Breaking News
September 19, 2018 - Bristol-Myers Squibb’s Novel, Oral, Selective TYK2 Inhibitor Delivered Significant Skin Clearance in Patients with Moderate to Severe Plaque Psoriasis in Phase 2 Trial
September 19, 2018 - Can work stress contribute to Parkinson’s disease risk?
September 19, 2018 - Global Climate Action Summit: A focus on kids and climate
September 19, 2018 - Targeted Lung Denervation procedure significantly reduces COPD problems
September 19, 2018 - FDA-approved ‘safe’ daily BPA exposure may contribute to insulin resistance
September 19, 2018 - Research finds physical connection between the brain’s fluid reservoirs and meningeal lymphatics
September 19, 2018 - UCalgary study could help physicians make better treatment decisions for stroke
September 19, 2018 - Biomedical review finds failure rates in some surgical mesh treatments to be unacceptably high
September 19, 2018 - Researchers develop more accurate measure of body fat
September 19, 2018 - Doctors and students rally to support gun violence research, education
September 19, 2018 - LEO Pharma and MorphoSys announce expansion of strategic alliance to develop peptide-derived drugs
September 19, 2018 - Seniors in pain hop aboard the canna-bus
September 19, 2018 - New compound could prevent malaria parasites from maturing inside mosquito
September 19, 2018 - Scientists find alterations in blood flow in response to body position change
September 19, 2018 - UNC Health Care extends free access to virtual care service in the aftermath of Hurricane Florence
September 19, 2018 - Opioid Refills Rare After Rhinoplasty
September 19, 2018 - Corn, obesity, and navigating healthy eating choices as a parent
September 19, 2018 - Journal editor aims to prompt thoughtful review of ethics in precision health
September 19, 2018 - Researchers identify key step in how plant cells respond to pathogens
September 18, 2018 - Researchers analyze how exposure to silver nanoparticles affects zebrafish
September 18, 2018 - Study shows air pollution may be bad for the fetus
September 18, 2018 - Coffee May Have Another Perk for Kidney Patients
September 18, 2018 - Tongue-in-cheek Nobels honor nutritional analysis of cannibalism, roller-coaster kidney stones treatment
September 18, 2018 - Progress, priorities, challenges are focus of State of Stanford Medicine | News Center
September 18, 2018 - Established Alzheimer’s Risk Gene Has a New Role
September 18, 2018 - Hospitalization after antibiotic initiation found to be higher for people with Alzheimer’s disease
September 18, 2018 - Many children with special healthcare needs do not have access to ‘PCMH-concordant’ care
September 18, 2018 - Investigational nasal influenza vaccine tested in children and teens
September 18, 2018 - Lymphatic vessels surrounding the brain play crucial role in multiple sclerosis, research suggests
September 18, 2018 - New fiber laser-based ultrasound sensor may have potential applications in medical diagnostics
September 18, 2018 - Protect your heart and health during ‘dog days’ of summer
September 18, 2018 - Faculty receive awards for promise in biomedical research, clinical care | News Center
September 18, 2018 - Digital games for CVD-related self-management improve exercise capacity and energy expenditure
September 18, 2018 - Aluminum inclusions help enhance adsorption of chemo drugs onto active carbon delivery capsule
September 18, 2018 - Adding PET scans to CT imaging can change treatment for women with cervical cancer
September 18, 2018 - UCSF awarded $20 million grant to study impacts of new, emerging tobacco products
September 18, 2018 - Human brains may be wired to prefer lying on the couch, suggests research
September 18, 2018 - Zika virus vaccine shows promise for treatment of fatal glioblastoma
September 18, 2018 - Theravance Biopharma and Mylan to Report New Data from Phase 3 Studies of Yupelri (revefenacin) in Oral Presentation at European Respiratory Society International Congress 2018
September 18, 2018 - INSiGHT identifies unique retinal regulatory genes
September 18, 2018 - Diversity, science leadership grants awarded to student-faculty pairs | News Center
September 18, 2018 - Many parents blame electronics for sleep problems among teens
September 18, 2018 - Researchers study neuronal activity in brain that prevents individuals from doing physical activity
September 18, 2018 - Purifying Proteins from Mammalian Cell Culture
September 18, 2018 - Researchers map 3D structure of toxic proteins used by Pseudomonas aeruginosa to trigger infection
September 18, 2018 - Outcome of ACL reconstruction related to the way you move post-surgery
September 18, 2018 - Study aims to investigate risk factors for PPCs in surgical patients with gastric cancer
September 18, 2018 - Ardelyx Submits New Drug Application for Tenapanor for IBS-C
September 18, 2018 - Sociodemographic disparities in eyeglass use among elderly
September 18, 2018 - New Drug Shows Promise for Progressive Form of MS
September 18, 2018 - Babies exposed to higher levels of organochlorine compounds in womb may have worse lung function
September 18, 2018 - Women exposed to trauma in their lives gave birth to underweight male infants
September 18, 2018 - Probiotic supplementation may reduce use of antibiotics, scientific analysis shows
September 18, 2018 - Resveratrol decreases pain severity and levels of inflammatory biomarkers in osteoarthritis patients
September 18, 2018 - Research shows pollution is reaching the placenta
September 18, 2018 - KAIST researchers develop heart-targeting drug delivery technology using tannin acid
September 18, 2018 - Muscle relaxants used during general anesthesia can increase risk of pulmonary complications
September 18, 2018 - Silicone breast implants may increase risk of rare adverse outcomes in women
September 18, 2018 - Pediatricians Have a Role in Encouraging Play Among Children
September 18, 2018 - California’s Medicaid program hits ‘print’ when the feds need info
September 18, 2018 - Genes, environment and schizophrenia—new study finds the placenta is the missing link
September 18, 2018 - Boehringer Ingelheim announces study results of COPD patients treated with Spiolto Respimat
September 18, 2018 - PAREXEL launches Patient Innovation Center to improve drug development process
September 18, 2018 - Children’s National and NIAID launch pediatric clinical research partnership
September 18, 2018 - Researchers may be overlooking complexities in social relations of primates
September 18, 2018 - Key signaling molecule that helps stem cells make healthy bone declines as we age
September 18, 2018 - More women veterans with chronic pain use CIH therapies than men
September 18, 2018 - As Earth Warms, Heat-Related Deaths Will Multiply
September 18, 2018 - Labetalol use up for patients with preeclampsia and asthma
September 18, 2018 - MoreGrasp project shows significant results in field of thought-controlled grasp neuroprosthetics
September 18, 2018 - Drumming can benefit school children with autism
September 18, 2018 - Busyness can help people to make virtuous choices, research shows
September 18, 2018 - Two-minute bursts of in-class exercise breaks do not disrupt learning and teaching
September 18, 2018 - New online tools aid surgeons and specialists who care for older people
September 18, 2018 - Researchers use CRISPR to identify gene that helps cells resist flavivirus infection
September 18, 2018 - Brain’s support cells may play a central role in repetitive behaviors related to OCD
September 18, 2018 - Scientists discover novel mechanism by which synthesized proteins reach target compartment in cell
September 18, 2018 - Easy and rapid test for viral infections can cut antibiotic use, hospitalizations
September 18, 2018 - Gunshot victims more likely to require blood transfusions and die than other trauma patients
September 18, 2018 - Cyclacel Pharmaceuticals Announces Initiation of Phase 1b/2 Clinical Trial of Sapacitabine With Olaparib in BRCA Mutant Breast Cancer
Scientists develop novel computational framework to support personalized cancer treatment

Scientists develop novel computational framework to support personalized cancer treatment

image_pdfDownload PDFimage_print

Researchers at Columbia University Irving Medical Center (CUIMC) have developed a highly innovative computational framework that can support personalized cancer treatment by matching individual tumors with the drugs or drug combinations that are most likely to kill them.

The study, published today on Nature Genetics, by Dr. Andrea Califano of Columbia University Irving Medical Center and Dr. Irvin Modlin of Yale University and Wren Laboratories LLC, co-senior author on the study, with collaborators from 17 research centers worldwide, details a proof of concept for a novel analytical platform applicable to any cancer type and validates its predictions on gastroenteropancreatic neuroendocrine tumors (GEP-NETs). The latter represent a rare class of tumors of the digestive system that, when metastatic, are associated with poor survival.

In a comprehensive analysis of samples from 212 patients, the team first identified a new class of drug-targets, called master regulators, which are rarely if ever mutated in cancer patients, and then predicted the drugs that can specifically invert their activity. Surprisingly, even though tumors were analyzed on an individual patient basis, the algorithm predicted the same top drug – Entinostat – for almost half of the metastatic patients. More importantly, when tested in a xenograft transplant of the tumor in a mouse, this drug induced dramatic shrinking of the tumor, while drugs predicted to have partial or no effect were also validated to produce results in line with predictions. These data led to rapid IND (Investigational New Drug) approval by the FDA for a metastatic GEP-NET clinical trial that is open and recruiting patients at Columbia University.

The innovative approach proposed in this manuscript, OncoTreat, is now available as a New York State Department of Health approved test through the Department of Pathology and Cell Biology at CUIMC. The test was co-developed with DarwinHealth, a precision oncology company born out of the Califano Lab work. It is the only such test designed to predict drugs that are optimally matched to individual patient tumors for 10 different aggressive tumor subtypes of ovarian, breast, pancreas, prostate, bladder, and lung cancer, as well as meningioma, sarcoma, glioblastoma, and GEP-NETs.

“This manuscript represents a first proof of concept of what may become a valuable new tool to deliver an effective and systematic precision medicine approach to cancer patients that may complement what we are currently doing with genetic mutations,” says Dr. Califano, the Clyde and Helen Wu Professor of Chemical and Systems Biology and chair of the Department of Systems Biology at CUIMC.

“Using novel systems biology methodologies, which combine the use of supercomputers with large-scale pharmacological assays, we can computationally predict and prioritize drugs and drug combinations that will most effectively kill cancer cells,” explains Dr. Califano. “Such an approach is especially promising for patients with aggressive tumors, who lack actionable mutations, fail to respond to targeted inhibitors or immune-checkpoint inhibitors, or relapse following initial response to a standard of care drug or drug combination. These patients, who unfortunately represent the majority of the aggressive tumor cases, present few, if any, effective therapeutic options. We hope that OncoTreat may offer the oncologist new alternatives when they run out of approved therapies, alternatives that are predicated on an increasingly mechanistic understanding of cancer cell regulation and response to drugs rather than on educated guesswork.”

Dr. Modlin, who had initially proposed the concept of addressing Neuroendocrine tumors using the innovative strategy developed by Dr. Califano, commented that the successful demonstration of the efficacy of a pre-treatment molecular identification strategy was a significant advance on previous practice where treatment agents were used based upon serendipitous selection rather than objective molecular evidence. This work combined with the use of molecular signature tools in blood to monitor real-time efficacy of therapy on disease are likely to change the face of therapeutic management in many diseases.

OncoTreat’s precision medicine approach

The OncoTreat framework centers on identifying and analyzing actionable proteins in cancer patients, independent of their genetic mutations. Called master regulators (MR), these proteins are organized into small regulatory modules – so-called tumor checkpoints – which are responsible for regulating and ensuring the stability of tumor cells. Master regulators and tumor checkpoints can be efficiently and systematically elucidated using the VIPER algorithm developed by the Califano Lab and published in an earlier Nature Genetics manuscript; critically, these analyses allow tracking their activity through metastatic progression, relapse, and development of drug resistance. These computational models were built based on mathematical concepts from information theory and Bayesian statistics and have been extensively validated over the past decade.

MR proteins represent a novel class of tumor vulnerabilities and potential therapeutic targets that are being increasingly adopted by pharmaceutical companies. Extensive research has demonstrated that shutting down the activity of these proteins is catastrophic for tumor cells, making it virtually impossible for them to survive and grow in their environment. In this study, drug compounds are prioritized based on their ability to revert the coordinated activity of 50 such master regulator proteins, as identified by the analysis of tumor samples. Predicted activity reversal was surveyed from an analysis of drug assays both in cell lines and in vivo, in PDX (Patient-Derived Xenografts) mice models.

“Master regulators–a new Achilles’ heel of cancer–represent the engine room of the cancer cell, where the effects of all tumorigenic mutations come together. What OncoTreat is able to do is attack this convergence point with a therapeutic intervention,” says collaborator Gary Schwartz, MD, division chief of hematology and oncology at CUIMC and associate director of the Herbert Irving Comprehensive Cancer Center. “By collapsing this tumor bottleneck, blocking this Achilles’ heel, the cancer can no longer survive. This method is so innovative, requiring a lot of mathematical modeling and understanding. It’s a whole new approach to cancer therapeutics, taking us in an entirely new direction.”

Califano and team validated the OncoTreat approach on a cohort of 212 gastroenteropancreatic neuroendocrine tumors, a deliberate choice since GEP-NETs are rare and poorly characterized, making them one of the more challenging tumors to research. Their analysis identified several MR proteins, including key immune function modulators, whose role as critical tumor dependencies was experimentally confirmed. The GEP-NET cells were screened against a library of 107 compounds, and found that the drug, Entinostat, proved to successfully invert the activity of the top 50 MR proteins in 42 percent of GEP-NET patients, providing the rationale for the follow up clinical trial.

“It is certainly our hope that this may provide a short cut to identify viable candidates for phase 2 trials in this and other malignancies,” says coauthor Edward Gelmann, MD, professor of medicine and of pathology and cell biology at CUIMC.

In addition to its potential therapeutic value, OncoTreat provides novel insight into the mechanisms and maintenance of GEP-NETs. In future work, Califano and collaborators intend to expand this approach to cover more than 80% of human malignancies and to develop clinical trials that will test the predictions in patients.

Source:

http://www.cumc.columbia.edu/

Tagged with:

About author

Related Articles