Data access committee for study - The subclonal architecture of metastatic breast cancer: Results from a prospective community-based rapid autopsy program "CASCADE".
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PROVIDER: EGAC00001000574 | EGA |
REPOSITORIES: EGA
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Project description:BackgroundUnderstanding the cancer genome is seen as a key step in improving outcomes for cancer patients. Genomic assays are emerging as a possible avenue to personalised medicine in breast cancer. However, evolution of the cancer genome during the natural history of breast cancer is largely unknown, as is the profile of disease at death. We sought to study in detail these aspects of advanced breast cancers that have resulted in lethal disease.Methods and findingsThree patients with oestrogen-receptor (ER)-positive, human epidermal growth factor receptor 2 (HER2)-negative breast cancer and one patient with triple negative breast cancer underwent rapid autopsy as part of an institutional prospective community-based rapid autopsy program (CASCADE). Cases represented a range of management problems in breast cancer, including late relapse after early stage disease, de novo metastatic disease, discordant disease response, and disease refractory to treatment. Between 5 and 12 metastatic sites were collected at autopsy together with available primary tumours and longitudinal metastatic biopsies taken during life. Samples underwent paired tumour-normal whole exome sequencing and single nucleotide polymorphism (SNP) arrays. Subclonal architectures were inferred by jointly analysing all samples from each patient. Mutations were validated using high depth amplicon sequencing. Between cases, there were significant differences in mutational burden, driver mutations, mutational processes, and copy number variation. Within each case, we found dramatic heterogeneity in subclonal structure from primary to metastatic disease and between metastatic sites, such that no single lesion captured the breadth of disease. Metastatic cross-seeding was found in each case, and treatment drove subclonal diversification. Subclones displayed parallel evolution of treatment resistance in some cases and apparent augmentation of key oncogenic drivers as an alternative resistance mechanism. We also observed the role of mutational processes in subclonal evolution. Limitations of this study include the potential for bias introduced by joint analysis of formalin-fixed archival specimens with fresh specimens and the difficulties in resolving subclones with whole exome sequencing. Other alterations that could define subclones such as structural variants or epigenetic modifications were not assessed.ConclusionsThis study highlights various mechanisms that shape the genome of metastatic breast cancer and the value of studying advanced disease in detail. Treatment drives significant genomic heterogeneity in breast cancers which has implications for disease monitoring and treatment selection in the personalised medicine paradigm.
| S-EPMC5189956 | biostudies-literature
Project description:Background: Understanding the cancer genome is seen as a key step in improving outcomes for cancer patients. Genomic assays are emerging as a possible avenue to personalised medicine in breast cancer. The majority of work in this area has targeted primary tumours however, and very few studies have performed comprehensive profiling of advanced disease. Evolution of the cancer genome during the natural history of breast cancer is largely unknown, as is the profile of disease at death. We sought to study in detail these aspects of advanced breast cancers that have resulted in lethal disease. Methods and Findings: Three patients with ER-positive, HER2-negative breast cancer and one patient with triple negative breast cancer underwent rapid autopsy as part of an institutional prospective community-based rapid autopsy program. Cases represented a range of management problems in breast cancer, including late relapse after early stage disease; de novo metastatic disease; discordant disease response and disease refractory to treatment. Between 5 and 12 metastatic sites were collected at autopsy together with available primary tumours and longitudinal metastatic biopsies taken during life. Samples underwent paired tumour-normal whole exome sequencing and single nucleotide polymorphism arrays. Subclonal architectures were inferred by jointly analysing all samples from each patient. Mutations were validated using high depth amplicon sequencing.Between cases, there were significant differences in mutational burden, driver mutations, mutational processes and copy number variation. Within each case, we found dramatic heterogeneity in subclonal structure from primary to metastatic disease and between metastatic sites, such that no single lesion captured the breadth of disease. Metastatic cross seeding was found in each case and treatment drove subclonal diversification. Subclones displayed parallel evolution of treatment resistance in some cases, and apparent augmentation of key oncogenic drivers as an alternative resistance mechanism. We also observed the key role of mutational processes in subclonal evolution.Limitations of this study include the potential for bias introduced by joint analysis of formalin fixed archival specimens with fresh specimens, and the difficulties in resolving subclones with whole exome sequencing. Other alterations that could define subclones such as structural variants or epigenetic modifications were not assessed. Conclusions: This study highlights the variety of mechanisms that shape the genome of metastatic breast cancer, and the value of studying advanced disease in detail. Treatment drives significant genomic heterogeneity in breast cancers which has implications for disease monitoring and treatment selection in the personalised medicine paradigm.
| EGAS00001002153 | EGA
Project description:Breast cancer affects 1/8 of women throughout their lifetimes, with over 90% of cancer deaths being caused by metastasis. However, metastasis poses unique challenges to research, as complex changes in the microenvironment in different metastatic sites and difficulty obtaining tissue for study hinder the ability to examine in depth the changes that occur during metastasis. Rapid autopsy programs thus fill a unique need in advancing metastasis research. Here, we describe our protocol and processes for establishing and improving the US-based Hope for OTHERS (Our Tissue Helping Enhance Research and Science) program for organ donation in metastatic breast cancer. As of August 2024, we consented 114 patients and performed 37 autopsies, from which we collected 551 unique metastatic frozen tumor samples, 1244 FFPE blocks, 90 longitudinal liquid biopsy samples and developed 14 patient-derived organoid and 8 patient-derived xenograft models. We report in-depth clinical and histopathological information and discuss extensive new research and novel findings in patient outcomes, metastatic phylogeny, and factors in successful living model development. Our results reveal key logistical and protocol improvements that are uniquely beneficial to certain programs based on identifiable features, such as working closely with patient advocates, methods to rescue RNA quality in cases where tissue quality may degrade due to time delays, as well as guidelines and future expansions of our program.
2025-06-25 | GSE291822 | GEO
Project description:Breast cancer affects 1/8 of women throughout their lifetimes, with 90% of cancer deaths being caused by metastasis. However, metastasis poses unique challenges to research, as complex changes in the microenvironment in different metastatic sites and difficulty obtaining tissue for study hinder the ability to examine in depth the changes that occur during metastasis. Rapid autopsy programs thus fill a unique need in advancing metastasis research. Here, we describe our protocol and processes for establishing and improving the US-based Hope for OTHERS (Our Tissue Helping Enhance Research and Science) program for organ donation in metastatic breast cancer. Our results reveal key logistical and protocol improvements that are uniquely beneficial to certain programs based on identifiable features, such as working closely with patient advocates, methods to rescue RNA quality in cases where tissue quality may degrade due to time delays, as well as guidelines and future expansions of our program with new research and novel research findings in patient outcomes, metastatic phylogeny, living model development and more.
| S-EPMC11580927 | biostudies-literature
Project description:The Cardiovascular Health Program (CHP) Registry is a 12-month, prospective study of therapeutic lifestyle change (TLC). Adult participants received comprehensive assessment of health behaviors and cardiovascular disease (CVD) risk factors. Personalized TLC action plans addressed modifiable health behaviors for diet, exercise, stress management, and sleep. Participants attended a half-day interactive workshop and met face-to-face with certified health coaches four times over 6 months. Monthly telephonic coaching for 6 more months completed the intervention. Measured outcomes included adherence to behavioral prescriptions, anthropometrics, CVD-relevant laboratory tests, and for a subset of participants, carotid intima-media thickness (CIMT). Of 965 participants, 648 (67%) completed the program and were included in the analysis. Participants were of mean age 55.4 ± 12.5 years, 57% women, and racially diverse. Adherence to prescribed TLC was substantial: dietary behaviors at goal rose from 53% to 86%, exercise 44% to 66%, perceived stress 65% to 79%, and sleep quality 28% to 49%. For participants with abnormal anthropometrics at baseline, there were improvements in body mass index in 63%, waist circumference (men 71%, women 74%), systolic BP 69%, and diastolic BP 71%. For participants with abnormal laboratory values at baseline, there were improvements in total cholesterol in 74%, LDL-cholesterol 65%, triglycerides 86%, fasting glucose 72%, and insulin resistance 71%. Improvements were not driven by prescribed medications. CIMT improved or showed no change in 70% of those measured, associated with significant improvements in sleep quality and longer total sleep time. Longer trials incorporating controls and major adverse CVD events are warranted.
| S-EPMC8020477 | biostudies-literature
Project description:BackgroundThe term "metabolic (dysfunction)-associated fatty liver disease" (MAFLD) is suggested alternative for "non-alcoholic fatty liver disease" (NAFLD), as it better reflects metabolic dysfunction. No study has compared outcomes of the two diagnostic criteria.MethodsIn an ongoing, community-based, cohort-study in suburban Sri Lanka, participants were randomly selected in 2007. They were reassessed in 2014 to evaluate new-onset metabolic traits (MTs) and cardiovascular-events (CVEs). Baseline characteristics, MTs and CVEs after 7-years were compared in NAFLD and MAFLD and vs. controls. Similarly, we compared these parameters in those excluded by the NAFLD definition but captured by the MAFLD definition and vice versa, and vs. controls.FindingsOf 2985 recruited in 2007, 940 (31.5%) had NAFLD, 990 (33.1%) had MAFLD and 362 (12.1%) were controls. When compared to NAFLD, MAFLD captured an additional 2.9% and lost 1.3% individuals. At baseline, anthropometric and metabolic traits were similar in NAFLD and MAFLD. At follow-up in 7-years, the risk of having new-onset MTs and fatal/non-fatal CVEs were similar in the groups, but were significantly higher compared to controls. Those excluded by the NAFLD definition but captured by the MAFLD definition showed higher baseline MTs compared to those excluded by the MAFLD definition but captured by the NAFLD definition, and had substantially higher risk for having new-onset MTs and CVEs compared to controls.InterpretationAlthough NAFLD and MAFLD had similar MTs at baseline, and similar outcomes after 7-years, those who were excluded by the NAFLD definition but captured by the MAFLD definition seem at higher risk of adverse outcomes than those excluded by the MAFLD definition but captured by the NAFLD definition. Although the increase in the index population was small, redefining NAFLD as MAFLD seemed to improve clinical utility.
| S-EPMC7857550 | biostudies-literature
Project description:Hope for Others: Research Results from the University of Pittsburgh Rapid Autopsy Program for Breast Cancer
| PRJNA1235297 | ENA
Project description:ImportanceCommunity-based COVID-19 testing and vaccination programs play a crucial role in mitigating racial and ethnic disparities in COVID-19 service delivery. They also represent a platform that can be leveraged to expand access to testing for chronic diseases, including diabetes, that disproportionately affect the Latinx community and other marginalized communities.ObjectiveTo evaluate outcomes associated with a diabetes testing strategy designed to reach low-income Latinx persons by leveraging COVID-19 testing infrastructure and community trust developed during the COVID-19 pandemic.Design, setting, and participantsThis health care improvement study was conducted from August 1 to October 5, 2021, at an outdoor, community-based COVID-19 testing site at a transport hub in the Mission Neighborhood in San Francisco, California. Because the program was designed to expand access to diabetes screening to the local community, all individuals presenting for on-site testing were eligible. Data were analyzed in November 2021.InterventionsIntegration of rapid, point-of-care hemoglobin A1c screening as a testing option in an existing low-barrier COVID-19 testing program.Main outcomes and measuresEvaluation was guided by the Reach, Effectiveness, Adoption, Implementation and Maintenance (RE-AIM) framework and utilized programmatic data and structured surveys among clients and staff.ResultsOf 6631 individuals tested (median [IQR] age 39.3 [29.7-51.3] years; 3417 [52.3%] female, 4348 [65.6%] Latinx), 923 (13.9%) underwent hemoglobin A1c testing with or without COVID-19 testing and 5708 (86.1%) underwent COVID-19 testing only. Individuals tested for diabetes were more likely to be Latinx (763 of 923 individuals [82.7%] who underwent testing were Latinx vs 3585 of 5708 [62.8%] not undergoing testing), have an annual household income of less than $50 000 (450 individuals [81.2%] vs 2409 individuals [66.0%]), and not have health insurance (381 individuals [47.2%] vs 1858 individuals [39.9%]), and 206 (48.0%) had never tested for diabetes before. Overall, 313 (33.9%) and 113 (12.2%) individuals had prediabetes and diabetes, respectively; only 141 of 354 of these individuals (39.8%) had a primary care clinician whom they had seen in the prior 12 months, which was lower among Latinx individuals (113 of 307 individuals [36.8%] vs 28 of 47 [59.6%]). Acceptability of the rapid testing program was high-98% were satisfied with their visit and 96% said they would return for future services; key factors underpinning acceptability included friendly staff, efficiency, and a convenient location.Conclusions and relevanceIn this health care improvement study conducted within an existing community-based COVID-19 testing program, integrating rapid testing for diabetes was feasible, reached low-income Latinx individuals, and identified many persons with prediabetes and diabetes, most of whom lacked access to services in formal health care settings. Leveraging pandemic-related public health responses represents an important opportunity for engaging socioeconomically disadvantaged populations into care for diabetes.
| S-EPMC9136625 | biostudies-literature
Project description:Rapid HIV tests are critical to HIV surveillance and universal testing and treatment programs. We assessed longitudinal patterns in indeterminate HIV rapid test results in an African population-based cohort. Prospective HIV rapid antibody test results, defined by two parallel rapid tests, among participants aged 15-49 years from three survey rounds of the Rakai Community Cohort Study, Uganda, from 2013 to 2018, were assessed. An indeterminate result was defined as any weak positive result or when one test was negative and the other was positive. A total of 31,405 participants contributed 54,459 person-visits, with 15,713 participants contributing multiple visits and 7,351 participants contributing 3 visits. The prevalence of indeterminate results was 2.7% (1,490/54,469). Of the participants with multiple visits who initially tested indeterminate (n = 591), 40.4% were negative, 18.6% were positive, and 41.0% were indeterminate at the subsequent visit. Of the participants with two consecutive indeterminate results who had a third visit (n = 67), 20.9% were negative, 9.0% were positive, and 70.2% remained indeterminate. Compared to a prior negative result, a prior indeterminate result was strongly associated with a subsequent indeterminate result [adjusted prevalence ratio, 23.0 (95% CI = 20.0-26.5)]. Compared to men, women were more likely to test indeterminate than negative [adjusted odds ratio, 2.3 (95% CI = 2.0-2.6)]. Indeterminate rapid HIV test results are highly correlated within an individual and 0.6% of the population persistently tested indeterminate over the study period. A substantial fraction of people with an indeterminate result subsequently tested HIV positive at the next visit, underscoring the importance of follow-up HIV testing protocols.IMPORTANCERapid HIV tests are a critical tool for expanding HIV testing and treatment to end the HIV epidemic. The interpretation and management of indeterminate rapid HIV test results pose a unique challenge for connecting all people living with HIV to the necessary care and treatment. Indeterminate rapid HIV test results are characterized by any weak positive result or discordant results (when one test is negative and the other is positive). We systematically tested all participants of a Ugandan population-based, longitudinal cohort study regardless of prior test results or HIV status to quantify longitudinal patterns in rapid HIV test results. We found that a substantial fraction (>15%) of participants with indeterminate rapid test results subsequently tested positive upon follow-up testing at the next visit. Our findings demonstrate the importance of follow-up HIV testing protocols for indeterminate rapid HIV test results.
| S-EPMC10845946 | biostudies-literature
Project description:AimsDiet is a major risk factor for type 2 diabetes mellitus. As cofactors necessary for enzyme function of all metabolic pathways, vitamins and minerals have the potential to improve glucose metabolism. We investigated the effects of a nutrient intervention program on glycemic status.MethodsWe used a form of natural experiment to compare Pure North program participants (n = 1018) that received vitamin D alone (Vital 1) or vitamin D in combination with other nutrients (Vital 2) during two different time periods. Changes in 25-hydroxyvitamin D [25(OH)D], high-sensitivity C reactive protein (hs-CRP), glycated hemoglobin (HbA1c) and glycemic status were characterized over one and two years.ResultsSerum 25(OH)D concentrations increased significantly in both Vital 1 (to 111 ± 49 nmol/L) and Vital 2 (to 119 ± 52 nmol/L) over one year. HbA1c and hs-CRP were significantly reduced over time in Vital 2. Higher 25(OH)D levels after one year were associated with larger decreases in HbA1c and hs-CRP in Vital 2. At one year, 8% of Vital 2 and 16% of Vital 1 participants progressed from normoglycemia to prediabetes/diabetes, whereas 44% of Vital 2 and 8% of Vital prediabetes/diabetes subjects regressed to normoglycemia.ConclusionsVitamin D combined with other nutrients was associated with a reduced risk of progression to diabetes and with an increased rate of reversion to normoglycemia in high risk participants. The results suggest that nutrient supplementation regimes may provide a safe, economical and effective means for lowering diabetes risk. Further examination of this potential via randomized controlled trials is warranted.
| S-EPMC5691218 | biostudies-literature