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Murgoitio-Esandi J, Tessone D, Naghdloo A, Shishido SN, Zhang B, Xu H, Dasgupta A, Mason J, Nagaraju RM, Hicks J, Kuhn P, Oberai A. Unsupervised Detection of Rare Events in Liquid Biopsy Assays. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.29.635501. [PMID: 39975209 PMCID: PMC11838382 DOI: 10.1101/2025.01.29.635501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
The use of liquid biopsies in the detection, diagnosis and treatment monitoring of different types of cancers and other diseases often requires identifying and enumerating instances of analytes that are rare. Most current techniques that aim to computationally isolate these rare instances or events first learn the signature of the event, and then scan the appropriate biological assay for this signature. While such techniques have proven to be very useful, they are limited because they must first establish what signature to look for, and only then identify events that are consistent with this signature. In contrast to this, in this study, we present an automated approach that does not require the knowledge of the signature of the rare event. It works by breaking the assay into a sequence of components, learning the probability distribution of these components, and then isolating those that are rare. This is done with the help of deep generative algorithms in an unsupervised manner, meaning without a-priori knowledge of the rare event associated with an analyte. In this study, this approach is applied to immunofluorescence microscopy images of peripheral blood, where it is shown that it successfully isolates biologically relevant events in blood from normal donors spiked with cancer-related cells and in blood from patients with late-stage breast cancer.
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Affiliation(s)
- Javier Murgoitio-Esandi
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, 90089, CA, USA
| | - Dean Tessone
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, 90089, CA, USA
- Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, 90089, CA, USA
| | - Amin Naghdloo
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, 90089, CA, USA
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, 90089, CA, USA
| | - Stephanie N Shishido
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, 90089, CA, USA
| | - Brian Zhang
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, 90089, CA, USA
| | - Haofeng Xu
- Department of Computer Science, Viterbi School of Engineering, University of Southern California, Los Angeles, 90089, CA, USA
| | - Agnimitra Dasgupta
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, 90089, CA, USA
| | - Jeremy Mason
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, 90089, CA, USA
- Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, 90033, CA, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, 90033, CA, USA
| | - Rajiv M Nagaraju
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, 90089, CA, USA
| | - James Hicks
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, 90089, CA, USA
| | - Peter Kuhn
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, 90089, CA, USA
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, 90089, CA, USA
- Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, 90089, CA, USA
- Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, 90033, CA, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, 90033, CA, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, 90089, CA, USA
| | - Assad Oberai
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, 90089, CA, USA
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Shishido SN, Marvit A, Pham D, Luo T, Xu L, Mason J, Priceman SJ, Portnow J, Kuhn P. Multi-Omic Characterization of Single Cells and Cell-Free Components Detected in the Cerebrospinal Fluid of Patients with Leptomeningeal Disease. Cancers (Basel) 2024; 16:3746. [PMID: 39594700 PMCID: PMC11592257 DOI: 10.3390/cancers16223746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 10/29/2024] [Accepted: 10/31/2024] [Indexed: 11/28/2024] Open
Abstract
BACKGROUND/OBJECTIVES Up to 30% of patients with breast cancers will develop brain or leptomeningeal metastases, and this risk is especially high with HER2-positive cancers. For patients with central nervous system metastases, cerebrospinal fluid (CSF) liquid biopsies are a promising opportunity to monitor disease, inform treatment, and predict prognosis. This pilot study investigated CSF liquid biopsy analytes from three patients diagnosed with central nervous system metastases based on imaging but not confirmed via clinical cytology. METHODS The detection of cellular analytes with the non-enrichment high-definition single-cell assay (HDSCA3.0) workflow was compared between the CSF and matched peripheral blood (PB) samples. RESULTS Circulating tumor cells (CTCs) were detected in the CSF but not the PB and were subsequently molecularly characterized using single-cell genomics and targeted multiplexed proteomics to reveal a clonal population of phenotypically heterogeneous cells. There was a lack of concordance in the copy number alteration profiles between CTCs and cell-free DNA (cfDNA) in the CSF. Extracellular vesicle surface marker analysis in CSF revealed a prominent signal among tetraspanins (CD9/CD63/CD81), with CD81 exhibiting the highest signal across all patients. CONCLUSIONS The data presented suggest that CSF could be a useful tool for diagnosing and assessing disease severity.
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Affiliation(s)
- Stephanie N. Shishido
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA (D.P.); (T.L.); (J.M.)
| | - Amelia Marvit
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA (D.P.); (T.L.); (J.M.)
| | - Doanna Pham
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA (D.P.); (T.L.); (J.M.)
| | - Theresa Luo
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA (D.P.); (T.L.); (J.M.)
| | - Liya Xu
- The Vision Center at Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA;
- USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jeremy Mason
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA (D.P.); (T.L.); (J.M.)
- Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Saul J. Priceman
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA;
- Department of Medicine, KSOM/NCCC Center for Cancer Cellular Immunotherapy, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Jana Portnow
- Department of Medical Oncology & Therapeutics Research, City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA;
| | - Peter Kuhn
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA (D.P.); (T.L.); (J.M.)
- Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA 90089, USA
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Resnick K, Shah A, Mason J, Kuhn P, Nieva J, Shishido SN. Circulation of rare events in the liquid biopsy for early detection of lung mass lesions. Thorac Cancer 2024; 15:2100-2109. [PMID: 39233479 PMCID: PMC11471425 DOI: 10.1111/1759-7714.15429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/30/2024] [Accepted: 08/05/2024] [Indexed: 09/06/2024] Open
Abstract
BACKGROUND Lung cancer screening with low-dose computed tomography (CT) scans (LDCT) has reduced mortality for patients with high-risk smoking histories, but it has significant limitations: LDCT screening implementation remains low, high rates of false-positive scans, and current guidelines exclude those without smoking histories. We sought to explore the utility of liquid biopsy (LBx) in early cancer screening and diagnosis of lung cancer. METHODS Using the high-definition single-cell assay workflow, we analyzed 99 peripheral blood samples from three cohorts: normal donors (NDs) with no known pathology (n = 50), screening CT patients (n = 25) with Lung-RADS score of 1-2, and biopsy (BX) patients (n = 24) with abnormal CT scans requiring tissue biopsy. RESULTS For CT and BX patients, demographic information was roughly equivalent; however, average pack-years smoked differed. A total of 14 (58%) BX patients were diagnosed with primary lung cancer (BX+). The comparison of the rare event enumerations among the cohorts revealed a greater incidence of total events, rare cells, and oncosomes, as well as specific cellular phenotypes in the CT and BX cohorts compared with the ND cohort. LBx analytes were also significantly elevated in the BX compared with the CT samples, but there was no difference between BX+ and BX- samples. CONCLUSIONS The data support the utility of the LBx in distinguishing patients with an alveolar lesion from those without, providing a potential avenue for prescreening before LDCT.
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Affiliation(s)
- Karen Resnick
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Anya Shah
- Convergent Science Institute for Cancer, Michelson Center, University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Jeremy Mason
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern CaliforniaLos AngelesCaliforniaUSA
- Convergent Science Institute for Cancer, Michelson Center, University of Southern CaliforniaLos AngelesCaliforniaUSA
- Institute of Urology, Catherine & Joseph Aresty Department of UrologyKeck School of Medicine, University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Peter Kuhn
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern CaliforniaLos AngelesCaliforniaUSA
- Convergent Science Institute for Cancer, Michelson Center, University of Southern CaliforniaLos AngelesCaliforniaUSA
- Institute of Urology, Catherine & Joseph Aresty Department of UrologyKeck School of Medicine, University of Southern CaliforniaLos AngelesCaliforniaUSA
- Department of Biomedical EngineeringViterbi School of Engineering, University of Southern CaliforniaLos AngelesCaliforniaUSA
- Department of Aerospace and Mechanical EngineeringViterbi School of Engineering, University of Southern CaliforniaLos AngelesCaliforniaUSA
- Department of Biological SciencesDornsife College of Letters, Arts, and Sciences, University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Jorge Nieva
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Stephanie N. Shishido
- Convergent Science Institute for Cancer, Michelson Center, University of Southern CaliforniaLos AngelesCaliforniaUSA
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Shishido SN, Suresh D, Courcoubetis G, Ye B, Lin E, Mason J, Park K, Lewis M, Wang R, Lo SK, Kuhn P, Pandol S. Determining the efficacy of ExThera Seraph100 blood filtration in patients diagnosed with pancreatic cancer through the liquid biopsy. BJC REPORTS 2024; 2:47. [PMID: 39516545 PMCID: PMC11524105 DOI: 10.1038/s44276-024-00069-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/22/2024] [Accepted: 06/02/2024] [Indexed: 11/16/2024]
Abstract
BACKGROUND Cancer becomes lethal as it spreads from the primary site to the rest of the body. Circulating tumor cells (CTCs) are biomarkers of disease progression and have been associated with decreased overall survival. Blood filtration is a novel concept for removing CTCs from circulation to improve patient prognosis. METHODS This study utilizes liquid biopsy to assess the efficacy of ExThera Medical's Seraph® 100 Microbind® Affinity Blood Filter on the blood of patients with pancreatic ductal adenocarcinoma (PDAC) using the third generation high-definition single cell assay workflow. Blood samples from treatment-naïve PDAC patients were collected and analyzed to characterize the CTCs and other rare cells present before and after filtration. RESULTS Examination of 6 paired portal vein blood (PoVB) samples demonstrated a statistically significant decrease in total rare cells, total cytokeratin (CK)+ cells, and CTCs across all patients due to filtration. Furthermore, analysis of 2 paired peripheral blood (PB) samples showed a decrease in total rare cells, total CK+ cells, and specific phenotypes of rare cells after filtration. DISCUSSION These preliminary results demonstrate initial proof of concept that this filtration device can remove CTCs from circulation and may therefore be useful as a therapy or adjunct in PDAC patient care.
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Affiliation(s)
- Stephanie N Shishido
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Divya Suresh
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - George Courcoubetis
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Brandon Ye
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Emmeline Lin
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jeremy Mason
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
- Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Ken Park
- Pancreatic and Biliary Diseases Program, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Michael Lewis
- Departments of Medicine and Pathology, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
- Department of Pathology, VA Greater Los Angeles Medical Center, Los Angeles, CA, 90073, USA
- Center for Cancer Research and Development, Clark Atlanta University, Atlanta, GA, 30314, USA
| | - Ruoxiang Wang
- Pancreatic and Biliary Diseases Program, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Simon K Lo
- Pancreatic and Biliary Diseases Program, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Peter Kuhn
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA.
- Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, 90089, USA.
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, 90089, USA.
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Stephen Pandol
- Pancreatic and Biliary Diseases Program, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
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Bai L, Courcoubetis G, Mason J, Hicks JB, Nieva J, Kuhn P, Shishido SN. Longitudinal tracking of circulating rare events in the liquid biopsy of stage III-IV non-small cell lung cancer patients. Discov Oncol 2024; 15:142. [PMID: 38700626 PMCID: PMC11068717 DOI: 10.1007/s12672-024-00984-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024] Open
Abstract
In the United States, lung cancer is the second most common type of cancer with non-small cell lung cancer (NSCLC) encompassing around 85% of total lung cancer cases. Late-stage patients with metastatic disease have worsening prognosis, highlighting the importance of longitudinal disease monitoring. Liquid biopsy (LBx) represents a way for physicians to non-invasively track tumor analytes, such as circulating tumor cells (CTCs), and understand tumor progression in real-time through analyzing longitudinal blood samples. CTCs have been shown to be effective predictive biomarkers in measuring treatment efficacy and survival outcomes. We used the third-generation High-Definition Single Cell Assay (HDSCA3.0) workflow to analyze circulating rare events longitudinally during treatment in a cohort of 10 late-stage NSCLC patients, identifying rare events including circulating cancer cells (i.e., CTCs), and oncosomes. Here, we show (1) that there is a cancer specific LBx profile, (2) there is considerable heterogeneity of rare cells and oncosomes, and (3) that LBx data elements correlated with patient survival outcomes. Additional studies are warranted to understand the biological significance of the rare events detected, and the clinical potential of the LBx to monitor and predict response to treatment in NSCLC patient care.
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Affiliation(s)
- Lily Bai
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - George Courcoubetis
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jeremy Mason
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
- Catherine and Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - James B Hicks
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jorge Nieva
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Peter Kuhn
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA.
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
- Catherine and Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
| | - Stephanie N Shishido
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA.
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Ghoreifi A, Shishido SN, Sayeed S, Courcoubetis G, Huang A, Schuckman A, Aron M, Desai M, Daneshmand S, Gill IS, Kuhn P, Djaladat H, Mason J. Blood-based liquid biopsy: A promising noninvasive test in diagnosis, surveillance, and prognosis of patients with upper tract urothelial carcinoma. Urol Oncol 2024; 42:118.e9-118.e17. [PMID: 38383240 DOI: 10.1016/j.urolonc.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/29/2024] [Accepted: 02/03/2024] [Indexed: 02/23/2024]
Abstract
OBJECTIVES To assess the efficacy of blood-based liquid biopsy in the diagnosis, surveillance, and prognosis of upper tract urothelial carcinoma (UTUC). METHODS AND MATERIALS In this prospective study, peripheral blood samples were collected from patients with primary UTUC before surgery with curative intent and follow-up visits at University of Southern California between May 2021 and September 2022. The samples were analyzed using the third-generation comprehensive high-definition single-cell assay (HDSCA3.0) to detect rare events, including circulating tumor cells (CTCs) and oncosomes, based on the immunofluorescence signals of DAPI (D), cytokeratin (CK), CD45/CD31 (CD), and vimentin (V). The findings of pre-surgery liquid biopsies were compared with those of blood samples from normal donors (NDs) and matched follow-up liquid biopsies. The association between liquid biopsy findings and clinical data, including recurrence-free survival (RFS), was also assessed. RESULTS Twenty-eight patients with UTUC were included, of whom 21 had follow-up samples. Significant differences in specific rare analytes were detected in the preoperative samples compared to the NDs. In the post- vs. presurgery matched analysis, a significant decrease was detected in total-, CK-, and CK|V oncosomes, as well as in D-, D|V-, and D|V|CD cells. With a median follow-up of 11 months, 8 patients had disease recurrence. Survival analysis demonstrated that patients with >1.95 preoperative CK|V oncosomes (p = 0.020) and those with >4.18 D|CK|V cells (p = 0.050) had worse RFS compared to other patients. CONCLUSIONS This study demonstrated promising initial evidence for the biomarker role of CTCs and oncosomes in the diagnosis and surveillance of patients with UTUC.
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Affiliation(s)
- Alireza Ghoreifi
- Catherine and Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Stephanie N Shishido
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA
| | - Salmaan Sayeed
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA
| | - George Courcoubetis
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA
| | - Amy Huang
- Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA
| | - Anne Schuckman
- Catherine and Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Monish Aron
- Catherine and Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Mihir Desai
- Catherine and Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Siamak Daneshmand
- Catherine and Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Inderbir S Gill
- Catherine and Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Peter Kuhn
- Catherine and Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA; Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA; Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA
| | - Hooman Djaladat
- Catherine and Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA.
| | - Jeremy Mason
- Catherine and Joseph Aresty Department of Urology, Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA; Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA.
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Shishido SN, Lin E, Nissen N, Courcoubetis G, Suresh D, Mason J, Osipov A, Hendifar AE, Lewis M, Gaddam S, Pandol S, Kuhn P, Lo SK. Cancer-related cells and oncosomes in the liquid biopsy of pancreatic cancer patients undergoing surgery. NPJ Precis Oncol 2024; 8:36. [PMID: 38360856 PMCID: PMC10869814 DOI: 10.1038/s41698-024-00521-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/15/2024] [Indexed: 02/17/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) has a five-year survival rate of less than 10% due to its late diagnosis, rapid metastasis, and chemotherapeutic resistance. For a small proportion (10-20%) of early-stage patients however, surgical resection of the pancreatic tumor offers the best chance for survival but the effect of surgery on disease dissemination is unknown. The primary objective of this study was to characterize cellular and acellular blood-based analytes in portal and peripheral blood before pancreatic manipulation, during tumor dissection and immediately after surgical resection to determine the effects of the surgery. This study used the non-enriching third generation High-Definition Single Cell Assay (HDSCA3.0) workflow to investigate heterogeneous circulating rare cell population in the blood. Blood from both sites taken before surgical manipulation of the pancreas had significantly greater incidence of total rare cellular and acellular analytes than normal donor samples. Post-surgery portal and peripheral blood had significantly greater incidence of specific cellular and acellular subtypes compared to the matched pre- and during-surgery samples. Our results reveal that in patients with PDAC liquid biopsy analytes are increased in both the portal and peripheral blood; portal blood contains a higher frequency of analytes than in the peripheral blood; total analytes in the portal and peripheral blood samples were significantly associated with the tumor volume and pathological T stage; and the surgical procedure increased the blood levels of circulating cellular and acellular analytes, but not Epi.CTCs or Mes.CTCs. This study demonstrates liquid biopsy's utility in monitoring patients with PDAC with surgically resectable disease.
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Affiliation(s)
- Stephanie N Shishido
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Emmeline Lin
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Nicholas Nissen
- Pancreatic and Biliary Diseases Program, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - George Courcoubetis
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Divya Suresh
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jeremy Mason
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA
- Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Arsen Osipov
- IM Hematology Oncology, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Andrew E Hendifar
- IM Hematology Oncology, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Michael Lewis
- Pancreatic and Biliary Diseases Program, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
- Greater Los Angeles Veterans Affairs System, Los Angeles, CA, 90073, USA
- Clark Atlanta University, Center for Cancer Research and Therapeutic Development, Atlanta, GA, 30314, USA
| | - Srinivas Gaddam
- Pancreatic and Biliary Diseases Program, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Stephen Pandol
- Pancreatic and Biliary Diseases Program, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Peter Kuhn
- Convergent Science Institute for Cancer, Michelson Center, University of Southern California, Los Angeles, CA, 90089, USA.
- Institute of Urology, Catherine & Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, 90089, USA.
- Department of Aerospace and Mechanical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, 90089, USA.
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Simon K Lo
- Pancreatic and Biliary Diseases Program, Cedars Sinai Medical Center, Los Angeles, CA, 90048, USA.
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8
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Badia-Ramentol J, Gimeno-Valiente F, Duréndez E, Martínez-Ciarpaglini C, Linares J, Iglesias M, Cervantes A, Calon A, Tarazona N. The prognostic potential of CDX2 in colorectal cancer: Harmonizing biology and clinical practice. Cancer Treat Rev 2023; 121:102643. [PMID: 37871463 DOI: 10.1016/j.ctrv.2023.102643] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023]
Abstract
Adjuvant chemotherapy following surgical intervention remains the primary treatment option for patients with localized colorectal cancer (CRC). However, a significant proportion of patients will have an unfavorable outcome after current forms of chemotherapy. While reflecting the increasing complexity of CRC, the clinical application of molecular biomarkers provides information that can be utilized to guide therapeutic strategies. Among these, caudal-related homeobox transcription factor 2 (CDX2) emerges as a biomarker of both prognosis and relapse after therapy. CDX2 is a key transcription factor that controls intestinal fate. Although rarely mutated in CRC, loss of CDX2 expression has been reported mostly in right-sided, microsatellite-unstable tumors and is associated with aggressive carcinomas. The pathological assessment of CDX2 by immunohistochemistry can thus identify patients with high-risk CRC, but the evaluation of CDX2 expression remains challenging in a substantial proportion of patients. In this review, we discuss the roles of CDX2 in homeostasis and CRC and the alterations that lead to protein expression loss. Furthermore, we review the clinical significance of CDX2 assessment, with a particular focus on its current use as a biomarker for pathological evaluation and clinical decision-making. Finally, we attempt to clarify the molecular implications of CDX2 deficiency, ultimately providing insights for a more precise evaluation of CDX2 protein expression.
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Affiliation(s)
- Jordi Badia-Ramentol
- Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Francisco Gimeno-Valiente
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, UK
| | - Elena Duréndez
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, CIBERONC, Spain
| | | | - Jenniffer Linares
- Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Mar Iglesias
- Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain; Department of Pathology, Hospital del Mar, Barcelona, CIBERONC, Spain
| | - Andrés Cervantes
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, CIBERONC, Spain
| | - Alexandre Calon
- Cancer Research Program, Hospital del Mar Research Institute (IMIM), Barcelona, Spain.
| | - Noelia Tarazona
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, CIBERONC, Spain.
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9
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Clinical, Pathological, and Molecular Characteristics in Colorectal Cancer. Cancers (Basel) 2022; 14:cancers14235958. [PMID: 36497440 PMCID: PMC9739916 DOI: 10.3390/cancers14235958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/03/2022] Open
Abstract
Colorectal cancer (CRC) is the third most diagnosed cancer worldwide, and the second leading cause of death in patients with cancer [...].
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