tbuckley/cabot-search huggingface dataset:
A new genomic framework to categorize pediatric acute myeloid leukemia
Authors: Masayuki Umeda, Jing Ma, Tamara Westover, Yonghui Ni, Guangchun Song, Jamie L. Maciaszek, Michael Rusch, Delaram Rahbarinia, Scott Foy, Benjamin J. Huang, Michael P. Walsh, Priyadarshini Kumar, Yanling Liu, Wenjian Yang, Yiping Fan, Gang Wu, Sharyn D. Baker, Xiaotu Ma, Lu Wang, Todd A. Alonzo, Jeffrey E. Rubnitz, Stanley Pounds, Jeffery M. Klco
Journal: Nature Genetics (2024)

Abstract Recent studies on pediatric acute myeloid leukemia (pAML) have revealed pediatric-specific driver alterations, many of which are underrepresented in the current classification schemas. To comprehensively define the genomic landscape of pAML, we systematically categorized 887 pAML into 23 mutually distinct molecular categories, including new major entities such as UBTF or BCL11B , covering 91.4% of the cohort. These molecular categories were associated with unique expression profiles and mutational patterns. For instance, molecular categories characterized by specific HOXA or HOXB expression signatures showed distinct mutation patterns of RAS pathway genes, FLT3 or WT1 , suggesting shared biological mechanisms. We show that molecular categories were strongly associated with clinical outcomes using two independent cohorts, leading to the establishment of a new prognostic framework for pAML based on these updated molecular categories and minimal residual disease. Together, this comprehensive diagnostic and prognostic framework forms the basis for future classification of pAML and treatment strategies.
Long COVID manifests with T cell dysregulation, inflammation and an uncoordinated adaptive immune response to SARS-CoV-2
Authors: Kailin Yin, Michael J. Peluso, Xiaoyu Luo, Reuben Thomas, Min-Gyoung Shin, Jason Neidleman, Alicer Andrew, Kyrlia C. Young, Tongcui Ma, Rebecca Hoh, Khamal Anglin, Beatrice Huang, Urania Argueta, Monica Lopez, Daisy Valdivieso, Kofi Asare, Tyler-Marie Deveau, Sadie E. Munter, Rania Ibrahim, Ludger Ständker, Scott Lu, Sarah A. Goldberg, Sulggi A. Lee, Kara L. Lynch, J. Daniel Kelly, Jeffrey N. Martin, Jan Münch, Steven G. Deeks, Timothy J. Henrich, Nadia R. Roan
Journal: Nature Immunology (2024)

Abstract Long COVID (LC) occurs after at least 10% of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, yet its etiology remains poorly understood. We used ‘omic” assays and serology to deeply characterize the global and SARS-CoV-2-specific immunity in the blood of individuals with clear LC and non-LC clinical trajectories, 8 months postinfection. We found that LC individuals exhibited systemic inflammation and immune dysregulation. This was evidenced by global differences in T cell subset distribution implying ongoing immune responses, as well as by sex-specific perturbations in cytolytic subsets. LC individuals displayed increased frequencies of CD4 + T cells poised to migrate to inflamed tissues and exhausted SARS-CoV-2-specific CD8 + T cells, higher levels of SARS-CoV-2 antibodies and a mis-coordination between their SARS-CoV-2-specific T and B cell responses. Our analysis suggested an improper crosstalk between the cellular and humoral adaptive immunity in LC, which can lead to immune dysregulation, inflammation and clinical symptoms associated with this debilitating condition.
Neutrophil extracellular traps induced by chemotherapy inhibit tumor growth in murine models of colorectal cancer
Authors: Yamu Li, Sulin Wu, Yiqing Zhao, Trang Dinh, Dongxu Jiang, J. Eva Selfridge, George Myers, Yuxiang Wang, Xuan Zhao, Suzanne Tomchuck, George Dubyak, Richard T. Lee, Bassam Estfan, Marc Shapiro, Suneel Kamath, Amr Mohamed, Stanley Ching-Cheng Huang, Alex Y. Huang, Ronald Conlon, Smitha Krishnamurthi, Jennifer Eads, Joseph E. Willis, Alok A. Khorana, David Bajor, Zhenghe Wang
Journal: Journal of Clinical Investigation (2024)

Neutrophil Extracellular Traps (NETs), a web-like structure of cytosolic and granule proteins assembled on decondensed chromatin, kill pathogens and causes tissue damage in diseases. Whether NETs can kill cancer cells is unexplored. Here, we report that a combination of glutaminase inhibitor CB-839 and 5-FU inhibits the growth of PIK3CA mutant colorectal cancers (CRCs) in xenograft, syngeneic, and genetically engineered mouse models in part through NETs. Disruption of NETs by either DNase I treatment or depletion of neutrophils in CRCs attenuated the efficacy of the drug combination. Moreover, NETs were present in tumor biopsies taken from patients treated with the drug combination in a phase II clinical trial. Increased NET levels in tumors are associated with longer progression-free survival. Mechanistically, the drug combination induced the expression of IL-8 preferentially in PIK3CA mutant CRCs to attract neutrophils into the tumors. Further, the drug combination increased the levels of reactive oxygen species in neutrophils, thereby inducing NETs. Cathepsin G (CTSG), a serine protease localized in NETs, enters CRC cells through the RAGE cell surface protein. The internalized CTSG cleaves 14-3-3 proteins, releases Bax, and triggers apoptosis in CRC cells. Thus, our studies illuminate a previously unrecognized mechanism by which chemotherapy-induced NETs kill cancer cells.
Abstract A031: ZEB2 induced EMT drives therapy resistance by activating nucleotide excision repair I gene ERCC1 And ERCC4 n colorectal cancer
Authors: Hajir Al Saihati
Journal: Cancer Research (2024)

Abstract Resistance to adjuvant chemotherapy is a major clinical problem in the treatment of colorectal cancer (CRC). The aim of this study was to elucidate the role of an epithelial to mesenchymal transition (EMT)-inducing protein, ZEB2, in chemoresistance of CRC, and to uncover the underlying mechanism. We performed IHC for ZEB2 and association analyses with clinical outcomes on primary CRC and matched CRC liver metastases in compliance with observational biomarker study guidelines. ZEB2 expression in primary tumors was an independent prognostic marker of reduced overall survival and disease-free survival in patients who received adjuvant FOLFOX chemotherapy. ZEB2 expression was retained in 96% of liver metastases. The ZEB2-dependent EMT transcriptional program activated nucleotide excision repair (NER) pathway largely via upregulation of the ERCC1 gene and other components in NER pathway, leading to enhanced viability of CRC cells upon oxaliplatin treatment. ERCC1-overexpressing CRC cells did not respond to oxaliplatin in vivo, as assessed using a murine orthotopic model in a randomized and blinded preclinical study. Our findings show that ZEB2 is a biomarker of tumor response to chemotherapy and risk of recurrence in CRC patients. We propose that the ZEB2-ERCC1 axis is a key determinant of chemoresistance in CRC. Citation Format: Hajir Al Saihati. ZEB2 induced EMT drives therapy resistance by activating nucleotide excision repair I gene ERCC1 And ERCC4 n colorectal cancer [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 A031.
Abstract B010: DNA-PKcs-dependent phosphorylation of RECQL4 promotes NHEJ by stabilizing the NHEJ machinery at DNA double-strand breaks
Authors: Anthony J. Davis
Journal: Cancer Research (2024)

Abstract RECQL4, one of the five RecQ helicases in mammalian cells, guards the genome by promoting DNA replication, DNA repair, and telomere maintenance. Mutations in human RECQL4 are associated with three genetic disorders, Rothmund-Thomson syndrome (RTS), Baller-Gerold syndrome (BGS), and RAPADILINO syndrome, which display accelerated aging, developmental abnormalities, and a predisposition to cancer. It is believed that accumulation of DNA damage contributes to the clinical features observed in patients with RECQL4 mutations. Previously, RECQL4 was implicated in promoting the DNA double strand break repair pathway non-homologous end joining (NHEJ), but its role in the pathway remains unresolved. In this study, we report that RECQL4 stabilizes the NHEJ machinery at DSBs to promote repair. Specifically, we find that RECQL4 interacts with the NHEJ core factor DNA-PKcs and the interaction is increased following IR. RECQL4 promotes DNA end bridging mediated by DNA-PKcs and Ku70/80 in vitro and the accumulation/retention of NHEJ factors at DSBs in vivo. Moreover, interaction between DNA-PKcs and the other core NHEJ proteins following IR treatment is attenuated in the absence of RECQL4. These data indicate that RECQL4 promotes the stabilization of the NHEJ factors at DSBs to support formation of the NHEJ long-range synaptic complex. In addition, we observed that the kinase activity of DNA-PKcs is required for accumulation of RECQL4 to DSBs and that DNA-PKcs phosphorylates RECQL4 at six serine/threonine residues. Blocking phosphorylation at these sites reduced the recruitment of RECQL4 to DSBs, attenuated the interaction between RECQL4 and NHEJ factors, destabilized interactions between the NHEJ machinery, and resulted in decreased NHEJ. Collectively, these data illustrate reciprocal regulation between RECQL4 and DNA-PKcs in NHEJ and the potential that dysfunctional NHEJ may play a role in RECQL4-associated genetic disorders and tumorigenesis. Citation Format: Anthony J. Davis. DNA-PKcs-dependent phosphorylation of RECQL4 promotes NHEJ by stabilizing the NHEJ machinery at DNA double-strand breaks [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 B010.
Long-term labeling and imaging of synaptically connected neuronal networks in vivo using double-deletion-mutant rabies viruses
Authors: Lei Jin, Heather A. Sullivan, Mulangma Zhu, Thomas K. Lavin, Makoto Matsuyama, Xin Fu, Nicholas E. Lea, Ran Xu, YuanYuan Hou, Luca Rutigliani, Maxwell Pruner, Kelsey R. Babcock, Jacque Pak Kan Ip, Ming Hu, Tanya L. Daigle, Hongkui Zeng, Mriganka Sur, Guoping Feng, Ian R. Wickersham
Journal: Nature Neuroscience (2024)

Abstract Rabies-virus-based monosynaptic tracing is a widely used technique for mapping neural circuitry, but its cytotoxicity has confined it primarily to anatomical applications. Here we present a second-generation system for labeling direct inputs to targeted neuronal populations with minimal toxicity, using double-deletion-mutant rabies viruses. Viral spread requires expression of both deleted viral genes in trans in postsynaptic source cells. Suppressing this expression with doxycycline following an initial period of viral replication reduces toxicity to postsynaptic cells. Longitudinal two-photon imaging in vivo indicated that over 90% of both presynaptic and source cells survived for the full 12-week course of imaging. Ex vivo whole-cell recordings at 5 weeks postinfection showed that the second-generation system perturbs input and source cells much less than the first-generation system. Finally, two-photon calcium imaging of labeled networks of visual cortex neurons showed that their visual response properties appeared normal for 10 weeks, the longest we followed them.
Abstract A029: DDR pathway genes in CRT resistance: Insights from longitudinal whole exome sequencing in cervical cancer
Authors: Shafqat F. Ehsan, Rui Wang, Xiaogang Wu, Tatiana V. Karpinets, Julianna K. Bronk, Chiraag Kapadia, Xingzhi Song, Andrew M. Futreal, Ann H. Klopp, Tim Harris, Jianhua Zhang, Lauren E. Colbert
Journal: Cancer Research (2024)

Abstract Background: Cervical cancer patients undergoing CRT face a 40% mortality rate, and the genetic underpinnings of radiation response variability remain under-explored. Our laboratory has developed a noninvasive cervical swab biopsy method, complemented by a custom computational pipeline that facilitates longitudinal whole-exome sequencing (WES) from samples with minimal tumor purity. This investigation used the pipeline for the identification of persistent or clonally expanded genes during CRT. The aim is to identify genes and pathways associated with radiation resistance. Methods: Tumor swabs from 30 cervical cancer patients were collected at baseline (week 1) and CRT completion (week 5) paired with corresponding buccal samples. We performed whole exome sequencing, adjusting for calculated tumor purity with strict mutation calling using several tools. Results: Our analysis revealed genes in known DNA damage and repair (DDR) pathways, in addition to unique genes not previously associated with DDR and radiation response, including BAGE3, CGREF1, XRCC5, ATM, LINP1, etc. Future work will include validation of these identified genes in vitro radiation sensitivity screening and validation in large-scale datasets, such as The Cancer Genome Atlas, and network and pathway analysis. Discussion: This exploratory analysis suggests that serial sequencing during chemoradiation to identify novel radiation sensitization targets is feasible and further study is needed. Their recurring involvement in DDR pathways underscores their pivotal role in CRT resistance mechanisms. Conclusions: Through longitudinal WES, we've deepened the understanding of CRT resistance and flagged potential targets for improved radiosensitization strategies in cervical cancer. Future Directions: We are moving towards experimental validation of these genes in patient-derived organoids using CRISPR/Cas9 and CyTOF. Additionally, we'll be screening FDA-approved drugs to pinpoint effective radiosensitizers. A major upcoming effort is the development of a CRT resistance map, enhanced by machine learning, promising a transformative impact on cervical cancer treatment. Citation Format: Shafqat F. Ehsan, Rui Wang, Xiaogang Wu, Tatiana V. Karpinets, Julianna K. Bronk, Chiraag Kapadia, Xingzhi Song, Andrew M. Futreal, Ann H. Klopp, Tim Harris, Jianhua Zhang, Lauren E. Colbert. DDR pathway genes in CRT resistance: Insights from longitudinal whole exome sequencing in cervical cancer [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 A029.
Novel strain of multidrug non-susceptible Neisseria gonorrhoeae in the USA
Authors: Jennifer L Reimche, Cau D Pham, Sandeep J Joseph, Shelby Hutton, John C Cartee, Yuheng Ruan, Mandy Breaux, Caryn Ivanof, Akita Joshi, Mary DeMartino, James E Kirby, Lindley A Barbee, Ellen N Kersh, Kathleen A Roosevelt, Katherine K Hsu
Journal: The Lancet Infectious Diseases (2024)
Lipid droplets, autophagy, and ageing: A cell-specific tale
Authors: Alice Maestri, Paolo Garagnani, Matteo Pedrelli, Carolina E. Hagberg, Paolo Parini, Ewa Ehrenborg
Journal: Ageing Research Reviews (2024)

Lipid droplets are the essential organelle for storing lipids in a cell. Within the variety of the human body, different cells store, utilize and release lipids in different ways, depending on their intrinsic function. However, these differences are not well characterized and, especially in the context of ageing, represent a key factor for cardiometabolic diseases. Whole body lipid homeostasis is a central interest in the field of cardiometabolic diseases. In this review we characterize lipid droplets and their utilization via autophagy and describe their diverse fate in three cells types central in cardiometabolic dysfunctions: adipocytes, hepatocytes, and macrophages.
Increased LL37 in psoriasis and other inflammatory disorders promotes LDL uptake and atherosclerosis
Authors: Yoshiyuki Nakamura, Nikhil N. Kulkarni, Toshiya Takahashi, Haleh Alimohamadi, Tatsuya Dokoshi, Edward Liu, Michael Shia, Tomofumi Numata, Elizabeth W.C. Luo, Adrian F. Gombart, Xiaohong Yang, Patrick Secrest, Philip L.S.M. Gordts, Sotirios Tsimikas, Gerard C.L. Wong, Richard L. Gallo
Journal: Journal of Clinical Investigation (2024)

Patients with chronic inflammatory disorders such as psoriasis have an increased risk of cardiovascular disease and elevated levels of LL37, a cathelicidin host defense peptide that has both antimicrobial and proinflammatory properties. To explore if LL37 could contribute to the risk of heart disease, we examined its effects on lipoprotein metabolism and show that LL37 enhances LDL uptake in macrophages through LDLR, SR-B1 and CD36. This interaction led to increased cytosolic cholesterol in macrophages and changes in expression of lipid metabolism genes consistent with increased cholesterol uptake. Structure-function analysis and synchrotron small angle X-ray scattering show structural determinants of the LL37-LDL complex that underlie its ability to bind its receptors and promote uptake. This function of LDL uptake is unique to cathelicidins from humans and some primates and was not observed with cathelicidins from mice or rabbits. Notably, Apoe-/- mice expressing LL37 develop larger atheroma plaques than control mice and a positive correlation between plasma LL37 and OxPL-apoB levels was observed in human subjects with cardiovascular disease. These findings provide evidence that LDL uptake can be increased via interaction with LL37 and may explain the increased risk of cardiovascular disease associated with the chronic inflammatory disorders.
Abstract B002: ALK signaling primes the DNA damage response sensitizing ALK-driven neuroblastoma to therapeutic ATR inhibition
Authors: Ruth H. Palmer, Bengt Hallberg, Marcus Borenäs, Ganesh Umapathy, Dan E. Lind, Wei-Yun Lai, Jikui Guan, Joel Johansson, Agata Aniszewska
Journal: Cancer Research (2024)

Abstract High-risk neuroblastoma (NB) currently presents significant clinical challenges. MYCN and ALK, which are often involved in high-risk NB, lead to increased replication stress in cancer cells, providing options for therapeutic exploitation. We previously identified an ATR/ALK inhibitor combination as an effective therapeutic approach in two independent genetically modified mouse NB models. Here, we identify an underlying molecular mechanism, in which ALK signaling leads to phosphorylation of ATR and CHK1, supporting an effective DNA damage response. The importance of ALK inhibition is supported by mouse data, in which monotreatment with ATRi resulted in a robust initial response, but subsequent relapse, in contrast to a 14-day ALKi/ATRi combination treatment that resulted in robust and sustained responses. Finally, we show that the remarkable response to the 14-day combined ATR/ALK inhibition protocol reflects a robust differentiation response in the tumor, reprogramming tumor cells to a neuronal/Schwann cell lineage identity. Our results identify a unique ability of ATR inhibition to trigger neuroblastoma differentiation and underscore the importance of further exploring combined ALK/ATR inhibition in NB, particularly in high-risk patient groups with oncogene-induced replication stress. Citation Format: Ruth H. Palmer, Bengt Hallberg, Marcus Borenäs, Ganesh Umapathy, Dan E. Lind, Wei-Yun Lai, Jikui Guan, Joel Johansson, Agata Aniszewska. ALK signaling primes the DNA damage response sensitizing ALK-driven neuroblastoma to therapeutic ATR inhibition [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 B002.
Fungicide-tolerant persister formation during cryptococcal pulmonary infection
Authors: Weixin Ke, Yuyan Xie, Yingying Chen, Hao Ding, Leixin Ye, Haoning Qiu, Hao Li, Lanyue Zhang, Lei Chen, Xiuyun Tian, Zhenghao Shen, Zili Song, Xin Fan, Jian-Fa Zong, Zhengyan Guo, Xiaoyu Ma, Meng Xiao, Guojian Liao, Cui Hua Liu, Wen-bing Yin, Zhiyang Dong, Feng Yang, Yuan-ying Jiang, David S. Perlin, Yihua Chen, Yu V Fu, Linqi Wang
Journal: Cell Host & Microbe (2024)
Heart Failure Readmission in Patients With ST-Segment Elevation Myocardial Infarction and Active Cancer
Authors: Mohamed Dafaalla, Dmitry Abramov, Harriette G.C. Van Spall, Arjun K. Ghosh, Chris P. Gale, Sarah Zaman, Muhammad Rashid, Mamas A. Mamas
Journal: JACC CardioOncology (2024)

Although numerous studies have examined readmission with heart failure (HF) after acute myocardial infarction (AMI), limited data are available on HF readmission in cancer patients post-AMI. This study aimed to assess the rates and factors associated with HF readmission in cancer patients presenting with ST-segment elevation myocardial infarction (STEMI). A nationally linked cohort of STEMI patients between January 2005 and March 2019 were obtained from the UK Myocardial Infarction National Audit Project registry and the UK national Hospital Episode Statistics Admitted Patient Care registry. Multivariable Fine-Gray competing risk models were used to evaluate HF readmission at 30 days and 1 year. A total of 326,551 STEMI indexed admissions were included, with 7,090 (2.2%) patients having active cancer. The cancer group was less likely to be admitted under the care of a cardiologist (74.5% vs 81.9%) and had lower rates of invasive coronary angiography (62.2% vs 72.7%; P < 0.001) and percutaneous coronary intervention (58.4% vs. 69.5%). There was a significant prescription gap in the administration of post-AMI medications upon discharge such as an angiotensin-converting enzyme inhibitor/angiotensin receptor blocker (49.5% vs 71.1%) and beta-blockers (58.4% vs 68.0%) in cancer patients. The cancer group had a higher rate of HF readmission at 30 days (3.2% vs 2.3%) and 1 year (9.4% vs 7.3%). However, after adjustment, cancer was not independently associated with HF readmission at 30 days (subdistribution HR: 1.05; 95% CI: 0.86-1.28) or 1 year (subdistribution HR: 1.03; 95% CI: 0.92-1.16). The opportunity-based quality indicator was associated with higher rates of HF readmission independent of cancer diagnosis. Cancer patients receive care that differs in important ways from patients without cancer. Greater implementation of evidence-based care may reduce HF readmissions, including in cancer patients.
Sfrp1 inhibits lung fibroblast invasion during transition to injury-induced myofibroblasts
Authors: Christoph H. Mayr, Arunima Sengupta, Sara Asgharpour, Meshal Ansari, Jeanine C. Pestoni, Paulina Ogar, Ilias Angelidis, Andreas Liontos, José Alberto Rodriguez-Castillo, Niklas J. Lang, Maximilian Strunz, Diana Porras-Gonzalez, Michael Gerckens, Laurens J. De Sadeleer, Bettina Oehrle, Valeria Viteri-Alvarez, Isis E. Fernandez, Michelle Tallquist, Martin Irmler, Johannes Beckers, Oliver Eickelberg, Gabriel Mircea Stoleriu, Jürgen Behr, Nikolaus Kneidinger, Wim A. Wuyts, Roxana Maria Wasnick, Ali Önder Yildirim, Katrin Ahlbrecht, Rory E. Morty, Christos Samakovlis, Fabian J. Theis, Gerald Burgstaller, Herbert B. Schiller
Journal: European Respiratory Journal (2024)

Fibroblast-to-myofibroblast conversion is a major driver of tissue remodelling in organ fibrosis. Distinct lineages of fibroblasts support homeostatic tissue niche functions, yet their specific activation states and phenotypic trajectories during injury and repair have remained unclear.