD) injury is a common clinical problem. Previous work examining early molecular changes post injury mainly used a candidate marker approach. In this study, gene expression in the injured and intact mouse tail IVDs was determined with a nonbiased whole transcriptome approach. DESIGN: Mouse tail IVD injury was induced by a needle puncture. Whole murine transcriptome was determined by RNASeq. Transcriptomes of injured IVDs were compared with those of intact controls by bioinformatic methods. RESULTS: Among the 18,078 murine genes examined, 592 genes were differentially expressed (P.adj < 0.01). Novel genes upregulated in injured compared with intact IVDs included Chl1, Lum, etc. Ontology study of upregulated genes revealed that leukocyte migration was the most enriched biological process, and network analysis showed that Tnfa had the most protein-protein interactions. Novel downregulated genes in the injured IVDs included 4833412C05Rik, Myoc, etc. The most enriched downregulated pathways were related to cytoskeletal organization. CONCLUSION: Novel genes highly regulated post disc injury were identified with an unbiased approach; they may serve as biomarkers of injury and response to treatments in future experiments. Enriched biological pathways and molecules with high numbers of connections may be targets for treatments post injury.

Elucidating immune-related gene transcriptional programs via factorization of large-scale RNA-profiles.

Recent developments in immunotherapy, including immune checkpoint blockade (ICB) and adoptive cell therapy (ACT), have encountered challenges such as immune-related adverse events and resistance, especially in solid tumors. To advance the field, a deeper understanding of the molecular mechanisms behind treatment responses and resistance is essential. However, the lack of functionally characterized immune-related gene sets has limited data-driven immunological research. To address this gap, we adopted non-negative matrix factorization on 83 human bulk RNA sequencing (RNA-seq) datasets and constructed 28 immune-specific gene sets. After rigorous immunologist-led manual annotations and orthogonal validations across immunological contexts and functional omics data, we demonstrated that these gene sets can be applied to refine pan-cancer immune subtypes, improve ICB response prediction and functionally annotate spatial transcriptomic data. These functional gene sets, informing diverse immune states, will advance our understanding of immunology and cancer research.

Phase II study of talazoparib in advanced cancers with BRCA1/2, DNA repair, and PTEN alterations.

Cancer cells with BRCA1/2 deficiencies are sensitive to poly (ADP-ribose) polymerase (PARP) inhibitors. We evaluated the efficacy of talazoparib in DNA-Damage Repair (DDR)-altered patients. In this phase II trial, patients were enrolled onto one of four cohorts based on molecular alterations: (1) somatic BRCA1/2, (2) other homologous recombination repair pathway, (3) PTEN and (4) germline BRCA1/2. The primary endpoint was a clinical benefit rate (CBR): complete response, partial response or stable disease ≥24 weeks. 79 patients with a median of 4 lines of therapy were enrolled. CBR for cohorts 1-4 were: 32.5%, 19.7%, 9.4% and 30.6%, respectively. PTEN mutations correlated with reduced survival and a trend towards shorter time to progression.Talazoparib demonstrated clinical benefit in selected DDR-altered patients. PTEN mutations/loss patients derived limited clinical benefit. Further study is needed to determine whether PTEN is prognostic or predictive of response to PARP inhibitors.

Free buccal fat pad graft for the bone defect filling of medication-related osteonecrosis of the jaws: A novel surgical approach.

Surgical intervention for medication-related jaw osteonecrosis (MRONJ) is currently the main treatment method, offering a higher healing rate than conservative approaches. However, the management of bony defects after sequestrectomy remains a challenging issue due to poor vascularization from the drug effect. The use of pedicled buccal fat pad (PBFP) for filling bone defects has become common and effective but is limited to the posterior maxillary region. To add to the advantages of the buccal fat pad, we explored a novel treatment approach using a free buccal fat pad (FBFP) to fill bone defects other than the posterior maxilla. While the FBFP has been employed in oral defect reconstruction, currently published cases have been utilized in recipient sites with good blood supply. There has yet to be any usage in poor vascularization defects like MRONJ. This article describes that the FBFP was used to fill the surgical defects of 8 patients who were diagnosed with MRONJ and who underwent sequestrectomy and saucerization. During follow-up visits, there was excellent wound healing and no significant tissue depression. Based on successful treatment experiences, FBFP is a reliable therapeutic option for the management of poor vascularization defects like MRONJ treated through surgical intervention.

Characteristics and biological responses of selective laser melted Ti6Al4V modified by micro-arc oxidation.

Background/purpose: Additive manufacturing (AM) technology, such as selective laser melting (SLM), has been used to fabricate medical devices of Ti-6wt.% Al-4wt.%V (Ti6Al4V) alloys in dentistry. Strontium (Sr) has been shown to have the potential to treat osteoporosis. The aim of this study was to investigate the physicochemical and biological properties of strontium-containing coatings on selective laser melted Ti6Al4V (SLM-Ti6Al4V) substrate. Materials and methods: The disk of Ti6Al4V was prepared by SLM method. The strontium-containing coatings were prepared by micro-arc oxidation (MAO) in aqueous electrolytes. The surface topography, chemical composition, and phase of strontium-containing MAO (SrMAO) coatings were performed by scanning electron microscope (SEM), energy dispersive X-ray spectrometer (EDS), and thin film X-ray diffraction (TF-XRD), respectively. The apatite-forming ability of the MAO coatings was conducted in simulating body fluid (SBF), and the cell proliferation was determined by methylthiazoletetrazolium (MTT) assay. Results: The microstructure of SLM-Ti6Al4V displays acicular α-phase organization. The TF-XRD results indicated that the phase of SrMAO coating was anatase, rutile, and titanium. The calcium, phosphorus, and strontium were detected in the coatings by EDS. Using the SEM, the surface morphology of SrMAO coatings exhibited a uniform 3D porous structure. The SrMAO coatings could induce a bone-like apatite layer after immersion in SBF, and presented significantly higher cell proliferation than untreated specimens in in-vitro experiments. Conclusion: All findings in this study indicate that SrMAO coatings formed on SLM-Ti6Al4V surfaces exhibit a benefit on biological responses and thereby are suitable for biomedical applications.