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Sepich-Poore GD, McDonald D, Kopylova E, Guccione C, Zhu Q, Austin G, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf JL, Song SJ, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Korem T, Knight R. Correction: Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene 2024:10.1038/s41388-024-03018-z. [PMID: 38580705 DOI: 10.1038/s41388-024-03018-z] [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: 04/07/2024]
Affiliation(s)
- Gregory D Sepich-Poore
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Clarity Genomics, Antwerp, Belgium
| | - Caitlin Guccione
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - George Austin
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Carolina Carpenter
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Serena Fraraccio
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
| | - Stephen Wandro
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Malopolska Centre of Biotechnology, Jagiellonian University in Kraków, Kraków, Poland
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Algorithmic Bioinformatics, Department of Biology and Chemistry, Justus Liebig University Gießen, Gießen, Germany
| | - Jessica L Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Jad Kanbar
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sandrine Miller-Montgomery
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
| | - Robert Heaton
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Rana Mckay
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Sandip Pravin Patel
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
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Sepich-Poore GD, McDonald D, Kopylova E, Guccione C, Zhu Q, Austin G, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf JL, Song SJ, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Korem T, Knight R. Robustness of cancer microbiome signals over a broad range of methodological variation. Oncogene 2024; 43:1127-1148. [PMID: 38396294 PMCID: PMC10997506 DOI: 10.1038/s41388-024-02974-w] [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: 11/23/2023] [Revised: 02/03/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024]
Abstract
In 2020, we identified cancer-specific microbial signals in The Cancer Genome Atlas (TCGA) [1]. Multiple peer-reviewed papers independently verified or extended our findings [2-12]. Given this impact, we carefully considered concerns by Gihawi et al. [13] that batch correction and database contamination with host sequences artificially created the appearance of cancer type-specific microbiomes. (1) We tested batch correction by comparing raw and Voom-SNM-corrected data per-batch, finding predictive equivalence and significantly similar features. We found consistent results with a modern microbiome-specific method (ConQuR [14]), and when restricting to taxa found in an independent, highly-decontaminated cohort. (2) Using Conterminator [15], we found low levels of human contamination in our original databases (~1% of genomes). We demonstrated that the increased detection of human reads in Gihawi et al. [13] was due to using a newer human genome reference. (3) We developed Exhaustive, a method twice as sensitive as Conterminator, to clean RefSeq. We comprehensively host-deplete TCGA with many human (pan)genome references. We repeated all analyses with this and the Gihawi et al. [13] pipeline, and found cancer type-specific microbiomes. These extensive re-analyses and updated methods validate our original conclusion that cancer type-specific microbial signatures exist in TCGA, and show they are robust to methodology.
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Affiliation(s)
- Gregory D Sepich-Poore
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Evguenia Kopylova
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Clarity Genomics, Antwerp, Belgium
| | - Caitlin Guccione
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - George Austin
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Carolina Carpenter
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Serena Fraraccio
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
| | - Stephen Wandro
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Malopolska Centre of Biotechnology, Jagiellonian University in Kraków, Kraków, Poland
| | - Stefan Janssen
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Algorithmic Bioinformatics, Department of Biology and Chemistry, Justus Liebig University Gießen, Gießen, Germany
| | - Jessica L Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Jad Kanbar
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sandrine Miller-Montgomery
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Micronoma, San Diego, CA, USA
| | - Robert Heaton
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Rana Mckay
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Sandip Pravin Patel
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego Health, La Jolla, CA, USA
| | - Austin D Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
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Chapman OS, Luebeck J, Sridhar S, Wong ITL, Dixit D, Wang S, Prasad G, Rajkumar U, Pagadala MS, Larson JD, He BJ, Hung KL, Lange JT, Dehkordi SR, Chandran S, Adam M, Morgan L, Wani S, Tiwari A, Guccione C, Lin Y, Dutta A, Lo YY, Juarez E, Robinson JT, Korshunov A, Michaels JEA, Cho YJ, Malicki DM, Coufal NG, Levy ML, Hobbs C, Scheuermann RH, Crawford JR, Pomeroy SL, Rich JN, Zhang X, Chang HY, Dixon JR, Bagchi A, Deshpande AJ, Carter H, Fraenkel E, Mischel PS, Wechsler-Reya RJ, Bafna V, Mesirov JP, Chavez L. Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma. Nat Genet 2023; 55:2189-2199. [PMID: 37945900 PMCID: PMC10703696 DOI: 10.1038/s41588-023-01551-3] [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: 06/01/2022] [Accepted: 09/22/2023] [Indexed: 11/12/2023]
Abstract
Circular extrachromosomal DNA (ecDNA) in patient tumors is an important driver of oncogenic gene expression, evolution of drug resistance and poor patient outcomes. Applying computational methods for the detection and reconstruction of ecDNA across a retrospective cohort of 481 medulloblastoma tumors from 465 patients, we identify circular ecDNA in 82 patients (18%). Patients with ecDNA-positive medulloblastoma were more than twice as likely to relapse and three times as likely to die within 5 years of diagnosis. A subset of tumors harbored multiple ecDNA lineages, each containing distinct amplified oncogenes. Multimodal sequencing, imaging and CRISPR inhibition experiments in medulloblastoma models reveal intratumoral heterogeneity of ecDNA copy number per cell and frequent putative 'enhancer rewiring' events on ecDNA. This study reveals the frequency and diversity of ecDNA in medulloblastoma, stratified into molecular subgroups, and suggests copy number heterogeneity and enhancer rewiring as oncogenic features of ecDNA.
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Affiliation(s)
- Owen S Chapman
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, San Diego, CA, USA
- Department of Medicine, University of California San Diego, San Diego, CA, USA
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Jens Luebeck
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, San Diego, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Sunita Sridhar
- Department of Medicine, University of California San Diego, San Diego, CA, USA
- Department of Pediatrics, UC San Diego and Rady Children's Hospital, San Diego, CA, USA
| | - Ivy Tsz-Lo Wong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Deobrat Dixit
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
- Department of Neurology and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Shanqing Wang
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Gino Prasad
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Utkrisht Rajkumar
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Meghana S Pagadala
- Medical Scientist Training Program, University of California San Diego, San Diego, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, San Diego, CA, USA
| | - Jon D Larson
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Britney Jiayu He
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - King L Hung
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Joshua T Lange
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Siavash R Dehkordi
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | | | - Miriam Adam
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ling Morgan
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Sameena Wani
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Ashutosh Tiwari
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | - Caitlin Guccione
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, San Diego, CA, USA
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Yingxi Lin
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Aditi Dutta
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Yan Yuen Lo
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital and Healthcare Center, San Diego, CA, USA
| | - Edwin Juarez
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - James T Robinson
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Andrey Korshunov
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 280, Heidelberg, Germany
| | - John-Edward A Michaels
- Papé Pediatric Research Institute, Department of Pediatrics and Knight Cancer Insitute, Oregon Health and Sciences University, Portland, OR, USA
| | - Yoon-Jae Cho
- Papé Pediatric Research Institute, Department of Pediatrics and Knight Cancer Insitute, Oregon Health and Sciences University, Portland, OR, USA
| | - Denise M Malicki
- Division of Pathology, UC San Diego and Rady Children's Hospital, San Diego, CA, USA
| | - Nicole G Coufal
- Department of Pediatrics, UC San Diego and Rady Children's Hospital, San Diego, CA, USA
| | - Michael L Levy
- Division of Pathology, UC San Diego and Rady Children's Hospital, San Diego, CA, USA
| | - Charlotte Hobbs
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital and Healthcare Center, San Diego, CA, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pathology, University of California San Diego, San Diego, CA, USA
| | - John R Crawford
- Department of Pediatrics, University of California Irvine and Children's Hospital Orange County, Irvine, CA, USA
| | - Scott L Pomeroy
- Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jeremy N Rich
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xinlian Zhang
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, San Diego, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jesse R Dixon
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Anindya Bagchi
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
| | | | - Hannah Carter
- Department of Medicine, University of California San Diego, San Diego, CA, USA
- Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paul S Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Robert J Wechsler-Reya
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA
- Department of Neurology and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
- Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Jill P Mesirov
- Department of Medicine, University of California San Diego, San Diego, CA, USA
- Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Lukas Chavez
- Department of Medicine, University of California San Diego, San Diego, CA, USA.
- Sanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA.
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital and Healthcare Center, San Diego, CA, USA.
- Moores Cancer Center, University of California San Diego, San Diego, CA, USA.
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Guccione C, McDonald D, Fielding-Miller R, Curtius K, Knight R. You are what you excrete. Nat Microbiol 2023; 8:1002-1003. [PMID: 37231087 DOI: 10.1038/s41564-023-01395-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Caitlin Guccione
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
- Center on Gender Equity and Health, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Division of Infectious Disease and Global Public Health, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kit Curtius
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
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Rahman G, Morton JT, Martino C, Sepich-Poore GD, Allaband C, Guccione C, Chen Y, Hakim D, Estaki M, Knight R. BIRDMAn: A Bayesian differential abundance framework that enables robust inference of host-microbe associations. bioRxiv 2023:2023.01.30.526328. [PMID: 36778470 PMCID: PMC9915500 DOI: 10.1101/2023.01.30.526328] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Quantifying the differential abundance (DA) of specific taxa among experimental groups in microbiome studies is challenging due to data characteristics (e.g., compositionality, sparsity) and specific study designs (e.g., repeated measures, meta-analysis, cross-over). Here we present BIRDMAn (Bayesian Inferential Regression for Differential Microbiome Analysis), a flexible DA method that can account for microbiome data characteristics and diverse experimental designs. Simulations show that BIRDMAn models are robust to uneven sequencing depth and provide a >20-fold improvement in statistical power over existing methods. We then use BIRDMAn to identify antibiotic-mediated perturbations undetected by other DA methods due to subject-level heterogeneity. Finally, we demonstrate how BIRDMAn can construct state-of-the-art cancer-type classifiers using The Cancer Genome Atlas (TCGA) dataset, with substantial accuracy improvements over random forests and existing DA tools across multiple sequencing centers. Collectively, BIRDMAn extracts more informative biological signals while accounting for study-specific experimental conditions than existing approaches.
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Affiliation(s)
- Gibraan Rahman
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - James T Morton
- Biostatistics & Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Cameron Martino
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | | | - Celeste Allaband
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Caitlin Guccione
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA
| | - Yang Chen
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Dermatology, University of California San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA
| | - Daniel Hakim
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Mehrbod Estaki
- Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
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6
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Ghosh P, Campos VJ, Vo DT, Guccione C, Goheen-Holland V, Tindle C, Mazzini GS, He Y, Alexandrov LB, Lippman SM, Gurski RR, Das S, Yadlapati R, Curtius K, Sahoo D. AI-assisted discovery of an ethnicity-influenced driver of cell transformation in esophageal and gastroesophageal junction adenocarcinomas. JCI Insight 2022; 7:e161334. [PMID: 36134663 PMCID: PMC9675486 DOI: 10.1172/jci.insight.161334] [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: 05/09/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
Although Barrett's metaplasia of the esophagus (BE) is the only known precursor lesion to esophageal adenocarcinomas (EACs), drivers of cellular transformation in BE remain incompletely understood. We use an artificial intelligence-guided network approach to study EAC initiation and progression. Key predictions are subsequently validated in a human organoid model, in patient-derived biopsy specimens of BE, a case-control study of genomics of BE progression, and in a cross-sectional study of 113 patients with BE and EACs. Our model classified healthy esophagus from BE and BE from EACs in several publicly available gene expression data sets (n = 932 samples). The model confirmed that all EACs must originate from BE and pinpointed a CXCL8/IL8↔neutrophil immune microenvironment as a driver of cellular transformation in EACs and gastroesophageal junction adenocarcinomas. This driver is prominent in White individuals but is notably absent in African Americans (AAs). Network-derived gene signatures, independent signatures of neutrophil processes, CXCL8/IL8 expression, and an absolute neutrophil count (ANC) are associated with risk of progression. SNPs associated with changes in ANC by ethnicity (e.g., benign ethnic neutropenia [BEN]) modify that risk. Findings define a racially influenced immunological basis for cell transformation and suggest that BEN in AAs may be a deterrent to BE→EAC progression.
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Affiliation(s)
- Pradipta Ghosh
- Department of Cellular and Molecular Medicine
- Department of Medicine
- HUMANOID Center of Research Excellence, and
- Moores Comprehensive Cancer Center, UCSD, La Jolla, California, USA
| | - Vinicius J. Campos
- Department of Gastrointestinal Surgery, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | | | - Caitlin Guccione
- Division of Biomedical Informatics, UCSD, La Jolla, California, USA
| | - Vanae Goheen-Holland
- Department of Cellular and Molecular Medicine
- HUMANOID Center of Research Excellence, and
| | - Courtney Tindle
- Department of Cellular and Molecular Medicine
- HUMANOID Center of Research Excellence, and
| | - Guilherme S. Mazzini
- Department of Gastrointestinal Surgery, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Postgraduate Program in Medicine, Surgical Scienceas, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Yudou He
- Department of Cellular and Molecular Medicine
- Moores Comprehensive Cancer Center, UCSD, La Jolla, California, USA
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine
- Moores Comprehensive Cancer Center, UCSD, La Jolla, California, USA
| | - Scott M. Lippman
- Department of Medicine
- Moores Comprehensive Cancer Center, UCSD, La Jolla, California, USA
| | - Richard R. Gurski
- Department of Gastrointestinal Surgery, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Postgraduate Program in Medicine, Surgical Scienceas, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
- Medical School of Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Soumita Das
- HUMANOID Center of Research Excellence, and
- Department of Pathology and
| | | | - Kit Curtius
- Department of Medicine
- Moores Comprehensive Cancer Center, UCSD, La Jolla, California, USA
- Division of Biomedical Informatics, UCSD, La Jolla, California, USA
| | - Debashis Sahoo
- Moores Comprehensive Cancer Center, UCSD, La Jolla, California, USA
- Department of Pediatrics and
- Department of Computer Science and Engineering, Jacob’s School of Engineering, UCSD, California, La Jolla, USA
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Sepich-Poore GD, Guccione C, Laplane L, Pradeu T, Curtius K, Knight R. Cancer's second genome: Microbial cancer diagnostics and redefining clonal evolution as a multispecies process: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution. Bioessays 2022; 44:e2100252. [PMID: 35253252 PMCID: PMC10506734 DOI: 10.1002/bies.202100252] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 10/23/2021] [Revised: 01/31/2022] [Accepted: 02/16/2022] [Indexed: 12/13/2022]
Abstract
The presence and role of microbes in human cancers has come full circle in the last century. Tumors are no longer considered aseptic, but implications for cancer biology and oncology remain underappreciated. Opportunities to identify and build translational diagnostics, prognostics, and therapeutics that exploit cancer's second genome-the metagenome-are manifold, but require careful consideration of microbial experimental idiosyncrasies that are distinct from host-centric methods. Furthermore, the discoveries of intracellular and intra-metastatic cancer bacteria necessitate fundamental changes in describing clonal evolution and selection, reflecting bidirectional interactions with non-human residents. Reconsidering cancer clonality as a multispecies process similarly holds key implications for understanding metastasis and prognosing therapeutic resistance while providing rational guidance for the next generation of bacterial cancer therapies. Guided by these new findings and challenges, this Review describes opportunities to exploit cancer's metagenome in oncology and proposes an evolutionary framework as a first step towards modeling multispecies cancer clonality. Also see the video abstract here: https://youtu.be/-WDtIRJYZSs.
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Affiliation(s)
| | - Caitlin Guccione
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Lucie Laplane
- Institut d’histoire et de philosophie des sciences et des techniques (UMR8590), CNRS & Panthéon-Sorbonne University, 75006 Paris, France
- Hematopoietic stem cells and the development of myeloid malignancies (UMR1287), Gustave Roussy Cancer Campus, 94800 Villejuif, France
| | - Thomas Pradeu
- ImmunoConcept (UMR5164), CNRS & University of Bordeaux, 33076 Bordeaux Cedex, France
| | - Kit Curtius
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
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Guccione C, Yadlapati R, Shah S, Knight R, Curtius K. Challenges in Determining the Role of Microbiome Evolution in Barrett's Esophagus and Progression to Esophageal Adenocarcinoma. Microorganisms 2021; 9:2003. [PMID: 34683324 PMCID: PMC8541168 DOI: 10.3390/microorganisms9102003] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/15/2021] [Accepted: 09/16/2021] [Indexed: 01/22/2023] Open
Abstract
Esophageal adenocarcinoma (EAC) claims the lives of half of patients within the first year of diagnosis, and its incidence has rapidly increased since the 1970s despite extensive research into etiological factors. The changes in the microbiome within the distal esophagus in modern populations may help explain the growth in cases that other common EAC risk factors together cannot fully explain. The precursor to EAC is Barrett's esophagus (BE), a metaplasia adapted to a reflux-mediated microenvironment that can be challenging to diagnose in patients who do not undergo endoscopic screening. Non-invasive procedures to detect microbial communities in saliva, oral swabs and brushings from the distal esophagus allow us to characterize taxonomic differences in bacterial population abundances within patients with BE versus controls, and may provide an alternative means of BE detection. Unique microbial communities have been identified across healthy esophagus, BE, and various stages of progression to EAC, but studies determining dynamic changes in these communities, including migration from proximal stomach and oral cavity niches, and their potential causal role in cancer formation are lacking. Helicobacter pylori is negatively associated with EAC, and the absence of this species has been implicated in the evolution of chromosomal instability, a main driver of EAC, but joint analyses of microbiome and host genomes are needed. Acknowledging technical challenges, future studies on the prediction of microbial dynamics and evolution within BE and the progression to EAC will require larger esophageal microbiome datasets, improved bioinformatics pipelines, and specialized mathematical models for analysis.
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Affiliation(s)
- Caitlin Guccione
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA;
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Rena Yadlapati
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; (R.Y.); (S.S.)
| | - Shailja Shah
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; (R.Y.); (S.S.)
- Veterans Affairs, San Diego Healthcare System, San Diego, CA 92161, USA
| | - Rob Knight
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA;
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Kit Curtius
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA;
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Loh JW, Guccione C, Di Clemente F, Riedlinger G, Ganesan S, Khiabanian H. All-FIT: allele-frequency-based imputation of tumor purity from high-depth sequencing data. Bioinformatics 2020; 36:2173-2180. [PMID: 31750888 PMCID: PMC7141867 DOI: 10.1093/bioinformatics/btz865] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 05/02/2019] [Revised: 11/13/2019] [Accepted: 11/19/2019] [Indexed: 01/14/2023] Open
Abstract
SUMMARY Clinical sequencing aims to identify somatic mutations in cancer cells for accurate diagnosis and treatment. However, most widely used clinical assays lack patient-matched control DNA and additional analysis is needed to distinguish somatic and unfiltered germline variants. Such computational analyses require accurate assessment of tumor cell content in individual specimens. Histological estimates often do not corroborate with results from computational methods that are primarily designed for normal-tumor matched data and can be confounded by genomic heterogeneity and presence of sub-clonal mutations. Allele-frequency-based imputation of tumor (All-FIT) is an iterative weighted least square method to estimate specimen tumor purity based on the allele frequencies of variants detected in high-depth, targeted, clinical sequencing data. Using simulated and clinical data, we demonstrate All-FIT's accuracy and improved performance against leading computational approaches, highlighting the importance of interpreting purity estimates based on expected biology of tumors. AVAILABILITY AND IMPLEMENTATION Freely available at http://software.khiabanian-lab.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jui Wan Loh
- Center for Systems and Computational Biology, Rutgers University, New Brunswick, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
- Graduate Program in Microbiology and Molecular Genetics, Rutgers University, Piscataway, NJ, USA
| | - Caitlin Guccione
- Center for Systems and Computational Biology, Rutgers University, New Brunswick, NJ, USA
| | - Frances Di Clemente
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Gregory Riedlinger
- Center for Systems and Computational Biology, Rutgers University, New Brunswick, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
- Department of Pathology and Laboratory Medicine, Rutgers University, New Brunswick, NJ, USA
| | - Shridar Ganesan
- Center for Systems and Computational Biology, Rutgers University, New Brunswick, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Hossein Khiabanian
- Center for Systems and Computational Biology, Rutgers University, New Brunswick, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
- Department of Pathology and Laboratory Medicine, Rutgers University, New Brunswick, NJ, USA
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Sideli L, Verdina A, Seminerio F, Barone M, La Cascia C, Sartorio C, Mule A, Guccione C, La Barbera D. Devaluation Towards People With Schizophrenia in Italian Medical, Nursing, and Psychology Students. Eur Psychiatry 2017. [DOI: 10.1016/j.eurpsy.2017.02.126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
IntroductionDiscrimination towards people with schizophrenia (PWS) by healthcare professionals is responsible of underdiagnosis and undertreatment of these patients. Negative attitudes toward PSW in health care professionals tend to be present since their university studies and are related to their knowledge and experience about the disease.Objectives and aimsTo assess opinion towards PSW in medical, nursing and psychology students and to investigate the relation with their knowledge of schizophrenia and its causes.MethodsThe study involved 133 medical, 200 nursing and 296 psychology undergraduate students. The opinion on mental illness questionnaire, the Devaluation Consumers Scale, and the Devaluation of Consumer Families Scale were administered to the sample. ANOVA and ANCOVA were used to test differences between groups and the relation between causal explanation of schizophrenia and discrimination towards PWS.ResultsPsychology students were more aware than the other student of public stigma towards PWS and their families (F 12.57, P < 0.001; F 32.69, P < 0.001) and expressed a more positive view on treatments’ effectiveness (F 30.74, P < 0.001). Psychology (OR 0.48, 95% CI 0.26–0.88) and nursing (OR 0.29, 95% CI 0.15–0.55) students were more likely to identify psychological and social risk factors as more frequent causes of schizophrenia (vs. biogenetics) and these, in turn, were related to a better opinion towards social equality of PWS.ConclusionsThese preliminary findings underline the relevance of biopsychosocial model of schizophrenia within stigma-reduction programs for health science students.Disclosure of interestThe authors have not supplied their declaration of competing interest.
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Karioti A, Giocaliere E, Guccione C, Pieraccini G, Gallo E, Vannacci A, Bilia A. Combined HPLC-DAD–MS, HPLC–MSn and NMR spectroscopy for quality control of plant extracts: The case of a commercial blend sold as dietary supplement. J Pharm Biomed Anal 2014; 88:7-15. [DOI: 10.1016/j.jpba.2013.07.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 07/26/2013] [Accepted: 07/29/2013] [Indexed: 10/26/2022]
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Catena V, Del Monte DD, Rubini A, Guccione C, Ricagna F, Gangeri G, De Zen GF. Anesthesia and myotonic dystrophy (Steinert's syndrome). The role of total intravenous anesthesia with propofol, cisatracurium and remifentanyl. Case report. Minerva Anestesiol 2007; 73:475-9. [PMID: 17660741] [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: 05/16/2023]
Abstract
Anesthesia for patients with Steinert's syndrome (myotonic dystrophy, MD) is a challenge for the anaesthetist. MD is a multisystemic disease and the neuromuscular symptoms can be associated with sleep apnea, endocrine disorders (diabetes, hypogonadism, hypothyroidism), cardiac, gastroenteric or cognitive disorders (mental deficiency, attention disorders). The diagnosis is facilitated when one or more of these symptoms are associated with the neuromuscular symptoms; however, the latter are not always present at the onset, which makes the diagnosis of MD a difficult and often late one. The choice of drugs and the choice of anesthesia in these patients can be very challenging for many reasons. A myotonic crisis can be triggered by several factors including hypothermia, shivering and mechanical or electrical stimulation. These patients are very sensitive to the usual anesthetics such as hypnotics and paralyzing agents (both depolarizing and nondepolarizing). The following case report describes pathophysiological considerations and a technique for anaesthesia during thoracic surgery that has been able to assure hemodynamic peroperative stability, early extubation and prolonged respiratory autonomy in a patient affected by this genetic disorder.
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Affiliation(s)
- V Catena
- Intensive Care Unit, ULSS 3, Bassano del Grappa Hospital, Vicenza, Italy.
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Maresca MC, Risica G, Calconi G, Vianello A, Guccione C, Chiara G, Mordacchini M, Bocci C. [Cardiac rhythm disorder in infection caused by cytomegalovirus in patients with kidney transplant]. Medicina (Firenze) 1989; 9:301-4. [PMID: 2559284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A higher incidence of arrhythmias was observed in 16 renal allograft recipients infected with Cytomegalovirus (CMV), as compared to 26 patients who were transplanted during the same period and did not contract the infection (43.7% vs. 3.8%; p less than 0.01). There was a highly significant difference in the incidence of sinus tachycardia (37.5% infected vs. 0% not infected; p less than 0.005), while the incidences of atrial fibrillation and ventricular ectopic beats were not significantly different. The arrhythmias always appeared in the early phases of the infection and disappeared after a certain period, lasting from one week to months. It is proposed that arrhythmias arising during CMV infection may be due to a myocardial CMV involvement.
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Ciarmiello G, Gava A, Sartori C, Dal Pozzo A, Dal Pos R, Caldato C, Guccione C, Lucernoni P, Salmaso L, Gimelli M. [Thin-needle aspiration cytology of palpable lymph nodes. Analysis of 702 consecutive cases]. Minerva Med 1988; 79:753-9. [PMID: 3173759] [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: 01/04/2023]
Abstract
Seven-hundred-two needle aspirates were taken from palpable lymph nodes between january 1982 and june 1987. Cytohistological correlation in about 70% of the preparations showed that the technique is capable of detecting neoplastic cells in 99% of metastases and in 90% of lymphoma cases. Certain technical aspects of smear preparation are pointed out with a view to reducing the percentage of inadequate samples (14% in the present series) and the position of the technique among other diagnostic procedures is discussed, with evaluation of advantages and limitations.
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Affiliation(s)
- G Ciarmiello
- Istituto di Anatomia Patologica, Presidio Ospedaliero Multizonale U.L.S.S. n. 10 - Treviso
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Abstract
Fournier's disease is an uncommon form of gas gangrene involving the scrotum and perineum. Described by Fournier as an idiopathic condition, it must be recognized as a synergistic gangrene secondary, in most cases, to a focus of perianal infection. Urinary tract infection and local trauma follow as possible causal factors. Five cases complicating a perianal abscess observed in a period of 11 years have been treated with urgent aggressive surgical debridement and intensive care support. Full-thickness skin grafts were required in three patients. Hospital mortality occurred in one case. Although combination antibiotic therapy and correct postoperative wound management are potentially successful, the mainstay of treatment is complete excision of all necrotic tissue. Colostomy and urinary diversion are not mandatory. Treatment with hyperbaric oxygen is controversial.
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Guccione C, Tonietto G, Actis Dato M. [Prognostic factors in thromboembolectomy with the Fogarty catheter for acute ischemia of the limbs]. Minerva Med 1979; 70:1399-404. [PMID: 450274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Authors describe the results obtained in 181 patients treated with thromboembolectomy by Fogarty catheter for acute limb ischaemia. Data were analyzed with the help of a set of computer programs for statistical computations, and some highly significant prognostic factors were determined: ischaemia duration and severity cause a substantial increase of both death and amputation probability; associate diseases or thrombosis are significant factors for amputation; occlusion level for death. The patients whose limb was saved without the pulse being present were characterized by ASO or thrombosis.
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Tessarolo N, Arrigoni G, Guccione C, Tonietto G, Ganassin L, Croce E. [Suprapubic femoro-femoral by-pass in the treatment of peripheral arterial insufficiency]. Angiologia 1978; 30:55-61. [PMID: 637364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Tonietto G, Ganassin L, Guccione C, Tessarolo N. [The aorto-inferior caval fistula syndrome]. Minerva Cardioangiol 1978; 26:75-86. [PMID: 643184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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