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Objective: This study aimed to determine whether characteristics detected by multi-detector computed tomography (MDCT) were predictive of highly infectious, smear-positive, active pulmonary tuberculosis (PTB).Methods: Among 124 patients with active PTB, 84 had positive (group 1) and 40 had negative (group 2) smear results for acid-fast bacilli. Multiplanar MDCT, axial conventional CT and chest X-ray images were analysed retrospectively for morphology, number, and segmental (lobe) distribution of lesions.Results: By multivariate analysis, consolidation over any segment of the upper, middle, or lingual lobes, cavitations, and clusters of nodules were associated with group 1, while centrilobular nodules were predictive of group 2. Using five independent variables associated with risk in group 1, a prediction model was created to distinguish between group 1 and group 2. ROC curve analysis showed an area under the curve of 0.951 +/- 0.021 for this prediction model. With the ideal cutoff point score of 1, the sensitivity, specificity, and positive predictive values were 84.5%, 97.5%, and 98.0%, respectively.Conclusions: A model to predict smear-positive active PTB on the basis of findings from MDCT may be a useful tool for clinical decisions about isolating patients pending sputum smear results. [ABSTRACT FROM AUTHOR]

Background and purpose Based on reported success with staged treatment of distal tibial fractures, we designed a 2-stage protocol including external/internal locked plating. We retrospectively assessed the outcome of open distal tibial fractures treated according to this protocol. Patients and methods From March 2006 through July 2008, 16 patients who sustained open distal tibial fractures were treated by a two-stage protocol. The first stage consisted of low-profile, locked plates for temporary external fixation after debridement and anatomic reduction, followed by soft tissue reconstruction. The second stage consisted of locked plates for definitive internal fixation, using minimally invasive percutaneous osteosynthesis. All fractures were followed for median 2 (1-3) years. Results The reduction was classified as being good in 15 patients and fair in 1 patient. All fractures united at a median of 6 (6-12) months. At the latest follow-up, 7 patients had excellent and 9 had good Iowa ankle scores; ankle motion ranged from a median of 10 (5-20) degrees of dorsiflexion to 40 (20-60) degrees of plantar flexion. Interpretation We believe that the 2-stage external/internal locked plating technique is an effective procedure for treatment of open distal tibial fractures in patients who need a long period of external fixation. We achieved good reduction with immediate ankle-sparing stable fixation. Soft tissue reconstruction and subsequent definitive fixation led to union of all fractures with good function. [ABSTRACT FROM AUTHOR]

Purpose: We conducted this study to investigate the value of the dual-time 2-[(18)F]fluoro-2-deoxy-d-glucose (FDG) positron emission tomography-computed tomography (PET-CT) in assessment of the primary tumor, loco-regional lymph node and distant metastasis in patients with esophageal squamous cell carcinoma. Methods: Twenty-six patients with histologically proved esophageal squamous cell carcinoma underwent dual-time FDG PET-CT before radical surgery. The standardized uptake values (SUV(max)) were obtained including early SUV(max) and delayed SUV(max), respectively. The retention index (RI) was also calculated. The results were evaluated retrospectively according to the final pathologic findings. Four diagnostic criteria including (1) early SUV(max)≧ 2.5 alone, (2) RI ≧ 10% alone, (3) a combination of early SUV(max)≧ 2.5 and RI ≧ 10%, and (4) a combination of early SUV(max)≧ 2.5 or RI ≧ 10% were used for differentiating malignancy from a benign lesion, respectively. Results: The sensitivity of FDG PET-CT in detecting the primary tumor with combination of early SUV(max)≧ 2.5 or RI ≧ 10% was 96.2%. It was statistically significantly higher than the results using the other three criteria (p<0.0001). For loco-regional lymph node detection, there was no significant difference among the 4 criteria. For distal metastases, the significantly higher specificity (100%) was found when using combination of early SUV(max)≧ 2.5 and RI ≧ 10% or using early SUV(max)≧ 2.5 alone than using the other two criteria (p=0.0058). With regard to accuracy, no significant correlations were observed among primary tumor, loco-regional lymph nodes and distant metastasis (p>0.05). Conclusion: The preliminary result of this study demonstrated that dual-time point FDG PET-CT had limited value in detection of primary tumor and loco-regional lymph nodes metastasis. For the distant metastasis, the sensitivity and specificity would be improved if RI ≧ 10% is used as a supplemental criterion. Efforts should be made to improve the ability of the dual-time FDG PET-CT technique to assess primary tumor and loco-regional lymph nodes metastasis. [ABSTRACT FROM AUTHOR]

Purpose: We found several cases with unexpected pulmonary abnormalities on the 18F-FDG PET scan after the gastrointestinal endoscopy with sedation during a compact health check-up course, interfering the interpretations of 18F-FDG PET scan for cancer screening. The current studies aimed to analyze the incidence and the clinical relevance of this pulmonary finding. Materials and Methods: From June to December 2009, 127 subjects undergoing the sequential gastrointestinal endoscopy with sedation and 18F-FDG PET scan within 48 h as part of routine health check-up were retrospectively enrolled in this study. The incidence of abnormal pulmonary findings and their SUVmax of FDG were calculated and correlated with the clinical manifestations. Results: Five subjects had abnormal 18F-FDG PET findings but pulmonary symptoms were only found in 2. The SUVmax did not seem to reflect the severity of pulmonary symptoms or the need of intervention. Although the incidence of unrecognized pulmonary aspiration featuring inflammation detected by the 18F-FDG PET scan was high (3.94%, 5/127), the incidence of events needed intervention remained low (0.79%, 1/127), similar to those previously reported literatures. Conclusions: Although higher incidence of pulmonary aspiration in this study, it probably reflects the better sensitivity of 18F-FDG PET for inflammation. The low incidence of clinical events needed intervention may still reflect the safety of sedation used for gastrointestinal endoscopy. Proper arrangement of the sequential examinations if subjects need both gastrointestinal endoscopy with sedation and 18F-FDG PET is important to reduce the interference degrading the performance of 18F-FDG PET in cancer screening, diagnosis or staging. [ABSTRACT FROM AUTHOR]

Background and Objectives: Studies show that new onset diabetes mellitus (DM) (NOD) predates the diagnosis of PDAC by up to 2 years. Two tumor-intrinsic molecular subtypes of PDAC that are prognostic and predictive of chemotherapy response have been described and validated. We hypothesize that patients with NOD may have different molecular subtypes and prognoses., Methods: This is a single-institution study of patients who underwent resection for PDAC from 2009 to 2022 with de-identified samples available for sequencing. Demographic and clinical factors were examined using bivariate and multivariate analysis., Results: A total of 97 patients met inclusion criteria: 70 with no history of DM, 11 with longstanding DM (> 2 years), and 16 with NOD. The demographics between groups were overall similar. After controlling for age, sex, race, BMI, and tobacco history, NOD was not a significant predictor of PDAC subtype. There were no survival differences between groups. Transcriptomic analysis suggests the upregulation of inflammatory and immune activation and regulation pathways in NOD., Conclusions: As continued interest in NOD and PDAC mounts, we are the first to examine if NOD may be associated with molecular subtypes and outcomes. Further investigation into the underlying pathophysiology of the NOD group is still needed., (© 2024 Wiley Periodicals LLC.)

The health impacts of the diurnal temperature range (DTR), which may be affected by climate change, have received little attention. The objectives of this study were (1) to evaluate the association of DTR and cardiopulmonary outcomes, (2) to select the proper thresholds for a DTR warning system, and (3) to identify vulnerable groups. The weather and health records in Taiwan from 2000 to 2019, with a maximum DTR of 12.8 °C, were analyzed using generalized additive models. The health outcomes included cardiovascular (CVD) and respiratory disease (RD) categories and several sub-categories, such as ischemic heart disease, stroke, pneumonia, asthma, and chronic obstructive pulmonary disease. The results showed that the associations of DTR and cardiopulmonary outcomes were as significant as, and sometimes even stronger than, those of the daily maximum temperature and daily minimum apparent temperature in the warm and cold seasons, respectively. The significant association began at DTR of 6 °C, lower than previously reported. The identified DTR warning thresholds were 8.5 and 11 °C for the warm and cold seasons, respectively. DTR is statistically significantly associated with a 5-36% and a 9-20% increase in cardiopulmonary emergency and hospitalized cases in the warm season with a 1 °C increase above 8.5 °C, respectively. In the cold season, DTR is significantly associated with 7-41%, 4-30%, and 36-100% increases in cardiopulmonary emergency, hospitalized, and mortality with a 1 °C increase above 11 °C, respectively. People with hypertension, hyperglycemia, and hyperlipidemia had even higher risks. Vulnerable age and sex groups were identified if they had a lower DTR-health threshold than the general population, which can be integrated into a warning system. In conclusion, DTR may be increased on a local or city scale under climate change; a DTR warning system and vulnerable group identification may be warranted in most countries for health risk reduction., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Effective therapies for pancreatic ductal adenocarcinoma (PDAC) have been largely elusive. Here, we perform Multiplexed kinase Inhibitor Bead Mass Spectrometry on 102 patient derived xenografts derived from 14 unique primary PDAC to define the tumor-intrinsic kinome landscape. Our findings uncover three kinome subgroups making up two tumor-intrinsic kinome subtypes that we call kinotypes. The kinotypes show enrichment of different kinase classes and recapitulate previously described molecular subtypes, basal-like and classical. The kinotype characterizing basal-like tumors shows enrichment of receptor tyrosine kinases, whereas the kinotype characterizing classical tumors is enriched in understudied kinases involved in Wnt signaling and immune pathways. We validate our findings in two clinical trials and show that only patients with basal-like tumors derive significant benefit from EGFR inhibitors. Our results provide a comprehensive tumor-intrinsic kinome landscape of PDAC that strongly supports actionable kinotype specific kinase targets and provides a roadmap for kinase inhibitor therapy in PDAC.

A noticeable characteristic of pancreatic ductal adenocarcinoma (PDAC) tumors is a dense tumor microenvironment with abundant and dense, desmoplastic stroma woven tightly with both cellular and matrix components. The high stromal density is associated with higher intratumor pressures which, until the last decade, was largely assumed to be tumor protective, confirmed by early studies demonstrating that altering the stroma was effective in genetically engineered models of PDAC. However, clinical trials using these approaches have been disappointing. There is increasing recognition that stroma heterogeneity is much greater than initially thought with an explosion of investigation into cancer-associated fibroblast (CAF) subpopulations led by experimental and single-cell transcriptomic studies. This review summarizes and attempts to harmonize the current transcriptomic data of CAF subpopulations. Understanding the heterogeneity of CAFs, the matrix, and other tumor microenvironment features will be critical to developing effective therapeutic approaches. Identifying model systems that best recapitulate the clinical behavior and treatment response of human PDAC will be important. Examining subpopulations as defined by clinical outcome will remain a critical step in defining clinically impactful CAF subtypes in larger clinical cohorts. The future of precision oncology in PDAC will depend on the integration of precision tumor epithelial and precision stroma approaches., (© The Author(s) 2024. Published by Oxford University Press. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

The two major molecular subtypes of pancreatic adenocarcinoma reportedly have differential response to FOLFIRINOX-based therapy. To promote rapid assignment of basal versus classical subtypes, an array-based single-sample classifier assay was developed and applied to 74 formalin-fixed, paraffin-embedded biopsy or resection specimens of known subtype based on transcriptomics. The Purity Independent Subtyping of Tumors (PurIST) algorithm assigns subtype based on relative expression of 16 RNAs counted by RNA sequencing (RNAseq) versus more practical array-based NanoString nCounter Elements XT technology. Subtype calls were largely concordant between RNAseq and array methods (72/74, 97% agreement). Compared with the lengthy RNAseq protocol, the array-based assay takes just 3 working days to analyze, permitting rapid reporting of tumor subtype. In conclusion, the PurIST pancreatic cancer classifier has robust performance to classify pancreatic adenocarcinoma into basal versus classical subtypes. Clinical validation studies are underway to evaluate outcome in patients whose standard-of-care chemotherapy regimen is selected on the basis of rapid subtype assignment (NCT04683315)., Competing Interests: Disclosure Statement N.U.R. and J.J.Y. are patent holders on Purity Independent Subtyping of Tumors (PurIST) technology for subtyping pancreatic ductal adenocarcinoma (US17/601,002). GeneCentric Therapeutics, Inc., had no involvement in the current study but acquired an exclusive license from the University of North Carolina at Chapel Hill related to PurIST technology., (Copyright © 2024 Association for Molecular Pathology and American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.)

The kinome is a dynamic system of kinases regulating signaling networks in cells and dysfunction of protein kinases contributes to many diseases. Regulation of the protein expression of kinases alters cellular responses to environmental changes and perturbations. We configured a library of 672 proteotypic peptides to quantify >300 kinases in a single LC-MS experiment using ten micrograms protein from human tissues including biopsies. This enables absolute quantitation of kinase protein abundance at attomole-femtomole expression levels, requiring no kinase enrichment and less than ten micrograms of starting protein from flash-frozen and formalin fixed paraffin embedded tissues. Breast cancer biopsies, organoids, and cell lines were analyzed using the SureQuant method, demonstrating the heterogeneity of kinase protein expression across and within breast cancer clinical subtypes. Kinome quantitation was coupled with nanoscale phosphoproteomics, providing a feasible method for novel clinical diagnosis and understanding of patient kinome responses to treatment.

Outcomes from pancreatic ductal adenocarcinoma (PDAC) remain poor and better methods of prognostication and therapeutic approaches are needed. Recent advances in cancer genomics have led to the development of molecular subtypes of PDAC associated with clinical outcomes. Current evidence also suggests that the subtypes have differential response to first-line chemotherapy regimens. PDAC is also characterized by different stroma and immune environments. Further work is needed to confirm the utility of these subtypes to predicting response to different systemic therapies., Competing Interests: Disclosure PurIST was licensed to GeneCentric Therapeutics Inc (JJY). Funding JJY is supported by R01 CA199064, U01 CA274298, U24 CA211000, and P50 CA257911., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Objective: To assess the utility of tumor-intrinsic and cancer-associated fibroblast (CAF) subtypes of pancreatic ductal adenocarcinoma (PDAC) in predicting response to neoadjuvant therapy (NAT) and overall survival (OS)., Background: PDAC remains a deadly disease with limited treatment options, and both the tumor as well as the microenvironment play an important role in pathogenesis. Gene expression-based tumor-intrinsic subtypes (classical and basal-like) have been shown to predict outcomes, but tumor microenvironment subtypes are still evolving., Methods: RNA-sequencing was performed on 114 deidentified resected PDAC tumors. Clinical data were collected by retrospective chart review. Single sample classifiers were used to determine classical and basal-like subtypes as well as tumor-permissive permCAF and tumor-restraining restCAF subtypes. Survival was analyzed using the log-rank test., Results: Patients who received NAT had an increase in OS, with a median survival of 27.9 months compared with 20.1 months for those who did not receive NAT, but the difference did not reach statistical significance (hazard ratio: 0.64, P =0.076). Either tumor-intrinsic or CAF subtypes alone were associated with OS regardless of NAT or no NAT, and patients with classical or restCAF subtypes had the best outcomes. When evaluated together, patients with the classical-restCAF subtype had the best OS and basal-permCAF the worst OS ( P <0.0001). Patients undergoing NAT with the classical-restCAF subtype demonstrated the longest OS compared with the other groups ( P =0.00041)., Conclusions: CAF subtypes have an additive effect over tumor-intrinsic subtypes in predicting survival with or without neoadjuvant FOLFIRINOX in PDAC. Molecular subtyping of both tumor and CAF compartments of PDAC may be important steps in selecting first-line systemic therapy., Competing Interests: J.J.Y., X.,L.,P., and N.U.R. are inventors of PurIST Subtype Classifier, which was licensed to GeneCentric Therapeutics, Inc. The remaining authors report no conflicts of interest., (Copyright © 2024 Wolters Kluwer Health, Inc. All rights reserved.)

The pleiotropic roles of nSMase2-generated ceramide include regulation of intracellular ceramide signaling and exosome biogenesis. We investigated the effects of eliminating nSMase2 on early and advanced PDA, including its influence on the microenvironment. Employing the KPC mouse model of pancreatic cancer, we demonstrate that pancreatic epithelial nSMase2 ablation reduces neoplasia and promotes a PDA subtype switch from aggressive basal-like to classical. nSMase2 elimination prolongs survival of KPC mice, hinders vasculature development, and fosters a robust immune response. nSMase2 loss leads to recruitment of cytotoxic T cells, N1-like neutrophils, and abundant infiltration of anti-tumorigenic macrophages in the pancreatic preneoplastic microenvironment. Mechanistically, we demonstrate that nSMase2-expressing PDA cell small extracellular vesicles (sEVs) reduce survival of KPC mice; PDA cell sEVs generated independently of nSMase2 prolong survival of KPC mice and reprogram macrophages to a proinflammatory phenotype. Collectively, our study highlights previously unappreciated opposing roles for exosomes, based on biogenesis pathway, during PDA progression.

Here, we introduce 'TICIT', targeted integration by CRISPR-Cas9 and integrase technologies, which utilizes the site-specific DNA recombinase - phiC31 integrase - to insert large DNA fragments into CRISPR-Cas9 target loci. This technique, which relies on first knocking in a 39-basepair phiC31 landing site via CRISPR-Cas9, enables researchers to repeatedly perform site-specific transgenesis at the exact genomic location with high precision and efficiency. We applied this approach to devise a method for the instantaneous determination of a zebrafish's genotype simply by examining its color. When a zebrafish mutant line must be propagated as heterozygotes due to homozygous lethality, employing this method allows facile identification of a population of homozygous mutant embryos even before the mutant phenotypes manifest. Thus, it should facilitate various downstream applications, such as large-scale chemical screens. We demonstrated that TICIT could also create reporter fish driven by an endogenous promoter. Further, we identified a landing site in the tyrosinase gene that could support transgene expression in a broad spectrum of tissue and cell types. In sum, TICIT enables site-specific DNA integration without requiring complex donor DNA construction. It can yield consistent transgene expression, facilitate diverse applications in zebrafish, and may be applicable to cells in culture and other model organisms., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2024. Published by The Company of Biologists Ltd.)

Numerous aspects of cellular signaling are regulated by the kinome-the network of over 500 protein kinases that guides and modulates information transfer throughout the cell. The key role played by both individual kinases and assemblies of kinases organized into functional subnetworks leads to kinome dysregulation driving many diseases, particularly cancer. In the case of pancreatic ductal adenocarcinoma (PDAC), a variety of kinases and associated signaling pathways have been identified for their key role in the establishment of disease as well as its progression. However, the identification of additional relevant therapeutic targets has been slow and is further confounded by interactions between the tumor and the surrounding tumor microenvironment. In this work, we attempt to link the state of the human kinome, or kinotype, with cell viability in treated, patient-derived PDAC tumor and cancer-associated fibroblast cell lines. We applied classification models to independent kinome perturbation and kinase inhibitor cell screen data, and found that the inferred kinotype of a cell has a significant and predictive relationship with cell viability. We further find that models are able to identify a set of kinases whose behavior in response to perturbation drive the majority of viability responses in these cell lines, including the understudied kinases CSNK2A1/3, CAMKK2, and PIP4K2C. We next utilized these models to predict the response of new, clinical kinase inhibitors that were not present in the initial dataset for model devlopment and conducted a validation screen that confirmed the accuracy of the models. These results suggest that characterizing the perturbed state of the human protein kinome provides significant opportunity for better understanding of signaling behavior and downstream cell phenotypes, as well as providing insight into the broader design of potential therapeutic strategies for PDAC., Competing Interests: Shawn M. Gomez is an Academic Editor for PeerJ., (©2024 Berginski et al.)

Background: Cholangiocarcinoma (CCA) features highly desmoplastic stroma that promotes structural and functional resistance to therapy. Lysyl oxidases (LOX, LOXL1-4) catalyze collagen cross-linking, thereby increasing stromal rigidity and facilitating therapeutic resistance. Here, we evaluate the role of lysyl oxidases in stromal desmoplasia and the effects of pan-lysyl oxidase (pan-LOX) inhibition in CCA., Methods: Resected CCA and normal liver specimens were analyzed from archival tissues. Spontaneous and orthotopic murine models of intrahepatic CCA (iCCA) were used to assess the impact of the pan-LOX inhibitor PXS-5505 in treatment and correlative studies. The functional role of pan-LOX inhibition was interrogated through in vivo and ex vivo assays., Results: All 5 lysyl oxidases are upregulated in CCA and reduced lysyl oxidase expression is correlated with an improved prognosis in resected patients with CCA. Spontaneous and orthotopic murine models of intrahepatic cholangiocarcinoma upregulate all 5 lysyl oxidase isoforms. Pan-LOX inhibition reversed mechanical compression of tumor vasculature, resulting in improved chemotherapeutic penetrance and cytotoxic efficacy. The combination of chemotherapy with pan-LOX inhibition increased damage-associated molecular pattern release, which was associated with improved antitumor T-cell responses. Pan-LOX inhibition downregulated macrophage invasive signatures in vitro, rendering tumor-associated macrophages more susceptible to chemotherapy. Mice bearing orthotopic and spontaneously occurring intrahepatic cholangiocarcinoma tumors exhibited delayed tumor growth and improved survival following a combination of pan-LOX inhibition with chemotherapy., Conclusions: CCA upregulates all 5 lysyl oxidase isoforms, and pan-LOX inhibition reverses tumor-induced mechanical forces associated with chemotherapy resistance to improve chemotherapeutic efficacy and reprogram antitumor immune responses. Thus, combination therapy with pan-LOX inhibition represents an innovative therapeutic strategy in CCA., (Copyright © 2024 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Association for the Study of Liver Diseases.)

CRISPR prime editing ( PE ) requires a Cas9 nickase-reverse transcriptase fusion protein (known as PE2) and a prime editing guide RNA ( pegRNA ), an extended version of a standard guide RNA ( gRNA ) that both specifies the intended target genomic sequence and encodes the desired genetic edit. Here, we show that sequence complementarity between the 5' and the 3' regions of a pegRNA can negatively impact its ability to complex with Cas9, thereby potentially reducing PE efficiency. We demonstrate this limitation can be overcome by a simple pegRNA refolding procedure, which improved ribonucleoprotein-mediated PE efficiencies in zebrafish embryos by up to nearly 25-fold. Further gains in PE efficiencies of as much as sixfold could also be achieved by introducing point mutations designed to disrupt internal interactions within the pegRNA. Our work defines simple strategies that can be implemented to improve the efficiency of PE., Competing Interests: WZ, JM, HL, CT, JY No competing interests declared, KP has a financial interest in SeQure Dx, Inc. KP's interests and relationships have been disclosed to Massachusetts General Hospital and Mass General Brigham in accordance with their conflict of interest policies, JJ has, or had during the course of this research, financial interests in several companies developing gene editing technology: Beam Therapeutics, Blink Therapeutics, Chroma Medicine, Editas Medicine, EpiLogic Therapeutics, Excelsior Genomics, Hera Biolabs, Monitor Biotechnologies, Nvelop Therapeutics (f/k/a ETx, Inc), Pairwise Plants, Poseida Therapeutics, SeQure Dx, Inc, and Verve Therapeutics. JKJ's interests were reviewed and are managed by Massachusetts General Hospital and Mass General Brigham in accordance with their conflict of interest policies. JKJ is a co-inventor on various patents and patent applications that describe gene editing and epigenetic editing technologies, (© 2023, Zhang et al.)

Cancer-associated fibroblast (CAF) subpopulations in pancreatic ductal adenocarcinoma (PDAC) have been identified using single-cell RNA sequencing (scRNAseq) with divergent characteristics, but their clinical relevance remains unclear. We translate scRNAseq-derived CAF cell-subpopulation-specific marker genes to bulk RNAseq data, and develop a single- sample classifier, DeCAF, for the classification of clinically rest raining and perm issive CAF subtypes. We validate DeCAF in 19 independent bulk transcriptomic datasets across four tumor types (PDAC, mesothelioma, bladder and renal cell carcinoma). DeCAF subtypes have distinct histology features, immune landscapes, and are prognostic and predict response to therapy across cancer types. We demonstrate that DeCAF is clinically replicable and robust for the classification of CAF subtypes in patients for multiple tumor types, providing a better framework for the future development and translation of therapies against permissive CAF subtypes and preservation of restraining CAF subtypes., Significance: We introduce a replicable and robust classifier, DeCAF, that delineates the significance of the role of permissive and restraining CAF subtypes in cancer patients. DeCAF is clinically tractable, prognostic and predictive of treatment response in multiple cancer types and lays the translational groundwork for the preclinical and clinical development of CAF subtype specific therapies.

Background: To determine the effect of colchicine on cancer risk in patients with the immune-mediated inflammatory diseases (IMIDs)-related to colchicine use., Methods: This is a time-dependent propensity-matched general population study based on the National Health Insurance Research Database (NHIRD) of Taiwan. We identified the IMIDs patients (n = 111,644) newly diagnosed between 2000 and 2012 based on the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM)-274,712, 135, 136.1, 279.49, 518.3, 287.0, 696.0, 696.1, 696.8, 420, 429.4, 710.0, 710.1, 710.3, 710.4, 714.0, 720, 55.0, 55.1, 55.9, 556., Inclusion Criteria: aged ≧ 20 years, if a patient had at least these disease diagnosis requirements within 1 year of follow-up, and, these patients had at least two outpatient visits or an inpatient visit. After propensity-matched according to age, sex, comorbidities, medications and index date, the IMIDs patients enter into colchicine users (N = 16,026) and colchicine nonusers (N = 16,026). Furthermore, time-dependent Cox models were used to analyze cancer risk in propensity-matched colchicine users compared with the nonusers. The cumulative cancer incidence was analyzed using Cox proportional regression analysis. We calculated adjusted hazard ratios (aHRs) and their 95% confidence intervals (95% CIs) for cancer after adjusting for sex, age, comorbidities, and use of medicine including acetylcysteine, medication for smoking cessation such as nicotine replacement medicines (the nicotine patch) and pill medicines (varenicline), anti-inflammatory drugs and immunosuppressant drugs., Results: Comparing the colchicine nonusers, all cancer risk were mildly attenuated, the (aHR (95% CI)) of all cancer is (0.84 (0.55, 0.99)). Meanwhile, the colchicine users were associated with the lower incidence of the colorectal cancer, the (aHRs (95% CI)) is (0.22 (0.19, 0.89)). Those aged < 65 years and male/female having the colchicine users were associated with lower risk the colorectal cancer also. Moreover, the colchicine > 20 days use with the lower aHR for colorectal cancer., Conclusion: Colchicine was associated with the lower aHR of the all cancer and colorectal cancer formation in patients with the IMIDs., (© 2024. The Author(s).)

Background: Pancreatic ductal adenocarcinoma (PDAC) has a fibrotic stroma that has both tumor-promoting and tumor-restraining properties. Different types of cancer-associated fibroblasts (CAFs) have been described. Here, we investigated whether CAFs within the same subtype exhibit heterogeneous functions., Methods: We evaluated the gene and protein expression differences in two myofibroblastic CAF (myCAF) lines using single-cell and bulk RNA-sequencing. We utilized proliferation and migration assays to determine the effect of different CAF lines on a tumor cell line., Results: We found that myCAF lines express an activated stroma subtype gene signature, which is associated with a shorter survival in patients. Although both myCAF lines expressed α-smooth muscle actin (α-SMA), platelet-derived growth factor-α (PDGFR-α), fibroblast-activated protein (FAP), and vimentin, we observed heterogeneity between the two lines. Similarly, despite being consistent with myCAF gene expression overall, heterogeneity within specific genes was observed. We found that these differences extended to the functional level where the two myCAF lines had different effects on the same tumor cell line. The myCAF216 line, which had slightly increased inflammatory CAF-like gene expression and higher protein expression of α-SMA, PDGFR-α, and FAP was found to restrain migration of tumor cells., Conclusions: We found that two myCAF lines with globally similar expression characteristics had different effects on the same tumor cell line, one promoting and the other restraining migration. Our study highlights that there may be unappreciated heterogeneity within CAF subtypes. Further investigation and attention to specific genes or proteins that may drive this heterogeneity will be important., (© 2024 Wiley Periodicals LLC.)

Alternatively spliced tissue factor (asTF) promotes the progression of pancreatic ductal adenocarcinoma (PDAC) by activating β1-integrins on PDAC cell surfaces. hRabMab1, a first-in-class humanized inhibitory anti-asTF antibody we recently developed, can suppress PDAC primary tumor growth as a single agent. Whether hRabMab1 has the potential to suppress metastases in PDAC is unknown. Following in vivo screening of three asTF-proficient human PDAC cell lines, we chose to make use of KRAS G12V-mutant human PDAC cell line PaCa-44, which yields aggressive primary orthotopic tumors with spontaneous spread to PDAC-relevant anatomical sites, along with concomitant severe leukocytosis. The experimental design featured orthotopic tumors formed by luciferase labeled PaCa-44 cells; administration of hRabMab1 alone or in combination with gemcitabine/paclitaxel (gem/PTX); and the assessment of the treatment outcomes on the primary tumor tissue as well as systemic spread. When administered alone, hRabMab1 exhibited poor penetration of tumor tissue; however, hRabMab1 was abundant in tumor tissue when co-administered with gem/PTX, which resulted in a significant decrease in tumor cell proliferation; leukocyte infiltration; and neovascularization. Gem/PTX alone reduced primary tumor volume, but not metastatic spread; only the combination of hRabMab1 and gem/PTX significantly reduced metastatic spread. RNA-seq analysis of primary tumors showed that the addition of hRabMab1 to gem/PTX enhanced the downregulation of tubulin binding and microtubule motor activity. In the liver, hRabMab1 reduced liver metastasis as a single agent. Only the combination of hRabMab1 and gem/PTX eliminated tumor cell-induced leukocytosis. We here demonstrate for the first time that hRabMab1 may help suppress metastasis in PDAC. hRabMab1's ability to improve the efficacy of chemotherapy is significant and warrants further investigation.

The purpose of this paper is to assess the effect of glucagon-like peptide-1 receptor agonists (GLP-1RAs) on stroke or heart disease in patients having chronic respiratory disease and diabetes (CD) with underlying diseases related to COVID-19. From 1998 to 2019, we adjusted competing risk by assessing the effect of GLP-1RAs on stroke or heart disease in a CD cohort after propensity matching based on the Taiwan National Health Insurance Research Database. We also used the time-dependent method to examine the results. GLP-1 RA and non-GLP-1 RA user groups included 15,801 patients (53% women and 46% men with a mean age of 52.6 ± 12.8 years). The time between the diagnoses of DM and the initial use of the GLP-1 RA among the stroke subcohort (<2000 days) was shorter than that of the heart disease subcohort (>2000 days) (all p -values < 0.05). The overall risks of stroke, ischemic, and hemorrhagic stroke were significantly lower in GLP-1 RA users than nonusers. The adjusted subhazard ratio (aSHR) was 0.76 [95% CI 0.65-0.90], 0.77 [95% CI 0.64-0.92], and 0.69 [95% CI 0.54-0.88] ( p < 0.05 for all). Furthermore, a ≥351-day use had a significantly lower stroke risk than GLP-1 RA nonusers (aSHR 0.35 [95% CI 0.26-0.49]). The time-dependent method revealed the same result, such as lower stroke, and ischemic or hemorrhagic stroke risk. In contrast, the cardiac arrhythmia incidence was higher in GLP-1 RA users with an aSHR of 1.36 [95% CI 1.16-1.59]. However, this risk disappeared after the ≥351-day use with 1.21 (0.98, 1.68) aSHR. Longer GLP-1 RA use was associated with a decreased risk of ischemic or hemorrhagic stroke and the risk of cardiac arrhythmia disappears in a CD cohort. Both a shorter lag time use of the GLP-1 RA and a longer time use of GLP-1 RA were associated with a decreased risk of ischemic or hemorrhagic stroke in the CD cohort. The GLP-1 RA use in the early stage and optimal time use in the CD cohort may avoid the stroke risk.

Modern biomedical datasets are increasingly high-dimensional and exhibit complex correlation structures. Generalized linear mixed models (GLMMs) have long been employed to account for such dependencies. However, proper specification of the fixed and random effects in GLMMs is increasingly difficult in high dimensions, and computational complexity grows with increasing dimension of the random effects. We present a novel reformulation of the GLMM using a factor model decomposition of the random effects, enabling scalable computation of GLMMs in high dimensions by reducing the latent space from a large number of random effects to a smaller set of latent factors. We also extend our prior work to estimate model parameters using a modified Monte Carlo Expectation Conditional Minimization algorithm, allowing us to perform variable selection on both the fixed and random effects simultaneously. We show through simulation that through this factor model decomposition, our method can fit high-dimensional penalized GLMMs faster than comparable methods and more easily scale to larger dimensions not previously seen in existing approaches., (© The Author(s) 2024. Published by Oxford University Press on behalf of The International Biometric Society.)

Advances in molecular genetics have revolutionized our understanding of the pathogenesis, progression, and therapeutic options for treating gastrointestinal (GI) cancers. This chapter provides a comprehensive overview of the molecular landscape of GI cancers, focusing on key genetic alterations implicated in tumorigenesis across various anatomical sites including GIST, colon and rectum, and pancreas. Emphasis is placed on critical oncogenic pathways, such as mutations in tumor suppressor genes, oncogenes, chromosomal instability, microsatellite instability, and epigenetic modifications. The role of molecular biomarkers in predicting prognosis, guiding treatment decisions, and monitoring therapeutic response is discussed, highlighting the integration of genomic profiling into clinical practice. Finally, we address the evolving landscape of precision oncology in GI cancers, considering targeted therapies and immunotherapies., (© 2024. The Author(s), under exclusive license to Springer Nature Switzerland AG.)

Protein kinase activity forms the backbone of cellular information transfer, acting both individually and as part of a broader network, the kinome. Their central role in signaling leads to kinome dysfunction being a common driver of disease, and in particular cancer, where numerous kinases have been identified as having a causal or modulating role in tumor development and progression. As a result, the development of therapies targeting kinases has rapidly grown, with over 70 kinase inhibitors approved for use in the clinic and over double this number currently in clinical trials. Understanding the relationship between kinase inhibitor treatment and their effects on downstream cellular phenotype is thus of clear importance for understanding treatment mechanisms and streamlining compound screening in therapy development. In this work, we combine two large-scale kinome profiling data sets and use them to link inhibitor-kinome interactions with cell line treatment responses (AUC/IC 50 ). We then built computational models on this data set that achieve a high degree of prediction accuracy (R 2 of 0.7 and RMSE of 0.9) and were able to identify a set of well-characterized and understudied kinases that significantly affect cell responses. We further validated these models experimentally by testing predicted effects in breast cancer cell lines and extended the model scope by performing additional validation in patient-derived pancreatic cancer cell lines. Overall, these results demonstrate that broad quantification of kinome inhibition state is highly predictive of downstream cellular phenotypes., Competing Interests: Shawn M. Gomez is an Academic Editor for PeerJ., (©2023 Joisa et al.)

Significant heat-related casualties underlie the urgency of establishing a heat-health warning system (HHWS). This paper presents an evidence-based pilot HHWS developed for Taipei City, Taiwan, through a co-design process engaging stakeholders. In the co-design process, policy concerns related to biometeorology, epidemiology and public health, and risk communication aspects were identified, with knowledge gaps being filled by subsequent findings. The biometeorological results revealed that Taipei residents were exposed to wet-bulb globe temperature (WBGT) levels of health concern for at least 100 days in 2016. The hot spots and periods identified using WBGT would be missed out if using temperature, underlining the importance of adopting an appropriate heat indicator. Significant increases in heat-related emergency were found in Taipei at WBGT exceeding 36°C with reference-adjusted risk ratio (RaRR) of 2.42, taking 30°C as the reference; and residents aged 0-14 had the highest risk enhancement (RaRR = 7.70). As for risk communication, occurring frequency was evaluated to avoid too frequent warnings, which would numb the public and exhaust resources. After integrating knowledge and reconciling the different preferences and perspectives, the pilot HHWS was co-implemented in 2018 by the science team and Taipei City officials; accompanying responsive measures were formulated for execution by ten city government departments/offices. The results of this pilot served as a useful reference for establishing a nationwide heat-alert app in 2021/2022. The lessons learnt during the interactive co-design processes provide valuable insights for establishing HHWSs worldwide., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Lung et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

BACKGROUND AND OBJECTIVES: Disparities in pancreas cancer care are multifactorial, but factors are often examined in isolation. Research that integrates these factors in a single conceptual framework is lacking. We use latent class analysis (LCA) to evaluate the association between intersectionality and patterns of care and survival in patients with resectable pancreas cancer., Methods: LCA was used to identify demographic profiles in resectable pancreas cancer (n = 140 344) diagnosed from 2004 to 2019 in the National Cancer Database (NCDB). LCA-derived patient profiles were used to identify differences in receipt of minimum expected treatment (definitive surgery), optimal treatment (definitive surgery and chemotherapy), time to treatment, and overall survival., Results: Minimum expected treatment (hazard ratio [HR] 0.69, 95% confidence interval [CI]: 0.65, 0.75) and optimal treatment (HR 0.58, 95% CI: 0.55, 0.62) were associated with improved overall survival. Seven latent classes were identified based on age, race/ethnicity, and socioeconomic status (SES) attributes (zip code-linked education and income, insurance, geography). Compared to the referent group (≥65 years + White + med/high SES), the ≥65 years + Black profile had the longest time-to-treatment (24 days vs. 28 days) and lowest odds of receiving minimum (odds ratio [OR] 0.67, 95% CI: 0.64, 0.71) or optimal treatment (OR 0.76, 95% CI: 0.72, 0.81). The Hispanic patient profile had the lowest median overall survival-55.3 months versus 67.5 months., Conclusions: Accounting for intersectionality in the NCDB resectable pancreatic cancer patient cohort identifies subgroups at higher risk for inequities in care. LCA demonstrates that older Black patients and Hispanic patients are at particular risk for being underserved and should be prioritiz for directed interventions., (© 2023 Wiley Periodicals LLC.)

Motivation: Single-cell RNA-sequencing (scRNA-seq) has enabled the molecular profiling of thousands to millions of cells simultaneously in biologically heterogenous samples. Currently, the common practice in scRNA-seq is to determine cell type labels through unsupervised clustering and the examination of cluster-specific genes. However, even small differences in analysis and parameter choosing can greatly alter clustering results and thus impose great influence on which cell types are identified. Existing methods largely focus on determining the optimal number of robust clusters, which can be problematic for identifying cells of extremely low abundance due to their subtle contributions toward overall patterns of gene expression., Results: Here, we present a carefully designed framework, SCISSORS, which accurately profiles subclusters within broad cluster(s) for the identification of rare cell types in scRNA-seq data. SCISSORS employs silhouette scoring for the estimation of heterogeneity of clusters and reveals rare cells in heterogenous clusters by a multi-step semi-supervised reclustering process. Additionally, SCISSORS provides a method for the identification of marker genes of high specificity to the cell type. SCISSORS is wrapped around the popular Seurat R package and can be easily integrated into existing Seurat pipelines., Availability and Implementation: SCISSORS, including source code and vignettes, are freely available at https://github.com/jr-leary7/SCISSORS., (© The Author(s) 2023. Published by Oxford University Press.)

Purpose: Timely radiographic studies are essential to oncology care. At our institution, a safety net hospital in a large metropolitan area, baseline assessment determined that the overwhelming majority of outpatient computed tomographic (CT) scans for oncology patients were overdue and not scheduled within 2 weeks of their first requested date., Methods: We conducted a series of structured, interdisciplinary meetings including staff from radiology, oncology, scheduling, and administration to critically review the scheduling process utilizing Lean Kaizen quality improvement methods. A new workflow was developed in which clinic staff scheduled CT scans before clinic discharge. Three months after our initial meeting, the new workflow was launched. We set a target of decreasing the percentage of overdue scans to below 20%., Results: At baseline, 87% (65 of 75) of CT scans awaiting scheduling were overdue. Data were gathered at 5 and 10 weeks after implementation of our workflow. The percentage of CT scans overdue for scheduling was 17% (9 of 53) at 5 weeks and 0.97% (1 of 103) at 10 weeks after implementation. Clinic visit durations were not affected., Conclusion: The Lean Kaizen QI model was successful in decreasing the rate of oncology patients overdue for CT scan scheduling with minimal effects on clinic visit durations. This study demonstrated the importance of interdepartmental collaboration and continuous monitoring for improvement. Given the success of this project, this workflow will be expanded to other outpatient clinics within our institution.

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease for which potent therapies have limited efficacy. Several studies have described the transcriptomic landscape of PDAC tumors to provide insight into potentially actionable gene expression signatures to improve patient outcomes. Despite centralization efforts from multiple organizations and increased transparency requirements from funding agencies and publishers, analysis of public PDAC data remains difficult. Bioinformatic pitfalls litter public transcriptomic data, such as subtle inclusion of low-purity and non-adenocarcinoma cases. These pitfalls can introduce non-specificity to gene signatures without appropriate data curation, which can negatively impact findings. To reduce barriers to analysis, we have created pdacR ( http://pdacR.bmi.stonybrook.edu , github.com/rmoffitt/pdacR), an open-source software package and web-tool with annotated datasets from landmark studies and an interface for user-friendly analysis in clustering, differential expression, survival, and dimensionality reduction. Using this tool, we present a multi-dataset analysis of PDAC transcriptomics that confirms the basal-like/classical model over alternatives., (© 2023. The Author(s).)

Little is understood about the embryonic development of sociality. We screened 1120 known drugs and found that embryonic inhibition of topoisomerase IIα (Top2a) resulted in lasting social deficits in zebrafish. In mice, prenatal Top2 inhibition caused defects in social interaction and communication, which are behaviors that relate to core symptoms of autism. Mutation of Top2a in zebrafish caused down-regulation of a set of genes highly enriched for genes associated with autism in humans. Both the Top2a-regulated and autism-associated gene sets have binding sites for polycomb repressive complex 2 (PRC2), a regulatory complex responsible for H3K27 trimethylation (H3K27me3). Moreover, both gene sets are highly enriched for H3K27me3. Inhibition of the PRC2 component Ezh2 rescued social deficits caused by Top2 inhibition. Therefore, Top2a is a key component of an evolutionarily conserved pathway that promotes the development of social behavior through PRC2 and H3K27me3.

Plasma cell responses are associated with anti-tumor immunity and favorable response to immunotherapy. B cells can amplify anti-tumor immune responses through antibody production; yet B cells in patients and tumor-bearing mice often fail to support this effector function. We identify dysregulated transcriptional program in B cells that disrupts differentiation of naive B cells into anti-tumor plasma cells. The signaling network contributing to this dysfunction is driven by interleukin (IL) 35 stimulation of a STAT3-PAX5 complex that upregulates the transcriptional regulator BCL6 in naive B cells. Transient inhibition of BCL6 in tumor-educated naive B cells is sufficient to reverse the dysfunction in B cell differentiation, stimulating the intra-tumoral accumulation of plasma cells and effector T cells and rendering pancreatic tumors sensitive to anti-programmed cell death protein 1 (PD-1) blockade. Our findings argue that B cell effector dysfunction in cancer can be due to an active systemic suppression program that can be targeted to synergize with T cell-directed immunotherapy., Competing Interests: Declaration of interests B.G.V. declares equity in GeneCentric Therapeutics., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

Objectives: We sought to fill the research gap on the effects of statins on the risks of ischemic stroke and heart disease among individuals with human immunodeficiency virus infection, influenza, and severe acute respiratory syndrome associated-coronavirus (HIS) disorders., Methods: We enrolled a HIS cohort treated with statins (n = 4921) and a HIS cohort not treated with statins (n = 4921). The cumulative incidence of ischemic stroke and heart disease was analyzed using a time-dependent Cox proportional regression analysis. We analyzed the adjusted hazard ratio (aHR) and 95% confidence interval (CI) of ischemic stroke and heart disease for statins users relative to nonusers based on sex, age, comorbidities and medications., Results: The aHR (95% CI) was 0.38 (0.22-0.65) for ischemic stroke. The aHR (95% CI) of heart disease was 0.50 (0.46-0.55). The aHRs (95% CI) of statin users with low, medium, and high adherence (statin use covering <33%, 33%-66%, and >66%, respectively, of the study period) for the risks of ischemic stroke were 0.50 (0.27-0.92), 0.31 (0.10-1.01), and 0.16 (0.04-0.68) and for heart disease were 0.56 (0.51-0.61), 0.40 (0.33-0.48), and 0.44 (0.38-0.51), respectively, compared with statin nonusers., Conclusion: Statin use was associated with lower aHRs for ischemic stroke and heart disease in those with HIS disorders with comorbidities.

Objective: Intrahepatic cholangiocarcinoma (iCCA) is rising in incidence, and at present, there are limited effective systemic therapies. iCCA tumours are infiltrated by stromal cells, with high prevalence of suppressive myeloid populations including tumour-associated macrophages (TAMs) and myeloid-derived suppressor cells (MDSCs). Here, we show that tumour-derived granulocyte-macrophage colony-stimulating factor (GM-CSF) and the host bone marrow is central for monopoiesis and potentiation of TAMs, and abrogation of this signalling axis facilitates antitumour immunity in a novel model of iCCA., Methods: Blood and tumours were analysed from iCCA patients and controls. Treatment and correlative studies were performed in mice with autochthonous and established orthotopic iCCA tumours treated with anti-GM-CSF monoclonal antibody., Results: Systemic elevation in circulating myeloid cells correlates with poor prognosis in patients with iCCA, and patients who undergo resection have a worse overall survival if tumours are more infiltrated with CD68 + TAMs. Mice with spontaneous iCCA demonstrate significant elevation of monocytic myeloid cells in the tumour microenvironment and immune compartments, and tumours overexpress GM-CSF. Blockade of GM-CSF with a monoclonal antibody decreased tumour growth and spread. Mice bearing orthotopic tumours treated with anti-GM-CSF demonstrate repolarisation of immunosuppressive TAMs and MDSCs, facilitating T cell response and tumour regression. GM-CSF blockade dampened inflammatory gene networks in tumours and TAMs. Human tumours with decreased GM-CSF expression exhibit improved overall survival after resection., Conclusions: iCCA uses the GM-CSF-bone marrow axis to establish an immunosuppressive tumour microenvironment. Blockade of the GM-CSF axis promotes antitumour T cell immunity., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Background: This study investigated the effect of colchicine use on the risks of heart disease (HD), pericarditis, endocarditis, myocarditis, cardiomyopathy, cardiac arrhythmia, and cardiac failure in patients having interstitial lung disease (ILD) with virus infection (ILD cohort)., Methods: We retrospectively enrolled ILD cohort between 2000 and 2013 from the Longitudinal Health Insurance Database and divided them into colchicine users ( n = 12,253) and colchicine non-users ( n = 12,253) through propensity score matching. The event of interest was the diagnosis of HD. The incidence of HD was analyzed using multivariate Cox proportional hazards models between colchicine users and the comparison cohort after adjustment for age, sex, medication, comorbidities, and index date based on the time-dependent analysis., Results: Colchicine users had a significantly lower risk of HD ( aHR = 0.87, 95% confidence interval (CI]) = 0.82-0.92) than did the colchicine non-user. For colchicine non-users as the reference, the aHR (95% CI) of the patients who received colchicine of 2-7, 8-30, 31-150, and > 150 days were 0.89 (0.81-0.98), 0.84 (0.76-0.94), 090 (0.80-0.99), and 0.83 (0.74-0.93), respectively; regardless of duration use, the lower risk of HD persisted in colchicine users. The cumulative incidence of HD in colchicine users was significantly lower than that in the colchicine non-users (log-rank p < 0.001)., Conclusion: The addition of short-term or long-term colchicine to standard medical therapy may have benefits to prevent the HD among the ILD patients concurrent with a virus infection or comorbidities even in elderly patients., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Yeh, Hung, Lin, Chen, Liw, Yu and Kao.)

This study aimed to determine the effect of colchicine use on the risk of stroke among patients with diabetes mellitus (DM). We retrospectively enrolled patients with DM between 2000 and 2013 from the Longitudinal Health Insurance Database and divided them into a colchicine cohort (n = 8761) and noncolchicine cohort (n = 8761) by using propensity score matching (PSM). The event of interest was a stroke, including ischemic stroke and hemorrhagic stroke. The incidence of stroke was analyzed using multivariate Cox proportional hazards models between the colchicine cohort and the comparison cohort after adjustment for several confounding factors. The subdistribution hazard model was also performed for examination of the competing risk. The colchicine cohort had a significantly lower incidence of stroke [adjusted hazard ratios (aHR), 95% confidence intervals (95%CI)] (aHR = 0.61, 95%CI = 0.55-0.67), ischemic stroke (aHR = 0.59, 95%CI = 0.53-0.66), and hemorrhagic stroke (aHR = 0.66, 95%CI = 0.53-0.82) compared with the noncolchicine cohort. Drug analysis indicated that patients in the colchicine cohort who received colchicine of cumulative daily defined dose (cDDD) > 14 and duration > 28 days had a lower risk of stroke and ischemic stroke compared with nonusers. The colchicine cohort (cDDD > 150, duration > 360 days) also had a lower risk of stroke, ischemic stroke, and hemorrhagic stroke. The cumulative incidence of stroke, ischemic stroke, and hemorrhagic stroke in the colchicine cohort was significantly lower than that in the noncolchicine cohort (log-rank P < 0.001). However, the subdistribution hazard model reveal the colchicine was not associated with the hemorrhagic stroke in DM patients without gout (aHR = 0.69, 95%CI = 0.47-1.00). Colchicine use with cDDD > 14 and duration > 28 days was associated with lower risk of stroke and ischemic stroke, and colchicine use with cDDD > 150 and duration > 360 days played an auxiliary role in the prevention of stroke, ischemic stroke, and hemorrhagic stroke in patients with DM. The colchicine for the hemorrhagic stroke in DM patients without gout seem to be null effect., (© 2022. The Author(s).)

To investigate the effects of hydroxychloroquine (HCQ) drug use on the risk of pulmonary vascular disease (PVD) in an interstitial lung disease cohort (ILD cohort, ILD+ virus infection), we retrospectively enrolled the ILD cohort with HCQ (HCQ users, N = 4703) and the ILD cohort without HCQ (non-HCQ users, N = 4703) by time-dependence after propensity score matching. Cox models were used to analyze the risk of PVD. We calculated the adjusted hazard ratios (aHRs) and their 95% confidence intervals (CIs) for PVD after adjusting for sex, age, comorbidities, index date and immunosuppressants, such as steroids, etc. Compared with the HCQ nonusers, in HCQ users, the aHRs (95% CIs) for PVD were (2.24 (1.42, 3.54)), and the women’s aHRs for PVD were (2.54, (1.49, 4.35)). The aHRs based on the days of HCQ use for PVD of 28−30 days, 31−120 days, and >120 days were (1.27 (0.81, 1.99)), (3.00 (1.81, 4.87)) and (3.83 (2.46, 5.97)), respectively. The medium or long-term use of HCQ or young women receiving HCQ were associated with a higher aHR for PVD in the ILD cohort. These findings indicated interplay of the primary immunologic effect of ILD, comorbidities, women, age and virus in the HCQ users.

Elevated levels of Mucin-16 (MUC16) in conjunction with a high expression of truncated O-glycans is implicated in playing crucial roles in the malignancy of pancreatic ductal adenocarcinoma (PDAC). However, the mechanisms by which such aberrant glycoforms present on MUC16 itself promote an increased disease burden in PDAC are yet to be elucidated. This study demonstrates that the CRISPR/Cas9-mediated genetic deletion of MUC16 in PDAC cells decreases tumor cell migration. We found that MUC16 enhances tumor malignancy by activating the integrin-linked kinase and focal adhesion kinase (ILK/FAK)-signaling axis. These findings are especially noteworthy in truncated O-glycan (Tn and STn antigen)-expressing PDAC cells. Activation of these oncogenic-signaling pathways resulted in part from interactions between MUC16 and integrin complexes (α4β1), which showed a stronger association with aberrant glycoforms of MUC16. Using a monoclonal antibody to functionally hinder MUC16 significantly reduced the migratory cascades in our model. Together, these findings suggest that truncated O-glycan containing MUC16 exacerbates malignancy in PDAC by activating FAK signaling through specific interactions with α4 and β1 integrin complexes on cancer cell membranes. Targeting these aberrant glycoforms of MUC16 can aid in the development of a novel platform to study and treat metastatic pancreatic cancer.

Background: It is sometimes difficult to distinguish between asthma and bronchiectasis as their symptoms overlap, and these two diseases are associated with pulmonary tuberculosis (PTB) or pneumonia. Objective: The purpose of this study is to determine the effects of bronchodilator drugs, steroids, antidepressants drugs, and antianxiety drugs on the risks of PTB or pneumonia in patients with bronchiectasis-asthma combination or bronchiectasis-asthma-chronic obstructive pulmonary disease combination-BCAS cohort. Methods: After propensity score matching, we retrospectively studied patients with BCAS ( N = 620) and without BCAS ( N = 2,314) through an analysis. The cumulative incidence of PTB or pneumonia was analyzed through Cox proportional regression. After adjustment for sex, age, comorbidities, and medications [including long-acting beta2 agonist/muscarinic antagonists (LABAs/LAMAs), short-acting beta2 agonist/muscarinic antagonists (SABAs/SAMAs), leukotriene receptor antagonist, montelukast, steroids (inhaled corticosteroids, ICSs; oral steroids, OSs), anti-depressants (fluoxetine), and anti-anxiety drugs (benzodiazepines, BZDs)], we calculated the adjusted hazard ratios (aHR) and their 95% confidence intervals (95% CI) for these risks. Similar to OSs, ICSs are associated with an increased risk of PTB or pneumonia, lumping these two as steroids (ICSs/OSs). Results: For the aHR (95% CI), with non-LABAs/non-OSs as the reference 1, the use of LABAs [0.70 (0.52-0.94)]/OSs [0.35 (0.29-0.44)] was associated with a lower risk of PTB or pneumonia. However, the current use of LABAs [2.39 (1.31-4.34)]/SABAs [1.61 (1.31-1.96)], steroids [ICSs 3.23 (1.96-5.29)]/OSs 1.76 (1.45-2.14)], and BZDs [alprazolam 1.73 (1.08-2.75)/fludiazepam 7.48 (1.93-28.9)] was associated with these risks. The current use of LAMAs [0.52 (0.14-1.84)]/SAMAs [1.45 (0.99-2.11)] was not associated with these risks. Conclusion: The current use of LAMAs/SAMAs is relatively safe with respect to PTB or pneumonia risks, but LABAs/SABAs, steroids, and BZDs could be used after evaluation of the benefit for the BCAS cohort. However, we must take the possible protopathic bias into account., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Yeh, Lin, Yang, Hsu and Kao.)

Objective: We investigated the effects of medication on heart disease and ischemic stroke (HDS) risk in patients with predominant bronchiectasis-asthma combination (BCAS)., Methods: BCAS and non-BCAS cohorts ( N = 588 and 1,118, respectively) were retrospectively enrolled. The cumulative incidence of HDS was analyzed using Cox proportional regression; propensity scores were estimated using non-parsimonious multivariable logistic regression. Adjusted hazard ratios (aHRs) and 95% confidence intervals (CIs) for HDS were calculated, adjusting for sex, age, comorbidities, and medication {long- and short-acting β2 agonists and muscarinic antagonists (LABAs/SABAs and LAMAs/SAMAs), steroids [inhaled corticosteroid steroids (ICSs), oral steroids (OSs)], antiarrhythmics, antidepressants (fluoxetine), benzodiazepines (alprazolam, fludiazepam), statins and antihypertensive drugs (diuretics, cardioselective beta blockers, calcium channel blockers (CCBs) and angiotensin converting enzyme inhibitors (ACEi), angiotensin II blockers)}., Results: Compared with the non-BCAS cohort, the BCAS cohort taking LABAs, SABAs, SAMAs, ICSs, OSs, antiarrhythmics, and alprazolam had an elevated HDS risk [aHRs (95% CIs): 2.36 (1.25-4.33), 2.65 (1.87-3.75), 2.66 (1.74-4.05), 2.53 (1.61-3.99), 1.76 (1.43-2.18), 9.88 (3.27-30.5), and 1.73 (1.15-2.58), respectively except fludiazepam 1.33 (0.73-2.40)]. The aHRs (95% CIs) for LABAs ≤ 30 days, DDDs <415, ICSs ≤ 30 days were 1.10 (0.38-3.15), 2.95 (0.22-38.8), 1.45 (0.76-2.77). The aHRs (95% CIs) for current and recent alprazolam were 1.78 (1.09-2.93) and 777.8 (1.34-451590.0); for current and past fludiazepam were 1.39 (0.75-2.59) and 1.29 (0.42-4.01) and for past alprazolam was 1.57 (0.55-4.46); respectively. The aHRs (95% CIs) for alprazolam >30 DDDs, fludiazepam >20 DDDs, ICSs ≦415 DDDs, and OSs DDDs ≦15 were 1.60 (0.78-3.29), 2.43 (0.90-6.55), 5.02 (1.76-14.3), and 2.28 (1.43-3.62), respectively., Conclusion: The bronchodilators, steroids, and antiarrhythmics were associated with higher risk of HDS, even low dose use of steroids. However, the current use of LABAs/ICSs were not associated with HDS. Benzodiazepines were relatively safe, except for current or recent alprazolam use. Notably, taking confounders into account is crucial in observational studies., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Yeh, Lai, Yang, Hsu and Kao.)

Prime editors have been delivered using DNA or RNA vectors. Here we demonstrate prime editing with purified ribonucleoprotein complexes. We introduced somatic mutations in zebrafish embryos with frequencies as high as 30% and demonstrate germline transmission. We also observed unintended insertions, deletions and prime editing guide RNA (pegRNA) scaffold incorporations. In HEK293T and primary human T cells, prime editing with purified ribonucleoprotein complexes introduced desired edits with frequencies of up to 21 and 7.5%, respectively., (© 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Introduction: Psychosocial distress screening of cancer patients is an American College of Surgeons Commission on Cancer mandate for accredited cancer programs. We evaluated psychosocial distress in breast cancer patients to characterize risk factors for high distress scores at a safety net hospital., Materials and Methods: The psychosocial distress screening form includes a list of potential issues and a distress score scaled from 1 through 10. Psychosocial distress screening results were retrospectively analyzed, along with patient demographics and clinical data. Cochran-Mantel-Haenszel test was applied to identify predictors for high distress scores, which were defined as a score of 5 and greater., Results: 775 distress screens were completed by 171 breast cancer patients. High distress scores were reported in 21.3%. Patients who had no evidence of disease at time of screening were less likely to report a high distress score compared to those who were newly diagnosed or in active treatment (odds ratio 0.51, 95% CI, 0.38-0.68, P< .0001). Patients with high distress scores were more likely to report concerns with insurance (29.1% vs. 7.6%, P< .0001), transportation (16.4% vs. 4.6%, P< .0001), housing (15.2% vs 2.1%, P< .0001), sadness/depression (63.6% vs. 14.1, P< .0001), and physical issues (89.1% vs. 52.8%, P< .0001)., Conclusion: Status of cancer at time of screening, particularly newly diagnosed cancer and active treatment of cancer were associated with high distress scores in this patient group. While there should be an emphasis to ensure patients with these risk factors receive psychosocial distress screening, routine periodic screening for all patients should continue to be implemented to ensure quality cancer care., (Copyright © 2021 Elsevier Inc. All rights reserved.)