Publications by authors named "Priya Velu"

19 Publications

  • Page 1 of 1

Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies and Spatial Omics Tissue Maps.

bioRxiv 2021 Mar 9. Epub 2021 Mar 9.

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus has infected over 115 million people and caused over 2.5 million deaths worldwide. Yet, the molecular mechanisms underlying the clinical manifestations of COVID-19, as well as what distinguishes them from common seasonal influenza virus and other lung injury states such as Acute Respiratory Distress Syndrome (ARDS), remains poorly understood. To address these challenges, we combined transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues, matched with spatial protein and expression profiling (GeoMx) across 357 tissue sections. These results define both body-wide and tissue-specific (heart, liver, lung, kidney, and lymph nodes) damage wrought by the SARS-CoV-2 infection, evident as a function of varying viral load (high vs. low) during the course of infection and specific, transcriptional dysregulation in splicing isoforms, T cell receptor expression, and cellular expression states. In particular, cardiac and lung tissues revealed the largest degree of splicing isoform switching and cell expression state loss. Overall, these findings reveal a systemic disruption of cellular and transcriptional pathways from COVID-19 across all tissues, which can inform subsequent studies to combat the mortality of COVID-19, as well to better understand the molecular dynamics of lethal SARS-CoV-2 infection and other viruses.
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http://dx.doi.org/10.1101/2021.03.08.434433DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7987017PMC
March 2021

Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions.

Nat Commun 2021 03 12;12(1):1660. Epub 2021 Mar 12.

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.

In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV-2 highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. We applied these methods to clinical specimens gathered from 669 patients in New York City during the first two months of the outbreak, yielding a broad molecular portrait of the emerging COVID-19 disease. We find significant enrichment of a NYC-distinctive clade of the virus (20C), as well as host responses in interferon, ACE, hematological, and olfaction pathways. In addition, we use 50,821 patient records to find that renin-angiotensin-aldosterone system inhibitors have a protective effect for severe COVID-19 outcomes, unlike similar drugs. Finally, spatial transcriptomic data from COVID-19 patient autopsy tissues reveal distinct ACE2 expression loci, with macrophage and neutrophil infiltration in the lungs. These findings can inform public health and may help develop and drive SARS-CoV-2 diagnostic, prevention, and treatment strategies.
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http://dx.doi.org/10.1038/s41467-021-21361-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7954844PMC
March 2021

CT derived radiomic score for predicting the added benefit of adjuvant chemotherapy following surgery in stage I, II resectable non-small cell lung cancer: a retrospective multicohort study for outcome prediction.

Lancet Digit Health 2020 03 13;2(3):e116-e128. Epub 2020 Feb 13.

Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA; Louis Stokes Cleveland Veterans Administration Medical Center, Cleveland, Ohio, USA. Electronic address:

Background: Use of adjuvant chemotherapy in patients with early-stage lung cancer is controversial because no definite biomarker exists to identify patients who would receive added benefit from it. We aimed to develop and validate a quantitative radiomic risk score (QuRiS) and associated nomogram (QuRNom) for early-stage non-small cell lung cancer (NSCLC) that is prognostic of disease-free survival and predictive of the added benefit of adjuvant chemotherapy following surgery.

Methods: We did a retrospective multicohort study of individuals with early-stage NSCLC (stage I and II) who either received surgery alone or surgery plus adjuvant chemotherapy. We selected patients for whom we had available pre-treatment diagnostic CT scans and corresponding survival information. We used radiomic texture features derived from within and outside the primary lung nodule on chest CT scans of patients from the Cleveland Clinic Foundation (Cleveland, OH, USA; cohort D) to develop QuRiS. A least absolute shrinkage and selection operator-Cox regularisation model was used for data dimension reduction, feature selection, and QuRiS construction. QuRiS was independently validated on a cohort of patients from the University of Pennsylvania (Philadephia, PA, USA; cohort D) and a cohort of patients whose CT scans were derived from The Cancer Imaging Archive (cohort D). QuRNom was constructed by integrating QuRiS with tumour and node descriptors (according to the tumour, node, metastasis staging system) and lymphovascular invasion. The primary endpoint of the study was the assessment of the performance of QuRiS and QuRNom in predicting disease-free survival. The added benefit of adjuvant chemotherapy estimated using QuRiS and QuRNom was validated by comparing patients who received adjuvant chemotherapy versus patients who underwent surgery alone in cohorts D-D.

Findings: We included: 329 patients in cohort D (73 [22%] had surgery plus adjuvant chemotherapy and 256 (78%) had surgery alone); 114 patients in cohort D (33 [29%] had surgery plus adjuvant chemotherapy and 81 (71%) had surgery alone); and 82 patients in cohort D (24 [29%] had surgery plus adjuvant chemotherapy and 58 (71%) had surgery alone). QuRiS comprised three intratumoral and 10 peritumoral CT-radiomic features and was found to be significantly associated with disease-free survival (ie, prognostic validation of QuRiS; hazard ratio for predicted high-risk vs predicted low-risk groups 1·56, 95% CI 1·08-2·23, p=0·016 for cohort D; 2·66, 1·24-5·68, p=0·011 for cohort D; and 2·67, 1·39-5·11, p=0·0029 for cohort D). To validate the predictive performance of QuRiS, patients were partitioned into three risk groups (high, intermediate, and low risk) on the basis of their corresponding QuRiS. Patients in the high-risk group were observed to have significantly longer survival with adjuvant chemotherapy than patients who underwent surgery alone (0·27, 0·08-0·95, p=0·042, for cohort D; 0·08, 0·01-0·42, p=0·0029, for cohorts D and D combined). As concerns QuRNom, the nomogram-estimated survival benefit was predictive of the actual efficacy of adjuvant chemotherapy (0·25, 0·12-0·55, p<0·0001, for cohort D; 0·13, <0·01-0·99, p=0·0019 for cohort D).

Interpretation: QuRiS and QuRNom were validated as being prognostic of disease-free survival and predictive of the added benefit of adjuvant chemotherapy, especially in clinically defined low-risk groups. Since QuRiS is based on routine chest CT imaging, with additional multisite independent validation it could potentially be employed for decision management in non-invasive treatment of resectable lung cancer.

Funding: National Cancer Institute of the US National Institutes of Health, National Center for Research Resources, US Department of Veterans Affairs Biomedical Laboratory Research and Development Service, Department of Defence, National Institute of Diabetes and Digestive and Kidney Diseases, Wallace H Coulter Foundation, Case Western Reserve University, and Dana Foundation.
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http://dx.doi.org/10.1016/S2589-7500(20)30002-9DOI Listing
March 2020

Rapid Implementation of Severe Acute Respiratory Syndrome Coronavirus 2 Emergency Use Authorization RT-PCR Testing and Experience at an Academic Medical Institution.

J Mol Diagn 2021 02 5;23(2):149-158. Epub 2020 Dec 5.

Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York. Electronic address:

An epidemic caused by an outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China in December 2019 has since rapidly spread internationally, requiring urgent response from the clinical diagnostics community. We present a detailed overview of the clinical validation and implementation of the first laboratory-developed real-time RT-PCR test offered in the NewYork-Presbyterian Hospital system following the Emergency Use Authorization issued by the US Food and Drug Administration. Nasopharyngeal and sputum specimens (n = 174) were validated using newly designed dual-target real-time RT-PCR (altona RealStar SARS-CoV-2 Reagent) for detecting SARS-CoV-2 in upper respiratory tract and lower respiratory tract specimens. Accuracy testing demonstrated excellent assay agreement between expected and observed values and comparable diagnostic performance to reference tests. The limit of detection was 2.7 and 23.0 gene copies per reaction for nasopharyngeal and sputum specimens, respectively. Retrospective analysis of 1694 upper respiratory tract specimens from 1571 patients revealed increased positivity in older patients and males compared with females, and an increasing positivity rate from approximately 20% at the start of testing to 50% at the end of testing 3 weeks later. Herein, we demonstrate that the assay accurately and sensitively identifies SARS-CoV-2 in multiple specimen types in the clinical setting and summarize clinical data from early in the epidemic in New York City.
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http://dx.doi.org/10.1016/j.jmoldx.2020.10.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7718583PMC
February 2021

Routine Laboratory Blood Tests Predict SARS-CoV-2 Infection Using Machine Learning.

Clin Chem 2020 11;66(11):1396-1404

Department of Population Health Sciences, Weill Cornell Medicine, New York, NY.

Background: Accurate diagnostic strategies to identify SARS-CoV-2 positive individuals rapidly for management of patient care and protection of health care personnel are urgently needed. The predominant diagnostic test is viral RNA detection by RT-PCR from nasopharyngeal swabs specimens, however the results are not promptly obtainable in all patient care locations. Routine laboratory testing, in contrast, is readily available with a turn-around time (TAT) usually within 1-2 hours.

Method: We developed a machine learning model incorporating patient demographic features (age, sex, race) with 27 routine laboratory tests to predict an individual's SARS-CoV-2 infection status. Laboratory testing results obtained within 2 days before the release of SARS-CoV-2 RT-PCR result were used to train a gradient boosting decision tree (GBDT) model from 3,356 SARS-CoV-2 RT-PCR tested patients (1,402 positive and 1,954 negative) evaluated at a metropolitan hospital.

Results: The model achieved an area under the receiver operating characteristic curve (AUC) of 0.854 (95% CI: 0.829-0.878). Application of this model to an independent patient dataset from a separate hospital resulted in a comparable AUC (0.838), validating the generalization of its use. Moreover, our model predicted initial SARS-CoV-2 RT-PCR positivity in 66% individuals whose RT-PCR result changed from negative to positive within 2 days.

Conclusion: This model employing routine laboratory test results offers opportunities for early and rapid identification of high-risk SARS-CoV-2 infected patients before their RT-PCR results are available. It may play an important role in assisting the identification of SARS-CoV-2 infected patients in areas where RT-PCR testing is not accessible due to financial or supply constraints.
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http://dx.doi.org/10.1093/clinchem/hvaa200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7499540PMC
November 2020

Clinical Performance of SARS-CoV-2 Molecular Tests.

J Clin Microbiol 2020 Jul 23;58(8). Epub 2020 Jul 23.

Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, New York, USA

Molecular testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the gold standard for diagnosis of coronavirus disease 2019 (COVID-19), but the clinical performance of these tests is still poorly understood, particularly with regard to disease course, patient-specific factors, and viral shedding. From 10 March to 1 May 2020, NewYork-Presbyterian laboratories performed 27,377 SARS-CoV-2 molecular assays from 22,338 patients. Repeat testing was performed for 3,432 patients, of which 2,413 had initial negative and 802 had initial positive results. Repeat-tested patients were more likely to have severe disease and low viral loads. The negative predictive value of the first-day result among repeat-tested patients was 81.3% The clinical sensitivity of SARS-CoV-2 molecular assays was estimated between 58% and 96%, depending on the unknown number of false-negative results in single-tested patients. Conversion to negative was unlikely to occur before 15 to 20 days after initial testing or 20 to 30 days after the onset of symptoms, with 50% conversion occurring at 28 days after initial testing. Conversion from first-day negative to positive results increased linearly with each day of testing, reaching 25% probability in 20 days. Sixty patients fluctuated between positive and negative results over several weeks, suggesting that caution is needed when single-test results are acted upon. In summary, our study provides estimates of the clinical performance of SARS-CoV-2 molecular assays and suggests time frames for appropriate repeat testing, namely, 15 to 20 days after a positive test and the same day or next 2 days after a negative test for patients with high suspicion for COVID-19.
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http://dx.doi.org/10.1128/JCM.00995-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7383556PMC
July 2020

Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions.

bioRxiv 2020 May 1. Epub 2020 May 1.

Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA.

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused thousands of deaths worldwide, including >18,000 in New York City (NYC) alone. The sudden emergence of this pandemic has highlighted a pressing clinical need for rapid, scalable diagnostics that can detect infection, interrogate strain evolution, and identify novel patient biomarkers. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs, plus a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, bacterial, and viral profiling. We applied both technologies across 857 SARS-CoV-2 clinical specimens and 86 NYC subway samples, providing a broad molecular portrait of the COVID-19 NYC outbreak. Our results define new features of SARS-CoV-2 evolution, nominate a novel, NYC-enriched viral subclade, reveal specific host responses in interferon, ACE, hematological, and olfaction pathways, and examine risks associated with use of ACE inhibitors and angiotensin receptor blockers. Together, these findings have immediate applications to SARS-CoV-2 diagnostics, public health, and new therapeutic targets.
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http://dx.doi.org/10.1101/2020.04.20.048066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7255793PMC
May 2020

Comparison of Two High-Throughput Reverse Transcription-PCR Systems for the Detection of Severe Acute Respiratory Syndrome Coronavirus 2.

J Clin Microbiol 2020 Jul 23;58(8). Epub 2020 Jul 23.

Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as the cause of a worldwide pandemic. Many commercial SARS-CoV-2 reverse transcription-PCR (RT-PCR) assays have received Emergency Use Authorization from the U.S. Food and Drug Administration. However, there are limited data describing their performance, in particular the performance of high-throughput SARS-CoV-2 RT-PCR systems. We analyzed the diagnostic performance of two high-throughput systems: cobas 6800 and Panther Fusion, and their associated RT-PCR assays, with a collection of 389 nasopharyngeal specimens. The overall agreement between the platforms was 96.4% (375/389). Cohen's kappa analysis rated the strength of agreement between the two platforms as "almost perfect" (κ = 0.922; standard error, 0.051). Furthermore, there was no significant difference between corresponding cycle threshold values generated on the two systems ( value = 0.88; Student's test). Taken together, these data imply that the two platforms can be considered comparable in terms of their clinical performance. We believe that this information will be useful for those who have already adopted these platforms or are seeking to implement high-throughput RT-PCR testing to stem the SARS-CoV-2 pandemic.
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http://dx.doi.org/10.1128/JCM.00890-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7383551PMC
July 2020

CT derived radiomic score for predicting the added benefit of adjuvant chemotherapy following surgery in Stage I, II resectable Non-Small Cell Lung Cancer: a retrospective multi-cohort study for outcome prediction.

Lancet Digit Health 2020 03 13;2(3):e116-e128. Epub 2020 Feb 13.

Case Western Reserve University, Cleveland, OH, USA 44106.

Summary:

Background: Development and validation of a quantitative radiomic risk score (QuRiS) and associated nomogram (QuRNom) for early-stage non-small cell lung cancer (ES-NSCLC) that is prognostic of disease-free survival (DFS) and predictive of the added benefit of adjuvant chemotherapy (ACT) following surgery.

Methods: QuRiS was developed using radiomic texture features derived from within and outside the primary lung nodule on chest CT scans using a cohort D of 329 patients from the Cleveland Clinic. A LASSO-Cox regularization model was used for data dimension reduction, feature selection, and QuRiS construction. QuRiS was independently validated on D(N=114; University of Pennsylvania) and D(N=82; TCIA). QuRNom was constructed by integrating QuRiS with T-, N-Descriptors, and LVI. The added benefit of ACT using QuRiS and QuRNom was validated by comparing patients who received ACT against patients who underwent surgery alone in D-D. To explore the underlying morphologic basis of the QuRiS, we explored associations with corresponding whole-slide tissue scans (WSIs) and mRNA sequencing data using subsets of D and D.

Findings: QuRiS consisted three intra- and ten peri-tumoral CT-radiomic features and was found to be significantly associated with DFS (D: HR=1.60 [1.10-2.20];p<·05; D:HR=2.70 [1.40-5.10]; p<·01; D:HR=2.70 [1.20-5.70];p<·01). Patients were partitioned into three risk groups (Q Q Q) based off their corresponding QuRiS score. High QuRiS group, Q patients were observed to have significantly prolonged survival with ACT when compared to surgery alone (D: HR=0·27[0.07-0.95],p<0.05; D+D: HR=0·08[0.01-0.42],p<0.01). For developed QuRNom, the actual efficacy of ACT was predictive of nomogram-estimated survival benefit (D: HR= D:0·25 [0·12-0·55], D: HR=0·13 [0·004-0·99]). QuRiS features were found to be associated with the spatial arrangement of TILs and cancer nuclei on corresponding WSIs (D: Rho=0·23,p<0·05, N=70). They were also observed to have an association with biological pathways implicated in chemotaxis (D,p<0·05, N=86) and other immune specific biological pathways.

Interpretation: QuRiS and QuRNom were validated as being prognostic of DFS and predictive of the added benefit of ACT.
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http://dx.doi.org/10.1016/s2589-7500(20)30002-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7051021PMC
March 2020

Stable and discriminating radiomic predictor of recurrence in early stage non-small cell lung cancer: Multi-site study.

Lung Cancer 2020 04 26;142:90-97. Epub 2020 Feb 26.

Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA. Electronic address:

Objectives: To evaluate whether combining stability and discriminability criteria in building radiomic classifiers will improve the prognosis of cancer recurrence in early stage non-small cell lung cancer on non-contrast computer tomography (CT).

Materials And Methods: CT scans of 610 patients with early stage (IA, IB, IIA) NSCLC from four independent cohorts were evaluated. A total of 350 patients from Cleveland Clinic Foundation and University of Pennsylvania were divided into two equal sets for training (D) and validation set (D). 80 patients from The Cancer Genome Atlas Lung Adenocarcinoma and Squamous Cell Carcinoma and 195 patients from The Cancer Imaging Archive, were used as independent second (D) and third (D) validation sets. A linear discriminant analysis (LDA) classifier was built based on the most stable and discriminate features. In addition, a radiomic risk score (RRS) was generated by using least absolute shrinkage and selection operator, Cox regression model to predict time to progression (TTP) following surgery.

Results: A feature selection strategy focusing on both feature discriminability and stability resulted in the classifier having a higher discriminability on validation datasets compared to the discriminability alone criteria in discriminating cancer recurrence (D, AUC of 0.75 vs. 0.65; D, 0.74 vs. 0.62; D, 0.76 vs. 0.63). The RRS generated by most stable-discriminating features was significantly associated with TTP compared to discriminating alone criteria (HR = 1.66, C-index of 0.72 vs. HR = 1.04, C-index of 0.62).

Conclusion: Accounting for both stability and discriminability yielded a more generalizable classifier for predicting cancer recurrence and TTP in early stage NSCLC.
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http://dx.doi.org/10.1016/j.lungcan.2020.02.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7141152PMC
April 2020

Changes in CT Radiomic Features Associated with Lymphocyte Distribution Predict Overall Survival and Response to Immunotherapy in Non-Small Cell Lung Cancer.

Cancer Immunol Res 2020 01 12;8(1):108-119. Epub 2019 Nov 12.

Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio.

No predictive biomarkers can robustly identify patients with non-small cell lung cancer (NSCLC) who will benefit from immune checkpoint inhibitor (ICI) therapies. Here, in a machine learning setting, we compared changes ("delta") in the radiomic texture (DelRADx) of CT patterns both within and outside tumor nodules before and after two to three cycles of ICI therapy. We found that DelRADx patterns could predict response to ICI therapy and overall survival (OS) for patients with NSCLC. We retrospectively analyzed data acquired from 139 patients with NSCLC at two institutions, who were divided into a discovery set (D = 50) and two independent validation sets (D = 62, D = 27). Intranodular and perinodular texture descriptors were extracted, and the relative differences were computed. A linear discriminant analysis (LDA) classifier was trained with 8 DelRADx features to predict RECIST-derived response. Association of delta-radiomic risk score (DRS) with OS was determined. The association of DelRADx features with tumor-infiltrating lymphocyte (TIL) density on the diagnostic biopsies ( = 36) was also evaluated. The LDA classifier yielded an AUC of 0.88 ± 0.08 in distinguishing responders from nonresponders in D, and 0.85 and 0.81 in D and D DRS was associated with OS [HR: 1.64; 95% confidence interval (CI), 1.22-2.21; = 0.0011; C-index = 0.72). Peritumoral Gabor features were associated with the density of TILs on diagnostic biopsy samples. Our results show that DelRADx could be used to identify early functional responses in patients with NSCLC.
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http://dx.doi.org/10.1158/2326-6066.CIR-19-0476DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7718609PMC
January 2020

Longitudinal targeted next-generation sequencing in a patient with acute myeloid leukaemia.

Br J Haematol 2019 09 17;186(6):801. Epub 2019 Jun 17.

Division of Precision and Computational Medicine, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.

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http://dx.doi.org/10.1111/bjh.16048DOI Listing
September 2019

Classes of ITD Predict Outcomes in AML Patients Treated with FLT3 Inhibitors.

Clin Cancer Res 2019 01 4;25(2):573-583. Epub 2018 Sep 4.

Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.

Purpose: Recurrent internal tandem duplication (ITD) mutations are observed in various cancers including acute myeloid leukemia (AML), where ITD mutations in tyrosine kinase receptor FLT3 are associated with poor prognostic outcomes. Several FLT3 inhibitors (FLT3i) are in clinical trials for high-risk -ITD-positive AML. However, the variability of survival following FLT3i treatment suggests that the mere presence of -ITD mutations might not guarantee effective clinical response. Motivated by the heterogeneity of -ITD mutations, we investigated the effects of -ITD structural features on the response of AML patients to treatment. We developed the HeatITup (HEAT diffusion for Internal Tandem dUPlication) algorithm to identify and quantitate ITD structural features including nucleotide composition. Using HeatITup, we studied the impact of ITD structural features on the clinical response to FLT3i and induction chemotherapy in -ITD-positive AML patients.

Results: HeatITup accurately identifies and classifies ITDs into newly defined categories of "typical" or "atypical" based on their nucleotide composition. A typical ITD's insert sequence completely matches the wild-type whereas an atypical ITD's insert contains nucleotides exogenous to the wild-type . Our analysis shows marked divergence between typical and atypical ITD mutation features. Furthermore, our data suggest that AML patients carrying typical -ITDs benefited significantly more from both FLT3i and induction chemotherapy treatments than patients with atypical -ITDs.

Conclusions: These results underscore the importance of structural discernment of complex somatic mutations such as ITDs in progressing toward personalized treatment of AML patients, and enable researchers and clinicians to unravel ITD complexity using the provided software..
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http://dx.doi.org/10.1158/1078-0432.CCR-18-0655DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6335170PMC
January 2019

Genomic heterogeneity of ALK fusion breakpoints in non-small-cell lung cancer.

Mod Pathol 2018 05 12;31(5):791-808. Epub 2018 Jan 12.

Department of Pathology and Immunology, Division of Anatomic and Molecular Pathology, Washington University School of Medicine, St Louis, MO, USA.

In lung adenocarcinoma, canonical EML4-ALK inversion results in a fusion protein with a constitutively active ALK kinase domain. Evidence of ALK rearrangement occurs in a minority (2-7%) of lung adenocarcinoma, and only ~60% of these patients will respond to targeted ALK inhibition by drugs such as crizotinib and ceritinib. Clinically, targeted anti-ALK therapy is often initiated based on evidence of an ALK genomic rearrangement detected by fluorescence in situ hybridization (FISH) of interphase cells in formalin-fixed, paraffin-embedded tissue sections. At the genomic level, however, ALK rearrangements are heterogeneous, with multiple potential breakpoints in EML4, and alternate fusion partners. Using next-generation sequencing of DNA and RNA together with ALK immunohistochemistry, we comprehensively characterized genomic breakpoints in 33 FISH-positive lung adenocarcinomas. Of these 33 cases, 29 (88%) had detectable DNA level ALK rearrangements involving EML4, KIF5B, or non-canonical partners including ASXL2, ATP6V1B1, PRKAR1A, and SPDYA. A subset of 12 cases had material available for RNA-Seq. Of these, eight of eight (100%) cases with DNA rearrangements showed ALK fusion transcripts from RNA-Seq; three of four cases (75%) without detectable DNA rearrangements were similarly negative by RNA-Seq, and one case was positive by RNA-Seq but negative by DNA next-generation sequencing. By immunohistochemistry, 17 of 19 (89%) tested cases were clearly positive for ALK protein expression; the remaining cases had no detectable DNA level rearrangement or had a non-canonical rearrangement not predicted to form a fusion protein. Survival analysis of patients treated with targeted ALK inhibitors demonstrates a significant difference in mean survival between patients with next-generation sequencing confirmed EML4-ALK rearrangements, and those without (20.6 months vs 5.4 months, P<0.01). Together, these data demonstrate abundant genomic heterogeneity among ALK-rearranged lung adenocarcinoma, which may account for differences in treatment response with targeted ALK inhibitors.
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http://dx.doi.org/10.1038/modpathol.2017.181DOI Listing
May 2018

Hippocampus, perirhinal cortex, and complex visual discriminations in rats and humans.

Learn Mem 2015 Feb 15;22(2):83-91. Epub 2015 Jan 15.

Department of Psychiatry, University of California, San Diego, La Jolla, California 92093, USA Veterans Affairs San Diego Healthcare System, San Diego, California 92161, USA

Structures in the medial temporal lobe, including the hippocampus and perirhinal cortex, are known to be essential for the formation of long-term memory. Recent animal and human studies have investigated whether perirhinal cortex might also be important for visual perception. In our study, using a simultaneous oddity discrimination task, rats with perirhinal lesions were impaired and did not exhibit the normal preference for exploring the odd object. Notably, rats with hippocampal lesions exhibited the same impairment. Thus, the deficit is unlikely to illuminate functions attributed specifically to perirhinal cortex. Both lesion groups were able to acquire visual discriminations involving the same objects used in the oddity task. Patients with hippocampal damage or larger medial temporal lobe lesions were intact in a similar oddity task that allowed participants to explore objects quickly using eye movements. We suggest that humans were able to rely on an intact working memory capacity to perform this task, whereas rats (who moved slowly among the objects) needed to rely on long-term memory.
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http://dx.doi.org/10.1101/lm.035840.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4341362PMC
February 2015

Effect of visual feedback on the occipital-parietal-motor network in Parkinson's disease with freezing of gait.

Front Neurol 2014 9;4:209. Epub 2014 Jan 9.

Cognitive Science Department, University of California , San Diego, CA , USA.

Freezing of gait (FOG) is an elusive phenomenon that debilitates a large number of Parkinson's disease (PD) patients regardless of stage of disease, medication status, or deep brain stimulation implantation. Sensory feedback cues, especially visual feedback cues, have been shown to alleviate FOG episodes or even prevent episodes from occurring. Here, we examine cortical information flow between occipital, parietal, and motor areas during the pre-movement stage of gait in a PD-with-FOG patient that had a strong positive behavioral response to visual cues, one PD-with-FOG patient without any behavioral response to visual cues, and age-matched healthy controls, before and after training with visual feedback. Results for this case study show differences in cortical information flow between the responding PD-with-FOG patient and the other two subject types, notably, an increased information flow in the beta range. Tentatively suggesting the formation of an alternative cortical sensory-motor pathway during training with visual feedback, these results are proposed as subject for further verification employing larger cohorts of patients.
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http://dx.doi.org/10.3389/fneur.2013.00209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3885816PMC
January 2014

Single-trial classification of gait and point movement preparation from human EEG.

Front Neurosci 2013 11;7:84. Epub 2013 Jun 11.

Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.

Neuroimaging studies provide evidence of cortical involvement immediately before and during gait and during gait-related behaviors such as stepping in place or motor imagery of gait. Here we attempt to perform single-trial classification of gait intent from another movement plan (point intent) or from standing in place. Subjects walked naturally from a starting position to a designated ending position, pointed at a designated position from the starting position, or remained standing at the starting position. The 700 ms of recorded electroencephalography (EEG) before movement onset was used for single-trial classification of trials based on action type and direction (left walk, forward walk, right walk, left point, right point, and stand) as well as action type regardless of direction (stand, walk, point). Classification using regularized LDA was performed on a principal components analysis (PCA) reduced feature space composed of coefficients from levels 1 to 9 of a discrete wavelet decomposition using the Daubechies 4 wavelet. We achieved significant classification for all conditions, with errors as low as 17% when averaged across nine subjects. LDA and PCA highly weighted frequency ranges that included movement related potentials (MRPs), with smaller contributions from frequency ranges that included mu and beta idle motor rhythms. Additionally, error patterns suggested a spatial structure to the EEG signal. Future applications of the cortical gait intent signal may include an additional dimension of control for prosthetics, preemptive corrective feedback for gait disturbances, or human computer interfaces (HCI).
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http://dx.doi.org/10.3389/fnins.2013.00084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3678086PMC
June 2013

Charges in the hydrophobic interior of proteins.

Proc Natl Acad Sci U S A 2010 Sep 26;107(37):16096-100. Epub 2010 Aug 26.

Department of Biophysics, Johns Hopkins University, 3400 N Charles Street, Baltimore, MD 21218, USA.

Charges are inherently incompatible with hydrophobic environments. Presumably for this reason, ionizable residues are usually excluded from the hydrophobic interior of proteins and are found instead at the surface, where they can interact with bulk water. Paradoxically, ionizable groups buried in the hydrophobic interior of proteins play essential roles, especially in biological energy transduction. To examine the unusual properties of internal ionizable groups we measured the pK(a) of glutamic acid residues at 25 internal positions in a stable form of staphylococcal nuclease. Two of 25 Glu residues titrated with normal pK(a) near 4.5; the other 23 titrated with elevated pK(a) values ranging from 5.2-9.4, with an average value of 7.7. Trp fluorescence and far-UV circular dichroism were used to monitor the effects of internal charges on conformation. These data demonstrate that although charges buried in proteins are indeed destabilizing, charged side chains can be buried readily in the hydrophobic core of stable proteins without the need for specialized structural adaptations to stabilize them, and without inducing any major conformational reorganization. The apparent dielectric effect experienced by the internal charges is considerably higher than the low dielectric constants of hydrophobic matter used to represent the protein interior in electrostatic continuum models of proteins. The high thermodynamic stability required for proteins to withstand the presence of buried charges suggests a pathway for the evolution of enzymes, and it underscores the need to mind thermodynamic stability in any strategy for engineering novel or altered enzymatic active sites in proteins.
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http://dx.doi.org/10.1073/pnas.1004213107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2941338PMC
September 2010

Hydration of the folding transition state ensemble of a protein.

Biochemistry 2006 Mar;45(11):3473-80

INSERM U554, Montpellier, F-34090 France.

A complete description of the mechanisms of protein folding requires knowledge of the structural and physical character of the folding transition state ensembles (TSEs). A key question concerning the role of hydration of the hydrophobic core in determining folding mechanisms remains. To address this, we probed the state of hydration of the TSE of staphylococcal nuclease (SNase) by examining the fluorescence-detected pressure-jump relaxation behavior of six SNase variants in which a residue in the hydrophobic core, Val-66, was replaced with polar or ionizable residues (Lys, Arg, His, Asp, Glu, and Asn). Because of a large positive activation volume for folding, the major effect of pressure on the wild-type protein is to decrease the folding rate. By the time wild-type SNase reaches the folding transition state, most water has already been expelled from its hydrophobic core. In contrast, the major effect of pressure on the variant proteins is an increase in the unfolding rate due to a large negative activation volume for unfolding. This results from a significant increase in the level of hydration of the TSE when an internal ionizable group is present. These data confirm that the role of water in the folding reaction can differ from protein to protein and that even a single substitution in a critical position can modulate significantly the properties of the TSE.
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http://dx.doi.org/10.1021/bi052638zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4442614PMC
March 2006