Engineered CD47 protects T cells for enhanced antitumour immunity.

Adoptively transferred T cells and agents designed to block the CD47-SIRPα axis are promising cancer therapeutics that activate distinct arms of the immune system1,2. Here we administered anti-CD47 antibodies in combination with adoptively transferred T cells with the goal of enhancing antitumour efficacy but observed abrogated therapeutic benefit due to rapid macrophage-mediated clearance of T cells expressing chimeric antigen receptors (CARs) or engineered T cell receptors. Anti-CD47-antibody-mediated CAR T cell clearance was potent and rapid enough to serve as an effective safety switch. To overcome this challenge, we engineered the CD47 variant CD47(Q31P) (47E), which engages SIRPα and provides a 'don't eat me' signal that is not blocked by anti-CD47 antibodies. TCR or CAR T cells expressing 47E are resistant to clearance by macrophages after treatment with anti-CD47 antibodies, and mediate substantial, sustained macrophage recruitment to the tumour microenvironment. Although many of the recruited macrophages manifested an M2-like profile3, the combined therapy synergistically enhanced antitumour efficacy. Our study identifies macrophages as major regulators of T cell persistence and illustrates the fundamental challenge of combining T-cell-directed therapeutics with those designed to activate macrophages. It delivers a therapeutic approach that is capable of simultaneously harnessing the antitumour effects of T cells and macrophages, offering enhanced potency against solid tumours.

Inosine induces stemness features in CAR-T cells and enhances potency.

Adenosine (Ado) mediates immune suppression in the tumor microenvironment and exhausted CD8+ CAR-T cells express CD39 and CD73, which mediate proximal steps in Ado generation. Here, we sought to enhance CAR-T cell potency by knocking out CD39, CD73, or adenosine receptor 2a (A2aR) but observed only modest effects. In contrast, overexpression of Ado deaminase (ADA-OE), which metabolizes Ado to inosine (INO), induced stemness and enhanced CAR-T functionality. Similarly, CAR-T cell exposure to INO augmented function and induced features of stemness. INO induced profound metabolic reprogramming, diminishing glycolysis, increasing mitochondrial and glycolytic capacity, glutaminolysis and polyamine synthesis, and reprogrammed the epigenome toward greater stemness. Clinical scale manufacturing using INO generated enhanced potency CAR-T cell products meeting criteria for clinical dosing. These results identify INO as a potent modulator of CAR-T cell metabolism and epigenetic stemness programming and deliver an enhanced potency platform for cell manufacturing.

Creating a Box-Cavity Defect Model in the Cortical Bone of Rat Femora.

Severe bone defects or complex fractures can result in serious complications such as nonunion or insufficient bone healing. Tissue engineering, which involves the application of cells, scaffolds, and cytokines, is considered a promising solution for bone regeneration. Consequently, various animal models that simulate bone defects play a crucial role in exploring the therapeutic potential of tissue engineering for bone healing. In this study, we established a box-shaped cortical bone defect model in the mid-femur of rats, which could serve as an ideal model for assessing the function of biomaterials in promoting bone healing. This box-shaped cortical bone defect was drilled using an oral low-speed handpiece and shaped by a lathe needle. Post-operative micro-CT analysis was immediately conducted to confirm the successful establishment of the box-cavity cortical bone defect. The femurs on the operated side of the rats were then harvested at multiple time points post-surgery (0 days, 2 weeks, 4 weeks, and 6 weeks). The healing process of each sample's defect area was evaluated using micro-CT, hematoxylin and eosin (H&E) staining, and Masson trichrome staining. These results demonstrated a healing pattern consistent with intramembranous ossification, with healing essentially complete by 6 weeks. The categorization of this animal model's healing process provides an effective in vivo method for investigating novel biomaterials and drugs that target intramembranous ossification during bone tissue defect healing.

Noncoding mutations cause super-enhancer retargeting resulting in protein synthesis dysregulation during B cell lymphoma progression.

Whole-genome sequencing of longitudinal tumor pairs representing transformation of follicular lymphoma to high-grade B cell lymphoma with MYC and BCL2 rearrangements (double-hit lymphoma) identified coding and noncoding genomic alterations acquired during lymphoma progression. Many of these transformation-associated alterations recurrently and focally occur at topologically associating domain resident regulatory DNA elements, including H3K4me3 promoter marks located within H3K27ac super-enhancer clusters in B cell non-Hodgkin lymphoma. One region found to undergo recurrent alteration upon transformation overlaps a super-enhancer affecting the expression of the PAX5/ZCCHC7 gene pair. ZCCHC7 encodes a subunit of the Trf4/5-Air1/2-Mtr4 polyadenylation-like complex and demonstrated copy number gain, chromosomal translocation and enhancer retargeting-mediated transcriptional upregulation upon lymphoma transformation. Consequently, lymphoma cells demonstrate nucleolar dysregulation via altered noncoding 5.8S ribosomal RNA processing. We find that a noncoding mutation acquired during lymphoma progression affects noncoding rRNA processing, thereby rewiring protein synthesis leading to oncogenic changes in the lymphoma proteome.

Confounding clinical picture in the diagnosis of left ventricular and valvular masses: a case report.

Background: Masses in the heart and valves have a broad differential diagnosis including infective and rheumatic causes as well as primary or metastatic tumours. Diagnosis involves delineating the location, shape, and origin of the mass/masses and considering the clinical context. This case outlines the work-up and approach to diagnosing a cardiac mass along with imaging findings of a unique secondary metastatic mass in the left ventricle (LV). Case summary: A 69-year-old female with past medical history of metastatic lung cancer treated with radiotherapy and breast cancer treated with mastectomy presented with dyspnoea and fever. Due to concern for infective endocarditis, transthoracic echocardiogram (TTE) was performed revealing 2 cm × 0.72 cm finger-like, echo-lucent, mobile mass, appearing to originate from LV lateral wall, protruding into the LV cavity, along with valvular masses on mitral and tricuspid valves. Initial differential diagnosis included benign pathologies, but due to the clinical suspicion of malignancy, cardiac MRI was performed which revealed a broad-based mass with invasion into the LV lateral wall and delayed gadolinium enhancement, suggestive of metastatic tumour. The patient was given Aspirin to prevent embolization and eventually underwent hospice care. Discussion: Atypical appearing cardiac masses can be seen on TTE. Cardiac magnetic resonance imaging (MRI) should be used for definite diagnosis in cases where clinical features do not match the echocardiographic findings.

Identifying cadmium and lead co-accumulation from living rice blade spectrum.

Neither cadmium (Cd) nor lead (Pb) is necessary for crop growth, but they both can accumulate in soil and crop tissues, resulting in land degradation and crop reduction. Few researchers have explored how to detect Cd-Pb co-accumulation in leaves using proximal sensing techniques, especially by low-cost, easy-to-use leaf clips that capture hyperspectral reflections at suitable foliar positions. In this study, a hyperspectral imager was employed to collect images of the rice canopy from a designed greenhouse experiment that included 16 pretreatments of Cd-Pb co-accumulation, followed by spectral extractions from 3 foliar positions: the blade root, the middle of the leaf, and the leaf apex. A support vector machine with leave-one-out cross-validation was performed to diagnose the contaminative levels based on the feature wavelengths selected by an improved successive projection algorithm. Partial least squares regression was used to predict Cd-Pb concentrations in rice blades. The results indicated that diagnostic accuracies were varied using spectra of different foliar positions. The blade root and leaf apex of rice blades were the optimal foliar position for detecting Cd and Pb contamination, respectively. At the optimal foliar positions, diagnostic accuracies exceeded 0.80 for distinguishing whether the rice is subject to Cd-Pb contamination. The Cd prediction performed 'very good' with a residual prediction deviation (RPD) of 2.21, a R2 of 0.79, and a root mean square error (RMSE)of 6.14, while that of Pb was 1.62, 0.61, and 186.54. Important wavelengths were identified at 659-694 nm and 667-694 nm to detect Cd and Pb contamination. In summary, our results verified the feasibility and clarified the optimal foliar positions of rice blades to detect Cd-Pb contamination. The wavelengths selecting have the great potential in the design of future leaf clips, and the optimal foliar position can provide suggestions to improve diagnostic performances in field applications.

Tumor-associated monocytes promote mesenchymal transformation through EGFR signaling in glioma.

The role of brain immune compartments in glioma evolution remains elusive. We profile immune cells in glioma microenvironment and the matched peripheral blood from 11 patients. Glioblastoma exhibits specific infiltration of blood-originated monocytes expressing epidermal growth factor receptor (EGFR) ligands EREG and AREG, coined as tumor-associated monocytes (TAMo). TAMo infiltration is mutually exclusive with EGFR alterations (p = 0.019), while co-occurring with mesenchymal subtype (p = 4.7 × 10-7) and marking worse prognosis (p = 0.004 and 0.032 in two cohorts). Evolutionary analysis of initial-recurrent glioma pairs and single-cell study of a multi-centric glioblastoma reveal association between elevated TAMo and glioma mesenchymal transformation. Further analyses identify FOSL2 as a TAMo master regulator and demonstrates that FOSL2-EREG/AREG-EGFR signaling axis promotes glioma invasion in vitro. Collectively, we identify TAMo in tumor microenvironment and reveal its driving role in activating EGFR signaling to shape glioma evolution.

Flagella of Tumor-Targeting Bacteria Trigger Local Hemorrhage to Reprogram Tumor-Associated Macrophages for Improved Antitumor Therapy.

Tumor-associated macrophages (TAMs) exhibit an immunosuppressive M2 phenotype and lead to failure of antitumor therapy. Infiltrated erythrocytes during hemorrhage are recognized as a promising strategy for polarizing TAMs. However, novel materials that precisely induce tumor hemorrhage without affecting normal coagulation still face challenges. Here, tumor-targeting bacteria (flhDC VNP) are genetically constructed to realize precise tumor hemorrhage. FlhDC VNP colonizes the tumor and overexpresses flagella during proliferation. The flagella promote the expression of tumor necrosis factor α, which induces local tumor hemorrhage. Infiltrated erythrocytes during the hemorrhage temporarily polarize macrophages to the M1 subtype. In the presence of artesunate, this short-lived polarization is transformed into a sustained polarization because artesunate and heme form a complex that continuously produces reactive oxygen species. Therefore, the flagella of active tumor-targeting bacteria may open up new strategies for reprogramming TAMs and improving antitumor therapy.

Structures of human TR4LBD-JAZF1 and TR4DBD-DNA complexes reveal the molecular basis of transcriptional regulation.

Testicular nuclear receptor 4 (TR4) modulates the transcriptional activation of genes and plays important roles in many diseases. The regulation of TR4 on target genes involves direct interactions with DNA molecules via the DNA-binding domain (DBD) and recruitment of coregulators by the ligand-binding domain (LBD). However, their regulatory mechanisms are unclear. Here, we report high-resolution crystal structures of TR4DBD, TR4DBD-DNA complexes and the TR4LBD-JAZF1 complex. For DNA recognition, multiple factors come into play, and a specific mutual selectivity between TR4 and target genes is found. The coactivators SRC-1 and CREBBP can bind at the interface of TR4 originally occupied by the TR4 activation function region 2 (AF-2); however, JAZF1 suppresses the binding through a novel mechanism. JAZF1 binds to an unidentified surface of TR4 and stabilizes an α13 helix never reported in the nuclear receptor family. Moreover, the cancer-associated mutations affect the interactions and the transcriptional activation of TR4 in vitro and in vivo, respectively. Overall, our results highlight the crucial role of DNA recognition and a novel mechanism of how JAZF1 reinforces the autorepressed conformation and influences the transcriptional activation of TR4, laying out important structural bases for drug design for a variety of diseases, including diabetes and cancers.

XPF activates break-induced telomere synthesis.

Alternative Lengthening of Telomeres (ALT) utilizes a recombination mechanism and break-induced DNA synthesis to maintain telomere length without telomerase, but it is unclear how cells initiate ALT. TERRA, telomeric repeat-containing RNA, forms RNA:DNA hybrids (R-loops) at ALT telomeres. We show that depleting TERRA using an RNA-targeting Cas9 system reduces ALT-associated PML bodies, telomere clustering, and telomere lengthening. TERRA interactome reveals that TERRA interacts with an extensive subset of DNA repair proteins in ALT cells. One of TERRA interacting proteins, the endonuclease XPF, is highly enriched at ALT telomeres and recruited by telomeric R-loops to induce DNA damage response (DDR) independent of CSB and SLX4, and thus triggers break-induced telomere synthesis and lengthening. The attraction of BRCA1 and RAD51 at telomeres requires XPF in FANCM-deficient cells that accumulate telomeric R-loops. Our results suggest that telomeric R-loops activate DDR via XPF to promote homologous recombination and telomere replication to drive ALT.

Intratumoral delivered novel circular mRNA encoding cytokines for immune modulation and cancer therapy.

The success of the two mRNA vaccines developed by Moderna and BioNTech during the COVID-19 pandemic increased research interest into the application of mRNA technologies. Compared with the canonical linear mRNA used in these vaccines, circular mRNA has been found to mediate more potent and durable protein expression and demands a simpler manufacturing procedure. However, the application of circular mRNA is still at the initiation stage, and proof of concept for its use as a future medicine or vaccine is required. In the current study, we established a novel type of circular mRNA, termed cmRNA, based on the echovirus 29-derived internal ribosome entry site element and newly designed homology arms and RNA spacers. Our results demonstrated that this type of circular mRNA could mediate strong and durable expression of various types of proteins, compared with typical linear mRNA. Moreover, for the first time, our study demonstrated that direct intratumoral administration of cmRNA encoding a mixture of cytokines achieved successful modulation of intratumoral and systematic anti-tumor immune responses and enhanced anti-programmed cell death protein 1 (PD-1) antibody-induced tumor repression in a syngeneic mouse model. This novel circular mRNA platform is thereby suitable for direct intratumoral administration for cancer therapy.

Healthy dietary patterns and risk of cardiovascular disease in US Hispanics/Latinos: the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).

BACKGROUND: Multiple dietary patterns have been recommended by the 2015-2020 Dietary Guidelines for Americans for the prevention of cardiovascular disease (CVD). The adherence to these patterns and its relation with risk of CVD remain unclear in the US Hispanic/Latino population. OBJECTIVES: We aimed to evaluate 3 healthy eating patterns measured by 3 dietary pattern scores [the Alternate Mediterranean diet (aMED), the Healthy Eating Index (HEI)-2015, and the healthful Plant-based Diet Index (hPDI)] across different Hispanic/Latino backgrounds and generations. We further examined the associations of these dietary scores with incident CVD in US Hispanics/Latinos. METHODS: We included 10,293 adult participants of US Hispanics/Latinos of 6 backgrounds (Mexican, Puerto Rican, Cuban, Dominican, Central American, and South American), free of CVD or cancer at baseline, in the Hispanic Community Health Study/Study of Latinos. Dietary pattern scores were derived at the baseline visit using two 24-h dietary recalls. The primary outcome was major incident CVD (n = 232), comprised of coronary heart disease and stroke, during an average 6-y follow-up. RESULTS: Mean levels of all 3 dietary scores were significantly different across the 6 Hispanic/Latino background groups (all P < 0.001), with the highest (i.e., healthiest) in those of Mexican background and lowest in those of Puerto Rican background. Compared with non-mainland-US-born Hispanics/Latinos, mainland-US-born Hispanics/Latinos had significantly lower dietary scores (P < 0.001). Differences in dietary scores between mainland-US-born and non-mainland-US-born Hispanics/Latinos were majorly driven by differences in dietary intakes of healthy plant-based foods. After adjusting for multiple covariates, significantly lower risk ratios (95% CI) of CVD were observed for 1-SD increments of the dietary scores, with 0.74 (0.60, 0.91) for aMED, 0.80 (0.63, 1.00) for HEI-2015, and 0.74 (0.60, 0.93) for hPDI. CONCLUSIONS: Although adherence to healthy eating patterns varied by Hispanic/Latino backgrounds and generations, greater adherence to these eating patterns was associated with lower risk of CVD across diverse US Hispanics/Latinos.

Ligand-Directed Caging Enables the Control of Endogenous DNA Alkyltransferase Activity with Light inside Live Cells.

The control of endogenous protein activity with light inside live cells is helpful for the high spatiotemporal probing of their dynamic roles. Herein, we report the first small-molecule-ligand-directed caging approach to control the endogenous human O6 -alkylguanine-DNA alkyltransferase (AGT) activity with light, and the caged AGT is constructed from the native intracellular AGT. The photo-responsive O6 -benzylguanine derivative O6 -NBG3 is developed to site-specifically cage the AGT's catalytic cysteine residue, and the light irradiation on-demand restores AGT's activity in vitro, in bacteria, and in mammalian cells. With O6 -NBG3, the alkylated AGT is dealkylated for the first time to recover the DNA repair activity in breast cancer MCF-7 cells by the dose-dependent light irradiation. This decaging strategy enables the localized modulation of endogenous AGT activity with high temporal precision without genetic engineering, which holds great potential for therapeutic applications.

BARD1 is an ATPase activating protein for OLA1.

OLA1 is a P-loop ATPase, implicated in centrosome duplication through the interactions with tumor suppressors BRCA1 and BARD1. Disruption of the interaction of OLA1 with BARD1 results in centrosome amplification. However, the molecular interplay and mechanism of the OLA1-BARD1 complex remain elusive. Here, we use a battery of biophysical, biochemical, and structural analyses to elucidate the molecular basis of the OLA1-BARD1 interaction. Our structural and enzyme kinetics analyses show this nucleotide-dependent interaction enhances the ATPase activity of OLA1 by increasing the turnover number (kcat). Unlike canonical GTPase activating proteins that act directly on the catalytic G domain, the BARD1 BRCT domain binds to the OLA1 TGS domain via a highly conserved BUDR motif. A cancer related mutation V695L on BARD1 is known to associate with centrosome abnormality. The V695L mutation reduces the BARD1 BRCT-mediated activation of OLA1. Crystallographic snapshot of the BRCT V695L mutant at 1.88 Å reveals this mutation perturbs the OLA1 binding site, resulting in reduced interaction. Altogether, our findings suggest the BARD1 BRCT domain serves as an ATPase activating protein to control OLA1 allosterically.

The catalytic activity of TCPTP is auto-regulated by its intrinsically disordered tail and activated by Integrin alpha-1.

T-Cell Protein Tyrosine Phosphatase (TCPTP, PTPN2) is a non-receptor type protein tyrosine phosphatase that is ubiquitously expressed in human cells. TCPTP is a critical component of a variety of key signaling pathways that are directly associated with the formation of cancer and inflammation. Thus, understanding the molecular mechanism of TCPTP activation and regulation is essential for the development of TCPTP therapeutics. Under basal conditions, TCPTP is largely inactive, although how this is achieved is poorly understood. By combining biomolecular nuclear magnetic resonance spectroscopy, small-angle X-ray scattering, and chemical cross-linking coupled with mass spectrometry, we show that the C-terminal intrinsically disordered tail of TCPTP functions as an intramolecular autoinhibitory element that controls the TCPTP catalytic activity. Activation of TCPTP is achieved by cellular competition, i.e., the intrinsically disordered cytosolic tail of Integrin-α1 displaces the TCPTP autoinhibitory tail, allowing for the full activation of TCPTP. This work not only defines the mechanism by which TCPTP is regulated but also reveals that the intrinsically disordered tails of two of the most closely related PTPs (PTP1B and TCPTP) autoregulate the activity of their cognate PTPs via completely different mechanisms.

Deep learning system compared with expert endoscopists in predicting early gastric cancer and its invasion depth and differentiation status (with videos).

BACKGROUND AND AIMS: We aimed to develop and validate a deep learning-based system that covers various aspects of early gastric cancer (EGC) diagnosis, including detecting gastric neoplasm, identifying EGC, and predicting EGC invasion depth and differentiation status. Herein, we provide a state-of-the-art comparison of the system with endoscopists using real-time videos in a nationwide human-machine competition. METHODS: This multicenter, prospective, real-time, competitive comparative, diagnostic study enrolled consecutive patients who received magnifying narrow-band imaging endoscopy at the Peking University Cancer Hospital from June 9, 2020 to November 17, 2020. The offline competition was conducted in Wuhan, China, and the endoscopists and the system simultaneously read patients' videos and made diagnoses. The primary outcomes were sensitivity in detecting neoplasms and diagnosing EGCs. RESULTS: One hundred videos, including 37 EGCs and 63 noncancerous lesions, were enrolled; 46 endoscopists from 44 hospitals in 19 provinces in China participated in the competition. The sensitivity rates of the system for detecting neoplasms and diagnosing EGCs were 87.81% and 100%, respectively, significantly higher than those of endoscopists (83.51% [95% confidence interval [CI], 81.23-85.79] and 87.13% [95% CI, 83.75-90.51], respectively). Accuracy rates of the system for predicting EGC invasion depth and differentiation status were 78.57% and 71.43%, respectively, slightly higher than those of endoscopists (63.75% [95% CI, 61.12-66.39] and 64.41% [95% CI, 60.65-68.16], respectively). CONCLUSIONS: The system outperformed endoscopists in identifying EGCs and was comparable with endoscopists in predicting EGC invasion depth and differentiation status in videos. This deep learning-based system could be a powerful tool to assist endoscopists in EGC diagnosis in clinical practice.

Diagnosis of cadmium contamination in urban and suburban soils using visible-to-near-infrared spectroscopy.

Previous studies have mostly focused on using visible-to-near-infrared spectral technique to quantitatively estimate soil cadmium (Cd) content, whereas little attention has been paid to identifying soil Cd contamination from a perspective of spectral classification. Here, we developed a framework to compare the potential of two spectral transformations (i.e., raw reflectance and continuum removal [CR]), three optimization strategies (i.e., full-spectrum, Boruta feature selection, and synthetic minority over-sampling technique [SMOTE]), and three classification algorithms (i.e., partial least squares discriminant analysis, random forest [RF], and support vector machine) for diagnosing soil Cd contamination. A total of 536 soil samples were collected from urban and suburban areas located in Wuhan City, China. Specifically, Boruta and SMOTE strategies were aimed at selecting the most informative predictors and obtaining balanced training datasets, respectively. Results indicated that soils contaminated by Cd induced decrease in spectral reflectance magnitude. Classification models developed after Boruta and SMOTE strategies out-performed to those from full-spectrum. A diagnose model combining CR preprocessing, SMOTE strategy, and RF algorithm achieved the highest validation accuracy for soil Cd (Kappa = 0.74). This study provides a theoretical reference for rapid identification of and monitoring of soil Cd contamination in urban and suburban areas.

Effect of a deep learning-based system on the miss rate of gastric neoplasms during upper gastrointestinal endoscopy: a single-centre, tandem, randomised controlled trial.

BACKGROUND: White light endoscopy is a pivotal first-line tool for the detection of gastric neoplasms. However, gastric neoplasms can be missed during upper gastrointestinal endoscopy due to the subtle nature of these lesions and varying skill among endoscopists. Here, we aimed to evaluate the effect of an artificial intelligence (AI) system designed to detect focal lesions and diagnose gastric neoplasms on reducing the miss rate of gastric neoplasms in clinical practice. METHODS: This single-centre, randomised controlled, tandem trial was done at Renmin Hospital of Wuhan University, China. We recruited consecutive patients (≥18 years old) undergoing routine upper gastrointestinal endoscopy for screening, surveillance, or investigation of symptoms. Same-day tandem upper gastrointestinal endoscopy was done where patients first underwent either AI-assisted (AI-first) or routine (routine-first) white light endoscopy, followed immediately by the other procedure, with targeted biopsies for all detected lesions taken at the end of the second examination. Patients were randomly assigned (1:1) to the AI-first or routine-first group using a computer-generated random numerical series and block randomisation (block size of four). Endoscopists were not blinded to randomisation status, whereas patients and pathologists were. The primary endpoint was the miss rate of gastric neoplasms and the analysis was done per protocol. This trial is registered with the Chinese Clinical Trial Registry, ChiCTR2000034453, and has been completed. FINDINGS: Between July 6, 2020, and Dec 11, 2020, 907 patients were randomly assigned to the AI-first group and 905 to the routine-first group. The gastric neoplasm miss rate was significantly lower in the AI-first group than in the routine-first group (6·1%, 95% CI 1·6-17·9 [3/49] vs 27·3%, 15·5-43·0 [12/44]; relative risk 0·224, 95% CI 0·068-0·744; p=0·015). The only reported adverse event was bleeding from a target lesion after biopsy. INTERPRETATION: The use of an AI system during upper gastrointestinal endoscopy significantly reduced the gastric neoplasm miss rate. AI-assisted endoscopy has the potential to improve the yield of gastric neoplasms by endoscopists. FUNDING: The Project of Hubei Provincial Clinical Research Center for Digestive Disease Minimally Invasive Incision and the Hubei Province Major Science and Technology Innovation Project.