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Popp CJ, Wang C, Hoover A, Gomez LA, Curran M, St-Jules DE, Barua S, Sevick MA, Kleinberg S. Objective Determination of Eating Occasion Timing: Combining Self-Report, Wrist Motion, and Continuous Glucose Monitoring to Detect Eating Occasions in Adults With Prediabetes and Obesity. J Diabetes Sci Technol 2024; 18:266-272. [PMID: 37747075 PMCID: PMC10973869 DOI: 10.1177/19322968231197205] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
BACKGROUND Accurately identifying eating patterns, specifically the timing, frequency, and distribution of eating occasions (EOs), is important for assessing eating behaviors, especially for preventing and managing obesity and type 2 diabetes (T2D). However, existing methods to study EOs rely on self-report, which may be prone to misreporting and bias and has a high user burden. Therefore, objective methods are needed. METHODS We aim to compare EO timing using objective and subjective methods. Participants self-reported EO with a smartphone app (self-report [SR]), wore the ActiGraph GT9X on their dominant wrist, and wore a continuous glucose monitor (CGM, Abbott Libre Pro) for 10 days. EOs were detected from wrist motion (WM) using a motion-based classifier and from CGM using a simulation-based system. We described EO timing and explored how timing identified with WM and CGM compares with SR. RESULTS Participants (n = 39) were 59 ± 11 years old, mostly female (62%) and White (51%) with a body mass index (BMI) of 34.2 ± 4.7 kg/m2. All had prediabetes or moderately controlled T2D. The median time-of-day first EO (and interquartile range) for SR, WM, and CGM were 08:24 (07:00-09:59), 9:42 (07:46-12:26), and 06:55 (04:23-10:03), respectively. The median last EO for SR, WM, and CGM were 20:20 (16:50-21:42), 20:12 (18:30-21:41), and 21:43 (20:35-22:16), respectively. The overlap between SR and CGM was 55% to 80% of EO detected with tolerance periods of ±30, 60, and 120 minutes. The overlap between SR and WM was 52% to 65% EO detected with tolerance periods of ±30, 60, and 120 minutes. CONCLUSION The continuous glucose monitor and WM detected overlapping but not identical meals and may provide complementary information to self-reported EO.
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Affiliation(s)
- Collin J. Popp
- Department of Population Health,
Institute for Excellence in Health Equity, NYU Langone Health, New York, NY,
USA
| | - Chan Wang
- Division of Biostatistics, Department
of Population Health, NYU Langone Health, New York, NY, USA
| | - Adam Hoover
- Holcombe Department of Electrical and
Computer Engineering, Clemson University, Clemson, SC, USA
| | - Louis A. Gomez
- Department of Computer Science, Stevens
Institute of Technology, Hoboken, NJ, USA
| | - Margaret Curran
- Department of Population Health,
Institute for Excellence in Health Equity, NYU Langone Health, New York, NY,
USA
| | | | - Souptik Barua
- Department of Medicine, NYU Langone
Health, New York, NY, USA
| | - Mary Ann Sevick
- Division of Precision Medicine,
Department of Medicine, NYU Langone Health, New York, NY, USA
- Department of Medicine, NYU Langone
Health, New York, NY, USA
| | - Samantha Kleinberg
- Department of Computer Science, Stevens
Institute of Technology, Hoboken, NJ, USA
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Barua S, Glantz N, Larez A, Bevier W, Sabharwal A, Kerr D. A probabilistic computation framework to estimate the dawn phenomenon in type 2 diabetes using continuous glucose monitoring. Sci Rep 2024; 14:2915. [PMID: 38316854 PMCID: PMC10844336 DOI: 10.1038/s41598-024-52461-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 01/18/2024] [Indexed: 02/07/2024] Open
Abstract
In type 2 diabetes (T2D), the dawn phenomenon is an overnight glucose rise recognized to contribute to overall glycemia and is a potential target for therapeutic intervention. Existing CGM-based approaches do not account for sensor error, which can mask the true extent of the dawn phenomenon. To address this challenge, we developed a probabilistic framework that incorporates sensor error to assign a probability to the occurrence of dawn phenomenon. In contrast, the current approaches label glucose fluctuations as dawn phenomena as a binary yes/no. We compared the proposed probabilistic model with a standard binary model on CGM data from 173 participants (71% female, 87% Hispanic/Latino, 54 ± 12 years, with either a diagnosis of T2D for six months or with an elevated risk of T2D) stratified by HbA1c levels into normal but at risk for T2D, with pre-T2D, or with non-insulin-treated T2D. The probabilistic model revealed a higher dawn phenomenon frequency in T2D [49% (95% CI 37-63%)] compared to pre-T2D [36% (95% CI 31-48%), p = 0.01] and at-risk participants [34% (95% CI 27-39%), p < 0.0001]. While these trends were also found using the binary approach, the probabilistic model identified significantly greater dawn phenomenon frequency than the traditional binary model across all three HbA1c sub-groups (p < 0.0001), indicating its potential to detect the dawn phenomenon earlier across diabetes risk categories.
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Affiliation(s)
- Souptik Barua
- Division of Precision Medicine, Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA.
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA.
| | - Namino Glantz
- Sansum Diabetes Research Institute, Santa Barbara, CA, USA
- Santa Barbara County Education Office, Santa Barbara, CA, USA
| | - Arianna Larez
- Sansum Diabetes Research Institute, Santa Barbara, CA, USA
| | - Wendy Bevier
- Sansum Diabetes Research Institute, Santa Barbara, CA, USA
| | - Ashutosh Sabharwal
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - David Kerr
- Sansum Diabetes Research Institute, Santa Barbara, CA, USA
- Center for Health Systems Research, Sutter Health, Santa Barbara, CA, USA
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Pai A, Santiago R, Glantz N, Bevier W, Barua S, Sabharwal A, Kerr D. Multimodal digital phenotyping of diet, physical activity, and glycemia in Hispanic/Latino adults with or at risk of type 2 diabetes. NPJ Digit Med 2024; 7:7. [PMID: 38212415 PMCID: PMC10784546 DOI: 10.1038/s41746-023-00985-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 12/04/2023] [Indexed: 01/13/2024] Open
Abstract
Digital phenotyping refers to characterizing human bio-behavior through wearables, personal devices, and digital health technologies. Digital phenotyping in populations facing a disproportionate burden of type 2 diabetes (T2D) and health disparities continues to lag compared to other populations. Here, we report our study demonstrating the application of multimodal digital phenotyping, i.e., the simultaneous use of CGM, physical activity monitors, and meal tracking in Hispanic/Latino individuals with or at risk of T2D. For 14 days, 36 Hispanic/Latino adults (28 female, 14 with non-insulin treated T2D) wore a continuous glucose monitor (CGM) and a physical activity monitor (Actigraph) while simultaneously logging meals using the MyFitnessPal app. We model meal events and daily digital biomarkers representing diet, physical activity choices, and corresponding glycemic response. We develop a digital biomarker for meal events that differentiates meal events into normal and elevated categories. We examine the contribution of daily digital biomarkers of elevated meal event count and step count on daily time-in-range 54-140 mg/dL (TIR54-140) and average glucose. After adjusting for step count, a change in elevated meal event count from zero to two decreases TIR54-140 by 4.0% (p = 0.003). An increase in 1000 steps in post-meal step count also reduces the meal event glucose response by 641 min mg/dL (p = 0.0006) and reduces the odds of an elevated meal event by 55% (p < 0.0001). The proposed meal event digital biomarkers may provide an opportunity for non-pharmacologic interventions for Hispanic/Latino adults facing a disproportionate burden of T2D.
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Affiliation(s)
- Amruta Pai
- Electrical and Computer Engineering, Rice University, Houston, TX, USA.
| | - Rony Santiago
- Sansum Diabetes Research Institute, Santa Barbara, CA, USA
| | - Namino Glantz
- Santa Barbara County Education Office, Children & Family Resource Services, Santa Barbara, CA, USA
| | - Wendy Bevier
- Sansum Diabetes Research Institute, Santa Barbara, CA, USA
| | - Souptik Barua
- Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | | | - David Kerr
- Sutter Center for Health Systems Research, Santa Barbara, CA, USA
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Shahnaz S, Hassanuzzaman M, Mazumder S, Rashid F, Hira HM, Hussain R, Barua S. Association of Posterior Reversible Encephalopathy Syndrome (PRES) with Preeclampsia with Severe Symptoms and Eclampsia in South East Part of Bangladesh. Mymensingh Med J 2024; 33:267-278. [PMID: 38163803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Posterior reversible encephalopathy syndrome (PRES) is a pathology seen not only in precelampsia with severe symptoms and eclampsia but in a varicty of diseases/ conditions. With the availability of neuroimaging, it is possible to know the exact underlying Central nervous system (CNS) pathology in preeclampsia with severe symptoms and eclampsia and thus therapy can be targeted. Preeclampsia with severe symptoms and eclampsia remains to be an important cause of maternal morbidity and mortality in both the developing and developed world. The objective of this study was to evaluate the association of Posterior reversible encephalopathy syndrome (PRES) by MRI (Magnetic resonance imaging) with preeclampsia with severe symptoms and eclampsia in south east part of Bangladesh. This cross-sectional observational study was performed among women suffering from preeclampsia with severe symptoms and eclampsia who attended at Obstetrics & Gynaecology department of Chittagong Medical College Hospital (CMCH), Bangladesh from January 2021 to June 2021. According to inclusion/exclusion criteria 50 samples were taken by convenient sampling for this study. A detail history was taken and complete general physical and gynecological examination was performed. Required data was collected through preset questionnaire. Neuroimaging reports were reviewed by both neurologist and radiologist. Data was analyzed by using windows based computer software device, SPSS 25.0. Results obtained from this study will be used to make a statement regarding aggressive management for cerebral vasospasm in severe preeclampsia and eclamptia related PRES. PRES has been reported to be reversible but late recognition or incorrect treatment can cause irreversible brain damage. Institution of early treatment leads to resolution of symptoms without any neurologic deficit and thus reduces maternal morbidity and mortality. PRES is a cliniconeuroradiologic entity. This study can aware doctors regarding prompt diagnosis of PRES in peripartum period among patient suffering from preeclampsia with severe symptoms and eclampsia by imaging aside clinical findings. A conclusive decision can be made to improve the outcome in this potentially life threatening but reversible condition.
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Affiliation(s)
- S Shahnaz
- Dr Shoyela Shahnaz, Assistant Professor, Department of Obstetrics & Gynaecology, Chittagong Medical College (CMC), Chittagong, Bangladesh; E-mail:
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Ismail HM, Barua S, Wang J, Sabharwal A, Libman I, Bacha F, Nadeau KJ, Tosur M, Redondo MJ. Baseline leptin predicts response to metformin in adolescents with type 1 diabetes and increased body mass index. Diabetes Obes Metab 2023; 25:3420-3423. [PMID: 37485878 PMCID: PMC10592422 DOI: 10.1111/dom.15218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/20/2023] [Accepted: 06/29/2023] [Indexed: 07/25/2023]
Affiliation(s)
- Heba M Ismail
- Department of Pediatrics, Indiana University, School of Medicine, Indianapolis, Indiana, USA
| | - Souptik Barua
- Division of Precision Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas, USA
| | - Johnny Wang
- Department of Biosciences, Rice University, Houston, Texas, USA
| | - Ashutosh Sabharwal
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas, USA
| | - Ingrid Libman
- Division of Pediatric Endocrinology and Diabetes, University of Pittsburgh, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Fida Bacha
- Diabetes & Endocrinology Division, Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas, USA
| | - Kristen J Nadeau
- University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Mustafa Tosur
- Diabetes & Endocrinology Division, Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas, USA
- Children's Nutrition Research Center, USDA/ARS, Houston, Texas, USA
| | - Maria J Redondo
- Diabetes & Endocrinology Division, Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas, USA
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Sato Imuro SE, Sabharwal A, Conneely C, Glantz N, Bevier W, Barua S, Pai A, Larez A, Kerr D. Temporal changes in bio-behavioral and glycemic outcomes following a produce prescription program among predominantly Hispanic/Latino adults with or at risk of type 2 diabetes. Heliyon 2023; 9:e18440. [PMID: 37533982 PMCID: PMC10391944 DOI: 10.1016/j.heliyon.2023.e18440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 08/04/2023] Open
Abstract
In the United States (U.S.), consumption of fresh vegetables and fruits is below recommended levels. Enhancing access to nutritious food through food prescriptions has been recognized as a promising approach to combat diet-related illnesses. However, the effectiveness of this strategy at a large scale remains untested, particularly in marginalized communities where food insecurity rates and the prevalence of health conditions such as type 2 diabetes (T2D) are higher compared to the background population. This study evaluated the impact of a produce prescription program for predominantly Hispanic/Latino adults living with or at risk of T2D. A total of 303 participants enrolled in a 3-month observational cohort received 21 medically prescribed portions/week of fresh produce. A subgroup of 189 participants used continuous glucose monitoring (CGM) to assess the relationship between CGM profile changes and HbA1c level changes. For 247 participants completing the study (76% female, 84% Hispanic/Latino, 32% with T2D, age 56·6 ± 11·9 years), there was a reduction in weight (-1·1 [-1·6 to -0·6] lbs., p < 0.001), waist circumference (-0·4 [-1·0 to 0·6] cm, p = 0·007) and systolic blood pressure (SBP) for participants with baseline SBP >120 mmHg (-4·2 [-6·8 to -1·8] mmHg, p = 0·001). For participants with an HbA1c ≥ 7·0% at baseline, HbA1c fell significantly (-0·5 [-0·9 to -0·1] %, p = 0·01). There were also improvements in food security (p < 0·0001), self-reported ratings of sleep, mood, pain (all p < 0·001), and measures of depression (p < 0·0001), anxiety (p = 0·045), and stress (p = 0·002) (DASS-21). There was significant correlation (r = 0·8, p = 0·001) between HbA1c change and the change in average glucose for participants with worsening HbA1c, but not for participants with an improvement in HbA1c. In conclusion, medical prescription of fresh produce is associated with significant improvements in cardio-metabolic and psycho-social risk factors for Hispanic/Latino adults with or at risk of T2D.
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Affiliation(s)
| | | | - Casey Conneely
- Sansum Diabetes Research Institute, Santa Barbara, CA, USA
| | - Namino Glantz
- Sansum Diabetes Research Institute, Santa Barbara, CA, USA
| | - Wendy Bevier
- Santa Barbara County Education Office, Children & Family Resource Services, Santa Barbara, CA, USA
| | - Souptik Barua
- Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - Amruta Pai
- Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - Arianna Larez
- Sansum Diabetes Research Institute, Santa Barbara, CA, USA
| | - David Kerr
- Diabetes Technology Society, Burlingame, CA, USA
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Kharmats AY, Popp C, Hu L, Berube L, Curran M, Wang C, Pompeii ML, Li H, Bergman M, St-Jules DE, Segal E, Schoenthaler A, Williams N, Schmidt AM, Barua S, Sevick MA. A randomized clinical trial comparing low-fat with precision nutrition-based diets for weight loss: impact on glycemic variability and HbA1c. Am J Clin Nutr 2023; 118:443-451. [PMID: 37236549 PMCID: PMC10447469 DOI: 10.1016/j.ajcnut.2023.05.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Recent studies have demonstrated considerable interindividual variability in postprandial glucose response (PPGR) to the same foods, suggesting the need for more precise methods for predicting and controlling PPGR. In the Personal Nutrition Project, the investigators tested a precision nutrition algorithm for predicting an individual's PPGR. OBJECTIVE This study aimed to compare changes in glycemic variability (GV) and HbA1c in 2 calorie-restricted weight loss diets in adults with prediabetes or moderately controlled type 2 diabetes (T2D), which were tertiary outcomes of the Personal Diet Study. METHODS The Personal Diet Study was a randomized clinical trial to compare a 1-size-fits-all low-fat diet (hereafter, standardized) with a personalized diet (hereafter, personalized). Both groups received behavioral weight loss counseling and were instructed to self-monitor diets using a smartphone application. The personalized arm received personalized feedback through the application to reduce their PPGR. Continuous glucose monitoring (CGM) data were collected at baseline, 3 mo and 6 mo. Changes in mean amplitude of glycemic excursions (MAGEs) and HbA1c at 6 mo were assessed. We performed an intention-to-treat analysis using linear mixed regressions. RESULTS We included 156 participants [66.5% women, 55.7% White, 24.1% Black, mean age 59.1 y (standard deviation (SD) = 10.7 y)] in these analyses (standardized = 75, personalized = 81). MAGE decreased by 0.83 mg/dL per month for standardized (95% CI: 0.21, 1.46 mg/dL; P = 0.009) and 0.79 mg/dL per month for personalized (95% CI: 0.19, 1.39 mg/dL; P = 0.010) diet, with no between-group differences (P = 0.92). Trends were similar for HbA1c values. CONCLUSIONS Personalized diet did not result in an increased reduction in GV or HbA1c in patients with prediabetes and moderately controlled T2D, compared with a standardized diet. Additional subgroup analyses may help to identify patients who are more likely to benefit from this personalized intervention. This trial was registered at clinicaltrials.gov as NCT03336411.
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Affiliation(s)
- Anna Y Kharmats
- Center for Healthful Behavior Change, Institute for Excellence in Health Equity, New York University Langone Health, New York, NY, United States; Department of Population Health, New York University Grossman School of Medicine, New York, NY, United States
| | - Collin Popp
- Center for Healthful Behavior Change, Institute for Excellence in Health Equity, New York University Langone Health, New York, NY, United States; Department of Population Health, New York University Grossman School of Medicine, New York, NY, United States
| | - Lu Hu
- Center for Healthful Behavior Change, Institute for Excellence in Health Equity, New York University Langone Health, New York, NY, United States; Department of Population Health, New York University Grossman School of Medicine, New York, NY, United States
| | - Lauren Berube
- Center for Healthful Behavior Change, Institute for Excellence in Health Equity, New York University Langone Health, New York, NY, United States; Department of Population Health, New York University Grossman School of Medicine, New York, NY, United States.
| | - Margaret Curran
- Center for Healthful Behavior Change, Institute for Excellence in Health Equity, New York University Langone Health, New York, NY, United States; Department of Population Health, New York University Grossman School of Medicine, New York, NY, United States
| | - Chan Wang
- Department of Population Health, New York University Grossman School of Medicine, New York, NY, United States
| | - Mary Lou Pompeii
- Center for Healthful Behavior Change, Institute for Excellence in Health Equity, New York University Langone Health, New York, NY, United States; Department of Population Health, New York University Grossman School of Medicine, New York, NY, United States
| | - Huilin Li
- Department of Population Health, New York University Grossman School of Medicine, New York, NY, United States
| | - Michael Bergman
- Department of Population Health, New York University Grossman School of Medicine, New York, NY, United States; Division of Endocrinology, Diabetes and Metabolism, New York University Grossman School of Medicine, New York, NY, United States
| | - David E St-Jules
- Department of Nutrition, University of Nevada, Reno, Reno, NV, United States
| | - Eran Segal
- Department of Computer Science and Applied Math, Weizmann Institute of Science, Rehovot, Israel
| | - Antoinette Schoenthaler
- Center for Healthful Behavior Change, Institute for Excellence in Health Equity, New York University Langone Health, New York, NY, United States; Department of Population Health, New York University Grossman School of Medicine, New York, NY, United States
| | - Natasha Williams
- Center for Healthful Behavior Change, Institute for Excellence in Health Equity, New York University Langone Health, New York, NY, United States; Department of Population Health, New York University Grossman School of Medicine, New York, NY, United States
| | - Ann Marie Schmidt
- Diabetes Research Program, Department of Medicine, New York University Langone Health, New York, NY, United States
| | - Souptik Barua
- Division of Precision Medicine, Department of Medicine, New York University Langone Health, New York, NY, United States
| | - Mary Ann Sevick
- Center for Healthful Behavior Change, Institute for Excellence in Health Equity, New York University Langone Health, New York, NY, United States; Department of Population Health, New York University Grossman School of Medicine, New York, NY, United States; Division of Endocrinology, Diabetes and Metabolism, New York University Grossman School of Medicine, New York, NY, United States
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Prasanna S, Barua S, Siller AF, Johnson JJ, Sabharwal A, DeSalvo DJ. Hypoglycemia risk with physical activity in type 1 diabetes: a data-driven approach. Front Digit Health 2023; 5:1142021. [PMID: 37274763 PMCID: PMC10237013 DOI: 10.3389/fdgth.2023.1142021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/03/2023] [Indexed: 06/06/2023] Open
Abstract
Physical activity (PA) provides numerous health benefits for individuals with type 1 diabetes (T1D). However, the threat of exercise-induced hypoglycemia may impede the desire for regular PA. Therefore, we aimed to study the association between three common types of PA (walking, running, and cycling) and hypoglycemia risk in 50 individuals with T1D. Real-world data, including PA duration and intensity, continuous glucose monitor (CGM) values, and insulin doses, were available from the Tidepool Big Data Donation Project. Participants' mean (SD) age was 38.0 (13.1) years with a mean (SD) diabetes duration of 21.4 (12.9) years and an average of 26.2 weeks of CGM data available. We developed a linear regression model for each of the three PA types to predict the average glucose deviation from 70 mg/dl for the 2 h after the start of PA. This is essentially a measure of hypoglycemia risk, for which we used the following predictors: PA duration (mins) and intensity (calories burned), 2-hour pre-exercise area under the glucose curve (adjusted AUC), the glucose value at the beginning of PA, and total bolus insulin (units) within 2 h before PA. Our models indicated that glucose value at the start of exercise and pre-exercise glucose adjusted AUC (p < 0.001 for all three activities) were the most significant predictors of hypoglycemia. In addition, the duration and intensity of PA and 2-hour bolus insulin were weakly associated with hypoglycemia for walking, running, and cycling. These findings may provide individuals with T1D with a data-driven approach to preparing for PA that minimizes hypoglycemia risk.
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Affiliation(s)
- Sahana Prasanna
- Department of Bioengineering, Rice University, Houston, TX, United States
| | - Souptik Barua
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, United States
- Division of Precision Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, NY, United States
| | - Alejandro F. Siller
- Department of Pediatrics, Diabetes, and Endocrinology, Baylor College of Medicine, Houston, TX, United States
| | - Jeremiah J. Johnson
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, United States
| | - Ashutosh Sabharwal
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, United States
| | - Daniel J. DeSalvo
- Department of Pediatrics, Diabetes, and Endocrinology, Baylor College of Medicine, Houston, TX, United States
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Barua S, Conte S, Cherrett C, Robson D, Bragg C, MacDonald P, Muthiah K, Hayward C. Major Adverse Kidney Events is a Predictor of Reduced Survival in Patients Supported with Ventricular Assist Devices. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Barua S, Lo P, Stephens M, Vazquez G, Diab S, James K, Heuring J, Muthiah K, Hayward C. A Mock Circulatory Loop Analysis of the Procyrion Aortix Pump. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Chavali S, Barua S, Adjii A, Robson D, Raven L, Greenfield J, Parvar S, MacDonald P, Hayward C, Muthiah K. Safety and Tolerability of Sodium-Glucose Cotransporter-2 Inhibitors (SGLT2i) in Patients Supported with Left Ventricular Assist Devices. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Jiang J, Jain P, Adji A, Barua S, Hayward C. Afterload and LV Function, but Not Circuit Flow, Determine LV Filling Pressure During VA-ECMO. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Jiang J, Jain P, Adji A, Barua S, Hayward C. Determinants of LV Filling Pressure During ECPR with VA-ECMO: A Mock Circulatory Loop Study. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
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Krishnan SN, Barua S, Frankel TL, Rao A. Towards the characterization of the tumor microenvironment through dictionary learning-based interpretable classification of multiplexed immunofluorescence images. Phys Med Biol 2023; 68:014002. [PMID: 36541756 PMCID: PMC9903331 DOI: 10.1088/1361-6560/aca86a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/02/2022] [Indexed: 12/03/2022]
Abstract
Objective.Histology image analysis is a crucial diagnostic step in staging and treatment planning, especially for cancerous lesions. With the increasing adoption of computational methods for image analysis, significant strides are being made to improve the performance metrics of image segmentation and classification frameworks. However, many developed frameworks effectively function as black boxes, granting minimal context to the decision-making process. Thus, there is a need to develop methods that offer reasonable discriminatory power and a biologically-informed intuition to the decision-making process.Approach.In this study, we utilized and modified a discriminative feature-based dictionary learning (DFDL) paradigm to generate a classification framework that allows for discrimination between two distinct clinical histologies. This framework allows us (i) to discriminate between 2 clinically distinct diseases or histologies and (ii) provides interpretable group-specific representative dictionary image patches, or 'atoms', generated during classifier training. This implementation is performed on multiplexed immunofluorescence images from two separate patient cohorts- a pancreatic cohort consisting of cancerous and non-cancerous tissues and a metastatic non-small cell lung cancer (mNSCLC) cohort of responders and non-responders to an immunotherapeutic treatment regimen. The analysis was done at both the image-level and subject-level. Five cell types were selected, namely, epithelial cells, cytotoxic lymphocytes, antigen presenting cells, HelperT cells, and T-regulatory cells, as our phenotypes of interest.Results.We showed that DFDL had significant discriminant capabilities for both the pancreatic pathologies cohort (subject-level AUC-0.8878) and the mNSCLC immunotherapy response cohort (subject-level AUC-0.7221). The secondary analysis also showed that more than 50% of the obtained dictionary atoms from the classifier contained biologically relevant information.Significance.Our method shows that the generated dictionary features can help distinguish patients presenting two different histologies with strong sensitivity and specificity metrics. These features allow for an additional layer of model interpretability, a highly desirable element in clinical applications for identifying novel biological phenomena.
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Affiliation(s)
- Santhoshi N Krishnan
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas-77005, United States of America,
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan-48109, United States of America
| | - Souptik Barua
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas-77005, United States of America
| | - Timothy L Frankel
- Department of Surgery, University of Michigan, Ann Arbor, Michigan-48109, United States of America
| | - Arvind Rao
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas-77005, United States of America,
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan-48109, United States of America,
Department of Biostatistics, University of Michigan, Ann Arbor, Michigan-48109, United States of America,
Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan-48109, United States of America,
Department of Radiology, University of Michigan, Ann Arbor, Michigan-48109, United States of America
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15
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Barua S, A Wierzchowska-McNew R, Deutz NEP, Sabharwal A. Discordance between postprandial plasma glucose measurement and continuous glucose monitoring. Am J Clin Nutr 2022; 116:1059-1069. [PMID: 35776949 DOI: 10.1093/ajcn/nqac181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 06/27/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND There has been growing interest in studying postprandial glucose responses using continuous glucose monitoring (CGM) in nondiabetic individuals. Accurate measurement of glucose responses to meals can facilitate applications such as precision nutrition and early detection of diabetes. OBJECTIVES We aimed to quantify the discordance between simultaneous postprandial glucose measurements made using plasma and CGM. METHODS We studied 10 nondiabetic older adults who randomly consumed 9 predefined meals of varying macronutrient compositions. Glucose was measured for 8 h after the meal by the CGM, blood samples for plasma collection were taken regularly, and plasma glucose was quantified using gold-standard laboratory measurement and a fingerstick blood glucose meter. The primary outcome measured was the mean absolute relative difference (MARD) of CGM and fingerstick measurements relative to the gold standard. Secondary outcomes were Bland-Altman statistics, Clarke Error Grid, and time in range metrics. Additional subgroup analyses were performed by stratifying the postprandial glucose measurements based on the macronutrient composition of the meals. RESULTS When compared against the gold-standard postprandial glucose measurements, the fingerstick meter was more accurate (MARD: 8.0%; 95% CI: 7.6%, 8.6%) than the CGM (MARD: 13.7%; 95% CI: 13.1%, 14.3%; P < 0.0001). After the meals, Bland-Altman analysis demonstrated that the CGM underestimated the 8-h gold-standard glucose rise by 12.8 mg/dL on average (P < 0.0001), whereas the fingerstick meter did so by 5.5 mg/dL on average (P < 0.0001). The CGM underestimated the time spent in the 70-180 mg/dL range (P = 0.002) and overestimated the time spent <70 mg/dL (P < 0.0001) compared with the other 2 methods. CONCLUSIONS We discovered discordance between gold standard, fingerstick, and CGM in measuring plasma glucose concentrations after a meal. Consequently, emerging applications of CGM in healthy individuals, such as precision nutrition and diabetes onset prediction, may need to account for these discordances.This trial was registered at clinicaltrials.gov as NCT04928872.
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Affiliation(s)
- Souptik Barua
- Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - Raven A Wierzchowska-McNew
- Center for Translational Research in Aging and Longevity, Texas A&M University, College Station, TX, USA
| | - Nicolaas E P Deutz
- Center for Translational Research in Aging and Longevity, Texas A&M University, College Station, TX, USA
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16
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Barua S, Yang T, Conte S, Bragg C, Macdonald P, Muthiah K, Hayward C. Value of Renal Histology for Predicting Cardiorenal Outcomes in Patients Listed for Cardiac Transplantation. J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.1677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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17
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Krishnaswamy R, Robson D, Ramanayake A, Gunawan A, Barua S, Adji A, Hayward C, Muthiah K. Using Pulsatility Responses to Breath-Hold Maneuvers to Predict Readmission Rates in Left Ventricular Assist Device Patients. J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.1435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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18
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Krishnaswamy R, Robson D, Ramanayake A, Gunawan A, Barua S, Jain P, Adji A, Macdonald P, Hayward C, Muthiah K. Using Pulsatility Responses to Breath-Hold Manoeuvres to Predict Readmission Rates in Continuous-Flow Left Ventricular Assist Device Patients. Heart Lung Circ 2022. [DOI: 10.1016/j.hlc.2022.06.139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Barua S, Lo P, Stevens M, Vazquez G, Diab S, Heuring J, Krisher J, Muthiah K, Hayward C. A Mock Circulatory Loop Analysis of an Intra-Aortic Cardiorenal Pump. Heart Lung Circ 2022. [DOI: 10.1016/j.hlc.2022.06.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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20
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Barua S, Sabharwal A, Glantz N, Conneely C, Larez A, Bevier W, Kerr D. The northeast glucose drift: Stratification of post-breakfast dysglycemia among predominantly Hispanic/Latino adults at-risk or with type 2 diabetes. EClinicalMedicine 2022; 43:101241. [PMID: 34988413 PMCID: PMC8703234 DOI: 10.1016/j.eclinm.2021.101241] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/16/2021] [Accepted: 11/29/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND There is minimal experience in continuous glucose monitoring (CGM) among underserved racial/ethnic minority populations with or at risk of type 2 diabetes (T2D), and therefore a lack of CGM-driven insight for these individuals. We analyzed breakfast-related CGM profiles of free-living, predominantly Hispanic/Latino individuals at-risk of T2D, with pre-T2D, or with non-insulin treated T2D. METHODS Starting February 2019, 119 participants in Santa Barbara, CA, USA, (93 female, 87% Hispanic/Latino [predominantly Mexican-American], age 54·4 [±12·1] years), stratified by HbA1c levels into (i) at-risk of T2D, (ii) with pre-T2D, and (iii) with non-insulin treated T2D, wore blinded CGMs for two weeks. We compared valid CGM profiles from 106 of these participants representing glucose response to breakfast using four parameters. FINDINGS A "northeast drift" was observed in breakfast glucose responses comparing at-risk to pre-T2D to T2D participants. T2D participants had a significantly higher pre-breakfast glucose level, glucose rise, glucose incremental area under the curve (all p < 0·0001), and time to glucose peak (p < 0·05) compared to pre-T2D and at-risk participants. After adjusting for demographic and clinical covariates, pre-breakfast glucose and time to peak (p < 0·0001) were significantly associated with HbA1c. The model predicted HbA1c within (0·55 ± 0·67)% of true laboratory HbA1c values. INTERPRETATION For predominantly Hispanic/Latino adults, the average two-week breakfast glucose response shows a progression of dysglycemia from at-risk of T2D to pre-T2D to T2D. CGM-based breakfast metrics have the potential to predict HbA1c levels and monitor diabetes progression. FUNDING US Department of Agriculture (Grant #2018-33800-28404), a seed grant from the industry board fees of the NSF Engineering Research Center for Precise Advanced Technologies and Health Systems for Underserved Populations (PATHS-UP) (Award #1648451), and the Elsevier foundation.
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Affiliation(s)
- Souptik Barua
- Electrical and Computer Engineering, Rice University, Houston, TX, United States
| | - Ashutosh Sabharwal
- Electrical and Computer Engineering, Rice University, Houston, TX, United States
| | - Namino Glantz
- Sansum Diabetes Research Institute, Santa Barbara, California, United States
| | - Casey Conneely
- Sansum Diabetes Research Institute, Santa Barbara, California, United States
| | - Arianna Larez
- Sansum Diabetes Research Institute, Santa Barbara, California, United States
| | - Wendy Bevier
- Sansum Diabetes Research Institute, Santa Barbara, California, United States
| | - David Kerr
- Sansum Diabetes Research Institute, Santa Barbara, California, United States
- Corresponding author.
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21
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Elhalawani H, Cardenas CE, Volpe S, Barua S, Stieb S, Rock CB, Lin T, Yang P, Wu H, Zaveri J, Elgohari B, Abdallah LE, Jethanandani A, Mohamed ASR, Court LE, Hutcheson KA, Brandon Gunn G, Rosenthal DI, Frank SJ, Garden AS, Rao A, Fuller CD. 18FDG positron emission tomography mining for metabolic imaging biomarkers of radiation-induced xerostomia in patients with oropharyngeal cancer. Clin Transl Radiat Oncol 2021; 29:93-101. [PMID: 34195391 PMCID: PMC8239739 DOI: 10.1016/j.ctro.2021.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/11/2021] [Accepted: 05/30/2021] [Indexed: 12/30/2022] Open
Abstract
Purpose Head and neck cancers radiotherapy (RT) is associated with inevitable injury to parotid glands and subsequent xerostomia. We investigated the utility of SUV derived from 18FDG-PET to develop metabolic imaging biomarkers (MIBs) of RT-related parotid injury. Methods Data for oropharyngeal cancer (OPC) patients treated with RT at our institution between 2005 and 2015 with available planning computed tomography (CT), dose grid, pre- & first post-RT 18FDG-PET-CT scans, and physician-reported xerostomia assessment at 3-6 months post-RT (Xero 3-6 ms) per CTCAE, was retrieved, following an IRB approval. A CT-CT deformable image co-registration followed by voxel-by-voxel resampling of pre & post-RT 18FDG activity and dose grid were performed. Ipsilateral (Ipsi) and contralateral (contra) parotid glands were sub-segmented based on the received dose in 5 Gy increments, i.e. 0-5 Gy, 5-10 Gy sub-volumes, etc. Median and dose-weighted SUV were extracted from whole parotid volumes and sub-volumes on pre- & post-RT PET scans, using in-house code that runs on MATLAB. Wilcoxon signed-rank and Kruskal-Wallis tests were used to test differences pre- and post-RT. Results 432 parotid glands, belonging to 108 OPC patients treated with RT, were sub-segmented & analyzed. Xero 3-6 ms was reported as: non-severe (78.7%) and severe (21.3%). SUV- median values were significantly reduced post-RT, irrespective of laterality (p = 0.02). A similar pattern was observed in parotid sub-volumes, especially ipsi parotid gland sub-volumes receiving doses 10-50 Gy (p < 0.05). Kruskal-Wallis test showed a significantly higher mean RT dose in the contra parotid in the patients with more severe Xero 3-6mo (p = 0.03). Multiple logistic regression showed a combined clinical-dosimetric-metabolic imaging model could predict the severity of Xero 3-6mo; AUC = 0.78 (95%CI: 0.66-0.85; p < 0.0001). Conclusion We sought to quantify pre- and post-RT 18FDG-PET metrics of parotid glands in patients with OPC. Temporal dynamics of PET-derived metrics can potentially serve as MIBs of RT-related xerostomia in concert with clinical and dosimetric variables.
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Affiliation(s)
- Hesham Elhalawani
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Department of Radiation Oncology, Brigham and Women's Hospital and Dana-Farber Cancer Institute, Boston, MA, United States
| | - Carlos E Cardenas
- Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Stefania Volpe
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Souptik Barua
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, United States.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | - Sonja Stieb
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Calvin B Rock
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Department of Radiation Oncology, University of Utah Huntsman Cancer Institute, Salt Lake City, UT, United States
| | - Timothy Lin
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Pei Yang
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital, Xiangya Medical School, Central South University, Changsha, China
| | - Haijun Wu
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jhankruti Zaveri
- Department of Head and Neck Surgery, Section of Speech Pathology and Audiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Baher Elgohari
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Department of Clinical Oncology & Nuclear Oncology, Mansoura University, Mansoura, Egypt
| | - Lamiaa E Abdallah
- Department of Clinical Oncology & Nuclear Oncology, Ain Shams University, Cairo, Egypt
| | - Amit Jethanandani
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Abdallah S R Mohamed
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Laurence E Court
- Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Katherine A Hutcheson
- Department of Head and Neck Surgery, Section of Speech Pathology and Audiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - G Brandon Gunn
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - David I Rosenthal
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Steven J Frank
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Adam S Garden
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Arvind Rao
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, United States.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States.,Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI, United States.,Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, United States.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Clifton D Fuller
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
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22
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Barua S, Sabharwal A, Glantz N, Conneely C, Larez A, Bevier W, Kerr D. Dysglycemia in adults at risk for or living with non-insulin treated type 2 diabetes: Insights from continuous glucose monitoring. EClinicalMedicine 2021; 35:100853. [PMID: 33997745 PMCID: PMC8093893 DOI: 10.1016/j.eclinm.2021.100853] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/22/2021] [Accepted: 03/31/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Continuous glucose monitoring (CGM) has demonstrable benefits for people living with diabetes, but the supporting evidence is almost exclusively from White individuals with type 1 diabetes. Here, we have quantified CGM profiles in Hispanic/Latino adults with or at-risk of non-insulin treated type 2 diabetes (T2D). METHODS 100 participants (79 female, 86% Hispanic/Latino [predominantly Mexican], age 54·6 [±12·0] years) stratified into (i) at risk of T2D, (ii) with pre-diabetes (pre-T2D), and (iii) with non-insulin treated T2D, wore blinded CGMs for 2 weeks. Beyond standardized CGM measures (average glucose, glucose variability, time in 70-140 mg/dL and 70-180 mg/dL ranges), we also examined additional CGM measures based on the time of day. FINDINGS Standardized CGM measures were significantly different for participants with T2D compared to at-risk and pre-T2D participants (p<0·0001). In addition, pre-T2D participants spent more time between 140 and 180 mg/dL during the day than at-risk participants (p<0·01). T2D participants spent more time between 140 and 180 mg/dL both during the day and overnight compared to at-risk and pre-T2D participants (both p<0·0001). Time in 70-140 mg/dL range during the day was significantly correlated with HbA1c (r=-0·72, p<0·0001), after adjusting for age, sex, BMI, and waist circumference (p<0·0001). INTERPRETATION Standardized CGM measures show a progression of dysglycemia from at-risk of T2D, to pre-T2D, and to T2D. Stratifying CGM readings by time of day and the range 140-180 mg/dL provides additional metrics to differentiate between the groups. FUNDING US Department of Agriculture (Grant #2018-33800-28404) and NSF PATHS-UP ERC (Award #1648451).
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Affiliation(s)
- Souptik Barua
- Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | | | - Namino Glantz
- Sansum Diabetes Research Institute, Santa Barbara, CA, USA
| | - Casey Conneely
- Sansum Diabetes Research Institute, Santa Barbara, CA, USA
| | - Arianna Larez
- Sansum Diabetes Research Institute, Santa Barbara, CA, USA
| | - Wendy Bevier
- Sansum Diabetes Research Institute, Santa Barbara, CA, USA
| | - David Kerr
- Sansum Diabetes Research Institute, Santa Barbara, CA, USA
- Corresponding author.
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23
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Carstens JL, Yang S, Correa de Sampaio P, Zheng X, Barua S, McAndrews KM, Rao A, Burks JK, Rhim AD, Kalluri R. Stabilized epithelial phenotype of cancer cells in primary tumors leads to increased colonization of liver metastasis in pancreatic cancer. Cell Rep 2021; 35:108990. [PMID: 33852841 PMCID: PMC8078733 DOI: 10.1016/j.celrep.2021.108990] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 01/25/2021] [Accepted: 03/23/2021] [Indexed: 12/30/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is therapeutically recalcitrant and metastatic. Partial epithelial to mesenchymal transition (EMT) is associated with metastasis; however, a causal connection needs further unraveling. Here, we use single-cell RNA sequencing and genetic mouse models to identify the functional roles of partial EMT and epithelial stabilization in PDAC growth and metastasis. A global EMT expression signature identifies ∼50 cancer cell clusters spanning the epithelial-mesenchymal continuum in both human and murine PDACs. The combined genetic suppression of Snail and Twist results in PDAC epithelial stabilization and increased liver metastasis. Genetic deletion of Zeb1 in PDAC cells also leads to liver metastasis associated with cancer cell epithelial stabilization. We demonstrate that epithelial stabilization leads to the enhanced collective migration of cancer cells and modulation of the immune microenvironment, which likely contribute to efficient liver colonization. Our study provides insights into the diverse mechanisms of metastasis in pancreatic cancer and potential therapeutic targets.
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Affiliation(s)
- Julienne L Carstens
- Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Sujuan Yang
- Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Pedro Correa de Sampaio
- Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Xiaofeng Zheng
- Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Souptik Barua
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77030, USA
| | - Kathleen M McAndrews
- Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Arvind Rao
- Department of Computational Medicine and Bioinformatics, Biostatistics, Radiation Oncology, University of Michigan, Ann Arbor, MI 48105, USA
| | - Jared K Burks
- Department of Leukemia, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Andrew D Rhim
- Department of Gastroenterology, Hepatology, and Nutrition, Division of Internal Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Raghu Kalluri
- Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Department of Bioengineering, Rice University, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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24
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Barua S, Elhalawani H, Volpe S, Al Feghali KA, Yang P, Ng SP, Elgohari B, Granberry RC, Mackin DS, Gunn GB, Hutcheson KA, Chambers MS, Court LE, Mohamed ASR, Fuller CD, Lai SY, Rao A. Computed Tomography Radiomics Kinetics as Early Imaging Correlates of Osteoradionecrosis in Oropharyngeal Cancer Patients. Front Artif Intell 2021; 4:618469. [PMID: 33898983 PMCID: PMC8063205 DOI: 10.3389/frai.2021.618469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 03/04/2021] [Indexed: 01/08/2023] Open
Abstract
Osteoradionecrosis (ORN) is a major side-effect of radiation therapy in oropharyngeal cancer (OPC) patients. In this study, we demonstrate that early prediction of ORN is possible by analyzing the temporal evolution of mandibular subvolumes receiving radiation. For our analysis, we use computed tomography (CT) scans from 21 OPC patients treated with Intensity Modulated Radiation Therapy (IMRT) with subsequent radiographically-proven ≥ grade II ORN, at three different time points: pre-IMRT, 2-months, and 6-months post-IMRT. For each patient, radiomic features were extracted from a mandibular subvolume that developed ORN and a control subvolume that received the same dose but did not develop ORN. We used a Multivariate Functional Principal Component Analysis (MFPCA) approach to characterize the temporal trajectories of these features. The proposed MFPCA model performs the best at classifying ORN vs. Control subvolumes with an area under curve (AUC) = 0.74 [95% confidence interval (C.I.): 0.61–0.90], significantly outperforming existing approaches such as a pre-IMRT features model or a delta model based on changes at intermediate time points, i.e., at 2- and 6-month follow-up. This suggests that temporal trajectories of radiomics features derived from sequential pre- and post-RT CT scans can provide markers that are correlates of RT-induced mandibular injury, and consequently aid in earlier management of ORN.
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Affiliation(s)
- Souptik Barua
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, United States.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | - Hesham Elhalawani
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Stefania Volpe
- Department of Radiation Oncology, European Institute of Oncology IRCSS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Karine A Al Feghali
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Pei Yang
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Sweet Ping Ng
- Department of Radiation Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Baher Elgohari
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Robin C Granberry
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Dennis S Mackin
- Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - G Brandon Gunn
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Katherine A Hutcheson
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Mark S Chambers
- Department of Oncologic Dentistry and Prosthodontics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Laurence E Court
- Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Abdallah S R Mohamed
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Clifton D Fuller
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Stephen Y Lai
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Arvind Rao
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, United States.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States.,Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, United States
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Conte S, Barua S, Cherrett C, Adji A, Engelman J, Robson D, Bragg C, Kearney K, Jain P, Macdonald P, Muthiah K, Hayward C. Flow Pulsatility and Outcomes in Continuous-Flow Ventricular Assist Devices. J Heart Lung Transplant 2021. [DOI: 10.1016/j.healun.2021.01.1177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Barua S, Conte S, Cherrett C, Adji A, Engelman J, Robson D, Kearney K, Bragg C, Jain P, Schnegg B, Macdonald P, Muthiah K, Hayward C. Predictors of Worsening Renal Function in Patients Supported with Ventricular Assist Devices. J Heart Lung Transplant 2021. [DOI: 10.1016/j.healun.2021.01.1205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Elhalawani H, Volpe S, Cardenas C, Stieb S, Rock C, Lin T, Yang P, Wu H, Barua S, Zaveri J, Elgohari B, Abdallah L, Jethanandani A, Mohamed A, Court L, Gunn G, Rosenthal D, Frank S, Garden A, Rao A, Hutcheson K, Fuller C. Investigation of Longitudinal Dose-weighted FDG-Positron Emission Tomography Metabolic Imaging Biomarkers (PET MIBs) of Radiation-associated Dysphagia in OPC Cohort. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Kerr D, Barua S, Glantz N, Conneely C, Kujan M, Bevier W, Larez A, Sabharwal A. Farming for life: impact of medical prescriptions for fresh vegetables on cardiometabolic health for adults with or at risk of type 2 diabetes in a predominantly Mexican-American population. BMJ Nutr Prev Health 2020; 3:239-246. [PMID: 33521534 PMCID: PMC7841821 DOI: 10.1136/bmjnph-2020-000133] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 12/18/2022] Open
Abstract
Introduction Poor diet is the leading cause of poor health in USA, with fresh vegetable consumption below recommended levels. We aimed to assess the impact of medical prescriptions for fresh (defined as picked within 72 hours) vegetables, at no cost to participants on cardiometabolic outcomes among adults (predominantly Mexican-American women) with or at risk of type 2 diabetes (T2D). Methods Between February 2019 and March 2020, 159 participants (122 female, 75% of Mexican heritage, 31% with non-insulin treated T2D, age 52.5 (13.2) years) were recruited using community outreach materials in English and Spanish, and received prescriptions for 21 servings/week of fresh vegetable for 10 weeks. Pre-post comparisons were made of weight; waist circumference; blood pressure; Hemoglobin A1c (HbA1c, a measure of long-term blood glucose control); self-reported sleep, mood and pain; vegetable, tortilla and soda consumption. After obtaining devices for this study, 66 of 72 participants asked, agreed to wear blinded continuous glucose monitors (CGM). Results Paired data were available for 131 participants. Over 3 months, waist circumference fell (−0.77 (95% CI −1.42 to 0.12) cm, p=0.022), as did systolic blood pressure (SBP) (−2.42 (95% CI −4.56 to 0.28) mm Hg, p=0.037), which was greater among individuals with baseline SBP >130 mm Hg (−7.5 (95% CI −12.4 to 2.6) mm Hg, p=0.005). Weight reduced by −0.4 (−0.7 to –0.04) kg, p=0.029 among women. For participants with baseline HbA1c >7.0%, HbA1c fell by −0.35 (-0.8 to –0.1), p=0.009. For participants with paired CGM data (n=40), time in range 70–180 mg/dL improved (from 97.4% to 98.9%, p<0.01). Food insecurity (p<0.001), tortilla (p<0.0001) and soda (p=0.013) consumption significantly decreased. Self-reported sleep, mood and pain level scores also improved (all p<0.01). Conclusions Medical prescriptions for fresh vegetables were associated with clinically relevant improvements in cardiovascular risk factors and quality of life variables (sleep, mood and pain level) in adults (predominantly Mexican-American and female) with or at risk of T2D. Trial registration number ClinicalTrials.gov Identifier: NCT03940300.
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Affiliation(s)
- David Kerr
- Sansum Diabetes Research Institute, Santa Barbara, California, USA
| | - Souptik Barua
- Electrical and Computer Engineering, Rice University, Houston, Texas, USA
| | - Namino Glantz
- Sansum Diabetes Research Institute, Santa Barbara, California, USA
| | - Casey Conneely
- Sansum Diabetes Research Institute, Santa Barbara, California, USA
| | - Mary Kujan
- Sansum Diabetes Research Institute, Santa Barbara, California, USA
| | - Wendy Bevier
- Sansum Diabetes Research Institute, Santa Barbara, California, USA
| | - Arianna Larez
- Sansum Diabetes Research Institute, Santa Barbara, California, USA
| | - Ashutosh Sabharwal
- Electrical and Computer Engineering, Rice University, Houston, Texas, USA
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Barua S, Muthiah K, Sevastos J, Macdonald P, Hayward C. 161 Renal Histology associated With Cardiorenal Syndrome in Patients With Advanced Heart Failure. Heart Lung Circ 2020. [DOI: 10.1016/j.hlc.2020.09.168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Barua S, Muthiah K, Macdonald P, Hayward C. 622 Renal Resistive Index and Acute Kidney Injury During Mechanical Circulatory Support. Heart Lung Circ 2020. [DOI: 10.1016/j.hlc.2020.09.629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Lazarus J, Oneka MD, Barua S, Maj T, Lanfranca MP, Delrosario L, Sun L, Smith JJ, D'Angelica MI, Shia J, Fang JM, Shi J, Di Magliano MP, Zou W, Rao A, Frankel TL. Mathematical Modeling of the Metastatic Colorectal Cancer Microenvironment Defines the Importance of Cytotoxic Lymphocyte Infiltration and Presence of PD-L1 on Antigen Presenting Cells. Ann Surg Oncol 2019; 26:2821-2830. [PMID: 31250346 PMCID: PMC6684475 DOI: 10.1245/s10434-019-07508-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND Although immune-based therapy has proven efficacious for some patients with microsatellite instability (MSI) colon cancers, a majority of patients receive limited benefit. Conversely, select patients with microsatellite stable (MSS) tumors respond to checkpoint blockade, necessitating novel ways to study the immune tumor microenvironment (TME). We used phenotypic and spatial data from infiltrating immune and tumor cells to model cellular mixing to predict disease specific outcomes in patients with colorectal liver metastases. METHODS Formalin fixed paraffin embedded metastatic colon cancer tissue from 195 patients were subjected to multiplex immunohistochemistry (mfIHC). After phenotyping, the G-function was calculated for each patient and cell type. Data was correlated with clinical outcomes and survival. RESULTS High tumor cell to cytotoxic T lymphocyte (TC-CTL) mixing was associated with both a pro-inflammatory and immunosuppressive TME characterized by increased CTL infiltration and PD-L1+ expression, respectively. Presence and engagement of antigen presenting cells (APC) and helper T cells (Th) were associated with greater TC-CTL mixing and improved 5-year disease specific survival compared to patients with a low degree of mixing (42% vs. 16%, p = 0.0275). Comparison of measured mixing to a calculated theoretical random mixing revealed that PD-L1 expression on APCs resulted in an environment where CTLs were non-randomly less associated with TCs, highlighting their biologic significance. CONCLUSION Evaluation of immune interactions within the TME of metastatic colon cancer using mfIHC in combination with mathematical modeling characterized cellular mixing of TCs and CTLs, providing a novel strategy to better predict clinical outcomes while identifying potential candidates for immune based therapies.
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Affiliation(s)
- Jenny Lazarus
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Morgan D Oneka
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Souptik Barua
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Tomasz Maj
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Lei Sun
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | - J Joshua Smith
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael I D'Angelica
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jiayun M Fang
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jiaqi Shi
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Weiping Zou
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Arvind Rao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
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Francisco-Cruz A, Parra ER, Krishnan SN, Barua S, Jiang M, Fujimoto J, Peterson CB, Das P, Chow CW, Rodriguez-Canales J, Behrens C, Kalhor N, Weissferdt A, Heymach J, Swisher S, Sepesi B, Rao A, Lee JJ, Moran C, Futreal A, Zhang J, Wistuba II. Abstract 1180: Impact of the spatial analysis of tumor-associated lymphocytes and tumor-associated macrophages on recurrence at early stage of non-small cell lung carcinoma. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-1180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction. The interaction between malignant cells (MCs), stromal cells, tumor-associated lymphocytes (TILs), and tumor-associated macrophages (TAMs) is relevant for non-small cell lung carcinoma (NSCLC) progression. The spatial distribution of those cells may affect the prognosis and can be related to genetic intra-tumor heterogeneity (ITH). The aim of this study was to characterize the immunologic ITH and the spatial distribution of immune cells to MCs in primary NSCLC tumors at early stages using multiplex immunofluorescence (mIF) and image analysis approaches.
Material and methods. We studied 33 surgically resected NSCLC cases (adenocarcinomas=23; squamous-cell carcinomas=10) with a history of recurrence in a follow-up of at least 60 months (recurrence, N=13; non-recurrence, N=15). Consecutive FFPE tissue sections were stained with two mIF panels (panel 1: cytokeratin (AE1/AE3), PD-L1, PD-1, CD3, CD8, and CD68; panel 2: AE1/AE3, CD3, CD8, granzyme-B, CD45RO, and FOXP3). Three intra-tumor regions (3mm2 each) per case were selected after gridding the whole tumor section. A total of 99 intratumor regions were scanned and analyzed using Vectra Multispectral-Microscope and InForm-software. From each intratumor region, TILs and TAMs densities, as well as the coefficient of variation, were evaluated. The median distance and the G-Cross area under the curve (AUC) for specific radial distances (10µm, 20µm, and 40µm) were obtained between TILs and TAMs phenotypes to MCs.
Results. Recurrence was associated with higher MCs density and TAMs/TILs ratio, and lower TIL densities. A high ITH of cytotoxic T-cells (CTLs) PD-L1+ was associated with worse survival. The distance of TAMs PD-L1+ to MCs PD-L1 negative (60µm vs 25µm) or to MCs PD-L1 positive (25µm vs 13µm) was higher in the non-recurrence group than in recurrence group. Close TAMs PD-L1+ to MCs was associated with worst survival. In a radial distance of 10µm, 20µm, and 40µm, a higher infiltration of CTLs PD-1+, was observed in the group of recurrence than non-recurrence group, surrounding MCs PD-L1 negative (AUC 0.49, 3.80, and 20.03; vs AUC 0.01, 0.16, and 1.29, respectively), and MCs PD-L1 positive (AUC 0.60, 4.35, and 19.90; vs AUC 0.01, 0.20, and 2.20, respectively). A high infiltration of CTLs PD-1+ surrounding MCs, with or without expression of PD-L1, was associated with worse survival. All the differences were statistically significant (P<0.05).
Conclusion. Close spatial proximity of antigen-experienced CTLs and TAMs PD-L1+ to MCs are associated with recurrence and poor survival in early stages of NSCLC. We determined that ITH of immune cell densities is associated with recurrence of surgically resected NSCLC. Tumor-immune cell spatial modeling offers a deep understanding of tumor microenvironment that impacts on clinical outcomes. Supported by CPRITRP160668 and UT Lung SPORE grants
Citation Format: Alejandro Francisco-Cruz, Edwin R. Parra, Santhoshi N. Krishnan, Souptik Barua, Mei Jiang, Junya Fujimoto, Christine B. Peterson, Priyam Das, Chi-Wan Chow, Jaime Rodriguez-Canales, Carmen Behrens, Neda Kalhor, Annikka Weissferdt, John Heymach, Stephen Swisher, Boris Sepesi, Arvind Rao, J. Jack Lee, Cesar Moran, Andrew Futreal, Jianjun Zhang, Ignacio I. Wistuba. Impact of the spatial analysis of tumor-associated lymphocytes and tumor-associated macrophages on recurrence at early stage of non-small cell lung carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1180.
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Affiliation(s)
| | - Edwin R. Parra
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Mei Jiang
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Junya Fujimoto
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Priyam Das
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chi-Wan Chow
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Carmen Behrens
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Neda Kalhor
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - John Heymach
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Stephen Swisher
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Boris Sepesi
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Arvind Rao
- 3University of Michigan Ann Arbor, Ann Arbor, MI
| | - J. Jack Lee
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Cesar Moran
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Andrew Futreal
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianjun Zhang
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
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Barua S, Rhee J, Cho E, Qureshi A, Walker J. 537 Psychosocial burden of skin caner is associated with age and sex. J Invest Dermatol 2019. [DOI: 10.1016/j.jid.2019.03.613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Reddy SM, Reuben A, Barua S, Jiang H, Zhang S, Wang L, Gopalakrishnan V, Hudgens CW, Tetzlaff MT, Reuben JM, Tsujikawa T, Coussens LM, Wani K, He Y, Villareal L, Wood A, Rao A, Woodward WA, Ueno NT, Krishnamurthy S, Wargo JA, Mittendorf EA. Poor Response to Neoadjuvant Chemotherapy Correlates with Mast Cell Infiltration in Inflammatory Breast Cancer. Cancer Immunol Res 2019; 7:1025-1035. [PMID: 31043414 DOI: 10.1158/2326-6066.cir-18-0619] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/18/2018] [Accepted: 04/22/2019] [Indexed: 12/28/2022]
Abstract
Our understanding is limited concerning the tumor immune microenvironment of inflammatory breast cancer (IBC), an aggressive form of primary cancer with low rates of pathologic complete response to current neoadjuvant chemotherapy (NAC) regimens. We retrospectively identified pretreatment (N = 86) and matched posttreatment tissue (N = 27) from patients with stage III or de novo stage IV IBC who received NAC followed by a mastectomy. Immune profiling was performed including quantification of lymphoid and myeloid infiltrates by IHC and T-cell repertoire analysis. Thirty-four of 86 cases in this cohort (39.5%) achieved a pathologic complete response. Characterization of the tumor microenvironment revealed that having a lower pretreatment mast cell density was significantly associated with achieving a pathologic complete response to NAC (P = 0.004), with responders also having more stromal tumor-infiltrating lymphocytes (P = 0.035), CD8+ T cells (P = 0.047), and CD20+ B cells (P = 0.054). Spatial analysis showed close proximity of mast cells to CD8+ T cells, CD163+ monocytes/macrophages, and tumor cells when pathologic complete response was not achieved. PD-L1 positivity on tumor cells was found in fewer than 2% of cases and on immune cells in 27% of cases, but with no correlation to response. Our results highlight the strong association of mast cell infiltration with poor response to NAC, suggesting a mechanism of treatment resistance and a potential therapeutic target in IBC. Proximity of mast cells to immune and tumor cells may suggest immunosuppressive or tumor-promoting interactions of these mast cells.
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Affiliation(s)
- Sangeetha M Reddy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Alexandre Reuben
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Souptik Barua
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Hong Jiang
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shaojun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Courtney W Hudgens
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael T Tetzlaff
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - James M Reuben
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, Texas
| | - Takahiro Tsujikawa
- Department of Cell, Developmental, and Cancer Biology, Oregon Health and Science University, Portland, Oregon.,Department of Otolaryngology-Head and Neck Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Lisa M Coussens
- Department of Cell, Developmental, and Cancer Biology, Oregon Health and Science University, Portland, Oregon
| | - Khalida Wani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yan He
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lily Villareal
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, Texas
| | - Anita Wood
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, Texas
| | - Arvind Rao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan.,Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan
| | - Wendy A Woodward
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, Texas.,Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Naoto T Ueno
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. .,Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, Texas
| | - Savitri Krishnamurthy
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, Texas. .,Department of Breast Surgical Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. .,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elizabeth A Mittendorf
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. .,Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts.,Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts
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Aung PP, Parra ER, Barua S, Sui D, Ning J, Mino B, Ledesma DA, Curry JL, Nagarajan P, Torres-Cabala CA, Efstathiou E, Hoang AG, Wong MK, Wargo JA, Lazar AJ, Rao A, Prieto VG, Wistuba I, Tetzlaff MT. B7-H3 Expression in Merkel Cell Carcinoma-Associated Endothelial Cells Correlates with Locally Aggressive Primary Tumor Features and Increased Vascular Density. Clin Cancer Res 2019; 25:3455-3467. [PMID: 30808776 DOI: 10.1158/1078-0432.ccr-18-2355] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 12/04/2018] [Accepted: 02/22/2019] [Indexed: 12/19/2022]
Abstract
PURPOSE Merkel cell carcinoma (MCC) is an aggressive cutaneous malignancy whose pathogenesis and prognosis are related to the integrity of the host immune system. Despite promising clinical responses to immune-checkpoint blockade, response and resistance remain unpredictable, underscoring a critical need to delineate novel prognostic biomarkers and/or therapeutic targets for this disease.Experimental Design: Expression of immune-regulatory markers (PD-L2, B7-H3, B7-H4, IDO-1, ICOS, TIM3, LAG3, VISTA, and OX-40) was assessed using singlet chromogenic IHC in 10 primary MCCs. Multiplex immunofluorescence quantified CD31 and B7-H3 expression in 52 primary and 25 metastatic MCCs. B7-H3 and CD31 expressions were tabulated as a series of independent (X,Y) cell centroids. A spatial G-function, calculated based on the distribution of distances of B7-H3+ (X,Y) cell centroids around the CD31+ (X,Y) cell centroids, was used to estimate a colocalization index equivalent to the percentage of CD31-positive cell centroids that overlap with a B7-H3-positive cell centroid. RESULTS Primary and metastatic MCCs exhibit a dynamic range of colocalized CD31 and B7-H3 expression. Increasing colocalized expression of B7-H3 with CD31 significantly associated with increased tumor size (P = 0.0060), greater depth of invasion (P = 0.0110), presence of lymphovascular invasion (P = 0.0453), and invasion beyond skin (P = 0.0428) in primary MCC. Consistent with these findings, increasing colocalized expression of B7-H3 and CD31 correlated with increasing vascular density in primary MCC, but not metastatic MCC. CONCLUSIONS Our results demonstrate that colocalized expression of B7-H3/CD31 is a poor prognostic indicator and suggest therapies targeting B7-H3 may represent an effective approach to augmenting immune-activating therapies for MCC.
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Affiliation(s)
- Phyu P Aung
- Department of Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Edwin Roger Parra
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Souptik Barua
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas
| | - Dawen Sui
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jing Ning
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Barbara Mino
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Debora Alejandra Ledesma
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jonathan L Curry
- Department of Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Carlos A Torres-Cabala
- Department of Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Eleni Efstathiou
- Department of Genitourinary Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anh G Hoang
- Department of Genitourinary Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael K Wong
- Department of Melanoma Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jennifer A Wargo
- Department of Surgical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexander J Lazar
- Department of Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Arvind Rao
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas.,Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Victor G Prieto
- Department of Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio Wistuba
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael T Tetzlaff
- Department of Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas. .,Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas
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Chandru P, Barua S, Dennis M, Eslick A, Kruit N, Coggins A. A Prospective 3-Year Review of out of Hospital Cardiac Arrest Presentations to a University-Affiliated Tertiary Centre. Heart Lung Circ 2019. [DOI: 10.1016/j.hlc.2019.06.151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Elhalawani H, Volpe S, Cardenas C, Barua S, Rock C, Lin T, Yang P, Wu H, Zaveri J, Elgohari B, Abdallah L, Jethanandani A, Mohamed A, Hutcheson K, Gunn G, Rosenthal D, Frank S, Garden A, Rao A, Fuller C. Development of Temporal Dose-Weighted Positron Emission Tomography Metabolic Imaging Biomarkers (PET MIBs) of Radiation-Related Parotid Glands Injury in Oropharyngeal Cancer Patients. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Barua S, Solis L, Parra ER, Uraoka N, Jiang M, Wang H, Rodriguez-Canales J, Wistuba I, Maitra A, Sen S, Rao A. A Functional Spatial Analysis Platform for Discovery of Immunological Interactions Predictive of Low-Grade to High-Grade Transition of Pancreatic Intraductal Papillary Mucinous Neoplasms. Cancer Inform 2018; 17:1176935118782880. [PMID: 30013304 PMCID: PMC6043922 DOI: 10.1177/1176935118782880] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/11/2018] [Indexed: 01/20/2023] Open
Abstract
Intraductal papillary mucinous neoplasms (IPMNs), critical precursors of the devastating tumor pancreatic ductal adenocarcinoma (PDAC), are poorly understood in the pancreatic cancer community. Researchers have shown that IPMN patients with high-grade dysplasia have a greater risk of subsequent development of PDAC in the remnant pancreas than do patients with low-grade dysplasia. In this study, we built a computational prediction model that encapsulates the spatial cellular interactions in IPMNs that play key roles in the transformation of low-grade IPMN cysts to high-grade cysts en route to PDAC. Using multiplex immunofluorescent images of IPMN cysts, we adopted algorithms from spatial statistics and functional data analysis to create metrics that summarize the spatial interactions in IPMNs. We showed that an ensemble of models learned using these spatial metrics can robustly predict, with high accuracy, (1) the dysplasia grade (low vs high grade) and (2) the risk of a low-grade cyst progressing to a high-grade cyst. We obtained high classification accuracies on both tasks, with areas under the curve of 0.81 (95% confidence interval: 0.71-0.9) for task 1 and 0.81 (95% confidence interval: 0.7-0.94) for task 2. To the best of our knowledge, this is the first application of an ensemble machine learning approach for discovering critical cellular spatial interactions in IPMNs using imaging data. We envision that our work can be used as a risk assessment tool for patients diagnosed with IPMNs and facilitate greater understanding and investigation of the cellular interactions that cause transition of IPMNs to PDAC.
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Affiliation(s)
- Souptik Barua
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Luisa Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edwin Roger Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Naohiro Uraoka
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mei Jiang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Huamin Wang
- Department of Anatomical Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaime Rodriguez-Canales
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anirban Maitra
- Department of Anatomical Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Subrata Sen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Arvind Rao
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
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Barua S, Saikia N. 2.1-O4Explaining the religious disparity and associated risk factors of diabetes in Southern India. Eur J Public Health 2018. [DOI: 10.1093/eurpub/cky047.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- S Barua
- Jawaharlal Nehru University, New Delhi, India
| | - N Saikia
- Jawaharlal Nehru University, New Delhi, India
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Elhalawani H, Volpe S, Barua S, Mohamed A, Yang P, Ng S, Lai S, Hutcheson K, Gunn G, Court L, Rao A, Fuller C. Exploration of an Early Imaging Biomarker of Osteoradionecrosis in Oropharyngeal Cancer Patients: Case-Control Study of the Temporal Changes of Mandibular Radiomics Features. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2017.12.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Barua S, Fang P, Sharma A, Fujimoto J, Wistuba I, Rao AUK, Lin SH. Spatial interaction of tumor cells and regulatory T cells correlates with survival in non-small cell lung cancer. Lung Cancer 2018; 117:73-79. [PMID: 29409671 PMCID: PMC6294443 DOI: 10.1016/j.lungcan.2018.01.022] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/14/2018] [Accepted: 01/29/2018] [Indexed: 12/18/2022]
Abstract
OBJECTIVES To determine the prognostic significance of spatial proximity of lung cancer cells and specific immune cells in the tumor microenvironment. MATERIALS AND METHODS We probed formalin-fixed, paraffin-embedded (FFPE) tissue microarrays using a novel tyramide signal amplification multiplexing technique labelling CD8, CD4, Foxp3, and CD68+ cells. Each multiplex stained immunohistochemistry slide was digitally processed by Vectra INFORMS software, and an X- and Y-coordinate assigned to each labeled cell type. The abundance and spatial location of each cell type and their proximity to one another was analyzed using a novel application of the G-cross spatial distance distribution method which computes the probability of finding at least one immune cell of any given type within a rμm radius of a tumor cell. Cox proportional hazards multiple regression was used for multivariate analysis of the influence of proximity of lymphocyte types. RESULTS Pathologic tumor specimens from 120 NSCLC patients with pathologic tumor stage I-III disease were analyzed. On univariate analysis, age (P = .0007) and number of positive nodes (P = .0014) were associated with overall survival. Greater area under the curve (AUC) of the G-cross function for tumor cell-Treg interactions was significantly associated with worse survival adjusting for age and number of positive nodes (HR 1.52 (1.11-2.07), P = .009). Greater G-cross AUC for T-reg-CD8 was significantly associated with better survival adjusting for age and number of positive lymph nodes (HR 0.96 (0.92-0.99), P = .042). CONCLUSION Increased infiltration of regulatory T cells into core tumor regions is an independent predictor of worse overall survival in NSCLC. However, increased infiltration of CD8+ cytotoxic T cells among regulatory T cells seems to mitigate this effect and was significantly associated with better survival. Validation of the G-cross method of measuring spatial proximity between tumor and immune cell types and exploration of its use as a prognostic factor in lung cancer treatment is warranted.
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Affiliation(s)
- Souptik Barua
- Department of Electrical Engineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA; Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Penny Fang
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Amrish Sharma
- Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center,1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Junya Fujimoto
- Molecular Pathology, The University of Texas MD Anderson Cancer Center,1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Ignacio Wistuba
- Molecular Pathology, The University of Texas MD Anderson Cancer Center,1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Arvind U K Rao
- Department of Electrical Engineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA; Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA; Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.
| | - Steven H Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA; Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center,1515 Holcombe Boulevard, Houston, TX, 77030, USA.
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Reddy SM, Reuben A, Jiang H, Roszik J, Tetzlaff MT, Reuben J, Wang L, Tsujikawa T, Barua S, Rao A, Villareal L, Wood A, Woodward W, Ueno NT, Krishnamurthy S, Wargo JA, Mittendorf EA. Abstract P3-05-08: Lymphoid and myeloid cell characterization of inflammatory breast cancer tumor microenvironment and correlation to pathological complete response. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p3-05-08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Inflammatory breast cancer (IBC) is an aggressive form of breast cancer with poor response rates to current chemotherapy regimens. With recent successes of immune targeted therapies in other solid tumors and a growing understanding of how the immune tumor microenvironment (TME) affects non-IBC outcomes, we sought to characterize the immune TME in IBC to identify biomarkers of treatment response and potential targets for drug development.
Methods: Pre-treatment core biopsy samples were identified from the MD Anderson Cancer Center IBC tissue bank from patients with stage III and de novo stage IV (with T4d) disease who received neoadjuvant chemotherapy (NAC) with intent to take to mastectomy. Lymphocytes were characterized by stromal tumor infiltrating lymphocyte (sTIL) quantification, CD8 T cell quantification, and T cell receptor sequencing. PD-L1 expression was assessed using DAKO 22C3 clone on tumor and immune cells. Myeloid cells were characterized using a multiplex immunohistochemistry approach, using CD68 and CD163 for macrophage markers, tryptase for mast cell marker, HLA-DR for class II antigen presentation marker, and cytokeratin as tumor marker. Spatial analyses were performed by determining probabilities of finding cell 1 of interest within 20 uM of cell 2 of interest and computing area under the curve for statistical comparison.
Results: 91 patients with stage III (N=62) or de novo stage IV (n=29) disease were identified. Breast cancer subtype included 25 triple negative, 34 HER2+ and 32 HER2-HR+. 86 patients received a mastectomy, of whom 33 (38.4%) patients experienced a pathologic complete response (pCR). sTIL was higher in stage III tumors (11.9 vs 4.8%, p<0.001) and in those having a pCR (13.8 vs 7.3%, p=0.019). CD8 T cell density (available in 48 cases) similarly was higher in stage III patients (360.3 vs 178.8 counts/mm2, p=0.040) and pCR cases (452.3 vs 219.2 counts/mm2, p=0.080) but also higher in HER2+ disease (560.9 for HER2+ vs 239.9 counts/mm2, p=0.087 for TNBC and 153.6 counts/mm2, p=0.005 for HER2-HR+). T cell clonality (available in 32 cases) ranged from 0.004 to 0.242 but showed no correlation to tumor characteristics or response. PD-L1 complete tumor membranous expression was seen in only 1 of 47 cases, whereas PD-L1 positivity on immune cells was seen on 36.2% of cases; neither correlated to response. Myeloid cell assessment (available in 25 cases) showed higher mast cell infiltration in non-pCR cases (63.8 vs 26.8 counts/mm2, p=0.008) and spatial analysis (performed on 10 cases) identified that closer proximity of mast cells to CD8 T cells correlates with response (AUC 6.0 vs 2.2, p=0.017), suggesting a possible immunosuppressive mechanism. HLA-DR analysis demonstrated no difference by response as a single stain marker, but co-localization of HLA-DR with cell type shows higher HLA-DR expression on tumor cells in non-responders (14.6 vs 1.6%, p=0.031).
Conclusions: Higher TIL and CD8 T cell density are correlated with improved responses to NAC in IBC. Mast cell infiltration and HLA-DR expression on tumor cells are inversely correlated to response and suggest possible mechanisms of resistance. Mast cells could present potential therapeutic target in IBC.
Citation Format: Reddy SM, Reuben A, Jiang H, Roszik J, Tetzlaff MT, Reuben J, Wang L, Tsujikawa T, Barua S, Rao A, Villareal L, Wood A, Woodward W, Ueno NT, Krishnamurthy S, Wargo JA, Mittendorf EA. Lymphoid and myeloid cell characterization of inflammatory breast cancer tumor microenvironment and correlation to pathological complete response [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-05-08.
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Affiliation(s)
- SM Reddy
- The University of Texas MD Anderson Cancer Center, Houston, TX; Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, TX; Oregon Health and Sciences University, Portland, OR; Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - A Reuben
- The University of Texas MD Anderson Cancer Center, Houston, TX; Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, TX; Oregon Health and Sciences University, Portland, OR; Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - H Jiang
- The University of Texas MD Anderson Cancer Center, Houston, TX; Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, TX; Oregon Health and Sciences University, Portland, OR; Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - J Roszik
- The University of Texas MD Anderson Cancer Center, Houston, TX; Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, TX; Oregon Health and Sciences University, Portland, OR; Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - MT Tetzlaff
- The University of Texas MD Anderson Cancer Center, Houston, TX; Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, TX; Oregon Health and Sciences University, Portland, OR; Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - J Reuben
- The University of Texas MD Anderson Cancer Center, Houston, TX; Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, TX; Oregon Health and Sciences University, Portland, OR; Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - L Wang
- The University of Texas MD Anderson Cancer Center, Houston, TX; Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, TX; Oregon Health and Sciences University, Portland, OR; Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - T Tsujikawa
- The University of Texas MD Anderson Cancer Center, Houston, TX; Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, TX; Oregon Health and Sciences University, Portland, OR; Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - S Barua
- The University of Texas MD Anderson Cancer Center, Houston, TX; Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, TX; Oregon Health and Sciences University, Portland, OR; Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - A Rao
- The University of Texas MD Anderson Cancer Center, Houston, TX; Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, TX; Oregon Health and Sciences University, Portland, OR; Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - L Villareal
- The University of Texas MD Anderson Cancer Center, Houston, TX; Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, TX; Oregon Health and Sciences University, Portland, OR; Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - A Wood
- The University of Texas MD Anderson Cancer Center, Houston, TX; Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, TX; Oregon Health and Sciences University, Portland, OR; Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - W Woodward
- The University of Texas MD Anderson Cancer Center, Houston, TX; Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, TX; Oregon Health and Sciences University, Portland, OR; Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - NT Ueno
- The University of Texas MD Anderson Cancer Center, Houston, TX; Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, TX; Oregon Health and Sciences University, Portland, OR; Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - S Krishnamurthy
- The University of Texas MD Anderson Cancer Center, Houston, TX; Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, TX; Oregon Health and Sciences University, Portland, OR; Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - JA Wargo
- The University of Texas MD Anderson Cancer Center, Houston, TX; Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, TX; Oregon Health and Sciences University, Portland, OR; Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - EA Mittendorf
- The University of Texas MD Anderson Cancer Center, Houston, TX; Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Houston, TX; Oregon Health and Sciences University, Portland, OR; Kyoto Prefectural University of Medicine, Kyoto, Japan
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Barik SK, Tiwari ON, Adhikari D, Singh PP, Tiwary R, Barua S. Geographic Distribution Pattern of Threatened Plants of India and Steps Taken for their Conservation. CURR SCI INDIA 2018. [DOI: 10.18520/cs/v114/i03/470-503] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Barua S, Macedo A, Kolb DS, Wynne-Edwards KE, Klein C. Milk-fat globule epidermal growth factor 8 (MFGE8) is expressed at the embryo– and fetal–maternal interface in equine pregnancy. Reprod Fertil Dev 2018; 30:585-590. [DOI: 10.1071/rd17094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 08/14/2017] [Indexed: 01/18/2023] Open
Abstract
Milk-fat globule epidermal growth factor (EGF) 8 protein (MFGE8), also known as lactadherin, promotes cell adhesion in an Arg-Gly-Asp (RGD)-dependent modus via integrins. In the present study, the expression of MFGE8 was examined in equine endometrium during oestrus and at Days 12 and 16 after ovulation in pregnant and non-pregnant mares and in mares during the 5th month of gestation. Results demonstrated that MFGE8 is expressed at the embryo– and fetal–maternal interface in equine pregnancy. In non-pregnant endometrium its expression was upregulated by oestrogen, a finding that was confirmed using endometrial explant culture. MFGE8 was expressed at similar levels by conceptuses collected 13 and 14 days after ovulation and by allantochorion sampled during the 5th month of gestation. Pericytes of endometrial blood vessels displayed strong MFGE8 expression upon in situ hybridisation. During the 5th month of gestation, the fetal side of the allantochorionic villi in particular displayed pronounced staining upon in situ hybridisation, confirming that MFGE8 expression is not restricted to early pregnancy but persists and is present at the fetal–maternal interface. Potential roles of MFGE8 in equine pregnancy include mediating cell–cell adhesion, promotion of angiogenesis and placental transfer of fatty acids.
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Barua S, Sivagangabalan G, Denniss A, Thomas S, Ross D, Chik W, Davis L. Characteristics of Patients with Cardiac Implantable Electronic Device Infection. Heart Lung Circ 2018. [DOI: 10.1016/j.hlc.2018.06.252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Affiliation(s)
- N.C. Sarkar
- Anthropological Survey of India , Shillong, 793 001, Meghalaya, India
| | - S. Barua
- Anthropological Survey of India, Indian Museum , Calcutta, 700 016, West Bengal, India
| | - R. Th. Varte
- Anthropological Survey of India , Shillong, 793 001, Meghalaya, India
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Knappett PSK, Mailloux BJ, Choudhury I, Khan MR, Michael HA, Barua S, Mondal DR, Steckler MS, Akhter SH, Ahmed KM, Bostick B, Harvey CF, Shamsudduha M, Shuai P, Mihajlov I, Mozumder R, van Geen A. VULNERABILITY OF LOW-ARSENIC AQUIFERS TO MUNICIPAL PUMPING IN BANGLADESH. J Hydrol (Amst) 2016; 539:674-686. [PMID: 28966395 PMCID: PMC5617134 DOI: 10.1016/j.jhydrol.2016.05.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Sandy aquifers deposited >12,000 years ago, some as shallow as 30 m, have provided a reliable supply of low-arsenic (As) drinking water in rural Bangladesh. This study concerns the potential risk of contaminating these aquifers in areas surrounding the city of Dhaka where hydraulic heads in aquifers >150 m deep have dropped by 70 m in a few decades due to municipal pumping. Water levels measured continuously from 2012 to 2014 in 12 deep (>150m), 3 intermediate (90-150 m) and 6 shallow (<90 m) community wells, 1 shallow private well, and 1 river piezometer show that the resulting drawdown cone extends 15-35 km east of Dhaka. Water levels in 4 low-As community wells within the 62-147 m depth range closest to Dhaka were inaccessible by suction for up to a third of the year. Lateral hydraulic gradients in the deep aquifer system ranged from 1.7×10-4 to 3.7×10-4 indicating flow towards Dhaka throughout 2012-2014. Vertical recharge on the edge of the drawdown cone was estimated at 0.21±0.06 m/yr. The data suggest that continued municipal pumping in Dhaka could eventually contaminate some relatively shallow community wells.
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Affiliation(s)
- P. S. K. Knappett
- Lamont-Doherty Earth Observatory of Columbia University, Palisades, NY 10964
- Department of Geology and Geophysics, Texas A&M University, College Station, TX 77843
| | - B. J. Mailloux
- Department of Environmental Science, Barnard College, New York, NY 10027
| | - I. Choudhury
- Department of Geology, University of Dhaka, Dhaka 1000, Bangladesh
| | - M. R. Khan
- Department of Geological Sciences, University of Delaware, Newark, DE 19716
| | - H. A. Michael
- Department of Civil and Environmental Engineering, University of Delaware, Newark, DE 19716
| | - S. Barua
- Department of Geology, Kansas State University, Manhattan, KS 66506
| | - D. R. Mondal
- School of Earth & Environmental Sciences, Queens College, Queens, NY 11367
| | - M. S. Steckler
- Lamont-Doherty Earth Observatory of Columbia University, Palisades, NY 10964
| | - S. H. Akhter
- Department of Geology, University of Dhaka, Dhaka 1000, Bangladesh
| | - K. M. Ahmed
- Department of Geology, University of Dhaka, Dhaka 1000, Bangladesh
| | - B. Bostick
- Lamont-Doherty Earth Observatory of Columbia University, Palisades, NY 10964
| | - C. F. Harvey
- Department of Civil & Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - M. Shamsudduha
- Institute for Risk & Disaster Reduction, University College London, London WC1E 6BT, UK
| | - P. Shuai
- Department of Geology and Geophysics, Texas A&M University, College Station, TX 77843
| | - I. Mihajlov
- Lamont-Doherty Earth Observatory of Columbia University, Palisades, NY 10964
| | - R. Mozumder
- Lamont-Doherty Earth Observatory of Columbia University, Palisades, NY 10964
| | - A. van Geen
- Lamont-Doherty Earth Observatory of Columbia University, Palisades, NY 10964
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Sankar MS, Vega MA, Defoe PP, Kibria MG, Ford S, Telfeyan K, Neal A, Mohajerin TJ, Hettiarachchi GM, Barua S, Hobson C, Johannesson K, Datta S. Elevated arsenic and manganese in groundwaters of Murshidabad, West Bengal, India. Sci Total Environ 2014; 488-489:570-9. [PMID: 24694939 DOI: 10.1016/j.scitotenv.2014.02.077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Revised: 02/14/2014] [Accepted: 02/14/2014] [Indexed: 05/02/2023]
Abstract
High levels of geogenic arsenic (As) and manganese (Mn) in drinking water has led to widespread health problems for the population of West Bengal, India. Here we delineate the extent of occurrences of As and Mn in Murshidabad, where the contaminated aquifers occur at shallow depths between 35 and 40 m and where access to safe drinking water is a critical issue for the local population. A total of 78 well-water samples were taken in 4 blocks on either side of the river Bhagirathi: Nabagram and Kandi (west, Pleistocene sediments), Hariharpara and Beldanga (east, Holocene sediments). High As, total iron (FeT) and low Mn concentrations were found in waters from the Holocene gray sediment aquifers east of the river Bhagirathi, while the opposite was found in the Pleistocene reddish-brown aquifer west of the river Bhagirathi in Murshidabad. Speciation of As in water samples from Holocene sediments revealed the dominant species to be As(III), with ratios of As(III):AsT ranging from 0.55 to 0.98 (average 0.74). There were indications from saturation index estimations that Mn solubility is limited by the precipitation of MnCO3. Tubewells from high As areas in proximity to anthropogenic waste influx sources showing high molar Cl/Br ratios, low SO4(2-) and low NO3(-) demonstrate relatively lower As concentrations, thereby reducing As pollution in those wells. Analyses of core samples (2 in each of the blocks) drilled to a depth of 45 m indicate that there is no significant variation in bulk As (5-20mg/kg) between the Holocene and Pleistocene sediments, indicating that favorable subsurface redox conditions conducive to mobilization are responsible for the release of As. The same applies to Mn, but concentrations vary more widely (20-2000 mg/kg). Sequential extraction of Holocene sediments showed As to be associated with 'specifically sorbed-phosphate-extractable' phases (10-15%) and with 'amorphous and well crystalline Fe-oxyhydroxide' phases (around 37%) at As-contaminated well depths, suggesting that the main As release mechanisms could be either competitive ion exchange with PO4(3-), or the dissolution of Fe oxyhydroxides. In the Pleistocene sediments Mn is predominantly found in the easily exchangeable fraction.
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Affiliation(s)
- M S Sankar
- Department of Geology, Kansas State University, Manhattan, KS 66506, USA
| | - M A Vega
- Department of Geology, Kansas State University, Manhattan, KS 66506, USA
| | - P P Defoe
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - M G Kibria
- Department of Geology, Kansas State University, Manhattan, KS 66506, USA
| | - S Ford
- Department of Geology, Kansas State University, Manhattan, KS 66506, USA
| | - K Telfeyan
- Department of Earth and Environmental Sciences, Tulane University, New Orleans 70118, USA
| | - A Neal
- Virginia Water Resources Research Center, Virginia Tech, VA 24061, USA
| | - T J Mohajerin
- Department of Earth and Environmental Sciences, Tulane University, New Orleans 70118, USA
| | - G M Hettiarachchi
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - S Barua
- Department of Geology, Kansas State University, Manhattan, KS 66506, USA
| | - C Hobson
- Department of Geology, Kansas State University, Manhattan, KS 66506, USA
| | - K Johannesson
- Department of Earth and Environmental Sciences, Tulane University, New Orleans 70118, USA
| | - S Datta
- Department of Geology, Kansas State University, Manhattan, KS 66506, USA.
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Barbosa J, Barua S, Daumerie D, Nakatani H, Noordeen S, Castália R. J Barbosa and colleagues reply to Diana N J Lockwood and colleagues. BMJ 2014; 348:g2114. [PMID: 24647166 DOI: 10.1136/bmj.g2114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- J Barbosa
- Ministério da Saúde, Brasilia, Brazil
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Bera BC, Virmani N, Shanmugasundaram K, Vaid RK, Singh BK, Gulati BR, Anand T, Barua S, Malik P, Singh RK. Genetic Analysis of the Neuraminidase (NA) Gene of Equine Influenza Virus (H3N8) from Epizootic of 2008-2009 in India. Indian J Virol 2013; 24:256-64. [PMID: 24426284 DOI: 10.1007/s13337-013-0137-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Accepted: 05/02/2013] [Indexed: 11/27/2022]
Abstract
The neuraminidase (NA) gene sequences of four Indian equine influenza viruses (EIVs) isolated from epizootic in 2008 and 2009 were analyzed. The phylogenetic relationship and selection pressure of NA genes were established in comparison to other EIVs circulating worldwide along with the domains and motifs of the encoded protein to find out the significance of mutational changes. Among Indian isolates, two amino acid (aa) changes each in Mysore/12/08 (Asn67Tyr & Asp396Gly), Gopeshwar/1/09 (Ile49Val & Asp396Gly), and Uttarkashi/1/09 (Ile49Val & Asp396Gly) isolates were observed in respect to Jammu-Katra/06/08 isolate. Amino acid (aa) sequence analysis also revealed five consistent aa residue changes viz, Gly/Arg40Glu, Tyr66His, Val191Ile, Val209Ile and Asp235Asn in Asian including Indian isolates, Spain/07 and Spain/09 isolates in comparison to other EIVs circulating worldwide. The topology of the phylogenetic tree revealed that the Indian, Chinese, Mongolian and Kazakhstan isolates together formed a subgroup with Yokohama/10 isolate. Spain/07 & Spain/09 isolates showed closest clustering with Asian isolates. This indicates that non-synonymous mutations in Asian isolates with temporal pattern originating from Spain/07, led to the subgroup of the Asian isolates within Florida clade 2 sublineage. The analysis of the predicted secondary structure has not shown any significant difference in the NA proteins of all Indian isolates. Fixed-effects likelihood (FEL) analysis of the selection pressure revealed three codons (43, 355 & 434) under positive selection pressure. The overall evolutionary changes (ω value) of 3.4 indicates NA gene to be under strong selection pressure. Further, seven putative N-glycosylation sites were observed in the NA protein. The mapping of specific aa changes, their mutational and functional analysis need to be carried out to ascertain their role in pathogenecity of the virus.
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Affiliation(s)
- B C Bera
- National Research Centre on Equines, Sirsa Road, Hisar, 125001 Haryana India
| | - N Virmani
- National Research Centre on Equines, Sirsa Road, Hisar, 125001 Haryana India
| | - K Shanmugasundaram
- National Research Centre on Equines, Sirsa Road, Hisar, 125001 Haryana India
| | - R K Vaid
- National Research Centre on Equines, Sirsa Road, Hisar, 125001 Haryana India
| | - B K Singh
- National Research Centre on Equines, Sirsa Road, Hisar, 125001 Haryana India
| | - B R Gulati
- National Research Centre on Equines, Sirsa Road, Hisar, 125001 Haryana India
| | - T Anand
- National Research Centre on Equines, Sirsa Road, Hisar, 125001 Haryana India
| | - S Barua
- National Research Centre on Equines, Sirsa Road, Hisar, 125001 Haryana India
| | - P Malik
- National Research Centre on Equines, Sirsa Road, Hisar, 125001 Haryana India
| | - R K Singh
- National Research Centre on Equines, Sirsa Road, Hisar, 125001 Haryana India
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