A Sonomyography-Based Muscle Computer Interface for Individuals With Spinal Cord Injury

Impairment of hand functions in individuals with spinal cord injury (SCI) severely disrupts activities of daily living. Recent advances have enabled rehabilitation assisted by robotic devices to augment the residual function of the muscles. Traditionally, electromyography-based muscle activity sensing interfaces have been utilized to sense volitional motor intent to drive robotic assistive devices. However, the dexterity and fidelity of control that can be achieved with electromyography-based control have been limited due to inherent limitations in signal quality. We have developed and tested a muscle-computer interface (MCI) utilizing sonomyography to provide control of a virtual cursor for individuals with motor-incomplete spinal cord injury. We demonstrate that individuals with SCI successfully gained control of a virtual cursor by utilizing contractions of muscles of the wrist joint. The sonomyography-based interface enabled control of the cursor at multiple graded levels demonstrating the ability to achieve accurate and stable endpoint control. Our sonomyography-based muscle-computer interface can enable dexterous control of upper-extremity assistive devices for individuals with motor-incomplete SCI.

Development, Content Validity and Reliability of Upper Extremity Functional Skill Measure in C5-C7 Spinal Cord Injury

STUDY DESIGN

A methodological research design.

OBJECTIVE

To create an objective measure for assessing hand functions in C5-C7 spinal cord injury (SCI) and estimation of its content validity and internal consistency reliability.

METHOD

This study was executed in three phases. Phase 1 included a thorough review of the literature, semi-structured in-depth interviews of participants with tetraplegia and interviews of caregivers of SCI individuals and healthcare workers dealing with SCI to understand the hand functions of individuals with C5-C7 SCI. Phase 2 consisted of the development of the tool. The content validity ratio (CVR) method and the opinion of the expert validated the content of the upper extremity functional skill measure (UEFSM). Phase 3 included a quantitative evaluation of the tool which was done on a targeted group of 30 subjects with C5-C7 SCI.

RESULTS

Through the review of the literature and in-depth interview of the participants, 11 items were developed under four content areas: grasp, grip, pinch and gross movement. Items with a minimum CVR of 0.56 were retained at a significance level of p = 0.05 resulting in a 10-item tool for assessing the hand function of individuals with C5-C7 SCI categorized under four subscales. Pilot testing on 10 subjects reveals an average time of 2 minutes and 25 seconds to complete the task. The Cronbach's alpha was found to be 0.878.

CONCLUSION

UEFSM is a 10-item tool with good content validity and internal consistency reliability for the assessment of hand functions in individuals with C5-C7 SCI.

Activation of RAS/MAPK pathway confers MCL-1 mediated acquired resistance to BCL-2 inhibitor venetoclax in acute myeloid leukemia

Despite high initial response rates, acute myeloid leukemia (AML) treated with the BCL-2-selective inhibitor venetoclax (VEN) alone or in combinations commonly acquires resistance. We performed gene/protein expression, metabolomic and methylation analyses of isogenic AML cell lines sensitive or resistant to VEN, and identified the activation of RAS/MAPK pathway, leading to increased stability and higher levels of MCL-1 protein, as a major acquired mechanism of VEN resistance. MCL-1 sustained survival and maintained mitochondrial respiration in VEN-RE cells, which had impaired electron transport chain (ETC) complex II activity, and MCL-1 silencing or pharmacologic inhibition restored VEN sensitivity. In support of the importance of RAS/MAPK activation, we found by single-cell DNA sequencing rapid clonal selection of RAS-mutated clones in AML patients treated with VEN-containing regimens. In summary, these findings establish RAS/MAPK/MCL-1 and mitochondrial fitness as key survival mechanisms of VEN-RE AML and provide the rationale for combinatorial strategies effectively targeting these pathways.

Epigenetic Forensics for Suspect Identification and Age Prediction

Background: Genetic testing at crime scenes is an instrumental molecular technique to identify or eliminate suspects, as well as to overturn wrongful convictions. Yet, genotyping alone cannot reveal the age of a sample, which could help advance the utility of crime scene samples for suspect identification. The distribution of cytosine methylation within a DNA sample can be leveraged to determine the epigenetic age of someone's blood. Methodology: We sought to demonstrate the ability of DNA methylation markers to accurately discern the age of blood spots from an actual crime scene, a "mock" crime scene, and also from a tube of blood stored in ethylenediaminetetraacetic acid for >20 years. This was achieved by quantifying methylation within known age-associated genetic loci across each DNA sample. We observed a strong linear coefficient (0.91) and high overall correlation (R ² = 0.963) between the known age of a sample and the predicted age. Conclusion: We show that novel methods for targeted methylation and low-input whole-genome bisulfite sequencing can enable a novel and improved forensic profile of a crime scene that discerns not only who was present at the crime, but also their age. Finally, we use this model to discern the age and provenance of a blood sample that was used in a criminal investigation.

Design and simulation of robot hand for writing and correction assistant applications

Purpose

The design of robot hand for writing and correction assistant applications work will be partially replaced as to develop the remote-assisted robot hand control needed to manipulate all this kind of work. As it is stress and strain full job for all teachers, which needs to bring a sustainable solution, hence robot hand which resembles the human hand which is teleoperated with the remote control is designed.

Design/methodology/approach

This work presents the design and simulation of a robot hand for correction assistant applications. To replace the work partially especially for the teachers who are undergoing the paper correction work like putting tick mark, cross mark, allocation of marks, etc.

Findings

In this paper the design of the same and its simulation of writing the horizontal line, vertical line and writing number two is presented, in further research, a prototype model and its analysis will be done.

Originality/value

The design is been done using the modelling software Creo 5.4 where the design will be used to print the prototype model which is physical using 3D printing technology and controlling and testing will be done on the same prototype model using simple Arduino.

Acquired Resistance to BET-PROTACs (Proteolysis-Targeting Chimeras) Caused by Genomic Alterations in Core Components of E3 Ligase Complexes

Proteolysis-targeting chimeras (PROTAC) are bifunctional molecules that hijack endogenous E3 ubiquitin ligases to induce ubiquitination and subsequent degradation of protein of interest. Recently, it has been shown that PROTACs with robust in vitro and in vivo activities and, in some cases, drug-like pharmaceutical properties can be generated using small-molecule ligands for the E3 ligases VHL and CRBN. These findings stoked tremendous enthusiasm on using PROTACs for therapeutics development. Innate and acquired drug resistance often underlies therapeutic failures, particularly for cancer therapy. With the PROTAC technology progressing rapidly toward therapeutic applications, it would be important to understand whether and how resistance to these novel agents may emerge. Using BET-PROTACs as a model system, we demonstrate that resistance to both VHL- and CRBN-based PROTACs can occur in cancer cells following chronic treatment. However, unlike what was often observed for many targeted therapeutics, resistance to BET-PROTACs did not result from secondary mutations that affect compound binding to the target. In contrast, acquired resistance to both VHL- and CRBN-based BET-PROTACs was primarily caused by genomic alterations that compromise core components of the relevant E3 ligase complexes.

Abstract 4749: Acquired resistance to BET-PROTACs caused by genomic alterations in core components of E3 ligase complexes

Proteolysis Targeting Chimeras (PROTACs) are bifunctional molecules that hijack endogenous E3 ubiquitin ligases to induce ubiquitination and subsequent degradation of protein of interest. Recently, it has been shown that PROTACs with robust in vitro and in vivo activities and, in some cases, drug-like pharmaceutical properties can be generated using small molecule ligands for the E3 ligases VHL and CRBN. These findings stoked tremendous enthusiasm on using PROTACs for therapeutics development. Innate and acquired drug resistance often underlies therapeutic failures, particularly for cancer therapy. With the PROTAC technology progressing rapidly towards therapeutic applications, it would be important to understand whether and how resistance to these novel agents may emerge. Using BET-PROTACs as a model system, we demonstrate that resistance to both VHL- and CRBN-based PROTACs can occur in cancer cells following chronic treatment. However, unlike what was often observed for many targeted therapeutics, resistance to BET-PROTACs did not result from secondary mutations that affect compound binding to the target. In contrast, acquired resistance to both VHL- and CRBN-based BET-PROTACs was primarily caused by genomic alterations that compromise core components of the relevant E3 ligase complexes.

Citation Format: Bridget Riley-Gillis, Lu Zhang, Priyanka Vijay, Yu Shen. Acquired resistance to BET-PROTACs caused by genomic alterations in core components of E3 ligase complexes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4749.

Abstract 1523: Repression of IRF4 and CYTIP unleashes anti-tumor interferon response in CDK4 inhibitor therapy in mantle cell lymphoma

Inhibition of CDK4/6 has emerged as an effective cancer therapy, but the underlying mechanism remains obscure. We have addressed this question in mantle cell lymphoma (MCL), a Non-Hodgkin's B cell lymphoma that remains incurable due to the development of drug resistance. As dysregulation of CDK4 (CDK6 is silenced) and cyclin D1 underlies unrestrained proliferation of MCL cells, targeting CDK4 also represents a rational approach to MCL therapy.

Previously we have demonstrated in preclinical studies that sustained inhibition of CDK4 with palbociclib led to prolonged early G1 arrest (pG1) that both prevented proliferation of MCL cells and reprogrammed them for killing by diverse agents. On this basis, we hypothesized that CDK4 inhibition may prolong and deepen the clinical response to its partner drug in combination therapy. Indeed, in a phase I clinical trial of palbociclib plus ibrutinib (BTK inhibitor) in recurrent MCL (n=28), complete response was observed in 43% of patients as compared with 23% in response to ibrutinib alone. Moreover, the responses were rapid and durable; only 4 of the 18 responding-patients have progressed in the 3.5 years since the trial opened.

To address how CDK4 inhibition enhances therapy vulnerability, in a separate phase I clinical trial palbociclib was administered to MCL patients for 12 days to induce pG1; bortezomib was given in pG1 and again after synchronous S phase reentry (pG1-S). At the optimal dose combination only one of 6 patients progressed and complete remission in one patient continues into its 6th year. Longitudinal integrative RNA and exome-sequencing (WTS/WES) of MCL cells isolated from lymph node biopsies at baseline, in pG1 (day 8) and in pG1-S (day 21) of individual patients showed that inhibition of CDK4 induced pG1 in all patients initially, regardless of the subsequent clinical response.

However, induction of pG1 led to a striking difference in cellular gene expression in pG1 (day 8/day 1) in MCL cells of responders (R) and non-responders (NR). There were 2041 genes upregulated and 1483 genes downregulated 1.5-fold or greater in R (N=4, EdgeR, FDR 0.05), but only 39 genes upregulated and 401 genes dowregulated in NR (N=3). Moreover, 5 genes were down regulated in R and upregulated in NR. Gene set enrichment analysis together with loss and gain of function studies revealed that among them, loss of IRF4 in R led to de-repression of IRF7 and induction of the interferon response. This in turn resulted in TRAIL mediated apoptosis due to repression of CYTIP downstream of IRF4 repression.

In summary, by longitudinal functional genomics of purified MCL cells and functional studies, we have discovered that CDK4 inhibition reprograms MCL for therapy vulnerability through induction of anti-tumor IFN response, and identified CYTIP and IRF4 as biomarkers that discriminate sensitivity from resistance to therapeutic targeting of CDK4.

Citation Format: Maurizio Di Liberto, Peter Martin, Xiangao Huang, Priyanka Vijay, David Chiron, Scott Ely, Christopher Mason, Olivier Elemento, John Leonard, Selina Chen-Kiang. Repression of IRF4 and CYTIP unleashes anti-tumor interferon response in CDK4 inhibitor therapy in mantle cell lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1523.

Abstract IA08: Reprogramming human cancer cells in CDK4/6 inhibitor therapy

CDK4 and CDK6 drive cell cycle progression through early G1 and are frequently deregulated in human cancer. Selective inhibition of CDK4/6 with palbociclib (PD 0332991) has demonstrated exciting clinical efficacy in diverse human cancers. However, the mechanism that discriminates sensitivity from resistance to targeting CDK4/6 remains obscure.

Mantle cell lymphoma (MCL) is an incurable non-Hodgkin's lymphoma where deregulated CDK4 activity and cyclin D1 expression underlies unrestrained proliferation and disease progression. In a phase I clinical trial in recurrent MCL, we demonstrated that palbociclib alone produced a durable clinical response with a favorable toxicity profile. To investigate the mechanism for targeting CDK4/6, we have now shown in primary cancer cells that 1) inhibition of CDK4/6 leads to early G1 arrest that requires Rb, the CDK4/6 substrate; 2) prolonged early G1 arrest (pG1) sensitizes Rb-proficient cancer cells to killing by diverse clinically-relevant agents; and 3) pG1 sensitization stems from continuous expression of genes scheduled for early G1 only. This leads to an imbalance in genes expression, which is exacerbated in synchronous progression to S phase (pG1-S) after palbociclib withdrawal, due to incomplete restoration of cell cycle-coupled gene expression.

In a hypothesis-driven phase Ib clinical trial, targeting CDK4 with palbociclib in sequential combination with the proteasome inhibitor bortezoimb was well tolerated (n=16). It exhibited a durable palbociclib dose-dependent clinical activity, including one complete remission for over 3 years with only one progression at the optimal dose combination (n=6). Longitudinal integrative whole transcriptome and whole exome sequencing of tumor cells isolated from serial lymph node biopsies demonstrated that palbociclib initially induced pG1 in MCL cells of all patients, regardless of copy number variation or mutation (ATM, p53). Cell cycle control by palbociclib is thus initially intact in MCL, but is insufficient to predict the clinical response.

As predicted, only genes programmed for early G1 were expressed pG1, concurrent PI3K inactivation in primary MCL cells. However, <1% of the 1400 genes suppressed (not programmed) in pG1 in clinically-responding patients were activated in non-responding patients. These genes were critical for redox homeostasis, suggesting that PI3K inactivation and redox stress mediates pG1 sensitization.

This study represents the first investigation of genes that discriminate sensitivity from resistance in targeting CDK4/CDK6 in human cancer, through integrative longitudinal analysis of whole exome and whole transcriptome sequencing in concert with protein expression analysis and functional studies. Selective inhibition of CDK4 induces pG1 in all MCL patients, which apparently reprograms MCL for clinical response to bortezomib through PI3K inactivation and suppression of genes for redox homeostasis.

Citation Format: Selina Chen-Kiang, Maurizio Di Liberto, Priyanka Vijay, David Chiron, Xiangao Huang, Scott Ely, Olivier Elemento, Christopher Mason, Lewis Cantley, John P. Leonard, Peter Martin. Reprogramming human cancer cells in CDK4/6 inhibitor therapy. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Cancer Cell Cycle - Tumor Progression and Therapeutic Response; Feb 28-Mar 2, 2016; Orlando, FL. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(11_Suppl):Abstract nr IA08.

Abstract LB-073: Epigenome evolution in relapsed acute myeloid leukemia

Acute myeloid leukemia (AML) is a predominantly fatal hematopoietic malignancy with high inter-patient and intra-patient genetic and epigenetic heterogeneity. The prognosis of relapsed AML remains dismal, yet the epigenetic basis of relapse is still unclear. Here we investigated whether and how the epigenome evolution impacts AML progression with biological and clinical relevance.

Methods: We obtained clinical annotation and AML specimens from 138 patients with paired diagnosis and relapsed samples. We used normal bone marrow (NBM) as epigenetic/transcriptomic controls and patients’ matched germline DNA as genetic controls. We then performed DNA methylation sequencing (ERRBS), RNA-seq, and Exome-seq. For one patient with 5 serial time points, we performed whole genome sequencing (WGS), ERRBS, and single cell RNA-seq. We measured the epigenetic allele burden using a compositional entropy-based approach (Methclone) and methylation heterogeneity using epipolymorphism.

Results: We found that diagnosis stage epigenetic allele burden (ΔS < -90) was linked to an inferior clinical outcome (p = 0.0064, log-rank test of relapse-free survival). The higher significance in promoter regions implies the functional impact of epigenetic dynamics. Promoter epiallele shift was associated with more differential expression events (p = 3.8 × 10−6, Wilcoxon signed-rank test) and promoter epiallele diversity is significantly associated with single cell resolution transcriptional heterogeneity (p < 2.2 × 10−16, ANOVA test). The global methylation heterogeneity is decreased from diagnosis to relapse, indicating a selective impact of chemotherapy on epigenetic variability (p = 0.0056, paired Wilcoxon test).

We investigated epigenetic allele burden progression from diagnosis to relapse by classifying patients into three clusters using K-means clustering: those with 1) decreased, 2) stable, or 3) increased abundance of epiallele burden. No association was seen between epigenetic clusters and patterns of genetic evolution, and the genetic abundance is higher in Cluster 3 than Cluster 1 (p = 0.048, Wilcoxon test), indicating divergent paths of genetic and epigenetic evolution. We next examined differential expression in the epigenetic cluster samples at diagnosis compared to NBM. Cluster 1 specific genes were enriched for cell cycle processes, while Cluster 3 genes were enriched for immune responses (p < 0.001, gene ontology hypergeometric tests). Integrating WGS and ERRBS data showed that epiallele burden is more dynamic than somatic mutations; a significant increase in epiallele burden preceded a major increase of somatic mutational abundance.

Summary: Our results indicate that epigenetic dynamics may provide leukemia cells greater evolutionary fitness via transcriptional adaptation and is associated with clinical outcome. This provides an alternative mechanism of AML resilience during progression and a potential predictor of relapse.

Citation Format: Sheng Li, Francine E. Garrett-Bakelman, Stephen S. Chung, Todd Hricik, Franck Rapaport, Jay Patel, Richard Dillon, Priyanka Vijay, Anna L. Brown, Alexander E. Perl, Joy Connon, Mathijs A. Sanders, Peter J.M. Valk, Lars Bullinger, Selina Luger, Michael W. Becker, Ian D. Lewis, Luen Bik To, Richard J. D’Andrea, David Grimwade, Ruud Delwel, Bob Löwenberg, Hartmut Döhner, Konstanze Döhner, Monica L. Guzman, Duane C. Hassane, Gail J. Roboz, Martin Carroll, Christopher Y. Park, Donna S. Neuberg, Ross L. Levine, Ari M. Melnick, Christopher E. Mason. Epigenome evolution in relapsed acute myeloid leukemia. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-073.

Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia

Genetic heterogeneity contributes to clinical outcome and progression of most tumors. Yet, little is known regarding allelic diversity for epigenetic compartments and almost no data exists for acute myeloid leukemia (AML). Here we examined epigenetic heterogeneity as assessed by cytosine methylation within defined genomic loci with four CpGs (epigenetic alleles), somatic mutations and transcriptomes of AML patient samples at serial time points. We observe that epigenetic allele burden is linked to inferior outcome and varies considerably during disease progression. Epigenetic and genetic allelic burden and patterning follow different patterns and kinetics during disease progression. We observed a subset of AMLs with high epiallele and low somatic mutation burden at diagnosis, a subset with high somatic mutation and lower epiallele burdens at diagnosis, and a subset with a mixed profile, suggesting distinct modes of tumor heterogeneity. Genes linked to promoter-associated epiallele shifts during tumor progression display increased single-cell transcriptional variance and differential expression, suggesting functional impact on gene regulation. Thus, genetic and epigenetic heterogeneity can occur with distinct kinetics, each likely able to impact biological and clinical features of tumors.

Clinical Genomics: Challenges and Opportunities

Next-generation sequencing (NGS) approaches are highly applicable to clinical studies. We review recent advances in sequencing technologies, as well as their benefits and tradeoffs, to provide an overview of clinical genomics from study design to computational analysis. Sequencing technologies enable genomic, transcriptomic, and epigenomic evaluations. Studies that use a combination of whole genome, exome, mRNA, and bisulfite sequencing are now feasible due to decreasing sequencing costs. Single-molecule sequencing increases read length, with the MinIONTM nanopore sequencer, which offers a uniquely portable option at a lower cost. Many of the published comparisons we review here address the challenges associated with different sequencing methods. Overall, NGS techniques, coupled with continually improving analysis algorithms, are useful for clinical studies in many realms, including cancer, chronic illness, and neurobiology. We, and others in the field, anticipate the clinical use of NGS approaches will continue to grow, especially as we shift into an era of precision medicine.

Abstract 3095: Longitudinal integrative whole transcriptome and exome sequencing identifies genes that reprogram lymphoma cells for clinical response to CDK4/6 inhibition in combination therapy

CDK4 and CDK6 drive cell cycle progression through early G1 and are frequently deregulated in human cancer. The selective inhibitor palbociclib (PD 0332991) demonstrated exciting clinical efficacy in diverse human cancers, notably in metastatic breast cancer where it more than doubled the progression free survival of patients treated with letrozole. In mantle cell lymphoma (MCL), deregulated CDK4 and cyclin D1 expression underlies unrestrained proliferation and disease progression. In a phase I clinical trial in recurrent MCL, we showed that palbociclib produced a durable clinical response. However, the mechanism that discriminates sensitivity from resistance to targeting CDK4/6 remains obscure.

To address this question, we demonstrated that 1) inhibition of CDK4/6 leads to early G1 arrest that requires Rb, the CDK4/6 substrate; 2) prolonged early G1 arrest (pG1) sensitizes Rb+ cancer cells to killing by diverse clinically-relevant agents; and 3) pG1 sensitization stems from continuous expression of genes scheduled for early G1 only. This sensitization is exacerbated in synchronous progression to S phase (pG1-S) after palbociclib withdrawal, due to incomplete restoration of cell cycle-coupled gene expression. In a hypothesis-driven phase Ib clinical trial we further showed that palbociclib induces pG1 and sensitizes MCL cells to the proteasome inhibitor bortezomib. At the optimal dose of palbociclib, only one in 6 patients progressed, and 4 patients had a durable responses including a complete remission for >800 days.

Longitudinal integrative whole transcriptome and whole exome sequencing of tumor cells from serial lymph node biopsies demonstrated that cell cycle control by palbociclib is initially intact in Rb+ MCL but is insufficient to predict clinical response. Palbociclib induced pG1 in all patients initially regardless of the subsequent clinical response or patient-specific copy number variation or mutation (ATM, p53). As expected, pG1 maintained the expression of cell cycle genes programmed for early G1 and suppressed those scheduled for other phases, and this was reversible upon release of the early G1 block.

However, expressing only genes scheduled for early G1 led to an imbalance in gene expression. Of the 1483 genes suppressed in pG1 compared with the baseline in Responders (Rs) (N = 4), 5 were up-regulated in Non-Responders (NRs) (N = 3); 11 of the 2041 genes up-regulated in pG1 in R were suppressed in NR. These oppositely expressed genes are involved in redox stress and metabolism based on functional analysis, suggesting a role for cell cycle-coupled metabolic imbalance in differential clinical response to targeting CDK4/6. Further validation of these candidate genes in the context of clinical response should advance the mechanism for therapeutic targeting of CDK4/6 as well as genome-based therapy and patient stratification.

Citation Format: Maurizio Di Liberto, Peter Martin, David Chiron, Priyanka Vijay, Xiangao Huang, Pedro Blecua, Scott Ely, Olivier Elemento, John P. Leonard, Christopher E. Mason, Selina Chen-Kiang. Longitudinal integrative whole transcriptome and exome sequencing identifies genes that reprogram lymphoma cells for clinical response to CDK4/6 inhibition in combination therapy. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3095. doi:10.1158/1538-7445.AM2015-3095

Abstract 3099: Longitudinal genomic and transcriptomic analysis of mantle cell lymphoma in a targeted combination trial of a selective CDK4/6 inhibitor

We used whole exome (WES) and whole transcriptome sequencing (WTS) to study progression of Mantle Cell Lymphoma (MCL) in the context of a clinical trial of targeted combination therapy of a CDK4 inhibitor PD0332991 (palbociclib) and a proteasome inhibitor bortezomib. Our longitudinal study design coupled with an integrative analysis approach enabled detailed molecular characterization of each subject's disease. This includes multiple time points for three therapy Responders (Rs) and two Non-Responders (NRs); a primary goal was to understand genetic reasons for differential response. To that end, we identified copy number variants (CNVs) and single nucleotide variants (SNVs) specific to NRs that are supported by both WES and WTS data and implicate pathways relevant to mechanisms of drug action.

CNVs were identified using multiple orthogonal methods that use read depth and genome-wide allele frequencies. These revealed a 29Mb chr9 hemizygous deletion unique to NRs. This region includes 15 interferon genes of the type 1 interferon signaling pathway (enrichment: p<10-9), which is involved in B cell differentiation and proliferation, and T cell and natural killer cell activation. Interferon signaling is implicated in bortezomib function and loss of interferon genes may contribute to resistance in non-responders. Additional key genes in deleted regions are JAK2, RPS6, and CDKN2A, a CDK2 inhibitor, loss of which may antagonize palbociclib-induced G1 arrest NRs also shared a 24Mb chr3 duplication resulting in gain of PIK3CA and PIK3CB. Amplification of these genes is common in cancers, including MCL (classical analysis) and DLBCL, and often associated with poor prognosis. But, this is the only longitudinal study of PI3K CNV in a targeted therapy. In context of PD+bortezomib treatment, higher levels of PI3K may affect sensitivity to proteasome inhibition activated autophagy since bortezomib's inhibitory activity involves suppression of the PI3K/AKT/mTOR pathway. PIK3CA is amplified in a responder as well, suggesting additional determinants for clinical response.

Other CNVs differentiating Rs and NRs are a 24Mb chr8 deletion found only in Rs and a 4Mb chr17 deletion found only in NRs, which includes p53 in a subject who also has a p53 mutation, resulting in 100% expression of the mutant allele. The described CNVs result in detectable shifts in expression of a large proportion of affected genes. Coupled with SNV data, where we identified 21 SNVs shared by NRs and absent in Rs, these results offer molecular clues to mechanisms of resistance in NRs, which we are currently pursuing with functional studies.

Overall, we performed a thorough genomic and transcriptomic analysis of a longitudinal investigation of MCL patients during a targeted combination therapy phase I clinical trial and identified potential biomarkers of response spanning CNVs, SNVs, and differentially expressed genes.

Citation Format: Priyanka Vijay, Pedro Blecua, Maurizio Di Liberto, David Chiron, Xiangao Huang, Olivier Elemento, Peter Martin, John P. Leonard, Christopher E. Mason, Selina Chen-Kiang. Longitudinal genomic and transcriptomic analysis of mantle cell lymphoma in a targeted combination trial of a selective CDK4/6 inhibitor. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3099. doi:10.1158/1538-7445.AM2015-3099

Meningoencephalocoele in a mastoid cavity: a case report and review of literature

A young adult male presented to us with a discharging mastoid cavity. Clinical and radiological examination revealed cholesteatoma recidivism along with a meningoencephalocoele (ME) which was managed successfully. Two year follow-up revealed no recurrence of the pathology.

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics

The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g., Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial signatures can reveal a station’s history, such as marine-associated bacteria in a hurricane-flooded station. Some evidence of pathogens was found (Bacillus anthracis), but a lack of reported cases in NYC suggests that the pathogens represent a normal, urban microbiome. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.

Cell-cycle reprogramming for PI3K inhibition overrides a relapse-specific C481S BTK mutation revealed by longitudinal functional genomics in mantle cell lymphoma

Despite the unprecedented clinical activity of the Bruton tyrosine kinase (BTK) inhibitor ibrutinib in mantle cell lymphoma (MCL), acquired resistance is common. By longitudinal integrative whole-exome and whole-transcriptome sequencing and targeted sequencing, we identified the first relapse-specific C481S mutation at the ibrutinib binding site of BTK in MCL cells at progression following a durable response. This mutation enhanced BTK and AKT activation and tissue-specific proliferation of resistant MCL cells driven by CDK4 activation. It was absent, however, in patients with primary resistance or progression following transient response to ibrutinib, suggesting alternative mechanisms of resistance. Through synergistic induction of PIK3IP1 and inhibition of PI3K-AKT activation, prolonged early G1 arrest induced by PD 0332991 (palbociclib) inhibition of CDK4 sensitized resistant lymphoma cells to ibrutinib killing when BTK was unmutated, and to PI3K inhibitors independent of C481S mutation. These data identify a genomic basis for acquired ibrutinib resistance in MCL and suggest a strategy to override both primary and acquired ibrutinib resistance.

SIGNIFICANCE

We have discovered the first relapse-specific BTK mutation in patients with MCL with acquired resistance, but not primary resistance, to ibrutinib, and demonstrated a rationale for targeting the proliferative resistant MCL cells by inhibiting CDK4 and the cell cycle in combination with ibrutinib in the presence of BTK(WT) or a PI3K inhibitor independent of BTK mutation. As drug resistance remains a major challenge and CDK4 and PI3K are dysregulated at a high frequency in human cancers, targeting CDK4 in genome-based combination therapy represents a novel approach to lymphoma and cancer therapy. Cancer Discov; 4(9); 1022-35. ©2014 AACR. This article is highlighted in the In This Issue feature, p. 973.

Response of chickpea genotypes to Agrobacterium-mediated delivery of Chickpea chlorotic dwarf virus (CpCDV) genome and identification of resistance source

Chickpea stunt disease caused by Chickpea chlorotic dwarf virus (CpCDV) (genus Mastrevirus, family Geminiviridae) is the most important biotic stress affecting chickpea crops worldwide. A survey conducted on the incidence of stunt disease clearly revealed high incidence of the disease with severe symptom expression in both indigenous and imported genotypes. To manage the disease in a sustainable way, resistant genotypes need to be bred by adopting objective and precise assessment of the disease response of chickpea genotypes. At present, evaluation of CpCDV resistance is conducted on the basis of natural infection in the field, which is bound to be erroneous due to vagaries in vector population. To circumvent the above problems, we devised an agroinoculation technique that involves the delivery of viral genomic DNA through Agrobacterium tumefaciens. An objective scoring system assigning quantitative value to different symptoms has been evolved to assess the response of chickpea genotypes to CpCDV inoculation. Using the inoculation and scoring techniques, we screened 70 genotypes, which helped in differentiating field resistance that is more due to resistance to vector feeding than resistance to the virus.

The effect of sodium valproate on the biochemical parameters of reproductive function in male albino Wistar rats

Objective:

To assess the effects of sodium valproate on intratesticular testosterone and lactic dehydrogenase level in rats.

Methods:

Male Wistar rats (12 weeks old) were treated with sodium valproate and sacrificed at the end of the 2^nd, 4^th, 5^th, 7^th, 10^th and 15^th week, after the last exposure to sodium valproate. The testes were removed, weighed and processed for biochemical analysis.

Results:

The intratesticular testosterone level was significantly (P<0.001) reduced in 200 mg/kg and 400 mg/kg treated rats. The intratesticular lactate dehydrogenase (LDH) level was significantly (P<0.001) increased by valproate in a time dependent manner.

Conclusion:

Valproate causes reversible change in intratesticular testosterone and LDH level.

An Antioxidant potential of Hingot and Hadjod

The antioxidant activity of two plants - Hadjod i.e. Cissus quadrangularis (CQ) and Hingot i.e. Balanites aegyptiaca (BA) was determined by the thiocyanate method. The antioxidant activity of both the plants increased with increasing amount of extract (200 g-1000 g) added to the linoleic emulsion. The ethanolic extract of CQ was more effective than the other. Like antioxidant activity, the reducing power was also dependent upon the concentration. The ethanolic extract of BA shows more reducing power than the other. The result obtained in the present study indicates that the both the plants are potential source of natural antioxidants. In addition, we could suggest that although the reducing power of a substance may be an indicator of its potential antioxidant activity, there is not necessarily a linear correlation between these two activities.

Modified Fontan operation in patients with anomalies of systemic and pulmonary venous connection

The presence of anomalies of the systemic and pulmonary venous connection associated with single ventricle anomalies has been considered a contraindication for the Fontan operation (FO). The aim of this study is to outline the technical considerations associated with the presence of anomalies of systemic and/or pulmonary venous connections and to identify the risk factors for mortality in this group of patients undergoing the modified FO. Between 1989 and 2004, 63 patients (median age, 3.2 years) with anomalous systemic or pulmonary venous connection underwent a Fontan procedure at our institution. Nine patients had a combination of anomalous systemic and pulmonary venous connection, 49 patients had anomalous drainage only from the systemic circulation, and 5 patients had isolated anomalies of pulmonary venous return. Visceral heterotaxy syndrome was diagnosed in 25 patients. Previous palliative operations had been performed in 51 patients (81%). There was 1 early death, and 2 patients required take down of Fontan procedures. Two patients required reoperation for revision of the atrial baffle. At a mean follow-up of 4.6 +/- 3.4 years, there have been 5 late deaths (8%) and 45 patients (71%) have undergone Fontan completion. Actuarial survival was 92% at 1 year and 91% at 5 and 10 years-not significantly different from the overall survival of the Fontan patients. We conclude that the modified FO can be successfully performed in patients with anomalous systemic or pulmonary venous connections, including those with visceral heterotaxy syndrome, with morbidity and mortality rates that do not differ significantly from those achieved in all patients with normal connections.

Surgical results in patients with double outlet right ventricle: a 20-year experience

BACKGROUND

The objective of this study was to review our surgical strategy in children with double outlet right ventricle and to assess risk factors for early and late mortality and reoperation.

METHODS

Patients (n = 124; June 1980 to January 2000; age range, 7 days to 16 years; mean, 2.8 years) who underwent repair of double outlet right ventricle. The patients were divided into three groups. Group 1 (n = 47) had noncomplex patients with atrioventricular concordance, a single ventricular septal defect, balanced ventricles, no straddling atrioventricular valves, and no major pulmonary artery anomalies. Group 2 (n = 39) included patients with double outlet right ventricle and a subpulmonary ventricular septal defect (Taussig-Bing). Group 3 (n = 38) had patients with complex anomalies including straddling atrioventricular valves, atrioventricular septal defects or a hypoplastic valve or ventricle, or a combination of atrioventricular septal defects and hypoplastic valve or ventricle.

RESULTS

Four types of definitive repairs were performed: (1) intraventricular tunnel repair with a baffle from the left ventricle to the aorta (n = 53); (2) use of a valved or nonvalved conduit (n = 20); (3) arterial switch operation with a patch committing the left ventricle to the neo-aorta (n = 16); and (4) cavopulmonary shunt and Fontan procedures (n = 33). Two patients with late postoperative cardiomyopathy had heart transplantation. Potential risk factors included location of the largest ventricular septal defect, presence of additional ventricular septal defects, ventricular outflow obstruction or hypoplasia, or both ventricular outflow obstruction and hypoplasia, previous palliation, and type of definitive operation. There were six early deaths (4.8%) and four late deaths (3.2%), and two heart transplants (1.6%). Overall 15-year survival was 95.8%, 89.7%, and 89.5% for groups 1, 2, and 3, respectively (p = 0.08). Thirteen patients (11.4%) have required 15 reoperations. Mean follow-up for survivors was 76.6 +/- 52.8 months. Up-to-date follow-ups are available on 114 surviving patients. Ninety-five of these patients (83.3%) were in New York Heart Association class I, and the remaining 19 patients (16.7%) were in New York Heart Association class II. Freedom from reoperation was 87%, 72%, and 100% at 15 years for groups 1, 2, and 3, respectively (p = 0.11).

CONCLUSIONS

Survival was high for all patients with double outlet right ventricle undergoing intraventricular tunnel repair, arterial switch operation, and repair with a conduit or a modified Fontan procedure. Careful attention to preoperative anatomy dictates the best surgical approach and will enhance outcomes.

Clinical outcomes and indicators of normalization of left ventricular dimensions after Ross procedure in children

Between 1993 and 2000, 50 patients (age range, 1 month to 18 years) who had left ventricular outflow tract (LVOT) disease and had undergone a Ross procedure were assessed using echocardiography. Aortic annulus size, valvular gradient, valve insufficiency, LV dimensions at end-systole and end-diastole, LV interventricular septal and posterior wall thickness, and LV mass index (LVMI) were measured. There was 1 early and 2 late deaths, and 5 reoperations. Aortic annulus size increased and degree of aortic insufficiency (AI) decreased, as did LV internal dimensions and LVMI. Peak pressure gradients declined from 73 +/- 18 mm Hg to 7 +/- 7 mm Hg, and LVMI regressed (167 +/- 6 g/m(2) v 108 +/- 6 g/m(2), P <.001) after 3 years. The degree of AI ranged from none to mild, and no patient has LVOT stenosis. Regression of LV dilatation and hypertrophy, good autograft valve function and durability, and a high survival rate suggest that the Ross procedure is preferred for most children who require aortic valve replacement.

Truncus arteriosus repair: outcomes, risk factors, reoperation and management

OBJECTIVES

Truncus arteriosus (TA) continues to be associated with significant morbidity and mortality, but there have been clinically significant improvements with early repair.

METHODS

Sixty patients underwent physiological correction of TA between November 1978 and January 2000. The average age was 76 days (range, 3 days--20 months). Associated cardiac anomalies were frequently encountered, the most common being severe truncal valve regurgitation (n=7), interrupted aortic arch (n=6), coronary artery anomalies (n=6), non-confluent pulmonary arteries (n=4), and total anomalous pulmonary venous return (n=1). Truncal valve replacement was performed initially or subsequently in seven patients with severe regurgitation (mechanical prostheses in six patients and a cryopreserved aortic homograft in one patient). Right ventricle--pulmonary artery continuity was established with an aortic (n=16) or pulmonary homograft (n=32) in 48 patients, a Dacron polyester porcine valved conduit in five, a non-valved polytetrafluoroethylene (PTFE) tube in three, direct anastomosis to the right ventricle with anterior patch arterioplasty in three, and a bovine jugular venous valve conduit in one patient.

RESULTS

There were ten hospital deaths (17%; 70% confidence limit, 7--25%). Multivariate and univariate analyses demonstrated a relationship between hospital mortality and associated cardiac anomalies. In the 43 patients without these associated cardiac anomalies, the early survival was 91% (group I). In the 17 patients with one or more of these risk factors, the survival was 71% (group II, P=0.002). There was one late death. Twenty-three patients (46%) required reoperation for right ventricular outflow tract (RVOT) obstruction at a mean follow-up time of 59.1 months. In 23 patients, the RVOT reconstruction was performed with a PTFE monocusp, and six patients had of a variety of replacement conduits inserted. Postoperatively, there were 34 (68%) patients in New York Heart Association functional class I and 16 (32%) in class II. Twenty-eight surviving patients are reported as doing well without any medication. The freedom of reoperation in the 39 hospital survivors (group I) without risk factors was 64% at 7 years; and 36% at 10 years in the 11 patients (group II) surviving with risk factors.

CONCLUSIONS

Associated cardiac anomalies were risk factors for death after the repair of TA. In the absence of these associated lesions, TA can be repaired with an excellent surgical outcome in the neonatal and early infancy period.

Biological versus mechanical aortic valve replacement in children

BACKGROUND

Aortic valve replacement in children remains challenging because of constraints imposed by available prosthetic devices. Potential risks of anticoagulation with mechanical valves and degeneration of other biological substitutes have kindled interest in the Ross procedure. This study outlines the evolution of our 27-year experience with prosthetic devices.

METHODS

Ninety-nine patients who underwent aortic valve replacement (January 1973 through September 2000) were included in this study. Procedures included implantation of pulmonary autograft (PA) (n = 42), aortic homograft (AH) (n = 3), mechanical valves (MV) (n = 41), and xenograft tissue valves (XG) (n = 13).

RESULTS

The mean follow-up times were: 3.8+/-1.3 years for PA, 3.5+/-1.5 years for AH, 7.7+/-4.7 years for MV, and 8.4+/-4.8 years for XG. There were no significant differences in perioperative outcomes among the groups (p < or = 0.05) or early deaths (2 each in the MV, AH, and PA groups). The incidence of valve-related complications and reoperations was high in the MV (n = 5), XG (n = 7), and AH (n = 1) groups as compared with the PA group (n = 3, p < 0.01). Early and late mortality for the series was 8.6% (n = 8). Overall, the reoperation rate was 20.7% (n = 18): 15.2% (5 of 33) MV, 70% (7 of 10) XG, 50% (1 of 2) AH, and 11.9% (5 of 42) for PA. The actuarial survival rate was 87.8% and 100% at 10 years for MV and XG, and 95.2% and 6.6% at 7 years for PA and AH.

CONCLUSIONS

Aortic valve replacement in children can be performed with acceptable mortality and good long-term results. The Ross procedure, although more complicated, has the advantage of not requiring anticoagulation therapy, can be performed in all age groups, possesses inherent growth potential, and exhibits the most normal left ventricular outflow tract hemodynamics.

Correlation of plasma adrenomedullin to myocardial preservation during open-heart surgery

Adrenomedullin (ADM) is a vasoactive peptide with potent dilatory effects. We studied whether perioperative myocardial injury could be altered by the presence of ADM. Blood samples from 19 children with congenital heart disease undergoing surgical repair were collected at six time points: preoperative, on cardiopulmonary bypass (CPB), and 0, 3, 6, and 12 hours after CPB. Blood levels of ADM (pg/ml) and troponin-I (Tn-I; ng/ml), a specific marker of myocardial injury, were measured. Patients were divided into three groups based on their 12-hour Tn-I levels (I, < 10, n = 6; II, 10-25, n = 6; III, >25, n = 7). Preoperative Tn-I levels were within the normal range for all patients. Preoperative ADM levels in group I (with little or no evidence of myocardial injury) were significantly greater than those of either group II or III (242.7 +/- 15.4 vs 83.8 +/- 18 and 85.2 +/- 5.5, respectively; p < or = 0.0001 for each). The 12-hour ADM levels in group I remained significantly lower than preoperative levels (242.7 +/- 15.4 vs 197.4 +/- 11.6, p < or = 0.03) but higher than in the other groups. In group III, ADM increased at the 12-hour time point (159.2 +/- 6.5, p < or = 0.0001 vs baseline). Higher preoperative ADM levels are associated with lower levels of myocardial injury (as assessed by troponin-I release) during congenital heart surgery.

Coronary sinus adrenomedullin rises in response to myocardial injury

Human adrenomedullin (ADM), a peptide comprising 52 amino acids, is a circulating hormone with vasodilator properties. We have evaluated its release by the heart following ischaemic myocardial damage, as indicated by elevated levels of the cardiospecific protein troponin-T (Tn-T) during cardiopulmonary bypass. ADM (pg/ml) and Tn-T (ng/ml) were measured in coronary sinus blood before and after aortic cross-clamp and in venous blood 6 h after surgery in 22 coronary-bypass patients. Based on the pre- and post-clamp Tn-T levels in the coronary sinus, the patients were divided into group I (no change; n=10) and group II (two times increase; n=12). Baseline ADM (362.7+/-106.2 and 303+/-58.7 pg/ml in groups I and II respectively; means+/-S.D.) and Tn-T (0.66+/-0.14 and 0.57+/-0.13 ng/ml respectively) levels were similar in both groups. In group I, the post-clamp ADM (317.6+/-80.8 pg/ml) and Tn-T (0.68+/-0.15 ng/ml) levels did not change significantly. In group II, the post-clamp ADM levels rose significantly above the baseline, mimicking the change in Tn-T (ADM, 541.4+/-89.4 pg/ml; Tn-T, 1.37+/-0.31 ng/ml; P=0.009). After 6 h, the systemic Tn-T levels were similar in both groups (2. 09+/-0.44 and 1.95+/-0.52 ng/ml in groups I and II respectively). We suggest that: (1) minor degrees of myocardial ischaemic damage result in release of ADM by the heart, and (2) ADM may play a protective role in the myocardium during an ischaemic insult. This suggests a possible therapeutic role for ADM in the management of intra-operative myocardial ischaemia.

Donor cardiac troponin T: a marker to predict heart transplant rejection

BACKGROUND

Noninvasive methodologies have shown poor sensitivity in predicting rejection when compared to serial endomyocardial biopsies. We studied the potential role of donor blood troponin T (Tn-T) as a marker for predicting heart transplant rejection.

METHODS

Blood cardiac Tn-T was measured from 16 heart donors. Transplant rejection and cardiac function in the recipients were monitored for 1 year.

RESULTS

When data were analyzed based on donor blood Tn-T levels, 6 patients who received hearts from donors with low Tn-T (<0.45+/-0.1 ng/mL) showed no rejection, and patients whose hearts came from donors with higher Tn-T (6.01+/-0.81 ng/mL) developed episodes of high-grade rejection (3A) within 38.5+/-2.1 days after transplantation. Eight patients who received hearts from donors with intermediate levels of Tn-T (3.57+/-0.55 ng/mL) showed mild rejection (grade 1). All recipients had qualitatively normal left ventricular systolic function by serial echocardiography. The mean donor ischemic time was 169+/-47 minutes.

CONCLUSIONS

The quality of the donor heart is an important prognostic factor in heart transplantation. It may be possible to identify severely damaged donor organs before transplantation and avoid their use or to develop more aggressive strategies for reducing recurrent acute rejection episodes in high-risk patients.