346 results on '"Aliya N. Husain"'
Search Results
2. Deep learning generates synthetic cancer histology for explainability and education
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James M. Dolezal, Rachelle Wolk, Hanna M. Hieromnimon, Frederick M. Howard, Andrew Srisuwananukorn, Dmitry Karpeyev, Siddhi Ramesh, Sara Kochanny, Jung Woo Kwon, Meghana Agni, Richard C. Simon, Chandni Desai, Raghad Kherallah, Tung D. Nguyen, Jefree J. Schulte, Kimberly Cole, Galina Khramtsova, Marina Chiara Garassino, Aliya N. Husain, Huihua Li, Robert Grossman, Nicole A. Cipriani, and Alexander T. Pearson
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Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Artificial intelligence methods including deep neural networks (DNN) can provide rapid molecular classification of tumors from routine histology with accuracy that matches or exceeds human pathologists. Discerning how neural networks make their predictions remains a significant challenge, but explainability tools help provide insights into what models have learned when corresponding histologic features are poorly defined. Here, we present a method for improving explainability of DNN models using synthetic histology generated by a conditional generative adversarial network (cGAN). We show that cGANs generate high-quality synthetic histology images that can be leveraged for explaining DNN models trained to classify molecularly-subtyped tumors, exposing histologic features associated with molecular state. Fine-tuning synthetic histology through class and layer blending illustrates nuanced morphologic differences between tumor subtypes. Finally, we demonstrate the use of synthetic histology for augmenting pathologist-in-training education, showing that these intuitive visualizations can reinforce and improve understanding of histologic manifestations of tumor biology.
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- 2023
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3. Uncertainty-informed deep learning models enable high-confidence predictions for digital histopathology
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James M. Dolezal, Andrew Srisuwananukorn, Dmitry Karpeyev, Siddhi Ramesh, Sara Kochanny, Brittany Cody, Aaron S. Mansfield, Sagar Rakshit, Radhika Bansal, Melanie C. Bois, Aaron O. Bungum, Jefree J. Schulte, Everett E. Vokes, Marina Chiara Garassino, Aliya N. Husain, and Alexander T. Pearson
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Science - Abstract
Safe clinical deployment of deep learning models for digital pathology requires reliable estimates of predictive uncertainty. Here the authors describe an algorithm for quantifying whole-slide image uncertainty, demonstrating their approach with models trained to distinguish lung cancer subtypes.
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- 2022
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4. Steroid-refractory dermatologic and pulmonary toxicity in a patient on rituximab treated with pembrolizumab for progressive urothelial carcinoma: a case report
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Jacobi Hines, Ellen Daily, Anh Khoa Pham, Christopher R. Shea, Urooba Nadeem, Aliya N. Husain, Walter M. Stadler, and Pankti Reid
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Immunotherapy ,Bullous skin diseases ,Medical oncology ,Case report ,Immune-related adverse effects ,Immune checkpoint inhibitors ,Medicine - Abstract
Abstract Background Increasingly widespread use of programmed cell death protein 1 (PD-1) immune checkpoint inhibitors (ICIs) for treatment of a variety of progressive malignancies continues to reveal a range of immune-related adverse events (irAEs), necessitating immunosuppressive therapy for management. While a single course of systemic corticosteroids may be sufficient for many irAEs, no clear standard-of-care guidelines exist for steroid-refractory cases. We present an unusual case of a patient who developed several steroid-refractory novel irAEs on pembrolizumab despite ongoing B cell-directed immunosuppressive therapy with rituximab, who ultimately noted resolution of symptoms with tacrolimus, a T-cell-directed immunosuppressant. Case presentation This 72-year-old Caucasian man with Waldenstrom’s macroglobulinemia and myelin-associated glycoprotein (MAG) immunoglobulin M (IgM) antibody-associated neuropathy was being treated with maintenance rituximab and intravenous immunoglobulin when he was started on pembrolizumab (2.26 mg/kg) for metastatic urothelial cancer 31 months after surgery and adjuvant chemotherapy. After his third dose of pembrolizumab, he developed a painful blistering papular rash of the distal extremities. He received two more doses of pembrolizumab before he also developed diarrhea, and it was held; he was initiated on 1 mg/kg prednisone for presumed ICI-induced dermatitis and colitis. Skin biopsy 10 weeks after cessation of pembrolizumab and taper of steroids to 20 mg daily revealed a unique bullous erythema multiforme. He was then admitted with dyspnea and imaging concerning for necrotizing pneumonia, but did not respond to antibiotic therapy. Bronchoscopy and biopsy revealed acute fibrinous organizing pneumonia. His symptoms failed to fully respond to multiple courses of high-dose systemic corticosteroids and a trial of azathioprine, but pneumonia, diarrhea, and skin rash all improved markedly with tacrolimus. The patient has since completed his therapy for tacrolimus, continues off of ICI, and has not experienced a recurrence of any irAEs, though has more recently experienced progression of his cancer. Conclusion Despite immunosuppression with rituximab and intravenous immunoglobulin, two immunomodulators targeting B cells, ICI cessation, and systemic corticosteroid therapy, our patient developed two high-grade unusual irAEs, bullous erythema multiforme and acute fibrinous organizing pneumonia. Our patient’s improvement with tacrolimus can offer critical insight into the pathophysiology of steroid-refractory irAEs.
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- 2021
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5. Educational Case: Myocardial Infarction: Histopathology and Timing of Changes
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Mariam Ghafoor MD, Maria Kamal MD, Urooba Nadeem MD, and Aliya N. Husain MD
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Pathology ,RB1-214 - Abstract
The following fictional case is intended as a learning tool within the Pathology Competencies for Medical Education (PCME), a set of national standards for teaching pathology. These are divided into three basic competencies: Disease Mechanisms and Processes, Organ System Pathology, and Diagnostic Medicine and Therapeutic Pathology. For additional information, and a full list of learning objectives for all three competencies, see http://journals.sagepub.com/doi/10.1177/2374289517715040 . 1
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- 2020
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6. IL-6 Inhibition in Critically Ill COVID-19 Patients Is Associated With Increased Secondary Infections
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Lucas M. Kimmig, David Wu, Matthew Gold, Natasha N. Pettit, David Pitrak, Jeffrey Mueller, Aliya N. Husain, Ece A. Mutlu, and Gökhan M. Mutlu
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COVID-19 ,SARS-CoV-2 ,tocilizumab ,cytokine release syndrome ,immunosuppression ,Medicine (General) ,R5-920 - Abstract
Background: Anti-inflammatory therapies such as IL-6 inhibition have been proposed for COVID-19 in a vacuum of evidence-based treatment. However, abrogating the inflammatory response in infectious diseases may impair a desired host response and pre-dispose to secondary infections.Methods: We retrospectively reviewed the medical record of critically ill COVID-19 patients during an 8-week span and compared the prevalence of secondary infection and outcomes in patients who did and did not receive tocilizumab. Additionally, we included representative histopathologic post-mortem findings from several COVID-19 cases that underwent autopsy at our institution.Results: One hundred eleven patients were identified, of which 54 had received tocilizumab while 57 had not. Receiving tocilizumab was associated with a higher risk of secondary bacterial (48.1 vs. 28.1%; p = 0.029 and fungal (5.6 vs. 0%; p = 0.112) infections. Consistent with higher number of infections, patients who received tocilizumab had higher mortality (35.2 vs. 19.3%; p = 0.020). Seven cases underwent autopsy. In three cases who received tocilizumab, there was evidence of pneumonia on pathology. Of the four cases that had not been given tocilizumab, two showed evidence of aspiration pneumonia and two exhibited diffuse alveolar damage.Conclusions: Experimental therapies are currently being applied to COVID-19 outside of clinical trials. Anti-inflammatory therapies such as anti-IL-6 therapy have the potential to impair viral clearance, pre-dispose to secondary infection, and cause harm. We seek to raise physician awareness of these issues and highlight the need to better understand the immune response in COVID-19.
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- 2020
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7. Educational Case: Asthma: Clinical Features and Morphologic Findings
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Maria Kamal MD, Mariam Ghafoor MD, Urooba Nadeem MD, and Aliya N. Husain MD
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Pathology ,RB1-214 - Abstract
The following fictional case is intended as a learning tool within the Pathology Competencies for Medical Education (PCME), a set of national standards for teaching pathology. These are divided into three basic competencies: Disease Mechanisms and Processes, Organ System Pathology, and Diagnostic Medicine and Therapeutic Pathology. For additional information, and a full list of learning objectives for all three competencies, see http://journals.sagepub.com/doi/10.1177/2374289517715040 . 1
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- 2020
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8. Differential responsiveness of MET inhibition in non-small-cell lung cancer with altered CBL
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Yi-Hung Carol Tan, Tamara Mirzapoiazova, Brian M. Won, Li Zhu, Minu K. Srivastava, Everett E. Vokes, Aliya N. Husain, Surinder K. Batra, Sherven Sharma, and Ravi Salgia
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Medicine ,Science - Abstract
Abstract Casitas B-lineage lymphoma (CBL) is an E3 ubiquitin ligase and a molecule of adaptor that we have shown is important for non-small-cell lung cancer (NSCLC). We investigated if MET is a target of CBL and if enhanced in CBL-altered NSCLC. We showed that CBL wildtype cells have lower MET expression than CBL mutant cells. Ubiquitination of MET was also decreased in CBL mutant cells compared to wildtype cells. Mutant cells were also more sensitive to MET inhibitor SU11274 than wild-type cells. sh-RNA-mediated knockdown of CBL enhanced cell motility and colony formation in NSCLC cells, and these activities were inhibited by SU11274. Assessment of the phospho-kinome showed decreased phosphorylation of pathways involving MET, paxillin, EPHA2, and VEGFR. When CBL was knocked down in the mutant cell line H1975 (erlotinib-resistant), it became sensitive to MET inhibition. Our findings suggest that CBL status is a potential positive indicator for MET-targeted therapeutics in NSCLC.
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- 2017
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9. Late presentation of constrictive pericarditis after limited epicardial ablation for inappropriate sinus tachycardia
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Adam Oesterle, MD, Amita Singh, MD, Husam Balkhy, MD, Aliya N. Husain, MD, Deborah Moyer, APN, Roderick Tung, MD, FHRS, and Hemal M. Nayak, MD, FHRS
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Inappropriate sinus tachycardia ,Catheter ablation ,Pericardial disease ,Magnetic resonance imaging ,Pericardial constriction ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Published
- 2016
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10. Autoimmune Hypothyroidism As a Predictor of Mortality in Chronic Hypersensitivity Pneumonitis
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Ayodeji Adegunsoye, Justin M. Oldham, Aliya N. Husain, Lena Chen, Scully Hsu, Steven Montner, Jonathan H. Chung, Rekha Vij, Imre Noth, and Mary E. Strek
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autoimmunity ,hypothyroidism ,hypersensitivity pneumonitis ,extrinsic allergic alveolitis ,pulmonary fibrosis ,Medicine (General) ,R5-920 - Abstract
BackgroundChronic hypersensitivity pneumonitis (CHP) is a fibrotic parenchymal lung disease that occurs when inhalation of environmental antigens leads to immune dysregulation. Autoimmune features have recently been identified as potentially important among patients with CHP. However, the relationship between hypothyroidism (HT) and CHP is unknown. In this study, we investigate the prevalence and impact of HT among patients with CHP.MethodsWe conducted a retrospective, case–control analysis. We identified 121 patients at the University of Chicago Interstitial Lung Disease Center with a multidisciplinary diagnosis of CHP. These patients were matched 3:1 according to age, sex, and race to 363 control subjects with asthma from 2006 to 2015. We analyzed demographics, clinical characteristics, and survival between both groups and assessed the relationship of HT with CHP. Survival analysis was performed using Cox proportional hazards modeling.ResultsPatients with CHP had higher prevalence of HT (25.6%, n = 31) compared to controls (10.7%, n = 39; OR, 2.86; 95% CI, 1.62–4.99; P
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- 2017
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11. Outcomes of immunosuppressive therapy in chronic hypersensitivity pneumonitis
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Ayodeji Adegunsoye, Justin M. Oldham, Evans R. Fernández Pérez, Mark Hamblin, Nina Patel, Mitchell Tener, Deepa Bhanot, Lacey Robinson, Sam Bullick, Lena Chen, Scully Hsu, Matthew Churpek, Donald Hedeker, Steven Montner, Jonathan H. Chung, Aliya N. Husain, Imre Noth, Mary E. Strek, and Rekha Vij
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Medicine - Abstract
In chronic hypersensitivity pneumonitis (CHP), lack of improvement or declining lung function may prompt use of immunosuppressive therapy. We hypothesised that use of azathioprine or mycophenolate mofetil with prednisone reduces adverse events and lung function decline, and improves transplant-free survival. Patients with CHP were identified. Demographic features, pulmonary function tests, incidence of treatment-emergent adverse events (TEAEs) and transplant-free survival were characterised, compared and analysed between patients stratified by immunosuppressive therapy. A multicentre comparison was performed across four independent tertiary medical centres. Among 131 CHP patients at the University of Chicago medical centre (Chicago, IL, USA), 93 (71%) received immunosuppressive therapy, and had worse baseline forced vital capacity (FVC) and diffusing capacity, and increased mortality compared with those who did not. Compared to patients treated with prednisone alone, TEAEs were 54% less frequent with azathioprine therapy (p=0.04) and 66% less frequent with mycophenolate mofetil (p=0.002). FVC decline and survival were similar between treatment groups. Analyses of datasets from four external tertiary medical centres confirmed these findings. CHP patients who did not receive immunosuppressive therapy had better survival than those who did. Use of mycophenolate mofetil or azathioprine was associated with a decreased incidence of TEAEs, and no difference in lung function decline or survival when compared with prednisone alone. Early transition to mycophenolate mofetil or azathioprine may be an appropriate therapeutic approach in CHP, but more studies are needed.
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- 2017
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12. Cardiotoxicity associated with CTLA4 and PD1 blocking immunotherapy
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Matthias Pauschinger, F. Stephen Hodi, Patrick A. Ott, Thomas F. Gajewski, Hussein Tawbi, Jason J. Luke, Lucie Heinzerling, Aliya N. Husain, Azadeh Tajmir-Riahi, and Evan J. Lipson
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Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Immune-checkpoint blocking antibodies have demonstrated objective antitumor responses in multiple tumor types including melanoma, non-small cell lung cancer (NSCLC), and renal cell cancer (RCC). In melanoma, an increase in overall survival has been demonstrated with anti-CTLA-4 and PD-1 inhibition. However, a plethora of immune-mediated adverse events has been reported with these agents. Immune-mediated cardiotoxicity induced by checkpoint inhibitors has been reported in single cases with variable presentation, including myocarditis and pericarditis.Among six clinical cancer centers with substantial experience in the administration of immune-checkpoint blocking antibodies, eight cases of immune-related cardiotoxicity after ipilimumab and/or nivolumab/pembrolizumab were identified. Diagnostic findings, treatment and follow-up are reported. A large variety of cardiotoxic events with manifestations such as heart failure, cardiomyopathy, heart block, myocardial fibrosis and myocarditis was documented.This is the largest case series to date describing cardiotoxicity of immune-checkpoint blocking antibodies. Awareness, monitoring of patients with pre-existing cardiac disorders and prompt evaluation by the treatment team is essential. Treatment including application of steroids is critical for patient safety.
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- 2016
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13. All Together Now
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Pari Jafari, Aliya N. Husain, and Namrata Setia
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Surgery ,Pathology and Forensic Medicine - Published
- 2023
14. Highly aneuploid non-small cell lung cancer shows enhanced responsiveness to concurrent radiation and immune checkpoint blockade
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Liam F. Spurr, Carlos A. Martinez, Wenjun Kang, Mengjie Chen, Yuanyuan Zha, Robyn Hseu, Stanley I. Gutiontov, William T. Turchan, Connor M. Lynch, Kelli B. Pointer, Paul Chang, Septimiu Murgu, Aliya N. Husain, Brittany Cody, Everett E. Vokes, Christine M. Bestvina, Jyoti D. Patel, Maximilian Diehn, Thomas F. Gajewski, Ralph R. Weichselbaum, Steven J. Chmura, and Sean P. Pitroda
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Cancer Research ,Lung Neoplasms ,Oncology ,Carcinoma, Non-Small-Cell Lung ,Humans ,Immune Checkpoint Inhibitors ,Combined Modality Therapy ,Biomarkers - Abstract
Over 500 clinical trials are investigating combination radiotherapy and immune checkpoint blockade (ICB) as cancer treatments; however, the majority of trials have found no positive interaction. Here we perform a comprehensive molecular analysis of a randomized phase I clinical trial of patients with non-small cell lung cancer (NSCLC) treated with concurrent or sequential ablative radiotherapy and ICB. We show that concurrent treatment is superior to sequential treatment in augmenting local and distant tumor responses and in improving overall survival in a subset of patients with immunologically cold, highly aneuploid tumors, but not in those with less aneuploid tumors. In addition, radiotherapy alone decreases intratumoral cytotoxic T cell and adaptive immune signatures, whereas radiotherapy and ICB upregulates key immune pathways. Our findings challenge the prevailing paradigm that local ablative radiotherapy beneficially stimulates the immune response. We propose the use of tumor aneuploidy as a biomarker and therapeutic target in personalizing treatment approaches for patients with NSCLC treated with radiotherapy and ICB.
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- 2022
15. Calretinin Staining in Anorectal Line Biopsies Accurately Distinguished Hirschsprung Disease in a Retrospective Study
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Suzanna J. Logan, Hong Yin, Beverly Rogers, Nicoleta Arva, Miriam R. Conces, Sandy Cope-Yokoyama, Louis P. Dehner, Carlos Galliani, Shipra Garg, Mai He, Aliya N. Husain, Matthew Keisling, Chandra Krishnan, Elena Puscasiu, Christopher Rossi, Faiza Siddiqui, Lisa Sutton, Jefferson Terry, Ameet I. Thaker, Yuan Huang, Jie Zhang, Courtney McCracken, and Heather Rytting
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Pediatrics, Perinatology and Child Health ,General Medicine ,Pathology and Forensic Medicine - Abstract
Introduction: The absence of submucosal ganglion cells does not reliably distinguish Hirschsprung disease from non Hirschsprung disease in anorectal line biopsies. Calretinin staining might be helpful in these biopsies. To determine its value, we analyzed calretinin positive mucosal neurites in anorectal line biopsies. Methods: Two pediatric pathologists, without access to patient data, evaluated calretinin positive mucosal neurites in anorectal line junctional mucosa in archival rectal biopsies contributed by 17 institutions. A separate investigator compiled patient information and sent data for statistical analysis. Results: Biopsies with anorectal junctional mucosa from 115 patients were evaluated for calretinin positive mucosal neurites. 20/20 Hirschsprung disease biopsies were negative. 87/88 non Hirschsprung disease biopsies and 7/7 post pullthrough Hirschsprung disease neorectal biopsies were positive. Statistical analysis of the 108 non pullthrough biopsies yielded an accuracy of 99.1% (sensitivity 100%, specificity 98.9%). Age range was preterm to 16 years. Biopsy size was less than 1 mm to over 1 cm. Conclusions: Absence of calretinin positive mucosal neurites at the anorectal line was highly accurate in distinguishing Hirschsprung disease from non Hirschsprung disease cases in this blinded retrospective study. Calretinin staining is useful for interpreting biopsies from the physiologic hypoganglionic zone up to the anorectal line.
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- 2022
16. Characterizing the distribution of alterations in mesothelioma and their correlation to morphology
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Heather I-Hsuan Chen-Yost, Melissa Y Tjota, Guimin Gao, Owen Mitchell, Hedy Kindler, Jeremy Segal, Aliya N Husain, Jeffrey Mueller, and Jefree J Schulte
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General Medicine - Abstract
Objectives Mesothelioma is a lethal disease that arises from the serosal lining of organ cavities. Several recurrent alterations have been observed in pleural and peritoneal mesotheliomas, including in BAP1, NF2, and CDKN2A. Although specific histopathologic parameters have been correlated with prognosis, it is not as well known whether genetic alterations correlate with histologic findings. Methods We reviewed 131 mesotheliomas that had undergone next-generation sequencing (NGS) at our institutions after pathologic diagnosis. There were 109 epithelioid mesotheliomas, 18 biphasic mesotheliomas, and 4 sarcomatoid mesotheliomas. All our biphasic and sarcomatoid cases arose in the pleura. Of the epithelioid mesotheliomas, 73 were from the pleura and 36 were from the peritoneum. On average, patients were 66 years of age (range, 26-90 years) and predominantly male (92 men, 39 women). Results The most common alterations identified were in BAP1, CDKN2A, NF2, and TP53. Twelve mesotheliomas did not show a pathogenic alteration on NGS. For epithelioid mesotheliomas in the pleura, the presence of an alteration in BAP1 correlated with low nuclear grade (P = .04), but no correlation was found in the peritoneum (P = .62). Similarly, there was no correlation between the amount of solid architecture in epithelioid mesotheliomas and any alterations in the pleura (P = .55) or peritoneum (P = .13). For biphasic mesotheliomas, cases with either no alteration detected or with an alteration in BAP1 were more likely to be epithelioid predominant (>50% of the tumor, P = .0001), and biphasic mesotheliomas with other alterations detected and no alteration in BAP1 were more likely to be sarcomatoid predominant (>50% of the tumor, P = .0001). Conclusions This study demonstrates a significant association between morphologic features associated with a better prognosis and an alteration in BAP1.
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- 2023
17. Surgical phenotype of patients with peritoneal mesothelioma and a germline mutation
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Yaniv Berger, Meghana Gadiraju, Ankit Dhiman, Katie Gilliam, Buerkley Opalecky, Heather Chen, Maria Helgeson, Oliver S. Eng, Aliya N. Husain, Michael W. Drazer, Hedy L. Kindler, Jane E. Churpek, and Kiran K. Turaga
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Cancer Research ,Oncology - Published
- 2023
18. Table S6 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma
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Erik Zmuda, Hongxin Zhang, Hailei Zhang, Jiashan Zhang, Jean C. Zenklusen, Marjorie G. Zauderer, Liming Yang, Shogo Yamamoto, Ye Wu, Tina Wong, Ignacio Wistuba, Lisa Wise, Matthew D. Wilkerson, Daniel J. Weisenberger, John N. Weinstein, Joellen Weaver, Jing Wang, Zhining Wang, Yunhu Wan, Douglas Voet, Luciano S. Viana, Umadevi Veluvolu, Nico van Zandwijk, David J. Van Den Berg, Federico Valdivieso, Tohru Tsujimura, Kane Tse, Anne Tsao, Eric Thompson, Nina Thiessen, Barry S Taylor, Kenji Tatsuno, Roy Tarnuzzer, Donghui Tan, Angela Tam, Qiang Sun, Josh Stuart, Chip Stewart, Paul Spellman, Matthew G. Soloway, Heidi J. Sofia, Tara Skelly, Payal Sipahimalani, Janae V. Simons, Henrique C. S. Silveira, Ilya Shmulevich, Yuichi Shiraishi, Yan Shi, Robert Sheridan, Troy Shelton, Candace Shelton, David T Severson, Tanguy Seiwert, Steven E. Schumacher, Nikolaus Schultz, Jacqueline E. Schein, Cristovam Scapulatempo-Neto, Ayuko Sato, Chris Sander, Gordon Saksena, Sara Sadeghi, Valerie Rusch, Jeffrey Roach, Robert C. Rintoul, William G Richards, David Rice, Sheila M. Reynolds, Rui M. Reis, Glen Reid, Gloria Ravegnini, Doris M. Rassl, Nilsa C. Ramirez, Todd Pihl, Charles M. Perou, Robert Penny, Nathan A. Pennell, Arjun Pennathur, Joseph Paulauskis, Harvey I. Pass, Joel S. Parker, Hatice Osmanbeyoglu, Angelica Ochoa, Yulia Newton, Rashi Naresh, Takashi Nakano, Karen Mungall, Andrew J. Mungall, Lisle E. Mose, Scott Morris, Cesar Moran, Richard A. Moore, Gordon B. Mills, Piotr A. Mieczkowski, Matthew Meyerson, Shaowu Meng, Jonathan Melamed, Sam Meier, Michael Mayo, Marco A. Marra, David Mallory, Dennis T. Maglinte, Yussanne Ma, James Luketich, Yiling Lu, Adhemar Longatto-Filho, Laxmi Lolla, Eric Minwei Liu, Wenbin Liu, Jia Liu, Pei Lin, Tara M. Lichtenberg, Kristen M. Leraas, Darlene Lee, Michael S. Lawrence, Peter W. Laird, Phillip H. Lai, David J. Kwiatkowski, Kozo Kuribayashi, Ritika Kundra, Thomas Krausz, Nobuyuki Kondo, Jaegil Kim, Katayoon Kasaian, Rupa S. Kanchi, Corbin D. Jones, Steven J.M. Jones, Stuart R. Jefferys, Carolyn M. Hutter, Aliya Husain, Alan P. Hoyle, Robert A. Holt, Katherine A. Hoadley, Zachary Heins, David I. Heiman, D. Neil Hayes, David Haussler, Seiki Hasegawa, Guangwu Guo, Benjamin Gross, Chandra Goparaju, Gad Getz, Mark Gerken, Nils Gehlenborg, Julie M. Gastier-Foster, Johanna Gardner, Jianjiong Gao, Françoise Galateau Sallé, Stacey B. Gabriel, Shiro Fukuda, Martin L. Ferguson, Michael Feldman, Rajiv Dhir, Noreen Dhalla, John A. Demchok, Timothy DeFreitas, Assunta De Rienzo, Ludmila Danilova, Erin Curley, Daniel Crain, Leslie Cope, Carrie Cibulskis, Sudha Chudamani, Eric Chuah, Juok Cho, Lucian Chirieac, Dorothy Cheung, Andrew D. Cherniack, Andre L. Carvalho, Rebecca Carlsen, Flávio M. Cárcano, Lauren Averett Byers, Denise Brooks, Moiz S. Bootwalla, Tom Bodenheimer, Craig Bielski, Rameen Beroukhim, Carmen Behrens, Michael Becich, Stephen B. Baylin, Saianand Balu, Miruna Balasundaram, J. Todd Auman, Joshua Armenia, Pavana Anur, Adrian Ally, Marc Ladanyi, Peter Campbell, Bruce W. Robinson, Hiroyuki Aburatani, Ronglai Shen, A. Gordon Robertson, Jonathan A. Fletcher, Michael S. Noble, Lauren A. Byers, Rehan Akbani, Jean Claude Zenklusen, Ina Felau, Jay Bowen, Kristen Leraas, Tara Lichtenberg, Jenette Creaney, Anne S. Tsao, Raphael Bueno, Hedy Kindler, Harvey Pass, Valerie W. Rusch, Henrique C. Silveira, Aliya N. Husain, Junya Fujimoto, Françoise Galateau-Sallé, Lucian R. Chirieac, Sanja Dacic, William D. Travis, Achim A. Jungbluth, Patrice Desmeules, David T. Severson, Havish Kantheti, Lisa Iype, Vesteinn Thorsson, David L. Gibbs, Lixia Diao, Carl M. Gay, Manaswi Gupta, Kiley Graim, Jumpei Takeshita, Yoshitaka Sekido, Hatice U. Osmanbeyoglu, Rupa Kanchi, Reanne Bowlby, Ewan A. Gibb, Esther Drill, Patrick Tarpey, David Heiman, Juliann Shih, Francisco Sanchez-Vega, and Julija Hmeljak
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Table S6 contains results from the analysis of DNA methylation in SETD2 mutated and BAP1 inactivated samples.
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- 2023
19. Data from Integrative Molecular Characterization of Malignant Pleural Mesothelioma
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Erik Zmuda, Hongxin Zhang, Hailei Zhang, Jiashan Zhang, Jean C. Zenklusen, Marjorie G. Zauderer, Liming Yang, Shogo Yamamoto, Ye Wu, Tina Wong, Ignacio Wistuba, Lisa Wise, Matthew D. Wilkerson, Daniel J. Weisenberger, John N. Weinstein, Joellen Weaver, Jing Wang, Zhining Wang, Yunhu Wan, Douglas Voet, Luciano S. Viana, Umadevi Veluvolu, Nico van Zandwijk, David J. Van Den Berg, Federico Valdivieso, Tohru Tsujimura, Kane Tse, Anne Tsao, Eric Thompson, Nina Thiessen, Barry S Taylor, Kenji Tatsuno, Roy Tarnuzzer, Donghui Tan, Angela Tam, Qiang Sun, Josh Stuart, Chip Stewart, Paul Spellman, Matthew G. Soloway, Heidi J. Sofia, Tara Skelly, Payal Sipahimalani, Janae V. Simons, Henrique C. S. Silveira, Ilya Shmulevich, Yuichi Shiraishi, Yan Shi, Robert Sheridan, Troy Shelton, Candace Shelton, David T Severson, Tanguy Seiwert, Steven E. Schumacher, Nikolaus Schultz, Jacqueline E. Schein, Cristovam Scapulatempo-Neto, Ayuko Sato, Chris Sander, Gordon Saksena, Sara Sadeghi, Valerie Rusch, Jeffrey Roach, Robert C. Rintoul, William G Richards, David Rice, Sheila M. Reynolds, Rui M. Reis, Glen Reid, Gloria Ravegnini, Doris M. Rassl, Nilsa C. Ramirez, Todd Pihl, Charles M. Perou, Robert Penny, Nathan A. Pennell, Arjun Pennathur, Joseph Paulauskis, Harvey I. Pass, Joel S. Parker, Hatice Osmanbeyoglu, Angelica Ochoa, Yulia Newton, Rashi Naresh, Takashi Nakano, Karen Mungall, Andrew J. Mungall, Lisle E. Mose, Scott Morris, Cesar Moran, Richard A. Moore, Gordon B. Mills, Piotr A. Mieczkowski, Matthew Meyerson, Shaowu Meng, Jonathan Melamed, Sam Meier, Michael Mayo, Marco A. Marra, David Mallory, Dennis T. Maglinte, Yussanne Ma, James Luketich, Yiling Lu, Adhemar Longatto-Filho, Laxmi Lolla, Eric Minwei Liu, Wenbin Liu, Jia Liu, Pei Lin, Tara M. Lichtenberg, Kristen M. Leraas, Darlene Lee, Michael S. Lawrence, Peter W. Laird, Phillip H. Lai, David J. Kwiatkowski, Kozo Kuribayashi, Ritika Kundra, Thomas Krausz, Nobuyuki Kondo, Jaegil Kim, Katayoon Kasaian, Rupa S. Kanchi, Corbin D. Jones, Steven J.M. Jones, Stuart R. Jefferys, Carolyn M. Hutter, Aliya Husain, Alan P. Hoyle, Robert A. Holt, Katherine A. Hoadley, Zachary Heins, David I. Heiman, D. Neil Hayes, David Haussler, Seiki Hasegawa, Guangwu Guo, Benjamin Gross, Chandra Goparaju, Gad Getz, Mark Gerken, Nils Gehlenborg, Julie M. Gastier-Foster, Johanna Gardner, Jianjiong Gao, Françoise Galateau Sallé, Stacey B. Gabriel, Shiro Fukuda, Martin L. Ferguson, Michael Feldman, Rajiv Dhir, Noreen Dhalla, John A. Demchok, Timothy DeFreitas, Assunta De Rienzo, Ludmila Danilova, Erin Curley, Daniel Crain, Leslie Cope, Carrie Cibulskis, Sudha Chudamani, Eric Chuah, Juok Cho, Lucian Chirieac, Dorothy Cheung, Andrew D. Cherniack, Andre L. Carvalho, Rebecca Carlsen, Flávio M. Cárcano, Lauren Averett Byers, Denise Brooks, Moiz S. Bootwalla, Tom Bodenheimer, Craig Bielski, Rameen Beroukhim, Carmen Behrens, Michael Becich, Stephen B. Baylin, Saianand Balu, Miruna Balasundaram, J. Todd Auman, Joshua Armenia, Pavana Anur, Adrian Ally, Marc Ladanyi, Peter Campbell, Bruce W. Robinson, Hiroyuki Aburatani, Ronglai Shen, A. Gordon Robertson, Jonathan A. Fletcher, Michael S. Noble, Lauren A. Byers, Rehan Akbani, Jean Claude Zenklusen, Ina Felau, Jay Bowen, Kristen Leraas, Tara Lichtenberg, Jenette Creaney, Anne S. Tsao, Raphael Bueno, Hedy Kindler, Harvey Pass, Valerie W. Rusch, Henrique C. Silveira, Aliya N. Husain, Junya Fujimoto, Françoise Galateau-Sallé, Lucian R. Chirieac, Sanja Dacic, William D. Travis, Achim A. Jungbluth, Patrice Desmeules, David T. Severson, Havish Kantheti, Lisa Iype, Vesteinn Thorsson, David L. Gibbs, Lixia Diao, Carl M. Gay, Manaswi Gupta, Kiley Graim, Jumpei Takeshita, Yoshitaka Sekido, Hatice U. Osmanbeyoglu, Rupa Kanchi, Reanne Bowlby, Ewan A. Gibb, Esther Drill, Patrick Tarpey, David Heiman, Juliann Shih, Francisco Sanchez-Vega, and Julija Hmeljak
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Malignant pleural mesothelioma (MPM) is a highly lethal cancer of the lining of the chest cavity. To expand our understanding of MPM, we conducted a comprehensive integrated genomic study, including the most detailed analysis of BAP1 alterations to date. We identified histology-independent molecular prognostic subsets, and defined a novel genomic subtype with TP53 and SETDB1 mutations and extensive loss of heterozygosity. We also report strong expression of the immune-checkpoint gene VISTA in epithelioid MPM, strikingly higher than in other solid cancers, with implications for the immune response to MPM and for its immunotherapy. Our findings highlight new avenues for further investigation of MPM biology and novel therapeutic options.Significance:Through a comprehensive integrated genomic study of 74 MPMs, we provide a deeper understanding of histology-independent determinants of aggressive behavior, define a novel genomic subtype with TP53 and SETDB1 mutations and extensive loss of heterozygosity, and discovered strong expression of the immune-checkpoint gene VISTA in epithelioid MPM.See related commentary by Aggarwal and Albelda, p. 1508.This article is highlighted in the In This Issue feature, p. 1494
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20. Supplementary Data from Integrative Molecular Characterization of Malignant Pleural Mesothelioma
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Erik Zmuda, Hongxin Zhang, Hailei Zhang, Jiashan Zhang, Jean C. Zenklusen, Marjorie G. Zauderer, Liming Yang, Shogo Yamamoto, Ye Wu, Tina Wong, Ignacio Wistuba, Lisa Wise, Matthew D. Wilkerson, Daniel J. Weisenberger, John N. Weinstein, Joellen Weaver, Jing Wang, Zhining Wang, Yunhu Wan, Douglas Voet, Luciano S. Viana, Umadevi Veluvolu, Nico van Zandwijk, David J. Van Den Berg, Federico Valdivieso, Tohru Tsujimura, Kane Tse, Anne Tsao, Eric Thompson, Nina Thiessen, Barry S Taylor, Kenji Tatsuno, Roy Tarnuzzer, Donghui Tan, Angela Tam, Qiang Sun, Josh Stuart, Chip Stewart, Paul Spellman, Matthew G. Soloway, Heidi J. Sofia, Tara Skelly, Payal Sipahimalani, Janae V. Simons, Henrique C. S. Silveira, Ilya Shmulevich, Yuichi Shiraishi, Yan Shi, Robert Sheridan, Troy Shelton, Candace Shelton, David T Severson, Tanguy Seiwert, Steven E. Schumacher, Nikolaus Schultz, Jacqueline E. Schein, Cristovam Scapulatempo-Neto, Ayuko Sato, Chris Sander, Gordon Saksena, Sara Sadeghi, Valerie Rusch, Jeffrey Roach, Robert C. Rintoul, William G Richards, David Rice, Sheila M. Reynolds, Rui M. Reis, Glen Reid, Gloria Ravegnini, Doris M. Rassl, Nilsa C. Ramirez, Todd Pihl, Charles M. Perou, Robert Penny, Nathan A. Pennell, Arjun Pennathur, Joseph Paulauskis, Harvey I. Pass, Joel S. Parker, Hatice Osmanbeyoglu, Angelica Ochoa, Yulia Newton, Rashi Naresh, Takashi Nakano, Karen Mungall, Andrew J. Mungall, Lisle E. Mose, Scott Morris, Cesar Moran, Richard A. Moore, Gordon B. Mills, Piotr A. Mieczkowski, Matthew Meyerson, Shaowu Meng, Jonathan Melamed, Sam Meier, Michael Mayo, Marco A. Marra, David Mallory, Dennis T. Maglinte, Yussanne Ma, James Luketich, Yiling Lu, Adhemar Longatto-Filho, Laxmi Lolla, Eric Minwei Liu, Wenbin Liu, Jia Liu, Pei Lin, Tara M. Lichtenberg, Kristen M. Leraas, Darlene Lee, Michael S. Lawrence, Peter W. Laird, Phillip H. Lai, David J. Kwiatkowski, Kozo Kuribayashi, Ritika Kundra, Thomas Krausz, Nobuyuki Kondo, Jaegil Kim, Katayoon Kasaian, Rupa S. Kanchi, Corbin D. Jones, Steven J.M. Jones, Stuart R. Jefferys, Carolyn M. Hutter, Aliya Husain, Alan P. Hoyle, Robert A. Holt, Katherine A. Hoadley, Zachary Heins, David I. Heiman, D. Neil Hayes, David Haussler, Seiki Hasegawa, Guangwu Guo, Benjamin Gross, Chandra Goparaju, Gad Getz, Mark Gerken, Nils Gehlenborg, Julie M. Gastier-Foster, Johanna Gardner, Jianjiong Gao, Françoise Galateau Sallé, Stacey B. Gabriel, Shiro Fukuda, Martin L. Ferguson, Michael Feldman, Rajiv Dhir, Noreen Dhalla, John A. Demchok, Timothy DeFreitas, Assunta De Rienzo, Ludmila Danilova, Erin Curley, Daniel Crain, Leslie Cope, Carrie Cibulskis, Sudha Chudamani, Eric Chuah, Juok Cho, Lucian Chirieac, Dorothy Cheung, Andrew D. Cherniack, Andre L. Carvalho, Rebecca Carlsen, Flávio M. Cárcano, Lauren Averett Byers, Denise Brooks, Moiz S. Bootwalla, Tom Bodenheimer, Craig Bielski, Rameen Beroukhim, Carmen Behrens, Michael Becich, Stephen B. Baylin, Saianand Balu, Miruna Balasundaram, J. Todd Auman, Joshua Armenia, Pavana Anur, Adrian Ally, Marc Ladanyi, Peter Campbell, Bruce W. Robinson, Hiroyuki Aburatani, Ronglai Shen, A. Gordon Robertson, Jonathan A. Fletcher, Michael S. Noble, Lauren A. Byers, Rehan Akbani, Jean Claude Zenklusen, Ina Felau, Jay Bowen, Kristen Leraas, Tara Lichtenberg, Jenette Creaney, Anne S. Tsao, Raphael Bueno, Hedy Kindler, Harvey Pass, Valerie W. Rusch, Henrique C. Silveira, Aliya N. Husain, Junya Fujimoto, Françoise Galateau-Sallé, Lucian R. Chirieac, Sanja Dacic, William D. Travis, Achim A. Jungbluth, Patrice Desmeules, David T. Severson, Havish Kantheti, Lisa Iype, Vesteinn Thorsson, David L. Gibbs, Lixia Diao, Carl M. Gay, Manaswi Gupta, Kiley Graim, Jumpei Takeshita, Yoshitaka Sekido, Hatice U. Osmanbeyoglu, Rupa Kanchi, Reanne Bowlby, Ewan A. Gibb, Esther Drill, Patrick Tarpey, David Heiman, Juliann Shih, Francisco Sanchez-Vega, and Julija Hmeljak
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Supplementary materials and methods, as well as supplementary figures S1-S7.
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21. Vascular Amyloid Deposition Is Highly Prevalent in Immunoglobulin Light Chain Cardiac Amyloidosis
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Jung Woo Kwon, Aliya N. Husain, Jeffrey Mueller, Varun Subashchandran, Nazia Alvi, Karolina M. Zareba, Nitasha Sarswat, Karima Addetia, Amit R. Patel, and Jeremy A. Slivnick
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Radiology, Nuclear Medicine and imaging ,Cardiology and Cardiovascular Medicine - Published
- 2023
22. Supplementary Table 2 from Paxillin Is a Target for Somatic Mutations in Lung Cancer: Implications for Cell Growth and Invasion
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Ravi Salgia, Aliya N. Husain, Mark K. Ferguson, Everett E. Vokes, John Minna, Viswanathan Natarajan, Wickii Vigneswaran, Thomas Krausz, Martin Sattler, Mark W. Lingen, David Sugarbaker, Raphael Bueno, Gavin J. Gordon, Livia L. Szeto, Vytas P. Bindokas, Lioubov Soulii, Osvaldo Zumba, Salman Ahmed, Maria S. Tretiakova, Luc Girard, Yi-Ching Wang, Leonardo Faoro, Stuart Schwartz, Vidya Nallasura, Trevor Reichman, Rajani Kanteti, Sivakumar Loganathan, Tanguy Y. Seiwert, A. Craig Mackinnon, Varalakshmi Janamanchi, Soundararajan Krishnaswamy, Hanna Surawska, and Ramasamy Jagadeeswaran
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Supplementary Table 2 from Paxillin Is a Target for Somatic Mutations in Lung Cancer: Implications for Cell Growth and Invasion
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- 2023
23. Supplementary Figure 5 from Paxillin Is a Target for Somatic Mutations in Lung Cancer: Implications for Cell Growth and Invasion
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Ravi Salgia, Aliya N. Husain, Mark K. Ferguson, Everett E. Vokes, John Minna, Viswanathan Natarajan, Wickii Vigneswaran, Thomas Krausz, Martin Sattler, Mark W. Lingen, David Sugarbaker, Raphael Bueno, Gavin J. Gordon, Livia L. Szeto, Vytas P. Bindokas, Lioubov Soulii, Osvaldo Zumba, Salman Ahmed, Maria S. Tretiakova, Luc Girard, Yi-Ching Wang, Leonardo Faoro, Stuart Schwartz, Vidya Nallasura, Trevor Reichman, Rajani Kanteti, Sivakumar Loganathan, Tanguy Y. Seiwert, A. Craig Mackinnon, Varalakshmi Janamanchi, Soundararajan Krishnaswamy, Hanna Surawska, and Ramasamy Jagadeeswaran
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Supplementary Figure 5 from Paxillin Is a Target for Somatic Mutations in Lung Cancer: Implications for Cell Growth and Invasion
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- 2023
24. Supplementary Figure 2 from Dramatic Antitumor Effects of the Dual MET/RON Small-Molecule Inhibitor LY2801653 in Non–Small Cell Lung Cancer
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Ravi Salgia, Everett E. Vokes, Aliya N. Husain, Erin Smithberger, Jeffrey Mueller, Qudsia Arif, Rifat Hasina, and Ichiro Kawada
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PDF file - 124K, Figure S2. Sub-network 'Calmodulin, c-Cbl, MET, PI3K reg class IA (p85), PDGF-R-beta' of Mitogenic signaling (Supplementary Table S1 No.1). Sub-network is made using 'Analyze network, Build Network' of GeneGo from the significant gene lists associated with H1993 treatment with LY2801653 (3 nM). STAT3 serves as both the divergence and convergence hub. Underexpressed genes (highlighted as blue targets) are significant genes from PamGene data. Eight out of 9 blue targets are represented. CD3Z was excluded from the network to simplify visualization because CD3Z is not related to NSCLC directly. The network objects to be placed in specific sectors of the network according to their sub-cellular localization. The localization sectors are Nucleus, Cytoplasm, Membrane, and Extracellular. Arrow between nodes describes positive (green), negative (red), and unspecified (black) interactions.
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- 2023
25. Supplementary Figure 1 from Paxillin Is a Target for Somatic Mutations in Lung Cancer: Implications for Cell Growth and Invasion
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Ravi Salgia, Aliya N. Husain, Mark K. Ferguson, Everett E. Vokes, John Minna, Viswanathan Natarajan, Wickii Vigneswaran, Thomas Krausz, Martin Sattler, Mark W. Lingen, David Sugarbaker, Raphael Bueno, Gavin J. Gordon, Livia L. Szeto, Vytas P. Bindokas, Lioubov Soulii, Osvaldo Zumba, Salman Ahmed, Maria S. Tretiakova, Luc Girard, Yi-Ching Wang, Leonardo Faoro, Stuart Schwartz, Vidya Nallasura, Trevor Reichman, Rajani Kanteti, Sivakumar Loganathan, Tanguy Y. Seiwert, A. Craig Mackinnon, Varalakshmi Janamanchi, Soundararajan Krishnaswamy, Hanna Surawska, and Ramasamy Jagadeeswaran
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Supplementary Figure 1 from Paxillin Is a Target for Somatic Mutations in Lung Cancer: Implications for Cell Growth and Invasion
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- 2023
26. Supplementary Figure 2 from Paxillin Is a Target for Somatic Mutations in Lung Cancer: Implications for Cell Growth and Invasion
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Ravi Salgia, Aliya N. Husain, Mark K. Ferguson, Everett E. Vokes, John Minna, Viswanathan Natarajan, Wickii Vigneswaran, Thomas Krausz, Martin Sattler, Mark W. Lingen, David Sugarbaker, Raphael Bueno, Gavin J. Gordon, Livia L. Szeto, Vytas P. Bindokas, Lioubov Soulii, Osvaldo Zumba, Salman Ahmed, Maria S. Tretiakova, Luc Girard, Yi-Ching Wang, Leonardo Faoro, Stuart Schwartz, Vidya Nallasura, Trevor Reichman, Rajani Kanteti, Sivakumar Loganathan, Tanguy Y. Seiwert, A. Craig Mackinnon, Varalakshmi Janamanchi, Soundararajan Krishnaswamy, Hanna Surawska, and Ramasamy Jagadeeswaran
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Supplementary Figure 2 from Paxillin Is a Target for Somatic Mutations in Lung Cancer: Implications for Cell Growth and Invasion
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- 2023
27. Supplementary Table 3 from Paxillin Is a Target for Somatic Mutations in Lung Cancer: Implications for Cell Growth and Invasion
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Ravi Salgia, Aliya N. Husain, Mark K. Ferguson, Everett E. Vokes, John Minna, Viswanathan Natarajan, Wickii Vigneswaran, Thomas Krausz, Martin Sattler, Mark W. Lingen, David Sugarbaker, Raphael Bueno, Gavin J. Gordon, Livia L. Szeto, Vytas P. Bindokas, Lioubov Soulii, Osvaldo Zumba, Salman Ahmed, Maria S. Tretiakova, Luc Girard, Yi-Ching Wang, Leonardo Faoro, Stuart Schwartz, Vidya Nallasura, Trevor Reichman, Rajani Kanteti, Sivakumar Loganathan, Tanguy Y. Seiwert, A. Craig Mackinnon, Varalakshmi Janamanchi, Soundararajan Krishnaswamy, Hanna Surawska, and Ramasamy Jagadeeswaran
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Supplementary Table 3 from Paxillin Is a Target for Somatic Mutations in Lung Cancer: Implications for Cell Growth and Invasion
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- 2023
28. Supplementary Figure 3 from Dramatic Antitumor Effects of the Dual MET/RON Small-Molecule Inhibitor LY2801653 in Non–Small Cell Lung Cancer
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Ravi Salgia, Everett E. Vokes, Aliya N. Husain, Erin Smithberger, Jeffrey Mueller, Qudsia Arif, Rifat Hasina, and Ichiro Kawada
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PDF file - 94K, Figure S3. Analysis of immunohistochemistry staining and evaluation. A. Scoring system is shown. A pathologist coded MET, p-MET, RON, and p-RON expression as the percentage of positive tumor cells (scale 0%-100%) with staining intensity from 0 to 3+. Positive IHC expression is defined as Scoring System. B. Phosphorylated MET was decreased modestly in LY2801653-treated mice in both A549 and H1993 studies. Moreover, in the treated arms of H1993, Phosphorylated RON was slightly decreased in LY2801653-treated mice.
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- 2023
29. Data from A Novel Algorithm for Simplification of Complex Gene Classifiers in Cancer
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Samuel L. Volchenboum, Stephen X. Skapek, James R. Anderson, Douglas S. Hawkins, Frederic G. Barr, Julie M. Gastier-Foster, Michele R. Wing, Timothy J. Triche, David M. Parham, Aliya N. Husain, Mei Lin Z. Bissonnette, Karen M. Bachmeyer, Ling Teng, and Raphael A. Wilson
- Abstract
The clinical application of complex molecular classifiers as diagnostic or prognostic tools has been limited by the time and cost needed to apply them to patients. Using an existing 50-gene expression signature known to separate two molecular subtypes of the pediatric cancer rhabdomyosarcoma, we show that an exhaustive iterative search algorithm can distill this complex classifier down to two or three features with equal discrimination. We validated the two-gene signatures using three separate and distinct datasets, including one that uses degraded RNA extracted from formalin-fixed, paraffin-embedded material. Finally, to show the generalizability of our algorithm, we applied it to a lung cancer dataset to find minimal gene signatures that can distinguish survival. Our approach can easily be generalized and coupled to existing technical platforms to facilitate the discovery of simplified signatures that are ready for routine clinical use. Cancer Res; 73(18); 5625–32. ©2013 AACR.
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30. Supplementary Figures 1 - 5, Tables 1 - 9 from A Novel Algorithm for Simplification of Complex Gene Classifiers in Cancer
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Samuel L. Volchenboum, Stephen X. Skapek, James R. Anderson, Douglas S. Hawkins, Frederic G. Barr, Julie M. Gastier-Foster, Michele R. Wing, Timothy J. Triche, David M. Parham, Aliya N. Husain, Mei Lin Z. Bissonnette, Karen M. Bachmeyer, Ling Teng, and Raphael A. Wilson
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PDF file - 714K, Supplementary Figure 1 Two-gene combinations from the 50-gene F1/F2 classifier with >98% classification efficiency in the Williamson data set. Supplementary Figure 2 Thirteen two-gene combinations with >99% classification efficiency, identified from exhaustive analysis of top 2000 genes. Supplementary Figure 3 Gene dyads with classification efficiency >95% identified through exhaustive search of all possible combinations. Supplementary Figure 4 Detection of gene expression is comparable for fresh-frozen and paraformaldehyde-fixed material with nCounter. Supplementary Figure 5 Gene expression detected in each case with the Williamson F1/F2 metagene nCounter Code set. Supplementary Table 1 Four-gene combinations with ≥ 99% accuracy. Supplementary Table 2 Dyad classifiers from T-test ranking of Williamson data set with ≥ 98% accuracy, applied to Davicioni data. Supplementary Table 3 T-test dyad classifier genes found in F1/F2 metagenes (L) and F1/F2 metagene probes excluded from dyad pairs (R). Supplementary Table 4 Top-scoring classifiers from exhaustive search of 1.5 billion gene pairs from Williamson data set, also applied to Davicioni and Exon data. Supplementary Table 5 Tumor sample characteristics. Supplementary Table 6 Genes in nCounter set. Supplementary Table 7 PCA Scores by tumor sample for nCounter Data. Supplementary Table 8 CA Loadings for nCounter Data. Supplementary Table 9 Top-scoring nCounter dyad classifiers. Supplementary Table 10 Top gene combinations - Lung cancer data
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- 2023
31. Supplementary Table 1 from Critical Role for the Receptor Tyrosine Kinase EPHB4 in Esophageal Cancers
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Ravi Salgia, Parkash Gill, Everett E. Vokes, Lyuba Varticovski, Mark K. Ferguson, Victoria M. Villaflor, Irving Waxman, Mitchell C. Posner, Aliya N. Husain, Mark W. Lingen, Yutaka Shimada, Dorothy Kane, Essam El Hashani, Rajani Kanteti, Jeffery Mueller, Elizabeth Hyjek, Kenneth S. Cohen, Vidya Nallasura, Benjamin D. Ferguson, Yue Zhou, Xiuqing Li, Ren Liu, Mosmi Surati, Soheil Yala, Geetanjali Kanade, Karun Mutreja, Ichiro Kawada, Nathan Mollberg, and Rifat Hasina
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PDF file - 66K, This table contains the detailed immunohistochemical data scoring depicted in Figure A and B
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32. Data from Critical Role for the Receptor Tyrosine Kinase EPHB4 in Esophageal Cancers
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Ravi Salgia, Parkash Gill, Everett E. Vokes, Lyuba Varticovski, Mark K. Ferguson, Victoria M. Villaflor, Irving Waxman, Mitchell C. Posner, Aliya N. Husain, Mark W. Lingen, Yutaka Shimada, Dorothy Kane, Essam El Hashani, Rajani Kanteti, Jeffery Mueller, Elizabeth Hyjek, Kenneth S. Cohen, Vidya Nallasura, Benjamin D. Ferguson, Yue Zhou, Xiuqing Li, Ren Liu, Mosmi Surati, Soheil Yala, Geetanjali Kanade, Karun Mutreja, Ichiro Kawada, Nathan Mollberg, and Rifat Hasina
- Abstract
Esophageal cancer incidence is increasing and has few treatment options. In studying receptor tyrosine kinases associated with esophageal cancers, we have identified EPHB4 to be robustly overexpressed in cell lines and primary tumor tissues. In total, 94 squamous cell carcinoma, 82 adenocarcinoma, 25 dysplasia, 13 Barrett esophagus, and 25 adjacent or unrelated normal esophageal tissues were evaluated by immunohistochemistry. EPHB4 expression was significantly higher in all the different histologic categories than in adjacent normal tissues. In 13 esophageal cancer cell lines, 3 of the 9 SCC cell lines and 2 of the 4 adenocarcinomas expressed very high levels of EPHB4. An increased gene copy number ranging from 4 to 20 copies was identified in a subset of the overexpressing patient samples and cell lines. We have developed a novel 4-nitroquinoline 1-oxide (4-NQO)-induced mouse model of esophageal cancer that recapitulates the EPHB4 expression in humans. A specific small-molecule inhibitor of EPHB4 decreased cell viability in a time- and dose-dependent manner in 3 of the 4 cell lines tested. The small-molecule inhibitor and an EPHB4 siRNA also decreased cell migration (12%–40% closure in treated vs. 60%–80% in untreated), with decreased phosphorylation of various tyrosyl-containing proteins, EphB4, and its downstream target p125FAK. Finally, in a xenograft tumor model, an EPHB4 inhibitor abrogated tumor growth by approximately 60% compared with untreated control. EphB4 is robustly expressed and potentially serves as a novel biomarker for targeted therapy in esophageal cancers. Cancer Res; 73(1); 184–94. ©2012 AACR.
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33. Supplementary Figure 1 from Dramatic Antitumor Effects of the Dual MET/RON Small-Molecule Inhibitor LY2801653 in Non–Small Cell Lung Cancer
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Ravi Salgia, Everett E. Vokes, Aliya N. Husain, Erin Smithberger, Jeffrey Mueller, Qudsia Arif, Rifat Hasina, and Ichiro Kawada
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PDF file - 62K, Figure S1. The protein tyrosine kinase activity profile obtained by using H1993 lysates treated with LY2801653 (10 nM) as tested on PamChip microarrays. For each of the 144 protein tyrosine kinase peptides on the array, treatment response was calculated as the log-transformed ratio of phosphorylation. 47 significant tyrosine kinase substrate modulation by LY2801653 (10 nM) treatment is shown (*: p-value
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- 2023
34. Supplementary Table 4 from Paxillin Is a Target for Somatic Mutations in Lung Cancer: Implications for Cell Growth and Invasion
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Ravi Salgia, Aliya N. Husain, Mark K. Ferguson, Everett E. Vokes, John Minna, Viswanathan Natarajan, Wickii Vigneswaran, Thomas Krausz, Martin Sattler, Mark W. Lingen, David Sugarbaker, Raphael Bueno, Gavin J. Gordon, Livia L. Szeto, Vytas P. Bindokas, Lioubov Soulii, Osvaldo Zumba, Salman Ahmed, Maria S. Tretiakova, Luc Girard, Yi-Ching Wang, Leonardo Faoro, Stuart Schwartz, Vidya Nallasura, Trevor Reichman, Rajani Kanteti, Sivakumar Loganathan, Tanguy Y. Seiwert, A. Craig Mackinnon, Varalakshmi Janamanchi, Soundararajan Krishnaswamy, Hanna Surawska, and Ramasamy Jagadeeswaran
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Supplementary Table 4 from Paxillin Is a Target for Somatic Mutations in Lung Cancer: Implications for Cell Growth and Invasion
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35. Data from Paxillin Is a Target for Somatic Mutations in Lung Cancer: Implications for Cell Growth and Invasion
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Ravi Salgia, Aliya N. Husain, Mark K. Ferguson, Everett E. Vokes, John Minna, Viswanathan Natarajan, Wickii Vigneswaran, Thomas Krausz, Martin Sattler, Mark W. Lingen, David Sugarbaker, Raphael Bueno, Gavin J. Gordon, Livia L. Szeto, Vytas P. Bindokas, Lioubov Soulii, Osvaldo Zumba, Salman Ahmed, Maria S. Tretiakova, Luc Girard, Yi-Ching Wang, Leonardo Faoro, Stuart Schwartz, Vidya Nallasura, Trevor Reichman, Rajani Kanteti, Sivakumar Loganathan, Tanguy Y. Seiwert, A. Craig Mackinnon, Varalakshmi Janamanchi, Soundararajan Krishnaswamy, Hanna Surawska, and Ramasamy Jagadeeswaran
- Abstract
Lung cancer is characterized by abnormal cell growth and invasion, and the actin cytoskeleton plays a major role in these processes. The focal adhesion protein paxillin is a target of a number of oncogenes involved in key signal transduction and important in cell motility and migration. In lung cancer tissues, we have found that paxillin was highly expressed (compared with normal lung), amplified (12.1%, 8 of 66) and correlated with increased MET and epidermal growth factor receptor (EGFR) gene copy numbers, or mutated (somatic mutation rate of 9.4%, 18 of 191). Paxillin mutations (19 of 21) were clustered between LD motifs 1 and 2 and the LIM domains. The most frequent point mutation (A127T) enhanced lung cancer cell growth, colony formation, focal adhesion formation, and colocalized with Bcl-2 in vitro. Gene silencing from RNA interference of mutant paxillin led to reduction of cell viability. A murine in vivo xenograft model of A127T paxillin showed an increase in tumor growth, cell proliferation, and invasion. These results establish an important role for paxillin in lung cancer. [Cancer Res 2007;68(1):132–42]
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36. Supplementary Table 1 from Paxillin Is a Target for Somatic Mutations in Lung Cancer: Implications for Cell Growth and Invasion
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Ravi Salgia, Aliya N. Husain, Mark K. Ferguson, Everett E. Vokes, John Minna, Viswanathan Natarajan, Wickii Vigneswaran, Thomas Krausz, Martin Sattler, Mark W. Lingen, David Sugarbaker, Raphael Bueno, Gavin J. Gordon, Livia L. Szeto, Vytas P. Bindokas, Lioubov Soulii, Osvaldo Zumba, Salman Ahmed, Maria S. Tretiakova, Luc Girard, Yi-Ching Wang, Leonardo Faoro, Stuart Schwartz, Vidya Nallasura, Trevor Reichman, Rajani Kanteti, Sivakumar Loganathan, Tanguy Y. Seiwert, A. Craig Mackinnon, Varalakshmi Janamanchi, Soundararajan Krishnaswamy, Hanna Surawska, and Ramasamy Jagadeeswaran
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Supplementary Table 1 from Paxillin Is a Target for Somatic Mutations in Lung Cancer: Implications for Cell Growth and Invasion
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37. Supplementary Figure 3 from Paxillin Is a Target for Somatic Mutations in Lung Cancer: Implications for Cell Growth and Invasion
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Ravi Salgia, Aliya N. Husain, Mark K. Ferguson, Everett E. Vokes, John Minna, Viswanathan Natarajan, Wickii Vigneswaran, Thomas Krausz, Martin Sattler, Mark W. Lingen, David Sugarbaker, Raphael Bueno, Gavin J. Gordon, Livia L. Szeto, Vytas P. Bindokas, Lioubov Soulii, Osvaldo Zumba, Salman Ahmed, Maria S. Tretiakova, Luc Girard, Yi-Ching Wang, Leonardo Faoro, Stuart Schwartz, Vidya Nallasura, Trevor Reichman, Rajani Kanteti, Sivakumar Loganathan, Tanguy Y. Seiwert, A. Craig Mackinnon, Varalakshmi Janamanchi, Soundararajan Krishnaswamy, Hanna Surawska, and Ramasamy Jagadeeswaran
- Abstract
Supplementary Figure 3 from Paxillin Is a Target for Somatic Mutations in Lung Cancer: Implications for Cell Growth and Invasion
- Published
- 2023
38. Supplementary Figure 4 from Paxillin Is a Target for Somatic Mutations in Lung Cancer: Implications for Cell Growth and Invasion
- Author
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Ravi Salgia, Aliya N. Husain, Mark K. Ferguson, Everett E. Vokes, John Minna, Viswanathan Natarajan, Wickii Vigneswaran, Thomas Krausz, Martin Sattler, Mark W. Lingen, David Sugarbaker, Raphael Bueno, Gavin J. Gordon, Livia L. Szeto, Vytas P. Bindokas, Lioubov Soulii, Osvaldo Zumba, Salman Ahmed, Maria S. Tretiakova, Luc Girard, Yi-Ching Wang, Leonardo Faoro, Stuart Schwartz, Vidya Nallasura, Trevor Reichman, Rajani Kanteti, Sivakumar Loganathan, Tanguy Y. Seiwert, A. Craig Mackinnon, Varalakshmi Janamanchi, Soundararajan Krishnaswamy, Hanna Surawska, and Ramasamy Jagadeeswaran
- Abstract
Supplementary Figure 4 from Paxillin Is a Target for Somatic Mutations in Lung Cancer: Implications for Cell Growth and Invasion
- Published
- 2023
39. Supplementary Methods, Table 1 from Dramatic Antitumor Effects of the Dual MET/RON Small-Molecule Inhibitor LY2801653 in Non–Small Cell Lung Cancer
- Author
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Ravi Salgia, Everett E. Vokes, Aliya N. Husain, Erin Smithberger, Jeffrey Mueller, Qudsia Arif, Rifat Hasina, and Ichiro Kawada
- Abstract
PDF file - 140K, Supplementary Table S1. Interactive gene networks of Mitogenic signaling of H1993 treatment with LY2801653 (3 nM). MetacoreTM (GeneGo) analysis using the tool 'Analyze network, Build Network'. Note: 'Size' represents the total number of genes evaluated in the Map Folder 'Mitogenic Signaling'. 'Target' denotes the number of genes out of the 12 significant genes that are common to that pathway.
- Published
- 2023
40. Prevalence of incidental germline variants detected via tumor-only mesothelioma genomic profiling
- Author
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Owen D. Mitchell, Katie Gilliam, Daniela del Gaudio, Kelsey E. McNeely, Shaili Smith, Maria Acevedo, Meghana Gaduraju, Rachel Hodge, Aubrianna S.S. Ramsland, Jeremy Segal, Soma Das, Darren S. Bryan, Sanjukta Tawde, Shelly Galasinski, Peng Wang, Melissa Y. Tjota, Aliya N. Husain, Samuel Armato, Jessica Donington, Mark K. Ferguson, Kiran Turaga, Jane E. Churpek, Hedy L. Kindler, and Michael W. Drazer
- Abstract
Structured AbstractImportancePatients with mesothelioma often have next generation sequencing (NGS) of their tumor. Tumor-only NGS may incidentally identify germline pathogenic or likely pathogenic (P/LP) variants despite not being designed for this purpose. It is unknown how frequently patients with mesothelioma have germline P/LP variants incidentally detected via tumor-only NGS.ObjectiveTo determine the prevalence of incidental germline P/LP variants detected via tumor-only NGS of mesothelioma.DesignA series of 161 unrelated patients with mesothelioma had tumor-only NGS and germline NGS. These assays were compared to determine which P/LP variants identified via tumor-only NGS were of germline origin.SettingThis was an observational study from a high-volume mesothelioma program. All patients enrolled on Institutional Review Board-approved protocols.Participants161 unrelated patients with pleural, peritoneal, or bicavitary mesothelioma.Intervention(s) (for clinical trials) or Exposure(s) (for observational studies)No therapeutic interventions were used.Main Outcome(s) and Measure(s)The proportion of patients with mesothelioma who had P/LP germline variants incidentally detected via tumor-only NGS.ResultsMost (78%) patients had potentially incidental P/LP germline variants. The positive predictive value of a potentially incidental germline P/LP variant on tumor-only NGS was 20%. Overall, 16% of patients carried a P/LP germline variant. Germline P/LP variants were identified inATM, ATR, BAP1, CHEK2, DDX41, FANCM, HAX1, MRE11A, MSH6, MUTYH, NF1, SAMD9L, andTMEM127.Conclusions and RelevanceMost (78%) patients with mesothelioma had potentially incidental germline P/LP variants on tumor NGS, but the positive predictive value of these was modest (20%). Of all patients, 16% had confirmed germline P/LP variants. Given the implications of a hereditary cancer syndrome diagnosis for preventive care and familial counseling, clinical approaches for addressing incidental P/LP germline variants in tumor-only NGS are needed.Tumor-only sequencing should not replace dedicated germline testing. Universal germline testing is likely needed for patients with mesothelioma.Key PointsQuestionWhat proportion of patients with mesothelioma have pathogenic or likely pathogenic germline variants incidentally identified by tumor-only genomic profiling?FindingsIn this cohort study of 161 patients with mesothelioma, 78% of patients had potential germline variants that warranted further evaluation. Overall, 16% of patients had pathogenic or likely pathogenic germline variants initially identified via tumor-only genomic profiling.MeaningTumor genomic profiling of mesothelioma frequently (78% of patients) identifies potential germline pathogenic/likely pathogenic variants that warrant dedicated germline evaluation. The high prevalence of germline variants (16%) in our series suggests universal genetic testing may be warranted for patients with mesothelioma.
- Published
- 2022
41. Reoperation for Hirschsprung Disease: Two cases of Vanishing Ganglion Cells and Review of the Literature
- Author
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Jasmine M. Vickery, Bahig M. Shehata, Eric P. Chang, and Aliya N. Husain
- Subjects
Pediatrics, Perinatology and Child Health ,General Medicine ,Pathology and Forensic Medicine - Abstract
Hirschsprung disease (HD) is characterized by circumferential aganglionosis of the rectum with variable proximal bowel involvement. The underlying pathogenesis is due to failure of caudal migration of neural crest cells during pre-natal development, causing functional bowel obstruction. Definitive therapy is surgical resection; however, a subset of patients will require reoperation. An important cause of reoperation is the rare but distinct entity described as the ganglion cell “vanishing” phenomenon. In this phenomenon, affected patients have normal circumferential ganglion cells present at the proximal margin during primary resection. They undergo a variable asymptomatic period post-primary resection but ultimately develop recurrent symptoms. Upon reoperation, ganglion cells seemingly vanish and are no longer present in the previously functioning and ganglionated bowel proximal to the initial anastomotic site. To further characterize and investigate this poorly understood pathology, here we present 2 cases of HD patients who required reoperation. Our small series implicates that an immune component may contribute as patient 2 had a brisk neurotrophic eosinophilic infiltrate only present in the reoperation specimen. However, this was not observed in patient 1. Other possible etiologies include post-operative ischemia/hypoxia, visceral neuropathy, or signaling abnormalities within the residual ganglion cells themselves.
- Published
- 2022
42. Updated Imaging Classification of Hypersensitivity Pneumonitis
- Author
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Lydia Chelala, Ayodeji Adegunsoye, Brittany A. Cody, Aliya N. Husain, and Jonathan H. Chung
- Subjects
Diagnostic Imaging ,Humans ,Radiology, Nuclear Medicine and imaging ,General Medicine ,Lung Diseases, Interstitial ,Lung ,Alveolitis, Extrinsic Allergic - Abstract
Hypersensitivity pneumonia (HP) refers to a heterogeneous group of interstitial lung diseases resulting from a non-IgE immune-mediated reaction to inhaled pathogens in susceptible and sensitized hosts. Environmental and genetic factors are important substrates of disease pathogenesis. A recurrent or ongoing airborne exposure results in activation of humoral and cellular immune responses. This article discusses key clinical, radiologic, and histopathologic features of HP and reviews current recommendations.
- Published
- 2022
43. SARS-CoV-2 Infection Is Associated with Reduced Krüppel-like Factor 2 in Human Lung Autopsy
- Author
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Gökhan M. Mutlu, Ayodeji Adegunsoye, Yun Fang, Tzu-Han Lee, Robert D. Guzy, Aliya N. Husain, Nathan Schoettler, Anne I. Sperling, Ru-Ting Huang, David Wu, and Jeffrey Mueller
- Subjects
Pulmonary and Respiratory Medicine ,2019-20 coronavirus outbreak ,Lung ,Kruppel-Like Transcription Factors ,Coronavirus disease 2019 (COVID-19) ,business.industry ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Clinical Biochemistry ,Autopsy ,Cell Biology ,Virology ,Human lung ,medicine.anatomical_structure ,Krüppel ,medicine ,business ,Molecular Biology - Published
- 2021
44. Membranous HEG1 expression is a useful marker in the differential diagnosis of epithelioid and biphasic malignant mesothelioma versus carcinomas
- Author
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Shoutaro Tsuji, Alberto M. Marchevsky, Aliya N. Husain, Ann E. Walts, Eitetsu Koh, Kohzoh Imai, Di Wu, Yohei Miyagi, Kenzo Hiroshima, Tadao Nakazawa, Daisuke Ozaki, Yasuo Sekine, and Toshikazu Yusa
- Subjects
Pathology ,medicine.medical_specialty ,Lung Neoplasms ,Cell ,Epithelium ,Pathology and Forensic Medicine ,Thyroid carcinoma ,Diagnosis, Differential ,Medicine ,Humans ,Mesothelioma ,Tissue microarray ,HEG1 ,business.industry ,Mesenchymal stem cell ,Mesothelioma, Malignant ,Membrane Proteins ,General Medicine ,Original Articles ,medicine.disease ,mesothelial marker ,Immunohistochemistry ,Staining ,medicine.anatomical_structure ,Tissue Array Analysis ,mesothelioma ,Carcinoma, Squamous Cell ,Original Article ,Differential diagnosis ,business - Abstract
Sialylated HEG1 has been reported as a highly specific and sensitive mesothelioma marker but a comprehensive evaluation of its expression in carcinomas in different organs, various sarcomas and reactive mesothelial proliferations has not been reported. The aim of this study was to evaluate the clinical applicability of HEG1 as a marker in the diagnosis of mesothelioma. HEG1 immunoreactivity was evaluated in whole sections of 122 mesotheliomas, 75 pulmonary carcinomas, 55 other carcinomas, 16 mesenchymal tumors, and 24 reactive mesothelial proliferations and in tissue microarrays containing 70 epithelioid (EM), 36 biphasic (BM), and 2 sarcomatoid mesotheliomas (SM). In whole sections and tissue microarrays, respectively, membranous HEG1 was expressed in 93.0% and 85.5% of EM, 81.3% and 69.4% of BM, 0% and 0% of SM. HEG1 was not expressed in pulmonary adenocarcinomas. HEG1 was expressed as cytoplasmic immunoreactivity in pulmonary squamous cell carcinomas (21.7%). Membranous HEG1 staining was seen in ovarian carcinomas (66.7%), thyroid carcinomas (100%), reactive conditions (16.7%), and mesenchymal tumors (18.8%). The sensitivity of membranous HEG1 expression to distinguish EM/BM from all carcinomas was 88.8%. The specificity for the differential diagnosis between EM/BM and all carcinomas and pulmonary carcinomas was 92.3% and 98.7%, respectively.
- Published
- 2021
45. Lymphatic coagulation and neutrophil extracellular traps in lung-draining lymph nodes of COVID-19 decedents
- Author
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Margo E. MacDonald, Rachel K. Weathered, Emma C. Stewart, Alexandra I. Magold, Anish Mukherjee, Sandeep Gurbuxani, Heather Smith, Phillip McMullen, Jeffrey Mueller, Aliya N. Husain, Calixto M. Salles, Priscilla S. Briquez, Sherin J. Rouhani, Jovian Yu, Jonathan Trujillo, Athalia R. Pyzer, Thomas F. Gajewski, Anne I. Sperling, Witold W. Kilarski, and Melody A. Swartz
- Subjects
Hematology - Abstract
Clinical manifestations of severe COVID-19 include coagulopathies that are exacerbated by the formation of neutrophil extracellular traps (NETs). Here, we report that pulmonary lymphatic vessels, which traffic neutrophils and other immune cells to the lung-draining lymph node (LDLN), can also be blocked by fibrin clots in severe COVID-19. Immunostained tissue sections from COVID-19 decedents revealed widespread lymphatic clotting not only in the lung but also in the LDLN, where the extent of clotting correlated with the presence of abnormal, regressed, or missing germinal centers (GCs). It strongly correlated with the presence of intralymphatic NETs. In mice, tumor necrosis factor α induced intralymphatic fibrin clots; this could be inhibited by DNase I, which degrades NETs. In vitro, TNF-α induced lymphatic endothelial cell upregulation of ICAM-1 and CXCL8, among other neutrophil-recruiting factors, as well as thrombomodulin downregulation; in decedents, lymphatic clotting in LDLNs. In a separate cohort of hospitalized patients, serum levels of Myeloperoxidase-DNA (MPO-DNA, a NET marker) inversely correlated with antiviral antibody titers, but D-dimer levels, indicative of blood thrombosis, did not correlate with either. Patients with high MPO-DNA but low D-dimer levels generated poor antiviral antibody titers. This study introduces lymphatic coagulation in lungs and LDLNs as a clinical manifestation of severe COVID-19 and suggests the involvement of NETosis of lymphatic-trafficking neutrophils. It further suggests that lymphatic clotting may correlate with impaired formation or maintenance of GCs necessary for robust antiviral antibody responses, although further studies are needed to determine whether and how lymphatic coagulation affects adaptive immune responses.
- Published
- 2022
46. Tumors of the Serosal Membranes
- Author
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Andrew G. Nicholson, Aliya N. Husain, and Alain C. Borczuk
- Published
- 2022
47. A series of <scp>COVID</scp> ‐19 autopsies with clinical and pathologic comparisons to both seasonal and pandemic influenza
- Author
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Lindsay Alpert, Alexis Snyder, David Wu, James Brainer, Thomas Krausz, Aliya N. Husain, Peter Pytel, Heather L. Smith, Nathan Schoettler, Anne I. Sperling, Jeffrey Mueller, Anthony Chang, Ayodeji Adegunsoye, John Hart, Jasmine Vickery, Robert D. Guzy, Phillip McMullen, and Sandeep Gurbuxani
- Subjects
Male ,Pathology ,medicine.medical_specialty ,Coronavirus disease 2019 (COVID-19) ,viral pneumonia ,Autopsy ,Lung injury ,Pathology and Forensic Medicine ,autopsy ,COVID‐19 ,Influenza, Human ,RB1-214 ,Humans ,Medicine ,Diffuse alveolar damage ,Lung ,Pandemics ,In Situ Hybridization ,Aged ,SARS-CoV-2 ,business.industry ,Pandemic influenza ,COVID-19 ,Histology ,Original Articles ,medicine.disease ,Immunohistochemistry ,diffuse alveolar damage ,viral sepsis ,Viral pneumonia ,Original Article ,Female ,Seasons ,influenza ,business - Abstract
Autopsies of patients who have died from COVID‐19 have been crucial in delineating patterns of injury associated with SARS‐CoV‐2 infection. Despite their utility, comprehensive autopsy studies are somewhat lacking relative to the global burden of disease, and very few comprehensive studies contextualize the findings to other fatal viral infections. We developed a novel autopsy protocol in order to perform postmortem examinations on victims of COVID‐19 and herein describe detailed clinical information, gross findings, and histologic features observed in the first 16 complete COVID‐19 autopsies. We also critically evaluated the role of ancillary studies used to establish a diagnosis of COVID‐19 at autopsy, including immunohistochemistry (IHC), in situ hybridization (ISH), and electron microscopy (EM). IHC and ISH targeting SARS‐CoV‐2 were comparable in terms of the location and number of infected cells in lung tissue; however, nonspecific staining of bacteria was seen occasionally with IHC. EM was unrevealing in blindly sampled tissues. We then compared the clinical and histologic features present in this series to six archival cases of fatal seasonal influenza and six archival cases of pandemic influenza from the fourth wave of the ‘Spanish Flu’ in the winter of 1920. In addition to routine histology, the inflammatory infiltrates in the lungs of COVID‐19 and seasonal influenza victims were compared using quantitative IHC. Our results demonstrate that the clinical and histologic features of COVID‐19 are similar to those seen in fatal cases of influenza, and the two diseases tend to overlap histologically. There was no significant difference in the composition of the inflammatory infiltrate in COVID‐19 and influenza at sites of acute lung injury at the time of autopsy. Our study underscores the relatively nonspecific clinical features and pathologic changes shared between severe cases of COVID‐19 and influenza, while also providing important caveats to ancillary methods of viral detection.
- Published
- 2021
48. Vessel-related structures predict UIP pathology in those with a non-IPF pattern on CT
- Author
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Aliya N. Husain, Rekha Vij, Justin M. Oldham, Mary E. Strek, Steven M. Montner, Ronald A. Karwoski, Ayodeji Adegunsoye, Jonathan H. Chung, and Brian J. Bartholmai
- Subjects
Univariate analysis ,medicine.medical_specialty ,Pathology ,Lung ,business.industry ,Interstitial lung disease ,General Medicine ,Lung biopsy ,respiratory system ,medicine.disease ,030218 nuclear medicine & medical imaging ,03 medical and health sciences ,0302 clinical medicine ,medicine.anatomical_structure ,Usual interstitial pneumonia ,030220 oncology & carcinogenesis ,medicine ,Radiology, Nuclear Medicine and imaging ,Honeycombing ,Radiology ,business ,Pathological ,Neuroradiology - Abstract
To determine if a quantitative imaging variable (vessel-related structures [VRS]) could identify subjects with a non-IPF diagnosis CT pattern who were highly likely to have UIP histologically. Subjects with a multidisciplinary diagnosis of interstitial lung disease including surgical lung biopsy and chest CT within 1 year of each other were included in the study. Non-contrast CT scans were analyzed using the Computer-Aided Lung Informatics for Pathology Evaluation and Rating (CALIPER) program, which quantifies the amount of various abnormal CT patterns on chest CT. Quantitative data were analyzed relative to pathological diagnosis as well as the qualitative CT pattern. CALIPER-derived volumes of reticulation (p = 0.012), honeycombing (p = 0.017), and VRS (p < 0.001) were associated with a UIP pattern on pathology on univariate analysis but only VRS was associated with a UIP pathology on multivariable analysis (p = 0.013). Using a VRS cut-off of 173 cm3, the sensitivity and specificity for pathological UIP were similar to those for standard qualitative CT assessment (55.9% and 80.4% compared to 60.6% and 80.4%, respectively). VRS differentiated pathological UIP cases in those with a non-IPF diagnosis CT category (p < 0.001) but not in other qualitative CT patterns (typical UIP, probable UIP, and indeterminate for UIP). The rate of pathological UIP in those with VRS greater than 173 cm3 (84.2%) was nearly identical to those who had a qualitative CT pattern of probable UIP (88.9%). VRS may be an adjunct to CT in predicting pathology in patients with interstitial lung disease. • Volume of vessel-related structures (VRS) was associated with usual interstitial pneumonia (UIP) on pathology. • This differentiation arose from those with CT scans with a non-IPF diagnosis imaging pattern. • Higher VRS has similar diagnostic ramifications for UIP as probable UIP, transitively suggesting in patients with high VRS, pathology may be obviated.
- Published
- 2021
49. Steroid-refractory dermatologic and pulmonary toxicity in a patient on rituximab treated with pembrolizumab for progressive urothelial carcinoma: a case report
- Author
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Anh Khoa Pham, Aliya N. Husain, Pankti Reid, Christopher R. Shea, Urooba Nadeem, Jacobi Hines, Ellen Daily, and Walter M. Stadler
- Subjects
0301 basic medicine ,Male ,medicine.medical_specialty ,Medical oncology ,medicine.medical_treatment ,lcsh:Medicine ,Azathioprine ,Pembrolizumab ,Antibodies, Monoclonal, Humanized ,03 medical and health sciences ,Immune checkpoint inhibitors ,0302 clinical medicine ,Bullous skin diseases ,Prednisone ,Case report ,Medicine ,Humans ,Aged ,Immune-related adverse effects ,business.industry ,lcsh:R ,Immunosuppression ,General Medicine ,medicine.disease ,Rash ,Dermatology ,Tacrolimus ,Pneumonia ,030104 developmental biology ,030220 oncology & carcinogenesis ,Rituximab ,Steroids ,Immunotherapy ,medicine.symptom ,Neoplasm Recurrence, Local ,business ,medicine.drug - Abstract
Background Increasingly widespread use of programmed cell death protein 1 (PD-1) immune checkpoint inhibitors (ICIs) for treatment of a variety of progressive malignancies continues to reveal a range of immune-related adverse events (irAEs), necessitating immunosuppressive therapy for management. While a single course of systemic corticosteroids may be sufficient for many irAEs, no clear standard-of-care guidelines exist for steroid-refractory cases. We present an unusual case of a patient who developed several steroid-refractory novel irAEs on pembrolizumab despite ongoing B cell-directed immunosuppressive therapy with rituximab, who ultimately noted resolution of symptoms with tacrolimus, a T-cell-directed immunosuppressant. Case presentation This 72-year-old Caucasian man with Waldenstrom’s macroglobulinemia and myelin-associated glycoprotein (MAG) immunoglobulin M (IgM) antibody-associated neuropathy was being treated with maintenance rituximab and intravenous immunoglobulin when he was started on pembrolizumab (2.26 mg/kg) for metastatic urothelial cancer 31 months after surgery and adjuvant chemotherapy. After his third dose of pembrolizumab, he developed a painful blistering papular rash of the distal extremities. He received two more doses of pembrolizumab before he also developed diarrhea, and it was held; he was initiated on 1 mg/kg prednisone for presumed ICI-induced dermatitis and colitis. Skin biopsy 10 weeks after cessation of pembrolizumab and taper of steroids to 20 mg daily revealed a unique bullous erythema multiforme. He was then admitted with dyspnea and imaging concerning for necrotizing pneumonia, but did not respond to antibiotic therapy. Bronchoscopy and biopsy revealed acute fibrinous organizing pneumonia. His symptoms failed to fully respond to multiple courses of high-dose systemic corticosteroids and a trial of azathioprine, but pneumonia, diarrhea, and skin rash all improved markedly with tacrolimus. The patient has since completed his therapy for tacrolimus, continues off of ICI, and has not experienced a recurrence of any irAEs, though has more recently experienced progression of his cancer. Conclusion Despite immunosuppression with rituximab and intravenous immunoglobulin, two immunomodulators targeting B cells, ICI cessation, and systemic corticosteroid therapy, our patient developed two high-grade unusual irAEs, bullous erythema multiforme and acute fibrinous organizing pneumonia. Our patient’s improvement with tacrolimus can offer critical insight into the pathophysiology of steroid-refractory irAEs.
- Published
- 2021
50. Malignant peritoneal mesothelioma: prognostic significance of clinical and pathologic parameters and validation of a nuclear-grading system in a multi-institutional series of 225 cases
- Author
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Kirin Turaga, Richard Attanoos, Alberto M. Marchevsky, Kazuki Nabeshima, Andrew Churg, Kenzo Hiroshima, Jefree J. Schulte, Hedy L. Kindler, Kelly J. Butnor, Luka Brcic, Thomas Krausz, Yin P Hung, Aliya N. Husain, Gudrun Absenger, David B. Chapel, Françoise Galateau-Sallé, Mari Mino-Kenudson, Lucian R. Chirieac, Ann E. Walts, and Jeffrey Mueller
- Subjects
Adult ,Male ,0301 basic medicine ,medicine.medical_specialty ,Pathology ,Mitotic index ,Adolescent ,Gastroenterology ,Disease-Free Survival ,Pathology and Forensic Medicine ,Metastasis ,Young Adult ,03 medical and health sciences ,0302 clinical medicine ,Internal medicine ,Biomarkers, Tumor ,Mitotic Index ,medicine ,Humans ,Mesothelioma ,Peritoneal Neoplasms ,Aged ,Aged, 80 and over ,Cell Nucleus ,Univariate analysis ,business.industry ,Mesothelioma, Malignant ,Middle Aged ,Prognosis ,medicine.disease ,030104 developmental biology ,030220 oncology & carcinogenesis ,Cohort ,Peritoneal mesothelioma ,Immunohistochemistry ,Female ,Hyperthermic intraperitoneal chemotherapy ,Neoplasm Grading ,business - Abstract
Malignant peritoneal mesothelioma historically carried a grim prognosis, but outcomes have improved substantially in recent decades. The prognostic significance of clinical, morphologic, and immunophenotypic features remains ill-defined. This multi-institutional cohort comprises 225 malignant peritoneal mesotheliomas, which were assessed for 21 clinical, morphologic, and immunohistochemical parameters. For epithelioid mesotheliomas, combining nuclear pleomorphism and mitotic index yielded a composite nuclear grade, using a previously standardized grading system. Correlation of clinical, morphologic, and immunohistochemical parameters with overall and disease-free survival was examined by univariate and multivariate analyses. On univariate analysis, longer overall survival was significantly associated with diagnosis after 2000 (P = 0.0001), age
- Published
- 2021
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