1
|
Willder S, Kelsey E, O'Connor E, Grills R. Expanding urological services into regional Australia and reducing interhospital transfers: how the nurse practitioner can help. ANZ J Surg 2024. [PMID: 38619216 DOI: 10.1111/ans.18993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 09/25/2023] [Accepted: 03/07/2024] [Indexed: 04/16/2024]
Abstract
BACKGROUND A visiting urology service has been in existence at Hamilton Base Hospital, Western Victoria, over the past 25 years, serving an unmet need. A Urology Nurse Practitioner (UNP) provides the care and management of urology patients working in close association with visiting urologists. We aim to assess the impact of the UNP's role in the delivery of regional urological care. METHODS A retrospective analysis of medical records identified all clinical interventions by the UNP between January 2016 and December 2019. Each encounter was graded according to a clinical severity scale from grade 1 to 5 and assessed for UNP management of patients and the prevention of interhospital transfers. RESULTS One hundred eighty-four patients with 654 individual assessments were identified for inclusion and classified according to the adapted clinical severity scale. Most interventions for category 3 and 4 patients related to major bleeding, catheter difficulties, and haemodynamic instability. A total of 19 patients whose urological issues would typically require interhospital transfer were able to be managed locally. CONCLUSIONS Transferring an acute patient from a regional to a tertiary hospital for specialist care is often necessary but not ideal for the patient and their family. The presence of a dedicated UNP in a regional centre is important for patient care and has an important role in preventing unnecessary transfers. This is a vital component of a visiting urological service to a rural community.
Collapse
Affiliation(s)
- S Willder
- Depatment of Surgery, Western District Health Service, Hamilton, Victoria, Australia
| | - E Kelsey
- Department of Urological Surgery, Barwon Health, University Hospital Geelong, Geelong, Victoria, Australia
| | - E O'Connor
- Department of Urological Surgery, Barwon Health, University Hospital Geelong, Geelong, Victoria, Australia
| | - R Grills
- Depatment of Surgery, Western District Health Service, Hamilton, Victoria, Australia
- Department of Urological Surgery, Barwon Health, University Hospital Geelong, Geelong, Victoria, Australia
- Department of Surgery, School of Medicine, Deakin University, Geelong, Victoria, Australia
| |
Collapse
|
2
|
Versace J, Tazrin S, O'Connor E, Sekibo J, Morey E, Kasinopoulou A, O'Donoghue D, Simblett SK. The role of spirituality and identity formation in personal recovery from traumatic brain injury: A qualitative analysis through the personal experiences of survivors. Neuropsychol Rehabil 2023:1-31. [PMID: 38006578 DOI: 10.1080/09602011.2023.2274624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 10/04/2023] [Indexed: 11/27/2023]
Abstract
Traumatic brain injury (TBI) is a type of acquired brain injury (ABI) that happens when a sudden, external, physical assault damages the brain. TBI can cause long-term cognitive impairments and other lifestyle changes that may affect psychological wellbeing. Among the psychological challenges people recovering from TBI often face is the subjective loss of their pre-injury identity. Quantitative and qualitative research suggests that spirituality can play a positive role in recovery from TBI, increasing the quality of life and overall mental health. However, thus far, the research into this topic has not directly addressed the relationship between identity and spirituality after TBI. The present study sought to do this by thematically analyzing 22 public podcasts featuring interviews of people recovering from TBI telling their stories. The authors review the spiritual themes discussed in the podcasts and then propose a hypothesis about how, through a sense of connection to something self-transcendent, spirituality may enable people to test new meanings and identities, relatively free from the consequences of discrepancy in meaning and identity after TBI.
Collapse
Affiliation(s)
- J Versace
- Department of Psychology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - S Tazrin
- Department of Psychology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - E O'Connor
- Department of Psychology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - J Sekibo
- Department of Psychology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - E Morey
- Department of Psychology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - A Kasinopoulou
- Department of Psychology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - D O'Donoghue
- Department of Psychology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - S K Simblett
- Department of Psychology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| |
Collapse
|
3
|
Singh B, Olds T, Curtis R, Dumuid D, Virgara R, Watson A, Szeto K, O'Connor E, Ferguson T, Eglitis E, Miatke A, Simpson CE, Maher C. Effectiveness of physical activity interventions for improving depression, anxiety and distress: an overview of systematic reviews. Br J Sports Med 2023; 57:1203-1209. [PMID: 36796860 PMCID: PMC10579187 DOI: 10.1136/bjsports-2022-106195] [Citation(s) in RCA: 73] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2023] [Indexed: 02/18/2023]
Abstract
OBJECTIVE To synthesise the evidence on the effects of physical activity on symptoms of depression, anxiety and psychological distress in adult populations. DESIGN Umbrella review. DATA SOURCES Twelve electronic databases were searched for eligible studies published from inception to 1 January 2022. ELIGIBILITY CRITERIA FOR SELECTING STUDIES Systematic reviews with meta-analyses of randomised controlled trials designed to increase physical activity in an adult population and that assessed depression, anxiety or psychological distress were eligible. Study selection was undertaken in duplicate by two independent reviewers. RESULTS Ninety-seven reviews (1039 trials and 128 119 participants) were included. Populations included healthy adults, people with mental health disorders and people with various chronic diseases. Most reviews (n=77) had a critically low A MeaSurement Tool to Assess systematic Reviews score. Physical activity had medium effects on depression (median effect size=-0.43, IQR=-0.66 to -0.27), anxiety (median effect size=-0.42, IQR=-0.66 to -0.26) and psychological distress (effect size=-0.60, 95% CI -0.78 to -0.42), compared with usual care across all populations. The largest benefits were seen in people with depression, HIV and kidney disease, in pregnant and postpartum women, and in healthy individuals. Higher intensity physical activity was associated with greater improvements in symptoms. Effectiveness of physical activity interventions diminished with longer duration interventions. CONCLUSION AND RELEVANCE Physical activity is highly beneficial for improving symptoms of depression, anxiety and distress across a wide range of adult populations, including the general population, people with diagnosed mental health disorders and people with chronic disease. Physical activity should be a mainstay approach in the management of depression, anxiety and psychological distress. PROSPERO REGISTRATION NUMBER CRD42021292710.
Collapse
Affiliation(s)
- Ben Singh
- Allied Health & Human Performance, University of South Australia, Adelaide, South Australia, Australia
| | - Timothy Olds
- Allied Health & Human Performance, University of South Australia, Adelaide, South Australia, Australia
| | - Rachel Curtis
- Allied Health & Human Performance, University of South Australia, Adelaide, South Australia, Australia
| | - Dorothea Dumuid
- Allied Health & Human Performance, University of South Australia, Adelaide, South Australia, Australia
| | - Rosa Virgara
- Allied Health & Human Performance, University of South Australia, Adelaide, South Australia, Australia
| | - Amanda Watson
- Allied Health & Human Performance, University of South Australia, Adelaide, South Australia, Australia
| | - Kimberley Szeto
- Allied Health & Human Performance, University of South Australia, Adelaide, South Australia, Australia
| | - Edward O'Connor
- Allied Health & Human Performance, University of South Australia, Adelaide, South Australia, Australia
| | - Ty Ferguson
- Allied Health & Human Performance, University of South Australia, Adelaide, South Australia, Australia
| | - Emily Eglitis
- Allied Health & Human Performance, University of South Australia, Adelaide, South Australia, Australia
| | - Aaron Miatke
- Allied Health & Human Performance, University of South Australia, Adelaide, South Australia, Australia
| | - Catherine Em Simpson
- Allied Health & Human Performance, University of South Australia, Adelaide, South Australia, Australia
| | - Carol Maher
- Health and Use of Time (HUT) Group, University of South Australia, Adelaide, South Australia, Australia
| |
Collapse
|
4
|
Nic An Ríogh E, McCombe G, Connolly SP, Fawsitt R, McHugh T, O'Connor E, Stewart S, Swan D, Tinago W, Cullen W, Lambert JS. A mixed methods study of attendance and treatment rates among patients with Hepatitis C. Ir Med J 2023; 116:742. [PMID: 37010498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
|
5
|
Nic An Ríogh E, McCombe G, Connolly SP, Fawsitt R, McHugh T, O'Connor E, Stewart S, Swan D, Tinago W, Cullen W, Lambert JS. A mixed methods study of Attendance and Treatment Rates among Patients with Hepatitis C. Ir Med J 2023; 116:742. [PMID: 36976262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
|
6
|
Nassar AH, Abou Alaiwi S, Baca SC, Adib E, Corona RI, Seo JH, Fonseca MAS, Spisak S, El Zarif T, Tisza V, Braun DA, Du H, He M, Flaifel A, Alchoueiry M, Denize T, Matar SG, Acosta A, Shukla S, Hou Y, Steinharter J, Bouchard G, Berchuck JE, O'Connor E, Bell C, Nuzzo PV, Mary Lee GS, Signoretti S, Hirsch MS, Pomerantz M, Henske E, Gusev A, Lawrenson K, Choueiri TK, Kwiatkowski DJ, Freedman ML. Epigenomic charting and functional annotation of risk loci in renal cell carcinoma. Nat Commun 2023; 14:346. [PMID: 36681680 PMCID: PMC9867739 DOI: 10.1038/s41467-023-35833-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/04/2023] [Indexed: 01/22/2023] Open
Abstract
While the mutational and transcriptional landscapes of renal cell carcinoma (RCC) are well-known, the epigenome is poorly understood. We characterize the epigenome of clear cell (ccRCC), papillary (pRCC), and chromophobe RCC (chRCC) by using ChIP-seq, ATAC-Seq, RNA-seq, and SNP arrays. We integrate 153 individual data sets from 42 patients and nominate 50 histology-specific master transcription factors (MTF) to define RCC histologic subtypes, including EPAS1 and ETS-1 in ccRCC, HNF1B in pRCC, and FOXI1 in chRCC. We confirm histology-specific MTFs via immunohistochemistry including a ccRCC-specific TF, BHLHE41. FOXI1 overexpression with knock-down of EPAS1 in the 786-O ccRCC cell line induces transcriptional upregulation of chRCC-specific genes, TFCP2L1, ATP6V0D2, KIT, and INSRR, implicating FOXI1 as a MTF for chRCC. Integrating RCC GWAS risk SNPs with H3K27ac ChIP-seq and ATAC-seq data reveals that risk-variants are significantly enriched in allelically-imbalanced peaks. This epigenomic atlas in primary human samples provides a resource for future investigation.
Collapse
Affiliation(s)
- Amin H Nassar
- Department of Hematology/Oncology, Yale New Haven Hospital, New Haven, CT, 06510, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sarah Abou Alaiwi
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sylvan C Baca
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Elio Adib
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Rosario I Corona
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Marcos A S Fonseca
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - Talal El Zarif
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Viktoria Tisza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - David A Braun
- Department of Hematology/Oncology, Yale New Haven Hospital, New Haven, CT, 06510, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA
| | - Heng Du
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Monica He
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Abdallah Flaifel
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Michel Alchoueiry
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Thomas Denize
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Sayed G Matar
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Andres Acosta
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Sachet Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yue Hou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - John Steinharter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Gabrielle Bouchard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jacob E Berchuck
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Edward O'Connor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Pier Vitale Nuzzo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Gwo-Shu Mary Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Mark Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Elizabeth Henske
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- McGraw/Patterson Center for Population Sciences, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Kate Lawrenson
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Toni K Choueiri
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - David J Kwiatkowski
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- The Eli and Edythe L. Broad Institute, Cambridge, MA, 02142, USA.
| |
Collapse
|
7
|
O'Mahony L, O'Shea E, O'Connor E, Tierney A, Dunne N, Harkin M, Harrington J, Tobin K, Kennelly S, Arendt E, O'Toole P, Timmons S. 36 WHAT DO OLDER ADULTS AND HEALTH CARE PROFESSIONALS LOOK FOR IN A FOOD PRODUCT? Age Ageing 2022. [DOI: 10.1093/ageing/afac218.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
The Mediterranean diet (Medi-diet) has proven benefits for healthy ageing but isn’t the habitual diet of most middle-aged or older adults in Ireland; there can be accessibility and tolerability issues with high amounts of fresh fruit and vegetables. Providing key Medi-diet nutrients in a food product is a novel approach to this challenge. This research aims to explore what ‘younger-old’ adults and healthcare professionals (HCPs) would value in such a novel food product.
Methods
Semi-structured 1:1 interviews and Focus Groups (FGs) were conducted remotely from July 2021 to January 2022. Older adults, defined as over 55’s, were recruited through relevant social, retirement and disease-support groups. Purposive sampling recruited a gender balance and a range of ages and disease profiles. HCPs were recruited through researcher networks and professional associations. Interviews/FGs were recorded, transcribed, and subsequently examined using inductive thematic analysis.
Results
Older adults (n=47; 50% male) were mostly aged 60-69 years (48.9%). Recruited HCPs (n=26) included dieticians (n=8); geriatricians (n=5); therapists (n=4); and nurses, pharmacists, catering managers (community; residential), and meal delivery service coordinators (n=2 each). Participants supported a food product for older adults requiring a nutrient-dense “boost”, or supplementary fibre or protein, but generally preferred a “food-first” approach, as opposed to a “silver bullet” product. Older adults largely associated functional foods with probiotic products “to repair the gut”, something to have “every now and then”. Product texture and portion size should consider changing dentition and appetite, and consider packaging (dexterity) and preparation ease, but should not stigmatize older adults through targeted branding. Participants felt pre-made soups or cake-type bars would be appealing, but not drinks.
Conclusion
A novel food product could supplement a balanced diet for older adults, providing high-protein content, and high-fibre for gut health, complimenting an overall lifestyle approach to health improvement and disease prevention.
Collapse
Affiliation(s)
- L O'Mahony
- University College Cork Centre for Gerontology and Rehabilitation, School of Medicine, , Cork, Ireland
| | - E O'Shea
- University College Cork Centre for Gerontology and Rehabilitation, School of Medicine, , Cork, Ireland
| | - E O'Connor
- University of Limerick Department of Biological Sciences, , Limerick, Ireland
- University of Limerick Health Research Institute, , Limerick, Ireland
- University College Cork APC Microbiome Ireland, Alimentary Pharmabiotic Centre, , Cork, Ireland
| | - A Tierney
- University of Limerick School of Allied Health, Health Implementation Science and Technology Research Group, , Limerick, Ireland
| | - N Dunne
- Family Carers Ireland , Dublin, Ireland
| | - M Harkin
- Age & Opportunity , Dublin, Ireland
| | - J Harrington
- University College Cork School of Public Health, , Cork, Ireland
| | - K Tobin
- Munster Technological University Clean Technology Centre, , Cork, Ireland
| | - S Kennelly
- National Primary Care Strategy and Planner, Health Service Executive, Ireland , Dublin, Ireland
| | - E Arendt
- University College Cork School of Food and Nutritional Sciences, , Cork, Ireland
| | - P O'Toole
- University College Cork School of Microbiology, , Cork, Ireland
- University College Cork APC Microbiome Ireland, Alimentary Pharmabiotic Centre, , Cork, Ireland
| | - S Timmons
- University College Cork Centre for Gerontology and Rehabilitation, School of Medicine, , Cork, Ireland
- University College Cork APC Microbiome Ireland, Alimentary Pharmabiotic Centre, , Cork, Ireland
| |
Collapse
|
8
|
Ferguson T, Olds T, Curtis R, Blake H, Crozier AJ, Dankiw K, Dumuid D, Kasai D, O'Connor E, Virgara R, Maher C. Effectiveness of wearable activity trackers to increase physical activity and improve health: a systematic review of systematic reviews and meta-analyses. Lancet Digit Health 2022; 4:e615-e626. [PMID: 35868813 DOI: 10.1016/s2589-7500(22)00111-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/22/2022] [Accepted: 05/27/2022] [Indexed: 05/27/2023]
Abstract
Wearable activity trackers offer an appealing, low-cost tool to address physical inactivity. This systematic review of systematic reviews and meta-analyses (umbrella review) aimed to examine the effectiveness of activity trackers for improving physical activity and related physiological and psychosocial outcomes in clinical and non-clinical populations. Seven databases (Embase, MEDLINE, Ovid Emcare, Scopus, SPORTDiscus, the Cochrane Library, and Web of Science) were searched from database inception to April 8, 2021. Systematic reviews of primary studies using activity trackers as interventions and reporting physical activity, physiological, or psychosocial outcomes were eligible for inclusion. In total, 39 systematic reviews and meta-analyses were identified, reporting results from 163 992 participants spanning all age groups, from both healthy and clinical populations. Taken together, the meta-analyses suggested activity trackers improved physical activity (standardised mean difference [SMD] 0·3-0·6), body composition (SMD 0·7-2·0), and fitness (SMD 0·3), equating to approximately 1800 extra steps per day, 40 min per day more walking, and reductions of approximately 1 kg in bodyweight. Effects for other physiological (blood pressure, cholesterol, and glycosylated haemoglobin) and psychosocial (quality of life and pain) outcomes were typically small and often non-significant. Activity trackers appear to be effective at increasing physical activity in a variety of age groups and clinical and non-clinical populations. The benefit is clinically important and is sustained over time. Based on the studies evaluated, there is sufficient evidence to recommend the use of activity trackers.
Collapse
Affiliation(s)
- Ty Ferguson
- Alliance for Research in Exercise, Nutrition, and Activity, University of South Australia, Adelaide, SA, Australia
| | - Timothy Olds
- Alliance for Research in Exercise, Nutrition, and Activity, University of South Australia, Adelaide, SA, Australia
| | - Rachel Curtis
- Alliance for Research in Exercise, Nutrition, and Activity, University of South Australia, Adelaide, SA, Australia
| | - Henry Blake
- Alliance for Research in Exercise, Nutrition, and Activity, University of South Australia, Adelaide, SA, Australia
| | - Alyson J Crozier
- Alliance for Research in Exercise, Nutrition, and Activity, University of South Australia, Adelaide, SA, Australia
| | - Kylie Dankiw
- Alliance for Research in Exercise, Nutrition, and Activity, University of South Australia, Adelaide, SA, Australia
| | - Dorothea Dumuid
- Alliance for Research in Exercise, Nutrition, and Activity, University of South Australia, Adelaide, SA, Australia
| | - Daiki Kasai
- Alliance for Research in Exercise, Nutrition, and Activity, University of South Australia, Adelaide, SA, Australia
| | - Edward O'Connor
- Alliance for Research in Exercise, Nutrition, and Activity, University of South Australia, Adelaide, SA, Australia
| | - Rosa Virgara
- Alliance for Research in Exercise, Nutrition, and Activity, University of South Australia, Adelaide, SA, Australia
| | - Carol Maher
- Alliance for Research in Exercise, Nutrition, and Activity, University of South Australia, Adelaide, SA, Australia.
| |
Collapse
|
9
|
Qiu X, Boufaied N, Hallal T, Feit A, de Polo A, Luoma AM, Alahmadi W, Larocque J, Zadra G, Xie Y, Gu S, Tang Q, Zhang Y, Syamala S, Seo JH, Bell C, O'Connor E, Liu Y, Schaeffer EM, Jeffrey Karnes R, Weinmann S, Davicioni E, Morrissey C, Cejas P, Ellis L, Loda M, Wucherpfennig KW, Pomerantz MM, Spratt DE, Corey E, Freedman ML, Shirley Liu X, Brown M, Long HW, Labbé DP. MYC drives aggressive prostate cancer by disrupting transcriptional pause release at androgen receptor targets. Nat Commun 2022; 13:2559. [PMID: 35562350 PMCID: PMC9106722 DOI: 10.1038/s41467-022-30257-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 04/22/2022] [Indexed: 12/30/2022] Open
Abstract
c-MYC (MYC) is a major driver of prostate cancer tumorigenesis and progression. Although MYC is overexpressed in both early and metastatic disease and associated with poor survival, its impact on prostate transcriptional reprogramming remains elusive. We demonstrate that MYC overexpression significantly diminishes the androgen receptor (AR) transcriptional program (the set of genes directly targeted by the AR protein) in luminal prostate cells without altering AR expression. Analyses of clinical specimens reveal that concurrent low AR and high MYC transcriptional programs accelerate prostate cancer progression toward a metastatic, castration-resistant disease. Data integration of single-cell transcriptomics together with ChIP-seq uncover an increase in RNA polymerase II (Pol II) promoter-proximal pausing at AR-dependent genes following MYC overexpression without an accompanying deactivation of AR-bound enhancers. Altogether, our findings suggest that MYC overexpression antagonizes the canonical AR transcriptional program and contributes to prostate tumor initiation and progression by disrupting transcriptional pause release at AR-regulated genes.
Collapse
Affiliation(s)
- Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Nadia Boufaied
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Tarek Hallal
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
- Department of Anatomy and Cell Biology, McGill University, Montréal, QC, Canada
| | - Avery Feit
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Anna de Polo
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
- Division of Urology, Department of Surgery, McGill University, Montréal, QC, Canada
| | - Adrienne M Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Walaa Alahmadi
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
- Division of Experimental Medicine, Department of Medicine, McGill University, Montréal, QC, Canada
| | - Janie Larocque
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
- Division of Experimental Medicine, Department of Medicine, McGill University, Montréal, QC, Canada
| | - Giorgia Zadra
- Departments of Oncologic Pathology and Pathology, Dana-Farber Cancer Institute and Brigham's Women Hospital, Boston, MA, USA
- Institute of Molecular Genetics, National Research Council, Pavia, Italy
| | - Yingtian Xie
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Shengqing Gu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Qin Tang
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yi Zhang
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Sudeepa Syamala
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Edward O'Connor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yang Liu
- Decipher Biosciences, San Diego, CA, USA
| | | | | | - Sheila Weinmann
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR, USA
| | | | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Leigh Ellis
- Division of Medical Oncology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Cedars-Sinai Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weil Cornell Medicine, New York Presbyterian-Weill Cornell Campus, New York, NY, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Daniel E Spratt
- Department of Radiation Oncology, University Hospitals Seidman Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Matthew L Freedman
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - X Shirley Liu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - David P Labbé
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada.
- Department of Anatomy and Cell Biology, McGill University, Montréal, QC, Canada.
- Division of Urology, Department of Surgery, McGill University, Montréal, QC, Canada.
- Division of Experimental Medicine, Department of Medicine, McGill University, Montréal, QC, Canada.
| |
Collapse
|
10
|
Hughes C, Barron F, O'Sullivan E, O'Connor E. Applying learning from 1st to the 3rd wave of the COVID19 pandemic: nutritional provision in critical care. Clin Nutr ESPEN 2022. [PMCID: PMC8937579 DOI: 10.1016/j.clnesp.2022.02.084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
11
|
Weaver E, O'Connor E, Cole DK, Hooker A, Uddin S, Lamprou DA. Microfluidic-mediated self-assembly of phospholipids for the delivery of biologic molecules. Int J Pharm 2022; 611:121347. [PMID: 34890709 DOI: 10.1016/j.ijpharm.2021.121347] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 12/31/2022]
Abstract
The encapsulation of biologic molecules using a microfluidic platform is a procedure that has been understudied but shows great promise from initial reported studies. The study focusses upon the encapsulation of bovine serum albumin (BSA) under various parameters and using multiple phospholipids to identify optimal conditions for the manufacturing of protein loaded lipid nanoparticles. Additionally, encapsulation of the enzyme trypsin (TRP) has been investigated to show the eligibility of the system to other biological medications. All liposomes were subject to rigorous physicochemical characterisation, including differential scanning calorimetry (DSC) and Fourier-transform infrared spectroscopy (FTIR), to document the successful synthesis of the liposomes. Drug-loaded liposome stability was investigated over a 28-day period at 5 °C and 37 °C, which showed encouraging results for 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) at all concentrations of BSA used. The sample containing 1 mg/ml BSA grew by only 10% over the study, which considering liposomes should be affected highly by biologic adsorption, shows great promise for the formulations. Encapsulation and in vitro release studies showed improved loading capacity for BSA compared to conventional methods, whilst maintaining a concise controlled release of the active pharmaceutical ingredient (API).
Collapse
Affiliation(s)
- Edward Weaver
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Edward O'Connor
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - David K Cole
- Immunocore, 92 Park Dr, Milton, Abingdon OX14 4RY, UK
| | - Andrew Hooker
- Immunocore, 92 Park Dr, Milton, Abingdon OX14 4RY, UK
| | - Shahid Uddin
- Immunocore, 92 Park Dr, Milton, Abingdon OX14 4RY, UK
| | - Dimitrios A Lamprou
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK.
| |
Collapse
|
12
|
Barron F, Hughes C, O'Sullivan E, Wrenne A, O'Connor E. An analysis of nutrition support in the intensive care unit during the covid19 pandemic. Clin Nutr ESPEN 2021. [PMCID: PMC8629537 DOI: 10.1016/j.clnesp.2021.09.308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
13
|
Hughes C, Barron F, O'Sullivan E, Wreene A, O'Connor E. Applying learning from 1st to the 3rd wave of the covid19 pandemic: nutritional provision in critical care. Clin Nutr ESPEN 2021. [PMCID: PMC8629574 DOI: 10.1016/j.clnesp.2021.09.294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
14
|
Cairns G, Burté F, Price R, O'Connor E, Toms M, Mishra R, Moosajee M, Pyle A, Sayer JA, Yu-Wai-Man P. A mutant wfs1 zebrafish model of Wolfram syndrome manifesting visual dysfunction and developmental delay. Sci Rep 2021; 11:20491. [PMID: 34650143 PMCID: PMC8516871 DOI: 10.1038/s41598-021-99781-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/28/2021] [Indexed: 11/09/2022] Open
Abstract
Wolfram syndrome (WS) is an ultra-rare progressive neurodegenerative disorder defined by early-onset diabetes mellitus and optic atrophy. The majority of patients harbour recessive mutations in the WFS1 gene, which encodes for Wolframin, a transmembrane endoplasmic reticulum protein. There is limited availability of human ocular and brain tissues, and there are few animal models for WS that replicate the neuropathology and clinical phenotype seen in this disorder. We, therefore, characterised two wfs1 zebrafish knockout models harbouring nonsense wfs1a and wfs1b mutations. Both homozygous mutant wfs1a-/- and wfs1b-/- embryos showed significant morphological abnormalities in early development. The wfs1b-/- zebrafish exhibited a more pronounced neurodegenerative phenotype with delayed neuronal development, progressive loss of retinal ganglion cells and clear evidence of visual dysfunction on functional testing. At 12 months of age, wfs1b-/- zebrafish had a significantly lower RGC density per 100 μm2 (mean ± standard deviation; 19 ± 1.7) compared with wild-type (WT) zebrafish (25 ± 2.3, p < 0.001). The optokinetic response for wfs1b-/- zebrafish was significantly reduced at 8 and 16 rpm testing speeds at both 4 and 12 months of age compared with WT zebrafish. An upregulation of the unfolded protein response was observed in mutant zebrafish indicative of increased endoplasmic reticulum stress. Mutant wfs1b-/- zebrafish exhibit some of the key features seen in patients with WS, providing a versatile and cost-effective in vivo model that can be used to further investigate the underlying pathophysiology of WS and potential therapeutic interventions.
Collapse
Affiliation(s)
- G Cairns
- International Centre for Life, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK.,Interdisciplinary School of Health Science, Faculty of Health Sciences, University of Ottawa, Ottawa, Canada
| | - F Burté
- International Centre for Life, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - R Price
- International Centre for Life, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - E O'Connor
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - M Toms
- UCL Institute of Ophthalmology, University College London, London, UK
| | - R Mishra
- John van Geest Centre for Brain Repair and MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - M Moosajee
- UCL Institute of Ophthalmology, University College London, London, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Great Ormond Street Hospital for Children NHS Foundation, Trust, London, UK
| | - A Pyle
- The Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - J A Sayer
- International Centre for Life, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK.,Department of Renal Medicine, Freeman Hospital, The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.,National Institute for Health Research Newcastle Biomedical Research Centre, Newcastle upon Tyne, UK
| | - P Yu-Wai-Man
- UCL Institute of Ophthalmology, University College London, London, UK. .,John van Geest Centre for Brain Repair and MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK. .,Moorfields Eye Hospital NHS Foundation Trust, London, UK. .,Cambridge Eye Unit, Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, UK.
| |
Collapse
|
15
|
O'Connor E, Mullins M, O'Connor D, Phelan S, Bruzzi J. The relationship between ultrasound microcalcifications and psammoma bodies in thyroid tumours: a single-institution retrospective study. Clin Radiol 2021; 77:e48-e54. [PMID: 34627599 DOI: 10.1016/j.crad.2021.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/10/2021] [Indexed: 11/29/2022]
Abstract
AIM To investigate the diagnostic accuracy of ultrasound microcalcifications for the detection of malignancy in thyroid nodules and determine the validity of the concept that ultrasound microcalcification reflects the presence of psammoma body calcification in thyroid nodules. MATERIALS AND METHODS The laboratory information system at University Hospital Galway, a tertiary referral hospital, was used to compile a list of patients who underwent thyroid lobectomy or complete thyroidectomy over a continuous 12-month period with both preoperative ultrasound and postoperative histology available (n=106) from January to December 2019. The haematoxylin and eosin-stained histology slides of each case were sourced and reviewed under light microscopy by a histopathologist to determine the presence of psammoma body calcification within both benign and malignant thyroid nodules. Two radiologists reviewed preoperative thyroid ultrasound images of each case independently and blindly, and reported on the presence of ultrasonographic microcalcification. RESULTS There was a strong and significant relationship between the presence of preoperative ultrasound microcalcification and thyroid malignancy (p<0.001). Ultrasound microcalcification had a high specificity (93%) and positive predictive value (75%) for thyroid malignancy, with a diagnostic accuracy of 76%. Negative predictive value was high at 76.7%, while sensitivity was low at 42.8%. There was a strong and significant association between the presence of preoperative ultrasound microcalcification in thyroid nodules and the presence of pathological psammoma bodies on histology (p<0.001). DISCUSSION Ultrasound microcalcification has a strong and significant association with malignancy in thyroid nodules. This study supported the theory that ultrasound microcalcification occurs secondary to the presence of psammoma bodies within thyroid nodules.
Collapse
Affiliation(s)
- E O'Connor
- Histopathology Department, University Hospital Galway, Newcastle Road, Galway, H91 YR71, Ireland.
| | - M Mullins
- Radiology Department, University Hospital Galway, Newcastle Road, Galway, H91 YR71, Ireland
| | - D O'Connor
- Histopathology Department, University Hospital Galway, Newcastle Road, Galway, H91 YR71, Ireland
| | - S Phelan
- Histopathology Department, University Hospital Galway, Newcastle Road, Galway, H91 YR71, Ireland
| | - J Bruzzi
- Radiology Department, University Hospital Galway, Newcastle Road, Galway, H91 YR71, Ireland
| |
Collapse
|
16
|
Baca SC, Takeda DY, Seo JH, Hwang J, Ku SY, Arafeh R, Arnoff T, Agarwal S, Bell C, O'Connor E, Qiu X, Alaiwi SA, Corona RI, Fonseca MAS, Giambartolomei C, Cejas P, Lim K, He M, Sheahan A, Nassar A, Berchuck JE, Brown L, Nguyen HM, Coleman IM, Kaipainen A, De Sarkar N, Nelson PS, Morrissey C, Korthauer K, Pomerantz MM, Ellis L, Pasaniuc B, Lawrenson K, Kelly K, Zoubeidi A, Hahn WC, Beltran H, Long HW, Brown M, Corey E, Freedman ML. Reprogramming of the FOXA1 cistrome in treatment-emergent neuroendocrine prostate cancer. Nat Commun 2021; 12:1979. [PMID: 33785741 PMCID: PMC8010057 DOI: 10.1038/s41467-021-22139-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/18/2021] [Indexed: 02/07/2023] Open
Abstract
Lineage plasticity, the ability of a cell to alter its identity, is an increasingly common mechanism of adaptive resistance to targeted therapy in cancer. An archetypal example is the development of neuroendocrine prostate cancer (NEPC) after treatment of prostate adenocarcinoma (PRAD) with inhibitors of androgen signaling. NEPC is an aggressive variant of prostate cancer that aberrantly expresses genes characteristic of neuroendocrine (NE) tissues and no longer depends on androgens. Here, we investigate the epigenomic basis of this resistance mechanism by profiling histone modifications in NEPC and PRAD patient-derived xenografts (PDXs) using chromatin immunoprecipitation and sequencing (ChIP-seq). We identify a vast network of cis-regulatory elements (N~15,000) that are recurrently activated in NEPC. The FOXA1 transcription factor (TF), which pioneers androgen receptor (AR) chromatin binding in the prostate epithelium, is reprogrammed to NE-specific regulatory elements in NEPC. Despite loss of dependence upon AR, NEPC maintains FOXA1 expression and requires FOXA1 for proliferation and expression of NE lineage-defining genes. Ectopic expression of the NE lineage TFs ASCL1 and NKX2-1 in PRAD cells reprograms FOXA1 to bind to NE regulatory elements and induces enhancer activity as evidenced by histone modifications at these sites. Our data establish the importance of FOXA1 in NEPC and provide a principled approach to identifying cancer dependencies through epigenomic profiling.
Collapse
Affiliation(s)
- Sylvan C Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David Y Takeda
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Justin Hwang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sheng Yu Ku
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rand Arafeh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Taylor Arnoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Supreet Agarwal
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Edward O'Connor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah Abou Alaiwi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rosario I Corona
- Department of Obstetrics and Gynecology and the Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Marcos A S Fonseca
- Department of Obstetrics and Gynecology and the Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Claudia Giambartolomei
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Istituto Italiano di Tecnologia, Genova, Italy
| | - Paloma Cejas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Klothilda Lim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Monica He
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anjali Sheahan
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Amin Nassar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jacob E Berchuck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lisha Brown
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Holly M Nguyen
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Ilsa M Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Arja Kaipainen
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Navonil De Sarkar
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Keegan Korthauer
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Leigh Ellis
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Kate Lawrenson
- Department of Obstetrics and Gynecology and the Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kathleen Kelly
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Vancouver, BC, Canada
- Department of Urologic Sciences, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Himisha Beltran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
| |
Collapse
|
17
|
Newman C, Egan AM, Ahern T, Al-Kiyumi M, Balan G, Brassill MJ, Brosnan E, Carmody L, Clarke H, Coogan Kelly C, Culliney L, Davern R, Durkan M, Fenlon M, Ferry P, Hanlon G, Higgins T, Hoashi S, Khamis A, Kinsley B, Kirwan B, Kyithar P, Liew A, Matthews L, McGurk C, McHugh C, Murphy MS, Murphy P, Nagodra D, Noctor E, Nolan M, O'Connor E, O'Halloran D, O'Mahoney L, O'Sullivan E, Peters M, Roberts G, Rooney H, Smyth A, Tarachand B, Todd M, Tuthill A, Wan Mahmood WA, Yousif O, Dunne FP. Diabetes care and pregnancy outcomes for women with pregestational diabetes in Ireland. Diabetes Res Clin Pract 2021; 173:108685. [PMID: 33548336 DOI: 10.1016/j.diabres.2021.108685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/16/2021] [Accepted: 01/22/2021] [Indexed: 12/13/2022]
Abstract
AIMS Pre-gestational diabetes mellitus (PGDM) is associated with adverse outcomes. We aimed to examine pregnancies affected by PGDM; report on these pregnancy outcomes and compare outcomes for patients with type 1 versus type 2 diabetes mellitus; compare our findings to published Irish and United Kingdom (UK) data and identify potential areas for improvement. METHODS Between 2016 and 2018 information on 679 pregnancies from 415 women with type 1 Diabetes Mellitus and 244 women with type 2 diabetes was analysed. Data was collected on maternal characteristics; pregnancy preparation; glycaemic control; pregnancy related complications; foetal and maternal outcomes; unscheduled hospitalisations; congenital anomalies and perinatal deaths. RESULTS Only 15.9% of women were adequately prepared for pregnancy. Significant deficits were identified in availability and attendance at pre-pregnancy clinic, use of folic acid, attaining appropriate glycaemic targets and appropriate retinal screening. The majority of pregnancies (n = 567, 83.5%) resulted in a live birth but the large number of infants born large for gestational age (LGA) (n = 280, 49.4%), born prematurely <37 weeks and requiring neonatal intensive care unit (NICU) admission continue to be significant issues. CONCLUSIONS This retrospective cohort study identifies multiple targets for improvements in the provision of care to women with pre-gestational DM which are likely to translate into better pregnancy outcomes.
Collapse
Affiliation(s)
- C Newman
- Galway University Hospital, Galway, Ireland.
| | - A M Egan
- Division of Endocrinology Mayo Clinic, Rochester, United States
| | - T Ahern
- Our Lady of Lourdes Hospital, Drogheda, Co Louth, Ireland
| | - M Al-Kiyumi
- Coombe Women and Infants University Hospital, Dublin, Ireland
| | - G Balan
- Coombe Women and Infants University Hospital, Dublin, Ireland
| | - M J Brassill
- South Tipperary General Hospital, Clonmel, Co Tipperary, Ireland
| | - E Brosnan
- Mayo University Hospital, Castlebar, Co Mayo, Ireland
| | - L Carmody
- Galway University Hospital, Galway, Ireland
| | - H Clarke
- Portiuncula University Hospital, Ballinasloe, Co Galway, Ireland
| | - C Coogan Kelly
- St Luke's General Hospital, Kilkenny, Co Kilkenny, Ireland
| | - L Culliney
- Cork University Hospital, Cork, Co Cork, Ireland
| | - R Davern
- St Luke's General Hospital, Kilkenny, Co Kilkenny, Ireland
| | - M Durkan
- Bons Secours Hospital, Cork, Co Cork, Ireland
| | - M Fenlon
- Wexford General Hospital, Co Wexford, Ireland
| | - P Ferry
- Letterkenny General Hospital, Letterkenny, Co Donegal, Ireland
| | - G Hanlon
- St Luke's General Hospital, Kilkenny, Co Kilkenny, Ireland
| | - T Higgins
- University Hospital Kerry, Tralee, Co Kerry, Ireland
| | - S Hoashi
- Mullingar Regional Hospital, Mullingar, Co Westmeath, Ireland
| | - A Khamis
- Letterkenny General Hospital, Letterkenny, Co Donegal, Ireland
| | - B Kinsley
- Coombe Women and Infants University Hospital, Dublin, Ireland
| | - B Kirwan
- Galway University Hospital, Galway, Ireland
| | - P Kyithar
- Portlaoise General Hospital, Portlaoise, Co Laois, Ireland
| | - A Liew
- Portiuncula University Hospital, Ballinasloe, Co Galway, Ireland
| | - L Matthews
- Our Lady of Lourdes Hospital, Drogheda, Co Louth, Ireland
| | - C McGurk
- St Luke's General Hospital, Kilkenny, Co Kilkenny, Ireland
| | - C McHugh
- Sligo University Hospital, Co Sligo, Ireland
| | - M S Murphy
- South Infirmary Victoria Hospital, Cork, Co Cork, Ireland
| | - P Murphy
- Cork University Hospital, Cork, Co Cork, Ireland
| | - D Nagodra
- Portlaoise General Hospital, Portlaoise, Co Laois, Ireland
| | - E Noctor
- Limerick University Hospital, Co Limerick, Ireland
| | - M Nolan
- University Hospital Kerry, Tralee, Co Kerry, Ireland
| | - E O'Connor
- Portiuncula University Hospital, Ballinasloe, Co Galway, Ireland
| | - D O'Halloran
- Cork University Hospital, Cork, Co Cork, Ireland
| | - L O'Mahoney
- Cork University Hospital, Cork, Co Cork, Ireland
| | | | - M Peters
- University Hospital Waterford, Co Waterford, Ireland
| | - G Roberts
- University Hospital Waterford, Co Waterford, Ireland
| | - H Rooney
- St Luke's General Hospital, Kilkenny, Co Kilkenny, Ireland
| | - A Smyth
- Coombe Women and Infants University Hospital, Dublin, Ireland
| | - B Tarachand
- University Hospital Waterford, Co Waterford, Ireland
| | - M Todd
- Mayo University Hospital, Castlebar, Co Mayo, Ireland
| | - A Tuthill
- Cork University Hospital, Cork, Co Cork, Ireland
| | - W A Wan Mahmood
- Coombe Women and Infants University Hospital, Dublin, Ireland
| | - O Yousif
- Wexford General Hospital, Co Wexford, Ireland
| | - F P Dunne
- Galway University Hospital, Galway, Ireland
| |
Collapse
|
18
|
Keane KG, Redmond EJ, McIntyre C, O'Connor E, Madden A, O'Connell C, Inder SM, Smyth LG, Thomas AZ, Flynn RJ, Manecksha RP. Does instillation of lidocaine gel following flexible cystoscopy decrease the severity of post procedure symptoms? A randomised controlled trial assessing the efficacy of lidocaine gel post flexible cystoscopy. Ir J Med Sci 2021; 190:1553-1559. [PMID: 33449326 PMCID: PMC7809241 DOI: 10.1007/s11845-020-02458-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/03/2020] [Indexed: 12/02/2022]
Abstract
Objective To assess whether instillation of lidocaine gel both before and after flexible cystoscopy is more effective at reducing post procedural symptoms than instillation of lidocaine gel pre flexible cystoscopy alone. We hypothesise that inadequate urethral dwell time and dilution of lidocaine gel by the irrigation fluid during flexible cystoscopy limits its anaesthetic efficacy. Only one other study has attempted to reduce bothersome urinary symptoms through an intervention after flexible cystoscopy. Methods This was a randomised controlled trial in which patients were randomised 1:1 to receive lidocaine gel pre and post flexible cystoscopy (treatment) or lidocaine gel pre flexible cystoscopy only (control). Patient-reported outcome measures were used to assess symptoms and quality of life prior to cystoscopy, on day 2 and day 7 post cystoscopy. Result Fifty patients were divided equally between the treatment and control groups. There were no significant differences in baseline characteristics between the groups (p = 1.000). An overall symptoms variable was measured, though no significant difference was found in the distribution of responses between the groups at baseline, 2 or 7 days after the flexible cystoscopy (p = 0.423, 0.651,0.735). In the treatment group, 1 patient (4.0%) presented to a doctor for review following flexible cystoscopy, and 4 patients (16.0%) presented in the control group (p = 0.349). Conclusion Initial study results suggest that post-operative lidocaine does not significantly limit the exacerbation of urinary symptoms following flexible cystoscopy; however, our results are not powered to detect a small difference. We do not recommend a change in practice based on our results.
Collapse
Affiliation(s)
- K G Keane
- Department of Urology, Tallaght University Hospital, Dublin, Ireland.
| | - E J Redmond
- Department of Urology, Tallaght University Hospital, Dublin, Ireland
| | - C McIntyre
- Department of Urology, Tallaght University Hospital, Dublin, Ireland
| | - E O'Connor
- Department of Urology, Tallaght University Hospital, Dublin, Ireland
| | - A Madden
- Department of Urology, Tallaght University Hospital, Dublin, Ireland
| | - C O'Connell
- Department of Urology, Tallaght University Hospital, Dublin, Ireland
| | - S M Inder
- Department of Urology, Tallaght University Hospital, Dublin, Ireland
| | - L G Smyth
- Department of Urology, Tallaght University Hospital, Dublin, Ireland
| | - A Z Thomas
- Department of Urology, Tallaght University Hospital, Dublin, Ireland.,Department of Surgery, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - R J Flynn
- Department of Urology, Tallaght University Hospital, Dublin, Ireland.,Department of Surgery, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - R P Manecksha
- Department of Urology, Tallaght University Hospital, Dublin, Ireland.,Department of Surgery, School of Medicine, Trinity College Dublin, Dublin, Ireland
| |
Collapse
|
19
|
|
20
|
Blake A, Collins D, O'Connor E, Bergin C, McLaughlin AM, Martin-Loeches I. Clinical and biochemical characteristics of patients admitted to ICU with SARS-CoV-2. Med Intensiva 2020; 44:589-590. [PMID: 32425288 PMCID: PMC7229922 DOI: 10.1016/j.medin.2020.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- A Blake
- Department of Intensive Care Medicine, St James's Hospital, Dublin, Ireland
| | - D Collins
- Department of Intensive Care Medicine, St James's Hospital, Dublin, Ireland
| | - E O'Connor
- Department of Intensive Care Medicine, St James's Hospital, Dublin, Ireland
| | - C Bergin
- Department of Infectious Diseases, St James's Hospital, Dublin, Ireland
| | - A M McLaughlin
- Department of Respiratory Medicine, St James's Hospital, Dublin, Ireland
| | - I Martin-Loeches
- Department of Intensive Care Medicine, St James's Hospital, Dublin, Ireland.
| |
Collapse
|
21
|
Sullivan R, Yau WY, Chelban V, Rossi S, O'Connor E, Wood NW, Cortese A, Houlden H. RFC1 Intronic Repeat Expansions Absent in Pathologically Confirmed Multiple Systems Atrophy. Mov Disord 2020; 35:1277-1279. [PMID: 32333430 DOI: 10.1002/mds.28074] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/24/2020] [Accepted: 04/06/2020] [Indexed: 11/10/2022] Open
Affiliation(s)
- Roisin Sullivan
- Department of Neuromuscular Disease, Queen's Square Institute of Neurology, London, United Kingdom
| | - Wai Yan Yau
- Department of Neuromuscular Disease, Queen's Square Institute of Neurology, London, United Kingdom.,The National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Viorica Chelban
- Department of Neuromuscular Disease, Queen's Square Institute of Neurology, London, United Kingdom.,The National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Salvatore Rossi
- Department of Neuromuscular Disease, Queen's Square Institute of Neurology, London, United Kingdom
| | - E O'Connor
- Department of Neuromuscular Disease, Queen's Square Institute of Neurology, London, United Kingdom.,The National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Nicholas W Wood
- Movement Disorders, Queen's Square Institute of Neurology, London, United Kingdom.,The National Hospital for Neurology and Neurosurgery, London, United Kingdom
| | - Andrea Cortese
- Department of Neuromuscular Disease, Queen's Square Institute of Neurology, London, United Kingdom.,Department of Brain and Behavioural Science, University of Pavia, Pavia, Italy
| | - Henry Houlden
- Department of Neuromuscular Disease, Queen's Square Institute of Neurology, London, United Kingdom.,The National Hospital for Neurology and Neurosurgery, London, United Kingdom
| |
Collapse
|
22
|
Francini E, Ou FS, Rhoades J, Wolfe EG, O'Connor E, Ha G, Gregory G, Kelleher K, Bhatt RS, Balk SP, Sweeney C, Adalsteinsson V, Taplin ME, Choudhury AD. Circulating-free DNA (cfDNA) as biomarker of taxane resistance in metastatic castration-resistant prostate cancer (mCRPC). J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.6_suppl.174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
174 Background: Docetaxel (D) and cabazitaxel (C) are standard chemotherapies for mCRPC. A reliable biomarker predictive of resistance to D or C is yet to be identified. We aimed to assess the association between genetic amplification of the multidrug resistance transporter ABCB1 (ABCB1 amp) and primary resistance (RES) to D or C for mCRPC, using cfDNA. Methods: A cohort (A) of 136 patients (pts) with at least 1 plasma sample drawn and stored within 1 year prior to starting D for mCRPC (2002-2014) and a cohort (B) of 42 pts with at least 1 plasma sample from within 1 year prior to starting C for mCRPC (2010-2016) were identified from the Dana-Farber Cancer Institute IRB approved database. Whole genome sequencing (WGS) at 0.1x coverage, termed ultra-low pass WGS (ULP-WGS), was performed on cfDNA extracted from the selected samples (1000μL/subject) and sequencing data were analyzed using a tool called ichorCNA to identify cases with sufficient tumor DNA content (>7%) for accurate detection of copy number alterations (CNAs) including ABCB1 amp. Primary objective was the association between ABCB1 amp and RES to D or C. RES was defined as lack of response (no PSA50 decline or radiologic response per RECIST criteria 1.1, within 4 months from treatment start). Odds ratio (OR) was used to compare odds of RES to D or C for pts with ABCB1 amp and P-values were calculated by Fisher’s exact test. Results: Of the selected 178 pts, 66 had tumor fraction >7%: 45 pts in cohort A and 21 in cohort B. No significant association was noted between ABCB1 amp and RES to D (P=0.7123; OR=1.600) or C (P=1.000; OR=1.0606). RES was observed in 26 pts (57.8%) of cohort A and 18 (85.7%) of cohort B. ABCB1 amp was found in 9 pts (20%; 95% CI, 9.6-34.6) in group A and 6 of them (66%) had RES to D. ABCB1 amp rate among D-resistant men was 23.1% (95% CI, 9.0-43.7). In group B, 2 pts (9.5%; 95% CI, 1.2-30.4) had ABCB1 amp and both of them had RES to C. ABCB1 rate among C-resistant pts was 11.1% (95% CI, 1.4-34.7). Conclusions: In this study, ABCB1 amp using cfDNA did not show statistically significant correlation with RES to D or C for pts with mCRPC. Future studies including ABCB1 amp in a suite of putative biomarkers and larger sample size may aid drawing definitive conclusions.
Collapse
Affiliation(s)
| | | | | | | | | | - Gavin Ha
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | | | - Christopher Sweeney
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | | | | |
Collapse
|
23
|
Wang AT, Shetty A, O'Connor E, Bell C, Pomerantz MM, Freedman ML, Gusev A. Allele-Specific QTL Fine Mapping with PLASMA. Am J Hum Genet 2020; 106:170-187. [PMID: 32004450 PMCID: PMC7011109 DOI: 10.1016/j.ajhg.2019.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/29/2019] [Indexed: 12/22/2022] Open
Abstract
Although quantitative trait locus (QTL) associations have been identified for many molecular traits such as gene expression, it remains challenging to distinguish the causal nucleotide from nearby variants. In addition to traditional QTLs by association, allele-specific (AS) QTLs are a powerful measure of cis-regulation that are concordant with traditional QTLs but typically less susceptible to technical/environmental noise. However, existing methods for estimating causal variant probabilities (i.e., fine mapping) cannot produce valid estimates from asQTL signals due to complexities in linkage disequilibrium (LD). We introduce PLASMA (Population Allele-Specific Mapping), a fine-mapping method that integrates QTL and asQTL information to improve accuracy. In simulations, PLASMA accurately prioritizes causal variants over a wide range of genetic architectures. Applied to RNA-seq data from 524 kidney tumor samples, PLASMA achieves a greater power at 50 samples than conventional QTL-based fine mapping at 500 samples, with more than 17% of loci fine mapped to within five causal variants, compared to 2% by QTL-based fine mapping, and a 6.9-fold overall reduction in median credible set size compared to QTL-based fine mapping when applied to H3K27AC ChIP-seq from just 28 prostate tumor/normal samples. Variants in the PLASMA credible sets for RNA-seq and ChIP-seq were enriched for open chromatin and chromatin looping, respectively, at a comparable or greater degree than credible variants from existing methods while containing far fewer markers. Our results demonstrate how integrating AS activity can substantially improve the detection of causal variants from existing molecular data.
Collapse
Affiliation(s)
- Austin T Wang
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Anamay Shetty
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cambridge University, Cambridge CB2 1TN, UK
| | - Edward O'Connor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA; Brigham & Women's Hospital, Division of Genetics, Boston, MA 02215, USA.
| |
Collapse
|
24
|
Haile-Mariam M, MacLeod IM, Bolormaa S, Schrooten C, O'Connor E, de Jong G, Daetwyler HD, Pryce JE. Value of sharing cow reference population between countries on reliability of genomic prediction for milk yield traits. J Dairy Sci 2019; 103:1711-1728. [PMID: 31864746 DOI: 10.3168/jds.2019-17170] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/24/2019] [Indexed: 01/08/2023]
Abstract
Increasing the reliability of genomic prediction (GP) of economic traits in the pasture-based dairy production systems of New Zealand (NZ) and Australia (AU) is important to both countries. This study assessed if sharing cow phenotype and genotype data of NZ and AU improves the reliability of GP for NZ bulls. Data from approximately 32,000 NZ genotyped cows and their contemporaries were included in the May 2018 routine genetic evaluation of the Australian Dairy cattle in an attempt to provide consistent phenotypes for both countries. After the genetic evaluation, deregressed proofs of cows were calculated for milk yield traits. The April 2018 multiple across-country evaluation of Interbull was also used to calculate deregressed proofs for bulls on the NZ scale. Approximately 1,178 Jersey (Jer) and 6,422 Holstein (Hol) bulls had genotype and phenotype data. In addition to NZ cows, phenotype data of close to 60,000 genotyped Australian (AU) cows from the same genetic evaluation run as NZ cows were used. All AU and NZ females were genotyped using low-density SNP chips (<10K SNP) and were imputed first to 50K and then to ∼600K (referred to as high density; HD). We used up to 98,000 animals in the reference populations, both by expanding the NZ reference set (cow, bull, single breed to multi-breed set) and by adding AU cows. Reliabilities of GP were calculated for 508 Jer and 1,251 Hol bulls whose sires are not included in the reference set (RS) to ensure that real differences are not masked by close relationships. The GP was tested using 50K or high-density SNP chip using genomic BLUP in bivariate (considering country as a trait) or single trait models. The RS that gave the highest reliability for each breed were also tested using a hybrid GP method that combines expectation maximization with Bayes R. The addition of the AU cows to an NZ RS that included either NZ cows only, or cows and bulls, improved the reliability of GP for both NZ Hol and Jer validation bulls for all traits. Using single breed reference populations also increased reliability when NZ crossbred cows were added to reference populations that included only purebred NZ bulls and cows and AU cows. The full multi-breed RS (all NZ cows and bulls and AU cows) provided similar reliabilities in NZ Hol bulls, when compared with the single breed reference with crossbred NZ cows. For Jer validation bulls, the RS that included Jer cows and bulls and crossbred cows from NZ and Jer cows from AU was marginally better than the all-breed, all-country RS. In terms of reliability, the advantage of the HD SNP chip was small but captured more of the genomic variance than the 50K, particularly for Hol. The expectation maximization Bayes R GP method was slightly (up to 3 percentage points) better than genomic BLUP. We conclude that GP of milk production traits in NZ bulls improves by up to 7 percentage points in reliability by expanding the NZ reference population to include AU cows.
Collapse
Affiliation(s)
- M Haile-Mariam
- Agriculture Victoria, Department of Jobs, Precincts and Regions, Bundoora, VIC 3083, Australia.
| | - I M MacLeod
- Agriculture Victoria, Department of Jobs, Precincts and Regions, Bundoora, VIC 3083, Australia
| | - S Bolormaa
- Agriculture Victoria, Department of Jobs, Precincts and Regions, Bundoora, VIC 3083, Australia
| | | | | | - G de Jong
- CRV, 6800 AL Arnhem, the Netherlands
| | - H D Daetwyler
- Agriculture Victoria, Department of Jobs, Precincts and Regions, Bundoora, VIC 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | - J E Pryce
- Agriculture Victoria, Department of Jobs, Precincts and Regions, Bundoora, VIC 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| |
Collapse
|
25
|
Houlahan KE, Shiah YJ, Gusev A, Yuan J, Ahmed M, Shetty A, Ramanand SG, Yao CQ, Bell C, O'Connor E, Huang V, Fraser M, Heisler LE, Livingstone J, Yamaguchi TN, Rouette A, Foucal A, Espiritu SMG, Sinha A, Sam M, Timms L, Johns J, Wong A, Murison A, Orain M, Picard V, Hovington H, Bergeron A, Lacombe L, Lupien M, Fradet Y, Têtu B, McPherson JD, Pasaniuc B, Kislinger T, Chua MLK, Pomerantz MM, van der Kwast T, Freedman ML, Mani RS, He HH, Bristow RG, Boutros PC. Genome-wide germline correlates of the epigenetic landscape of prostate cancer. Nat Med 2019; 25:1615-1626. [PMID: 31591588 PMCID: PMC7418214 DOI: 10.1038/s41591-019-0579-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 08/13/2019] [Indexed: 12/16/2022]
Abstract
Oncogenesis is driven by germline, environmental and stochastic factors. It is unknown how these interact to produce the molecular phenotypes of tumors. We therefore quantified the influence of germline polymorphisms on the somatic epigenome of 589 localized prostate tumors. Predisposition risk loci influence a tumor's epigenome, uncovering a mechanism for cancer susceptibility. We identified and validated 1,178 loci associated with altered methylation in tumoral but not nonmalignant tissue. These tumor methylation quantitative trait loci influence chromatin structure, as well as RNA and protein abundance. One prominent tumor methylation quantitative trait locus is associated with AKT1 expression and is predictive of relapse after definitive local therapy in both discovery and validation cohorts. These data reveal intricate crosstalk between the germ line and the epigenome of primary tumors, which may help identify germline biomarkers of aggressive disease to aid patient triage and optimize the use of more invasive or expensive diagnostic assays.
Collapse
Affiliation(s)
- Kathleen E Houlahan
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
| | - Yu-Jia Shiah
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Alexander Gusev
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jiapei Yuan
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Musaddeque Ahmed
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Anamay Shetty
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- University of Cambridge, Cambridge, UK
| | - Susmita G Ramanand
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Cindy Q Yao
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Edward O'Connor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Vincent Huang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Michael Fraser
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | | | | | | | - Adrien Foucal
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Ankit Sinha
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Michelle Sam
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Lee Timms
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jeremy Johns
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Ada Wong
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Alex Murison
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Michèle Orain
- Department of Pathology, Centre de recheche du CHU de Québec-Université Laval, Québec City, Québec, Canada
| | - Valérie Picard
- Division of Urology, Centre de recheche du CHU de Québec-Université Laval, Québec City, Québec, Canada
| | - Hélène Hovington
- Division of Urology, Centre de recheche du CHU de Québec-Université Laval, Québec City, Québec, Canada
| | - Alain Bergeron
- Division of Urology, Centre de recheche du CHU de Québec-Université Laval, Québec City, Québec, Canada
| | - Louis Lacombe
- Division of Urology, Centre de recheche du CHU de Québec-Université Laval, Québec City, Québec, Canada
| | - Mathieu Lupien
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yves Fradet
- Division of Urology, Centre de recheche du CHU de Québec-Université Laval, Québec City, Québec, Canada
| | - Bernard Têtu
- Department of Pathology, Centre de recheche du CHU de Québec-Université Laval, Québec City, Québec, Canada
| | | | - Bogdan Pasaniuc
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Thomas Kislinger
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Melvin L K Chua
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Theodorus van der Kwast
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ram S Mani
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Housheng H He
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Robert G Bristow
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada.
- Division of Cancer Sciences, Faculty of Biology, Health and Medicine, University of Manchester, Manchester, UK.
- The Christie NHS Foundation Trust, Manchester, UK.
- Cancer Research UK Manchester Institute, Manchester, UK.
- Manchester Cancer Research Centre, Manchester, UK.
| | - Paul C Boutros
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Vector Institute, Toronto, Ontario, Canada.
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.
- Department of Urology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
26
|
Mazzu YZ, Armenia J, Chakraborty G, Yoshikawa Y, Coggins SA, Nandakumar S, Gerke TA, Pomerantz MM, Qiu X, Zhao H, Atiq M, Khan N, Komura K, Lee GSM, Fine SW, Bell C, O'Connor E, Long HW, Freedman ML, Kim B, Kantoff PW. A Novel Mechanism Driving Poor-Prognosis Prostate Cancer: Overexpression of the DNA Repair Gene, Ribonucleotide Reductase Small Subunit M2 (RRM2). Clin Cancer Res 2019; 25:4480-4492. [PMID: 30996073 DOI: 10.1158/1078-0432.ccr-18-4046] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/14/2019] [Accepted: 04/08/2019] [Indexed: 01/23/2023]
Abstract
PURPOSE Defects in genes in the DNA repair pathways significantly contribute to prostate cancer progression. We hypothesize that overexpression of DNA repair genes may also drive poorer outcomes in prostate cancer. The ribonucleotide reductase small subunit M2 (RRM2) is essential for DNA synthesis and DNA repair by producing dNTPs. It is frequently overexpressed in cancers, but very little is known about its function in prostate cancer. EXPERIMENTAL DESIGN The oncogenic activity of RRM2 in prostate cancer cells was assessed by inhibiting or overexpressing RRM2. The molecular mechanisms of RRM2 function were determined. The clinical significance of RRM2 overexpression was evaluated in 11 prostate cancer clinical cohorts. The efficacy of an RRM2 inhibitor (COH29) was assessed in vitro and in vivo. Finally, the mechanism underlying the transcriptional activation of RRM2 in prostate cancer tissue and cells was determined. RESULTS Knockdown of RRM2 inhibited its oncogenic function, whereas overexpression of RRM2 promoted epithelial mesenchymal transition in prostate cancer cells. The prognostic value of RRM2 RNA levels in prostate cancer was confirmed in 11 clinical cohorts. Integrating the transcriptomic and phosphoproteomic changes induced by RRM2 unraveled multiple oncogenic pathways downstream of RRM2. Targeting RRM2 with COH29 showed excellent efficacy. Thirteen putative RRM2-targeting transcription factors were bioinformatically identified, and FOXM1 was validated to transcriptionally activate RRM2 in prostate cancer. CONCLUSIONS We propose that increased expression of RRM2 is a mechanism driving poor patient outcomes in prostate cancer and that its inhibition may be of significant therapeutic value.
Collapse
Affiliation(s)
- Ying Z Mazzu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joshua Armenia
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, United Kingdom
| | - Goutam Chakraborty
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yuki Yoshikawa
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Si'Ana A Coggins
- Center for Drug Discovery, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Subhiksha Nandakumar
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Huiyong Zhao
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mohammad Atiq
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nabeela Khan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kazumasa Komura
- Translational Research Program and Department of Urology, Osaka Medical College, Osaka, Japan
| | - Gwo-Shu Mary Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Samson W Fine
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Edward O'Connor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Baek Kim
- Center for Drug Discovery, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia.,Department of Pharmacy, Kyung-Hee University, Seoul, South Korea
| | - Philip W Kantoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| |
Collapse
|
27
|
Wolters M, Volkert D, Streicher M, Kiesswetter E, Torbahn G, O'Connor E, O'Keeffe M, O'Herlihy E, O'Toole P, Timmons S, O'Shea E, Kearney P, van Zwienen-Pot J, Visser M, Maitre I, van Wymelbeke V, Sulmont-Rossé C, Nagel G, Flechtner-Mors M, Teh R, Hebestreit A. Prevalence rates of malnutrition using harmonized definitions in older adults from different settings in Europe and New Zealand – a manuel study. Clin Nutr 2018. [DOI: 10.1016/j.clnu.2018.06.1486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
28
|
Kelly M, Purtill H, Leahy S, Grace M, O'Toole P, O'Herlihy E, O'Connor E. Determinants of malnutrition in older Irish adults. Clin Nutr 2018. [DOI: 10.1016/j.clnu.2018.06.1645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
29
|
Takeda DY, Spisák S, Seo JH, Bell C, O'Connor E, Korthauer K, Ribli D, Csabai I, Solymosi N, Szállási Z, Stillman DR, Cejas P, Qiu X, Long HW, Tisza V, Nuzzo PV, Rohanizadegan M, Pomerantz MM, Hahn WC, Freedman ML. A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer. Cell 2018; 174:422-432.e13. [PMID: 29909987 PMCID: PMC6046260 DOI: 10.1016/j.cell.2018.05.037] [Citation(s) in RCA: 196] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/11/2018] [Accepted: 05/16/2018] [Indexed: 12/26/2022]
Abstract
Increased androgen receptor (AR) activity drives therapeutic resistance in advanced prostate cancer. The most common resistance mechanism is amplification of this locus presumably targeting the AR gene. Here, we identify and characterize a somatically acquired AR enhancer located 650 kb centromeric to the AR. Systematic perturbation of this enhancer using genome editing decreased proliferation by suppressing AR levels. Insertion of an additional copy of this region sufficed to increase proliferation under low androgen conditions and to decrease sensitivity to enzalutamide. Epigenetic data generated in localized prostate tumors and benign specimens support the notion that this region is a developmental enhancer. Collectively, these observations underscore the importance of epigenomic profiling in primary specimens and the value of deploying genome editing to functionally characterize noncoding elements. More broadly, this work identifies a therapeutic vulnerability for targeting the AR and emphasizes the importance of regulatory elements as highly recurrent oncogenic drivers.
Collapse
Affiliation(s)
- David Y Takeda
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | - Sándor Spisák
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Connor Bell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Edward O'Connor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Keegan Korthauer
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Biostatistics & Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dezső Ribli
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest 1117, Hungary
| | - István Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest 1117, Hungary
| | - Norbert Solymosi
- Centre for Bioinformatics, University of Veterinary Medicine, István str. 2, Budapest 1078, Hungary
| | - Zoltán Szállási
- Computational Health Informatics Program (CHIP) Boston Children's Hospital Harvard Medical School, Boston, MA 02215, USA; Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark; 2nd Department of Pathology, MTA-SE NAP, Brain Metastasis Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest 1091, Hungary
| | - David R Stillman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Viktória Tisza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Computational Health Informatics Program (CHIP) Boston Children's Hospital Harvard Medical School, Boston, MA 02215, USA
| | - Pier Vitale Nuzzo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Internal Medicine, School of Medicine, University of Genoa, Genoa, Lgo R. Benzi 10, 16132, Italy
| | - Mersedeh Rohanizadegan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Mark M Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L. Broad Institute, Cambridge, MA 02142, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| |
Collapse
|
30
|
Borhan F, Borhan N, Ahmed S, Varghese L, O'Connor E. Identifying factors that influence the '6-hour target' in the Emergency Department by applying Regression Analysis. Ir Med J 2018; 111:699. [PMID: 29952447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
AIM To determine factors within the Emergency Department (ED) that have maximum influence on the '6-hour target'. METHODS Regression Analysis methodology employed to analyse the influence of 9 ED variables on the '6-hour target' compliance. RESULTS The number of patients waiting to be seen an ED physician at 8pm exerts maximum influence on the '6-hour target' (r = -0.581, p<0.05). CONCLUSION The '6-hour target' compliance rises with lesser number of patients waiting to be seen by an ED physician at 8pm. Also, the '6-hour target' compliance rises by increasing the number of ED Registrar working hours and the number of ED SHO working hours per day.
Collapse
Affiliation(s)
- F Borhan
- Emergency Department, Connolly Hospital, Blanchardstown, Dublin 15, Ireland
| | - N Borhan
- Emergency Department, Connolly Hospital, Blanchardstown, Dublin 15, Ireland
| | - S Ahmed
- Government Health and Human Services Analytics, IBM Watson Health, Dublin 15, Ireland
| | - L Varghese
- Emergency Department, Connolly Hospital, Blanchardstown, Dublin 15, Ireland
| | - E O'Connor
- Emergency Department, Connolly Hospital, Blanchardstown, Dublin 15, Ireland
| |
Collapse
|
31
|
Wentlandt K, Weiss A, O'Connor E, Kaya E. Palliative and end of life care in solid organ transplantation. Am J Transplant 2017; 17:3008-3019. [PMID: 28976070 DOI: 10.1111/ajt.14522] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 09/17/2017] [Accepted: 09/22/2017] [Indexed: 01/25/2023]
Abstract
Palliative care is an interprofessional approach that focuses on quality of life of patients who are facing life-threatening illness. Palliative care is consistently associated with improvements in advance care planning, patient and caregiver satisfaction, quality of life, symptom burden, and lower healthcare utilization. Most transplant patients have advanced chronic disease, significant symptom burden, and mortality awaiting transplant. Transplantation introduces new risks including perioperative death, organ rejection, infection, renal insufficiency, and malignancy. Numerous publications over the last decade identify that palliative care is well-suited to support these patients and their caregivers, yet access to palliative care and research within this population are lacking. This review describes palliative care and summarizes existing research supporting palliative intervention in advanced organ failure and transplant populations. A proposed model to provide palliative care in parallel with disease-directed therapy in a transplant program has the potential to improve symptom burden, quality of life, and healthcare utilization. Further studies are needed to elucidate specific benefits of palliative care for this population. In addition, there is a tremendous need for education, specifically for clinicians, patients, and families, to improve understanding of palliative care and its benefits for patients with advanced disease.
Collapse
Affiliation(s)
- K Wentlandt
- Division of Palliative Care, Department of Supportive Care, University Health Network, Toronto, ON, Canada.,Multi-Organ Transplant Program, University Health Network, Toronto, ON, Canada.,Department of Family and Community Medicine, University of Toronto, Toronto, ON, Canada
| | - A Weiss
- Division of Palliative Care, Department of Supportive Care, University Health Network, Toronto, ON, Canada.,Department of Family and Community Medicine, University of Toronto, Toronto, ON, Canada
| | - E O'Connor
- Division of Palliative Care, Department of Supportive Care, University Health Network, Toronto, ON, Canada.,Division of Emergency Medicine, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - E Kaya
- Division of Palliative Care, Department of Supportive Care, University Health Network, Toronto, ON, Canada.,Division of Medical Oncology, Department of Medicine, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
32
|
Topf A, Azuma Y, Gorokhova S, O'Connor E, Porter A, Harris E, Evangelista T, Cox D, Lorenzoni P, McMacken G, Bartoli M, McArthur D, Magnusson O, Abicht A, Senderek J, Roos A, Abicht A, Lochmüller H. Next generation sequencing technologies in the genetic diagnosis of congenital myasthenic syndrome. Neuromuscul Disord 2017. [DOI: 10.1016/j.nmd.2017.06.373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
33
|
Niermeyer M, Franchow E, Barron C, Heyrend R, Ray A, Meredith S, Ziemnik R, O'Connor E, Suchy Y. A-07Reported Expressive Suppression in Daily Life is Related to Lower Executive Functioning and Slower Action Planning Among Older Adults. Arch Clin Neuropsychol 2017. [DOI: 10.1093/arclin/acx076.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
34
|
Ziemnik R, Niermeyer M, Nilssen R, Ocanovic Z, Bateman C, O'Connor E, Suchy Y. C-34Expressive Suppression as Predictors of Medication Management in Healthy Older Adults. Arch Clin Neuropsychol 2017. [DOI: 10.1093/arclin/acx076.201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
35
|
Fraser S, Shih JY, Ware M, O'Connor E, Cameron MJ, Schwickart M, Zhao X, Regnstrom K. Current Trends in Ligand Binding Real-Time Measurement Technologies. AAPS J 2017; 19:682-691. [PMID: 28321830 DOI: 10.1208/s12248-017-0067-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 02/24/2017] [Indexed: 01/01/2023]
Abstract
Numerous advances in ligand binding assay (LBA) real-time measurement technologies have been made within the last several years, ranging from the development of novel platforms to drive technology expansion to the adaptation of existing platforms to optimize performance and throughput. In this review, we have chosen to focus on technologies that provide increased value to two distinct segments of the LBA community. First, experimentally, by measuring real-time binding events, these technologies provide data that can be used to interrogate receptor/ligand binding interactions. While overall the platforms are not new, they have made significant advances in throughput, multiplexing, and/or sensitivity. Second, clinically, these point-of-care (POC) technologies provide instantaneous information which facilitates rapid treatment decisions.
Collapse
Affiliation(s)
| | - Judy Y Shih
- Amgen Inc., One Amgen Center Drive, Thousand Oaks, California, 91320, USA
| | - Mark Ware
- Janssen Research & Development, LLC, 1400 McKean Road, Spring House, Pennsylvania, 19477, USA
| | - Edward O'Connor
- AegisBioconsult, 78 Marbern Dr., Suffield, Connecticut, 06078, USA
| | - Mark J Cameron
- Lumigen, 22900 8 Mile Road, Southfield, Michigan, 48033, USA
| | - Martin Schwickart
- MedImmune, 319 N. Bernardo Ave, Mountain View, California, 94043, USA
| | - Xuemei Zhao
- Merck Research Laboratories, Rahway, New Jersey, 07065, USA
| | - Karin Regnstrom
- Boehringer Ingelheim, 6701 Kaiser Drive, Fremont, California, 94555, USA
| |
Collapse
|
36
|
Borhan F, Ahmed S, Varghese L, O'Connor E. A Statistical Methodology to determine factors affecting Patient Experience Time Targets in the Emergency Department. Ir Med J 2017; 110:506. [PMID: 28657283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- F Borhan
- Department of Emergency Medicine, Connolly Hospital , Blanchardstown, Dublin 15, Ireland
| | - S Ahmed
- Department of Emergency Medicine, Connolly Hospital , Blanchardstown, Dublin 15, Ireland
| | - L Varghese
- Department of Emergency Medicine, Connolly Hospital, Blanchardstown, Dublin 15, Ireland
| | - E O'Connor
- Department of Emergency Medicine, Connolly Hospital , Blanchardstown, Dublin 15, Ireland
| |
Collapse
|
37
|
Di Capua-Sacoto C, Sanchez-Llopis A, O'Connor E, Martinez A, Ruiz-Cerdá JL. Study of the apoptotic effect of urine as a diagnostic biomarker in patients with interstitial cystitis. Actas Urol Esp 2016; 40:570-576. [PMID: 27174573 DOI: 10.1016/j.acuro.2016.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 03/15/2016] [Accepted: 03/17/2016] [Indexed: 11/19/2022]
Abstract
INTRODUCTION The main objective of the study was to assess the apoptotic effect of urine from patients with interstitial cystitis (IC) in cell cultures and to study its value as a diagnostic biomarker for IC. MATERIAL AND METHODS A prospective study was conducted between January 2010 and January 2015 and included 57 patients diagnosed with IC and 50 healthy patients from the Hospital Clinic of Barcelona and the La Paz University Hospital. The urine of these patients was exposed to cell cultures, and its ability to induce apoptosis in the cultures was analysed. Using flow cytometry, we then measured the degree of apoptosis, quantified by the percentage of cells of the cell cycle in phase sub G0. RESULTS The cell cultures exposed to the urine of patients with IC had a sub G1 peak and a G2 phase, which was significantly greater than that of the control group, and a significantly lower percentage in the S phase than the control group. The mean apoptosis values in the urine cultures from patients with IC were significantly higher than those of the control group. Using a value >10% of the apoptosis test as a positive result, we observed a specificity of 96% and a positive predictive value of 92%. CONCLUSIONS The urine of patients with IC exerts an apoptotic effect on tumour cell cultures that is significantly greater than that exerted by the urine of healthy control patients. A≥10% cutoff for the apoptosis test presented very low sensitivity (40%) but had a very high specificity (96%), thereby able to confirm the diagnosis of IC when positive.
Collapse
Affiliation(s)
- C Di Capua-Sacoto
- Departamento de Urología, Hospital La Plana de Villarreal, Castellón, España
| | - A Sanchez-Llopis
- Departamento de Urología, Hospital Universitario General de Castellón, Castellón, España.
| | - E O'Connor
- Departamento de Citómica, Instituto de Investigación Príncipe Felipe, Valencia, España
| | - A Martinez
- Departamento de Citómica, Instituto de Investigación Príncipe Felipe, Valencia, España
| | - J L Ruiz-Cerdá
- Departamento de Urología, Hospital Universitario La Fe, Valencia, España
| |
Collapse
|
38
|
Hofstra LM, Sauvageot N, Albert J, Alexiev I, Garcia F, Struck D, Van de Vijver DAMC, Åsjö B, Beshkov D, Coughlan S, Descamps D, Griskevicius A, Hamouda O, Horban A, Van Kasteren M, Kolupajeva T, Kostrikis LG, Liitsola K, Linka M, Mor O, Nielsen C, Otelea D, Paraskevis D, Paredes R, Poljak M, Puchhammer-Stöckl E, Sönnerborg A, Staneková D, Stanojevic M, Van Laethem K, Zazzi M, Zidovec Lepej S, Boucher CAB, Schmit JC, Wensing AMJ, Puchhammer-Stockl E, Sarcletti M, Schmied B, Geit M, Balluch G, Vandamme AM, Vercauteren J, Derdelinckx I, Sasse A, Bogaert M, Ceunen H, De Roo A, De Wit S, Echahidi F, Fransen K, Goffard JC, Goubau P, Goudeseune E, Yombi JC, Lacor P, Liesnard C, Moutschen M, Pierard D, Rens R, Schrooten Y, Vaira D, Vandekerckhove LPR, Van den Heuvel A, Van Der Gucht B, Van Ranst M, Van Wijngaerden E, Vandercam B, Vekemans M, Verhofstede C, Clumeck N, Van Laethem K, Beshkov D, Alexiev I, Lepej SZ, Begovac J, Kostrikis L, Demetriades I, Kousiappa I, Demetriou V, Hezka J, Linka M, Maly M, Machala L, Nielsen C, Jørgensen LB, Gerstoft J, Mathiesen L, Pedersen C, Nielsen H, Laursen A, Kvinesdal B, Liitsola K, Ristola M, Suni J, Sutinen J, Descamps D, Assoumou L, Castor G, Grude M, Flandre P, Storto A, Hamouda O, Kücherer C, Berg T, Braun P, Poggensee G, Däumer M, Eberle J, Heiken H, Kaiser R, Knechten H, Korn K, Müller H, Neifer S, Schmidt B, Walter H, Gunsenheimer-Bartmeyer B, Harrer T, Paraskevis D, Hatzakis A, Zavitsanou A, Vassilakis A, Lazanas M, Chini M, Lioni A, Sakka V, Kourkounti S, Paparizos V, Antoniadou A, Papadopoulos A, Poulakou G, Katsarolis I, Protopapas K, Chryssos G, Drimis S, Gargalianos P, Xylomenos G, Lourida G, Psichogiou M, Daikos GL, Sipsas NV, Kontos A, Gamaletsou MN, Koratzanis G, Sambatakou H, Mariolis H, Skoutelis A, Papastamopoulos V, Georgiou O, Panagopoulos P, Maltezos E, Coughlan S, De Gascun C, Byrne C, Duffy M, Bergin C, Reidy D, Farrell G, Lambert J, O'Connor E, Rochford A, Low J, Coakely P, O'Dea S, Hall W, Mor O, Levi I, Chemtob D, Grossman Z, Zazzi M, de Luca A, Balotta C, Riva C, Mussini C, Caramma I, Capetti A, Colombo MC, Rossi C, Prati F, Tramuto F, Vitale F, Ciccozzi M, Angarano G, Rezza G, Kolupajeva T, Vasins O, Griskevicius A, Lipnickiene V, Schmit JC, Struck D, Sauvageot N, Hemmer R, Arendt V, Michaux C, Staub T, Sequin-Devaux C, Wensing AMJ, Boucher CAB, van de Vijver DAMC, van Kessel A, van Bentum PHM, Brinkman K, Connell BJ, van der Ende ME, Hoepelman IM, van Kasteren M, Kuipers M, Langebeek N, Richter C, Santegoets RMWJ, Schrijnders-Gudde L, Schuurman R, van de Ven BJM, Åsjö B, Kran AMB, Ormaasen V, Aavitsland P, Horban A, Stanczak JJ, Stanczak GP, Firlag-Burkacka E, Wiercinska-Drapalo A, Jablonowska E, Maolepsza E, Leszczyszyn-Pynka M, Szata W, Camacho R, Palma C, Borges F, Paixão T, Duque V, Araújo F, Otelea D, Paraschiv S, Tudor AM, Cernat R, Chiriac C, Dumitrescu F, Prisecariu LJ, Stanojevic M, Jevtovic D, Salemovic D, Stanekova D, Habekova M, Chabadová Z, Drobkova T, Bukovinova P, Shunnar A, Truska P, Poljak M, Lunar M, Babic D, Tomazic J, Vidmar L, Vovko T, Karner P, Garcia F, Paredes R, Monge S, Moreno S, Del Amo J, Asensi V, Sirvent JL, de Mendoza C, Delgado R, Gutiérrez F, Berenguer J, Garcia-Bujalance S, Stella N, de Los Santos I, Blanco JR, Dalmau D, Rivero M, Segura F, Elías MJP, Alvarez M, Chueca N, Rodríguez-Martín C, Vidal C, Palomares JC, Viciana I, Viciana P, Cordoba J, Aguilera A, Domingo P, Galindo MJ, Miralles C, Del Pozo MA, Ribera E, Iribarren JA, Ruiz L, de la Torre J, Vidal F, Clotet B, Albert J, Heidarian A, Aperia-Peipke K, Axelsson M, Mild M, Karlsson A, Sönnerborg A, Thalme A, Navér L, Bratt G, Karlsson A, Blaxhult A, Gisslén M, Svennerholm B, Bergbrant I, Björkman P, Säll C, Mellgren Å, Lindholm A, Kuylenstierna N, Montelius R, Azimi F, Johansson B, Carlsson M, Johansson E, Ljungberg B, Ekvall H, Strand A, Mäkitalo S, Öberg S, Holmblad P, Höfer M, Holmberg H, Josefson P, Ryding U. Transmission of HIV Drug Resistance and the Predicted Effect on Current First-line Regimens in Europe. Clin Infect Dis 2015; 62:655-663. [PMID: 26620652 PMCID: PMC4741360 DOI: 10.1093/cid/civ963] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 11/06/2015] [Indexed: 11/13/2022] Open
Abstract
Transmitted human immunodeficiency virus drug resistance in Europe is stable at around 8%. The impact of baseline mutation patterns on susceptibility to antiretroviral drugs should be addressed using clinical guidelines. The impact on baseline susceptibility is largest for nonnucleoside reverse transcriptase inhibitors. Background. Numerous studies have shown that baseline drug resistance patterns may influence the outcome of antiretroviral therapy. Therefore, guidelines recommend drug resistance testing to guide the choice of initial regimen. In addition to optimizing individual patient management, these baseline resistance data enable transmitted drug resistance (TDR) to be surveyed for public health purposes. The SPREAD program systematically collects data to gain insight into TDR occurring in Europe since 2001. Methods. Demographic, clinical, and virological data from 4140 antiretroviral-naive human immunodeficiency virus (HIV)–infected individuals from 26 countries who were newly diagnosed between 2008 and 2010 were analyzed. Evidence of TDR was defined using the WHO list for surveillance of drug resistance mutations. Prevalence of TDR was assessed over time by comparing the results to SPREAD data from 2002 to 2007. Baseline susceptibility to antiretroviral drugs was predicted using the Stanford HIVdb program version 7.0. Results. The overall prevalence of TDR did not change significantly over time and was 8.3% (95% confidence interval, 7.2%–9.5%) in 2008–2010. The most frequent indicators of TDR were nucleoside reverse transcriptase inhibitor (NRTI) mutations (4.5%), followed by nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations (2.9%) and protease inhibitor mutations (2.0%). Baseline mutations were most predictive of reduced susceptibility to initial NNRTI-based regimens: 4.5% and 6.5% of patient isolates were predicted to have resistance to regimens containing efavirenz or rilpivirine, respectively, independent of current NRTI backbones. Conclusions. Although TDR was highest for NRTIs, the impact of baseline drug resistance patterns on susceptibility was largest for NNRTIs. The prevalence of TDR assessed by epidemiological surveys does not clearly indicate to what degree susceptibility to different drug classes is affected.
Collapse
Affiliation(s)
- L Marije Hofstra
- Luxembourg Institute of Health, Luxembourg.,Department of Virology, University Medical Center Utrecht, The Netherlands
| | | | - Jan Albert
- Karolinska Institute, Solna.,Karolinska University Hospital, Stockholm, Sweden
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Federico Garcia
- Complejo Hospitalario Universitario de Granada, Instituto de Investigación IBS Granada; on behalf of Cohorte de Adultos de la Red de Investigación en SIDA, Spain
| | | | | | | | - Danail Beshkov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Diane Descamps
- AP-HP Groupe hospitalier Bichat-Claude Bernard, IAME INSERM UMR 1137, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | | | | | | | | | | | | | - Kirsi Liitsola
- Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki, Finland
| | - Marek Linka
- National Reference Laboratory for HIV/AIDS, National Institute of Public Health, Prague, Czech Republic
| | - Orna Mor
- National HIV Reference Laboratory, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | | | - Dan Otelea
- National Institute for Infectious Diseases "Prof. dr. Matei Bals", Bucharest, Romania
| | | | | | - Mario Poljak
- Faculty of Medicine, Slovenian HIV/AIDS Reference Centre, University of Ljubljana, Slovenia
| | | | - Anders Sönnerborg
- Karolinska Institute, Solna.,Karolinska University Hospital, Stockholm, Sweden
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Font A, Grimmond CSB, Kotthaus S, Morguí JA, Stockdale C, O'Connor E, Priestman M, Barratt B. Daytime CO2 urban surface fluxes from airborne measurements, eddy-covariance observations and emissions inventory in Greater London. Environ Pollut 2015; 196:98-106. [PMID: 25463702 DOI: 10.1016/j.envpol.2014.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 10/01/2014] [Accepted: 10/04/2014] [Indexed: 06/04/2023]
Abstract
Airborne measurements within the urban mixing layer (360 m) over Greater London are used to quantify CO(2) emissions at the meso-scale. Daytime CO(2) fluxes, calculated by the Integrative Mass Boundary Layer (IMBL) method, ranged from 46 to 104 μmol CO(2) m(-2) s(-1) for four days in October 2011. The day-to-day variability of IMBL fluxes is at the same order of magnitude as for surface eddy-covariance fluxes observed in central London. Compared to fluxes derived from emissions inventory, the IMBL method gives both lower (by 37%) and higher (by 19%) estimates. The sources of uncertainty of applying the IMBL method in urban areas are discussed and guidance for future studies is given.
Collapse
|
40
|
Doherty M, O'Connor E, Hannon D, O'Reilly A, Grogan L, Hennessy B, Breathnach O, Morris P. Effect of Thyroid Transcription Factor-1 (TTF-1) on Outcome Following Chemotherapy for Advanced Pulmonary Adenocarcinoma. Int J Radiat Oncol Biol Phys 2014. [DOI: 10.1016/j.ijrobp.2014.08.243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
41
|
Doherty M, Keenan L, McHugh J, O'Brien M, O'Reilly A, Reilly C, Hannan E, De Golden PH, O'Connor E, Hannon D, Tierney N, Henderson R, Doyle P, McHugh C, Grogan W, Hennessy B, Morris P, Breathnach O. Patterns of Treatment and Rates of Admission in a Specialist Oncology Clinic. Ann Oncol 2014. [DOI: 10.1093/annonc/mdu353.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
42
|
Fraser S, Cameron M, O'Connor E, Schwickart M, Tanen M, Ware M. Next generation ligand binding assays-review of emerging real-time measurement technologies. AAPS J 2014; 16:914-24. [PMID: 25060773 DOI: 10.1208/s12248-014-9643-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 06/23/2014] [Indexed: 12/20/2022]
Abstract
Over the last few years, numerous ligand binding assay technologies that utilize real-time measurement have been introduced; however, an assemblage and evaluation of these technologies has not previously been published. Herein, we describe six emerging real-time measurement technologies: Maverick™, MX96 SPR™, NanoDLSay™, AMMP®/ViBE®, SoPrano™, and two Lab-on-a-Chip (LoC) microfluidic devices. The development stage gate of these technologies ranges from pre-commercial to commercially available. Due to the novelty, the application and utility of some of the technologies regarding bioanalysis are likely to evolve but it is our hope that this review will provide insight into the direction the development of real-time measurement technologies is moving and the vision of those that are taking us there. Following the technology discussions, a comprehensive summary table is presented.
Collapse
Affiliation(s)
- Stephanie Fraser
- Pfizer Global Research and Development, Groton, Connecticut, USA,
| | | | | | | | | | | |
Collapse
|
43
|
Abstract
Hyperlactataemia and lactic acidosis are commonly encountered during and after cardiac surgery. Perioperative lactate production increases in the myocardium, skeletal muscle, lungs and in the splanchnic circulation during cardiopulmonary bypass. Hyperlactataemia has a bimodal distribution in the perioperative period. An early increase in lactate levels, arising intraoperatively or soon after intensive care unit admission, is a familiar and concerning finding for most clinicians. It is highly suggestive of tissue ischaemia and is associated with a prolonged intensive care unit stay, a prolonged requirement for respiratory and cardiovascular support and increased postoperative mortality. Its presence should prompt a thorough search for potential causes of tissue hypoxia. In contrast, late-onset hyperlactataemia, a less well recognised complication, occurs 4 to 24 hours after completion of surgery and is typically associated with preserved cardiac output and oxygen delivery. Risk factors for late-onset hyperlactataemia include hyperglycaemia, long cardiopulmonary bypass time and elevated endogenous catecholamines. Although patients with this complication may have a longer duration of ventilation and intensive care unit length of stay than those with normolactataemia, an association with increased mortality has not been demonstrated. The discovery of late-onset hyperlactataemia should not delay the postoperative progress of an otherwise stable patient following cardiac surgery.
Collapse
Affiliation(s)
- E O'Connor
- Adult Intensive Care Services, Prince Charles Hospital, Chermside, Queensland, Australia.
| | | |
Collapse
|
44
|
Ott CD, Reisswig C, Schnetter E, O'Connor E, Sperhake U, Löffler F, Diener P, Abdikamalov E, Hawke I, Burrows A. Dynamics and gravitational wave signature of collapsar formation. Phys Rev Lett 2011; 106:161103. [PMID: 21599351 DOI: 10.1103/physrevlett.106.161103] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Indexed: 05/21/2023]
Abstract
We perform 3+1 general relativistic simulations of rotating core collapse in the context of the collapsar model for long gamma-ray bursts. We employ a realistic progenitor, rotation based on results of stellar evolution calculations, and a simplified equation of state. Our simulations track self-consistently collapse, bounce, the postbounce phase, black hole formation, and the subsequent early hyperaccretion phase. We extract gravitational waves from the spacetime curvature and identify a unique gravitational wave signature associated with the early phase of collapsar formation.
Collapse
Affiliation(s)
- C D Ott
- TAPIR, California Institute of Technology, Pasadena, California 91125, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Medrano JV, Marqués-Marí AI, Aguilar CE, Riboldi M, Garrido N, Martínez-Romero A, O'Connor E, Gil-Salom M, Simón C. Comparative analysis of the germ cell markers c-KIT, SSEA-1 and VASA in testicular biopsies from secretory and obstructive azoospermias. Mol Hum Reprod 2010; 16:811-7. [PMID: 20508065 DOI: 10.1093/molehr/gaq044] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Testicular biopsy is needed to confirm diagnosis in azoospermic patients and to recover spermatozoa, if possible. This report aims to quantitatively analyse the germline markers stage-specific embryonic antigen (SSEA-1), c-KIT and VASA in testicular biopsies with distinct azoospermic aetiologies. Twenty-three testicular biopsies were analysed by flow cytometry and RT-qPCR for c-KIT, SSEA-1 and VASA. In all the Sertoli cell-only (SCO) samples, significantly lower VASA mRNA expression and fewer VASA+ cells were found compared with obstructive controls. Maturation arrest (MA) cases showed significant differences only with the non-mosaic SCO samples when compared for VASA mRNA expression and percentage of VASA+ cells, but not with the mosaics. However, the normalized VASA-KIT parameter obtained by subtracting the percentage of c-KIT+ cells from the percentage of VASA+ cells showed significant differences between the MA and all the SCO samples. RT-qPCR consistently found differences for the VASA expression between SCO mosaic and non-mosaic samples. However, by flow cytometry, only VASA-KIT showed significant differences between them. Conversely, the percentage of SSEA-1+ cells revealed no inter-group differences. In conclusion, testicular biopsies display different expression profiles for c-KIT and VASA depending on the azoospermic aetiology. These results can be used as a complementary tool to create new molecular categories for diagnoses in azoospermic patients, particularly useful to discriminate between mosaic and non-mosaic SCO patients.
Collapse
Affiliation(s)
- J V Medrano
- Valencia Stem Cell Bank, Centro de Investigación Príncipe Felipe (CIPF), Valencia 46012, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
46
|
O'Connor E, Freeman TCA, Margrain TH. Sensitivity to retinal and extra-retinal motion signals as a function of age. J Vis 2010. [DOI: 10.1167/8.6.669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
47
|
O'Connor E. Explorations in the social history of medicine. CMAJ 2009. [DOI: 10.1503/cmaj.091706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
|
48
|
Buckland KF, O'Connor E, Murray LA, Hogaboam CM. Toll like receptor-2 modulates both innate and adaptive immune responses during chronic fungal asthma in mice. Inflamm Res 2008; 57:379-87. [PMID: 18787777 DOI: 10.1007/s00011-008-8004-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
OBJECTIVE AND DESIGN We investigated the effect of TLR2 gene deletion in a murine model of chronic fungal asthma. METHODS TLR2 wildtype (TLR2(+/+)) and TLR2 deficient (TLR2(-/-)) mice were sensitized to soluble A. fumigatus antigens and challenged with live A. fumigatus conidia, and the extent of allergic airways disease was analyzed in both groups of mice at 3, 7, 14, and 30 days after conidia. RESULTS At day 7 post-conidia, TLR2(-/-) mice exhibited significantly lower airway hyperresponsiveness, airway inflammation, and whole lung Th2 cytokine levels compared with the TLR2(+ / +) group. TLR2 deletion also significantly reduced mucus cell metaplasia and peribronchial fibrosis at day 30 after conidia. However, fungal material persisted in the TLR2(-/-) group, and at day 30 after conidia TLR2(-/-) mice exhibited enhanced airway neutrophil recruitment and airway hyperresponsiveness. CONCLUSION Thus, during chronic fungal asthma in mice, TLR2 is a major contributor to the maintenance of the adaptive Th2-cytokine driven and anti-fungal innate responses.
Collapse
Affiliation(s)
- K F Buckland
- Immunology Program, Department of Pathology, University of Michigan Medical School, Rm 4057, BSRB, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200, USA
| | | | | | | |
Collapse
|
49
|
Skolnik J, Jayaraman B, Patel D, O'Connor E, Barrett JS, Adamson PC. A clinical trial simulation study of a new pediatric phase I trial methodology: The rolling six design. J Clin Oncol 2007. [DOI: 10.1200/jco.2007.25.18_suppl.9564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
9564 Background: Phase I cancer trials have traditionally used the 3+3 study design in which cohorts of three patients at a time are enrolled. The study is suspended to accrual with every 3rd patient, and again suspended to replace inevaluable patients. As the pediatric phase I starting dose is based on adult phase I safety data, we hypothesized that pediatric study timelines could be shortened without increasing risk using a novel rolling six design, in which up to 6 patients are concurrently enrolled per dose level. Methods: A trial simulation approach comparing the standard 3+3 design to the rolling six design was performed. Discrete time events (accrual/enrollment, evaluation and/or time to dose limiting toxicity (DLT) or inevaluability) with outcome probabilities (DLT/inevaluability) assigned to each subject based on historical data from phase I pediatric oncology trials. The probability of DLT was a function of dose level and varied distributions were used to assign discrete time elements. Metrics for study efficiency (time to complete study, total number of patients required) were determined for each design. Simulated trials and decision rule logic were coded using PC/Windows SAS v9.1. Results: The rolling six design outperformed the 3+3 design for the most relevant metrics. Average (±SD) time to study completion was 373±90 days vs. 431±98 days and the total number of patients required was 20±5 vs. 17±4 for the rolling six vs. 3+3 designs, respectively. There was no difference in the number of DLTs per study (3±1) between designs. Conclusions: The rolling six design is predicted to shorten pediatric phase 1 study timelines and will be tested prospectively in upcoming COG phase I trials. No significant financial relationships to disclose.
Collapse
Affiliation(s)
- J. Skolnik
- Children's Hospital of Philadelphia, Philadelphia, PA; Children's Oncology Group, Arcadia, CA
| | - B. Jayaraman
- Children's Hospital of Philadelphia, Philadelphia, PA; Children's Oncology Group, Arcadia, CA
| | - D. Patel
- Children's Hospital of Philadelphia, Philadelphia, PA; Children's Oncology Group, Arcadia, CA
| | - E. O'Connor
- Children's Hospital of Philadelphia, Philadelphia, PA; Children's Oncology Group, Arcadia, CA
| | - J. S. Barrett
- Children's Hospital of Philadelphia, Philadelphia, PA; Children's Oncology Group, Arcadia, CA
| | - P. C. Adamson
- Children's Hospital of Philadelphia, Philadelphia, PA; Children's Oncology Group, Arcadia, CA
| |
Collapse
|
50
|
O'Connor E, Allen LE, Bradshaw K, Boylan J, Moore AT, Trump D. Congenital stationary night blindness associated with mutations in GRM6 encoding glutamate receptor MGluR6. Br J Ophthalmol 2006; 90:653-4. [PMID: 16622103 PMCID: PMC1857053 DOI: 10.1136/bjo.2005.086678] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|