National trends in utilisation of glucose lowering medicines by older people with diabetes in long-term care facilities

AIMS

To examine national trends in glucose lowering medicine (GLM) use among older people with diabetes in long-term care facilities (LTCFs) during 2009-2019.

METHODS

A repeated cross-sectional study of individuals ≥65 years with diabetes in Australian LTCFs (n = 140,322) was conducted. Annual age-sex standardised prevalence of GLM use and number of defined daily doses (DDDs)/1000 resident-days were estimated. Multivariable Poisson or Negative binomial regression models were used to estimate adjusted rate ratios (aRRs) and 95 % confidence intervals (CIs).

RESULTS

Prevalence of GLM use remained steady between 2009 (63.9%, 95 %CI 63.3-64.4) and 2019 (64.3%, 95 %CI 63.9-64.8) (aRR 1.00, 95 %CI 1.00-1.00). The percentage of residents receiving metformin increased from 36.0% (95 %CI 35.3-36.7) to 43.5% (95 %CI 42.9-44.1) (aRR 1.01, 95 %CI 1.01-1.01). Insulin use also increased from 21.5% (95 %CI 21.0-22.0) to 27.0% (95 %CI 26.5-27.5) (aRR 1.02, 95 %CI 1.02-1.02). Dipeptidyl peptidase-4 inhibitor use increased from 1.0% (95 %CI 0.9-1.1) to 21.1% (95 %CI 20.7-21.5) (aRR 1.24, 95 %CI 1.24-1.25), while sulfonylurea use decreased from 34.4% (95 %CI 33.8-35.1) to 19.3% (95 %CI 18.9-19.7) (aRR 0.93, 95 %CI 0.93-0.94). Similar trends were observed in DDDs/1000 resident days.

CONCLUSIONS

The increasing use of insulin and ongoing use of sulfonylureas suggests a need to implement evidence-based strategies to optimise diabetes care in LTCFs.

Predictors of mortality shortly after entering a long-term care facility

OBJECTIVE

Moving into a long-term care facility (LTCF) requires substantial personal, societal and financial investment. Identifying those at high risk of short-term mortality after LTCF entry can help with care planning and risk factor management. This study aimed to: (i) examine individual-, facility-, medication-, system- and healthcare-related predictors for 90-day mortality at entry into an LTCF and (ii) create risk profiles for this outcome.

DESIGN

Retrospective cohort study using data from the Registry of Senior Australians.

SUBJECTS

Individuals aged ≥ 65 years old with first-time permanent entry into an LTCF in three Australian states between 01 January 2013 and 31 December 2016.

METHODS

A prediction model for 90-day mortality was developed using Cox regression with the purposeful variable selection approach. Individual-, medication-, system- and healthcare-related factors known at entry into an LTCF were examined as predictors. Harrell's C-index assessed the predictive ability of our risk models.

RESULTS

116,192 individuals who entered 1,967 facilities, of which 9.4% (N = 10,910) died within 90 days, were studied. We identified 51 predictors of mortality, five of which were effect modifiers. The strongest predictors included activities of daily living category (hazard ratio [HR] = 5.41, 95% confidence interval [CI] = 4.99-5.88 for high vs low), high level of complex health conditions (HR = 1.67, 95% CI = 1.58-1.77 for high vs low), several medication classes and male sex (HR = 1.59, 95% CI = 1.53-1.65). The model out-of-sample Harrell's C-index was 0.773.

CONCLUSIONS

Our mortality prediction model, which includes several strongly associated factors, can moderately well identify individuals at high risk of mortality upon LTCF entry.

National Trends in Antidepressant Use in Australian Residential Aged Care Facilities (2006-2019)

OBJECTIVES

Antipsychotics have been the focus of reforms for improving the appropriateness of psychotropic medicine use in residential aged care facilities (RACFs). Comprehensive evaluation of antidepressant use in RACFs is required to inform policy and practice initiatives targeting psychotropic medicines. This study examined national trends in antidepressant use among older people living in RACFs from 2006 to 2019.

DESIGN

National repeated cross-sectional study.

SETTING AND PARTICIPANTS

Individuals aged 65 to 105 years who were permanent, long-term (≥100 days) residents of Australian RACFs between January 2006 and December 2019 were included.

METHODS

Annual age- and sex-adjusted antidepressant prevalence rates and defined daily doses (DDDs) supplied per 1000 resident-days from 2006 to 2019 were determined. Age- and sex-adjusted prevalence rate ratios (aRRs) and 95% confidence intervals (CIs) were estimated using Poisson and negative binomial regression models.

RESULTS

A total of 779,659 residents of 3371 RACFs were included (786,227,380 resident-days). Overall, antidepressant use increased from 46.1% (95% CI, 45.9-46.4) in 2006 to 58.5% (95% CI, 58.3-58.8) of residents in 2019 (aRR, 1.02; 95% CI, 1.02-1.02). Mirtazapine use increased from 8.4% (95% CI, 8.2-8.5) to 20.9% (95% CI, 20.7-21.1) from 2006 to 2019 (aRR, 1.07; 95% CI, 1.07-1.07). Antidepressant use increased from 350.3 (95% CI, 347.6-353.1) to 506.0 (95% CI, 502.8-509.3) DDDs/1000 resident-days (aRR, 1.03; 95% CI, 1.03-1.03), with mirtazapine utilization increasing by 6% annually (aRR, 1.06; 95% CI, 1.06-1.06).

CONCLUSIONS AND IMPLICATIONS

This nationwide study identified a substantial increase in antidepressant use among residents of Australian RACFs, largely driven by mirtazapine. With nearly 3 in every 5 residents treated with an antidepressant in 2019, findings highlight potential off-label use and suggest that interventions to optimize care are urgently needed.

Historical Trends and Future Projections of Demand for Permanent Residential Aged Care for Older People in Australia, 2008-2052

OBJECTIVES

To examine the historical trends and predict the future rates and total volumes of permanent residential aged care (PRAC) service utilization in Australia.

DESIGN

A population-based repeated cross-sectional and projection study of non-indigenous older people (≥65 years) accessing PRAC in Australia was conducted.

SETTING AND PARTICIPANTS

Publicly available aged care admissions from the Australian Institute of Health and Welfare and population estimates from the Australian Bureau of Statistics were used.

METHODS

Historical incidence rates (per 1000 people), incidence rate ratios (IRRs) and 95% CIs of PRAC admission from 2008-2009 to 2020-2021 were estimated using negative binomial regression models. The future incidence and prediction intervals (PIs) of PRAC admission between 2021-2022 and 2051-2052 were projected using a generalized additive model-negative binomial regression. All estimates were adjusted or standardized by sex and age.

RESULTS

Between 2008-2009 and 2020-2021, the adjusted admission to PRAC decreased (from 23.6/1000 people to 15.7/1000 people with an IRR = 0.97/year, 95% CI 0.97-0.98). The projected PRAC admission rate will decrease to 12.1/1000 (95%PI 10.8-13.3) by 2037-2038 and 9.0/1000 (95%PI 7.6-10.4) by 2051-2052. The projected volume of PRAC admission will be 73,988 (95%PI 65,960-81,425) at its highest point in 2037-2038 and 64,579 (95%PI 54,258-74,543) in 2051-2052.

CONCLUSIONS AND IMPLICATIONS

The utilization of PRAC has decreased in the past decade, and a predicted decrease in PRAC use in future years is estimated. However, the volume of PRAC utilization will still increase for the next 15 years (until 2037-2038) due to our increasingly older population. These findings can inform service planning of PRAC access in Australia.

Trends in utilisation of ultrasound by older Australians (2010-2019)

BACKGROUND

Older people have increasingly complex healthcare needs, often requiring appropriate access to diagnostic imaging, an essential component of their health and disease management planning. Ultrasound is a safe imaging tool used to diagnose several conditions commonly experienced by older people such as deep vein thrombosis.

PURPOSE

To evaluate the utilisation of major ultrasound services by Australians ≥ 65 years old between 2009- and 2019.

METHODS

This population-based and yearly cross-sectional study of ultrasound utilisation per 1,000 Australians ≥ 65 years old was conducted using publicly available data sources. Overall, examination site and age- and sex-specific incidence rate (IR) of ultrasound per 1,000 people, adjusted incidence rate ratios (IRRs) and 95% confidence intervals (CIs) were calculated using negative binomial regression models.

RESULTS

Over the study period, the crude utilisation of ultrasound increased by 83% in older Australians. Most ultrasound examinations were conducted on extremities (39%) and the chest (21%), with 25% of all ultrasounds investigating the vascular system. More men than women use ultrasounds of the chest (184/1,000 vs 268/1,000 people), particularly echocardiograms (177/1,000 vs 261/1,000 people), and abdomen (88/1,000 vs 92/1,000 people), especially in those ≥ 85 years old. Hip and pelvic ultrasound were used more by women than men (212/1,000 vs 182/1,000 people). There were increases in vascular abdominal (IRR:1.07, 95%CI:1.06-1.08) and extremeties (IRR:1.06, 95%CI:1.05-1.07) ultrasounds over the study period, particularly in ≥ 75 years old men.

CONCLUSIONS

Ultrasound is a common and increasingly used diagnostic tool for conditions commonly experienced by older Australians.

Trends in utilisation of plain X-rays by older Australians (2010-2019)

BACKGROUND

Older Australians are major health service users and early diagnosis is key in the management of their health. Radiological services are an important component of diagnosis and disease management planning in older Australians, but their national utilisation of diagnostic services has never been investigated in Australia.

PURPOSE

This study aims to evaluate the utilisation of major plain X-rays by Australians ≥ 65 years old.

METHODS

A population-based epidemiological evaluation and yearly cross-sectional analyses of X-ray examinations per 1,000 Australians aged ≥ 65 years old between 2009 and 2019 were conducted using publicly available Medicare Benefits Schedule and Australian Bureau of Statistics data sources. Age and sex specific incidence rate (IR) of plain X-rays per 1,000 Australians, adjusted incidence rate ratios (IRR) and 95% confidence intervals (CI) were estimated using a negative binomial regression model.

RESULTS

During the study period, the Australian population over 65 years old increased by 39% while the crude plain X-ray utilisation by this population increased by 63%. Most X-rays were conducted on extremities or the chest. Men used chest radiography more than women, and particularly for lungs, where the incidence increased the most in those ≥ 85 years old. There was an increase in X-rays of extremities and the hip joint between 2009-10 and 2013-14 in people ≥ 85 years old.

CONCLUSION

The utilisation of plain X-rays of the chest, the gastro-intestinal tract and extremities was high and has increased among older Australians between 2009-10 and 2018-19. Plain X-rays remain a commonly used diagnostic tool for conditions affecting the older population.

Predictors of hospitalisations and emergency department presentations shortly after entering a residential aged care facility in Australia: a retrospective cohort study

OBJECTIVES

To: (1) examine the 90-day incidence of unplanned hospitalisation and emergency department (ED) presentations after residential aged care facility (RACF) entry, (2) examine individual-related, facility-related, medication-related, system-related and healthcare-related predictors of these outcomes and (3) create individual risk profiles.

DESIGN

Retrospective cohort study using the Registry of Senior Australians. Fine-Gray models estimated subdistribution HRs and 95% CIs. Harrell's C-index assessed risk models' predictive ability.

SETTING AND PARTICIPANTS

Individuals aged ≥65 years old entering a RACF as permanent residents in three Australian states between 1 January 2013 and 31 December 2016 (N=116 192 individuals in 1967 RACFs).

PREDICTORS EXAMINED

Individual-related, facility-related, medication-related, system and healthcare-related predictors ascertained at assessments or within 90 days, 6 months or 1 year prior to RACF entry.

OUTCOME MEASURES

90-day unplanned hospitalisation and ED presentation post-RACF entry.

RESULTS

The cohort median age was 85 years old (IQR 80-89), 62% (N=71 861) were women, and 50.5% (N=58 714) had dementia. The 90-day incidence of unplanned hospitalisations was 18.0% (N=20 919) and 22.6% (N=26 242) had ED presentations. There were 34 predictors of unplanned hospitalisations and 34 predictors of ED presentations identified, 27 common to both outcomes and 7 were unique to each. The hospitalisation and ED presentation models out-of-sample Harrell's C-index was 0.664 (95% CI 0.657 to 0.672) and 0.655 (95% CI 0.648 to 0.662), respectively. Some common predictors of high risk of unplanned hospitalisation and ED presentations included: being a man, age, delirium history, higher activity of daily living, behavioural and complex care needs, as well as history, number and recency of healthcare use (including hospital, general practitioners attendances), experience of a high sedative load and several medications.

CONCLUSIONS

Within 90 days of RACF entry, 18.0% of individuals had unplanned hospitalisations and 22.6% had ED presentations. Several predictors, including modifiable factors, were identified at the time of care entry. This is an actionable period for targeting individuals at risk of hospitalisations.

Effect of Dementia on Outcomes After Surgically Treated Hip Fracture in Older Adults

BACKGROUND

Hip fractures are associated with increased mortality and functional limitations. However, the effect that dementia has on these outcomes in individuals in aged care settings after fracture is not well established. This study examined the association of dementia with post-hip fracture mortality, permanent residential aged care entry, transition care use, and change in activities of daily living (ADL) needs.

METHODS

A retrospective cohort study using data from the Registry of Senior Australians (2003-2015) was conducted. Individuals with a hip fracture while receiving aged care services were included. Associations of dementia with mortality, risks of transition and permanent care use, and ADL needs progression were estimated using multivariable Cox, Fine-Gray, and logistic regression methods, respectively.

RESULTS

Of 4771 individuals evaluated, 76% were women, the median age was 86 years (IQR 82-90), and 71% already lived in permanent residential aged care at the time of fracture. Within two years of their hip fracture, 50.4% (95% CI 48.9%-51.8%) of individuals died, 16.2% (95% CI 14.2%-18.2%) entered a transition care program, 59.1% (95% CI 56.5%-61.7%) entered permanent residential aged care, and 32% had greater ADL needs. Dementia was associated with higher risk of two-year mortality (HR = 1.19, 95% CI 1.09-1.30), 90-day entry into permanent care (sHR = 1.96, 95% CI 1.60-2.38), and increased likelihood of ADL limitations (OR = 1.36, 95% CI 1.00-1.85). Minor differences were seen in transition care use by dementia status.

CONCLUSION

Dementia is a strong risk factor for mortality after hip fractures in individuals in aged care settings and associated with a high risk of entry into permanent care.

LEVEL OF EVIDENCE

Prognostic level III.

Hospitalisation for lower respiratory viral infections in older people in residential aged care facilities

OBJECTIVE

To quantify incidence, trends and outcomes associated with lower respiratory viral infection (LRVI) hospitalisations in Australian residential aged care facilities (RACFs).

METHODS

A population-based cohort study of residents in RACFs aged ≥65 years from New South Wales (NSW), South Australia (SA) and Victoria (VIC) using data from the Registry of Senior Australians (2013-2016) was conducted. Age- and sex-standardised monthly and yearly LRVI hospitalisation incidences were calculated, and time trends and risk factors were assessed.

RESULTS

Of 268 657 residents included over the study period, 12% had ≥1 LRVI hospitalisation. Average annual incidence/1000 residents was 7.1 [6.9-7.2] in 2013, increasing to 7.8 [7.7-8.1] in 2016. Males, increasing co-morbidity, presence of CHF, respiratory disease and hypertension had a higher incidence of LRVI hospitalisation. In-hospital mortality was 14%. Within 30 days following discharge, 15% died and 8% were readmitted.

CONCLUSION

Prior to COVID-19, incidence of hospitalisation for LRVI in Australia's residential aged care population was increasing and was associated with significant morbidity and mortality.

Predictors of short-term hospitalization and emergency department presentations in aged care

OBJECTIVES

To examine individual, medication, system, and healthcare related predictors of hospitalization and emergency department (ED) presentation within 90 days of entering the aged care sector, and to create risk-profiles associated with these outcomes.

DESIGN AND SETTING

Retrospective population-based cohort study using data from the Registry of Senior Australians.

PARTICIPANTS

Older people (aged 65 and older) with an aged care eligibility assessment in South Australia between January 1, 2013 and May 31, 2016 (N = 22,130).

MEASUREMENTS

Primary outcomes were unplanned hospitalization and ED presentation within 90 days of assessment. Individual, medication, system, and healthcare related predictors of the outcomes at the time of assessment, within 90 days or 1-year prior. Fine-Gray models were used to calculate subdistribution hazard ratios (sHR) and 95% confidence intervals (CI). Harrell's C-index assessed predictive ability.

RESULTS

Four thousand nine-hundred and six (22.2%) individuals were hospitalized and 5028 (22.7%) had an ED presentation within 90 days. Predictors of hospitalization included: being a man (hospitalization sHR = 1.33, 95% CI 1.26-1.42), ≥3 urgent after-hours attendances (hospitalization sHR = 1.21, 95% CI 1.06-1.39), increasing frailty index score (hospitalization sHR = 1.19, 95% CI 1.11-1.28), individuals using glucocorticoids (hospitalization sHR = 1.11, 95% CI 1.02-1.20), sulfonamides (hospitalization sHR = 1.18, 95% CI 1.10-1.27), trimethoprim antibiotics (hospitalization sHR = 1.15, 95% CI 1.03-1.29), unplanned hospitalizations 30 days prior (hospitalization sHR = 1.13, 95% CI 1.04-1.23), and ED presentations 1 year prior (hospitalization sHR = 1.07, 95% CI 1.04-1.10). Similar predictors and hazard estimates were also observed for ED presentations. The hospitalization models out-of-sample predictive ability (C-index = 0.653, 95% CI 0.635-0.670) and ED presentations (C-index = 0.647, 95% CI 0.630-0.663) were moderate.

CONCLUSIONS

One in five individuals with aged care eligibility assessments had unplanned hospitalizations and/or ED presentation within 90 days with several predictors identified at the time of aged care eligibility assessment. This is an actionable period for targeting at-risk individuals to reduce hospitalizations.

An integrated knowledge translation approach to address avoidable rehospitalisations and unplanned admissions for older people in South Australia: implementation and evaluation program plan

Background

Repeated admission to hospital can be stressful for older people and their families and puts additional pressure on the health care system. While there is some evidence about strategies to better integrate care, improve older patients’ experiences at transitions of care, and reduce preventable hospital readmissions, implementing these strategies at scale is challenging. This program of research comprises multiple, complementary research activities with an overall goal of improving the care for older people after discharge from hospital. The program leverages existing large datasets and an established collaborative network of clinicians, consumers, academics, and aged care providers.

Methods

The program of research will take place in South Australia focusing on people aged 65 and over. Three inter-linked research activities will be the following: (1) analyse existing registry data to profile individuals at high risk of emergency department encounters and hospital admissions; (2) evaluate the cost-effectiveness of existing ‘out-of-hospital’ programs provided within the state; and (3) implement a state-wide quality improvement collaborative to tackle key interventions likely to improve older people’s care at points of transitions. The research is underpinned by an integrated approach to knowledge translation, actively engaging a broad range of stakeholders to optimise the relevance and sustainability of the changes that are introduced.

Discussion

This project highlights the uniqueness and potential value of bringing together key stakeholders and using a multi-faceted approach (risk profiling; evaluation framework; implementation and evaluation) for improving health services. The program aims to develop a practical and scalable solution to a challenging health service problem for frail older people and service providers.

The effect of frailty on outcomes of surgically treated hip fractures in older people

BACKGROUND

Hip fractures are associated with mortality, disability, and loss of independence in older adults. While several risk factors associated with poor outcomes following a hip fracture have been identified, the effect of frailty status prior to hip fracture is not well established.

AIM

To examine the associations of frailty with mortality, change in activities of daily living (ADL) limitations, and transition to permanent residential aged care in older people following a hip fracture.

METHODS

A retrospective cohort study was conducted on people aged 65 years and older with a surgically treated hip fracture between 2003 and 2015. Frailty was estimated using a cumulative deficit-based frailty index and categorized into quartiles. Cox multivariable regression, logistic regression, and Fine-Gray multivariable regression models estimated associations of frailty with mortality, ADL limitations, and entry into permanent residential aged care, respectively. Hazard ratios (HR), odds ratios (OR), subdistribution hazard ratios (SHR), and 95% confidence intervals (95%CI) are reported.

RESULTS

Out of 4771 individuals with hip fractures, 75.6% were female and the median age was 86 (interquartile range 82-90) years old. The two-year survival of patients following hip fracture was 43.7% (95%CI 40.9-46.7%) in those in the highest quartile of frailty, compared to 54.4% (95%CI 51.8-57.2%) for those in the lowest quartile (HR = 1.25, 95%CI 1.11-1.41, p < 0.001). No associations between pre-fracture frailty and post-fracture ADL limitations were observed. Additionally, no association of frailty with transition to permanent residential aged care for patients living in the community (n = 1361) was observed (SHR = 0.98, 95%CI 0.81-1.18, p = 1.000).

CONCLUSIONS

Older patients with the highest level of frailty had an increased risk of mortality after hip fracture. Consideration for appropriate clinical interventions, including fall and frailty prevention measures, may be appropriate for this identified group of vulnerable individuals.

Lymphocytic response to tumour and deficient DNA mismatch repair identify subtypes of stage II/III colorectal cancer associated with patient outcomes

OBJECTIVE

Tumour-infiltrating lymphocyte (TIL) response and deficient DNA mismatch repair (dMMR) are determinants of prognosis in colorectal cancer. Although highly correlated, evidence suggests that these are independent predictors of outcome. However, the prognostic significance of combined TIL/MMR classification and how this compares to the major genomic and transcriptomic subtypes remain unclear.

DESIGN

A prospective cohort of 1265 patients with stage II/III cancer was examined for TIL/MMR status and BRAF/KRAS mutations. Consensus molecular subtype (CMS) status was determined for 142 cases. Associations with 5-year disease-free survival (DFS) were evaluated and validated in an independent cohort of 602 patients.

RESULTS

Tumours were categorised into four subtypes based on TIL and MMR status: TIL-low/proficient-MMR (pMMR) (61.3% of cases), TIL-high/pMMR (14.8%), TIL-low/dMMR (8.6%) and TIL-high/dMMR (15.2%). Compared with TIL-high/dMMR tumours with the most favourable prognosis, both TIL-low/dMMR (HR=3.53; 95% CI=1.88 to 6.64; P_multivariate<0.001) and TIL-low/pMMR tumours (HR=2.67; 95% CI=1.47 to 4.84; P_multivariate=0.001) showed poor DFS. Outcomes of patients with TIL-low/dMMR and TIL-low/pMMR tumours were similar. TIL-high/pMMR tumours showed intermediate survival rates. These findings were validated in an independent cohort. TIL/MMR status was a more significant predictor of prognosis than National Comprehensive Cancer Network high-risk features and was a superior predictor of prognosis compared with genomic (dMMR, pMMR/BRAF^wt /KRAS^wt , pMMR/BRAF^mut /KRAS^wt , pMMR/BRAF^wt /KRAS^mut ) and transcriptomic (CMS 1-4) subtypes.

CONCLUSION

TIL/MMR classification identified subtypes of stage II/III colorectal cancer associated with different outcomes. Although dMMR status is generally considered a marker of good prognosis, we found this to be dependent on the presence of TILs. Prognostication based on TIL/MMR subtypes was superior compared with histopathological, genomic and transcriptomic subtypes.

Evaluation of the transferability of survival calculators for stage II/III colon cancer across healthcare systems

Adjuvant! Online Inc (A!O), the Memorial Sloan Kettering Cancer Center (MSKCC), MD Anderson (MDA) and Mayo Clinic (MC) provide calculators to predict survival probabilities for patients with resected early-stage colon cancer, trained on data from United States (US) patient cohorts or patients enrolled in international clinical trials. Limited data exist on the transferability of calculators across healthcare systems. Calculator transferability to Australian community practice was evaluated for 1,401 stage II/III patients. Calibration and discrimination were assessed for overall (OS), cancer-specific (CSS) or recurrence-free survival (RFS). The US patient cohort-based calculators, A!O, MSKCC and MDA, significantly overestimated risks of recurrence and death in Australian patients, with 5-year OS, CSS and RFS prediction differences of -6.5% to -9.9%, -9.1% to -14.4% and - 3.8% to -6.8%, respectively (p < 0.001). Significant heterogeneity in calibration was observed for subgroups by tumor stage and treatment, age, gender, tumor location, ECOG and ASA score. Calibration appeared acceptable for the clinical trial patient-based MC calculator, but restricted tool applicability (stage III patients, ≥12 examined lymph nodes, receiving adjuvant treatment) limited the sample size. Compared to AJCC 7th edition tumor staging, calculators showed improved discrimination for OS, but no improvement for CSS and RFS. In conclusion, deficiencies in calibration limited transferability of US patient cohort-based survival calculators for early-stage colon cancer to the setting of Australian community practice. Our results demonstrate the utility for multi-feature survival calculators to improve OS predictions but highlight the importance for performance assessment of tools prior to implementation in an external health care setting.

MACROD2 Haploinsufficiency Impairs Catalytic Activity of PARP1 and Promotes Chromosome Instability and Growth of Intestinal Tumors

ADP-ribosylation is an important posttranslational protein modification that regulates diverse biological processes, controlled by dedicated transferases and hydrolases. Here, we show that frequent deletions (∼30%) of the MACROD2 mono-ADP-ribosylhydrolase locus in human colorectal cancer cause impaired PARP1 transferase activity in a gene dosage-dependent manner. MACROD2 haploinsufficiency alters DNA repair and sensitivity to DNA damage and results in chromosome instability. Heterozygous and homozygous depletion of Macrod2 enhances intestinal tumorigenesis in Apc^Min/+ mice and the growth of human colorectal cancer xenografts. MACROD2 deletion in sporadic colorectal cancer is associated with the extent of chromosome instability, independent of clinical parameters and other known genetic drivers. We conclude that MACROD2 acts as a haploinsufficient tumor suppressor, with loss of function promoting chromosome instability, thereby driving cancer evolution.Significance: Chromosome instability (CIN) is a hallmark of cancer. We identify MACROD2 deletion as a cause of CIN in human colorectal cancer. MACROD2 loss causes repression of PARP1 activity, impairing DNA repair. MACROD2 haploinsufficiency promotes CIN and intestinal tumor growth. Our results reveal MACROD2 as a major caretaker tumor suppressor gene. Cancer Discov; 8(8); 988-1005. ©2018 AACR.See related commentary by Jin and Burkard, p. 921This article is highlighted in the In This Issue feature, p. 899.

Relative telomere lengths in tumor and normal mucosa are related to disease progression and chromosome instability profiles in colorectal cancer

Telomeric dysfunction is linked to colorectal cancer (CRC) initiation. However, the relationship of normal tissue and tumor telomere lengths with CRC progression, molecular features and prognosis is unclear. Here, we measured relative telomere length (RTL) by real-time quantitative PCR in 90 adenomas (aRTL), 419 stage I-IV CRCs (cRTL) and adjacent normal mucosa (nRTL). Age-adjusted RTL was analyzed against germline variants in telomere biology genes, chromosome instability (CIN), microsatellite instability (MSI), CpG island methylator phenotype (CIMP), TP53, KRAS, BRAF mutations and clinical outcomes. In 509 adenoma or CRC patients, nRTL decreased with advancing age. Female gender, proximal location and the TERT rs2736100 G allele were independently associated with longer age-adjusted nRTL. Adenomas and carcinomas exhibited telomere shortening in 79% and 67% and lengthening in 7% and 15% of cases. Age-adjusted nRTL and cRTL were independently associated with tumor stage, decreasing from adenoma to stage III and leveling out or increasing from stage III to IV, respectively. Cancer MSI, CIMP, TP53, KRAS and BRAF status were not related to nRTL or cRTL. Near-tetraploid CRCs exhibited significantly longer cRTLs than CIN- and aneuploidy CRCs, while cRTL was significantly shorter in CRCs with larger numbers of chromosome breaks. Age-adjusted nRTL, cRTL or cRTL:nRTL ratios were not associated with disease-free or overall survival in stage II/III CRC. Taken together, our data show that both normal mucosa and tumor RTL are independently associated with CRC progression, and highlight divergent associations of CRC telomere length with tumor CIN profiles.

Colorectal Cancer Cell Line Proteomes Are Representative of Primary Tumors and Predict Drug Sensitivity

BACKGROUND AND AIMS

Proteomics holds promise for individualizing cancer treatment. We analyzed to what extent the proteomic landscape of human colorectal cancer (CRC) is maintained in established CRC cell lines and the utility of proteomics for predicting therapeutic responses.

METHODS

Proteomic and transcriptomic analyses were performed on 44 CRC cell lines, compared against primary CRCs (n=95) and normal tissues (n=60), and integrated with genomic and drug sensitivity data.

RESULTS

Cell lines mirrored the proteomic aberrations of primary tumors, in particular for intrinsic programs. Tumor relationships of protein expression with DNA copy number aberrations and signatures of post-transcriptional regulation were recapitulated in cell lines. The 5 proteomic subtypes previously identified in tumors were represented among cell lines. Nonetheless, systematic differences between cell line and tumor proteomes were apparent, attributable to stroma, extrinsic signaling, and growth conditions. Contribution of tumor stroma obscured signatures of DNA mismatch repair identified in cell lines with a hypermutation phenotype. Global proteomic data showed improved utility for predicting both known drug-target relationships and overall drug sensitivity as compared with genomic or transcriptomic measurements. Inhibition of targetable proteins associated with drug responses further identified corresponding synergistic or antagonistic drug combinations. Our data provide evidence for CRC proteomic subtype-specific drug responses.

CONCLUSIONS

Proteomes of established CRC cell line are representative of primary tumors. Proteomic data tend to exhibit improved prediction of drug sensitivity as compared with genomic and transcriptomic profiles. Our integrative proteogenomic analysis highlights the potential of proteome profiling to inform personalized cancer medicine.

The transcription cofactor c-JUN mediates phenotype switching and BRAF inhibitor resistance in melanoma

Most patients with BRAF-mutant metastatic melanoma display remarkable but incomplete and short-lived responses to inhibitors of the BRAF kinase or the mitogen-activated protein kinase kinase (MEK), collectively BRAF/MEK inhibitors. We found that inherent resistance to these agents in BRAF(V600)-mutant melanoma cell lines was associated with high abundance of c-JUN and characteristics of a mesenchymal-like phenotype. Early drug adaptation in drug-sensitive cell lines grown in culture or as xenografts, and in patient samples during therapy, was consistently characterized by down-regulation of SPROUTY4 (a negative feedback regulator of receptor tyrosine kinases and the BRAF-MEK signaling pathway), increased expression of JUN and reduced expression of LEF1. This coincided with a switch in phenotype that resembled an epithelial-mesenchymal transition (EMT). In cultured cells, these BRAF inhibitor-induced changes were reversed upon removal of the drug. Knockdown of SPROUTY4 was sufficient to increase the abundance of c-JUN in the absence of drug treatment. Overexpressing c-JUN in drug-naïve melanoma cells induced similar EMT-like phenotypic changes to BRAF inhibitor treatment, whereas knocking down JUN abrogated the BRAF inhibitor-induced early adaptive changes associated with resistance and enhanced cell death. Combining the BRAF inhibitor with an inhibitor of c-JUN amino-terminal kinase (JNK) reduced c-JUN phosphorylation, decreased cell migration, and increased cell death in melanoma cells. Gene expression data from a panel of melanoma cell lines and a patient cohort showed that JUN expression correlated with a mesenchymal gene signature, implicating c-JUN as a key mediator of the mesenchymal-like phenotype associated with drug resistance.

Impact of regular aspirin use on overall and cancer-specific survival in patients with colorectal cancer harboring a PIK3CA mutation

BACKGROUND

Recent data have suggested that regular aspirin use improves overall and cancer-specific survival in the subset of colorectal cancer (CRC) patients harboring PIK3CA mutations. However, the number of PIK3CA-mutated CRC patients examined in these studies was modest. Our collaborative study aims to validate the association between regular aspirin use and survival in patients with PIK3CA-mutated CRC.

PATIENTS AND METHODS

Patients with PIK3CA-mutated CRC were identified at Moffitt Cancer Center (MCC) in the United States and Royal Melbourne Hospital (RMH) in Australia. Prospective clinicopathological data and survival data were available. At MCC, PIK3CA mutations were identified by targeted exome sequencing using the Illumina GAIIx Next Generation Sequencing platform. At RMH, Sanger sequencing was utilized. Multivariate survival analyses were conducted using Cox logistic regression.

RESULTS

From a cohort of 1487 CRC patients, 185 patients harbored a PIK3CA mutation. Median age of patients with PIK3CA-mutated tumors was 72 years (range: 34-92) and median follow up was 54 months. Forty-nine (26%) patients used aspirin regularly. Regular aspirin use was not associated with improved overall survival (multivariate HR 0.96, p = 0.86). There was a trend towards improved cancer-specific survival (multivariate HR 0.60, p = 0.14), but this was not significant.

CONCLUSIONS

Despite examining a large number of patients, we did not confirm that regular aspirin use was associated with statistically significant improvements in survival in PIK3CA-mutated CRC patients. Prospective evaluation of this relationship is warranted.

Colorectal cancer cell lines are representative models of the main molecular subtypes of primary cancer

Human colorectal cancer cell lines are used widely to investigate tumor biology, experimental therapy, and biomarkers. However, to what extent these established cell lines represent and maintain the genetic diversity of primary cancers is uncertain. In this study, we profiled 70 colorectal cancer cell lines for mutations and DNA copy number by whole-exome sequencing and SNP microarray analyses, respectively. Gene expression was defined using RNA-Seq. Cell line data were compared with those published for primary colorectal cancers in The Cancer Genome Atlas. Notably, we found that exome mutation and DNA copy-number spectra in colorectal cancer cell lines closely resembled those seen in primary colorectal tumors. Similarities included the presence of two hypermutation phenotypes, as defined by signatures for defective DNA mismatch repair and DNA polymerase ε proofreading deficiency, along with concordant mutation profiles in the broadly altered WNT, MAPK, PI3K, TGFβ, and p53 pathways. Furthermore, we documented mutations enriched in genes involved in chromatin remodeling (ARID1A, CHD6, and SRCAP) and histone methylation or acetylation (ASH1L, EP300, EP400, MLL2, MLL3, PRDM2, and TRRAP). Chromosomal instability was prevalent in nonhypermutated cases, with similar patterns of chromosomal gains and losses. Although paired cell lines derived from the same tumor exhibited considerable mutation and DNA copy-number differences, in silico simulations suggest that these differences mainly reflected a preexisting heterogeneity in the tumor cells. In conclusion, our results establish that human colorectal cancer lines are representative of the main subtypes of primary tumors at the genomic level, further validating their utility as tools to investigate colorectal cancer biology and drug responses.

Regular aspirin (ASA) use and survival in patients with PIK3CA-mutated metastatic colorectal cancer (CRC)

386

Background: Recent data has demonstrated that regular ASA use improves overall and cancer-specific survival in the subset of CRC patients harboring PIK3CA mutations. However, as this series only analyzed 15 PIK3CA mutant CRC patients with metastatic disease at diagnosis, it remains uncertain whether the survival benefit associated with regular ASA use extends to patients with metastatic disease. We combined data from two large academic institutions to explore the association between regular ASA use and survival in metastatic CRC. Methods: Patients with PIK3CA mutated CRC were identified at Moffitt Cancer Center (MCC) in Tampa, FL and Royal Melbourne Hospital (RMH) in Australia. Prospective clinicopathological data (including age, sex, site of disease) and survival data were available. At MCC, PIK3CA mutations were identified by exome sequencing using an Illumina Next Generation Sequencing platform with 50-100X coverage. At RMH, Sanger sequencing was used to identify PIK3CA mutations. Survival analyses were conducted using Cox regression. Results: We identified 187 CRC patients who harbored a PIK3CA mutation. Median age was 72 years and median follow up was 48 months. 49 (26%) patients used ASA regularly. 47 (25%) patients had metastatic disease at diagnosis. In univariate analyses, regular ASA use was not associated with improved overall survival (HR 0.87, p = 0.60), although there was a trend towards improved cancer-specific survival (HR 0.48, p = 0.06). In patients with stage-II or stage-III disease, regular ASA use did not improve overall, cancer-specific or recurrence-free survival. However, in stage-IV patients, regular ASA use was significantly associated with improved overall (HR 0.35, p = 0.04) and cancer-specific (HR 0.28, p = 0.02) survival in a univariate analysis. Conclusions: Our study demonstrates that in patients with metastatic CRC harboring a PIK3CA mutation, regular ASA use is associated with a significant overall and cancer-specific survival advantage. However, we were not able to confirm the survival advantage across all stages. To our knowledge, our study is the largest to examine ASA use in PIK3CA mutated CRC.

Survival in stage II/III colorectal cancer is independently predicted by chromosomal and microsatellite instability, but not by specific driver mutations

OBJECTIVES

Microsatellite instability (MSI) is an established marker of good prognosis in colorectal cancer (CRC). Chromosomal instability (CIN) is strongly negatively associated with MSI and has been shown to be a marker of poor prognosis in a small number of studies. However, a substantial group of "double-negative" (MSI-/CIN-) CRCs exists. The prognosis of these patients is unclear. Furthermore, MSI and CIN are each associated with specific molecular changes, such as mutations in KRAS and BRAF, that have been associated with prognosis. It is not known which of MSI, CIN, and the specific gene mutations are primary predictors of survival.

METHODS

We evaluated the prognostic value (disease-free survival, DFS) of CIN, MSI, mutations in KRAS, NRAS, BRAF, PIK3CA, FBXW7, and TP53, and chromosome 18q loss-of-heterozygosity (LOH) in 822 patients from the VICTOR trial of stage II/III CRC. We followed up promising associations in an Australian community-based cohort (N=375).

RESULTS

In the VICTOR patients, no specific mutation was associated with DFS, but individually MSI and CIN showed significant associations after adjusting for stage, age, gender, tumor location, and therapy. A combined analysis of the VICTOR and community-based cohorts showed that MSI and CIN were independent predictors of DFS (for MSI, hazard ratio (HR)=0.58, 95% confidence interval (CI) 0.36-0.93, and P=0.021; for CIN, HR=1.54, 95% CI 1.14-2.08, and P=0.005), and joint CIN/MSI testing significantly improved the prognostic prediction of MSI alone (P=0.028). Higher levels of CIN were monotonically associated with progressively poorer DFS, and a semi-quantitative measure of CIN was a better predictor of outcome than a simple CIN+/- variable. All measures of CIN predicted DFS better than the recently described Watanabe LOH ratio.

CONCLUSIONS

MSI and CIN are independent predictors of DFS for stage II/III CRC. Prognostic molecular tests for CRC relapse should currently use MSI and a quantitative measure of CIN rather than specific gene mutations.

Different APC genotypes in proximal and distal sporadic colorectal cancers suggest distinct WNT/β-catenin signalling thresholds for tumourigenesis

Biallelic protein-truncating mutations in the adenomatous polyposis coli (APC) gene are prevalent in sporadic colorectal cancer (CRC). Mutations may not be fully inactivating, instead producing WNT/β-catenin signalling levels 'just-right' for tumourigenesis. However, the spectrum of optimal APC genotypes accounting for both hits, and the influence of clinicopathological features on genotype selection remain undefined. We analysed 630 sporadic CRCs for APC mutations and loss of heterozygosity (LOH) using sequencing and single-nucleotide polymorphism microarrays, respectively. Truncating APC mutations and/or LOH were detected in 75% of CRCs. Most truncating mutations occurred within a mutation cluster region (MCR; codons 1282-1581) leaving 1-3 intact 20 amino-acid repeats (20AARs) and abolishing all Ser-Ala-Met-Pro (SAMP) repeats. Cancers commonly had one MCR mutation plus either LOH or another mutation 5' to the MCR. LOH was associated with mutations leaving 1 intact 20AAR. MCR mutations leaving 1 vs 2-3 intact 20AARs were associated with 5' mutations disrupting or leaving intact the armadillo-repeat domain, respectively. Cancers with three hits had an over-representation of mutations upstream of codon 184, in the alternatively spliced region of exon 9, and 3' to the MCR. Microsatellite unstable cancers showed hyper-mutation at MCR mono- and di-nucleotide repeats, leaving 2-3 intact 20AARs. Proximal and distal cancers exhibited different preferred APC genotypes, leaving a total of 2 or 3 and 0 to 2 intact 20AARs, respectively. In conclusion, APC genotypes in sporadic CRCs demonstrate 'fine-tuned' interdependence of hits by type and location, consistent with selection for particular residual levels of WNT/β-catenin signalling, with different 'optimal' thresholds for proximal and distal cancers.

Aspirin use and survival outcomes in patients (pts) with PIK3CA mutant colorectal cancer (CRC)

3598

Background: Aspirin has an established role in preventing CRC. Recent data suggests aspirin use may also benefit a subset of pts diagnosed with CRC. In one series, the authors identified PIK3CA mutations as a potential predictive biomarker for aspirin use, reporting that PIK3CA mutant CRC pts receiving aspirin had superior cancer specific survival (CSS) compared to those not receiving aspirin (HR 0.18, p<0.001), whereas in pts with wildtype PIK3CA, aspirin had no survival impact. Our study aims to confirm the survival benefit associated with aspirin use in pts with PIK3CA mutant CRC. Methods: A cohort of CRC pts with PIK3CA mutations (Sanger sequencing) was identified. Prospectively collected clinicopathological, treatment and outcome data was available. Aspirin use was confirmed by chart review. CSS and overall survival (OS) analyses were conducted using Cox proportional hazards in univariate and multivariate settings. Recurrence free survival (RFS) analyses were limited to early stage CRC pts (Stage A-C). Statistical differences in 5-year CSS (5YS) rates were calculated using Fisher’s exact test. Results: From a cohort of 1,019 CRC pts with known PIK3CA mutation status, 121 (12%) harbored PIK3CA mutations. Of these, 112 (92%) had aspirin usage data available: 27 (24%) pts used aspirin, 85 (76%) did not. In the aspirin group, there were 22 (81%) early stage and 5 (19%) metastatic CRC pts; in the no-aspirin group, there were 59 (69%) early stage and 26 (31%) metastatic CRC pts. In univariate analyses, aspirin use was not associated with superior CSS (HR 0.57, p=0.21), OS (HR 0.83, p=0.57), or RFS (HR 0.72, p=0.57). In multivariate analyses, aspirin use was not associated with improved OS (HR 1.07, p=0.86), CSS (HR 1.04, p=0.94) or RFS (HR 0.54, p=0.34). In 69 (62%) pts with mature follow-up, there was a trend towards superior 5YS for aspirin users (69% v 42%, p=0.09), but this may reflect imbalances in stage at diagnosis. Conclusions: Our study was unable to confirm the recently reported survival benefit associated with aspirin use in pts with PIK3CA mutant CRC. Given the small numbers of pts, a modest survival benefit associated with aspirin use cannot be excluded. Analyses in an expanded cohort of early stage pts are underway.

PIK3CA and PTEN gene and exon mutation-specific clinicopathologic and molecular associations in colorectal cancer

PURPOSE

PIK3CA and PTEN mutations are prevalent in colorectal cancer and potential markers of response to mitogen-activated protein/extracellular signal-regulated kinase inhibitors and anti-EGF receptor antibody therapy. Relationships between phosphoinositide 3-kinase (PI3K) pathway mutation, clinicopathologic characteristics, molecular features, and prognosis remain controversial.

EXPERIMENTAL DESIGN

A total of 1,093 stage I-IV colorectal cancers were screened for PIK3CA (exons 9 and 20), KRAS (codons 12-13), BRAF (codon 600) mutations, and microsatellite instability (MSI). PTEN (exons 3-8) and CpG island methylator phenotype (CIMP) status were determined in 744 and 489 cases. PIK3CA data were integrated with 17 previous reports (n = 5,594).

RESULTS

PIK3CA and PTEN mutations were identified in 11.9% and 5.8% of colorectal cancers. PTEN mutation was associated with proximal tumors, mucinous histology, MSI-high (MSI-H), CIMP-high (CIMP-H), and BRAF mutation (P < 0.02). PIK3CA mutation was related to older age, proximal tumors, mucinous histology, and KRAS mutation (P < 0.04). In integrated cohort analysis, PIK3CA exon 9 and 20 mutations were overrepresented in proximal, CIMP-low (CIMP-L), and KRAS-mutated cancers (P ≤ 0.011). Comparing PIK3CA exonic mutants, exon 20 mutation was associated with MSI-H, CIMP-H, and BRAF mutation, and exon 9 mutation was associated with KRAS mutation (P ≤ 0.027). Disease-free survival for stage II/III colorectal cancers did not differ by PI3K pathway status.

CONCLUSION

PI3K pathway mutation is prominent in proximal colon cancers, with PIK3CA exon 20 and PTEN mutations associated with features of the sessile-serrated pathway (MSI-H/CIMP-H/BRAF(mut)), and PIK3CA exon 9 (and to a lesser extent exon 20) mutation associated with features of the traditional serrated pathway (CIMP-L/KRAS(mut)) of tumorigenesis. Our data highlight the PI3K pathway as a therapeutic target in distinct colorectal cancer subtypes.

Quantitative threefold allele-specific PCR (QuanTAS-PCR) for highly sensitive JAK2 V617F mutant allele detection

Background

The JAK2 V617F mutation is the most frequent somatic change in myeloproliferative neoplasms, making it an important tumour-specific marker for diagnostic purposes and for the detection of minimal residual disease. Sensitive quantitative assays are required for both applications, particularly for the monitoring of minimal residual disease, which requires not only high sensitivity but also very high specificity.

Methods

We developed a highly sensitive probe-free quantitative mutant-allele detection method, Quantitative Threefold Allele-Specific PCR (QuanTAS-PCR), that is performed in a closed-tube system, thus eliminating the manipulation of PCR products. QuantTAS-PCR uses a threefold approach to ensure allele-specific amplification of the mutant sequence: (i) a mutant allele-specific primer, (ii) a 3′dideoxy blocker to suppress false-positive amplification from the wild-type template and (iii) a PCR specificity enhancer, also to suppress false-positive amplification from the wild-type template. Mutant alleles were quantified relative to exon 9 of JAK2.

Results

We showed that the addition of the 3′dideoxy blocker suppressed but did not eliminate false-positive amplification from the wild-type template. However, the addition of the PCR specificity enhancer near eliminated false-positive amplification from the wild-type allele. Further discrimination between true and false positives was enabled by using the quantification cycle (Cq) value of a single mutant template as a cut-off point, thus enabling robust distinction between true and false positives. As 10,000 JAK2 templates were used per replicate, the assay had a sensitivity of 1/10^-4 per replicate. Greater sensitivity could be reached by increasing the number of replicates analysed. Variation in replicates when low mutant-allele templates were present necessitated the use of a statistics-based approach to estimate the load of mutant JAK2 copies. QuanTAS-PCR showed comparable quantitative results when validated against a commercial assay.

Conclusions

QuanTAS-PCR is a simple, cost-efficient, closed-tube method for JAK2 V617F mutation quantification that can detect very low levels of the mutant allele, thus enabling analysis of minimal residual disease. The approach can be extended to the detection of other recurrent single nucleotide somatic changes in cancer.

Impact of diabetes on clinicopathologic and genetic features of colorectal cancer formation

426

Background: Diabetes mellitus is reported to increase the risk of colorectal cancer (CRC) development and has been associated with poor tumour-specific outcomes. Here we assessed the impact of diabetes on the clinicopathologic features and tumour mutation profiles of CRC. Methods: Analysis of a prospective series of patients diagnosed with CRC between January 2000 and December 2010. Fresh-frozen and formalin-fixed, paraffin-embedded tumour specimens were retrieved and genomic DNA extracted for analysis of microsatellite instability (MSI), CpG island methylator phenotype (CIMP) and mutations in BRAF, KRAS, PIK3CA, TP53 and APC genes. Propensity-score matching and logistic regression were used to estimate the association of diabetes with tumour molecular profile, controlling for age, sex, tumour stage, body mass index (BMI), smoking and socio-economic status. Results: Of the 1,348 patients assessed, 288 (21.4%) had a history of diabetes mellitus. Compared to patients without diabetes, diabetics were more likely to be older (age > 70 yrs: 56% vs 47%, p = 0.006), male (57% vs 47%, p = 0.002) and have a higher BMI (BMI > 25: 82% vs 65%, p < 0.0001). There were no statistically significant differences in tumour site, differentiation or lymphovascular invasion. Propensity scores were used to match 260 diabetic patients to an equal number of nondiabetics. In multivariate regression analysis, diabetes was associated with BRAF-mutated tumours (OR 2.81, 95% CI 1.16-7.59, p = 0.029) and showed a trend towards MSI-high tumours (OR 1.54, 95% CI 0.91-2.63, p = 0.110). Results are shown in the Table. Survival analysis is planned. Conclusions: CRC patients with diabetes are older, more likely male and have higher BMI than non-diabetics. In this preliminary analysis, an association between diabetes and BRAF-mutant CRC was found, and may explain reported differences in outcomes for diabetic CRC patients. [Table: see text]

SMAD2, SMAD3 and SMAD4 mutations in colorectal cancer

Activation of the canonical TGF-β signaling pathway provides growth inhibitory signals in the normal intestinal epithelium. Colorectal cancers (CRCs) frequently harbor somatic mutations in the pathway members TGFBR2 and SMAD4, but to what extent mutations in SMAD2 or SMAD3 contribute to tumorigenesis is unclear. A cohort of 744 primary CRCs and 36 CRC cell lines were sequenced for SMAD4, SMAD2, and SMAD3 and analyzed for allelic loss by single-nucleotide polymorphism (SNP) microarray analysis. Mutation spectra were compared between the genes, the pathogenicity of mutations was assessed, and relationships with clinicopathologic features were examined. The prevalence of SMAD4, SMAD2, and SMAD3 mutations in sporadic CRCs was 8.6% (64 of 744), 3.4% (25 of 744), and 4.3% (32 of 744), respectively. A significant overrepresentation of two genetic hits was detected for SMAD4 and SMAD3, consistent with these genes acting as tumor suppressors. SMAD4 mutations were associated with mucinous histology. The mutation spectra of SMAD2 and SMAD3 were highly similar to that of SMAD4, both in mutation type and location within the encoded proteins. In silico analyses suggested the majority of the mutations were pathogenic, with most missense changes predicted to reduce protein stability or hinder SMAD complex formation. The latter altered interface residues or disrupted the phosphorylation-regulated Ser-Ser-X-Ser motifs within SMAD2 and SMAD3. Functional analyses of selected mutations showed reductions in SMAD3 transcriptional activity and SMAD2-SMAD4 complex formation. Joint biallelic hits in SMAD2 and SMAD3 were overrepresented and mutually exclusive to SMAD4 mutation, underlining the critical roles of these three proteins within the TGF-β signaling pathway.

Clinicopathologic and molecular associations of PIK3CA and PTEN mutation in colorectal cancer

3623

Background: The phosphatidylinositol 3-kinase (PI3K) signaling pathway has been implicated in the development of colorectal cancer (CRC), however a systematic analysis of pathway members and their association with clinical, pathological and other molecular features has been lacking. Methods: We determined the prevalence of PIK3CA (exons 9, 20) mutations in a large cohort (n=1092) of community-based patients (pts) with stage I-IV CRCs. A subset (n=744, 68%) were also tested for mutation in PTEN (exons 3,4,5,6,7,8), PTEN LOH and CIMP. All tumors were characterised for MSI, KRAS and BRAF mutations, and annotated for clinico-pathologic features and patient outcomes in a prospectively-recorded database. Detected novel PIK3CA exon-specific correlates were further explored in a combined analysis integrating the data of other published cohorts (total n=3677). Results: PIK3CA mutations occurred in 11.6% of primary tumors and were associated with older pt age (p=0.009), proximal site (p<0.001), lower lymphovascular invasion (p=0.018) and KRAS mutation (p<0.001), but not with gender, tumor stage or differentiation. Direct comparison of PIK3CA exon 9 and 20 mutations in the combined analysis (mixed effect logistic regression) finds both at increased frequency in KRAS-mutant tumors (p=0.098 for difference); however PIK3CA exon 20 mutations uniquely correlated with BRAF mutation (p=0.002 for difference), MSI (p<0.001) and CIMP-high status (p=0.031). PTEN mutations were present in 5.8% of tumors and associated with proximal site (p=0.013), mucinous histology (p=0.013), MSI (p<0.001), CIMP-high (p<0.001), and BRAF mutation (p<0.001). There was a trend toward mutation of both PIK3CA and PTEN and strong selection for two hits to PTEN (mut/mut or mut/LOH, p<0.001). In our cohort neither PIK3CA or PTEN mutation were associated with pt survival outcomes. Conclusions: In CRC, common mutations in the PI3K signaling pathway are universally associated with proximal site, however display unique gene- and exon-specific associations with tumor histology, MSI, CIMP, KRAS and BRAF mutation. These need to be considered when exploring targeted therapeutic options for pts with CRC.

Optimizing targeted therapeutic development: analysis of a colorectal cancer patient population with the BRAF(V600E) mutation

BRAF(V600E) mutations are found in 10% of colorectal cancers (CRCs). The low frequency of this mutation therefore makes it a challenging target for drug development, unless subsets of patients with higher rates of BRAF(V600E) can be defined. Knowledge of the concordance between primary-metastasis pairs and the impact of BRAF(V600E) on outcome would also assist in optimal drug development. We selected primary CRCs from 525 patients (stages I-IV) evenly matched for age (<70 and ≥70), gender and tumor location (right, left and rectum), and 81 primary-metastasis pairs. BRAF(V600E), KRAS mutation and microsatellite instability (MSI) were determined and correlated with clinical features and patient outcomes. In multivariate analyses, increasing patient age (p = 0.04), female gender (p = 0.0005) and right-sided tumor location (p < 0.0001) were independently associated with BRAF(V600E). The prevalence of BRAF(V600E) was considerably higher in older (age > 70) females with KRAS wild-type right-sided colon cancers (50%) compared to the unselected cohort (10%). BRAF(V600E) was associated with inferior overall survival in metastatic CRC (HR = 2.02; 95% CI 1.26-3.26), particularly evident in patients treated with chemotherapy, and is independent of MSI status. BRAF status was concordant in all primary tumors and matched metastases (79 wild-type pairs and two mutant pairs). Clinicopathological and molecular features can identify CRC patients with a higher prevalence of BRAF(V600E). Patients with BRAF(V600E) wild-type primary tumor do not appear to acquire the mutation in their metastases, and BRAF(V600E) is associated with poorer outcomes in metastatic patients. Our findings are timely and will help inform the rational development of BRAF(V600E) inhibitors in CRC.

KRAS mutation is associated with lung metastasis in patients with curatively resected colorectal cancer

PURPOSE

Oncogene mutations contribute to colorectal cancer development. We searched for differences in oncogene mutation profiles between colorectal cancer metastases from different sites and evaluated these as markers for site of relapse.

EXPERIMENTAL DESIGN

One hundred colorectal cancer metastases were screened for mutations in 19 oncogenes, and further 61 metastases and 87 matched primary cancers were analyzed for genes with identified mutations. Mutation prevalence was compared between (a) metastases from liver (n = 65), lung (n = 50), and brain (n = 46), (b) metastases and matched primary cancers, and (c) metastases and an independent cohort of primary cancers (n = 604). Mutations differing between metastasis sites were evaluated as markers for site of relapse in 859 patients from the VICTOR trial.

RESULTS

In colorectal cancer metastases, mutations were detected in 4 of 19 oncogenes: BRAF (3.1%), KRAS (48.4%), NRAS (6.2%), and PIK3CA (16.1%). KRAS mutation prevalence was significantly higher in lung (62.0%) and brain (56.5%) than in liver metastases (32.3%; P = 0.003). Mutation status was highly concordant between primary cancer and metastasis from the same individual. Compared with independent primary cancers, KRAS mutations were more common in lung and brain metastases (P < 0.005), but similar in liver metastases. Correspondingly, KRAS mutation was associated with lung relapse (HR = 2.1; 95% CI, 1.2 to 3.5, P = 0.007) but not liver relapse in patients from the VICTOR trial.

CONCLUSIONS

KRAS mutation seems to be associated with metastasis in specific sites, lung and brain, in colorectal cancer patients. Our data highlight the potential of somatic mutations for informing surveillance strategies.

Nonsense mediated decay resistant mutations are a source of expressed mutant proteins in colon cancer cell lines with microsatellite instability

Background

Frameshift mutations in microsatellite instability high (MSI-High) colorectal cancers are a potential source of targetable neo-antigens. Many nonsense transcripts are subject to rapid degradation due to nonsense-mediated decay (NMD), but nonsense transcripts with a cMS in the last exon or near the last exon-exon junction have intrinsic resistance to nonsense-mediated decay (NMD). NMD-resistant transcripts are therefore a likely source of expressed mutant proteins in MSI-High tumours.

Methods

Using antibodies to the conserved N-termini of predicted mutant proteins, we analysed MSI-High colorectal cancer cell lines for examples of naturally expressed mutant proteins arising from frameshift mutations in coding microsatellites (cMS) by immunoprecipitation and Western Blot experiments. Detected mutant protein bands from NMD-resistant transcripts were further validated by gene-specific short-interfering RNA (siRNA) knockdown. A genome-wide search was performed to identify cMS-containing genes likely to generate NMD-resistant transcripts that could encode for antigenic expressed mutant proteins in MSI-High colon cancers. These genes were screened for cMS mutations in the MSI-High colon cancer cell lines.

Results

Mutant protein bands of expected molecular weight were detected in mutated MSI-High cell lines for NMD-resistant transcripts (CREBBP, EP300, TTK), but not NMD-sensitive transcripts (BAX, CASP5, MSH3). Expression of the mutant CREBBP and EP300 proteins was confirmed by siRNA knockdown. Five cMS-bearing genes identified from the genome-wide search and without existing mutation data (SFRS12IP1, MED8, ASXL1, FBXL3 and RGS12) were found to be mutated in at least 5 of 11 (45%) of the MSI-High cell lines tested.

Conclusion

NMD-resistant transcripts can give rise to expressed mutant proteins in MSI-High colon cancer cells. If commonly expressed in primary MSI-High colon cancers, MSI-derived mutant proteins could be useful as cancer specific immunological targets in a vaccine targeting MSI-High colonic tumours.

Structural elements and allosteric mechanisms governing regulation and catalysis of CSK-family kinases and their inhibition of Src-family kinases

C-terminal Src kinase (CSK) and CSK-homologous kinase (CHK) are endogenous inhibitors constraining the activity of the oncogenic Src-family kinases (SFKs) in cells. Both kinases suppress SFKs by selectively phosphorylating their consensus C-terminal regulatory tyrosine. In addition to phosphorylation, CHK can suppress SFKs by a unique non-catalytic inhibitory mechanism that involves tight binding of CHK to SFKs to form stable complexes. In this review, we discuss how allosteric regulators, phosphorylation, and inter-domain interactions interplay to govern the activity of CSK and CHK and their ability to inhibit SFKs. In particular, based upon the published results of structural and biochemical analysis of CSK and CHK, we attempt to chart the allosteric networks in CSK and CHK that govern their catalysis and ability to inhibit SFKs. We also discuss how the published three-dimensional structure of CSK complexed with an SFK member sheds light on the structural basis of substrate recognition by protein kinases.

A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data

We describe a statistical method for the characterization of genomic aberrations in single nucleotide polymorphism microarray data acquired from cancer genomes. Our approach allows us to model the joint effect of polyploidy, normal DNA contamination and intra-tumour heterogeneity within a single unified Bayesian framework. We demonstrate the efficacy of our method on numerous datasets including laboratory generated mixtures of normal-cancer cell lines and real primary tumours.

Metastasis-Associated Gene Expression Changes Predict Poor Outcomes in Patients with Dukes Stage B and C Colorectal Cancer

PURPOSE: Colorectal cancer prognosis is currently predicted from pathologic staging, providing limited discrimination for Dukes stage B and C disease. Additional markers for outcome are required to help guide therapy selection for individual patients. EXPERIMENTAL DESIGN: A multisite single-platform microarray study was done on 553 colorectal cancers. Gene expression changes were identified between stage A and D tumors (three training sets) and assessed as a prognosis signature in stage B and C tumors (independent test and external validation sets). RESULTS: One hundred twenty-eight genes showed reproducible expression changes between three sets of stage A and D cancers. Using consistent genes, stage B and C cancers clustered into two groups resembling early-stage and metastatic tumors. A Prediction Analysis of Microarray algorithm was developed to classify individual intermediate-stage cancers into stage A-like/good prognosis or stage D-like/poor prognosis types. For stage B patients, the treatment adjusted hazard ratio for 6-year recurrence in individuals with stage D-like cancers was 10.3 (95% confidence interval, 1.3-80.0; P = 0.011). For stage C patients, the adjusted hazard ratio was 2.9 (95% confidence interval, 1.1-7.6; P = 0.016). Similar results were obtained for an external set of stage B and C patients. The prognosis signature was enriched for downregulated immune response genes and upregulated cell signaling and extracellular matrix genes. Accordingly, sparse tumor infiltration with mononuclear chronic inflammatory cells was associated with poor outcome in independent patients. CONCLUSIONS: Metastasis-associated gene expression changes can be used to refine traditional outcome prediction, providing a rational approach for tailoring treatments to subsets of patients. (Clin Cancer Res 2009;15(24):7642-51).

Additivity in the analysis and design of HIV protease inhibitors

We explore the applicability of an additive treatment of substituent effects to the analysis and design of HIV protease inhibitors. Affinity data for a set of inhibitors with a common chemical framework were analyzed to provide estimates of the free energy contribution of each chemical substituent. These estimates were then used to design new inhibitors whose high affinities were confirmed by synthesis and experimental testing. Derivations of additive models by least-squares and ridge-regression methods were found to yield statistically similar results. The additivity approach was also compared with standard molecular descriptor-based QSAR; the latter was not found to provide superior predictions. Crystallographic studies of HIV protease-inhibitor complexes help explain the perhaps surprisingly high degree of substituent additivity in this system, and allow some of the additivity coefficients to be rationalized on a structural basis.

DNA copy-number alterations underlie gene expression differences between microsatellite stable and unstable colorectal cancers

PURPOSE

About 15% of colorectal cancers harbor microsatellite instability (MSI). MSI-associated gene expression changes have been identified in colorectal cancers, but little overlap exists between signatures hindering an assessment of overall consistency. Little is known about the causes and downstream effects of differential gene expression.

EXPERIMENTAL DESIGN

DNA microarray data on 89 MSI and 140 microsatellite-stable (MSS) colorectal cancers from this study and 58 MSI and 77 MSS cases from three published reports were randomly divided into test and training sets. MSI-associated gene expression changes were assessed for cross-study consistency using training samples and validated as MSI classifier using test samples. Differences in biological pathways were identified by functional category analysis. Causation of differential gene expression was investigated by comparison to DNA copy-number data.

RESULTS

MSI-associated gene expression changes in colorectal cancers were found to be highly consistent across multiple studies of primary tumors and cancer cell lines from patients of different ethnicities (P < 0.001). Clustering based on consistent changes separated additional test cases by MSI status, and classification of individual samples predicted MSI status with a sensitivity of 96% and specificity of 85%. Genes associated with immune response were up-regulated in MSI cancers, whereas genes associated with cell-cell adhesion, ion binding, and regulation of metabolism were down-regulated. Differential gene expression was shown to reflect systematic differences in DNA copy-number aberrations between MSI and MSS tumors (P < 0.001).

CONCLUSIONS

Our results show cross-study consistency of MSI-associated gene expression changes in colorectal cancers. DNA copy-number alterations partly cause the differences in gene expression between MSI and MSS cancers.

BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities

BindingDB () is a publicly accessible database currently containing ∼20 000 experimentally determined binding affinities of protein–ligand complexes, for 110 protein targets including isoforms and mutational variants, and ∼11 000 small molecule ligands. The data are extracted from the scientific literature, data collection focusing on proteins that are drug-targets or candidate drug-targets and for which structural data are present in the Protein Data Bank. The BindingDB website supports a range of query types, including searches by chemical structure, substructure and similarity; protein sequence; ligand and protein names; affinity ranges and molecular weight. Data sets generated by BindingDB queries can be downloaded in the form of annotated SDfiles for further analysis, or used as the basis for virtual screening of a compound database uploaded by the user. The data in BindingDB are linked both to structural data in the PDB via PDB IDs and chemical and sequence searches, and to the literature in PubMed via PubMed IDs.

Virtual screening of molecular databases using a support vector machine

The Support Vector Machine (SVM) is an algorithm that derives a model used for the classification of data into two categories and which has good generalization properties. This study applies the SVM algorithm to the problem of virtual screening for molecules with a desired activity. In contrast to typical applications of the SVM, we emphasize not classification but enrichment of actives by using a modified version of the standard SVM function to rank molecules. The method employs a simple and novel criterion for picking molecular descriptors and uses cross-validation to select SVM parameters. The resulting method is more effective at enriching for active compounds with novel chemistries than binary fingerprint-based methods such as binary kernel discrimination.

CR1/CR2 Interactions Modulate the Functions of the Cell Surface Epidermal Growth Factor Receptor

Recent crystallographic data on the isolated extracellular domain of the epidermal growth factor receptor (EGFR) have suggested a model for its activation by ligand. We have tested this model in the context of the full-length EGFR displayed at the cell surface, by introducing mutations in two regions (CR1 and CR2) of the extracellular domain thought to be critical for regulation of receptor activation. Mutations in the CR1 and CR2 domains have opposing effects on ligand binding affinity, receptor dimerization, tyrosine kinase activation, and signaling competence. Tyr(246) is a critical residue in the CR1 loop, which is implicated in the positioning and stabilization of the receptor dimer interface after ligand binding; mutations of Tyr(246) impair or abolish receptor function. Mutations in CR2, which weaken the interaction that restricts the receptor to the tethered (inactive) state, enhance responsiveness to EGF by increasing affinity for the ligand. However, weakening of the CR1/CR2 interaction does not result in spontaneous activation of the receptors' kinase. We have used an antibody (mAb 806), which recognizes a transition state of the EGF receptor between the negatively constrained, tethered state and the fully active back-to-back dimer conformation, to follow conformational changes in the wild-type and mutant EGF receptors after ligand binding. Our results suggest that EGFR on the cell surface can be untethered, but this form is inactive; thus, untethering of the receptor is not sufficient for activation, and ligand binding is essential for the correct positioning of the two receptor subunits to achieve kinase activation.

Epidermal growth factor receptor: mechanisms of activation and signalling

The epidermal growth factor (EGF) receptor (EGFR) is one of four homologous transmembrane proteins that mediate the actions of a family of growth factors including EGF, transforming growth factor-alpha, and the neuregulins. We review the structure and function of the EGFR, from ligand binding to the initiation of intracellular signalling pathways that lead to changes in the biochemical state of the cell. The recent crystal structures of different domains from several members of the EGFR family have challenged our concepts of these processes.

The crystal structure of a truncated ErbB2 ectodomain reveals an active conformation, poised to interact with other ErbB receptors

ErbB2 does not bind ligand, yet appears to be the major signaling partner for other ErbB receptors by forming heteromeric complexes with ErbB1, ErbB3, or ErbB4. The crystal structure of residues 1-509 of ErbB2 at 2.5 A resolution reveals an activated conformation similar to that of the EGFR when complexed with ligand and very different from that seen in the unactivated forms of ErbB3 or EGFR. The structure explains the inability of ErbB2 to bind known ligands and suggests why ErbB2 fails to form homodimers. Together, the data suggest a model in which ErbB2 is already in the activated conformation and ready to interact with other ligand-activated ErbB receptors.

Crystal structure of a truncated epidermal growth factor receptor extracellular domain bound to transforming growth factor alpha

We report the crystal structure, at 2.5 A resolution, of a truncated human EGFR ectodomain bound to TGFalpha. TGFalpha interacts with both L1 and L2 domains of EGFR, making many main chain contacts with L1 and interacting with L2 via key conserved residues. The results indicate how EGFR family members can bind a family of highly variable ligands. In the 2:2 TGFalpha:sEGFR501 complex, each ligand interacts with only one receptor molecule. There are two types of dimers in the asymmetric unit: a head-to-head dimer involving contacts between the L1 and L2 domains and a back-to-back dimer dominated by interactions between the CR1 domains of each receptor. Based on sequence conservation, buried surface area, and mutagenesis experiments, the back-to-back dimer is favored to be biologically relevant.

The K252a derivatives, inhibitors for the PAK/MLK kinase family selectively block the growth of RAS transformants

BACKGROUND

Oncogenic RAS mutants such as v-Ha-RAS activate members of Rac/CDC42-dependent kinases (PAKs) and appear to contribute to the development of more than 30% of all human cancers. PAK1 activation is essential for oncogenic RAS transformation, and several chemical compounds that inhibit Tyr kinases essential for the RAS-induced activation of PAK1 strongly suppress RAS transformation either in cell culture or in vivo (nude mice). Although we have developed a cell-permeable PAK-specific peptide inhibitor called WR-PA18, so far no chemical (metabolically stable) compound has been developed that directly inhibits PAK1 in a highly selective manner. Thus, we have explored such a PAK1 inhibitor(s) among synthetic derivatives of an adenosine triphosphate antagonist.

RESULTS

From the naturally occurring adenosine triphosphate antagonist K252a, we have developed two bulky derivatives, called CEP-1347 and KT D606 (a K252a dimer), which selectively inhibit PAKs or mixed-lineage kinases both in vitro and in cell culture and convert v-Ha-RAS-transformed NIH 3T3 cells to flat fibroblasts similar to the parental normal cells. Furthermore, these two K252a analogues suppress the proliferation of v-Ha-RAS transformants, but not the normal cells.

CONCLUSION

These bulky adenosine triphosphate antagonists derived from K252a or related indolocarbazole compounds such as staurosporine would be potentially useful for the treatment of RAS/ PAK1-induced cancers, once their anti-PAK1 activity is significantly potentiated by a few additional chemical modifications at the sugar ring suggested in this paper.