Predicting radiographic outcomes of vertebral body tethering in adolescent idiopathic scoliosis patients using machine learning.

Anterior Vertebral Body Tethering (AVBT) is a growing alternative treatment for adolescent idiopathic scoliosis (AIS), offering an option besides spinal fusion. While AVBT aims to correct spinal deformity through growth correction, its outcomes have been mixed. To improve surgical outcomes, this study aimed to develop a machine learning-based tool to predict short- and midterm spinal curve correction in AIS patients who underwent AVBT surgery, using the most predictive clinical, radiographic, and surgical parameters. After institutional review board approval and based on inclusion criteria, 91 AIS patients who underwent AVBT surgery were selected from the Shriners Hospitals for Children, Philadelphia. For all patients, longitudinal standing (PA or AP, and lateral) and side bending spinal Radiographs were retrospectively obtained at six visits: preop and first standing, one year, two years, five years postop, and at the most recent follow-up. Demographic, radiographic, and surgical features associated with curve correction were collected. The sequential backward feature selection method was used to eliminate correlated features and to provide a rank-ordered list of the most predictive features of the AVBT correction. A Gradient Boosting Regressor (GBR) model was trained and tested using the selected features to predict the final correction of the curve in AIS patients. Eleven most predictive features were identified. The GBR model predicted the final Cobb angle with an average error of 6.3 ± 5.6 degrees. The model also provided a prediction interval, where 84% of the actual values were within the 90% prediction interval. A list of the most predictive features for AVBT curve correction was provided. The GBR model, trained on these features, predicted the final curve magnitude with a clinically acceptable margin of error. This model can be used as a clinical tool to plan AVBT surgical parameters and improve outcomes.

Direct Linear Transformation for the Measurement of In-Situ Peripheral Nerve Strain During Stretching.

Peripheral nerves undergo physiological and non-physiological stretch during development, normal joint movement, injury, and more recently while undergoing surgical repair. Understanding the biomechanical response of peripheral nerves to stretch is critical to the understanding of their response to different loading conditions and thus, to optimizing treatment strategies and surgical interventions. This protocol describes in detail the calibration process of the stereo-imaging camera system via direct linear transformation and the tracking of the three-dimensional in-situ tissue displacement of peripheral nerves during stretch, obtained from three-dimensional coordinates of the video files captured by the calibrated stereo-imaging camera system. From the obtained three-dimensional coordinates, the nerve length, change in the nerve length, and percent strain with respect to time can be calculated for a stretched peripheral nerve. Using a stereo-imaging camera system provides a non-invasive method for capturing three-dimensional displacements of peripheral nerves when stretched. Direct linear transformation enables three-dimensional reconstructions of peripheral nerve length during stretch to measure strain. Currently, no methodology exists to study the in-situ strain of stretched peripheral nerves using a stereo-imaging camera system calibrated via direct linear transformation. Capturing the in-situ strain of peripheral nerves when stretched can not only aid clinicians in understanding underlying injury mechanisms of nerve damage when overstretched but also help optimize treatment strategies that rely on stretch-induced interventions. The methodology described in the paper has the potential to enhance our understanding of peripheral nerve biomechanics in response to stretch to improve patient outcomes in the field of nerve injury management and rehabilitation.

Studying the Effects of Shoulder Dystocia and Neonate-Focused Delivery Maneuvers on Brachial Plexus Strain: A Computational Study.

The purpose of this computational study was to investigate the effects of neonate-focused clinical delivery maneuvers on brachial plexus (BP) during shoulder dystocia. During shoulder dystocia, the anterior shoulder of the neonate is obstructed behind the symphysis pubis of the maternal pelvis, postdelivery of the neonate's head. This is managed by a series of clinical delivery maneuvers. The goal of this study was to simulate these delivery maneuvers and study their effects on neonatal BP strain. Using madymo models of a maternal pelvis and a 90th-percentile neonate, various delivery maneuvers and positions were simulated including the lithotomy position alone of the maternal pelvis, delivery with the application of various suprapubic pressures (SPPs), neonate in an oblique position, and during posterior arm delivery maneuver. The resulting BP strain (%) along with the required maternal delivery force was reported in these independently simulated scenarios. The lithotomy position alone served as the baseline. Each of the successive maneuvers reported a decrease in the required delivery force and resulting neonatal BP strain. As the applied SPP force increased (three scenarios simulated), the required maternal delivery force and neonatal BP strain decreased. A further decrease in both delivery force and neonatal BP strain was observed in the oblique position, with the lowest delivery force and neonatal BP strain reported during the posterior arm delivery maneuver. Data obtained from the improved computational models in this study enhance our understanding of the effects of clinical maneuvers on neonatal BP strain during complicated birthing scenarios such as shoulder dystocia.

In vitro coupled motions of the whole human thoracic and lumbar spine with rib cage.

Study design: In vitro biomechanical study investigating the coupled motions of the whole normative human thoracic spine (TS) and lumbar spine (LS) with rib cage. Objective: To quantify the region-specific coupled motion patterns and magnitudes of the TS, thoracolumbar junction (TLJ), and LS simultaneously. Background: Studying spinal coupled motions is important in understanding the development of complex spinal deformities and providing data for validating computational models. However, coupled motion patterns reported in vitro are controversial, and no quantitative data on region-specific coupled motions of the whole human TS and LS are available. Methods: Pure, unconstrained bending moments of 8 Nm were applied to seven fresh-frozen human cadaveric TS and LS specimens (mean age: 70.3 ± 11.3 years) with rib cages to elicit flexion-extension (FE), lateral bending (LB), and axial rotation (AR). During each primary motion, region-specific rotational range of motion (ROM) data were captured. Results: No statistically significant, consistent coupled motion patterns were observed during primary FE. During primary LB, there was significant (p < 0.05) ipsilateral AR in the TS and a general pattern of contralateral coupled AR in the TLJ and LS. There was also a tendency for the TS to extend and the LS to flex. During primary AR, significant coupled LB was ipsilateral in the TS and contralateral in both the TLJ and LS. Significant coupled flexion in the LS was also observed. Coupled LB and AR ROMs were not significantly different between the TS and LS or from one another. Conclusions: The findings support evidence of consistent coupled motion patterns of the TS and LS during LB and AR. These novel data may serve as reference for computational model validations and future in vitro studies investigating spinal deformities and implants.

In vivo biomechanical responses of neonatal brachial plexus when subjected to stretch.

Neonatal brachial plexus palsy (NBPP) results from over-stretching of the neonatal brachial plexus during complicated birthing scenarios. The lack of information on the biomechanical response of the neonatal brachial plexus complex when subjected to stretch limits our understanding of the NBPP injury mechanism. This study aims to fill that critical gap by using a neonatal piglet animal model and providing the in vivo biomechanical properties of the neonatal brachial plexus complex when subjected to stretch. Forty-seven brachial plexus levels (identified by the four brachial plexus terminal nerve branches namely musculocutaneous, median, ulnar, and radial), obtained from 16 neonatal Yorkshire piglets (3-5 days old), were subjected to stretch-induced failure. The average maximum load and corresponding strain were reported to be 16.6 ± 1.3 N and 36.1 ± 1.6%, respectively. Maximum loads reported at the musculocutaneous level were significantly lower than the median and radial levels. No differences in strains at failure were reported at all four tested levels. Proximal or distal failure locations were reported in 83% of the tests with 17% mid-length ruptures that were primarily reported at the bifurcation of the median and ulnar brachial plexus levels. Histological studies reported an overall loss of wavy pattern of the nerve fibers, an increase in nerve spacing, fiber disruptions, and blood vessel ruptures in the stretched tissue. This in vivo piglet animal study offers insight into the NBPP mechanism by reporting biomechanical, injury location, and structural damage responses in neonatal brachial plexus when subjected to stretch.

Patient-specific finite element modeling of scoliotic curve progression using region-specific stress-modulated vertebral growth.

PURPOSE: This study describes the creation of patient-specific (PS) osteo-ligamentous finite element (FE) models of the spine, ribcage, and pelvis, simulation of up to three years of region-specific, stress-modulated growth, and validation of simulated curve progression with patient clinical angle measurements. RESEARCH QUESTION: Does the inclusion of region-specific, stress-modulated vertebral growth, in addition to scaling based on age, weight, skeletal maturity, and spine flexibility allow for clinically accurate scoliotic curve progression prediction in patient-specific FE models of the spine, ribcage, and pelvis? METHODS: Frontal, lateral, and lateral bending X-Rays of five AIS patients were obtained for approximately three-year timespans. PS-FE models were generated by morphing a normative template FE model with landmark points obtained from patient X-rays at the initial X-ray timepoint. Vertebral growth behavior and response to stress, as well as model material properties were made patient-specific based on several prognostic factors. Spine curvature angles from the PS-FE models were compared to the corresponding X-ray measurements. RESULTS: Average FE model errors were 6.3 ± 4.6°, 12.2 ± 6.6°, 8.9 ± 7.7°, and 5.3 ± 3.4° for thoracic Cobb, lumbar Cobb, kyphosis, and lordosis angles, respectively. Average error in prediction of vertebral wedging at the apex and adjacent levels was 3.2 ± 2.2°. Vertebral column stress ranged from 0.11 MPa in tension to 0.79 MPa in compression. CONCLUSION: Integration of region-specific stress-modulated growth, as well as adjustment of growth and material properties based on patient-specific data yielded clinically useful prediction accuracy while maintaining physiological stress magnitudes. This framework can be further developed for PS surgical simulation.

Automated Clustering Technique (ACT) for Early Onset Scoliosis: A preliminary report.

PURPOSE: While the C-EOS system helps organize and classify Early Onset Scoliosis (EOS) pathology, it is not data-driven and does not help achieve consensus for surgical treatment. The current study aims to create an automated method to cluster EOS patients based on pre-operative clinical indices. METHODS: A total of 1114 EOS patients were used for the study, with the following distribution by etiology: congenital (240), idiopathic (217), neuromuscular (417), syndromic (240). Pre-operative clinical indices used for clustering were age, major curve (Cobb) angle, kyphosis, number of levels involved in a major curve (Cobb angle) and kyphosis along with deformity index (defined as the ratio of major Cobb angle and kyphosis). Fuzzy C-means clustering was performed for each etiology individually, with one-way ANOVA performed to assess statistical significance (p < 0.05). RESULTS: The automated clustering method resulted in three clusters per etiology as the optimal number based on the highest average membership values. Statistical analyses showed that the clusters were significantly different for all the clinical indices within and between etiologies. Link to the ACT-EOS web application: https://biomed.drexel.edu/labs/obl/toolkits/act-eos-application . CONCLUSION: An automated method to cluster EOS patients based on pre-operative clinical indices was developed identifying three unique, data-driven subgroups for each C-EOS etiology category. Adoption of such an automated clustering framework can help improve the standardization of clinical decision-making for EOS.

Clinical impact of ibrutinib plus R-CHOP in untreated DLBCL coexpressing BCL2 and MYC in the phase 3 PHOENIX trial.

Diffuse large B-cell lymphoma (DLBCL), with high coexpression of BCL2 and MYC proteins (DE lymphoma), is considered an adverse prognostic indicator associated mostly with non-germinal center B-cell-like (non-GCB) DLBCL. BCL2/MYC overexpression is associated with B-cell receptor (BCR) pathway activation; consequently, DE DLBCL may be sensitive to BCR inhibitors. We assessed whether high BCL2/MYC coexpression by RNA sequencing could identify a patient subset responsive to ibrutinib using baseline biopsies from the PHOENIX trial, which evaluated the addition of ibrutinib to rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) in untreated non-GCB DLBCL. BCL2/MYC RNA expression was correlated with lower event-free survival (EFS) and overall survival (OS) using Kaplan-Meier estimates with Cox regression and log-rank testing. In total, 234 of 766 (30.5%) patients had high BCL2/MYC coexpression: 123 of 386 (31.9%) received ibrutinib plus R-CHOP and 111 of 380 (29.2%) received R-CHOP. EFS was superior with ibrutinib plus R-CHOP compared with R-CHOP alone in patients with high BCL2/MYC coexpression, but there was no significant impact on OS. However, EFS and OS showed clinically meaningful improvement with ibrutinib plus R-CHOP over R-CHOP alone in patients aged <60 years with high BCL2/MYC coexpression. We observed a significant association between high BCL2/MYC coexpression and activated B-cell-like and MYD88L265P/CD79B-mutated subtypes of DLBCL. Consequently, high BCL2/MYC coexpression identified a subset of non-GCB DLBCL that may be preferentially responsive to ibrutinib and warrants further investigation. This trial was registered at www.clinicaltrials.gov as #NCT01855750.

Longitudinal expression profiling identifies a poor risk subset of patients with ABC-type diffuse large B-cell lymphoma.

Despite the effectiveness of immuno-chemotherapy, 40% of patients with diffuse large B-cell lymphoma (DLBCL) experience relapse or refractory disease. Longitudinal studies have previously focused on the mutational landscape of relapse but fell short of providing a consistent relapse-specific genetic signature. In our study, we have focused attention on the changes in GEP accompanying DLBCL relapse using archival paired diagnostic/relapse specimens from 38 de novo patients with DLBCL. COO remained stable from diagnosis to relapse in 80% of patients, with only a single patient showing COO switching from activated B-cell-like (ABC) to germinal center B-cell-like (GCB). Analysis of the transcriptomic changes that occur following relapse suggest ABC and GCB relapses are mediated via different mechanisms. We developed a 30-gene discriminator for ABC-DLBCLs derived from relapse-associated genes that defined clinically distinct high- and low-risk subgroups in ABC-DLBCLs at diagnosis in datasets comprising both population-based and clinical trial cohorts. This signature also identified a population of <60-year-old patients with superior PFS and OS treated with ibrutinib-R-CHOP as part of the PHOENIX trial. Altogether this new signature adds to the existing toolkit of putative genetic predictors now available in DLBCL that can be readily assessed as part of prospective clinical trials.

Ibrutinib and rituximab plus cyclophosphamide, doxorubicin, vincristine and prednisone in patients with previously untreated non-germinal centre B-cell-like diffuse large B-cell lymphoma: A Chinese subgroup analysis of the phase III PHOENIX trial.

In this post hoc subgroup analysis of 200 patients enrolled in China from the phase III PHOENIX trial (N = 838, NCT01855750), addition of ibrutinib to rituximab plus cyclophosphamide, doxorubicin, vincristine and prednisone (R-CHOP) did not improve event-free survival (EFS) versus placebo+R-CHOP in the intent-to-treat (ITT; n = 200, hazard ratio [HR] = 0.83, 95% confidence interval [CI]: 0·509-1.349; p = 0.4495) or activated B-cell-like (ABC; n = 141 [based on available gene-expression profiling data], HR = 0.86, 95% CI: 0.467-1.570; p = 0.6160) subpopulations. However, ibrutinib+R-CHOP improved EFS (HR = 0·50, 95% CI: 0.251-1.003) and progression-free survival (PFS; HR = 0.48, 95% CI: 0.228-1.009) versus placebo+R-CHOP in patients aged <60 but not ≥60 years. Grade ≥3 serious treatment-emergent adverse events occurred more with ibrutinib+R-CHOP (45·6% vs. 31·3%). The percentage of patients receiving ≥6 cycles of R-CHOP was similar across treatment arms in those <60 years. A numerical trend was seen towards improved EFS and PFS with ibrutinib+R-CHOP versus placebo+R-CHOP in patients with MYC-high/BCL2-high co-expression. In this slightly younger Chinese subgroup, ibrutinib+R-CHOP did not improve EFS in the ITT and ABC subpopulations but improved outcomes with manageable safety in patients <60 years, consistent with overall PHOENIX study outcomes.

Investigating Stress-relaxation and Failure Responses in the Trachea.

The biomechanical properties of the trachea directly affect the airflow and contribute to the biological function of the respiratory system. Understanding these properties is critical to understanding the injury mechanism in this tissue. This protocol describes an experimental approach to study the stress-relaxation behavior of porcine trachea that were pre-stretched to 0% or 10% strain for 300 s, followed by mechanical tensile loading until failure. This study provides details of the experimental design, data acquisition, analyses, and preliminary results from the porcine tracheae biomechanical testing. Using the detailed steps provided in this protocol and the data analysis MATLAB code, future studies can investigate the time-dependent viscoelastic behavior of trachea tissue, which is critical to understanding its biomechanical responses during physiological, pathological, and traumatic conditions. Furthermore, in-depth studies of the biomechanical behavior of the trachea will critically aid in improving the design of related medical devices such as endotracheal implants that are widely used during surgeries.

Discovery of JNJ-64264681: A Potent and Selective Covalent Inhibitor of Bruton's Tyrosine Kinase.

Bruton's tyrosine kinase (BTK) is a Tec family kinase that plays an essential role in B-cell receptor (BCR) signaling as well as Fcγ receptor signaling in leukocytes. Pharmacological inhibition of BTK has been shown to be effective in treating hematological malignancies and is hypothesized to provide an effective strategy for the treatment of autoimmune diseases such as rheumatoid arthritis and systemic lupus erythematosus. We report the discovery and preclinical properties of JNJ-64264681 (13), a covalent, irreversible BTK inhibitor with potent whole blood activity and exceptional kinome selectivity. JNJ-64264681 demonstrated excellent oral efficacy in both cancer and autoimmune models with sustained in vivo target coverage amenable to once daily dosing and has advanced into human clinical studies to investigate safety and pharmacokinetics.

Molecular determinants of outcomes in relapsed or refractory mantle cell lymphoma treated with ibrutinib or temsirolimus in the MCL3001 (RAY) trial.

Mantle cell lymphoma (MCL) is a rare, incurable lymphoma subtype characterized by heterogeneous outcomes. To better understand the clinical behavior and response to treatment, predictive biomarkers are needed. Using residual archived material from patients enrolled in the MCL3001 (RAY) study, we performed detailed analyses of gene expression and targeted genetic sequencing. This phase III clinical trial randomized patients with relapsed or refractory MCL to treatment with either ibrutinib or temsirolimus. We confirmed the prognostic capability of the gene expression proliferation assay MCL35 in this cohort treated with novel agents; it outperformed the simplified MCL International Prognostic Index in discriminating patients with different outcomes. Regardless of treatment arm, our data demonstrated that this assay captures the risk conferred by known biological factors, including increased MYC expression, blastoid morphology, aberrations of TP53, and truncated CCND1 3' untranslated region. We showed the negative impact of BIRC3 mutations/deletions on outcomes in this cohort and identified that deletion of chromosome 8p23.3 also negatively impacts survival. Restricted to patients with deletions/alterations in TP53, ibrutinib appeared to abrogate the deleterious impact on outcome. These data illustrate the potential to perform a molecular analysis of predictive biomarkers on routine patient samples that can meaningfully inform clinical practice.

Predicting curve progression for adolescent idiopathic scoliosis using random forest model.

BACKGROUND: Adolescent Idiopathic Scoliosis (AIS) is a three-dimensional (3D) spinal deformity characterized by coronal curvature and rotational deformity. Predicting curve progression is important for the selection and timing of treatment. Although there is a consensus in the literature regarding prognostic factors associated with curve progression, the order of importance, as well as the combination of factors that are most predictive of curve progression is unknown. OBJECTIVES: (1) create an ordered list of prognostic factors that most contribute to curve progression, and (2) develop and validate a Machine Learning (ML) model to predict the final major Cobb angle in AIS patients. METHODS: 193 AIS patients were selected for the current study. Preoperative PA, lateral and lateral bending radiographs were retrospectively obtained from the Shriners Hospitals for Children. Demographic and radiographic features, previously reported to be associated with curve progression, were collected. Sequential Backward Floating Selection (SBFS) was used to select a subset of the most predictive features. Based on the performance of several machine learning methods, a Random Forest (RF) regressor model was used to provide the importance rank of prognostic features and to predict the final major Cobb angle. RESULTS: The seven most predictive prognostic features in the order of importance were initial major Cobb angle, flexibility, initial lumbar lordosis angle, initial thoracic kyphosis angle, age at last visit, number of levels involved, and Risser "+" stage at the first visit. The RF model predicted the final major Cobb angle with a Mean Absolute Error (MAE) of 4.64 degrees. CONCLUSION: A RF model was developed and validated to identify the most important prognostic features for curve progression and predict the final major Cobb angle. It is possible to predict the final major Cobb angle value within 5 degrees error from 2D radiographic features. Such methods could be directly applied to guide intervention timing and optimization for AIS treatment.

Development of a Finite Element Model of the Pediatric Thoracic and Lumbar Spine, Ribcage, and Pelvis With Orthotropic Region-Specific Vertebral Growth.

Finite element (FE) modeling of the spine has increasingly been applied in orthopedic precision-medicine approaches. Previously published FE models of the pediatric spine growth have made simplifications in the geometry of anatomical structures, material properties, and representation of vertebral growth. To address those limitations, a comprehensive FE model of a pediatric (10-year-old) osteo-ligamentous thoracic and lumbar spine (T1-L5 with intervertebral discs (IVDs) and ligaments), ribcage, and pelvis with age- and level-specific ligament properties and orthotropic region-specific vertebral growth was developed and validated. Range of motion (ROM) measures, namely, lateral bending, flexion-extension, and axial rotation, of the current 10 YO FE model were generally within reported ranges of scaled in vitro adult ROM data. Changes in T1-L5 spine height, as well as kyphosis (T2-T12) and lordosis (L1-L5), angles in the current FE model for two years of growth (from ages 10 to 12 years) were within ranges reported from corresponding pediatric clinical data. The use of such comprehensive pediatric FE models can provide clinically relevant insights into normative and pathological biomechanical responses of the spine, and also contribute to the development and optimization of clinical interventions for spine deformities.

Effects of Prestretch on Neonatal Peripheral Nerve: An In Vitro Study.

Background Characterizing the biomechanical failure responses of neonatal peripheral nerves is critical in understanding stretch-related peripheral nerve injury mechanisms in neonates. Objective This in vitro study investigated the effects of prestretch magnitude and duration on the biomechanical failure behavior of neonatal piglet brachial plexus (BP) and tibial nerves. Methods BP and tibial nerves from 32 neonatal piglets were harvested and prestretched to 0, 10, or 20% strain for 90 or 300 seconds. These prestretched samples were then subjected to tensile loading until failure. Failure stress and strain were calculated from the obtained load-displacement data. Results Prestretch magnitude significantly affected failure stress but not the failure strain. BP nerves prestretched to 10 or 20% strain, exhibiting significantly lower failure stress than those prestretched to 0% strain for both prestretch durations (90 and 300 seconds). Likewise, tibial nerves prestretched to 10 or 20% strain for 300 seconds, exhibiting significantly lower failure stress than the 0% prestretch group. An effect of prestretch duration on failure stress was also observed in the BP nerves when subjected to 20% prestretch strain such that the failure stress was significantly lower for 300 seconds group than 90 seconds group. No significant differences in the failure strains were observed. When comparing BP and tibial nerve failure responses, significantly higher failure stress was reported in tibial nerve prestretched to 20% strain for 300 seconds than BP nerve. Conclusion These data suggest that neonatal peripheral nerves exhibit lower injury thresholds with increasing prestretch magnitude and duration while exhibiting regional differences.

Identification of a genetic signature enriching for response to ibrutinib in relapsed/refractory follicular lymphoma in the DAWN phase 2 trial.

BACKGROUND: The single-arm DAWN trial (NCT01779791) of ibrutinib monotherapy in patients with relapsed/refractory follicular lymphoma (FL) showed an overall response rate (ORR) of 20.9% and a median response duration of 19.4 months. This biomarker analysis of the DAWN dataset sought to determine genetic classifiers for prediction of response to ibrutinib treatment. METHODS: Whole exome sequencing was performed on baseline tumor samples. Potential germline variants were excluded; a custom set of 1216 cancer-related genes was examined. Responder- versus nonresponder-associated variants were identified using Fisher's exact test. Classifiers with increasing numbers of genes were created using a greedy algorithm that repeatedly selected genes, adding the most nonresponders to the existing "predicted nonresponders" set and were evaluated with 10-fold cross-validation. RESULTS: Exome data were generated from 88 patient samples and 13,554 somatic mutation variants were inferred. Response data were available for 83 patients (17 responders, 66 nonresponders). Each sample showed 100 to >500 mutated genes, with greater variance across nonresponders. The overall variant pattern was consistent with previous FL studies; 75 genes had mutations in >10% of patients, including genes previously reported as associated with FL. Univariate analysis yielded responder-associated genes FANCA, HISTH1B, ANXA6, BTG1, and PARP10, highlighting the importance of functions outside of B-cell receptor signaling, including epigenetic processes, DNA damage repair, cell cycle/proliferation, and cell motility/invasiveness. While nonresponder-associated genes included well-known TP53 and CARD11, genetic classifiers developed using nonresponder-associated genes included ATP6AP1, EP400, ARID1A, SOCS1, and TBL1XR1, suggesting resistance to ibrutinib may be related to broad biological functions connected to epigenetic modification, telomere maintenance, and cancer-associated signaling pathways (mTOR, JAK/STAT, NF-κB). CONCLUSION: The results from univariate and genetic classifier analyses provide insights into genes associated with response or resistance to ibrutinib in FL and identify a classifier developed using nonresponder-associated genes, which warrants further investigation. TRIAL REGISTRATION: NCT01779791.

Effect of ibrutinib with R-CHOP chemotherapy in genetic subtypes of DLBCL.

In diffuse large B cell lymphoma (DLBCL), tumors belonging to the ABC but not GCB gene expression subgroup rely upon chronic active B cell receptor signaling for viability, a dependency that is targetable by ibrutinib. A phase III trial ("Phoenix;" ClinicalTrials.gov: NCT01855750) showed a survival benefit of ibrutinib addition to R-CHOP chemotherapy in younger patients with non-GCB DLBCL, but the molecular basis for this benefit was unclear. Analysis of biopsies from Phoenix trial patients revealed three previously characterized genetic subtypes of DLBCL: MCD, BN2, and N1. The 3-year event-free survival of younger patients (age ≤60 years) treated with ibrutinib plus R-CHOP was 100% in the MCD and N1 subtypes while the survival of patients with these subtypes treated with R-CHOP alone was significantly inferior (42.9% and 50%, respectively). This work provides a mechanistic understanding of the benefit of ibrutinib addition to chemotherapy, supporting its use in younger patients with non-GCB DLBCL.

Combined ibrutinib and venetoclax treatment vs single agents in the TCL1 mouse model of chronic lymphocytic leukemia.

The covalent inhibitor of Bruton's tyrosine kinase ibrutinib and the specific Bcl-2 inhibitor venetoclax are both highly efficacious single-agent drugs in the treatment of chronic lymphocytic leukemia (CLL). Based on their complementary modes of action, ibrutinib and venetoclax are hypothesized to act in a synergistic fashion. Currently, it is unclear whether combined treatment is indeed superior to continuous single-agent treatment and what mechanisms underlie the resistance to combination treatment. In addition, the effects of such treatment on the skewed T-cell compartment characteristic of CLL are as yet unknown. In the murine Eµ-TCL1 adoptive transfer model resembling aggressive CLL, we found that combined treatment resulted in the deepest responses, with the longest duration related to a combination of decreased proliferation and increased induction of apoptosis. In addition, alterations in T-cell subsets were most prominent after combination treatment, with increased naive cells and reduced effector memory cells. Remarkably, effects of single agents but also combination treatment were eventually interrupted by relapse, and we found downregulation of BIM expression as a plausible cause of acquired drug resistance. Nevertheless, in this murine model, the combination of venetoclax and ibrutinib has increased efficacy over single agents, accompanied by a restoration of the T-cell compartment.

Circulating tumor DNA for comprehensive noninvasive monitoring of lymphoma treated with ibrutinib plus nivolumab.

To advance the use of circulating tumor DNA (ctDNA) applications, their broad clinical validity must be tested in different treatment settings, including targeted therapies. Using the prespecified longitudinal systematic collection of plasma samples in the phase 1/2a LYM1002 trial (registered on www.clinicaltrials.gov as NCT02329847), we tested the clinical validity of ctDNA for baseline mutation profiling, residual tumor load quantification, and acquisition of resistance mutations in patients with lymphoma treated with ibrutinib+nivolumab. Inclusion criterion for this ancillary biological study was the availability of blood collected at baseline and cycle 3, day 1. Overall, 172 ctDNA samples from 67 patients were analyzed by the LyV4.0 ctDNA Cancer Personalized Profiling Deep Sequencing Assay. Among baseline variants in ctDNA, only TP53 mutations (detected in 25.4% of patients) were associated with shorter progression-free survival; clones harboring baseline TP53 mutations did not disappear during treatment. Molecular response, defined as a >2-log reduction in ctDNA levels after 2 cycles of therapy (28 days), was achieved in 28.6% of patients with relapsed diffuse large B-cell lymphoma who had ≥1 baseline variant and was associated with best response and improved progression-free survival. Clonal evolution occurred frequently during treatment, and 10.3% new mutations were identified after 2 treatment cycles in nonresponders. PLCG2 was the topmost among genes that acquired new mutations. No patients acquired the C481S BTK mutation implicated in resistance to ibrutinib in CLL. Collectively, our results provide the proof of concept that ctDNA is useful for noninvasive monitoring of lymphoma treated with targeted agents in the clinical trial setting.