tbuckley/cabot-search huggingface dataset:
DNA methylation-based biological age and time to relapse in triple negative breast cancer.
Authors: Drew Robert Nannini, Nitish Nandu, Gerhard Hildebrandt, Rene Cortese
Journal: Journal of Clinical Oncology (2024)

e13126 Background: Triple negative breast cancer (TNBC) represents 15% of all breast cancer cases and is one of the most aggressive forms of breast cancer with a poorer prognosis. Due to the lack of receptors, TNBC is not amendable to hormonal or anti-HER2 therapies and current gene expression arrays have limited clinical utility in TNBC. The identification of biomarkers associated with TNBC may aid in elucidating the underlying biological mechanisms of this disease and may also have implications for risk stratification, diagnosis, and prognosis of TNBC. The purpose of this study was to investigate the association between markers of biological aging and time to relapse in TNBC. Methods: DNA methylation and clinical data from a publicly available dataset (GSE141441) were used in this analysis. Breast tissue specimens in female TNBC patients who received (n=56) and who did not receive (n=110) chemotherapy underwent DNA methylation profiling using the Illumina Infinium HumanMethylation450K BeadChip. Five DNA methylation-based biological age metrics were calculated: intrinsic epigenetic age acceleration (IEAA), extrinsic epigenetic age acceleration (EEAA), PhenoAge acceleration (PhenoAA), GrimAge acceleration (GrimAA), and DunedinPACE (Pace of Aging Calculated from the Epigenome). Multiple linear and quantile regression analyses were performed to examine the association between the aging metrics and time to TNBC relapse. Interaction and stratified analyses by Ki-67 was additionally performed. Results: After adjusting for chronological age, GrimAA ( P=0.024) and DunedinPACE ( P=0.019) were negatively associated with time to relapse among patients who did not receive chemotherapy. Specifically, a 1-year increase in GrimAA and 1 unit increase in the pace of aging were associated with a 1.77-month and a 53.62-month shorter relapse of TNBC, respectively. Additionally, Ki-67 significantly modified the association between IEAA ( P=0.023) and DunedinPACE ( P=0.035) among patients who received chemotherapy with a 2.75- and a 42.17-month shorter relapse of TNBC among those with a Ki-67 index greater than 50% per unit increase in IEAA and DunedinPACE, respectively. Conclusions: We observed DNA methylation markers of biological age were associated with time to relapse in TNBC patients and these associations were modified by Ki-67. These biomarkers may have prognostic utility in TNBC relapse and potentially, may aid in oncological precision medicine efforts for personalized treatment regimens and surveillance. [Table: see text]
Real-world data of efficacy and safety of denosumab on patients with breast cancer with bone metastasis: Results from Chinese clinical experience.
Authors: Xu Liang, Ruyan Zhang, Anjie Zhu, Xin-Yu Gui, Huiping Li, Guohong Song
Journal: Journal of Clinical Oncology (2024)

e13103 Background: Bone is the most common metastasis site in advanced metastatic breast cancer disease. Denosumab is advocated by various guidelines with high-quality of evidence for the treatment of breast cancer patients with bone metastases (BM) to delay or reduce the occurrence of skeletal related events (SRE). Data for bone lesion repair after treatment on image is still needed in real world. This retrospective study aims to evaluate the efficacy of denosumab on breast cancer with BM by MD Anderson (MDA) criteria which is specific to BM and its safety in real world. Methods: Data of patients age ≥18 years diagnosed with advanced breast cancer with BM and treated with denosumab from June 1 st 2020 to Dec 31 st 2022 were retrospectively analyzed. The primary endpoint was the objective response rate (ORR) for bone lesions by MDA criteria in evaluable patients. Secondary endpoints include disease control rate (DCR) for bone lesions, risk of SRE occurrence and safety in total population. Subgroup analysis investigated the impact of the time of denosumab treatment initiation post-diagnosis of BM as well as the duration of treatment with denosumab on efficacy. Comparative analysis was performed using Chi-squared test and a p value of &lt;0.05 was considered statistically significant. Results: Atotal of 185 patients were enrolled with median age of 52.45 (SD: 12.02) years. The median follow-up time was 25.2 months. 49 out of the 130 evaluable patients achieved partial response, resulting in an ORR of 37.69% (95% CI: 0.29-0.47), and a DCR of 90% (95% CI: 0.84-0.95). 16 out of 185 (8.65%) patients developed SRE after denosumab treatment with the median time to the first occurrence of SRE not reached. The ORR and DCR for bone lesions of starting denosumab after diagnosis of BM in ≤3 months vs. &gt;3 months were 31.54% vs. 6.15% (p&lt;0.001) and 68.46% vs. 21.54% (p&lt;0.001), respectively. The ORR and DCR for bone lesions of the duration of denosumab treatment &lt;6 months vs. ≥6 months were 4.62% vs. 33.08% (p&lt;0.001) and 37.69% vs. 76.92% (p&lt;0.001), respectively. Renal function impairment decreased from 33 patients before treatment to 8 patients post-treatment, while hypocalcemia increased from 1.62% to 11.35%. Osteonecrosis of the jaw occurred in one patient (1/185,0.54%) post-treatment. Conclusions: Denosumab was found to be effective and safe for breast cancer patients with BM in this large retrospective study. Early initiation and longer duration of denosumab treatment may generate better clinical outcomes for bone lesions by MDA criteria.
Ethnic and clinical differences in gBRCA and HRD mutated breast and ovarian cancers and their response to PARP inhibitors.
Authors: Ashok Uttamchandani, Naveed Syed, Ashish Vittalrao Chintakuntlawar, Imrana Afrooz, Kanishka Uttam Chandani, Riad Al Hasan, Deepthi Vilasini, Aisha Mohamed Al Salami, Aref Ahmad Chehal
Journal: Journal of Clinical Oncology (2024)

e13102 Background: Hereditary mutations of the homologous recombination (HR), the key DNA double-strand break repair pathway, are one of the well-known causes of breast and ovarian cancers. Few reports exist on these mutations and the utilization of PARP inhibitors in the Middle Eastern region. Methods: This is a single-center retrospective study of breast and ovarian cancer patients who underwent genetic testing for g BRCA and HR defects (HRD) respectively between August 2021 and May 2023. Data was summarized using descriptive statistics and compared using counts and percentages. Response to treatment was assessed using RECIST criteria. Results: The prevalence of pathogenic mutations was 22.8%, with 26.3% of breast cancers harboring g BRCA mutations and 24% of ovarian cancers showing HRD positivity. Middle Eastern patients comprised 40% of the g BRCA-positive breast cancer group, while Asians accounted for 66% of the HRD-positive ovarian cancer patients. In mutated breast cancer, 53.3% had a positive family history of cancer. 33.3% of mutated breast cancer group and 66.6% of the ovarian cancer group received PARPis. Objective response to PARPi was 40% and 100% in breast and ovarian cancers, respectively. Conclusions: Our study revealed a high prevalence of g BRCA mutations (26.3%) in breast cancer and HRD positivity (24%) in ovarian cancer). Ethnic profiles differed between these cancers, with Middle Eastern and Southeast Asian patients dominating the breast and ovarian groups, respectively. Interestingly, the TNBC rate in breast cancer remained around 20% regardless of g BRCA status. While disparities between HRD groups were more pronounced in ovarian cancer, as expected, unexpected trends emerged in breast cancer. Further research with larger cohorts is needed to confirm these findings. [Table: see text]
Subclonal mutational signatures in breast cancer brain metastases.
Authors: Muriele Bertagna Varuzza, Helena Winata, Yash Patel, Mohammed Faizal Eeman Mootor, Cristiano de Padua Souza, Paul Christopher Boutros, Marcia Maria Chiquitelli Marques Silveira
Journal: Journal of Clinical Oncology (2024)

e13108 Background: Breast cancer is the leading cause of cancer-related deaths among women in Brazil and the cancer type with highest incidence. When diagnosed at early stages, it has an overall five-year survival rate of up to 90%. However, in advanced stages, survival rate is reduced to about 24%, and 90% of women in stage IV die of metastatic complications. Brain is one of the most common metastatic sites in breast cancer patients, and even though it is a site with poor prognosis, the mutational profile of brain tumors is poorly described in the literature. Therefore, we understand that the identification of this profile may contribute to elucidate mechanisms associated with tumor progression. The aim of this study was to reconstruct the subclonal evolution of breast cancer metastases in the brain. Methods: To carry out this study, the whole exome was accessed through Next Generation Sequencing (NGS) using the Illumina platform in DNA samples extracted from buffy coat cryopreserved and paraffin material of breast tumors and paired brain metastases (n=10). The median read coverage was 68x. DNA was aligned to a Human Reference Genome using the Burrows–Wheeler Aligner, Genome Analysis Toolkit was used for germline short variants calling, and Mutect2 and MuSE were used for variant calling with somatic character (SNVs and INDELs). FACETS was used for assessing the somatic DNA copy number (Copy Number Aberrations). PyClone-VI tool was used for the subclonal reconstruction and to infer the phylogeny it was considered the mutation loci, Cancer Cell Fraction (CCF) and clustering assignments, using R Statistical Environment and Stats, Argparse, and Devtools packages. Results: We identified the mutational signature in these patients with subclonal and clonal mutations that segregated in approximately two clusters with a median between ten and forty variants related with tumor progression process. Conclusions: These findings show a set of variants with driver potential for breast cancer brain metastasis, bringing new perspectives in identifying mechanisms associated with disease progression.
Percutaneous cryoablation of breast cancer metastases: Analysis of long-term single center experience, efficacy and outcomes.
Authors: Jie Chi, Hussein Aoun, Wei Chen, Yu Zong, Gorica Ristic, Hyejeong Jang, Michael S. Simon, Hadeel Assad
Journal: Journal of Clinical Oncology (2024)

e13105 Background: Percutaneous image-guided cryoablation is a minimally invasive loco-regional treatment modality with wide availability and advantages of minimal sedation, short recovery, and ability to continue concurrent systemic therapy. However, there is a paucity of data about its long-term effects in the treatment of metastatic breast cancer despite evidence suggesting a potential survival advantage with loco-regional therapy for oligo-metastatic disease. Methods: We conducted retrospective analysis of patients who underwent CT-guided percutaneous cryoablation for metastatic breast cancer and had at least 1 follow up post cryoablation. Patient data including demographics, cancer treatment history and outcomes were extracted by chart review after IRB approval. Descriptive analyses of overall survival (OS), progression-free survival (PFS), and time to next-line treatment (TTNL) was performed. Results: The study encompassed 37 metastatic breast cancer patients who underwent cryotherapy between 2004-2021. These ablation procedures targeted various metastatic sites, which included the liver, lung, renal, lymph nodes, subcutaneous nodules, and bone. Their median age at the time of cryoablation was 58 years (range: 34-90). Among them, 46% had triple-negative breast cancer (TNBC), 41% were HR+/HER2-, and 8% were HER2+. Prior to first cryoablation procedure, 59% of patients had received more than one line of systemic therapy, and 73% were actively undergoing systemic treatment. The median size of the metastatic lesions treated with cryoablation was 1.8 cm (range: 0.4-6.5 cm). The most frequent site for cryotherapy was the liver (38%), followed by lymph nodes (30%). For the entire cohort, median PFS, TTNL, and OS were 7.1, 14, and 65.7 months, respectively. Subgroup analysis revealed mPFS of 3.1, 7.4 and 14.2 months for TNBC, Her2+ and HR+/Her2- cohorts respectively. Subgroup analysis for OS was not reported due to the small number of events and premature follow up time. Among the 27 patients who experienced disease progression, the majority (74%) had distant progression, with 22% occurring within the same organ but outside the ablation zone. Local recurrence within the ablation zone was rare, observed in only 4% of cases. Conclusions: Percutaneous image-guided cryoablation of metastatic breast cancer lesions demonstrated durable local response, prolonged PFS, TTNL and OS. Future studies investigating cryoablation as part of a multidisciplinary treatment approach for patients with metastatic breast cancer are worthwhile to confirm disease control rate and improvement in survival.
Binary oncolytic adenovirus in combination with HER2-specific autologous CAR VST for treatment of advanced HER2-positive solid tumors (VISTA).
Authors: Shalini Makawita, Jerry M Gibbs, Dustin R. McFadden, Caroline Porter, Amanda Rosewell Shaw, Catherine Robertson, Mae Louise Woods, Tao Wang, Bambi J Grilley, Helen E Heslop, Malcolm K Brenner, Masataka Suzuki
Journal: Journal of Clinical Oncology (2024)

TPS2679 Background: Urgent therapies are needed for patients with refractory Human Epidermal Growth Factor Receptor 2 (HER2) positive solid malignancies. Our group has previously shown potent antitumor effect of a binary oncolytic/helper-dependent adenovirus (CAdVEC) with dual expression of IL-12 and PD-L1 blocker. Initial preclinical and clinical studies with direct tumor injection of CAdVEC has shown it to be safe and result in increased infiltration of CD8 T cells into the tumor microenvironment, with antitumor effect on locoregional and distant metastatic sites. 1 Based on these results, we describe an ongoing study with addition of HER2-specific autologous chimeric antigen receptor (CAR)-T cell therapy to CAdVEC. Methods: This is a single arm, dose escalation phase I clinical trial guided by Bayesian Optimal Interval Design (BOIN) for patients with advanced HER2 positive solid tumors. Patients who are deemed unsuitable for curative treatments and progressed after at least one standard first line therapy are eligible. HER2 positivity is determined by IHC and defined as ≥2+. Patients are required to have at least one tumor site appropriate for intratumor injection and radiographically measurable disease per RECIST v1.1. Patients with autoimmune disease requiring systemic corticosteroids greater than 10mg/day and those with active/untreated CNS metastasis are excluded. Patients will receive increasing doses of CAdVEC intratumor injection alone (first two dose levels) or in combination with HER2 specific autologous CAR-T cells (dose levels 3-7). A total of 45 patients are planned. The primary endpoint of the study is to evaluate safety and maximum tolerated dose as assessed by incidence of dose limiting toxicities (DLT) of CAdVEC intratumor injection in combination with HER2-specific autologous CAR T cells. Secondary endpoints include anti-tumor activity of the combination measured by overall response rate (ORR), disease control rate (DCR), median progression free survival (PFS) and median overall survival (OS). Exploratory endpoints include assessing the immunogenicity of combination therapy by determining the impact of treatment on cellular and humoral immunity, as well as assessing long-term persistence and functional status of HER2 CAR T-cells. Correlative analysis of levels of adenovirus antibodies with clinical outcomes and immunological findings are also planned. This study is currently enrolling. 1. Wang D, Porter CE, Lim B, et al: Science Advances 9, 2023. Clinical trial information: NCT03740256 .
Cancers with epidemiologic signatures of viral oncogenicity among immunocompromised populations in the United States
Authors: Cameron B Haas, Meredith S Shiels, Ruth M Pfeiffer, Monica D’Arcy, Qianlai Luo, Kelly Yu, April A Austin, Colby Cohen, Paige Miller, Bozena M Morawski, Karen Pawlish, William T Robinson, Eric A Engels
Journal: JNCI Journal of the National Cancer Institute (2024)

Immunosuppressed individuals have elevated risk of virus-related cancers. Identifying cancers with elevated risk in people with HIV and solid organ transplant recipients, 2 immunosuppressed populations, may help identify novel etiologic relationships with infectious agents.
Cross-circulation combined with rapidly deployable veno-venous bypass grafts for multi-organ biosystemic support in liver failure: Experimental studies
Authors: Peng Liu, Lifei Yang, Qiang Lu, Yerong Qian, Aihua Shi, Xin Liu, Shasha Wei, Shujuan Fan, Yi Lv, Junxi Xiang
Journal: International Journal of Surgery (2024)

Background: Liver failure remains a critical clinical challenge with limited treatment options. Cross-circulation, the establishment of vascular connections between individuals, has historically been explored as a potential supportive therapy but with limited success. This study investigated the feasibility of combining cross-circulation with a rapidly deployable veno-venous bypass (VVB) graft for multi-organ support in a rat model of total hepatectomy, representing the most severe form of liver failure. Materials and Methods: A Y-shaped VVB graft was fabricated using coaxial electrospinning of PLCL/heparin nanofibers and magnetic rings for rapid anastomosis. After total hepatectomy in rats, the VVB graft was implanted to divert blood flow. Cross-circulation was then established between anhepatic and normal host rats. Hemodynamics, biochemical parameters, blood gases, and survival were analyzed across three groups: hepatectomy with blocked vessels (block group), hepatectomy with VVB only (VVB group), and hepatectomy with VVB and cross-circulation (VVB/cross-circulation group). Results: The VVB graft exhibited suitable mechanical properties and hemocompatibility. VVB rapidly restored hemodynamic stability and mitigated abdominal congestion post-hepatectomy. Cross-circulation further ameliorated liver dysfunction, metabolic derangements, and coagulation disorders in anhepatic rats, significantly prolonging survival compared to the VVB group (mean 6.56±0.58 vs 4.05±0.51 h, P &lt;0.05) and the block group (mean 1.01±0.05 h, P &lt;0.05). Conclusion: Combining cross-circulation with a rapidly deployed VVB graft provided effective multi-organ biosystemic support in a rat model of total hepatectomy, substantially improving the biochemical status and survival time. This approach holds promise for novel liver failure therapies and could facilitate liver transplantation procedures.
Political restoration
Authors: None The Lancet Planetary Health
Journal: The Lancet Planetary Health (2024)

Restoring natural environments and biodiversity over the coming decades will be a vital part of fighting climate change and maintaining a liveable planet. In most parts of the globe, industrialization and urbanization have denuded nature and continue to push species and natural environments to the margins. In a political climate dominated by war, economic uncertainty, and other geopolitical tensions, environmental concerns can drop down the political agenda. However, the adoption of the Nature Restoration Law (NRL) by the European Union Council on 17th June 2024 offers some hope that political agreements that prioritise nature can still progress.
Ambient air pollution and daily mortality in ten cities of India: a causal modelling study
Authors: Jeroen de Bont, Bhargav Krishna, Massimo Stafoggia, Tirthankar Banerjee, Hem Dholakia, Amit Garg, Vijendra Ingole, Suganthi Jaganathan, Itai Kloog, Kevin Lane, Rajesh Kumar Mall, Siddhartha Mandal, Amruta Nori-Sarma, Dorairaj Prabhakaran, Ajit Rajiva, Abhiyant Suresh Tiwari, Yaguang Wei, Gregory A Wellenius, Joel Schwartz, Poornima Prabhakaran, Petter Ljungman
Journal: The Lancet Planetary Health (2024)
Mapping the distribution of Nipah virus infections: a geospatial modelling analysis
Authors: Yan-Qun Sun, Yuan-Yuan Zhang, Mei-Chen Liu, Jin-Jin Chen, Ting-Ting Li, Yan-Ning Liu, Ling-Yu Zhang, Tao Wang, Lin-Jie Yu, Tian-Le Che, Tian Tang, Qiang Xu, Chen-Long Lv, Bao-Gui Jiang, Nick Golding, Max L Mehlman, Simon I Hay, Li-Qun Fang, Wei Liu
Journal: The Lancet Planetary Health (2024)
High ambient temperature in pregnancy and risk of childhood acute lymphoblastic leukaemia: an observational study
Authors: Tormod Rogne, Rong Wang, Pin Wang, Nicole C Deziel, Catherine Metayer, Joseph L Wiemels, Kai Chen, Joshua L Warren, Xiaomei Ma
Journal: The Lancet Planetary Health (2024)

BackgroundHigh ambient temperature is increasingly common due to climate change and is associated with risk of adverse pregnancy outcomes. Acute lymphoblastic leukaemia is the most common malignancy in children, the incidence is increasing, and in the USA disproportionately affects Latino children. We aimed to investigate the potential association between high ambient temperature in pregnancy and risk of childhood acute lymphoblastic leukaemia.MethodsWe used data from California birth records (children born from Jan 1, 1982, to Dec 31, 2015) and California Cancer Registry (those diagnosed with childhood cancer in California from Jan 1, 1988, to Dec 31, 2015) to identify acute lymphoblastic leukaemia cases diagnosed in infants and children aged 14 years and younger and controls matched by sex, race, ethnicity, and date of last menstrual period. Ambient temperatures were estimated on a 1-km grid. The association between ambient temperature and acute lymphoblastic leukaemia was evaluated per gestational week, restricted to May–September, adjusting for confounders. Bayesian meta-regression was applied to identify critical exposure windows. For sensitivity analyses, we evaluated a 90-day pre-pregnancy period (assuming no direct effect before pregnancy), adjusted for relative humidity and particulate matter less than 2·5 microns in aerodynamic diameter, and constructed an alternatively matched dataset for exposure contrast by seasonality.Findings6849 cases of childhood acute lymphoblastic leukaemia were identified and, of these, 6258 had sufficient data for study inclusion. We also included 307 579 matched controls. Most of the study population were male (174 693 [55·7%] of the 313 837 included in the study) and of Latino ethnicity (174 906 [55·7%]). The peak association between ambient temperature and risk of acute lymphoblastic leukaemia was observed in gestational week 8, where a 5°C increase was associated with an odds ratio of 1·07 (95% CI 1·04–1·11). A slightly larger effect was seen among Latino children (OR 1·09 [95% CI 1·04–1·14]) than non-Latino White children (OR 1·05 [1·00–1·11]). The sensitivity analyses supported the results of the main analysis.InterpretationOur findings suggest an association between high ambient temperature in early pregnancy and risk of childhood acute lymphoblastic leukaemia. Further replication and investigation of mechanistic pathways might inform mitigation strategies.FundingYale Center on Climate Change and Health, The National Center for Advancing Translational Science, National Institutes of Health.