tbuckley/cabot-search huggingface dataset:
Abstract IA009: Scars of faulty DNA repair in cancer whole genomes
Authors: Jeremy Setton, Simon Powell, Marcin Imielinski
Journal: Cancer Research (2024)

Abstract Cancer genomes provide a record of the genetic alterations acquired from DNA damage and DNA repair defects during normal cell development and carcinogenesis. Genome-wide somatic alteration patterns in BRCA1-deficient (BRCA1d) and BRCA2-deficient (BRCA2d) cancers are attributed to a deficiency in homologous recombination (HR), a major pathway for the repair of double-strand breaks (DSBs) in human cells. Some of these mutational patterns may reflect specific error-prone repair mechanisms of DSB repair that cells use in the absence of HR. Such mutational patterns can provide biomarkers of HR-deficiency and help identify clinically relevant therapeutic vulnerabilities. HRD is has been associated with specific DNA rearrangements and cytogenetic aberrations. Paradoxically, the types of DNA rearrangements specifically associated with HR-deficient (HRD) cancers only minimally impact chromosomal structure. Addressing this, we combined a genome graph analysis of short-read whole genome sequencing (WGS) profiles across thousands of tumors with deep linked-read (LR) WGS of 46 BRCA1- or BRCA2-mutant breast cancers to discover a distinct class of HR deficiency-enriched rearrangements called reciprocal pairs. LR WGS showed that reciprocal pairs with identical rearrangement orientations gave rise to one of two distinct chromosomal outcomes, distinguishable only with long molecule data. While one (cis) outcome corresponded to the copy and pasting of a small segment to a distant site, a second (trans) outcome was a quasi-balanced translocation or multi-megabase inversion with substantial (10kb) duplications at each junction. We propose an HR-independent replication restart repair mechanism to explain the full spectrum of reciprocal pair outcomes. LR WGS additionally identified single-strand annealing (SSA) as a BRCA2-deficiency specific repair pathway in human cancers. Integrating these features in a classifier improved discrimination between BRCA1- vs. BRCA2-deficient genomes. In conclusion, our data reveal classes of BRCA1- and BRCA2-deficiency specific rearrangements as a source of cytogenetic aberrations in HRD cells. Citation Format: Jeremy Setton, Simon Powell, Marcin Imielinski. Scars of faulty DNA repair in cancer whole genomes [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Damage Repair: From Basic Science to Future Clinical Application; 2024 Jan 9-11; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2024;84(1 Suppl):Abstract nr IA009.
Safety and protective efficacy of PfSPZ Vaccine administered to HIV-negative and -positive Tanzanian adults
Authors: Said Jongo, L.W. Preston Church, Florence Milando, Munira Qassim, Tobias Schindler, Mohammed Rashid, Anneth Tumbo, Gloria Nyaulingo, Bakari M. Bakari, Thabit Athuman Mbaga, Latipha Mohamed, Kamaka Kassimu, Beatus S. Simon, Maxmillian Mpina, Irfan Zaidi, Patrick E. Duffy, Phillip A. Swanson, Robert Seder, Jonathan D. Herman, Maanasa Mendu, Yonatan Zur, Galit Alter, Natasha KC, Pouria Riyahi, Yonas Abebe, Tooba Murshedkar, Eric R. James, Peter F. Billingsley, B. Kim Lee Sim, Thomas L. Richie, Claudia Daubenberger, Salim Abdulla, Stephen L. Hoffman
Journal: Journal of Clinical Investigation (2024)

BACKGROUND. Sanaria PfSPZ Vaccine, composed of attenuated Plasmodium falciparum (Pf) sporozoites (SPZ), protects against malaria. We conducted this clinical trial to assess the safety and efficacy of PfSPZ Vaccine in HIV positive (HIV+) individuals since the HIV infection status of participants in mass vaccination programs may be unknown.
Simple use of Y-connector for proper positioning and contrast aspiration in biliary metal stent placement
Authors: Kiyoyuki Kobayashi, Hideki Kobara, Takako Nomura, Tomohiro Ogi, Hideki Kamada, Masafumi Ono, Tsutomu Masaki
Journal: Endoscopy (2024)

Endoscopic biliary drainage for unresectable malignant hilar biliary obstruction often requires multiple metal stents, and stent-in-stent placement is an effective drainage method [1] [2]. Although multiple stent placement requires more cholangiograms for proper positioning, post-endoscopic retrograde cholangiopancreatography (ERCP) cholangitis remains a concern. Moreover, the over-injection of contrast medium and residual contrast medium increase post-ERCP cholangitis [3] [4] [5]. To overcome these issues, we introduced a simple method using a Y-connector attached to an existing metal stent ([Fig. 1]).
Abstract PR010: Understanding extrachromosomal telomere generation in ALT cancers
Authors: Junyeop Lee, Jina Lee, Eric J. Sohn, Angelo Taglialatela, Roderick J. O’Sullivan, Alberto Ciccia, Jaewon Min
Journal: Cancer Research (2024)

Abstract Introduction: Alternative Lengthening of Telomeres (ALT) is a telomere maintenance mechanism mediated by break-induced replication (BIR), evident in approximately 15% of human cancers. A characteristic feature of ALT cancers is the presence of C-circles, circular single-stranded telomeric DNAs composed of Cytosine-rich (CCCTAA) sequences. These C-circles are unique biomarkers of ALT cells and may be generated from extrachromosomal telomeric single-stranded DNAs (ssDNAs), also unique to ALT cells, but the generation process remains undefined. Methods and results: In order to investigate C-rich ssDNA, we developed a highly sensitive method to detect single stranded telomeric DNA, called 4SET (Strand-Specific Southern-blot for Single-stranded Extrachromosomal Telomeres) assay. Utilizing 4SET, we are able to capture C-rich single stranded DNAs that are near 200 to 1500 nucleotides in size. Both telomeric ssDNAs and C-circles are abundant in cytoplasm and nucleoplasm fractions, which supports the hypothesis that telomeric ssDNA accumulation may indeed precede C-circle formation. We also found that telomeric ssDNAs originate during Okazaki fragment processing during C-rich lagging strand DNA synthesis at telomere ends during telomere elongation in ALT cancers. During lagging strand priming and synthesis, the CST-PP complex (CTC1/STN1/TEN1-PRIMASE-Polymerase alpha) primes the telomeric C-rich strand; then, Polymerase delta and BLM helicase facilitate excessive strand displacement, leading to the accumulation of telomeric ssDNAs in the nucleoplasm and cytoplasm which is potential precursor material for C-circles in ALT cancers. Conclusion: Here, we introduce a highly sensitive 4SET method for studying telomeric ssDNA, which we used to propose a new model for the generation of telomeric C-rich ssDNAs and C-circles during ALT-mediated telomere elongation. Our work contributes to a growing body of knowledge pertaining to the idiosyncrasies of the ALT mechanism based on investigation of its unique biomarkers. Citation Format: Junyeop Lee, Jina Lee, Eric J. Sohn, Angelo Taglialatela, Roderick J. O’Sullivan, Alberto Ciccia, Jaewon Min. Understanding extrachromosomal telomere generation in ALT cancers [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Damage Repair: From Basic Science to Future Clinical Application; 2024 Jan 9-11; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2024;84(1 Suppl):Abstract nr PR010.
Abstract A016: <i>LINC00261 is functionally linked to tumor DNA mutational burden and tumor immune microenvironment composition in lung adenocarcinoma</i>
Authors: Jonathan Castillo, Tianchun Xue, Mayela Norwood, Samantha Joseph, Alan L. Epstein, W. Dean Wallace, Anthony W. Kim, Crystal N. Marconett
Journal: Cancer Research (2024)

Abstract Immunotherapy has emerged as a breakthrough in the improvement of survival outcomes for lung adenocarcinoma (LUAD), however effective response requires the combination of blocking inhibitory signals on the tumor surface and antigen presentation to the tumor surface for proper immune recognition. Several commercially available and robust methods exist for identification of tumors displaying immune-inhibitory surface receptors, such as PD-L1, however it is currently difficult to predict effectiveness of antigen presentation on the cell surface. To address this, we utilized clinical and next-generation sequencing data from The Cancer Genome Atlas (TCGA) to identify gene signatures that are correlated to tumor mutational burden (TMB) within cancers of epithelial origins as a surrogate for neoantigen signatures. We identified LINC00261 as a top gene correlated to TMB, whose expression activates DNA damage response pathways in vitro along with resistance to cisplatin. LINC00261 expression was also significantly correlated to MHC class I and II genes involved in endogenous neoantigen presentation expression within the TCGA-LUAD cohort. This relationship was confirmed in vitro through ectopic reintroduction of LINC00261 for key MHC class II presentation genes. Interferon gamma-induced MHC gene activation in vitro was also able to induce endogenous expression of LINC00261. The staining of primary human lung cancer sections suggested that loss of LINC00261 is associated with an immunosuppressive tumor microenvironment. Taken together, our results suggest there is a mechanistic relationship in the silencing of LINC00261 in LUAD and compromised DNA repair, accumulation of mutations, and reduced antitumor immune response. Citation Format: Jonathan Castillo, Tianchun Xue, Mayela Norwood, Samantha Joseph, Alan L. Epstein, W. Dean Wallace, Anthony W. Kim, Crystal N. Marconett. LINC00261 is functionally linked to tumor DNA mutational burden and tumor immune microenvironment composition in lung adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Damage Repair: From Basic Science to Future Clinical Application; 2024 Jan 9-11; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2024;84(1 Suppl):Abstract nr A016.
Abstract B023: SMARCAL1 is a novel candidate therapeutic target for ALT-positive osteosarcoma
Authors: Angelo Taglialatela, Xiao Chen, Zahra Fatema Khan, Filemon Dela Cruz, Dua Shivi, Dillon Oswald, Azeroglu Benura, Eros Lazzerini Denchi, Min Jaewon, Andrew L. Kung, Alberto Ciccia
Journal: Cancer Research (2024)

Abstract The DNA translocase SMARCAL1 has been characterized by our laboratory and others as a DNA replication-associated factor that promotes the remodeling of stalled replication forks to facilitate the repair of DNA damage and the restart of DNA synthesis. Recent genome-wide analyses of CRISPR-Cas9 loss-of-function screens in pediatric cancer cell lines have suggested an essential function for SMARCAL1 in a subset of pediatric tumors (Dharia NV et al., Nature Genetics, 2021). In agreement with these observations, pan-cancer analysis of dependency scores in over 1,000 cell lines from the DepMap project revealed an important role for SMARCAL1 in tumors of mesenchymal origin and especially in osteosarcoma. We found that SMARCAL1 dependency in osteosarcoma is selectively associated with lack of telomerase expression. In the absence of telomerase, cancer cells mostly rely on a recombination-based mechanism, known as ALT (Alternative Lengthening of Telomeres), for the maintenance of their telomere length. Surprisingly, by comparing genome-wide CRISPR screening data of known ALT-positive vs ALT-negative osteosarcoma cell lines, we found that SMARCAL1 is among the genes that are most selectively essential in ALT-positive tumors. We validated in multiple cellular models a strict correlation and functional relationship between ALT status and SMARCAL1 dependency. In line with previous findings (Cox KE et al., Cell Reports, 2016), we observed that SMARCAL1 localizes to a subset of telomeres in ALT-positive cells and loss of SMARCAL1 induces accumulation of telomere damage. SMARCAL1 enzymatic activity and its RPA-binding function contribute to suppress DNA damage in ALT-positive cells. Furthermore, our studies suggest that SMARCAL1 protects telomere stability in ALT-positive cancer cells by limiting PRIMPOL-mediated restart of stalled replication forks. In addition, SMARCAL1 deficiency enhances cell-intrinsic immune response and anti-tumor immunity. Collectively, our studies have uncovered SMARCAL1 as a novel candidate therapeutic target for the treatment of ALT-positive cancer patients. In these patients, SMARCAL1 inhibition may have a dual beneficial effect by promoting selective cancer cell toxicity combined with stimulation of anti-tumor immunity and enhancement of immunotherapy response. Citation Format: Angelo Taglialatela, Xiao Chen, Zahra Fatema Khan, Filemon Dela Cruz, Dua Shivi, Dillon Oswald, Azeroglu Benura, Eros Lazzerini Denchi, Min Jaewon, Andrew L. Kung, Alberto Ciccia. SMARCAL1 is a novel candidate therapeutic target for ALT-positive osteosarcoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Damage Repair: From Basic Science to Future Clinical Application; 2024 Jan 9-11; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2024;84(1 Suppl):Abstract nr B023.
Perinatal depression and its health impact
Authors: Emma Bränn, Qing Shen, Donghao Lu
Journal: BMJ (2024)

Perinatal depression and its health impact Fast FactsMaternity care typically prioritises pregnancy outcomes, often sidelining women's mental wellbeing.Results from our nationwide, population based, matched, cohort study in Sweden showed increased mortality over 18 years among women who were clinically diagnosed with perinatal depression.These findings underscore the imperative need to deepen our understanding of the health consequences of perinatal depression, especially over the long term.
TRIM56 protects against nonalcoholic fatty liver disease by promoting the degradation of fatty acid synthase
Authors: Suowen Xu, Xiumei Wu, Sichen Wang, Mengyun Xu, Tingyu Fang, Xiaoxuan Ma, Meijie Chen, Jiajun Fu, Juan Guo, Song Tian, Tian Tian, Xu Cheng, Hailong Yang, Junjie Zhou, Zhenya Wang, Yanjun Yin, Wen Xu, Fen Xu, Jinhua Yan, Zhihua Wang, Sihui Luo, Xiao-Jing Zhang, Yan-Xiao Ji, Jianping Weng
Journal: Journal of Clinical Investigation (2024)

Nonalcoholic liver disease (NAFLD) encompasses a disease continuum from simple steatosis, to non-alcoholic steatohepatitis (NASH). However, there are currently no approved pharmacotherapies for NAFLD although several drugs are in advanced stages of clinical development. Because of the complex pathophysiology and heterogeneity of NALFD, identification of potential therapeutic targets is clinically important. Here, we demonstrated that TRIM56 protein abundance is markedly downregulated in the livers of individuals with NAFLD and mice fed a high-fat diet. Hepatocyte-specific ablation of TRIM56 exacerbated the progression of NAFLD, while hepatic TRIM56 overexpression suppressed it. Integrative analyses of interactomic and transcriptomic profiling revealed a pivotal role of TRIM56 in lipid metabolism and identified lipogenesis factor FASN as a direct binding partner of TRIM56. TRIM56 directly interacts with FASN and triggers its K48-linked ubiquitination-dependent degradation. Finally, by using AI-based virtual screening, we discovered an orally bioavailable small-molecule inhibitor of FASN (named FASstatin) which potentiates TRIM56-mediated FASN ubiquitination. Therapeutic administration of FASstatin improved NAFLD and NASH pathologies in mice with optimal safety, tolerability and pharmacokinetic profile. Our findings provide the proof-of-concept that targeting the TRIM56/FASN axis in hepatocytes may offer potential therapeutic avenues to treat NAFLD.
The Digital 1-Minute Walk Test: A New Patient-centered Cardiorespiratory Endpoint
Authors: Lucy Robertson, Joseph Newman, Shaun Clayton, Mary Ferguson, Joanna Pepke-Zaba, John Cannon, Karen Sheares, Dolores Taboada, Katherine Bunclark, Iain Armstrong, Elisa Ferrer Mallol, Elin Haf Davies, Mark Toshner
Journal: American Journal of Respiratory and Critical Care Medicine (2024)

"The Digital 1-Minute Walk Test: A New Patient-centered Cardiorespiratory Endpoint." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.
Phototherapy for age-related brain diseases: Challenges, successes and future
Authors: Ling Ding, Ziqi Gu, Haishu Chen, Panpan Wang, Yilan Song, Xincheng Zhang, Mengyu Li, Jinhan Chen, Hongbin Han, Jianhua Cheng, Zhiqian Tong
Journal: Ageing Research Reviews (2024)

Brain diseases present a significant obstacle to both global health and economic progress, owing to their elusive pathogenesis and the limited effectiveness of pharmaceutical interventions. Phototherapy has emerged as a promising non-invasive therapeutic modality for addressing age-related brain disorders, including stroke, Alzheimer's disease (AD), and Parkinson's disease (PD), among others. This review examines the recent progressions in phototherapeutic interventions. Firstly, the article elucidates the various wavelengths of visible light that possess the capability to penetrate the skin and skull, as well as the pathways of light stimulation, encompassing the eyes, skin, veins, and skull. Secondly, it deliberates on the molecular mechanisms of visible light on photosensitive proteins, within the context of brain disorders and other molecular pathways of light modulation. Lastly, the practical application of phototherapy in diverse clinical neurological disorders is indicated. Additionally, this review presents novel approaches that combine phototherapy and pharmacological interventions. Moreover, it outlines the limitations of phototherapeutics and proposes innovative strategies to improve the treatment of cerebral disorders.
Advisory Committee on Immunization Practices Recommended Immunization Schedule for Adults Aged 19 Years or Older — United States, 2024
Authors: Neil Murthy, A. Patricia Wodi, Veronica V. McNally, Matthew F. Daley, Sybil Cineas
Journal: MMWR Morbidity and Mortality Weekly Report (2024)

At its October 2023 meeting, the Advisory Committee on Immunization Practices* (ACIP) approved the Recommended Adult Immunization Schedule for Ages 19 Years or Older, United States, 2024. The adult immunization schedule, which can be found on the CDC immunization schedule website (https://www.cdc.gov/vaccines/schedules), is published annually to consolidate and summarize updates to ACIP recommendations on the vaccination of adults and to assist health care providers in implementing current ACIP recommendations. The 2024 immunization schedule includes several changes to the cover page, tables, notes, and appendix from the 2023 immunization schedule.
Endotypic traits of supine position and supine-predominant obstructive sleep apnoea in Asian patients
Authors: Wan-Ju Cheng, Eysteinn Finnsson, Jón S. Ágústsson, Scott A. Sands, Liang-Wen Hang
Journal: European Respiratory Journal (2024)

Background Over half of all cases of obstructive sleep apnoea (OSA) are classified as supine-related OSA; however, the pathological endotype during supine position is not fully understood. This study aims to investigate the endotypic traits of supine-predominant OSA and explore the variations in endotypic traits between the supine and lateral positions. Methods We prospectively recruited 689 adult patients with OSA from a single sleep centre between April 2020 and December 2022. Endotypic traits, namely arousal threshold, collapsibility, loop gain and upper airway muscle compensation, were retrieved from polysomnographic signals. We identified spOSA by a supine to non-supine apnoea–hypopnoea index (AHI) ratio &gt;2. We cross-sectionally compared demographic and endotypic traits between supine-predominant OSA and non-positional OSA and examined the associations between supine-predominant OSA and endotypic traits. Additionally, we compared the changes in endotypic traits between supine and lateral positions in patients with supine-predominant OSA and non-positional OSA. Results In our study sample, 75.8% of patients were identified as having supine-predominant OSA. Compared to non-positional OSA, supine-predominant OSA was associated with low collapsibility (β= −3.46 % eupnoea , 95% CI −5.93– −1.00 % eupnoea ) and reduced compensation (β= −6.79 % eupnoea , 95% CI −10.60– −2.99 % eupnoea ). When transitioning from the lateral to supine position, patients with supine-predominant OSA had a substantial decrease in compensation compared to those with non-positional OSA (−11.98 versus −6.28 % eupnoea ). Conclusions Supine-predominant OSA is the prevalent phenotype of OSA in Asian patients. Inadequate upper airway compensation appears to be a crucial underlying pathology in patients with supine-predominant OSA.
The performance of a deep learning system in assisting junior ophthalmologists in diagnosing 13 major fundus diseases: a prospective multi-center clinical trial
Authors: Bing Li, Huan Chen, Weihong Yu, Ming Zhang, Fang Lu, Jingxue Ma, Yuhua Hao, Xiaorong Li, Bojie Hu, Lijun Shen, Jianbo Mao, Xixi He, Hao Wang, Dayong Ding, Xirong Li, Youxin Chen
Journal: npj Digital Medicine (2024)

Abstract Artificial intelligence (AI)-based diagnostic systems have been reported to improve fundus disease screening in previous studies. This multicenter prospective self-controlled clinical trial aims to evaluate the diagnostic performance of a deep learning system (DLS) in assisting junior ophthalmologists in detecting 13 major fundus diseases. A total of 1493 fundus images from 748 patients were prospectively collected from five tertiary hospitals in China. Nine junior ophthalmologists were trained and annotated the images with or without the suggestions proposed by the DLS. The diagnostic performance was evaluated among three groups: DLS-assisted junior ophthalmologist group (test group), junior ophthalmologist group (control group) and DLS group. The diagnostic consistency was 84.9% (95%CI, 83.0% ~ 86.9%), 72.9% (95%CI, 70.3% ~ 75.6%) and 85.5% (95%CI, 83.5% ~ 87.4%) in the test group, control group and DLS group, respectively. With the help of the proposed DLS, the diagnostic consistency of junior ophthalmologists improved by approximately 12% (95% CI, 9.1% ~ 14.9%) with statistical significance ( P &lt; 0.001). For the detection of 13 diseases, the test group achieved significant higher sensitivities (72.2% ~ 100.0%) and comparable specificities (90.8% ~ 98.7%) comparing with the control group (sensitivities, 50% ~ 100%; specificities 96.7 ~ 99.8%). The DLS group presented similar performance to the test group in the detection of any fundus abnormality (sensitivity, 95.7%; specificity, 87.2%) and each of the 13 diseases (sensitivity, 83.3% ~ 100.0%; specificity, 89.0 ~ 98.0%). The proposed DLS provided a novel approach for the automatic detection of 13 major fundus diseases with high diagnostic consistency and assisted to improve the performance of junior ophthalmologists, resulting especially in reducing the risk of missed diagnoses. ClinicalTrials.gov NCT04723160
Mortality Due to Hyperglycemic Crises in the US, 1999-2022
Authors: Matthew A. Crane, Audrey Lam, Emil Ekanayake, Yazan Y. Alshawkani, Colleen Christmas, Alison Gemmill, John A. Romley
Journal: JAMA (2024)

This study analyzes trends in US mortality attributed to both diabetic ketoacidosis and hyperosmolar hyperglycemic state from 1999-2022.
Characteristics of Medical School Deans and University Hospital Directors in Japan
Authors: Takashi Watari, Ashwin Gupta, Maika Hayashi, Kotoko Mizuno, Yasuhisa Nakano, Yasuharu Tokuda, Kota Sakaguchi
Journal: JAMA Network Open (2024)

This cross-sectional study investigates characteristics, including sex, postgraduate experience, and specialty, of medical school deans and university hospital directors in Japan.
Mirtazapine as Appetite Stimulant in Patients With Non–Small Cell Lung Cancer and Anorexia
Authors: Oscar Arrieta, Daniela Cárdenas-Fernández, Oscar Rodriguez-Mayoral, Salvador Gutierrez-Torres, Diana Castañares, Diana Flores-Estrada, Edgar Reyes, Dennis López, Pablo Barragán, Pamela Soberanis Pina, Andres F. Cardona, Jenny G. Turcott
Journal: JAMA Oncology (2024)

Currently there is no standard therapy to improve cancer-related anorexia, hampering survival. Mirtazapine has been suggested as a feasible option in this context.