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Latest deaths in Juno trial underscore the need for greater transparency in clinical trials
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In recent years, numerous states have passed so-called “right-to-try” laws that encourage patients to seek access to experimental drugs outside of the clinical trial framework. In addition, libertarian activists and even some individuals associated with the incoming Trump administration continue to propose moving new medicines out into widespread use after only scant safety testing. That would increase the number of patients at risk for adverse outcomes, like the ones observed in the Juno trials, before we even know whether the drugs work.
The best way to identify transformative new medicines, protect patients from unexpectedly dangerous drugs, and avoid wasting health care resources is by subjecting experimental products to well-designed clinical trials that enroll sufficient numbers of patients and test relevant clinical outcomes that can then be independently reviewed by the experts at the FDA. When severe, unanticipated problems arise, the FDA needs a transparent and systematic evaluation process that can provide public insight into what happened and why. That would contribute to the progress of science and the development of the next generation of safer, better therapies.
Juno Therapeutics to Resume JCAR015 Phase II ROCKET Trial
SEATTLE–(BUSINESS WIRE)–Jul. 12, 2016– Juno Therapeutics, Inc. (Nasdaq: JUNO), a biopharmaceutical company focused on re-engaging the body’s immune system to revolutionize the treatment of cancer, today announced that the U.S. Food and Drug Administration has removed the clinical hold on the Phase II clinical trial of JCAR015 (known as the “ROCKET” trial) in adult patients with relapsed or refractory B cell acute lymphoblastic leukemia (r/r ALL).
Under the revised protocol, the ROCKET trial will continue enrollment using JCAR015 with cyclophosphamide pre-conditioning only.
Juno Therapeutics (NASDAQ:JUNO) acquires privately held Boston, MA-based RedoxTherapies. Juno’s primary aim of the deal was to secure an exclusive license to vipadenant, a small molecule adenosine A2a receptor antagonist that may disrupt key immunosuppressive pathways in the tumor microenvironment in certain cancers.
Redox licensed vipadenant from London-based Vernalis in October 2014. It was under development for the treatment of Parkinson’s disease by Biogen (NASDAQ:BIIB) but safety concerns scuppered the effort in 2010 despite encouraging efficacy in mid-stage studies. Biogen returned the rights to Vernalis in 2011.
Under the terms of the transaction, Juno will pay $10M in upfront cash plus undisclosed milestones.
Other related articles published in this open Access Online Scientific Journal include the following:
What does this mean for Immunotherapy? FDA put a temporary hold on Juno’s JCAR015, Three Death of Celebral Edema in CAR-T Clinical Trial and Kite Pharma announced Phase II portion of its CAR-T ZUMA-1 trial
Reporters and Curators: Stephen J Williams, PhD and Aviva Lev-Ari, PhD, RN
Johnson & Johnson has entered into a definitive agreement to acquire Abiomed in a deal valued at approximately $16.6 billion. The boards of directors of both companies have unanimously approved the transaction.
Johnson & Johnson agreed to an upfront payment of $380 per share. Abiomed shareholders will also receive a non-tradeable contingent value of up to $35 per share if certain milestones are met. For example, if the company receives FDA premarket application approval for the use of its Impella heart pumps to treat ST-elevation myocardial infarction (STEMI) patients without cardiogenic shock by Jan. 1, 2028, each shareholder will receive $7.50 per share. If Impella devices receive a Class 1 recommendation for the treatment of high-risk percutaneous coronary intervention or STEMI patients with or without cardiogenic shock by Dec. 31, 2029, shareholders will receive an additional $10 per share.
“The addition of Abiomed is an important step in the execution of our strategic priorities and our vision for the new Johnson & Johnson focused on pharmaceutical and MedTech,” Johnson & Johnson CEO Joaquin Duato said in a prepared statement. “We have committed to enhancing our position in MedTech by entering high-growth segments. The addition of Abiomed provides a strategic platform to advance breakthrough treatments in cardiovascular disease and helps more patients around the world while driving value for our shareholders.”
Michael R. Minogue, Abiomed’s chairman, president and CEO, said in the same statement. “It will enable us to leverage Johnson & Johnson’s global scale, commercial strength and clinical expertise to accelerate our mission of making heart recovery the global standard of care.”
This acquisition is expected to be finalized by the end of the first quarter of 2023.
Abiomed Impella® Therapy Receives FDA Approval for Cardiogenic Shock After Heart Attack or Heart Surgery
Entire Family of Impella Left Side Heart Pumps FDA Approved To Enable Heart Recovery
DANVERS, Mass., April 07, 2016 (GLOBE NEWSWIRE) — Abiomed, Inc. (NASDAQ:ABMD), a leading provider of breakthrough heart support technologies, today announced that it has received U.S. Food and Drug Administration (FDA) Pre-Market Approval (PMA) for its Impella 2.5™, Impella CP®, Impella 5.0™ and Impella LD™ heart pumps to provide treatment of ongoing cardiogenic shock. In this setting, the Impella heart pumps stabilize the patient’s hemodynamics, unload the left ventricle, perfuse the end organs and allow for recovery of the native heart. This latest approval adds to the prior FDA indication of Impella 2.5 for high risk percutaneous coronary intervention (PCI), or Protected PCI™, received in March 2015.
With this approval, these are the first and only percutaneous temporary ventricular support devices that are FDA-approved as safe and effective for the cardiogenic shock indication, as stated below:
The Impella 2.5, Impella CP, Impella 5.0 and Impella LD catheters, in conjunction with the Automated Impella Controller console, are intended for short-term use (<4 days for the Impella 2.5 and Impella CP and <6 days for the Impella 5.0 and Impella LD) and indicated for the treatment of ongoing cardiogenic shock that occurs immediately (<48 hours) following acute myocardial infarction (AMI) or open heart surgery as a result of isolated left ventricular failure that is not responsive to optimal medical management and conventional treatment measures with or without an intra-aortic balloon pump. The intent of the Impella system therapy is to reduce ventricular work and to provide the circulatory support necessary to allow heart recovery and early assessment of residual myocardial function.
The product labeling also allows for the clinical decision to leave Impella 2.5, Impella CP, Impella 5.0 and Impella LD in place beyond the intended duration of four to six days due to unforeseen circumstances.
The Impella products offer the unique ability to both stabilize the patient’s hemodynamics before or during a PCI procedure and unload the heart, which allows the muscle to rest and potentially recover its native function. Heart recovery is the ideal option for a patient’s quality of life and as documented in several clinical papers, has the ability to save costs for the healthcare system1,2,3.
Cardiogenic shock is a life-threatening condition in which the heart is suddenly unable to pump enough blood and oxygen to support the body’s vital organs. For this approval, it typically occurs during or after a heart attack or acute myocardial infarction (AMI) or cardiopulmonary bypass surgery as a result of a weakened or damaged heart muscle. Despite advancements in medical technology, critical care guidelines and interventional techniques, AMI cardiogenic shock and post-cardiotomy cardiogenic shock (PCCS) carry a high mortality risk and has shown an incremental but consistent increase in occurrence in recent years in the United States.
“This approval sets a new standard for the entire cardiovascular community as clinicians continue to seek education and new approaches to effectively treat severely ill cardiac patients with limited options and high mortality risk,” said William O’Neill, M.D., medical director of the Center for Structural Heart Disease at Henry Ford Hospital. “The Impella heart pumps offer the ability to provide percutaneous hemodynamic stability to high-risk patients in need of rapid and effective treatment by unloading the heart, perfusing the end organs and ultimately, allowing for the opportunity to recover native heart function.”
“Abiomed would like to recognize our customers, physicians, nurses, scientists, regulators and employees for their last fifteen years of circulatory support research and clinical applications. This FDA approval marks a significant milestone in the treatment of heart disease. The new medical field of heart muscle recovery has begun,” said Michael R. Minogue, President, Chairman and Chief Executive Officer of Abiomed. “Today, Abiomed only treats around 5% of this AMI cardiogenic shock patient population, which suffers one of the highest mortality risks of any patient in the heart hospital. Tomorrow, Abiomed will be able to educate and directly partner with our customers and establish appropriate protocols to improve the patient outcomes focused on native heart recovery.”
Abiomed Data Supporting FDA Approval
The data submitted to the FDA in support of the PMA included an analysis of 415 patients from the RECOVER 1 study and the U.S. Impella registry (cVAD Registry™), as well as an Impella literature review including 692 patients treated with Impella from 17 clinical studies. A safety analysis reviewed over 24,000 Impella treated patients using the FDA medical device reporting (“MDR”) database, which draws from seven years of U.S. experience with Impella.
In addition, the Company also provided a benchmark analysis of Impella patients in the real-world Impella cVAD registry vs. these same patient groups in the Abiomed AB5000/BVS 5000 Registry. The Abiomed BVS 5000 product was the first ventricular assist device (VAD) ever approved by the FDA in 1991 based on 83 patient PMA study. In 2003, the AB5000 Ventricle received FDA approval and this also included a PMA study with 60 patients.
For this approval, the data source for this benchmark analysis was a registry (“AB/BVS Registry”) that contained 2,152 patients that received the AB5000 and BVS 5000 devices, which were originally approved for heart recovery. The analysis examined by the FDA used 204 patients that received the AB5000 device for the same indications. This analysis demonstrated significantly better outcomes with Impella in these patients.
The Company believes this is the most comprehensive review ever submitted to the FDA for circulatory support in the cardiogenic shock population.
Maini B, Gregory D, Scotti DJ, Buyantseva L. Percutaneous cardiac assist devices compared with surgical hemodynamic support alternatives: Cost-Effectiveness in the Emergent Setting.Catheter Cardiovasc Interv. 2014 May 1;83(6):E183-92.
Cheung A, Danter M, Gregory D. TCT-385 Comparative Economic Outcomes in Cardiogenic Shock Patients Managed with the Minimally Invasive Impella or Extracorporeal Life Support. J Am Coll Cardiol. 2012;60(17_S):. doi:10.1016/j.jacc.2012.08.413.
Gregory D, Scotti DJ, de Lissovoy G, Palacios I, Dixon, Maini B, O’Neill W. A value-based analysis of hemodynamic support strategies for high-risk heart failure patients undergoing a percutaneous coronary intervention. Am Health Drug Benefits. 2013 Mar;6(2):88-99
ABOUT IMPELLA
Impella 2.5 received FDA PMA approval for high risk PCI in March 2015, is supported by clinical guidelines, and is reimbursed by the Centers for Medicare & Medicaid Services (CMS) under ICD-9-CM code 37.68 for multiple indications. The Impella RP® device received Humanitarian Device Exemption (HDE) approval in January 2015. The Impella product portfolio, which is comprised of Impella 2.5, Impella CP, Impella 5.0, Impella LD, and Impella RP, has supported over 35,000 patients in the United States.
The ABIOMED logo, ABIOMED, Impella, Impella CP, and Impella RP are registered trademarks of Abiomed, Inc. in the U.S.A. and certain foreign countries. Impella 2.5, Impella 5.0, Impella LD, and Protected PCI are trademarks of Abiomed, Inc.
ABOUT ABIOMED
Based in Danvers, Massachusetts, Abiomed, Inc. is a leading provider of medical devices that provide circulatory support. Our products are designed to enable the heart to rest by improving blood flow and/or performing the pumping of the heart. For additional information, please visit: www.abiomed.com
FORWARD-LOOKING STATEMENTS
This release includes forward-looking statements. These forward-looking statements generally can be identified by the use of words such as “anticipate,” “expect,” “plan,” “could,” “may,” “will,” “believe,” “estimate,” “forecast,” “goal,” “project,” and other words of similar meaning. These forward-looking statements address various matters including, the Company’s guidance for fiscal 2016 revenue. Each forward-looking statement contained in this press release is subject to risks and uncertainties that could cause actual results to differ materially from those expressed or implied by such statement. Applicable risks and uncertainties include, among others, uncertainties associated with development, testing and related regulatory approvals, including the potential for future losses, complex manufacturing, high quality requirements, dependence on limited sources of supply, competition, technological change, government regulation, litigation matters, future capital needs and uncertainty of additional financing, and the risks identified under the heading “Risk Factors” in the Company’s Annual Report on Form 10-K for the year ended March 31, 2015 and the Company’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2015, each filed with the Securities and Exchange Commission, as well as other information the Company files with the SEC. We caution investors not to place considerable reliance on the forward-looking statements contained in this press release. You are encouraged to read our filings with the SEC, available at www.sec.gov, for a discussion of these and other risks and uncertainties. The forward-looking statements in this press release speak only as of the date of this release and the Company undertakes no obligation to update or revise any of these statements. Our business is subject to substantial risks and uncertainties, including those referenced above. Investors, potential investors, and others should give careful consideration to these risks and uncertainties.
For more information, please contact: Aimee Genzler Director, Corporate Communications 978-646-1553 agenzler@abiomed.com Ingrid Goldberg Director, Investor Relations igoldberg@abiomed.com
FDA approved Absorb GT1 Bioresorbable Vascular Scaffold System (BVS), Everolimus releasing and Absorbed by the body in 3 years
Reporter: Aviva Lev-Ari, PhD, RN
FDA approves first absorbable stent for coronary artery disease
For Immediate Release
July 5, 2016
Release
The U.S. Food and Drug Administration today approved the first fully absorbable stent to treat coronary artery disease. The Absorb GT1 Bioresorbable Vascular Scaffold System (BVS), which releases the drug everolimus to limit the growth of scar tissue, is gradually absorbed by the body in approximately three years.
“The FDA’s approval of the Absorb GT1 BVS offers a new treatment option for individuals who are candidates for angioplasty, but would prefer an absorbable device rather than a permanent metallic coronary stent,” said Bram Zuckerman, M.D., director of the division of cardiovascular devices at the FDA’s Center for Devices and Radiological Health.
Coronary heart disease is responsible for about 370,000 deaths each year in the U.S., according to the National Heart, Lung, and Blood Institute. The condition develops when cholesterol-containing deposits build up and narrow the coronary arteries, decreasing blood flow to the heart. This can cause chest pain (angina), shortness of breath, fatigue or other heart disease symptoms. Doctors often treat coronary artery disease with a procedure called angioplasty to widen the artery using a metal stent. Scar tissue can form within the stent causing the artery to narrow again (restenosis). Drug-eluting stents temporarily release a drug, typically for a few months after stent placement, to combat the formation of scar tissue.
The Absorb GT1 BVS is manufactured from a biodegradable polymer called poly(L-lactide), which is similar to materials used in other types of absorbable medical devices, such as sutures. The device’s absorption by the body gradually eliminates the presence of foreign material in the artery once the stent is no longer needed. After absorption, there are only four very small platinum markers embedded in the walls of the artery, which help cardiologists identify where the Absorb GT1 BVS was originally placed.
In approving the Absorb GT1 BVS, the FDA evaluated data from a randomized trial of 2,008 patients, which compared the rate of major adverse cardiac events between the Absorb GT1 BVS and a drug-eluting metallic stent. After one year, the Absorb GT1 BVS group showed a major cardiac adverse event rate of 7.8 percent, which was clinically comparable to the rate of 6.1 percent observed in the control group. In addition, after one year, the rate of blood clots forming within the devices was 1.54 percent for the Absorb GT1 BVS and 0.74 percent rate for the control.
Possible adverse events that may be associated with the procedure to insert the Absorb GT1 BVS or with the Absorb GT1 BVS itself include allergic reactions to materials in the device or medications used during the procedure, allergic reaction to the drug everolimus, infection or irritation at the catheter insertion site, internal bleeding, the development of abnormal connections between arteries and veins, embolism, or other coronary artery complications that may require medical intervention and that could lead to death.
The Absorb GT1 BVS is contraindicated for patients who have a known hypersensitivity or allergy to everolimus or the materials used in the device, such as poly(L-lactide), poly(D,L-lactide), or platinum. It is also contraindicated for those who are not candidates for angioplasty, have sensitivity to contrast, or who cannot take long-term aspirin therapy along with other blood-thinning medications (antiplatelet agents).
The Absorb GT1 BVS is manufactured by Abbott Vascular in Santa Clara, California.
The FDA, an agency within the U.S. Department of Health and Human Services, protects the public health by assuring the safety, effectiveness, and security of human and veterinary drugs, vaccines and other biological products for human use, and medical devices. The agency also is responsible for the safety and security of our nation’s food supply, cosmetics, dietary supplements, products that give off electronic radiation, and for regulating tobacco products.
Chest pain patients are often evaluated for acute myocardial infarction through troponin testing, which may prompt downstream services (cascades) of uncertain value.
Objective
Determine the association of high-sensitivity cardiac troponin (hs-cTn) assay implementation with cascade events.
Methods
Using electronic health record and billing data, we examined patient-visits to five emergency departments, April 1, 2017 – April 1, 2019. Difference-in-differences analysis compared patient-visits for chest pain (n=7,564) to patient-visits for other symptoms (n=100,415) (irrespective of troponin testing) before and after hs-cTn assay implementation. Outcomes included presence of any cascade event potentially associated with an initial hs-cTn test (primary), individual cascade events, length of stay, and spending on cardiac services.
Results
Following hs-cTn implementation, patients with chest pain had a 2.8% (95%CI 0.72, 4.9) net increase in experiencing any cascade event. They were more likely to have multiple troponin tests (10.5%, 95%CI 9.0, 12.0) and electrocardiograms (7.1 per 100 patient-visits, 95%CI 1.8, 12.4). However, they received net fewer computed tomography scans (-1.5 per 100 patient-visits, 95%CI -1.8, -1.1), stress tests (-5.9 per 100 patient-visits, 95%CI -6.5, -5.3), and cardiac catheterizations (-0.65 per 100 patient-visits, 95%CI -1.01, -0.30) and were less likely to receive cardiac medications, undergo cardiology evaluation (-3.5%, 95%CI -4.5, 2.6), or be hospitalized (-5.8%, 95%CI -7.7, -3.8). Chest pain patients had lower net mean length of stay (-0.24 days, 95%CI -0.32, -0.16) but no net change in spending.
Conclusions
Hs-cTn assay implementation was associated with more net upfront tests yet fewer net stress tests, catheterizations, cardiology evaluations, and hospital admissions in chest pain patients relative to patients with other symptoms.
Background: We assessed whether plasma troponin I measured by a high-sensitivity assay (hs-TnI) is associated with incident cardiovascular disease (CVD) and mortality in a community-based sample without prior CVD.
Methods: ARIC study (Atherosclerosis Risk in Communities) participants aged 54 to 74 years without baseline CVD were included in this study (n=8121). Cox proportional hazards models were constructed to determine associations between hs-TnI and incident coronary heart disease (CHD; myocardial infarction and fatal CHD), ischemic stroke, atherosclerotic CVD (CHD and stroke), heart failure hospitalization, global CVD (atherosclerotic CVD and heart failure), and all-cause mortality. The comparative association of hs-TnI and high-sensitivity troponin T with incident CVD events was also evaluated. Risk prediction models were constructed to assess prediction improvement when hs-TnI was added to traditional risk factors used in the Pooled Cohort Equation.
Results: The median follow-up period was ≈15 years. Detectable hs-TnI levels were observed in 85% of the study population. In adjusted models, in comparison to low hs-TnI (lowest quintile, hs-TnI ≤1.3 ng/L), elevated hs-TnI (highest quintile, hs-TnI ≥3.8 ng/L) was associated with greater incident CHD (hazard ratio [HR], 2.20; 95% CI, 1.64-2.95), ischemic stroke (HR, 2.99; 95% CI, 2.01-4.46), atherosclerotic CVD (HR, 2.36; 95% CI, 1.86-3.00), heart failure hospitalization (HR, 4.20; 95% CI, 3.28-5.37), global CVD (HR, 3.01; 95% CI, 2.50-3.63), and all-cause mortality (HR, 1.83; 95% CI, 1.56-2.14). hs-TnI was observed to have a stronger association with incident global CVD events in white than in black individuals and a stronger association with incident CHD in women than in men. hs-TnI and high-sensitivity troponin T were only modestly correlated (r=0.47) and were complementary in prediction of incident CVD events, with elevation of both troponins conferring the highest risk in comparison with elevation in either one alone. The addition of hsTnI to the Pooled Cohort Equation model improved risk prediction for atherosclerotic CVD, heart failure, and global CVD.
Conclusions: Elevated hs-TnI is strongly associated with increased global CVD incidence in the general population independent of traditional risk factors. hs-TnI and high-sensitivity troponin T provide complementary rather than redundant information.
Siemens Launches High-sensitivity Troponin Test for Faster Diagnosis of Heart Attacks
The new troponin I assays can detect lower levels of troponin compared to conventional testing
July 25, 2018 — The U.S. Food and Drug Administration (FDA) cleared Siemens Healthineers high-sensitivity troponin I assays (TnIH) for the Atellica IM and ADVIA Centaur XP/XPT in vitro diagnostic analyzers from Siemens Healthineers to aid in the early diagnosis of myocardial infarctions.
The new tests can shorten the time doctors need to diagnose a life-threatening heart attacks. The time to first results is 10 minutes. When a patient experiencing chest pain enters the emergency department, a physician orders a blood test to determine whether troponin is present. As blood flow to the heart is blocked, the heart muscle begins to die in as few as 30 to 60 minutes and releases troponin into the bloodstream.
The company said its high-sensitivity performance of the two new Siemens TnIH assays offers the ability to detect lower levels of troponin at significantly improved precision at the 99th percentile, and detect smaller changes in a patient’s troponin level as repeat testing occurs. This design affords clinicians greater confidence in the results with precision that provides the ability to measure slight, yet critical, changes to begin treatment.[1,2]
Chest pain is the cause of more than 8 million visits annually nationwide to emergency departments, but only 5.5 percent of those visits lead to serious diagnoses such as heart attacks.[3] Armed with data to properly triage patients sooner or to exclude myocardial infarctions, the Siemens Healthineers TnIH assays can help support testing initiatives tied to improving patient experience.
“Our emergency department is overcrowded with patients. If we can do a more efficient job at triaging patients to receive the proper level of care and to discharge the patients who do not need to stay in the emergency department, this will have a tremendous economic advantage for our healthcare system,” said Alan Wu, M.D., chief of clinical chemistry and toxicology at Zuckerberg San Francisco General Hospital and Trauma Center.
Siemens is launching the product at the 70th AACC Annual Scientific Meeting and Clinical Lab Expo taking place July 31 to Aug. 2 in Chicago.
Increases in levels of cardiac troponin T by high-sensitivity assay (hs-cTnT) over time are associated with later risk of death, coronary heart disease (CHD), and especially heart failure in apparently healthy middle-aged people, according to a report published June 8, 2016 in JAMA Cardiology[1].
The novel findings, based on a cohort of >8000 participants from the Atherosclerosis Risk in Communities (ARIC) study followed up to 16 years, are the first to show “an association between temporal hs-cTnT change and incident CHD events” in asymptomatic middle-aged adults,” write the authors, led by Dr John W McEvoy (Johns Hopkins University School of Medicine, Baltimore, MD).
Individuals with the greatest troponin increases over time had the highest risk for poor cardiac outcomes. The strongest association was for risk of heart failure, which reached almost 800% for those with the sharpest hs-cTnT rises.
Intriguingly, those in whom troponin levels fell at least 50% had a reduced mortality risk and may have had a slightly decreased risk of later HF or CHD.
“Serial testing over time with high-sensitivity cardiac troponins provided additional prognostic information over and above the usual clinical risk factors, [natriuretic peptide] levels, and a single troponin measurement. Two measurements appear better than one when it comes to informing risk for future coronary heart disease, heart failure, and death,” McEvoy told heartwirefrom Medscape.
He cautioned, though, that the conclusion is based on observational data and would need to be confirmed in clinical trials. Moreover, high-sensitivity cardiac troponin assays are widely used in Europe but are not approved in the US.
An important next step after this study, according to an accompanying editorial from Dr James Januzzi (Massachusetts General Hospital, Boston, MA), would be to evaluate whether the combination of hs-troponin and natriuretic peptides improves predictive value in this population[2].
“To the extent prevention is ultimately the holy grail for defeating the global pandemic of CHD, stroke, and HF, the main reason to do a biomarker study such as this would be to set the stage for a biomarker-guided strategy to improve the medical care for those patients at highest risk, as has been recently done with [natriuretic peptides],” he wrote.
The ARIC prospective cohort study entered and followed 8838 participants (mean age 56, 59% female, 21.4% black) in North Carolina, Mississippi, Minneapolis, and Maryland from January 1990 to December 2011. At baseline, participants had no clinical signs of CHD or heart failure.
Levels of hs-cTnT, obtained 6 years apart, were categorized as undetectable (<0.005 ng/mL), detectable (≥0.005 ng/mL to <0.014 ng/mL), and elevated (>0.014 ng/mL).
Troponin increases from <0.005 ng/mL to 0.005 ng/mL or higher independently predicted development of CHD (HR 1.41; 95% CI 1.16–1.63), HF (HR 1.96; 95% CI 1.62–2.37), and death (HR 1.50; 95% CI 1.31–1.72), compared with undetectable levels at both measurements.
Hazard ratios were adjusted for age, sex, race, body-mass index, C-reactive protein, smoking status, alcohol-intake history, systolic blood pressure, current antihypertensive therapy, diabetes, serum lipid and cholesterol levels, lipid-modifying therapy, estimated glomerular filtration rate, and left ventricular hypertrophy.
Subjects with >50% increase in hs-cTnT had a significantly increased risk of CHD (HR 1.28; 95% CI 1.09–1.52), HF (HR 1.60; 95% CI 1.35–1.91), and death (HR 1.39; 95% CI 1.22–1.59).
Risks for those end points fell somewhat for those with a >50% decrease in hs-cTnT (CHD: HR 0.47; 95% CI 0.22–1.03; HF: HR 0.49 95% CI 0.23–1.01; death: HR 0.57 95% CI 0.33–0.99).
Among participants with an adjudicated HF hospitalization, the group writes, associations of hs-cTnT changes with outcomes were of similar magnitude for those with HF with preserved ejection fraction (HFpEF) and HF with reduced ejection fraction (HFrEF).
Few biomarkers have been linked to increased risk for HFpEF, and few effective therapies exist for it. That may be due to problems identifying and enrolling patients with HFpEF in clinical trials, Dr McEvoy pointed out.
“We think the increased troponin over time reflects progressive myocardial injury or progressive myocardial damage,” Dr McEvoy said. “This is a window into future risk, particularly with respect to heart failure but other outcomes as well. It may suggest high-sensitivity troponins as a marker of myocardial health and help guide interventions targeting the myocardium.”
Moreover, he said, “We think that high-sensitivity troponin may also be a useful biomarker along with [natriuretic peptides] for emerging trials of HFpEF therapy.”
But whether hs-troponin has the potential for use as a screening tool is a question for future studies, according to McEvoy.
In his editorial, Januzzi pointed out several implications of the study, including the possibility for lowering cardiac risk in those with measurable hs-troponin, and that HF may be the most obvious outcome to target. Also, optimizing treatment and using cardioprotective therapies may reduce risk linked to increases in hs-troponin. Finally, long-term, large clinical trials on this issue will require a multidisciplinary team effort from various sectors.
“What is needed now are efforts toward developing strategies to upwardly bend the survival curves of those with a biomarker signature of risk, leveraging the knowledge gained from studies such as the report by McEvoy et al to improve public health,” he concluded.
mRNA Data Survival Analysis, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 1: Next Generation Sequencing (NGS)
mRNA Data Survival Analysis
Curators: Larry H. Bernstein, MD, FCAP and Aviva Lev-Ari, PhD, RN
SURVIV for survival analysis of mRNA isoform variation
The rapid accumulation of clinical RNA-seq data sets has provided the opportunity to associate mRNA isoform variations to clinical outcomes. Here we report a statistical method SURVIV (Survival analysis of mRNA Isoform Variation), designed for identifying mRNA isoform variation associated with patient survival time. A unique feature and major strength of SURVIV is that it models the measurement uncertainty of mRNA isoform ratio in RNA-seq data. Simulation studies suggest that SURVIV outperforms the conventional Cox regression survival analysis, especially for data sets with modest sequencing depth. We applied SURVIV to TCGA RNA-seq data of invasive ductal carcinoma as well as five additional cancer types. Alternative splicing-based survival predictors consistently outperform gene expression-based survival predictors, and the integration of clinical, gene expression and alternative splicing profiles leads to the best survival prediction. We anticipate that SURVIV will have broad utilities for analysing diverse types of mRNA isoform variation in large-scale clinical RNA-seq projects.
Eukaryotic cells generate remarkable regulatory and functional complexity from a finite set of genes. Production of mRNA isoforms through alternative processing and modification of RNA is essential for generating this complexity. A prevalent mechanism for producing mRNA isoforms is the alternative splicing of precursor mRNA1. Over 95% of the multi-exon human genes undergo alternative splicing2, 3, resulting in an enormous level of plasticity in the regulation of gene function and protein diversity. In the last decade, extensive genomic and functional studies have firmly established the critical role of alternative splicing in cancer4, 5, 6. Alternative splicing is involved in a full spectrum of oncogenic processes including cell proliferation, apoptosis, hypoxia, angiogenesis, immune escape and metastasis7, 8. These cancer-associated alternative splicing patterns are not merely the consequences of disrupted gene regulation in cancer but in numerous instances actively contribute to cancer development and progression. For example, alternative splicing of genes encoding the Bcl-2 family of apoptosis regulators generates both anti-apoptotic and pro-apoptotic protein isoforms9. Alternative splicing of the pyruvate kinase M (PKM) gene has a significant impact on cancer cell metabolism and tumour growth10. A transcriptome-wide switch of the alternative splicing programme during the epithelial–mesenchymal transition plays an important role in cancer cell invasion and metastasis11, 12.
RNA sequencing (RNA-seq) has become a popular and cost-effective technology to study transcriptome regulation and mRNA isoform variation13, 14. As the cost of RNA-seq continues to decline, it has been widely adopted in large-scale clinical transcriptome projects, especially for profiling transcriptome changes in cancer. For example, as of April 2015 The Cancer Genome Atlas (TCGA) consortium had generated RNA-seq data on over 11,000 cancer patient specimens from 34 different cancer types. Within the TCGA data, breast invasive carcinoma (BRCA) has the largest sample size of RNA-seq data covering over 1,000 patients, and clinical information such as survival times, tumour stages and histological subtypes is available for the majority of the BRCA patients15. Moreover, the median follow-up time of BRCA patients is ~400 days, and 25% of the patients have more than 1,200 days of follow-up. Collectively, the large sample size and long follow-up time of the TCGA BRCA data set allow us to correlate genomic and transcriptomic profiles to clinical outcomes and patient survival times.
To date, systematic analyses have been performed to reveal the association between copy number variation, DNA methylation, gene expression and microRNA expression profiles with cancer patient survival16, 17. By contrast, despite the importance of mRNA isoform variation and alternative splicing, there have been limited efforts in transcriptome-wide survival analysis of alternative splicing in cancer patients. Most RNA-seq studies of alternative splicing in cancer transcriptomes focus on identifying ‘cancer-specific’ alternative splicing events by comparing cancer tissues with normal controls (see refs 18, 19, 20, 21, 22, 23 for examples). A recent analysis of TCGA RNA-seq data identified 163 recurrent differential alternative splicing events between cancer and normal tissues of three cancer types, among which five were found to have suggestive survival signals for breast cancer at a nominal P-value cutoff of 0.05 (ref. 21). Some other studies reported a significant survival difference between cancer patient subgroups after stratifying patients with overall mRNA isoform expression profiles24, 25. However, systematic cancer survival analyses of alternative splicing at the individual exon resolution have been lacking. Two main challenges exist for survival analyses of mRNA isoform variation and alternative splicing using RNA-seq data. The first challenge is to account for the estimation uncertainty of mRNA isoform ratios inferred from RNA-seq read counts. The statistical confidence of mRNA isoform ratio estimation depends on the RNA-seq read coverage for the events of interest, with larger read coverage leading to a more reliable estimation14. Modelling the estimation uncertainty of mRNA isoform ratio is an essential component of RNA-seq analyses of alternative splicing, as shown by various statistical algorithms developed for detecting differential alternative splicing from multi-group RNA-seq data14, 26, 27, 28,29. The second challenge, which is a general issue in survival analysis, is to properly model the association of mRNA isoform ratio with survival time, while accounting for missing data in survival time because of censoring, that is, patients still alive at the end of the survival study, whose precise survival time would be uncertain. To date, no algorithm has been developed for survival analyses of mRNA isoform variation that accounts for these sources of uncertainty simultaneously.
Here we introduce SURVIV (Survival analysis of mRNA Isoform Variation), a statistical model for identifying mRNA isoform ratios associated with patient survival times in large-scale cancer RNA-seq data sets. SURVIV models the estimation uncertainty of mRNA isoform ratios in RNA-seq data and tests the survival effects of isoform variation in both censored and uncensored survival data. In simulation studies, SURVIV consistently outperforms the conventional Cox regression survival analysis that ignores the measurement uncertainty of mRNA isoform ratio. We used SURVIV to identify alternatively spliced exons whose exon-inclusion levels significantly correlated with the survival times of invasive ductal carcinoma (IDC) patients from the TCGA breast cancer cohort. Survival-associated alternative splicing events are identified in gene pathways associated with apoptosis, oxidative stress and DNA damage repair. Importantly, we show that alternative splicing-based survival predictors outperform gene expression-based survival predictors in the TCGA IDC RNA-seq data set, as well as in TCGA data of five additional cancer types. Moreover, the integration of clinical information, gene expression and alternative splicing profiles leads to the best prediction of survival time.
SURVIV statistical model
The statistical model of SURVIV assesses the association between mRNA isoform ratio and patient survival time. While the model is generic for many types of alternative isoform variation, here we use the exon-skipping type of alternative splicing to illustrate the model (Fig. 1a). For each alternative exon involved in exon-skipping, we can use the RNA-seq reads mapping to its exon-inclusion or -skipping isoform to estimate its exon-inclusion level (denoted as ψ, or PSI that is Per cent Spliced In14). A key feature of SURVIV is that it models the RNA-seq estimation uncertainty of exon-inclusion level as influenced by the sequencing coverage for the alternative splicing event of interest. This is a critical issue in accurate quantitative analyses of mRNA isoform ratio in large-scale RNA-seq data sets14, 26, 27, 28, 29. Therefore, SURVIV contains two major components: the first to model the association of mRNA isoform ratio with patient survival time across all patients, and the second to model the estimation uncertainty of mRNA isoform ratio in each individual patient (Fig. 1a).
Figure 1: The statistical framework of the SURVIV model.
(a) For each patient k, the patient’s hazard rate λk(t) is associated with the baseline hazard rate λ0(t) and this patient’s exon-inclusion level ψk. The association of exon-inclusion level with patient survival is estimated by the survival coefficient β. The exon-inclusion level ψk is estimated from the read counts for the exon-inclusion isoform ICk and the exon-skipping isoform SCk. The proportion of the inclusion and skipping reads is adjusted by a normalization function f that considers the lengths of the exon-inclusion and -skipping isoforms (see details in Results and Supplementary Methods). (b) A hypothetical example to illustrate the association of exon-inclusion level with patient survival probability over time Sk(t), with the survival coefficient β=−1 and a constant baseline hazard rate λ0(t)=1. In this example, patients with higher exon-inclusion levels have lower hazard rates and higher survival probabilities. (c) The schematic diagram of an exon-skipping event. The exon-inclusion reads ICk are the reads from the upstream splice junction, the alternative exon itself and the downstream splice junction. The exon-skipping reads SCk are the reads from the skipping splice junction that directly connects the upstream exon to the downstream exon.
Briefly, for any individual exon-skipping event, the first component of SURVIV uses a proportional hazards model to establish the relationship between patient k’s exon-inclusion level ψk and hazard rate λk(t).
For each exon, the association between the exon-inclusion level and patient survival time is reflected by the survival coefficient β. A positive β means increased exon inclusion is associated with higher hazard rate and poorer survival, while a negative β means increased exon inclusion is associated with lower hazard rate and better survival. λ0(t) is the baseline hazard rate estimated from the survival data of all patients (see Supplementary Methods for the detailed estimation procedure). A particular patient’s survival probability over time Sk(t) can be calculated from the patient-specific hazard rate λk(t) as . Figure 1b illustrates a simple example with a negative β=−1 and a constant baseline hazard rate λ0(t)=1, where higher exon-inclusion levels are associated with lower hazard rates and higher survival probabilities.
The second component of SURVIV models the exon-inclusion level and its estimation uncertainty in individual patient samples. As illustrated in Fig. 1c, the exon-inclusion level ψk of a given exon in a particular sample can be estimated by the RNA-seq read count specific to the exon inclusion isoform (ICk) and the exon-skipping isoform (SCk). Other types of alternative splicing and mRNA isoform variation can be similarly modelled by this framework29. Given the effective lengths (that is, the number of unique isoform-specific read positions) of the exon-inclusion isoform (lI) and the exon-skipping isoform (lS), the exon-inclusion level ψk can be estimated as . Assuming that the exon-inclusion read count ICk follows a binomial distribution with the total read count nk=ICk+SCk, we have:
The binomial distribution models the estimation uncertainty of ψk as influenced by the total read count nk, in which the parameter pk represents the proportion of reads from the exon-inclusion isoform, given the exon-inclusion level ψk adjusted by a length normalization function f(ψk) based on the effective lengths of the isoforms. The definitions of effective lengths for all basic types of alternative splicing patterns are described in ref. 29.
Distinct from conventional survival analyses in which predictors do not have estimation uncertainty, the predictors in SURVIV are exon-inclusion levels ψk estimated from RNA-seq count data, and the confidence of ψk estimate for a given exon in a particular sample depends on the RNA-seq read coverage. We use the statistical framework of survival measurement error model30 to incorporate the estimation uncertainty of isoform ratio in the proportional hazards model. Using a likelihood ratio test, we test whether the exon-inclusion levels have a significant association with patient survival over the null hypothesis H0:β=0. The false discovery rate (FDR) is estimated using the Benjamini and Hochberg approach31. Details of the parameter estimation and likelihood ratio test in SURVIV are described in Supplementary Methods.
Figure 2: Simulation studies to assess the performance of SURVIV and the importance of modelling the estimation uncertainty of mRNA isoform ratio.
We compared our SURVIV model with Cox regression using point estimates of exon-inclusion levels, which does not consider the estimation uncertainty of the mRNA isoform ratio. (a) To study the effect of RNA-seq depth, we simulated the mean total splice junction read counts equal to 5, 10, 20, 50, 80 and 100 reads. We generated two sets of simulations with and without data-censoring. For each simulation, the true-positive rate (TPR) at 5% false-positive rate is plotted. The inset figure shows the empirical distribution of the mean total splice junction read counts in the TCGA IDC RNA-seq data (x axis in the log10 scale). (b) To faithfully represent the read count distribution in a real data set, we performed another simulation with read counts directly sampled from the TCGA IDC data. Sampled read counts were then multiplied by different factors ranging from 10 to 300% to simulate data sets with different RNA-seq read depth. Continuous and dashed lines represent the performance of SURVIV and Cox regression, respectively. Red lines represent the area under curve (AUC) of the ROC curve (TPR versus false-positive rate plot). Black lines represent the TPR at 5% false-positive rate.
Using these simulated data, we compared SURVIV with Cox regression in two settings, without or with censoring of the survival time. In the setting without censoring, the death and survival time of each individual is known. In the setting with censoring, certain individuals are still alive at the end of the survival study. Consequently, these patients have unknown death and survival time. Here, in the simulation with censoring, we assumed that 85% of the patients were still alive at the end of the study, similar to the censoring rate of the TCGA IDC data set. In both settings and with different depths of RNA-seq coverage, SURVIV consistently outperformed Cox regression in the true-positive rate at the same false-positive rate of 5% (Fig. 2a). As expected, we observed a more significant improvement in SURVIV over Cox regression when the RNA-seq read coverage was low (Fig. 2a).
To more faithfully recapitulate the read count distribution in a real cancer RNA-seq data set, we performed another simulation study with read counts directly sampled from the TCGA IDC data. To assess the influence of RNA-seq read depth on the performance of SURVIV and Cox regression, sampled read counts were then multiplied by different factors ranging from 10 to 300% to simulate data sets with different RNA-seq read depths (Fig. 2b). The TCGA IDC data set has an average RNA-seq depth of ~60 million paired-end reads per patient. Thus, the read depth of these simulated RNA-seq data sets ranged from ~6 million reads to 180 million reads per patient, representing low-coverage RNA-seq studies designed primarily for gene expression analysis32 up to high-coverage RNA-seq studies designed primarily for alternative isoform analysis29. At all levels of RNA-seq depth, SURVIV consistently outperformed Cox regression, as reflected by the area under curve of the receiver operating characteristic (ROC) curve as well as the true-positive rate at 5% false-positive rate (Fig. 2b). The improvement of SURVIV over Cox regression was particularly prominent when the read depth was low. For example, at 10% read depth, SURVIV had 7% improvement in area under curve (68% versus 61%) and 8% improvement in the true-positive rate at 5% false-positive rate (46% versus 38%). Collectively, these simulation results suggest that SURVIV achieves a higher accuracy by accounting for the estimation uncertainty of mRNA isoform ratio in RNA-seq data.
SURVIV analysis of TCGA IDC breast cancer data
To illustrate the practical utility of SURVIV, we used it to analyse the overall survival time of 682 IDC patients from the TCGA breast cancer (BRCA) RNA-seq data set (see Methods for details of the data source and processing pipeline). We chose to analyse IDC because it is the most frequent type of breast cancer33, comprising ~70% of patients in the TCGA breast cancer data set. To control for the effects of significant clinical parameters such as tumour stage and subtype and identify alternative splicing events associated with patient outcomes across multiple molecular and clinical subtypes, we followed the procedure of Croce and colleagues in analysing mRNA and microRNA prognostic signature of IDC33 and stratified the patients according to their clinical parameters. We then conducted SURVIV analysis in 26 clinical subgroups with at least 50 patients in each subgroup. We identified 229 exon-skipping events associated with patient survival in multiple clinical subgroups that met the criteria of SURVIV P-value≤0.01 in at least two subgroups of the same clinical parameter (cancer subtype, stage, lymph node, metastasis, tumour size, oestrogen receptor status, progesterone receptor status, HER2 status and age as shown in Fig. 3). DAVID (Database for Annotation, Visualization and Integrated Discovery) Gene Ontology analyses34 of the 229 alternative splicing events suggest an enrichment of genes in cancer-related functional categories such as intracellular signalling, apoptosis, oxidative stress and response to DNA damage (Supplementary Fig. 1). Table 1 shows a few selected examples of survival-associated alternative splicing events in cancer-related genes. Using two-means clustering of each individual exon’s inclusion levels, the 682 IDC patients can be segregated into two subgroups with significantly different survival times as illustrated by the Kaplan–Meier survival plot (Fig. 4). We also carried out hierarchical clustering of IDC patients using 176 survival-associated alternative exons (P≤0.01; SURVIV analysis of all IDC patients). Using the exon-inclusion levels of these 176 exons, we clustered IDC patients into three major subgroups, with 95, 194 and 389 patients, respectively. As illustrated by the Kaplan–Meier survival plots, the three subgroups had significantly different survival times (Supplementary Fig. 2).
Figure 3: SURVIV analysis of exon-skipping events in the TCGA IDC RNA-seq data set.
IDC patients are stratified into multiple clinical subgroups based on clinical parameters including cancer subtype, stage, lymph node status, metastasis, tumour size, oestrogen receptor status, progesterone receptor status, HER2 status and age. Only clinical subgroups with at least 50 patients are included in further analyses. Numbers of patients in the subgroups are indicated next to the names of the subgroups. Shown in the heatmap are the log10 SURVIV P-values of the 229 exons associated with patient survival (P≤0.01) in at least two subgroups of the same class of clinical parameters. Turquoise colour indicates positive correlation that higher exon-inclusion levels are associated with higher survival probabilities. Magenta colour indicates negative correlation that lower exon-inclusion levels are associated with higher survival probabilities.
Figure 4: Kaplan–Meier survival plots of IDC patients stratified by two-means clustering of the exon-inclusion levels of four survival-associated alternative splicing events.
Clustering was generated for each of the four exons separately. Black lines represent patients with high exon-inclusion levels. Red lines represent patients with low exon-inclusion levels. The P-values are from SURVIV analysis of the TCGA IDC RNA-seq data. (a) ATRIP. (b) BCL2L11. (c) CD74. (d) PCBP4.
Figure 5: Alternative splicing of STAT5A exon 5 is significantly associated with IDC patient survival.
(a) The gene structure of the STAT5A full-length isoform compared to the ΔEx5 isoform skipping the 5th exon. (b) Kaplan–Meier survival plot of IDC patients stratified by two-means clustering using exon-inclusion levels of STAT5A exon 5. The 420 patients in Group 1 (average exon 5 inclusion level=95%) have significantly higher survival probabilities than the 262 patients in Group 2 (average exon 5 inclusion level=85%) (SURVIV P=6.8e−4). (c) Exon 5 inclusion levels of IDC patients stratified by two-means clustering using exon 5 inclusion levels. Group 1 has 420 patients with average exon-inclusion level at 95%. Group 2 has 262 patients with average exon-inclusion level at 85%. (d) STAT5A exon 5 inclusion levels in normal breast tissues versus breast cancer tumour samples. Exon-inclusion levels are extracted from 86 TCGA breast cancer patients with matched normal and tumour samples. Normal breast tissues have average exon 5 inclusion level at 95%, compared to 91% average exon-inclusion level in tumour samples. Error bars represent 95% confidence interval of the mean.
Figure 6: Splicing factor regulatory network of survival-associated alternative splicing events in IDC.
(a–c) Kaplan–Meier survival plots of IDC patients stratified by the gene expression levels of three splicing factors: TRA2B (a, Cox regression P=1.8e−4), HNRNPH1 (b, P=3.4e−4) and SFRS3 (c, P=2.8e−3). Black lines represent patients with high gene expression levels. Red lines represent patients with low gene expression levels. (d) The exon-inclusion levels of a DHX30 alternative exon are negatively correlated with TRA2B gene expression levels (robust correlation coefficient r=−0.26, correlation P=1.2e−17). (e) The exon-inclusion levels of a MAP3K4 alternative exon are positively correlated withHNRNPH1 gene expression levels (robust correlation coefficient r=0.16, correlation P=2.6e−06). (f) A splicing co-expression network of the three splicing factors and their correlated survival-associated alternative exons. In total, 84 survival-associated alternative exons are significantly correlated with the three splicing factors. The positive/negative correlation between splicing factors and alternative exons is represented by blue/red lines, respectively. Exons whose inclusion levels are positively/negatively correlated with survival times are represented by blue/red dots, respectively. The size of the splicing factor circles is proportional to the number of correlated exons within the network.
Figure 7: Cross-validation of different classes of IDC survival predictors measured by the C-index
A C-index of 1 indicates perfect prediction accuracy and a C-index of 0.5 indicates random guess. The plots indicate the distribution of C-indexes from 100 rounds of cross-validation. The centre value of the box plot is the median C-index from 100 rounds of cross-validation. The notch represents the 95%confidence interval of the median. The box represents the 25 and 75% quantiles. The whiskers extended out from the box represent the 5 and 95% quantiles. Two-sided Wilcoxon test was used to compare different survival predictors. The different classes of predictors are: (a) clinical information (median C-index 0.67). (b) Gene expression (median C-index 0.68). (c) Alternative splicing (median C-index 0.71). (d) Clinical information+gene expression (median C-index 0.69). (e) Clinical information+alternative splicing (median C-index 0.73). (f) Clinical information+gene expression+alternative splicing (median C-index 0.74). Note that ‘Gene’ refers to ‘Gene-level expression’ in these plots.
Next, we carried out the SURVIV analysis in five additional cancer types in TCGA, including GBM (glioblastoma multiforme), KIRC (kidney renal clear cell carcinoma), LGG (lower grade glioma), LUSC (lung squamous cell carcinoma) and OV (ovarian serous cystadenocarcinoma). As expected, the number of significant events at different FDR or P-value significance cutoffs varied across cancer types, with LGG having the strongest survival-associated alternative splicing signals with 660 significant exon-skipping events at FDR≤5% (Supplementary Data 3 and 4). Strikingly, regardless of the number of significant events, alternative splicing-based survival predictors outperformed gene expression-based survival predictors across all cancer types (Supplementary Fig. 3), consistent with our initial observation on the IDC data set.
Alternative processing and modification of mRNA, such as alternative splicing, allow cells to generate a large number of mRNA and protein isoforms with diverse regulatory and functional properties. The plasticity of alternative splicing is often exploited by cancer cells to produce isoform switches that promote cancer cell survival, proliferation and metastasis7, 8. The widespread use of RNA-seq in cancer transcriptome studies15, 47, 48 has provided the opportunity to comprehensively elucidate the landscape of alternative splicing in cancer tissues. While existing studies of alternative splicing in large-scale cancer transcriptome data largely focused on the comparison of splicing patterns between cancer and normal tissues or between different subtypes of cancer18, 21, 49, additional computational tools are needed to characterize the clinical relevance of alternative splicing using massive RNA-seq data sets, including the association of alternative splicing with phenotypes and patient outcomes.
We have developed SURVIV, a novel statistical model for survival analysis of alternative isoform variation using cancer RNA-seq data. SURVIV uses a survival measurement error model to simultaneously model the estimation uncertainty of mRNA isoform ratio in individual patients and the association of mRNA isoform ratio with survival time across patients. Compared with the conventional Cox regression model that uses each patient’s mRNA isoform ratio as a point estimate, SURVIV achieves a higher accuracy as indicated by simulation studies under a variety of settings. Of note, we observed a particularly marked improvement of SURVIV over Cox regression for low- and moderate-depth RNA-seq data (Fig. 2b). This has important practical value because many clinical RNA-seq data sets have large sample size but relatively modest sequencing depth.
Using the TCGA IDC breast cancer RNA-seq data of 682 patients, SURVIV identified 229 alternative splicing events associated with patient survival time, which met the criteria of SURVIVP-values≤0.01 in multiple clinical subgroups. While the statistical threshold seemed loose, several lines of evidence suggest the functional and clinical relevance of these survival-associated alternative splicing events. These alternative splicing events were frequently identified and enriched in the gene functional groups important for cancer development and progression, including apoptosis, DNA damage response and oxidative stress. While some of these events may simply reflect correlation but not causal effect on cancer patient survival, other events may play an active role in regulating cancer cell phenotypes. For example, a survival-associated alternative splicing event involving exon 5 of STAT5A is known to regulate the activity of this transcription factor with important roles in epithelial cell growth and apoptosis37. Using a co-expression network analysis of splicing factor to exon correlation across all patients, we identified three splicing factors (TRA2B, HNRNPH1 and SFRS3) as potential hubs of the survival-associated alternative splicing network of IDC. The expression levels of all three splicing factors were negatively associated with patient survival times (Fig. 6a–c), and both TRA2B and HNRNPH1 were previously reported to have an impact on cancer-related molecular pathways40, 41, 42, 43, 44, 45. Finally, despite the limited power in detecting individual events, we show that the survival-associated alternative splicing events can be used to construct a predictor for patient survival, with an accuracy higher than predictors based on clinical parameters or gene expression profiles (Fig. 7). This further demonstrates the potential biological relevance and clinical utility of the identified alternative splicing events.
We performed cross-validation analyses to evaluate and compare the prognostic value of alternative splicing, gene expression and clinical information for predicting patient survival, either independently or in combination. As expected, the combined use of all three types of information led to the best prediction accuracy. Because we used penalized regression to build the prediction model, combining information from multiple layers of data did not necessarily increase the number of predictors in the model. The perhaps more surprising and intriguing result is that alternative splicing-based predictors appear to outperform gene expression-based predictors when used alone and when either type of data was combined with clinical information (Fig. 7). We observed the same trend in five additional cancer types (Supplementary Fig. 3). We note that this finding was consistent with a previous report that cancer subtype classification based on splicing isoform expression performed better than gene expression-based classification25. While this trend seems counterintuitive because accurate estimation of gene expression requires much lower RNA-seq depth than accurate estimation of alternative splicing29, one possible explanation may be the inherent characteristic of isoform ratio data. By definition, mRNA isoform ratio is estimated as the ratio of multiple mRNA isoforms from a single gene. Therefore, mRNA isoform ratio data have a ‘built-in’ internal control that could be more robust against certain artefacts and confounding issues that influence gene expression estimates across large clinical RNA-seq data sets, such as poor sample quality and RNA degradation12. Regardless of the reasons, our data call for further studies to fully explore the utility of mRNA isoform ratio data for various clinical research applications.
The SURVIV source code is available for download at https://github.com/Xinglab/SURVIV. SURVIV is a general statistical model for survival analysis of mRNA isoform ratio using RNA-seq data. The current statistical framework of SURVIV is applicable to RNA-seq based count data for all basic types of alternative splicing patterns involving two isoform choices from an alternatively spliced region, such as exon-skipping, alternative 5′ splice sites, alternative 3′ splice sites, mutually exclusive exons and retained introns, as well as other forms of alternative isoform variation such as RNA editing. With the rapid accumulation of clinical RNA-seq data sets, SURVIV will be a useful tool for elucidating the clinical relevance and potential functional significance of alternative isoform variation in cancer and other diseases.
CHICAGO — A new class of cancer immunotherapies, led by pembrolizumab (Keytruda), has taken the oncology world by storm. But with this novel type of treatment comes a new challenge.
The Association of Community Cancer Centers (ACCC) wants to ensure that non-oncologist physicians know how to take care of their patients receiving these agents since doctors in other specialties may not be aware of the side effects related to the immunotherapies.
The initiative is one of the steps taken by the association’s Institute of Clinical Immuno-Oncology’s (ICLIO) in making immunotherapy available in the community.
ICLIO was launched 1 year ago to help prepare community cancer teams and centers to deal with the clinical, coverage, and reimbursement issues related to immunotherapy.
During the American Society of Clinical Oncology annual meeting here MedPage Todayspoke with ACCC President Jennie R. Crews, MD, and ICLIO Chair Lee S. Schwartzberg, MD, about the institute’s growth and future plans.
Schwartzberg, chief of the division of hematology and oncology at the University of Tennessee, as well as executive director of the West Cancer Center in Memphis, said that the field of immunotherapy “is moving so fast that we can’t have enough education.”
“Needs change over time and last year many cancer practices became familiar with immuno-oncology and now we have to go deeper and broader.”
The broadening, he explained, involves educating other medical subspecialists about immune-related toxicities from the new agents.
“The problem is that we see related toxicities that are not managed well, and we’re having trouble with this.”
He cited as two primary examples toxic side effects such as colitis and pneumonitis and the necessity of educating gastroenterologists and pulmonologists about their relationship to immunotherapy.
Many times these subspecialists, as well as dermatologists, endocrinologists, emergency physicians, and internists see autoimmune-related toxicities and first think they are from chemotherapy or infection, according to Schwartzberg.
“But they are going to be going down a very bad path with these patients if they think this way,” noting that a colleague from a leading cancer center had recently mentioned that the institution’s emergency room staff didn’t always understand about immunotherapy reactions.
He said that, although ICLIO does not have direct access to reaching many other subspecialists, it was beginning to develop educational materials that oncologists could share with other medical colleagues, as well as to work with some of the subspecialty societies.
“Education, however, has to be across the board, and has to include patients as well,” he said, adding that many cancer immunotherapy patients were being provided with cards that explained their immunotherapy and could be handed to nurses and physicians at the outset of their medical intervention, saving time and the risk of undergoing the wrong treatment.
In a separate interview, Crews, medical director for Cancer Services PeaceHealth at St. Joseph Medical Center in Bellingham, Wash., said that ACCC members include both academic centers and community practices including both hospital-based and private. (An ACCC public relations representative monitored the interview.)
“We are not focused on what the science is, but rather on how do we take this technology out to the community to bring cancer to where patients are,” she said, adding that she and others are very passionate in the belief that cancer care should be delivered wherever cancer patients live.
She said since ICLIO started in June 2015, much of its infrastructure and programs have been established, including a webinar series, eNewsletters, eLearning Modules, tumor subcommittee working groups, an on-site preceptorship program, an ICLIO stakeholder summit, and an upcoming second national conference this fall in Philadelphia.
That conference will be preceded by a stakeholder summit bringing together providers, patient advocates, payers, pharmaceutical producers, and others, which the ACCC hopes will produce a white paper.
The last year has seen the growth of the initiative’s Scholars Program to about 50 oncologists who have received training through ICLIO’s learning modules.
These scholars will in turn eventually be able to serve as mentors to the 2,000 cancer programs with some 20,000 individual members that make up ACCC’s membership.
Crews said that to date about 700 cancer programs involving some 1,900 individuals have participated in the webinars, and about 100 people attended ICLIO’s first annual conference last October.
She said that in addition to the charitable contribution initially made by Bristol-Myers Squibb last year to help launch ICLIO, Merck has also provided an educational grant, but she would not disclose the amount of the funding.
First Drug in Checkpoint Inhibitor Class of Cancer Immunotherapies has demonstrated Superiority over Standard of care in the treatment of First-line Lung Cancer Patients: Merck’s Keytryda
Reporter: Aviva Lev-Ari, PhD, RN
A comprehensive classification of all Immunotherapy Molecules in Development is presented in
Immune-Oncology Molecules In Development & Articles on Topic in @pharmaceuticalintelligence.com
Curators: Stephen J Williams, PhD and Aviva Lev-Ari, PhD, RN
Our goal is to translate breakthrough science into innovative oncology medicines to help people with cancer worldwide. At Merck Oncology, helping people fight cancer is our passion and supporting accessibility to our cancer medicines is our commitment. Our focus is on pursuing research in immuno-oncology and we are accelerating every step in the journey – from lab to clinic – to potentially bring new hope to people with cancer.
As part of our focus on cancer, Merck is committed to exploring the potential of immuno-oncology with one of the fastest-growing development programs in the industry. We are currently executing an expansive research program that includes more than 270 clinical trials evaluating our anti-PD-1 therapy across more than 30 tumor types. We also continue to strengthen our immuno-oncology portfolio through strategic acquisitions and are prioritizing the development of several promising immunotherapeutic candidates with the potential to improve the treatment of advanced cancers.
Merck’s KEYTRUDA® (pembrolizumab) Demonstrates Superior Progression-Free and Overall Survival Compared to Chemotherapy as First-Line Treatment in Patients with Advanced Non-Small Cell Lung Cancer
KEYNOTE-024 Studied Patients Whose Tumors Expressed High Levels of PD-L1
KENILWORTH, N.J.–(BUSINESS WIRE)–Merck (NYSE:MRK), known as MSD outside the United States and Canada, today announced that the KEYNOTE-024 trial investigating the use of KEYTRUDA® (pembrolizumab), in patients with previously untreated advanced non-small cell lung cancer (NSCLC) whose tumors expressed high levels of PD-L1 (tumor proportion score of 50 percent or more), met its primary endpoint. In this trial, KEYTRUDA was superior compared to chemotherapy for both the primary endpoint of progression-free survival (PFS), and the secondary endpoint of overall survival (OS). Based on these results, an independent Data Monitoring Committee (DMC) has recommended that the trial be stopped, and that patients receiving chemotherapy in KEYNOTE-024 be offered the opportunity to receive KEYTRUDA.
“We believe that the KEYNOTE-024 results have the potential to change the therapeutic paradigm in first-line treatment of non-small-cell lung cancer,” said Dr. Roger M. Perlmutter, president, Merck Research Laboratories. “We look forward to sharing these data with the medical community and with regulatory authorities around the world.”
The safety profile of KEYTRUDA in this trial was consistent with that observed in previously reported studies in patients with advanced NSCLC. Results from KEYNOTE-024 will be presented at an upcoming medical meeting.
Merck currently has the largest immuno-oncology clinical development program across the industry and is advancing five registration-enabling studies for NSCLC with KEYTRUDA as a monotherapy and in combination.
About KEYNOTE-024
KEYNOTE-024 is a randomized, pivotal, phase 3 study (ClinicalTrials.gov, NCT02142738) evaluating KEYTRUDA (pembrolizumab) monotherapy compared to standard of care (SOC) platinum-based chemotherapies in the treatment of patients with advanced NSCLC. Patients enrolled were those who had received no prior systemic chemotherapy treatment for their advanced disease and whose tumors expressed high levels of PD-L1 (defined as a tumor proportion score of 50 percent or more) as determined by a central laboratory using an immunohistochemistry assay. The study randomized 305 patients to receive KEYTRUDA (200 mg every three weeks) or SOC platinum-based chemotherapies: paclitaxel+carboplatin, pemetrexed+carboplatin, pemetrexed+cisplatin, gemcitabine+carboplatin, or gemcitabine+cisplatin. Pemetrexed maintenance therapy was permitted for patients with non-squamous histologies. In addition, patients randomized to the control had the option of crossing over to pembrolizumab upon disease progression. The primary endpoint is PFS; secondary endpoints are OS and overall response rate (ORR).
About KEYTRUDA®(pembrolizumab) Injection 100 mg
KEYTRUDA is a humanized monoclonal antibody that works by increasing the ability of the body’s immune system to help detect and fight tumor cells. KEYTRUDA blocks the interaction between PD-1 and its ligands, PD-L1 and PD-L2, thereby activating T lymphocytes which may affect both tumor cells and healthy cells.
KEYTRUDA is indicated for the treatment of patients with unresectable or metastatic melanoma.
KEYTRUDA is also indicated for the treatment of patients with metastatic non-small cell lung cancer (NSCLC) whose tumors express PD-L1 as determined by an FDA-approved test with disease progression on or after platinum-containing chemotherapy. Patients with EGFR or ALK genomic tumor aberrations should have disease progression on FDA-approved therapy for these aberrations prior to receiving KEYTRUDA. This indication is approved under accelerated approval based on tumor response rate and durability of response. An improvement in survival or disease-related symptoms has not yet been established. Continued approval for this indication may be contingent upon verification and description of clinical benefit in the confirmatory trials.
KEYTRUDA is administered at a dose of 2 mg/kg as an intravenous infusion over 30 minutes every three weeks for the approved indications.
Selected Important Safety Information for KEYTRUDA® (pembrolizumab)
Immune-mediated pneumonitis occurred in 19 (3.5%) of 550 patients, including Grade 2 (1.1%), 3 (1.3%), 4 (0.4%), or 5 (0.2%) pneumonitis and occurred more frequently in patients with a history of asthma/chronic obstructive pulmonary disease (5.4%) or prior thoracic radiation (6.0%). Monitor patients for signs and symptoms of pneumonitis. Evaluate suspected pneumonitis with radiographic imaging. Administer corticosteroids for Grade 2 or greater pneumonitis. Withhold KEYTRUDA for Grade 2; permanently discontinue KEYTRUDA for Grade 3 or 4 or recurrent Grade 2 pneumonitis.
Immune-mediated colitis occurred in 4 (0.7%) of 550 patients, including Grade 2 (0.2%) or 3 (0.4%) colitis. Monitor patients for signs and symptoms of colitis. Administer corticosteroids for Grade 2 or greater colitis. Withhold KEYTRUDA for Grade 2 or 3; permanently discontinue KEYTRUDA for Grade 4 colitis.
Immune-mediated hepatitis occurred in patients receiving KEYTRUDA. Monitor patients for changes in liver function. Administer corticosteroids for Grade 2 or greater hepatitis and, based on severity of liver enzyme elevations, withhold or discontinue KEYTRUDA.
Hypophysitis occurred in 1 (0.2%) of 550 patients, which was Grade 3 in severity. Monitor patients for signs and symptoms of hypophysitis (including hypopituitarism and adrenal insufficiency). Administer corticosteroids and hormone replacement as clinically indicated. Withhold KEYTRUDA for Grade 2; withhold or discontinue for Grade 3 or 4 hypophysitis.
Hyperthyroidism occurred in 10 (1.8%) of 550 patients, including Grade 2 (0.7%) or 3 (0.3%) hyperthyroidism. Hypothyroidism occurred in 38 (6.9%) of 550 patients, including Grade 2 (5.5%) or 3 (0.2%) hypothyroidism. Thyroid disorders can occur at any time during treatment. Monitor patients for changes in thyroid function (at the start of treatment, periodically during treatment, and as indicated based on clinical evaluation) and for clinical signs and symptoms of thyroid disorders. Administer replacement hormones for hypothyroidism and manage hyperthyroidism with thionamides and beta-blockers as appropriate. Withhold or discontinue KEYTRUDA (pembrolizumab) for Grade 3 or 4 hyperthyroidism.
Type 1 diabetes mellitus, including diabetic ketoacidosis, occurred in 3 (0.1%) of 2117 patients. Monitor patients for hyperglycemia or other signs and symptoms of diabetes. Administer insulin for type 1 diabetes, and withhold KEYTRUDA and administer anti-hyperglycemics in patients with severe hyperglycemia.
Immune-mediated nephritis occurred in patients receiving KEYTRUDA. Monitor patients for changes in renal function. Administer corticosteroids for Grade 2 or greater nephritis. Withhold KEYTRUDA (pembrolizumab) for Grade 2; permanently discontinue KEYTRUDA for Grade 3 or 4 nephritis.
Other clinically important immune-mediated adverse reactions can occur. For suspected immune mediated adverse reactions, ensure adequate evaluation to confirm etiology or exclude other causes. Based on the severity of the adverse reaction, withhold KEYTRUDA and administer corticosteroids. Upon improvement to Grade 1 or less, initiate corticosteroid taper and continue to taper over at least 1 month. Based on limited data from clinical studies in patients whose immune-related adverse reactions could not be controlled with corticosteroid use, administration of other systemic immunosuppressants can be considered. Resume KEYTRUDA when the adverse reaction remains at Grade 1 or less following corticosteroid taper. Permanently discontinue KEYTRUDA for any Grade 3 immune-mediated adverse reaction that recurs and for any life-threatening immune-mediated adverse reaction.
The following clinically significant, immune-mediated adverse reactions occurred in less than 1% of 550 patients: rash, vasculitis, hemolytic anemia, serum sickness, and myasthenia gravis.
Severe and life-threatening infusion-related reactions have been reported in 3 (0.1%) of 2117 patients. Monitor patients for signs and symptoms of infusion-related reactions including rigors, chills, wheezing, pruritus, flushing, rash, hypotension, hypoxemia, and fever. For Grade 3 or 4 reactions, stop infusion and permanently discontinue KEYTRUDA.
Based on its mechanism of action, KEYTRUDA can cause fetal harm when administered to a pregnant woman. If used during pregnancy, or if the patient becomes pregnant during treatment, apprise the patient of the potential hazard to a fetus. Advise females of reproductive potential to use highly effective contraception during treatment and for 4 months after the last dose of KEYTRUDA.
KEYTRUDA was discontinued due to adverse reactions in 14% of 550 patients. Serious adverse reactions occurred in 38% of patients. The most frequent serious adverse reactions reported in at least 2% of patients were pleural effusion, pneumonia, dyspnea, pulmonary embolism, and pneumonitis. The most common adverse reactions (reported in at least 20% of patients) were fatigue (44%), cough (29%), decreased appetite (25%), and dyspnea (23%).
No formal pharmacokinetic drug interaction studies have been conducted with KEYTRUDA.
It is not known whether KEYTRUDA is excreted in human milk. Because many drugs are excreted in human milk, instruct women to discontinue nursing during treatment with KEYTRUDA and for 4 months after the final dose.
Safety and effectiveness of KEYTRUDA (pembrolizumab) have not been established in pediatric patients.
Dive Brief:
Merck’s cancer immunotherapy Keytruda beat out standard of care chemotherapy in extending time without worsening symptoms and overall survival among patients with previously untreated non-small cell lung cancer (NSCLC), the company said Thursday.
After reviewing the positive results, an independent data monitoring committee recommended halting Keytruda’s Phase 3 trial ahead of schedule.
These results mark the first time a checkpoint inhibitor has been proven more effective than standard of care in a first-line setting, according to The Street.
Merck Extends Cancer Immunotherapy Reach to First-Line Lung Cancer
Merck’s (MRK) flagship cancer immunotherapy Keytruda delayed the re-growth of tumors and prolonged survival in patients with newly diagnosed non-small cell lung cancer compared to chemotherapy, the company said Thursday.
The new phase III study results from Merck are significant because they represent the first time that a drug belonging to the so-called checkpoint inhibitor class of cancer immunotherapies has demonstrated superiority over standard of care in the treatment of first-line lung cancer patients.
Lung cancer is the most prevalent cancer globally, with more than 200,000 patients in the U.S. and 1.5 million patients globally diagnosed each year. As such, lung cancer is an important commercial market for the drug companies developing new therapies which harness the immune system to target and kill cancer cells.
Cancer immunotherapy sales will reach $34 billion to $35 billion by 2026, of which almost half will come from lung cancer, predicts Leerink, the health care investment bank.
Merck is the first of the Big Pharma companies to demonstrate the efficacy of a checkpoint inhibitor in newly diagnosed lung cancer, but it will likely have company soon.
Bristol-Myers Squibb (BMY) is expected to announce results from a phase III study of Opdivo in first-line lung cancer in the third quarter.Roche (RHHBY) is also making an aggressive push with its own checkpoint inhibitor into lung cancer.
For now, Merck is not saying much about how well Keytruda performed in the phase III, study known as Keyote-024. The study compared Keytruda against a doublet chemotherapy in patients with non-small cell lung cancer who had not yet received any systemic therapy.
Keytruda beat chemotherapy on the study’s primary endpoint of progression-free survival and the secondary endpoint of overall survival, the company said. The magnitude of Keytruda’s benefit was not disclosed Thursday, but Merck said the data are strong enough to support approval filings in the U.S. and Europe.
Importantly, the patients enrolled in Merck’s Keytruda study also had to have lung cancers that expressed high levels of the protein PD-L1, defined as a tumor proportion score of 50% or more.
Checkpoint inhibitors like Keytruda and Opdivo work by blocking the interaction between PD-L1, a protein found on the surface of tumor cells. with PD-1, a receptor found on immune cells. Blocking the PD-1/PD-L1 connection allows a patient’s immune system to recognize and kill cancer cells.
Bristol is enrolling a larger, more inclusive group of first-line lung cancer patients with tumors expressing lower levels of PD-L1 in its studies of Opdivo. Depending on the study results, this may give Bristol a competitive advantage in the commercial market.
That’s what has already happened in the treatment market for more advanced, second-line lung cancer, where Bristol enjoys a significant market share advantage over Merck.
Preclinical Data Presented at ASCO 2016 Annual Meeting Demonstrate that Single-Agent NKTR-214 Produces a Large Increase in Tumor-Infiltrating Lymphocytes to Provide Durable Anti-Tumor Activity
SAN FRANCISCO, June 6, 2016 /PRNewswire/ — Nektar Therapeutics (NASDAQ: NKTR) today announced new preclinical data for NKTR-214, an immuno-stimulatory CD-122 biased cytokine currently being evaluated in cancer patients with solid tumors in a Phase 1/2 clinical trial being conducted at MD Anderson Cancer Center and Yale Cancer Center. The new preclinical data presented demonstrate that treatment with single-agent NKTR-214 mobilizes tumor-killing T cells into colon cancer tumors. In addition, mouse pharmacodynamics data demonstrated that a single dose of NKTR-214 can increase and sustain STAT5 phosphorylation (a marker of IL-2 pathway activation) through one week post-dose. These data were presented at the American Society of Clinical Oncology (ASCO) Annual Meeting in Chicago, IL from June 3-7, 2016.
“These latest data build upon our growing body of preclinical evidence demonstrating the unique mechanism of NKTR-214,” added Jonathan Zalevsky, PhD, Vice President, Biology and Preclinical Development at Nektar Therapeutics. “The studies presented at ASCO show that NKTR-214 promotes tumor-killing immune cell accumulation directly in the tumor, providing a mechanistic basis for its significant anti-tumor activity in multiple preclinical tumor models. The ability to grow TILs1 in vivo and replenish the immune system is exceptionally important. We’ve now learned that many human tumors lack sufficient TIL populations and the addition of the NKTR-214 TIL-enhancing MOA could improve the success of many checkpoint inhibitors and other agents, and allow more patients to benefit from immuno-therapy.”
In studies previously published for NKTR-214, when mice bearing established breast cancer tumors are treated with NKTR-214 and anti-CTLA4 (a checkpoint inhibitor therapy known as ipilimumab for human treatment), a large proportion of mice become tumor-free. Anti-tumor immune memory was demonstrated when tumor-free mice were re-challenged by implant with a new breast cancer tumor and then found to clear the new tumor, without further therapy. The new data presented at ASCO demonstrate that upon re-challenge, there is a rapid expansion of newly proliferative CD8 T cells and particularly CD8 effector memory T cells. Both cell populations were readily detectable in multiple tissues (blood, spleen, and lymph nodes) and likely contribute to the anti-tumor effect observed in these animals. Adoptive transfer studies confirmed the immune-memory effect as transplant of splenocytes from tumor-free mice into naïve recipients provided the ability to resist tumor growth.
“NKTR-214 provides a highly unique immune activation profile that allows it to access the IL-2 pathway without pushing the immune system into pathological overdrive,” said Dr. Steve Doberstein, Senior Vice President and Chief Scientific Officer. “NKTR-214’s unique immune-stimulatory profile and antibody-like dosing schedule positions it as a potentially important medicine within the immuno-oncology landscape.”
The data presentation at ASCO entitled, “Immune memory in nonclinical models after treatment with NKTR-214, an engineered cytokine biased towards expansion of CD8+ T cells in tumor,” can be accessed at http://www.nektar.com/2016_NKTR-214_ASCO_poster.pdf
NKTR-214 is a CD122-biased agonist designed to stimulate the patient’s own immune system to kill tumor cells by preferentially activating production of specific immune cells which promote tumor killing, including CD8-positive T cells and Natural Killer (NK) cells, within the tumor micro-environment. CD122, which is also known as the Interleukin-2 receptor beta subunit, is a key signaling receptor that is known to increase proliferation of these types of T cells.2
In preclinical studies, NKTR-214 demonstrated a highly favorable mean ratio of 450:1 within the tumor micro-environment of CD8-positive effector T cells relative to regulatory T cells.3 Furthermore, the pro-drug design of NKTR-214 enables an antibody-like dosing regimen for an immuno-stimulatory cytokine.4
About the NKTR-214 Phase 1/2 Clinical Study
A Phase 1/2 clinical study is underway to evaluate NKTR-214 in patients with advanced solid tumors, including melanoma, renal cell carcinoma and non-small cell lung cancer. The first stage of this study, which is expected to be complete in the second half of 2016, is evaluating escalating doses of single-agent NKTR-214 treatment in approximately 20 patients with solid tumors. The primary objective of the first stage of the study is to evaluate the safety and efficacy of NKTR-214 and to identify a recommended Phase 2 dose. In addition, the study will also assess the immunologic effect of NKTR-214 on TILs and other immune cells in both blood and tumor tissue, and it will also include TCR repertoire profiling. Dose expansion cohorts are planned to evaluate NKTR-214 in specific tumor types, including melanoma, renal cell carcinoma and non-small cell lung cancer.
The NKTR-214 clinical study is being conducted initially at two primary investigator sites: MD Anderson Cancer Center under Drs. Patrick Hwu and Adi Diab; and Yale Cancer Center, under Drs. Mario Sznol and Michael Hurwitz. Patients and physicians interested in the ongoing NKTR-214 study can visit the “Clinical Trials” section of www.mdanderson.org using identifier 2015-0573 or visit https://medicine.yale.edu/cancer/research/trials/active/858.trial.
About Nektar
Nektar Therapeutics has a robust R&D pipeline and portfolio of approved partnered medicines in oncology, pain, immunology and other therapeutic areas. In the area of oncology, Nektar is developing NKTR-214, an immuno-stimulatory CD122-biased agonist, that is in Phase 1/2 clinical development for patients with solid tumors. ONZEALD™ (etirinotecan pegol), a long-acting topoisomerase I inhibitor, is being developed for patients with advanced breast cancer and brain metastases and is partnered with Daiichi Sankyo in Europe. In the area of pain, Nektar has an exclusive worldwide license agreement with AstraZeneca for MOVANTIK™ (naloxegol), the first FDA-approved once-daily oral peripherally-acting mu-opioid receptor antagonist (PAMORA) medication for the treatment of opioid-induced constipation (OIC), in adult patients with chronic, non-cancer pain. The product is also approved in the European Union as MOVENTIG® (naloxegol) and is indicated for adult patients with OIC who have had an inadequate response to laxatives. The AstraZeneca agreement also includes NKTR-119, an earlier stage development program that is a co-formulation of MOVANTIK and an opioid. NKTR-181, a wholly owned mu-opioid analgesic molecule for chronic pain conditions, is in Phase 3 development. In hemophilia, Nektar has a collaboration agreement with Baxalta for ADYNOVATE™ [Antihemophilic Factor (Recombinant)], a longer-acting PEGylated Factor VIII therapeutic approved in the U.S. and Japan for patients over 12 with hemophilia A. In anti-infectives, the company has two collaborations with Bayer Healthcare, Cipro Inhale in Phase 3 for non-cystic fibrosis bronchiectasis and Amikacin Inhale in Phase 3 for patients with Gram-negative pneumonia.
Immune memory in nonclinical models after treatment with NKTR-214, an engineered cytokine biased towards expansion of CD8+ T cells in tumor
Deborah H. Charych, Vidula Dixit, Peiwen Kuo, Werner Rubas, Janet Cetz, Rhoneil Pena, John L. Langowski, Ute Hoch, Murali Addepalli, Stephen K. Doberstein, Jonathan Zalevsky | Nektar Therapeutics, San Francisco, CA
INTRODUCTION
• Recombinant human IL-2 (aldesleukin) is an effective immunotherapy for metastatic melanoma and renal cell carcinoma with durable responses in ~ 10% of patients, but side effects limit its use
• IL-2 has pleiotropic immune modulatory effects[1] which may limit its anti-tumor activity
• Binding to the heterodimeric receptor IL-2Rβγ leads to expansion of tumor-killing CD8+ memory effector T cells and NK cells
• Binding to the heterotrimeric IL-2Rαβγ leads to expansion of suppressive Treg which antagonizes anti-tumor immunity
• NKTR-214 delivers a controlled, sustained and biased signal through the IL-2 receptor pathway.
• The prodrug design of NKTR-214 comprises recombinant human IL-2 chemically conjugated with multiple releasable chains of polyethylene glycol (PEG)
• Slow release of PEG chains over time generates active PEG-conjugated IL-2 metabolites of increasing bioactivity, improving pharmacokinetics and tolerability compared to aldesleukin
• Active NKTR-214 metabolites bias IL-2R activation towards CD8 T cells over Treg[2]
NKTR-214 was engineered to release PEG at physiological pH with predictable kinetics.
The kinetics of PEG release was evaluated in vitro by quantifying free PEG over time using HPLC.
The release of PEG from IL-2 followed predictable kinetics. Symbols = measured data; Line = curve fit based on first order kinetic model. R2 =0.997
In mice, a single dose of NKTR-214 gradually builds and sustains pSTAT5 levels through seven days post-dose. In contrast, IL-2 produces a rapid burst of pSTAT5 that declines four hours post-dose
C57BL/6 mice were treated with either one dose of NKTR-214 (blue) or aldesleukin (red); blood samples were collected at various time points post-dose. pSTAT5 in peripheral blood CD3+ T cells was assessed using flow cytometry. Top graph is an inset showing the 0-4 hour time period. Bottom graph shows the full 10 day time course of the experiment. Histograms on right depict pSTAT5 MFI for IL-2 (red) and NKTR-214 (blue)
Mobilization of lymphocytes from the periphery into the tumor is an inherent property of NKTR-214
A. C57BL/6 mice bearing established subcutaneous B16F10 melanoma tumors were dosed with either NKTR-214 (2 mg/kg, i.v., q9d x2) or aldesleukin (3 mg/kg, i.p. bid x5, two cycles)
B. Tumor infiltrating lymphocytes were analyzed by flow cytometry from treated tumors (*, p<0.05 relative to vehicle; ‡, p<0.05 relative to aldesleukin)
C. Tumor growth inhibition from NKTR-214 was compromised when NKTR-214 was co-administered with Fingolimod, an agent that blocks lymphocyte trafficking.[3], (C57BL/6 mice, B16F10 subcutaneous mouse melanoma). Fingolimod was dosed qd p.o. 5 ug/animal. Lymphocyte count in blood was significantly reduced as expected, for study duration. Tumor growth inhibition (TGI) shown at study endpoint. (One-way ANOVA, Dunnets multiple comparison test ***=p<0.001, ****=p<0.0001 vs. vehicle; #=p<0.05 vs. NKTR-214)
D. Balb/c mice bearing established subcutaneous CT26 colon tumors were dosed with NKTR-214, 0.8 mg/kg i.v. q9dx3 or checkpoint inhibitors, 200 ug/mouse 2x/week. (*, p<0.05 relative to vehicle) E. T cell infiltration into mouse CT26 colon tumors was determined by TIL DNA fraction 7 days post-dose, Adaptive Biotechnologies, n=4 per group
The combination of NKTR-214 and anti-CTLA4 delivers durable anti-tumor activity and vigorous immune memory recall Durable treatment-induced immune memory demonstrated by:
A. Rejection of new tumors implanted into tumor-free mice without further therapy,
Durable anti-tumor immune memory demonstrated by rechallenging treated tumor-free mice with new tumors. New tumors can be eliminated without further treatment.
Balb/c mice initially were implanted with EMT6 murine breast tumors and treated with NKTR-214 0.8mg/kg q9dx3 and anti-CTLA4 200ug/mouse 2x/week. Several weeks later, tumor-free mice were rechallenged with tumor cells EMT6 (blue), CT26 (red) or vehicle (black). Tumor outgrowth occurred when non-related CT26 tumors were implanted. In contrast, tumors were rejected by up to 100% of mice when the same EMT6 tumors were implanted (2×106 EMT6 or CT26 cells)
B. Production of proliferating CD8 effector memory T cells in 3 tissues after tumor rechallenge and
Durable anti-tumor immune memory demonstrated by vigorous proliferative (Ki67+) CD8 T cell responses. The increased activity of these cells is greatest for mice previously treated with NKTR-214 and anti-CTLA4, rechallenged with the same tumor type (blue) compared to a different tumor (red) or mice who were never treated (brown, gray). Treated mice received therapy ~6 months prior. Top row shows total CD8+ cells, bottom row shows effector memory CD8+ in 3 tissues. The role of CD8 and NK cells in mediating the anti-tumor response was previously shown using depletion antibodies.[2]
Mice that became tumor-free from NKTR-214+anti-CTLA4 therapy and treatment naïve controls were rechallenged ~6 months later with either EMT6, CT26 or Sham buffer. No further treatment was given. Immune cells in spleen, lymph and blood were enumerated by flow cytometry, n=4/group. Graphs indicate proliferating Ki67+ total CD8 T cells (top) and effector memory CD8+ CD44hi CD67L-lo (bottom).
C. Transference of immune memory from tumor-free mice to recipient mice.
Durable anti-tumor immune memory demonstrated by adoptive spleen transfer from tumor-free mice to recipient mice. The recipients resist tumor growth without further treatment.
Mouse EMT6 breast tumors were implanted in recipient mice 1 day after receiving spleens from tumor-free mice or naïve mice; (****=p<0.0001 vs. normal control , two way ANOVA Tukey’s multiple comparison test, ns = non-significant)
CONCLUSIONS
• NKTR-214 mechanism of action delivers a controlled, sustained and biased signal to the IL-2 pathway, potentially mitigating systemic toxicities observed from bolus activation by IL-2 (aldesleukin)
• NKTR-214 provides marked efficacy in multiple tumor models, alone or in combination, using lower doses of reduced administration frequency
• Mobilization of T cells from the periphery into the tumor is an inherent property of NKTR-214
• NKTR-214 mechanism enables durable complete anti-tumor response with immune memory recall when combined with anti-CTLA4
• Treatment provides tumor-free mice that consistently eliminate new tumors even in the absence of further therapy • Mice becoming tumor-free from prior treatment reject new tumors by mounting a vigorous CD8+ effector memory response up to 6 months post-therapy
• Adoptive spleen transfer from tumor-free mice confers an anti-tumor response in recipient mice in the absence of further therapy
• NKTR-214 is being evaluated in an ongoing outpatient Phase 1/2 clinical trial for the treatment of solid tumors
Nonin Medical, Inc., the inventor of finger pulse oximetry, today announced the results of a new independent hypoxia lab study in humans that demonstrates that Nonin’s PureSAT pulse oximetry technology captures and reports worsening patient conditions better than other Food and Drug Administration (FDA)-cleared oximeter brands.1Nonin made the results available in a white paper at the American Thoracic Society (ATS) and American Telemedicine Association (ATA) conferences this week.
Not all FDA-cleared finger pulse oximeters perform alike, says a new study. Nonin Medical’s pulse oximetry technology was found to be more accurate in patients with challenging conditions, such as COPD.
In the study, conducted independently by Clinimark Laboratories in Boulder, Colo., three finger pulse oximeters were tested; one from Nonin Medical and two from large, private-labeled manufacturers. All oximeters had FDA 510(k) clearance as “medical devices,” but two of them did not provide the clinical accuracy required to track desaturations in patients with low blood circulation and labored breathing. Only the Nonin Medical oximeter was able to accurately track the desaturation events as compared to an independent hospital tabletop oximeter control device.
Not all FDA-cleared finger pulse oximeters perform alike, says a new study. Nonin Medical’s pulse oximetry technology was found to be more accurate in patients with challenging conditions, such as COPD. (Credit: PRNewsFoto/Nonin Medical, Inc.)
“Over the years, a number of inexpensive, imported FDA-cleared oximeters have flooded the market, all claiming to be accurate,” said Jim Russell, vice president of quality, regulatory and clinical affairs for Nonin Medical. “This study dispels the myth that all pulse oximeters perform alike, especially on challenging patients such as those with chronic obstructive pulmonary disease (COPD).
“Clinicians, hospitals and telemedicine providers can better manage COPD patients and potentially reduce readmission rates by choosing pulse oximeters that provide early and accurate data on all patients, including the sickest patients. Nonin Medical’s oximeter performance is proven,” Russell said.
References 1Batchelder, P.B., Fingertip Pulse Oximeter Performance in Dyspnea and Low Perfusion During Hypoxic Events. Clinimark Laboratories, Boulder, Colorado. 2016. White Paper.
hysical chemists have devised a rolling DNA-based motor that’s 1,000 times faster than any other synthetic DNA motor, giving it potential for real-world applications, such as disease diagnostics. Nature Nanotechnology is publishing the finding.
“Unlike other synthetic DNA-based motors, which use legs to ‘walk’ like tiny robots, ours is the first rolling DNA motor, making it far faster and more robust,” says Khalid Salaita, the Emory University chemist who led the research. “It’s like the biological equivalent of the invention of the wheel for the field of DNA machines.”
The speed of the new DNA-based motor, which is powered by ribonuclease H, means a simple smart phone microscope can capture its motion through video. The researchers have filed an invention disclosure patent for the concept of using the particle motion of their rolling molecular motor as a sensor for everything from a single DNA mutation in a biological sample to heavy metals in water.
“Our method offers a way of doing low-cost, low-tech diagnostics in settings with limited resources,” Salaita says.
The field of synthetic DNA-based motors, also known as nano-walkers, is about 15 years old. Researchers are striving to duplicate the action of nature’s nano-walkers. Myosin, for example, are tiny biological mechanisms that “walk” on filaments to carry nutrients throughout the human body.
“It’s the ultimate in science fiction,” Salaita says of the quest to create tiny robots, or nano-bots, that could be programmed to do your bidding. “People have dreamed of sending in nano-bots to deliver drugs or to repair problems in the human body.”
So far, however, mankind’s efforts have fallen far short of nature’s myosin, which speeds effortlessly about its biological errands. “The ability of myosin to convert chemical energy into mechanical energy is astounding,” Salaita says. “They are the most efficient motors we know of today.”
Some synthetic nano-walkers move on two legs. They are essentially enzymes made of DNA, powered by the catalyst RNA. These nano-walkers tend to be extremely unstable, due to the high levels of Brownian motion at the nano-scale. Other versions with four, and even six, legs have proved more stable, but much slower. In fact, their pace is glacial: A four-legged DNA-based motor would need about 20 years to move one centimeter.
Kevin Yehl, a post-doctoral fellow in the Salaita lab, had the idea of constructing a DNA-based motor using a micron-sized glass sphere. Hundreds of DNA strands, or “legs,” are allowed to bind to the sphere. These DNA legs are placed on a glass slide coated with the reactant: RNA.
The DNA legs are drawn to the RNA, but as soon as they set foot on it they destroy it through the activity of an enzyme called RNase H. As the legs bind and then release from the substrate, they guide the sphere along, allowing more of the DNA legs to keep binding and pulling.
“It’s called a burnt-bridge mechanism,” Salaita explains. “Wherever the DNA legs step, they trample and destroy the reactant. They have to keep moving and step where they haven’t stepped in order to find more reactant.”
The combination of the rolling motion, and the speed of the RNase H enzyme on a substrate, gives the new DNA motor its stability and speed.
“Our DNA-based motor can travel one centimeter in seven days, instead of 20 years, making it 1,000 times faster than the older versions,” Salaita says. “In fact, nature’s myosin motors are only 10 times faster than ours, and it took them billions of years to evolve.”
Emory post-doctoral fellow Kevin Yehl sets up a smart-phone microscope to get a readout for the particle motion of the rolling DNA-based motor.
The researchers demonstrated that their rolling motors can be used to detect a single DNA mutation by measuring particle displacement. They simply glued lenses from two inexpensive laser pointers to the camera of a smart phone to turn the phone into a microscope and capture videos of the particle motion.
“Using a smart phone, we can get a readout for anything that’s interfering with the enzyme-substrate reaction, because that will change the speed of the particle,” Salaita says. “For instance, we can detect a single mutation in a DNA strand.”
This simple, low-tech method could come in handy for doing diagnostic sensing of biological samples in the field, or anywhere with limited resources.
The proof that the motors roll came by accident, Salaita adds. During their experiments, two of the glass spheres occasionally became stuck together, or dimerized. Instead of making a wandering trail, they left a pair of straight, parallel tracks across the substrate, like a lawn mower cutting grass. “It’s the first example of a synthetic molecular motor that goes in a straight line without a track or a magnetic field to guide it,” Salaita says.
In addition to Salaita and Yehl, the co-authors on the Nature Nanotechnology paper include Emory researchers Skanda Vivek, Yang Liu, Yun Zhang, Megzhen Fan, Eric Weeks and Andrew Mugler (who is now at Purdue University).
DNA-based machines that walk by converting chemical energy into controlled motion could be of use in applications such as next-generation sensors, drug-delivery platforms and biological computing. Despite their exquisite programmability, DNA-based walkers are challenging to work with because of their low fidelity and slow rates (∼1 nm min–1). Here we report DNA-based machines that roll rather than walk, and consequently have a maximum speed and processivity that is three orders of magnitude greater than the maximum for conventional DNA motors. The motors are made from DNA-coated spherical particles that hybridize to a surface modified with complementary RNA; the motion is achieved through the addition of RNase H, which selectively hydrolyses the hybridized RNA. The spherical motors can move in a self-avoiding manner, and anisotropic particles, such as dimerized or rod-shaped particles, can travel linearly without a track or external force. We also show that the motors can be used to detect single nucleotide polymorphism by measuring particle displacement using a smartphone camera.
A 3-D rendering of a fluorescence image mapping the piconewton forces applied by T cells. The height and color indicates the magnitude of the applied force. (Microscopy image by Yang Liu.)
By Carol Clark
T cells, the security guards of the immune system, use a kind of mechanical “handshake” to test whether a cell they encounter is a friend or foe, a new study finds.
“We’ve provided the first direct evidence that a T cell gives precise mechanical tugs to other cells,” Salaita says. “And we’ve shown that these tugs are central to a T cell’s process of deciding whether to mount an immune response. A tug that releases easily, similar to a casual handshake, signals a friend. A stronger grip indicates a foe.”
T cells continuously patrol through the body in search of foreign invaders. They have molecules known as T-cell receptors (TCR) that can recognize specific antigenic peptides on the surface of a pathogenic or cancerous cell. When a T cell detects an antigen-presenting cell (APC), its TCR connects to a ligand, or binding molecule, of the APC. If the T cell determines the ligand is foreign, it becomes activated and starts pumping calcium. The calcium is part of a signaling chain that recruits other cells to come and help mount an immune response.
Scientists have known about this process for decades, but they have not fully understood how the T cell distinguishes small modifications to the antigenic ligand and how it decides to respond to it. “If you view this T cell response purely as a chemical process, it does not fully explain the remarkable specifity of the binding,” Salaita says. “When you take the two components – the TCR and the ligand on the surface of cells – and just let them chemically bind in a solution, for example, you can’t predict what will trigger a strong or a weak immune response.”
The researchers hypothesized that mechanical strain might also play a role in a T cell response, since the T cell continues to move even as it locks into a bind with an antigenic ligand.
To test this idea, the Salaita lab developed DNA-based gold nanoparticle tension sensors that light up, or fluoresce, in response to a miniscule mechanical force of a piconewton – about one million-millionth the weight of an apple.
The researchers designed experiments using T cells from a mouse and allowed them to test ligands containing eight amino acid peptides that had slight mutations.
“We swapped out the fourth amino acid position to create really subtle chemical changes in the ligand that would be very difficult to distinguish without a mechanical component,” Salaita says.
Some of the mutated ligands were given a firmer anchor to give them a tighter “grip” to the moving TCR.
Through the experiments, captured on microscopy video, the researchers were able to see, record and measure the responses of the T cells as they moved across the ligands.
“As a T cell moves across a cell’s surface and encounters a ligand, it pulls on it,” Salaita explains. “It doesn’t pull very hard, it’s a very precise and tiny tug that is not sustained. The T cell pulls and stops, pulls and stops, all across the surface. It’s like the T cell is doing a mechanical test of the ligand.”
During the experiments, the T cells did not activate fully when they encountered ligands with weak anchors. In contrast, when a T cell encountered a ligand with a firm anchor, the T cell became activated, showing that it experienced a piconewton level of resistance.
The amount of force that was applied by the T cell was mapped by using tension probes of different stiffness. Probes that responded to 19 piconewtons did not fluoresce, while softer, 12-piconewton probes produced high signal.
Following the fluorescence of the probe, the T cells switched on their calcium pumps and increased the calcium concentration within the cell, indicating that the T cell is mounting an immune response.
“We were able to map out the order of the cascade of chemical and mechanical reactions,” Salaita says. “First, the T cell uses a very specific and finely tuned mechanical tug to distinguish friend from foe. And when it senses a precise, piconewton level of force in response to that tug, the T cell realizes that it has encountered a foreign body and gives the signal for attack.”
The discovery could help in the search for treatments of auto-immune diseases and the development of immune therapies for cancer.
“Cancer cells have an extra molecule that can make T cell security guards ‘drunk’ or ‘sleepy’ so that they are not able to function properly,” Salaita says. “Learning more about the mechanical forces involved in an effective immune response may help us develop ways to evade this defense system of cancer cells.”
Co-authors on the study include Yang Liu, Victor Pui-Yan Ma, Kornelia Galior and Zheng Liu (from the Salaita lab); and Lori Blanchfield and Rakieb Andargachew (from the Evavold lab).
T cells protect the body against pathogens and cancer by recognizing specific foreign peptides on the cell surface. Because antigen recognition occurs at the junction between a migrating T cell and an antigen-presenting cell (APC), it is likely that cellular forces are generated and transmitted through T-cell receptor (TCR)-ligand bonds. Here we develop a DNA-based nanoparticle tension sensor producing the first molecular maps of TCR-ligand forces during T cell activation. We find that TCR forces are orchestrated in space and time, requiring the participation of CD8 coreceptor and adhesion molecules. Loss or damping of TCR forces results in weakened antigen discrimination, showing that T cells harness mechanics to optimize the specificity of response to ligand.
T cells are triggered when the T-cell receptor (TCR) encounters its antigenic ligand, the peptide-major histocompatibility complex (pMHC), on the surface of antigen presenting cells (APCs). Because T cells are highly migratory and antigen recognition occurs at an intermembrane junction where the T cell physically contacts the APC, there are long-standing questions of whether T cells transmit defined forces to their TCR complex and whether chemomechanical coupling influences immune function. Here we develop DNA-based gold nanoparticle tension sensors to provide, to our knowledge, the first pN tension maps of individual TCR-pMHC complexes during T-cell activation. We show that naïve T cells harness cytoskeletal coupling to transmit 12–19 pN of force to their TCRs within seconds of ligand binding and preceding initial calcium signaling. CD8 coreceptor binding and lymphocyte-specific kinase signaling are required for antigen-mediated cell spreading and force generation. Lymphocyte function-associated antigen 1 (LFA-1) mediated adhesion modulates TCR-pMHC tension by intensifying its magnitude to values >19 pN and spatially reorganizes the location of TCR forces to the kinapse, the zone located at the trailing edge of migrating T cells, thus demonstrating chemomechanical crosstalk between TCR and LFA-1 receptor signaling. Finally, T cells display a dampened and poorly specific response to antigen agonists when TCR forces are chemically abolished or physically “filtered” to a level below ∼12 pN using mechanically labile DNA tethers. Therefore, we conclude that T cells tune TCR mechanics with pN resolution to create a checkpoint of agonist quality necessary for specific immune response.
Andrej Kosmrlj et al., Proc Natl Acad Sci U S A, 2008
Larry H. Bernstein, MD, FCAP, Curator
LPBI
The two articles above are connected in an interesting way by the fact that cellular forces are generated and transmitted through T-cell receptor (TCR)-ligand bonds. The T-cell receptor (TCR) encounters its antigenic ligand, the peptide-major histocompatibility complex (pMHC), on the surface of antigen presenting cells (APCs). The movement detected by the fluorescent sensor may be based on only a single amino acid at the cell surface ligand. The result is chemomechanical crosstalk between TCR and LFA-1 receptor signaling
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