5-Hydroxymethylcytosine in Cell-Free DNA Predicts Immunotherapy Response in Lung Cancer.

Immune checkpoint inhibitors (ICIs) drastically improve therapeutic outcomes for lung cancer, but accurately predicting individual patient responses to ICIs remains a challenge. We performed the genome-wide profiling of 5-hydroxymethylcytosine (5hmC) in 85 plasma cell-free DNA (cfDNA) samples from lung cancer patients and developed a 5hmC signature that was significantly associated with progression-free survival (PFS). We built a 5hmC predictive model to quantify the 5hmC level and validated the model in the validation, test, and control sets. Low weighted predictive scores (wp-scores) were significantly associated with a longer PFS compared to high wp-scores in the validation [median 7.6 versus 1.8 months; p = 0.0012; hazard ratio (HR) 0.12; 95% confidence interval (CI), 0.03-0.54] and test (median 14.9 versus 3.3 months; p = 0.00074; HR 0.10; 95% CI, 0.02-0.50) sets. Objective response rates in patients with a low or high wp-score were 75.0% (95% CI, 42.8-94.5%) versus 0.0% (95% CI, 0.0-60.2%) in the validation set (p = 0.019) and 80.0% (95% CI, 44.4-97.5%) versus 0.0% (95% CI, 0.0-36.9%) in the test set (p = 0.0011). The wp-scores were also significantly associated with PFS in patients receiving single-agent ICI treatment (p < 0.05). In addition, the 5hmC predictive signature demonstrated superior predictive capability to tumor programmed death-ligand 1 and specificity to ICI treatment response prediction. Moreover, we identified novel 5hmC-associated genes and signaling pathways integral to ICI treatment response in lung cancer. This study provides proof-of-concept evidence that the cfDNA 5hmC signature is a robust biomarker for predicting ICI treatment response in lung cancer.

A Phase 2 Study of In Situ Oncolytic Virus Therapy and Stereotactic Body Radiation Therapy Followed by Pembrolizumab in Metastatic Non-Small Cell Lung Cancer.

PURPOSE: A phase 2 study of stereotactic body radiation therapy (SBRT) and in situ oncolytic virus therapy in metastatic non-small cell lung cancer (mNSCLC) followed by pembrolizumab (STOMP) was designed to explore the dual approach in enhancing single pembrolizumab with ADV/HSV-tk plus valacyclovir gene therapy and SBRT in mNSCLC. METHODS AND MATERIALS: STOMP is a single-arm, open-label phase 2 study. Patients with mNSCLC received intratumoral injections of ADV/HSV-tk (5 × 1011 vp) and SBRT (30 Gy in 5 fractions) followed by pembrolizumab 200 mg IV every 3 weeks until disease progression or intolerable toxicity. The primary endpoint was overall response rate (ORR) (complete response [CR] and partial response [PR]). Secondary endpoints included clinical benefit rate (CBR) (CR, PR and stable disease [SD]), progression-free survival (PFS), overall survival (OS), and safety. RESULTS: 28 patients were enrolled, of whom 27 were evaluated for response. The ORR was 33.3%, including 2 CR (7.4%) and 7 PR (25.9%). CBR was 70.4%. Six of eight (75.0%) patients who were immune checkpoint inhibitor (ICI) refractory derived clinical benefits. Responders had durable responses with median PFS, and OS not reached. The entire cohort had a median PFS of 7.4 months (95% CI, 5.1-9.6 months), and median OS of 18.1 months (95% CI, 15.4-20.9 months). The combination was well tolerated, with grade 3 or higher toxicity in 6 (21.4%) patients. CONCLUSIONS: The dual approach of in situ ADV/HSV-tk plus valacyclovir gene therapy and SBRT as a chemotherapy-sparing strategy to enhance the antitumor effect of pembrolizumab is a well-tolerated encouraging treatment in patients with mNSCLC.

Treatment at Twilight: An Analysis of Therapy Patterns and Outcomes in Adults 80 Years and Older With Advanced or Metastatic NSCLC.

Introduction: The aim of this study is to evaluate treatment patterns, survival outcomes, and factors influencing systemic treatment decisions in adults 80 years and older with NSCLC. Methods: This was a retrospective National Cancer Database study evaluating outcomes in adults aged 80 years and older with advanced NSCLC. Patients were analyzed on the basis of systemic therapy, including none, chemotherapy or immunotherapy (IO) alone, and chemotherapy plus IO (chemotherapy + IO). Median overall survival (OS) was compared using Kaplan-Meier methodology. Hazard ratio with 95% confidence interval (CI) was used to assess differences in outcomes, and OR with 95% CI was used to assess factors contributing to systemic therapy provision. Results: Patients 80 years and older (OR = 1.135 [95% CI: 1.127-1.142], p = 0.000), females (OR = 1.129 [95% CI: 1.085-1.175], p < 0.001), blacks (OR = 1.272 [95% CI: 1.179-1.372], p < 0.001), non-Hispanic whites (OR = 1.210 [95% CI: 1.075-1.362], p = 0.002), and those with increasing Charlson-Deyo Comorbidity Index score (p < 0.001) were less likely to receive systemic therapy. Median OS for no therapy, IO alone, chemotherapy alone, and chemotherapy plus IO was 2.63 (95% CI: 2.57-2.69), 10.68 (95% CI: 9.96-11.39), 12.35 (95% CI: 11.98-12.72), and 14.03 (95% CI: 13.87-14.88) months, respectively. In chemotherapy alone, mean OS was 1.12 months (95% CI: 0.55-1.70) (p < 0.001) longer with multiagent versus single agent. There was no difference between IO plus single agent versus IO plus multiagent chemotherapy (0.67 mo [95% CI -1.18 to 2.54], p = 1.00). Conclusions: Age, comorbidities, patient race, and sex affected systemic therapy provision. Multiagent chemotherapy and chemotherapy plus IO significantly improved survival; with the latter, survival was similar with IO plus single or multiagent chemotherapy.

Long-term outcomes in patients with Burkitt lymphoma older than 65 years: an analysis of the Texas Cancer Registry.

Burkitt lymphoma (BL) is an extremely aggressive but curable subtype of non-Hodgkin lymphoma. While younger patients have excellent outcomes in response to aggressive chemoimmunotherapy, the rarity of this disease in older patients and limitations caused by age, comorbidities, and performance status may negate survival advantages. This analysis assessed outcomes of older adults with BL through data provided by the Texas Cancer Registry (TCR). Patients ≥65 years with BL were assessed. Patients were dichotomized into 1997-2007 and 2008-2018. Median overall survival (OS) and disease-specific survival (DSS) were assessed using Kaplan-Meier methodology, and covariates including age, race, sex, stage, primary site, and poverty index were analyzed using Pearson Chi-squared analysis. Odds ratio (OR) with 95% confidence intervals (CI) was used to assess factors contributing to patients not offered systemic therapy. P value <0.05 was considered statistically significant. Non-BL mortality events were also categorized. There were 325 adults, 167 in 1997-2007 and 158 in 2008-2018; 106 (63.5%) and 121 (76.6%) received systemic therapy, a trend that increased with time (p = 0.010). Median OS for 1997-2007 and 2008-2018 was 5 months (95% CI 2.469, 7.531) and 9 months (95% CI 0.000, 19.154) (p = 0.013), and DSS was 72 months (95% CI 56.397, 87.603) (p = 0.604) and not reached, respectively. For patients that received systemic therapy, median OS was 8 months (95% CI 1.278, 14.722) and 26 months (95% CI 5.824, 46.176) (p = 0.072), respectively, and DSS was 79 months (95% CI: 56.416, 101.584) and not reached, respectively (p = 0.607). Age ≥75 years (HR 1.39 [95% CI 1.078, 1.791], p = 0.011) and non-Hispanic whites (HR 1.407 [95% CI 1.024, 1.935], p = 0.035) had poorer outcomes, and patients at the 20-100% poverty index (OR 0.387 [95% CI 0.163, 0.921], p = 0.032) and increasing age at diagnosis (OR 0.947 [95% CI 0.913, 0.983], p = 0.004) were less likely to receive systemic therapy. Of 259 (79.7%) deaths, 62 (23.9%) were non-BL deaths, and 6 (9.6%) of these were from a second cancer. This two-decade analysis of older Texas patients with BL indicates a significant improvement in OS over time. Although patients were more likely to receive systemic therapy over time, treatment disparities existed in patients residing in poverty-stricken regions of Texas and in advancing age. These statewide findings reflect an unmet national need to find a systemic therapeutic strategy that can be tolerated by and augment outcomes in the growing elderly population.

Long term outcomes in older patients with primary central nervous system lymphoma: an analysis of the Texas Cancer Registry.

Primary central nervous system lymphoma (PCNSL) is an aggressive subtype of non-Hodgkin lymphoma that carries a poor prognosis in the elderly. The aim of this study is to investigate treatment patterns and survival trends in patients ≥ 65 years with PCNSL through data provided by the Texas Cancer Registry. Adults ≥ 65 years diagnosed with PCNSL and followed between 1995-2017 were identified and separated into three eras: 1995-2003, 2004-2012, and 2013-2017. Baseline covariates compared included patient demographics and treatments administered. Pearson's chi-squared test and Cox proportional hazard models compared covariates; overall survival (OS) and disease-specific survival (DSS) were assessed via Kaplan-Meier methodology. There were 375 patients; 104 (27.7%) in 1995-2003, 146 (38.9%) in 2004-2012, and 125 (33.3%) in 2013-2017. There were 50 (48.1%), 55 (37.7%), and 31 (24.8%) in 1995-2003, 2004-2012, and 2013-2017, respectively, that did not receive treatment. At last follow up, 101 (97.1%), 130 (89.0%), and 94 (75.2%) in each era died, of which 89 (85.6%), 112 (76.7%), and 70 (56.0%) were attributed to PCNSL. Median OS per era was eight (95% confidence interval [CI] 5.06-10.93), six (95% CI, 2.30-9.69), and five months (95% CI, 2.26-7.73) (p = 0.638). DSS per era was nine (95% CI: 0.00, 26.53), 10 (95% CI: 5.14, 14.86), and 19 (95% CI, 0.00-45.49) (p = 0.931) months. Spinal cord as primary disease site (HR: 0.668 [95% CI, 0.45-0.99], p = 0.049), and chemotherapy (HR 0.532 [95% CI, 0.42-0.673], p = < 0.001) or chemotherapy + radiation (HR, 0.233 [95% CI, 0.11-0.48] p < 0.001) had better outcomes compared to no therapy or radiation therapy alone. Survival in older patients ≥ 65 with PCNSL has not improved per our analysis of the TCR from 1995-2017 despite increasing trends of treatment utilization. Strategies to augment recruitment of older individuals in trials are needed in order to determine who would derive treatment benefit and minimize treatment toxicities.

A Phase 2 Trial of Enhancing Immune Checkpoint Blockade by Stereotactic Radiation and In Situ Virus Gene Therapy in Metastatic Triple-Negative Breast Cancer.

PURPOSE: A Phase 2 trial of stereotactic radiotherapy and in situ cytotoxic virus therapy in patients with metastatic triple-negative breast cancer (mTNBC) followed by pembrolizumab (STOMP) was designed to evaluate dual approach of enhancing single-agent immune checkpoint blockade with adenovirus-mediated expression of herpes-simplex-virus thymidine-kinase (ADV/HSV-tk) plus valacyclovir gene therapy and stereotactic body radiotherapy (SBRT) in patients with mTNBC. PATIENTS AND METHODS: In this single-arm, open-label Phase 2 trial, patients with mTNBC were treated with ADV/HSV-tk [5 × 1011 virus particles (vp)] intratumoral injection, followed by SBRT to the injected tumor site, then pembrolizumab (200 mg, every 3 weeks). The primary endpoint was clinical benefit rate [CBR; complete response (CR), partial response (PR), or stable disease (SD) ≥ 24 weeks per RECIST version1.1 at non-irradiated site]. Secondary endpoints included duration on treatment (DoT), overall survival (OS), and safety. Exploratory endpoints included immune response to treatment assessed by correlative tissue and blood-based biomarkers. RESULTS: Twenty-eight patients were enrolled and treated. CBR was seen in 6 patients (21.4%), including 2 CR (7.1%), 1 PR (3.6%), and 3 SD (10.7%). Patients with clinical benefit had durable responses, with median DoT of 9.6 months and OS of 14.7 months. The median OS was 6.6 months in the total population. The combination was well tolerated. Correlative studies with Cytometry by Time of Flight (CyTOF) and imaging mass cytometry (IMC) revealed a significant increase of CD8 T cells in responders and of myeloid cells in non-responders. CONCLUSIONS: The median OS increased by more than 2-fold in patients with clinical benefit. The therapy is a well-tolerated treatment in heavily pretreated patients with mTNBC. Early detection of increased effector and effector memory CD8 T cells and myeloids correlate with response and non-response, respectively.

Photocrosslinking Activity-Based Probes for Ubiquitin RING E3 Ligases.

Activity-based protein profiling is an invaluable technique for studying enzyme biology and facilitating the development of therapeutics. Ubiquitin E3 ligases (E3s) are one of the largest enzyme families and regulate a host of (patho)physiological processes. The largest subtype are the RING E3s of which there are >600 members. RING E3s have adaptor-like activity that can be subject to diverse regulatory mechanisms and have become attractive drug targets. Activity-based probes (ABPs) for measuring RING E3 activity do not exist. Here we re-engineer ubiquitin-charged E2 conjugating enzymes to produce photocrosslinking ABPs. We demonstrate activity-dependent profiling of two divergent cancer-associated RING E3s, RNF4 and c-Cbl, in response to their native activation signals. We also demonstrate profiling of endogenous RING E3 ligase activation in response to epidermal growth factor (EGF) stimulation. These photocrosslinking ABPs should advance E3 ligase research and the development of selective modulators against this important class of enzymes.

Personalized medicine could transform healthcare.

Personalized medicine (PM) is about tailoring a treatment as individualized as the disease. The approach relies on identifying genetic, epigenomic, and clinical information that allows the breakthroughs in our understanding of how a person's unique genomic portfolio makes them vulnerable to certain diseases. PM approach is a complete extension of traditional approach (One-Size-Fits-All) to increasing our ability to predict which medical treatments will be safe and effective for individual patient, and which ones will not be, based on the patient's unique genetic profile. Implementation of PM has the potential to reduce financial and time expenditure, and increase quality of life and life extension of patients. Knowledge of PM facilitates earlier disease detection via enhanced use of existing biomarkers and detection of early genomic and epigenomic events in disease development, particularly carcinogenesis. The PM approach predominantly focuses on preventative medicine and favours taking pro-active actions rather than just reactive. This approach delays or prevents the need to apply more severe treatments which are usually less tolerated and with increased quality of life and financial considerations. Increasing healthcare costs have placed additional pressure on government funded healthcare systems globally, especially regarding end of life care. PM may increase the effectiveness of existing treatments and negate the inherent problems associated with non-PM approaches. PM is a young but rapidly expanding field of healthcare where a physician can select a treatment based on a patient's genetic profile that may not only minimize harmful side effects and guarantee a more successful result, but can be less cost effective compared with a 'trial-and-error' approach to disease treatment. The less efficient non-PM ('trial-and-error') approach, which can lead to drug toxicity, severe side effects, reactive treatment and misdiagnosis continue to contribute to increasing healthcare costs. Increased patient stratification will allow for the enhanced application of PM and pro-active treatment regimens, resulting in reduced costs and quality of life enhancement.

Outcomes following routine antithrombin III replacement during neonatal extracorporeal membrane oxygenation.

BACKGROUND: We sought to examine the effect of routine antithrombin III (AT3) infusion on hemorrhagic and thrombotic complications, blood product utilization, and circuit lifespan in neonatal extracorporeal membrane oxygenation (ECMO). METHODS: We performed a retrospective cohort study of 162 infants placed on ECMO for hypoxic respiratory failure. Infants requiring ECMO for primary cardiac support were excluded. Demographic data, time on ECMO, blood product usage, coagulation profile, and complications were compared between 90 control patients and 72 patients treated with AT3. RESULTS: Infants receiving AT3 during ECMO had less thrombotic and similar bleeding complications as compared to infants receiving standard anticoagulation therapy. Total blood product infusion during ECMO was decreased (54.7±20.1 vs. 67.4±34.9mL/kg per day, p=0.001) in infants receiving AT3 during ECMO. Tighter control of activated clotting time and higher serum heparin anti-Xa levels were observed in the AT3 cohort during the first days of ECMO support. 1st ECMO circuit lifespan did not differ between groups. CONCLUSIONS: Routine administration of AT3 in neonates receiving ECMO therapy was associated with tighter control of anticoagulation and a reduction in thrombotic events without increasing unwanted bleeding. However, circuit lifespan was unaffected. LEVEL OF EVIDENCE: Level III.

TIMP-1 overexpression in lung carcinoma enhances tumor kinetics and angiogenesis in brain metastasis.

Tissue inhibitors of matrix metalloproteinase (TIMP) orchestrate many biologic activities, including inhibition of matrix metalloproteinase activity, activation of pro-matrix metalloproteinases, and regulation of cell proliferation, angiogenesis, and apoptosis induction. Tissue inhibitors of matrix metalloproteinase can play a protective role during tumor invasion and metastasis, but elevated TIMP messenger RNA levels have also been associated with aggressive cancers and poor clinical outcome. We examined the potential roles of TIMP-1 in H2009 lung adenocarcinoma cells and in cells transfected with a human TIMP-1-overexpressing vector (HB-6 and HB-1). Tumors resulting from the implantation of parental cell lines and transfected HB-1 cells into the brains of nude mice had a typical carcinoma profile, but human TIMP-1-overexpressing tumors showed enhanced tumor kinetics and focally more infiltrative features; vessel density assessed with anti-CD31 immunohistochemistry was also greater within HB-1 tumor implants. Similar effects on HB-6 and HB-1 cells versus parental cell lines and empty vector clones were observed in endothelial cell assays. Anchorage-independent growth and invasion through Matrigel were also increased in TIMP-1-overexpressing cells. Together, these results indicate tumor-promoting functions of TIMP-1 through alterations in angiogenesis, increased tumorigenicity, and invasive behavior. Although matrix metalloproteinase inhibition has been the traditionally identified function of TIMP-1, matrix metalloproteinase-independent interactions may contribute to the growth of metastatic carcinomas in the brain.

Developing a novel test to detect cancer genes from microarray data.

DNA microarray technology can simultaneously screen thousands of gene expression profiles, transforming how genetics is applied in medicine. However, the lack of normality in microarray data renders common statistical methods ineffective. We propose a novel statistical method which does not require stringent assumptions but is still more powerful than some of its competitors. Using both simulation studies and clinical data, we show that our novel method outperforms previous methods. The limiting distribution for the proposed test is obtained for under null and alternative hypotheses. The proposed test will help make cancer treatment and gene therapy more successful, and it may facilitate research regarding cancer vaccinations. The proposed test may also help in the development of a prediction model in genetic profiling studies built on a subset of differentially expressed genes and the clinical data to assess the accuracy of the clinical prediction.

The management of secondary pelvi-ureteric junction obstruction - a comparison of pyeloplasty and endopyelotomy.

OBJECTIVE: To review our experience in the management of secondary pelvi-ureteric junction obstruction (PUJO) comparing endopyelotomy with pyeloplasty. PATIENTS AND METHODS: We retrospectively analysed our database of 58 patients having undergone operative management of PUJO after failed primary management, including 41 with failed pyeloplasty and 17 failed endopyelotomy. Outcomes included mercapto-acetyltriglycine (MAG3) drainage capacity, symptomatic control and need for further intervention. Success was defined as freedom from failure in all three. RESULTS: Patients undergoing secondary pyeloplasty had better outcomes than endopyelotomy for symptomatic success (87.5% vs 74%), resolution of obstruction on MAG3 renography (96% vs 74%), and no need for further intervention (96% vs 71%). Overall success was 87.5% for pyeloplasty compared with 44% after secondary endopyelotomy. CONCLUSION: Outcomes of pyelopasty for secondary PUJO were superior when compared with endopyelotomy.

Developing a strategy to reduce the high morbidity of patients with long-term urinary catheters: the BioMed catheter research clinic.

OBJECTIVE: To assess the idea of managing patients having problems with long-term catheterization (LTC, normally used when all other methods of bladder management have failed or are unsuitable) in a dedicated clinic, to present a prospective analysis of consecutive new patients attending between February 2002 and October 2006, and to establish the incidence of bladder stones in patients who have recurrent catheter encrustation and blockage. PATIENTS AND METHODS: Patients treated with LTC are a large heterogeneous group, mainly consisting of elderly people who have chronic disabilities, and catheter-associated complications occur in > 70% of them. In all, 260 consecutive new patients having problems with LTC were assessed; the evaluation consisted of basic demographics, a detailed history, clinical examination, urine analysis and flexible cystoscopy (FC) via the catheterization route. Patients with bladder stones were screened with FC for recurrence of stones at 3, 6 and 12 months after treatment. RESULTS: In all, 117 men and 143 women (mean age 67.7 years, range 23-97) were assessed; 147 (55.5%) had catheter encrustation. FC showed that 66 of the 147 patients (45%) had bladder stones. Forty-eight patients (73%) were successfully treated at the same clinic appointment and their stones were removed with the help of a tip-less stone basket. Eighteen patients (27%) were referred for inpatient treatment of bladder stones under general anaesthesia. Twenty of 66 patients with bladder stones (30%) formed recurrent bladder stones at a mean (range) follow-up of 8.1 (3-18 months). In addition, 36 patients had successful insertion of suprapubic catheter (SPC) under local anaesthetic in the clinic, and 11 were referred for SPC insertion under general anaesthesia. Two patients were diagnosed with bladder transitional cell carcinoma. CONCLUSION: The introduction of a dedicated catheter clinic, equipped with facilities such as FC and a hoist, enables patients to be treated in an environment that meets their needs and potentially reduces the risk of more complex stone removal and catheter problems at a later date. It can also act as a potential source of data for use in research and development. A significant proportion (45%) of patients with catheter encrustation and blockage had formed bladder stones. Our study provides a rationale for FC of all such patients to detect and remove stones.

A nonparametric likelihood ratio test to identify differentially expressed genes from microarray data.

Microarray experiments contribute significantly to the progress in disease treatment by enabling a precise and early diagnosis. One of the major objectives of microarray experiments is to identify differentially expressed genes under various conditions. The statistical methods currently used to analyse microarray data are inadequate, mainly due to the lack of understanding of the distribution of microarray data. We present a nonparametric likelihood ratio (NPLR) test to identify differentially expressed genes using microarray data. The NPLR test is highly robust against extreme values and does not assume the distribution of the parent population. Simulation studies show that the NPLR test is more powerful than some of the commonly used methods, such as the two-sample t-test, the Mann-Whitney U-test and significance analysis of microarrays (SAM). When applied to microarray data, we found that the NPLR test identifies more differentially expressed genes than its competitors. The asymptotic distribution of the NPLR test statistic and the p-value function is presented. The application of the NPLR method is shown, using both synthetic and real-life data. The biological significance of some of the genes detected only by the NPLR method is discussed.