1
|
Monjé N, Dragomir MP, Sinn BV, Hoffmann I, Makhmut A, Simon T, Kunze CA, Ihlow J, Schmitt WD, Pohl J, Piwonski I, Marchenko S, Keunecke C, Calina TG, Tiso F, Kulbe H, Kreuzinger C, Cacsire Castillo-Tong D, Sehouli J, Braicu EI, Denkert C, Darb-Esfahani S, Kübler K, Capper D, Coscia F, Morkel M, Horst D, Sers C, Taube ET. AHRR and SFRP2 in primary versus recurrent high-grade serous ovarian carcinoma and their prognostic implication. Br J Cancer 2024; 130:1249-1260. [PMID: 38361045 PMCID: PMC11014847 DOI: 10.1038/s41416-023-02550-1] [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: 12/04/2022] [Revised: 12/03/2023] [Accepted: 12/11/2023] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND The aim of this study was to analyse transcriptomic differences between primary and recurrent high-grade serous ovarian carcinoma (HGSOC) to identify prognostic biomarkers. METHODS We analysed 19 paired primary and recurrent HGSOC samples using targeted RNA sequencing. We selected the best candidates using in silico survival and pathway analysis and validated the biomarkers using immunohistochemistry on a cohort of 44 paired samples, an additional cohort of 504 primary HGSOCs and explored their function. RESULTS We identified 233 differential expressed genes. Twenty-three showed a significant prognostic value for PFS and OS in silico. Seven markers (AHRR, COL5A2, FABP4, HMGCS2, ITGA5, SFRP2 and WNT9B) were chosen for validation at the protein level. AHRR expression was higher in primary tumours (p < 0.0001) and correlated with better patient survival (p < 0.05). Stromal SFRP2 expression was higher in recurrent samples (p = 0.009) and protein expression in primary tumours was associated with worse patient survival (p = 0.022). In multivariate analysis, tumour AHRR and SFRP2 remained independent prognostic markers. In vitro studies supported the anti-tumorigenic role of AHRR and the oncogenic function of SFRP2. CONCLUSIONS Our results underline the relevance of AHRR and SFRP2 proteins in aryl-hydrocarbon receptor and Wnt-signalling, respectively, and might lead to establishing them as biomarkers in HGSOC.
Collapse
Affiliation(s)
- Nanna Monjé
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Mihnea P Dragomir
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Bruno V Sinn
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Inga Hoffmann
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Anuar Makhmut
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany
| | - Tincy Simon
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Catarina A Kunze
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Jana Ihlow
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Wolfgang D Schmitt
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Jonathan Pohl
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Iris Piwonski
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Sofya Marchenko
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Carlotta Keunecke
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department for Gynecology with the Center for Oncologic Surgery Charité Campus Virchow-Klinikum, Charitéplatz 1, 10117, Berlin, Germany
| | | | - Francesca Tiso
- Center of Functional Genomics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- Department of Hematology, Oncology and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
| | - Hagen Kulbe
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department for Gynecology with the Center for Oncologic Surgery Charité Campus Virchow-Klinikum, Charitéplatz 1, 10117, Berlin, Germany
| | - Caroline Kreuzinger
- Translational Gynecology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Dan Cacsire Castillo-Tong
- Translational Gynecology Group, Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Jalid Sehouli
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department for Gynecology with the Center for Oncologic Surgery Charité Campus Virchow-Klinikum, Charitéplatz 1, 10117, Berlin, Germany
| | - Elena I Braicu
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department for Gynecology with the Center for Oncologic Surgery Charité Campus Virchow-Klinikum, Charitéplatz 1, 10117, Berlin, Germany
| | - Carsten Denkert
- Institute of Pathology, University Hospital Gießen and Marburg, Marburg, Germany
| | - Silvia Darb-Esfahani
- Institute of Pathology, Berlin-Spandau, Stadtrandstraße 555, 13589, Berlin, Germany
| | - Kirsten Kübler
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Center of Functional Genomics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- Department of Hematology, Oncology and Cancer Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Hindenburgdamm 30, 12203, Berlin, Germany
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School Teaching Hospital, Charlestown, MA, USA
| | - David Capper
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Fabian Coscia
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany
| | - Markus Morkel
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - David Horst
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Christine Sers
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Eliane T Taube
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Pathology, Charitéplatz 1, 10117, Berlin, Germany.
| |
Collapse
|
2
|
Prete AA, Angerilli V, Bergamo F, Vettore V, De Toni C, Intini R, Cerma K, Ricagno G, Cerantola R, Perissinotto E, De Rosa A, Ceccon C, Gasparello J, Denaro L, D'Amico A, Chioffi F, Carcea E, Fassan M, Lonardi S. HER2 expression and genOmic characterization of rESected brain metastases from colorectal cancer: the HEROES study. Br J Cancer 2024; 130:1316-1323. [PMID: 38347094 PMCID: PMC11014920 DOI: 10.1038/s41416-023-02569-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Little is known about prognostic factors of brain metastases (BM) from colorectal cancer (CRC). HER2 amplification/overexpression (HER2+) was previously described; its impact on prognosis remains uncertain. METHODS In the translational study HEROES, extensive molecular analysis was performed on primary CRC (prCRC) and their matched resected BM by means of NGS comprehensive genomic profiling and HER2 status as assessed by immunohistochemical/ in situ hybridization. Count of tumour-infiltrating lymphocytes (TILs) was also performed. PRIMARY OBJECTIVE to describe the molecular landscape of paired BM/prCRC. SECONDARY OBJECTIVES to search for new prognostic biomarkers of outcome after BM resection: intracranial-only Progression-Free Survival (BM-iPFS), Progression-Free Survival (BM-PFS), and Overall Survival (BM-OS). RESULTS Out of 22 patients having paired samples of prCRC and BM, HER2+ was found on 4 (18%) BM, 3 (75%) of which also HER2+ in matched prCRC. Lower tumour mutation burden (HR 3.08; 95%CI 1.06-8.93; p = 0.0386) and HER2-negative BM (HER2neg) (HR 7.75;95%CI 1.97-30.40; p = 0.0033) were associated with longer BM-iPFS; HER2neg BM (HR 3.44; 95%CI 1.03-11.53; p = 0.0449) and KRASmut BM (HR 0.31; 95%CI 0.12-0.80; p = 0.0153) conferred longer BM-PFS. Longer BM-OS was found in pts with TILs-enriched (≥1.6/HPF) BM (HR 0.11; 95%CI0.01-0.91; p = 0.0403). CONCLUSIONS This study shows HER2+ enrichment in both BM and their prCRC. TILs-enriched BM conferred better BM-OS.
Collapse
Affiliation(s)
| | - Valentina Angerilli
- Department of Medicine (DIMED), Surgical Pathology & Cytopathology Unit, University of Padua, Padua, Italy
| | - Francesca Bergamo
- Medical Oncology 1, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy.
| | - Valentina Vettore
- Medical Oncology 1, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Chiara De Toni
- Medical Oncology 1, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Rossana Intini
- Medical Oncology 1, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Krisida Cerma
- Medical Oncology 1, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | | | - Riccardo Cerantola
- Medical Oncology 1, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | | | - Antonio De Rosa
- Medical Oncology 1, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Carlotta Ceccon
- Department of Medicine (DIMED), Surgical Pathology & Cytopathology Unit, University of Padua, Padua, Italy
| | - Jessica Gasparello
- Department of Medicine (DIMED), Surgical Pathology & Cytopathology Unit, University of Padua, Padua, Italy
| | - Luca Denaro
- Academic Neurosurgery, Department of Neurosciences, University of Padua, Padua, Italy
| | - Alberto D'Amico
- Academic Neurosurgery, Department of Neurosciences, University of Padua, Padua, Italy
| | - Franco Chioffi
- Division of Neurosurgery, Azienda Ospedaliera Università di Padova, Padua, Italy
| | - Elena Carcea
- Medical Oncology 1, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology & Cytopathology Unit, University of Padua, Padua, Italy
- Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Sara Lonardi
- Medical Oncology 3, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| |
Collapse
|
3
|
Karapetis CS, Liu H, Sorich MJ, Pederson LD, Van Cutsem E, Maughan T, Douillard JY, O'Callaghan CJ, Jonker D, Bokemeyer C, Sobrero A, Cremolini C, Chibaudel B, Zalcberg J, Adams R, Buyse M, Peeters M, Yoshino T, de Gramont A, Shi Q. Fluoropyrimidine type, patient age, tumour sidedness and mutation status as determinants of benefit in patients with metastatic colorectal cancer treated with EGFR monoclonal antibodies: individual patient data pooled analysis of randomised trials from the ARCAD database. Br J Cancer 2024; 130:1269-1278. [PMID: 38402342 PMCID: PMC11015038 DOI: 10.1038/s41416-024-02604-y] [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: 09/26/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/26/2024] Open
Abstract
BACKGROUND KRAS mutations in metastatic colorectal cancer (mCRC) are used as predictive biomarkers to select therapy with EGFR monoclonal antibodies (mAbs). Other factors may be significant determinants of benefit. METHODS Individual patient data from randomised trials with a head-to-head comparison between EGFR mAb versus no EGFR mAb (chemotherapy alone or best supportive care) in mCRC, across all lines of therapy, were pooled. Overall survival (OS) and progression-free survival (PFS) were compared between groups. Treatment effects within the predefined KRAS biomarker subsets were estimated by adjusted hazard ratio (HRadj) and 95% confidence interval (CI). EGFR mAb efficacy was measured within the KRAS wild-type subgroup according to BRAF and NRAS mutation status. In both KRAS wild-type and mutant subgroups, additional factors that could impact EGFR mAb efficacy were explored including the type of chemotherapy, line of therapy, age, sex, tumour sidedness and site of metastasis. RESULTS 5675 patients from 8 studies were included, all with known mCRC KRAS mutation status. OS (HRadj 0.90, 95% CI 0.84-0.98, p = 0.01) and PFS benefit (HRadj 0.73, 95% CI 0.68-0.79, p < 0.001) from EGFR mAbs was observed in the KRAS wild-type group. PFS benefit was seen in patients treated with fluorouracil (HRadj 0.75, 95% CI 0.68-0.82) but not with capecitabine-containing regimens (HRadj 1.04, 95% CI 0.86-1.26) (pinteraction = 0.002). Sidedness also interacted with EGFR mAb efficacy, with survival benefit restricted to left-sided disease (pinteraction = 0.038). PFS benefits differed according to age, with benefits greater in those under 70 (pinteraction = 0.001). The survival benefit was not demonstrated in those patients with mutations found in the KRAS, NRAS or BRAF genes. The presence of liver metastases interacted with EGFR mAb efficacy in patients with KRAS mutant mCRC (pinteraction = 0.004). CONCLUSION The benefit provided by EGFR mAbs in KRAS WT mCRC is associated with left-sided primary tumour location, younger patient age and absence of NRAS or BRAF mutations. Survival benefit is observed with fluorouracil but not capecitabine. Exploratory results support further research in KRAS mutant mCRC without liver metastases.
Collapse
Affiliation(s)
- C S Karapetis
- Flinders Medical Centre, Adelaide, SA, Australia.
- Flinders University, Adelaide, SA, Australia.
| | - H Liu
- Mayo Clinic, Rochester, NY, USA
| | - M J Sorich
- Flinders University, Adelaide, SA, Australia
| | | | - E Van Cutsem
- University Hospitals Gasthuisberg Leuven and University of Leuven, Leuven, Belgium
| | - T Maughan
- University of Liverpool, Liverpool, UK
| | - J Y Douillard
- University of Nantes and Integrated Centers of Oncology ICO Rene Gauducheau Cancer Nantes, Nantes, France
| | | | - D Jonker
- The Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - C Bokemeyer
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | | | - B Chibaudel
- Franco-British Institute Levallois-Perre, Levallois-Perre, France
| | - J Zalcberg
- Dept of Medical Oncology, Alfred Health and School of Public Health, Monash University, Melbourne, VIC, Australia
| | - R Adams
- Velindre Cancer Centre Cardiff University, Cardiff, UK
| | - M Buyse
- International Drug Development Institute, Louvain-la-Neuve, Belgium
| | - M Peeters
- Antwerp University and Antwerp University Hospital, Antwerp, Belgium
| | - T Yoshino
- National Cancer Centre Hospital East, Kashiwa, Japan
| | - A de Gramont
- Franco-British Institute Levallois-Perre, Levallois-Perre, France
| | - Q Shi
- Mayo Clinic, Rochester, NY, USA
| |
Collapse
|
4
|
Shool S, Rahmani S, Habibi MA, Piri SM, Lotfinia M, Jashnani D, Asaadi S. Acute spinal cord injury serum biomarkers in human and rat: a scoping systematic review. Spinal Cord Ser Cases 2024; 10:21. [PMID: 38615029 PMCID: PMC11016077 DOI: 10.1038/s41394-024-00636-3] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 03/28/2024] [Accepted: 04/08/2024] [Indexed: 04/15/2024] Open
Abstract
STUDY DESIGN Scoping systematic review. OBJECTIVES To summarize the available experimental clinical and animal studies for the identification of all CSF and serum-derived biochemical markers in human and rat SCI models. SETTING Tehran, Iran. METHODS In this scoping article, we systematically reviewed the electronic databases of PubMed, Scopus, WOS, and CENTRAL to retrieve current literature assessing the levels of different biomarkers in human and rat SCI models. RESULTS A total of 19,589 articles were retrieved and 6897 duplicated titles were removed. The remaining 12,692 studies were screened by their title/abstract and 12,636 were removed. The remaining 56 were considered for full-text assessment, and 11 papers did not meet the criteria, and finally, 45 studies were included. 26 studies were human observational studies comprising 1630 patients, and 19 articles studied SCI models in rats, including 832 rats. Upon reviewing the literature, we encountered a remarkable heterogeneity in terms of selected biomarkers, timing, and method of measurement, studied models, extent, and mechanism of injury as well as outcome assessment measures. CONCLUSIONS The specific expression and distribution patterns of biomarkers in relation to spinal cord injury (SCI) phases, and their varied concentrations over time, suggest that cerebrospinal fluid (CSF) and blood biomarkers are effective measures for assessing the severity of SCI.
Collapse
Affiliation(s)
- Sina Shool
- Department of Neurosurgery, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Sina Trauma and Surgery Research Center, Sina Hospital, Tehran University of Medical Sciences, Hassan-Abad Square, Imam Khomeini Ave, 11365-3876, Tehran, Iran
| | - Saeed Rahmani
- Department of Neurosurgery, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Amin Habibi
- Department of Neurosurgery, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Sina Trauma and Surgery Research Center, Sina Hospital, Tehran University of Medical Sciences, Hassan-Abad Square, Imam Khomeini Ave, 11365-3876, Tehran, Iran
| | - Seyed Mohammad Piri
- Sina Trauma and Surgery Research Center, Sina Hospital, Tehran University of Medical Sciences, Hassan-Abad Square, Imam Khomeini Ave, 11365-3876, Tehran, Iran
| | - Mahmoud Lotfinia
- Resident of Neurosurgery, Department of Neurosurgery, Klinikum Saarbrücken, University of Saarland, Saarbrücken, Germany
| | - Delara Jashnani
- Department of Neurosurgery, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sina Asaadi
- Department of Surgery, Division of Acute Care Surgery, Loma Linda University, Loma Linda, CA, USA.
| |
Collapse
|
5
|
Kolbinger FR, Veldhuizen GP, Zhu J, Truhn D, Kather JN. Reporting guidelines in medical artificial intelligence: a systematic review and meta-analysis. Commun Med (Lond) 2024; 4:71. [PMID: 38605106 PMCID: PMC11009315 DOI: 10.1038/s43856-024-00492-0] [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: 08/18/2023] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
BACKGROUND The field of Artificial Intelligence (AI) holds transformative potential in medicine. However, the lack of universal reporting guidelines poses challenges in ensuring the validity and reproducibility of published research studies in this field. METHODS Based on a systematic review of academic publications and reporting standards demanded by both international consortia and regulatory stakeholders as well as leading journals in the fields of medicine and medical informatics, 26 reporting guidelines published between 2009 and 2023 were included in this analysis. Guidelines were stratified by breadth (general or specific to medical fields), underlying consensus quality, and target research phase (preclinical, translational, clinical) and subsequently analyzed regarding the overlap and variations in guideline items. RESULTS AI reporting guidelines for medical research vary with respect to the quality of the underlying consensus process, breadth, and target research phase. Some guideline items such as reporting of study design and model performance recur across guidelines, whereas other items are specific to particular fields and research stages. CONCLUSIONS Our analysis highlights the importance of reporting guidelines in clinical AI research and underscores the need for common standards that address the identified variations and gaps in current guidelines. Overall, this comprehensive overview could help researchers and public stakeholders reinforce quality standards for increased reliability, reproducibility, clinical validity, and public trust in AI research in healthcare. This could facilitate the safe, effective, and ethical translation of AI methods into clinical applications that will ultimately improve patient outcomes.
Collapse
Grants
- UM1 TR004402 NCATS NIH HHS
- JNK is supported by the German Federal Ministry of Health (DEEP LIVER, ZMVI1-2520DAT111) and the Max-Eder-Programme of the German Cancer Aid (grant #70113864), the German Federal Ministry of Education and Research (PEARL, 01KD2104C; CAMINO, 01EO2101; SWAG, 01KD2215A; TRANSFORM LIVER, 031L0312A), the German Academic Exchange Service (SECAI, 57616814), the German Federal Joint Committee (Transplant.KI, 01VSF21048) the European Union (ODELIA, 101057091; GENIAL, 101096312) and the National Institute for Health and Care Research (NIHR, NIHR213331) Leeds Biomedical Research Centre.
Collapse
Affiliation(s)
- Fiona R Kolbinger
- Else Kroener Fresenius Center for Digital Health, TUD Dresden University of Technology, Dresden, Germany
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
- Regenstrief Center for Healthcare Engineering, Purdue University, West Lafayette, IN, USA
- Department of Biostatistics and Health Data Science, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Gregory P Veldhuizen
- Else Kroener Fresenius Center for Digital Health, TUD Dresden University of Technology, Dresden, Germany
| | - Jiefu Zhu
- Else Kroener Fresenius Center for Digital Health, TUD Dresden University of Technology, Dresden, Germany
| | - Daniel Truhn
- Department of Diagnostic and Interventional Radiology, University Hospital Aachen, Aachen, Germany
| | - Jakob Nikolas Kather
- Else Kroener Fresenius Center for Digital Health, TUD Dresden University of Technology, Dresden, Germany.
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany.
- Department of Medicine I, University Hospital Dresden, Dresden, Germany.
- Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany.
| |
Collapse
|
6
|
Sujit SJ, Aminu M, Karpinets TV, Chen P, Saad MB, Salehjahromi M, Boom JD, Qayati M, George JM, Allen H, Antonoff MB, Hong L, Hu X, Heeke S, Tran HT, Le X, Elamin YY, Altan M, Vokes NI, Sheshadri A, Lin J, Zhang J, Lu Y, Behrens C, Godoy MCB, Wu CC, Chang JY, Chung C, Jaffray DA, Wistuba II, Lee JJ, Vaporciyan AA, Gibbons DL, Heymach J, Zhang J, Cascone T, Wu J. Enhancing NSCLC recurrence prediction with PET/CT habitat imaging, ctDNA, and integrative radiogenomics-blood insights. Nat Commun 2024; 15:3152. [PMID: 38605064 PMCID: PMC11009351 DOI: 10.1038/s41467-024-47512-0] [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: 06/27/2023] [Accepted: 03/21/2024] [Indexed: 04/13/2024] Open
Abstract
While we recognize the prognostic importance of clinicopathological measures and circulating tumor DNA (ctDNA), the independent contribution of quantitative image markers to prognosis in non-small cell lung cancer (NSCLC) remains underexplored. In our multi-institutional study of 394 NSCLC patients, we utilize pre-treatment computed tomography (CT) and 18F-fluorodeoxyglucose positron emission tomography (FDG-PET) to establish a habitat imaging framework for assessing regional heterogeneity within individual tumors. This framework identifies three PET/CT subtypes, which maintain prognostic value after adjusting for clinicopathologic risk factors including tumor volume. Additionally, these subtypes complement ctDNA in predicting disease recurrence. Radiogenomics analysis unveil the molecular underpinnings of these imaging subtypes, highlighting downregulation in interferon alpha and gamma pathways in the high-risk subtype. In summary, our study demonstrates that these habitat imaging subtypes effectively stratify NSCLC patients based on their risk levels for disease recurrence after initial curative surgery or radiotherapy, providing valuable insights for personalized treatment approaches.
Collapse
Affiliation(s)
- Sheeba J Sujit
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Muhammad Aminu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tatiana V Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pingjun Chen
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maliazurina B Saad
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Morteza Salehjahromi
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John D Boom
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Mohamed Qayati
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James M George
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Haley Allen
- Natural Sciences, Rice University, Houston, TX, USA
| | - Mara B Antonoff
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lingzhi Hong
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xin Hu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Simon Heeke
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hai T Tran
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiuning Le
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yasir Y Elamin
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mehmet Altan
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Natalie I Vokes
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ajay Sheshadri
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Julie Lin
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yang Lu
- Department of Nuclear Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Myrna C B Godoy
- Department of Thoracic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carol C Wu
- Department of Thoracic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joe Y Chang
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Caroline Chung
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Institute of Data Science in Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David A Jaffray
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Institute of Data Science in Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ara A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Lung Cancer Genomics Program, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Lung Cancer Interception Program, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tina Cascone
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jia Wu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Institute of Data Science in Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| |
Collapse
|
7
|
Ram S, Mojtahedzadeh S, Aguilar JK, Coskran T, Powell EL, O'Neil SP. Quantitative performance assessment of Ultivue multiplex panels in formalin-fixed, paraffin-embedded human and murine tumor specimens. Sci Rep 2024; 14:8496. [PMID: 38605049 PMCID: PMC11009312 DOI: 10.1038/s41598-024-58372-5] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/28/2024] [Indexed: 04/13/2024] Open
Abstract
We present a rigorous validation strategy to evaluate the performance of Ultivue multiplex immunofluorescence panels. We have quantified the accuracy and precision of four different multiplex panels (three human and one mouse) in tumor specimens with varying levels of T cell density. Our results show that Ultivue panels are typically accurate wherein the relative difference in cell proportion between a multiplex image and a 1-plex image is less than 20% for a given biomarker. Ultivue panels exhibited relatively high intra-run precision (CV ≤ 25%) and relatively low inter-run precision (CV >> 25%) which can be remedied by using local intensity thresholding to gate biomarker positivity. We also evaluated the reproducibility of cell-cell distance estimates measured from multiplex images which show high intra- and inter-run precision. We introduce a new metric, multiplex labeling efficiency, which can be used to benchmark the overall fidelity of the multiplex data across multiple batch runs. Taken together our results provide a comprehensive characterization of Ultivue panels and offer practical guidelines for analyzing multiplex images.
Collapse
Affiliation(s)
- Sripad Ram
- Drug Safety Research and Development, Pfizer Inc., Groton, CT, USA.
| | | | | | - Timothy Coskran
- Drug Safety Research and Development, Pfizer Inc., Groton, CT, USA
| | - Eric L Powell
- Oncology Research and Development, Pfizer Inc., San Diego, CA, USA
| | - Shawn P O'Neil
- Drug Safety Research and Development, Pfizer Inc., Groton, CT, USA
| |
Collapse
|
8
|
Yin Y, Niu Q, Wei Z, Wang Y, Li G, Zhang W, Guo K, Yao X. Research on the toxicological prognostic significance of age-related genes in endometrial cancer unveiling key factors in patient prognosis. Environ Toxicol 2024. [PMID: 38591852 DOI: 10.1002/tox.24219] [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] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/11/2024] [Accepted: 03/04/2024] [Indexed: 04/10/2024]
Abstract
This study investigates the influence of aging-related genes on endometrial cancer, a prominent gynecological malignancy with rising incidence and mortality. By analyzing gene expression differences between cancerous and normal endometrial tissues, 42 aging-related genes were identified as differentially expressed. Utilizing the TCGA-UCEC sample, consensus clustering divided the samples into two molecular subgroups, Aging low and Aging high, based on their expression profiles. These subgroups showed distinct prognoses and survival rates, with the Aging high group associated with DNA repair and cell cycle pathways, and the Aging low group showing suppressed metabolic pathways and increased immune cell infiltration, suggesting a potential for better immunotherapy outcomes. Mutation analysis did not find significant differences in mutation frequencies between the groups, but a high Tumor Mutation Burden (TMB) correlated with better prognosis. A risk score model was also developed, showcasing significant prognostic power. Further analysis of the SIX1 gene revealed its overexpression in cancer cells. Drug sensitivity tests indicated that the low-risk group might respond better to chemotherapy. This research underscores the significance of aging-related genes in endometrial cancer, offering insights into their prognostic value and therapeutic potential, which could lead to personalized treatment approaches and enhanced patient management.
Collapse
Affiliation(s)
- Yongchao Yin
- Department of Second Ward of Gynecology, Xingtai People's Hospital, Xingtai, China
| | - Qian Niu
- Department of Ouclar Trauma, Hebei Provincial Eye Hospital, Xingtai, China
| | - Zhiqiang Wei
- Department of Operating Room, Xingtai People's Hospital, Xingtai, China
| | - Yefei Wang
- Department of Operating Room, Xingtai People's Hospital, Xingtai, China
| | - Gang Li
- Department of Operating Room, Xingtai People's Hospital, Xingtai, China
| | - Weican Zhang
- Department of Fourth Ward of Gynecology, Xingtai People's Hospital, Xingtai, China
| | - Kai Guo
- Department of Neurosurgery, Xingtai People's Hospital, Xingtai, China
| | - Xinyu Yao
- Department of Anesthesiology, Xingtai People's Hospital, Xingtai, China
| |
Collapse
|
9
|
Xin J, Gu D, Li S, Qian S, Cheng Y, Shao W, Ben S, Chen S, Zhu L, Jin M, Chen K, Hu Z, Zhang Z, Du M, Shen H, Wang M. Integration of pathologic characteristics, genetic risk and lifestyle exposure for colorectal cancer survival assessment. Nat Commun 2024; 15:3042. [PMID: 38589358 PMCID: PMC11002003 DOI: 10.1038/s41467-024-47204-9] [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: 08/31/2023] [Accepted: 03/20/2024] [Indexed: 04/10/2024] Open
Abstract
The development of an effective survival prediction tool is key for reducing colorectal cancer mortality. Here, we apply a three-stage study to devise a polygenic prognostic score (PPS) for stratifying colorectal cancer overall survival. Leveraging two cohorts of 3703 patients, we first perform a genome-wide survival association analysis to develop eight candidate PPSs. Further using an independent cohort with 470 patients, we identify the 287 variants-derived PPS (i.e., PPS287) achieving an optimal prediction performance [hazard ratio (HR) per SD = 1.99, P = 1.76 × 10-8], accompanied by additional tests in two external cohorts, with HRs per SD of 1.90 (P = 3.21 × 10-14; 543 patients) and 1.80 (P = 1.11 × 10-9; 713 patients). Notably, the detrimental impact of pathologic characteristics and genetic risk could be attenuated by a healthy lifestyle, yielding a 7.62% improvement in the 5-year overall survival rate. Therefore, our findings demonstrate the integrated contribution of pathologic characteristics, germline variants, and lifestyle exposure to the prognosis of colorectal cancer patients.
Collapse
Affiliation(s)
- Junyi Xin
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Dongying Gu
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Shuwei Li
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Sangni Qian
- Department of Epidemiology and Biostatistics at School of Public Health, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yifei Cheng
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Wei Shao
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuai Ben
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Silu Chen
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Linjun Zhu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mingjuan Jin
- Department of Epidemiology and Biostatistics at School of Public Health, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kun Chen
- Department of Epidemiology and Biostatistics at School of Public Health, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhibin Hu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Mulong Du
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongbing Shen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, China.
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.
- The Affiliated Suzhou Hospital of, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China.
| |
Collapse
|
10
|
Sornsamdang G, Shobana J, Chanprapaph K, Chantratita W, Chotewutmontri S, Limtong P, O-Charoen P, Sukasem C. Novel genetic variants of HLA gene associated with Thai Behcet's disease (BD) patients using next generation sequencing technology. Sci Rep 2024; 14:7967. [PMID: 38575661 PMCID: PMC10995258 DOI: 10.1038/s41598-024-58254-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: 09/17/2023] [Accepted: 03/27/2024] [Indexed: 04/06/2024] Open
Abstract
Behçet's disease (BD) manifests as an autoimmune disorder featuring recurrent ulcers and multi-organ involvement, influenced by genetic factors associated with both HLA and non-HLA genes, including TNF-α and ERAP1. The study investigated the susceptible alleles of both Class I and II molecules of the HLA gene in 56 Thai BD patients and 192 healthy controls through next-generation sequencing using a PacBio kit. The study assessed 56 BD patients, primarily females (58.9%), revealing diverse manifestations including ocular (41.1%), vascular (35.7%), skin (55.4%), CNS (5.4%), and GI system (10.7%) involvement. This study found associations between BD and HLA-A*26:01:01 (OR 3.285, 95% CI 1.135-9.504, P-value 0.028), HLA-B*39:01:01 (OR 6.176, 95% CI 1.428-26.712, P-value 0.015), HLA-B*51:01:01 (OR 3.033, 95% CI 1.135-8.103, P-value 0.027), HLA-B*51:01:02 (OR 6.176, 95% CI 1.428-26.712, P-value 0.015), HLA-C*14:02:01 (OR 3.485, 95% CI 1.339-9.065, P-value 0.01), HLA-DRB1*14:54:01 (OR 1.924, 95% CI 1.051-3.522, P-value 0.034), and HLA-DQB1*05:03:01 (OR 3.00, 95% CI 1.323-6.798, P-value 0.008). However, after Bonferroni correction none of these alleles were found to be associated with BD. In haplotype analysis, we found a strong linkage disequilibrium in HLA-B*51:01:01, HLA-C*14:02:01 (P-value 0.0, Pc-value 0.02). Regarding the phenotype, a significant association was found between HLA-DRB1*14:54:01 (OR 11.67, 95% CI 2.86-47.57, P-value 0.001) and BD with ocular involvement, apart from this, no distinct phenotype-HLA association was documented. In summary, our study identifies specific HLA associations in BD. Although limited by a small sample size, we acknowledge the need for further investigation into HLA relationships with CNS, GI, and neurological phenotypes in the Thai population.
Collapse
Affiliation(s)
- Gaidganok Sornsamdang
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - John Shobana
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Kumutnart Chanprapaph
- Division of Dermatology, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sasithorn Chotewutmontri
- Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Preeyachat Limtong
- Division of Dermatology, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pichaya O-Charoen
- Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Chonlaphat Sukasem
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand.
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand.
- Pharmacogenomics and Precision Medicine, The Preventive Genomics & Family Check-Up Services Center, Bumrungrad International Hospital, Bangkok, Thailand.
- Department of Pharmacology and Therapeutics, MRC Centre for Drug Safety Science, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
| |
Collapse
|
11
|
Gonzalez-Ortiz F, Kirsebom BE, Contador J, Tanley JE, Selnes P, Gísladóttir B, Pålhaugen L, Suhr Hemminghyth M, Jarholm J, Skogseth R, Bråthen G, Grøndtvedt G, Bjørnerud A, Tecelao S, Waterloo K, Aarsland D, Fernández-Lebrero A, García-Escobar G, Navalpotro-Gómez I, Turton M, Hesthamar A, Kac PR, Nilsson J, Luchsinger J, Hayden KM, Harrison P, Puig-Pijoan A, Zetterberg H, Hughes TM, Suárez-Calvet M, Karikari TK, Fladby T, Blennow K. Plasma brain-derived tau is an amyloid-associated neurodegeneration biomarker in Alzheimer's disease. Nat Commun 2024; 15:2908. [PMID: 38575616 PMCID: PMC10995141 DOI: 10.1038/s41467-024-47286-5] [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: 08/09/2023] [Accepted: 03/26/2024] [Indexed: 04/06/2024] Open
Abstract
Staging amyloid-beta (Aβ) pathophysiology according to the intensity of neurodegeneration could identify individuals at risk for cognitive decline in Alzheimer's disease (AD). In blood, phosphorylated tau (p-tau) associates with Aβ pathophysiology but an AD-type neurodegeneration biomarker has been lacking. In this multicenter study (n = 1076), we show that brain-derived tau (BD-tau) in blood increases according to concomitant Aβ ("A") and neurodegeneration ("N") abnormalities (determined using cerebrospinal fluid biomarkers); We used blood-based A/N biomarkers to profile the participants in this study; individuals with blood-based p-tau+/BD-tau+ profiles had the fastest cognitive decline and atrophy rates, irrespective of the baseline cognitive status. Furthermore, BD-tau showed no or much weaker correlations with age, renal function, other comorbidities/risk factors and self-identified race/ethnicity, compared with other blood biomarkers. Here we show that blood-based BD-tau is a biomarker for identifying Aβ-positive individuals at risk of short-term cognitive decline and atrophy, with implications for clinical trials and implementation of anti-Aβ therapies.
Collapse
Affiliation(s)
- Fernando Gonzalez-Ortiz
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden.
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.
| | - Bjørn-Eivind Kirsebom
- Department of Neurology, University Hospital of North Norway, Tromsø, Norway
- Department of Psychology, Faculty of Health Sciences, The Arctic University of Norway, Tromsø, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - José Contador
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
- Hospital del Mar Research Institute, Barcelona, Spain
- Cognitive Decline and Movement Disorders Unit, Neurology Department, Hospital del Mar, Barcelona, Spain
| | - Jordan E Tanley
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Per Selnes
- Department of Neurology, Akershus University Hospital, Lørenskog, Norway
| | | | - Lene Pålhaugen
- Department of Neurology, Akershus University Hospital, Lørenskog, Norway
| | - Mathilde Suhr Hemminghyth
- Research Group for Age-Related Medicine, Haugesund Hospital, Haugesund, Norway
- Department of Neuropsychology, Haugesund Hospital, Haugesund, Norway
- Department of Clinical Medicine (K1), University of Bergen, Bergen, Norway
| | - Jonas Jarholm
- Department of Neurology, Akershus University Hospital, Lørenskog, Norway
| | - Ragnhild Skogseth
- Department of Geriatric Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
- Department of Clinical Sciences, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Geir Bråthen
- Department of Neurology and Clinical Neurophysiology, University Hospital of Trondheim, Trondheim, Norway
- Department of Neuromedicine and Movement Science, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Gøril Grøndtvedt
- Department of Neurology and Clinical Neurophysiology, University Hospital of Trondheim, Trondheim, Norway
- Department of Neuromedicine and Movement Science, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Atle Bjørnerud
- Department of Physics, University of Oslo, Oslo, Norway
- Unit for Computational Radiology and Artificial Intelligence, Oslo University hospital, Oslo, Norway
- Department of Psychology, Faculty for Social Sciences, University of Oslo, Oslo, Norway
| | - Sandra Tecelao
- Department of Neurology, Akershus University Hospital, Lørenskog, Norway
| | - Knut Waterloo
- Department of Neurology, University Hospital of North Norway, Tromsø, Norway
- Department of Psychology, Faculty of Health Sciences, The Arctic University of Norway, Tromsø, Norway
| | - Dag Aarsland
- Department of Old Age Psychiatry. Institute of psychiatry, Psychology and Neuroscience King's College London, London, UK
- Centre for Age-Related Diseases, University Hospital Stavanger, Stavanger, Norway
| | - Aida Fernández-Lebrero
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
- Hospital del Mar Research Institute, Barcelona, Spain
- Cognitive Decline and Movement Disorders Unit, Neurology Department, Hospital del Mar, Barcelona, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, 08003, Spain
- ERA-Net on Cardiovascular Diseases (ERA-CVD) consortium, Barcelona, Spain
| | - Greta García-Escobar
- Hospital del Mar Research Institute, Barcelona, Spain
- ERA-Net on Cardiovascular Diseases (ERA-CVD) consortium, Barcelona, Spain
| | - Irene Navalpotro-Gómez
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
- Hospital del Mar Research Institute, Barcelona, Spain
- Cognitive Decline and Movement Disorders Unit, Neurology Department, Hospital del Mar, Barcelona, Spain
- ERA-Net on Cardiovascular Diseases (ERA-CVD) consortium, Barcelona, Spain
| | - Michael Turton
- Bioventix Plc, 7 Romans Business Park, East Street, Farnham, Surrey, GU9 7SX, UK
| | - Agnes Hesthamar
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Przemyslaw R Kac
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Johanna Nilsson
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Jose Luchsinger
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Kathleen M Hayden
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Peter Harrison
- Bioventix Plc, 7 Romans Business Park, East Street, Farnham, Surrey, GU9 7SX, UK
| | - Albert Puig-Pijoan
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
- Hospital del Mar Research Institute, Barcelona, Spain
- ERA-Net on Cardiovascular Diseases (ERA-CVD) consortium, Barcelona, Spain
- Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK
- UK Dementia Research Institute at UCL, London, UK
- Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Timothy M Hughes
- Department of Internal Medicine, Section on Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Marc Suárez-Calvet
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
- Hospital del Mar Research Institute, Barcelona, Spain
- Cognitive Decline and Movement Disorders Unit, Neurology Department, Hospital del Mar, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), Madrid, Spain
| | - Thomas K Karikari
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tormod Fladby
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
- Department of Neurology, Akershus University Hospital, Lørenskog, Norway
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| |
Collapse
|
12
|
Riganati M, Zotta F, Candino A, Conversano E, Gargiulo A, Scarsella M, Lo Russo A, Bettini C, Emma F, Vivarelli M, Colucci M. A novel flow cytometry panel to identify prognostic markers for steroid-sensitive forms of idiopathic nephrotic syndrome in childhood. Front Immunol 2024; 15:1379924. [PMID: 38629076 PMCID: PMC11018947 DOI: 10.3389/fimmu.2024.1379924] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/14/2024] [Indexed: 04/19/2024] Open
Abstract
Introduction The clinical evolution of steroid-sensitive forms of pediatric idiopathic nephrotic syndrome (INS) is highly heterogeneous following the standard treatment with prednisone. To date, no prognostic marker has been identified to predict the severity of the disease course starting from the first episode. Methods In this monocentric prospective cohort study we set up a reproducible and standardized flow cytometry panel using two sample tubes (one for B-cell and one for T-cell subsets) to extensively characterized the lymphocyte repertoire of INS pediatric patients. A total of 44 children with INS at disease onset were enrolled, sampled before and 3 months after standard induction therapy with prednisone and followed for 12 months to correctly classify their disease based on relapses. Age-matched controls with non immune-mediated renal diseases or with urological disorders were also enrolled. Demographical, clinical, laboratory and immunosuppressive treatment data were registered. Results We found that children with INS at disease onset had significantly higher circulating levels of total CD19+ and specific B-cell subsets (transitional, mature-naïve, plasmablasts/plasmacells, CD19+CD27+, unswitched, switched and atypical memory B cells) and reduced circulating levels of Tregs, when compared to age-matched controls. Prednisone therapy restored most B- and T-cell alterations. When patients were subdivided based on disease relapse, relapsing patients had significantly more transitional, CD19+CD27+ memory and in particular unswitched memory B cells at disease onset, which were predictive of a higher risk of relapse in steroid-sensitive patients by logistic regression analysis, irrespective of age. In accordance, B-cell dysregulations resulted mainly associated with steroid-dependence when patients were stratified in different disease severity forms. Of note, Treg levels were reduced independently from the disease subgroup and were not completely normalized by prednisone treatment. Conclusion We have set up a novel, reproducible, disease-specific flow cytometry panel that allows a comprehensive characterization of circulating lymphocytes. We found that, at disease onset, relapsing patients had significantly more transitional, CD19+CD27+ memory and unswitched memory B cells and those who are at higher risk of relapse had increased circulating levels of unswitched memory B cells, independently of age. This approach can allow prediction of clinical evolution, monitoring of immunosuppression and tailored treatment in different forms of INS.
Collapse
Affiliation(s)
- Martina Riganati
- Laboratory of Nephrology, Bambino Gesù Children’s Hospital Scientific Institute for Research and Health Care (IRCCS), Rome, Italy
| | - Federica Zotta
- Division of Nephrology, Bambino Gesù Children’s Hospital Scientific Institute for Research and Health Care (IRCCS), Rome, Italy
| | - Annalisa Candino
- Division of Nephrology, Bambino Gesù Children’s Hospital Scientific Institute for Research and Health Care (IRCCS), Rome, Italy
| | - Ester Conversano
- Division of Nephrology, Bambino Gesù Children’s Hospital Scientific Institute for Research and Health Care (IRCCS), Rome, Italy
| | - Antonio Gargiulo
- Division of Nephrology, Bambino Gesù Children’s Hospital Scientific Institute for Research and Health Care (IRCCS), Rome, Italy
| | - Marco Scarsella
- Research Laboratories, Bambino Gesù Children’s Hospital Scientific Institute for Research and Health Care (IRCCS), Rome, Italy
| | - Anna Lo Russo
- Research Laboratories, Bambino Gesù Children’s Hospital Scientific Institute for Research and Health Care (IRCCS), Rome, Italy
| | - Chiara Bettini
- Division of Nephrology, Bambino Gesù Children’s Hospital Scientific Institute for Research and Health Care (IRCCS), Rome, Italy
| | - Francesco Emma
- Laboratory of Nephrology, Bambino Gesù Children’s Hospital Scientific Institute for Research and Health Care (IRCCS), Rome, Italy
- Division of Nephrology, Bambino Gesù Children’s Hospital Scientific Institute for Research and Health Care (IRCCS), Rome, Italy
| | - Marina Vivarelli
- Laboratory of Nephrology, Bambino Gesù Children’s Hospital Scientific Institute for Research and Health Care (IRCCS), Rome, Italy
- Division of Nephrology, Bambino Gesù Children’s Hospital Scientific Institute for Research and Health Care (IRCCS), Rome, Italy
| | - Manuela Colucci
- Laboratory of Nephrology, Bambino Gesù Children’s Hospital Scientific Institute for Research and Health Care (IRCCS), Rome, Italy
| |
Collapse
|
13
|
Ali MM, Tank N, Bawa M. Antenatally Detected Thoracic Lesions: Prognosis, Management and Outcome. Afr J Paediatr Surg 2024; 21:117-122. [PMID: 38546250 PMCID: PMC11003573 DOI: 10.4103/ajps.ajps_116_22] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/05/2022] [Accepted: 01/09/2023] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Foetal thoracic lesions are uncommon, with the incidence of 1 in 15,000 live births. Antenatal monitoring of these lesions is required to prognosticate the parents about the postnatal outcome of the lesions and about the well-being of the baby. Foetal ultrasound and magnetic resonance imaging (MRI) are the modalities to detect these lesions and follow-up during pregnancy and postnatally. Congenital pulmonary adenomatoid malformations (CPAM), congenital diaphragmatic hernia (CDH) and bronchopulmonary sequestrations (BPS) are the commonly detected foetal thoracic lesions. Parameters such as congenital cystic adenomatoid malformation (CCAM) volume ratio (CVR) and lung-to-head ratio (LHR) determine the prognosis of these lesions. With this background, we planned to study the prognosis and outcome of antenatally detected thoracic lesions. MATERIALS AND METHODS This was a prospective study carried out for 2 years (January 2017 to December 2018). Pregnant females with foetuses diagnosed to have thoracic lesions on the second- and third-trimester ultrasound and foetal MRI were enrolled for the study. CVR and LHR were noted. Outcomes were analysed in terms of the need of termination of pregnancy, foetal or neonatal demise and need of surgery or conservative management. RESULTS Of a total of 521 pregnancies, thoracic lesions were detected in 22 (4.22%) cases. Individually, the incidence of each lesion was: CPAM-10 (45.45%), BPS-5 (22.73%), CDH-5 (22.73%) and congenital higher airway obstruction-2 (9.1%). Chromosomal screening was normal in 100% of cases. Follow-up was done for 2 years. Termination of pregnancy was required in 3 (13.64%) cases, postnatal death occurred in 4 (18.2%) cases, surgery was required in three cases of CDH soon after birth and two cases of extralobar BPS at 2 years of age. 10 (45.45%) cases were managed conservatively, who are doing well at 2-year follow-up. CONCLUSION CPAMs, BPSs and CDH are the commonly detected antenatal thoracic lesions. Ultrasonography and MRI help detect and prognosticate the parents about the outcomes of these lesions. CVR and LHR with associated congenital malformations are important prognostic markers for these lesions. There is a need of long-term prospective studies to delineate the natural history of these lesions.
Collapse
Affiliation(s)
| | - Nilesh Tank
- Department of Pediatric Surgery, Geetanjali Medical College and Hospital, Udaipur, Rajasthan, India
| | - Monika Bawa
- Department of Pediatric Surgery, PGIMER, Chandigarh, India
| |
Collapse
|
14
|
Zhuang M, Li F, Liang H, Su Y, Cheng L, Lin B, Zhou J, Deng R, Chen L, Lyu P, Lu Z. Targeting RCC1 to block the human soft-tissue sarcoma by disrupting nucleo-cytoplasmic trafficking of Skp2. Cell Death Dis 2024; 15:241. [PMID: 38561375 PMCID: PMC10985091 DOI: 10.1038/s41419-024-06629-2] [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: 10/11/2023] [Revised: 03/16/2024] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
Abstract
Soft-tissue sarcomas (STS) emerges as formidable challenges in clinics due to the complex genetic heterogeneity, high rates of local recurrence and metastasis. Exploring specific targets and biomarkers would benefit the prognosis and treatment of STS. Here, we identified RCC1, a guanine-nucleotide exchange factor for Ran, as an oncogene and a potential intervention target in STS. Bioinformatics analysis indicated that RCC1 is highly expressed and correlated with poor prognosis in STS. Functional studies showed that RCC1 knockdown significantly inhibited the cell cycle transition, proliferation and migration of STS cells in vitro, and the growth of STS xenografts in mice. Mechanistically, we identified Skp2 as a downstream target of RCC1 in STS. Loss of RCC1 substantially diminished Skp2 abundance by compromising its protein stability, resulting in the upregulation of p27Kip1 and G1/S transition arrest. Specifically, RCC1 might facilitate the nucleo-cytoplasmic trafficking of Skp2 via direct interaction. As a result, the cytoplasmic retention of Skp2 would further protect it from ubiquitination and degradation. Notably, recovery of Skp2 expression largely reversed the phenotypes induced by RCC1 knockdown in STS cells. Collectively, this study unveils a novel RCC1-Skp2-p27Kip1 axis in STS oncogenesis, which holds promise for improving prognosis and treatment of this formidable malignancy.
Collapse
Affiliation(s)
- Mingzhi Zhuang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350108, P. R. China
| | - Fengyue Li
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350108, P. R. China
| | - Hong Liang
- College of Geography and Oceanography, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, Fujian, 350108, P. R. China
| | - Yongfu Su
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350108, P. R. China
| | - Lei Cheng
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350108, P. R. China
| | - Bingkai Lin
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350108, P. R. China
| | - Jun Zhou
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350108, P. R. China
| | - Runzhi Deng
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350108, P. R. China
| | - Linying Chen
- Department of Pathology, the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, 350005, P. R. China
| | - Peng Lyu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350108, P. R. China.
| | - Zhonglei Lu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, 350108, P. R. China.
| |
Collapse
|
15
|
Yii FS, He M, Chappell F, Bernabeu MO, MacGillivray T, Dhillon B, Tatham A, Strang N. Higher intraocular pressure is associated with slower axial growth in children with non-pathological high myopia. Eye (Lond) 2024; 38:1208-1214. [PMID: 38081936 PMCID: PMC11009290 DOI: 10.1038/s41433-023-02872-7] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 04/13/2024] Open
Abstract
OBJECTIVES To investigate the association between intraocular pressure (IOP) and axial elongation rate in highly myopic children from the ZOC-BHVI High Myopia Cohort Study. METHODS 162 eyes of 81 healthy children (baseline spherical equivalent: -6.25 D to -15.50 D) aged 7-12 years with non-pathological high myopia were studied over five biennial visits. The mean (SD) follow-up duration was 5.2 (3.3) years. A linear mixed-effects model (LMM) was used to assess the association between IOP (at time point t-1) and axial elongation rate (annual rate of change in AL from t-1 to t), controlling for a pre-defined set of covariates including sex, age, central corneal thickness, anterior chamber depth and lens thickness (at t-1). LMM was also used to assess the contemporaneous association between IOP and axial length (AL) at t, controlling for the same set of covariates (at t) as before. RESULTS Higher IOP was associated with slower axial growth (β = -0.01, 95% CI -0.02 to -0.005, p = 0.001). There was a positive contemporaneous association between IOP and AL (β = 0.03, 95% CI 0.01-0.05, p = 0.004), but this association became progressively less positive with increasing age, as indicated by a negative interaction effect between IOP and age on AL (β = -0.01, 95% CI -0.01 to -0.003, p = 0.001). CONCLUSIONS Higher IOP is associated with slower rather than faster axial growth in children with non-pathological high myopia, an association plausibly confounded by the increased influence of ocular compliance on IOP.
Collapse
Affiliation(s)
- Fabian Sl Yii
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK.
- Curle Ophthalmology Laboratory, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK.
| | - Mingguang He
- School of Optometry, The Hong Kong Polytechnic University, Hong Kong, China
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
- Centre for Eye Research Australia, The University of Melbourne, Melbourne, Australia
| | - Francesca Chappell
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Miguel O Bernabeu
- Centre for Medical Informatics, Usher Institute, The University of Edinburgh, Edinburgh, UK
- The Bayes Centre, The University of Edinburgh, Edinburgh, UK
| | - Tom MacGillivray
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
- Curle Ophthalmology Laboratory, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Baljean Dhillon
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
- Curle Ophthalmology Laboratory, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
- Princess Alexandra Eye Pavilion, NHS Lothian, Edinburgh, UK
| | - Andrew Tatham
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
- Princess Alexandra Eye Pavilion, NHS Lothian, Edinburgh, UK
| | - Niall Strang
- Department of Vision Sciences, Glasgow Caledonian University, Glasgow, UK
| |
Collapse
|
16
|
Xiao H, Weng Z, Sun K, Shen J, Lin J, Chen S, Li B, Shi Y, Kuang M, Song X, Weng W, Peng S. Predicting 5-year recurrence risk in colorectal cancer: development and validation of a histology-based deep learning approach. Br J Cancer 2024; 130:951-960. [PMID: 38245662 PMCID: PMC10951272 DOI: 10.1038/s41416-024-02573-2] [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: 04/27/2023] [Revised: 12/15/2023] [Accepted: 01/03/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Accurate estimation of the long-term risk of recurrence in patients with non-metastatic colorectal cancer (CRC) is crucial for clinical management. Histology-based deep learning is expected to provide more abundant information for risk stratification. METHODS We developed and validated a weakly supervised deep-learning model for predicting 5-year relapse-free survival (RFS) to stratify patients with different risks based on histological images from three hospitals of 614 cases with non-metastatic CRC. A deep prognostic factor (DL-RRS) was established to stratify patients into high and low-risk group. The areas under the curve (AUCs) were calculated to evaluate the performances of models. RESULTS Our proposed model achieves the AUCs of 0.833 (95% CI: 0.736-0.905) and 0.715 (95% CI: 0.647-0.776) on validation cohort and external test cohort, respectively. The 5-year RFS rate was 45.7% for high DL-RRS patients, and 82.5% for low DL-RRS patients respectively in the external test cohort (HR: 3.89, 95% CI: 2.51-6.03, P < 0.001). Adjuvant chemotherapy was associated with improved RFS in Stage II patients with high DL-RRS (HR: 0.15, 95% CI: 0.06-0.38, P < 0.001). CONCLUSIONS DL-RRS has a good predictive performance of 5-year recurrence risk in CRC, and will better serve the clinical decision-making.
Collapse
Affiliation(s)
- Han Xiao
- Department of Medical Ultrasonics, Institute of Diagnostic and Interventional Ultrasound, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zongpeng Weng
- Clinical Trials Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Kaiyu Sun
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jingxian Shen
- Department of Medical Imaging, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jie Lin
- Department of Liver and Pancreatobiliary Surgery, Shunde Hospital of Southern Medical University, Shunde, China
| | - Shuling Chen
- Department of Medical Ultrasonics, Institute of Diagnostic and Interventional Ultrasound, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Bin Li
- Clinical Trials Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yiyu Shi
- University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Ming Kuang
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xinming Song
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Weixiang Weng
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Sui Peng
- Clinical Trials Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
| |
Collapse
|
17
|
Gorgulho J, Roderburg C, Beier F, Bokemeyer C, Brümmendorf TH, Loosen SH, Luedde T. Soluble lymphocyte activation gene-3 (sLAG3) and CD4/CD8 ratio dynamics as predictive biomarkers in patients undergoing immune checkpoint blockade for solid malignancies. Br J Cancer 2024; 130:1013-1022. [PMID: 38233492 PMCID: PMC10951205 DOI: 10.1038/s41416-023-02558-7] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 12/05/2023] [Accepted: 12/13/2023] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND The search for biomarkers to identify suitable candidates for immune checkpoint inhibitor (ICI) therapy remains ongoing. We evaluate how soluble levels of the next generation immune checkpoint Lymphocyte Activation Gene-3 (sLAG-3) and its association with circulating T lymphocyte subsets could pose as a novel biomarker to predict outcome to ICI therapy. METHODS Circulating levels of sLAG3 were analyzed using multiplex immunoassay in n = 84 patients undergoing ICI therapy for advanced solid cancer, accompanied by flow cytometry analyses of peripheral blood mononuclear cells (PBMCs). RESULTS Uni- and multivariate analysis shows that patients with higher sLAG3 concentrations before ICI therapy had a significantly impaired progression-free (PFS) and overall survival (OS) (HRPFS: 1.005 [95%CI: 1.000-1.009], p = 0.039; HROS: 1.006 [95%CI: 1.001-1.011], p = 0.015). The CD4/CD8 cell ratio and its dynamics during therapy were strong predictors of PFS and OS with patients with a decreasing ratio between baseline and after 1-2 cycles having an improved median OS compared to patients with increasing values (p = 0.012, HR: 3.32). An immunological score combining sLAG3 and the CD4/CD8 ratio showed the highest predictive potential (HROS: 10.3). CONCLUSION Pending prospective validation, sLAG3 and correlating circulating T-cell subsets can be used as a non-invasive predictive marker to predict outcome to ICI therapy to help identifying ideal ICI candidates in the future.
Collapse
Affiliation(s)
- Joao Gorgulho
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section of Pneumology, University Medical Centre Hamburg-Eppendorf, Martinistraße 52, 20251, Hamburg, Germany
- Mildred Scheel Cancer Career Center, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Roderburg
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
- Center for Integrated Oncology Aachen-Bonn-Cologne-Düsseldorf (CIOABCD), Aachen, Germany
| | - Fabian Beier
- Center for Integrated Oncology Aachen-Bonn-Cologne-Düsseldorf (CIOABCD), Aachen, Germany
- Department of Medicine IV, University Hospital RWTH Aachen, Pauwelsstrasse 30, 52074, Aachen, Germany
| | - Carsten Bokemeyer
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section of Pneumology, University Medical Centre Hamburg-Eppendorf, Martinistraße 52, 20251, Hamburg, Germany
| | - Tim H Brümmendorf
- Center for Integrated Oncology Aachen-Bonn-Cologne-Düsseldorf (CIOABCD), Aachen, Germany
- Department of Medicine IV, University Hospital RWTH Aachen, Pauwelsstrasse 30, 52074, Aachen, Germany
| | - Sven H Loosen
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany.
- Center for Integrated Oncology Aachen-Bonn-Cologne-Düsseldorf (CIOABCD), Aachen, Germany.
| | - Tom Luedde
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany.
- Center for Integrated Oncology Aachen-Bonn-Cologne-Düsseldorf (CIOABCD), Aachen, Germany.
| |
Collapse
|
18
|
Cong L, Zhao Q, Sun H, Zhou Z, Hu Y, Li C, Hao M, Cong X. A novel long non-coding RNA SLNCR1 promotes proliferation, migration, and invasion of melanoma via transcriptionally regulating SOX5. Cell Death Discov 2024; 10:160. [PMID: 38561355 PMCID: PMC10984963 DOI: 10.1038/s41420-024-01922-7] [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: 07/06/2023] [Revised: 03/13/2024] [Accepted: 03/19/2024] [Indexed: 04/04/2024] Open
Abstract
Steroid receptor RNA activator (SRA)-like non-coding RNA (SLNCR1) has been implicated in various tumorigenic processes, but the precise regulatory role in melanoma progression remains uncertain. We performed a comprehensive analysis to investigate the prognostic value of SLNCR1 expression in patients with melanoma by TCGA database and melanoma tissue samples via the Kaplan-Meier method. Subsequently, we conducted qRT-PCR and Fluorescence in Situ Hybridization (FISH) assays to identify SLNCR1 expression levels and localization in tissues and cells, respectively. Loss-of-function assays utilizing shRNAs vectors were used to investigate the potential impact of SLNCR1. Our data showed that SLNCR1 is significantly up-regulated in human malignant melanoma tissues and cell lines and functions as an oncogene. Silencing of SLNCR1 suppressed melanoma cell proliferation, migration, invasion, and inhibited tumorigenesis in a mouse xenograft model. Additionally, we employed bioinformatic predictive analysis, combined with dual-luciferase reporter analysis and functional rescue assays, to elucidate the mechanistic target of the SLNCR1/SOX5 axis in melanoma. Mechanistically, we discovered that SLNCR1 promotes EMT of human melanoma by targeting SOX5, as downregulation of SLNCR1 expression leads to a decrease in SOX5 protein levels and inhibits melanoma tumorigenesis. Our research offers promising insights for more precise diagnosis and treatment of human melanoma.
Collapse
Affiliation(s)
- Lele Cong
- Department of Dermatology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Qing Zhao
- Department of Neurology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Hongyan Sun
- Department of Biobank, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Zilong Zhou
- Department of Biobank, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Yue Hu
- Department of Biobank, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Chunyi Li
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Changchun, China
| | - Miao Hao
- Scientific Research Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China.
| | - Xianling Cong
- Department of Biobank, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China.
| |
Collapse
|
19
|
Vasseur A, Cabel L, Hego C, Takka W, Trabelsi Grati O, Renouf B, Lerebours F, Loirat D, Brain E, Cottu P, Sablin MP, Pierga JY, Callens C, Renault S, Bidard FC. Fulvestrant and everolimus efficacy after CDK4/6 inhibitor: a prospective study with circulating tumor DNA analysis. Oncogene 2024; 43:1214-1222. [PMID: 38413796 PMCID: PMC11014798 DOI: 10.1038/s41388-024-02986-6] [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: 09/11/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/29/2024]
Abstract
In a prospective study (NCT02866149), we assessed the efficacy of fulvestrant and everolimus in CDK4/6i pre-treated mBC patients and circulating tumor DNA (ctDNA) changes throughout therapy. Patients treated with fulvestrant and everolimus had their ctDNA assessed at baseline, after 3-5 weeks and at disease progression. Somatic mutations were identified in archived tumor tissues by targeted NGS and tracked in cell-free DNA by droplet digital PCR. ctDNA detection was then associated with clinicopathological characteristics and patients' progression-free survival (PFS), overall survival (OS) and best overall response (BOR). In the 57 included patients, median PFS and OS were 6.8 (95%CI [5.03-11.5]) and 38.2 (95%CI [30.0-not reached]) months, respectively. In 47 response-evaluable patients, BOR was a partial response or stable disease in 15 (31.9%) and 11 (23.4%) patients, respectively. Among patients with trackable somatic mutation and available plasma sample, N = 33/47 (70.2%) and N = 19/36 (52.8%) had ctDNA detected at baseline and at 3 weeks, respectively. ctDNA detection at baseline and PIK3CA mutation had an adverse prognostic impact on PFS and OS in multivariate analysis. This prospective cohort study documents the efficacy of fulvestrant and everolimus in CDK4/6i-pretreated ER + /HER2- mBC and highlights the clinical validity of early ctDNA changes as pharmacodynamic biomarker.
Collapse
Affiliation(s)
- Antoine Vasseur
- Department of Medical Oncology, Institut Curie, Paris & Saint-Cloud, France
- Circulating Tumor Biomarkers Laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
| | - Luc Cabel
- Department of Medical Oncology, Institut Curie, Paris & Saint-Cloud, France
| | - Caroline Hego
- Circulating Tumor Biomarkers Laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
| | - Wissam Takka
- Circulating Tumor Biomarkers Laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
| | - Olfa Trabelsi Grati
- Department of Genetics, Institut Curie, Paris Sciences & Lettres University, Paris, France
| | | | - Florence Lerebours
- Department of Medical Oncology, Institut Curie, Paris & Saint-Cloud, France
| | - Delphine Loirat
- Department of Medical Oncology, Institut Curie, Paris & Saint-Cloud, France
| | - Etienne Brain
- Department of Medical Oncology, Institut Curie, Paris & Saint-Cloud, France
| | - Paul Cottu
- Department of Medical Oncology, Institut Curie, Paris & Saint-Cloud, France
| | - Marie-Paule Sablin
- Department of Medical Oncology, Institut Curie, Paris & Saint-Cloud, France
| | - Jean-Yves Pierga
- Department of Medical Oncology, Institut Curie, Paris & Saint-Cloud, France
- Université Paris Cité, Paris, France
| | - Céline Callens
- Department of Genetics, Institut Curie, Paris Sciences & Lettres University, Paris, France
| | - Shufang Renault
- Circulating Tumor Biomarkers Laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France.
| | - François-Clément Bidard
- Department of Medical Oncology, Institut Curie, Paris & Saint-Cloud, France.
- Circulating Tumor Biomarkers Laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France.
- UVSQ, Paris-Saclay University, Saint Cloud, France.
| |
Collapse
|
20
|
Menon PJ, Sambin S, Criniere-Boizet B, Courtin T, Tesson C, Casse F, Ferrien M, Mariani LL, Carvalho S, Lejeune FX, Rebbah S, Martet G, Houot M, Lanore A, Mangone G, Roze E, Vidailhet M, Aasly J, Gan Or Z, Yu E, Dauvilliers Y, Zimprich A, Tomantschger V, Pirker W, Álvarez I, Pastor P, Di Fonzo A, Bhatia KP, Magrinelli F, Houlden H, Real R, Quattrone A, Limousin P, Korlipara P, Foltynie T, Grosset D, Williams N, Narendra D, Lin HP, Jovanovic C, Svetel M, Lynch T, Gallagher A, Vandenberghe W, Gasser T, Brockmann K, Morris HR, Borsche M, Klein C, Corti O, Brice A, Lesage S, Corvol JC. Genotype-phenotype correlation in PRKN-associated Parkinson's disease. NPJ Parkinsons Dis 2024; 10:72. [PMID: 38553467 PMCID: PMC10980707 DOI: 10.1038/s41531-024-00677-3] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 03/07/2024] [Indexed: 04/02/2024] Open
Abstract
Bi-allelic pathogenic variants in PRKN are the most common cause of autosomal recessive Parkinson's disease (PD). 647 patients with PRKN-PD were included in this international study. The pathogenic variants present were characterised and investigated for their effect on phenotype. Clinical features and progression of PRKN-PD was also assessed. Among 133 variants in index cases (n = 582), there were 58 (43.6%) structural variants, 34 (25.6%) missense, 20 (15%) frameshift, 10 splice site (7.5%%), 9 (6.8%) nonsense and 2 (1.5%) indels. The most frequent variant overall was an exon 3 deletion (n = 145, 12.3%), followed by the p.R275W substitution (n = 117, 10%). Exon3, RING0 protein domain and the ubiquitin-like protein domain were mutational hotspots with 31%, 35.4% and 31.7% of index cases presenting mutations in these regions respectively. The presence of a frameshift or structural variant was associated with a 3.4 ± 1.6 years or a 4.7 ± 1.6 years earlier age at onset of PRKN-PD respectively (p < 0.05). Furthermore, variants located in the N-terminus of the protein, a region enriched with frameshift variants, were associated with an earlier age at onset. The phenotype of PRKN-PD was characterised by slow motor progression, preserved cognition, an excellent motor response to levodopa therapy and later development of motor complications compared to early-onset PD. Non-motor symptoms were however common in PRKN-PD. Our findings on the relationship between the type of variant in PRKN and the phenotype of the disease may have implications for both genetic counselling and the design of precision clinical trials.
Collapse
Affiliation(s)
- Poornima Jayadev Menon
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France.
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France.
- School of Postgraduate Studies, Royal College of Surgeons in Ireland, Dublin, Ireland.
| | - Sara Sambin
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
| | - Baptiste Criniere-Boizet
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Thomas Courtin
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Genetics, Hôpital Pitié-Salpêtrière, Paris, France
| | - Christelle Tesson
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Fanny Casse
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Melanie Ferrien
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Louise-Laure Mariani
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
| | - Stephanie Carvalho
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Francois-Xavier Lejeune
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Sana Rebbah
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Gaspard Martet
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Marion Houot
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
- Centre of Excellence of Neurodegenerative Disease (CoEN), AP-HP, Pitié-Salpêtrière Hospital, Paris, France
- Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Aymeric Lanore
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
| | - Graziella Mangone
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
- Department of Neurology, Movement Disorder Division, Rush University Medical Center, 1725 W. Harrison Street, Chicago, IL, USA
| | - Emmanuel Roze
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
| | - Marie Vidailhet
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
| | - Jan Aasly
- Department of Neurology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ziv Gan Or
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Eric Yu
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Yves Dauvilliers
- Department of Neurology, Gui-de-Chauliac Hospital, CHU Montpellier, University of Montpellier, Institute for Neurosciences of Montpellier (INM), INSERM, Montpellier, France
| | | | | | - Walter Pirker
- Department of Neurology, Ottakring Clinic, Vienna, Austria
| | - Ignacio Álvarez
- Department of Neurology, Hospital Universitari Mutua de Terrassa, and Fundació per a la Recerca Biomèdica i Social Mútua de Terrassa, Terrassa, Barcelona, Spain
| | - Pau Pastor
- Unit of Neurodegenerative diseases, Department of Neurology, University Hospital Germans Trias i Pujol and The Germans Trias i Pujol Research Institute (IGTP) Badalona, Barcelona, Spain
| | - Alessio Di Fonzo
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Kailash P Bhatia
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Francesca Magrinelli
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Raquel Real
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
- UCL Movement Disorders Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Andrea Quattrone
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
- Institute of Neurology, Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Patricia Limousin
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Prasad Korlipara
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Thomas Foltynie
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Donald Grosset
- Institute of Neurological Sciences, University of Glasgow, Glasgow, UK
| | - Nigel Williams
- Department of Psychological Medicine and Neurology, Cardiff University, Cardiff, UK
| | - Derek Narendra
- Inherited Disorders Unit, Neurogenetics Branch, Division of Intramural Research, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Hsin-Pin Lin
- Inherited Disorders Unit, Neurogenetics Branch, Division of Intramural Research, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Carna Jovanovic
- University Clinical Center of Serbia, Neurology Clinic, Belgrade, Serbia
| | - Marina Svetel
- University Clinical Center of Serbia, Neurology Clinic, Belgrade, Serbia
| | - Timothy Lynch
- The Dublin Neurological Institute at the Mater Misericordiae University Hospital, Dublin Ireland and University College Dublin, Dublin, Ireland
| | - Amy Gallagher
- The Dublin Neurological Institute at the Mater Misericordiae University Hospital, Dublin Ireland and University College Dublin, Dublin, Ireland
| | - Wim Vandenberghe
- Department of Neurology, University Hospitals Leuven; Department of Neurosciences, KU Leuven; Leuven Brain Institute, Leuven, Belgium
| | - Thomas Gasser
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- DZNE, German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Kathrin Brockmann
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- DZNE, German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Huw R Morris
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Max Borsche
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Olga Corti
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Alexis Brice
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Genetics, Hôpital Pitié-Salpêtrière, Paris, France
| | - Suzanne Lesage
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Jean Christophe Corvol
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Hôpital Pitié-Salpêtrière, Paris, France
| |
Collapse
|
21
|
Leon-Ferre RA, Carter JM, Zahrieh D, Sinnwell JP, Salgado R, Suman VJ, Hillman DW, Boughey JC, Kalari KR, Couch FJ, Ingle JN, Balkenhol M, Ciompi F, van der Laak J, Goetz MP. Automated mitotic spindle hotspot counts are highly associated with clinical outcomes in systemically untreated early-stage triple-negative breast cancer. NPJ Breast Cancer 2024; 10:25. [PMID: 38553444 PMCID: PMC10980681 DOI: 10.1038/s41523-024-00629-3] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 03/08/2024] [Indexed: 04/02/2024] Open
Abstract
Operable triple-negative breast cancer (TNBC) has a higher risk of recurrence and death compared to other subtypes. Tumor size and nodal status are the primary clinical factors used to guide systemic treatment, while biomarkers of proliferation have not demonstrated value. Recent studies suggest that subsets of TNBC have a favorable prognosis, even without systemic therapy. We evaluated the association of fully automated mitotic spindle hotspot (AMSH) counts with recurrence-free (RFS) and overall survival (OS) in two separate cohorts of patients with early-stage TNBC who did not receive systemic therapy. AMSH counts were obtained from areas with the highest mitotic density in digitized whole slide images processed with a convolutional neural network trained to detect mitoses. In 140 patients from the Mayo Clinic TNBC cohort, AMSH counts were significantly associated with RFS and OS in a multivariable model controlling for nodal status, tumor size, and tumor-infiltrating lymphocytes (TILs) (p < 0.0001). For every 10-point increase in AMSH counts, there was a 16% increase in the risk of an RFS event (HR 1.16, 95% CI 1.08-1.25), and a 7% increase in the risk of death (HR 1.07, 95% CI 1.00-1.14). We corroborated these findings in a separate cohort of systemically untreated TNBC patients from Radboud UMC in the Netherlands. Our findings suggest that AMSH counts offer valuable prognostic information in patients with early-stage TNBC who did not receive systemic therapy, independent of tumor size, nodal status, and TILs. If further validated, AMSH counts could help inform future systemic therapy de-escalation strategies.
Collapse
Affiliation(s)
| | | | | | | | - Roberto Salgado
- GZA-ZNA-Hospitals, Antwerp, Belgium
- Peter Mac Callum Cancer Centre, Melbourne, Australia
| | | | | | | | | | | | | | | | | | - Jeroen van der Laak
- Radboud University Medical Center, Nijmegen, Netherlands
- Center for Medical Image Science and Visualization, Linköping University, Linköping, Sweden
| | | |
Collapse
|
22
|
Kim Y, You JH, Ryu Y, Park G, Lee U, Moon HE, Park HR, Song CW, Ku JL, Park SH, Paek SH. ELAVL2 loss promotes aggressive mesenchymal transition in glioblastoma. NPJ Precis Oncol 2024; 8:79. [PMID: 38548861 PMCID: PMC10978835 DOI: 10.1038/s41698-024-00566-1] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 03/08/2024] [Indexed: 04/01/2024] Open
Abstract
Glioblastoma (GBM), the most lethal primary brain cancer, exhibits intratumoral heterogeneity and molecular plasticity, posing challenges for effective treatment. Despite this, the regulatory mechanisms underlying such plasticity, particularly mesenchymal (MES) transition, remain poorly understood. In this study, we elucidate the role of the RNA-binding protein ELAVL2 in regulating aggressive MES transformation in GBM. We found that ELAVL2 is most frequently deleted in GBM compared to other cancers and associated with distinct clinical and molecular features. Transcriptomic analysis revealed that ELAVL2-mediated alterations correspond to specific GBM subtype signatures. Notably, ELAVL2 expression negatively correlated with epithelial-to-mesenchymal transition (EMT)-related genes, and its loss promoted MES process and chemo-resistance in GBM cells, whereas ELAVL2 overexpression exerted the opposite effect. Further investigation via tissue microarray analysis demonstrated that high ELAVL2 protein expression confers a favorable survival outcome in GBM patients. Mechanistically, ELAVL2 was shown to directly bind to the transcripts of EMT-inhibitory molecules, SH3GL3 and DNM3, modulating their mRNA stability, potentially through an m6A-dependent mechanism. In summary, our findings identify ELAVL2 as a critical tumor suppressor and mRNA stabilizer that regulates MES transition in GBM, underscoring its role in transcriptomic plasticity and glioma progression.
Collapse
Affiliation(s)
- Yona Kim
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Neuroscience, Seoul National University College of Biological Sciences, Seoul, Korea
| | - Ji Hyeon You
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Caner Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Yeonjoo Ryu
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Neuroscience, Seoul National University College of Biological Sciences, Seoul, Korea
| | - Gyuri Park
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Caner Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Urim Lee
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Caner Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Hyo Eun Moon
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hye Ran Park
- Department of Neurosurgery, Soonchunhyang University Seoul Hospital, Seoul, Korea
| | - Chang W Song
- Department of Radiation Oncology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Ja-Lok Ku
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University Hospital, Seoul, Korea
| | - Sun Ha Paek
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea.
- Advanced Institute of Convergence Technology, Seoul National University, Suwon, Korea.
| |
Collapse
|
23
|
Scaini MC, Catoni C, Poggiana C, Pigozzo J, Piccin L, Leone K, Scarabello I, Facchinetti A, Menin C, Elefanti L, Pellegrini S, Aleotti V, Vidotto R, Schiavi F, Fabozzi A, Chiarion-Sileni V, Rosato A. A multiparameter liquid biopsy approach allows to track melanoma dynamics and identify early treatment resistance. NPJ Precis Oncol 2024; 8:78. [PMID: 38548846 PMCID: PMC10978909 DOI: 10.1038/s41698-024-00567-0] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 03/14/2024] [Indexed: 04/01/2024] Open
Abstract
Melanoma heterogeneity is a hurdle in metastatic disease management. Although the advent of targeted therapy has significantly improved patient outcomes, the occurrence of resistance makes monitoring of the tumor genetic landscape mandatory. Liquid biopsy could represent an important biomarker for the real-time tracing of disease evolution. Thus, we aimed to correlate liquid biopsy dynamics with treatment response and progression by devising a multiplatform approach applied to longitudinal melanoma patient monitoring. We conceived an approach that exploits Next Generation Sequencing (NGS) and droplet digital PCR, as well as the FDA-cleared platform CellSearch, to analyze circulating tumor DNA (ctDNA) trend and circulating melanoma cell (CMC) count, together with their customized genetic and copy number variation analysis. The approach was applied to 17 stage IV melanoma patients treated with BRAF/MEK inhibitors, followed for up to 28 months. BRAF mutations were detected in the plasma of 82% of patients. Single nucleotide variants known or suspected to confer resistance were identified in 70% of patients. Moreover, the amount of ctDNA, both at baseline and during response, correlated with the type and duration of the response itself, and the CMC count was confirmed to be a prognostic biomarker. This work provides proof of principle of the power of this approach and paves the way for a validation study aimed at evaluating early ctDNA-guided treatment decisions in stage IV melanoma. The NGS-based molecular profile complemented the analysis of ctDNA trend and, together with CMC analysis, revealed to be useful in capturing tumor evolution.
Collapse
Affiliation(s)
- Maria Chiara Scaini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy.
| | - Cristina Catoni
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Cristina Poggiana
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy.
| | - Jacopo Pigozzo
- Medical Oncology 2, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Luisa Piccin
- Medical Oncology 2, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Kevin Leone
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Ilaria Scarabello
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Antonella Facchinetti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), Oncology Section, University of Padua, Padua, Italy
| | - Chiara Menin
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Lisa Elefanti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Stefania Pellegrini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Valentina Aleotti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Riccardo Vidotto
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Francesca Schiavi
- Familial Cancer Clinic, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Alessio Fabozzi
- Oncology Unit 3, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | | | - Antonio Rosato
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), Oncology Section, University of Padua, Padua, Italy
| |
Collapse
|
24
|
Chen Z, Wang X, Jin Z, Li B, Jiang D, Wang Y, Jiang M, Zhang D, Yuan P, Zhao Y, Feng F, Lin Y, Jiang L, Wang C, Meng W, Ye W, Wang J, Qiu W, Liu H, Huang D, Hou Y, Wang X, Jiao Y, Ying J, Liu Z, Liu Y. Deep learning on tertiary lymphoid structures in hematoxylin-eosin predicts cancer prognosis and immunotherapy response. NPJ Precis Oncol 2024; 8:73. [PMID: 38519580 PMCID: PMC10959936 DOI: 10.1038/s41698-024-00579-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/14/2024] [Indexed: 03/25/2024] Open
Abstract
Tertiary lymphoid structures (TLSs) have been associated with favorable immunotherapy responses and prognosis in various cancers. Despite their significance, their quantification using multiplex immunohistochemistry (mIHC) staining of T and B lymphocytes remains labor-intensive, limiting its clinical utility. To address this challenge, we curated a dataset from matched mIHC and H&E whole-slide images (WSIs) and developed a deep learning model for automated segmentation of TLSs. The model achieved Dice coefficients of 0.91 on the internal test set and 0.866 on the external validation set, along with intersection over union (IoU) scores of 0.819 and 0.787, respectively. The TLS ratio, defined as the segmented TLS area over the total tissue area, correlated with B lymphocyte levels and the expression of CXCL13, a chemokine associated with TLS formation, in 6140 patients spanning 16 tumor types from The Cancer Genome Atlas (TCGA). The prognostic models for overall survival indicated that the inclusion of the TLS ratio with TNM staging significantly enhanced the models' discriminative ability, outperforming the traditional models that solely incorporated TNM staging, in 10 out of 15 TCGA tumor types. Furthermore, when applied to biopsied treatment-naïve tumor samples, higher TLS ratios predicted a positive immunotherapy response across multiple cohorts, including specific therapies for esophageal squamous cell carcinoma, non-small cell lung cancer, and stomach adenocarcinoma. In conclusion, our deep learning-based approach offers an automated and reproducible method for TLS segmentation and quantification, highlighting its potential in predicting immunotherapy response and informing cancer prognosis.
Collapse
Affiliation(s)
- Ziqiang Chen
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Xiaobing Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zelin Jin
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Bosen Li
- Department of General Surgery/Gastric Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Dongxian Jiang
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yanqiu Wang
- Departments of Pathology, International Peace Maternity and Child Health Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mengping Jiang
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Dandan Zhang
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Pei Yuan
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yahui Zhao
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Feiyue Feng
- Thoracic Surgery Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yicheng Lin
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Liping Jiang
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chenxi Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weida Meng
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
| | - Wenjing Ye
- Division of Rheumatology and Immunology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jie Wang
- Departments of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wenqing Qiu
- Shanghai Xuhui Central Hospital, Shanghai, China
| | - Houbao Liu
- Shanghai Xuhui Central Hospital, Shanghai, China
- Department of General Surgery/Biliary Tract Disease Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Dan Huang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Institute of Pathology, Fudan University, Shanghai, China
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xuefei Wang
- Department of General Surgery/Gastric Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
- Department of General Surgery, Zhongshan Hospital (Xiamen), Fudan University, Shanghai, China
| | - Yuchen Jiao
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Yun Liu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China.
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China.
| |
Collapse
|
25
|
Engström J, Koozi H, Didriksson I, Larsson A, Friberg H, Frigyesi A, Spångfors M. Plasma neutrophil gelatinase-associated lipocalin independently predicts dialysis need and mortality in critical COVID-19. Sci Rep 2024; 14:6695. [PMID: 38509165 PMCID: PMC10954663 DOI: 10.1038/s41598-024-57409-z] [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: 11/15/2023] [Accepted: 03/18/2024] [Indexed: 03/22/2024] Open
Abstract
Neutrophil gelatinase-associated lipocalin (NGAL) is a novel kidney injury and inflammation biomarker. We investigated whether NGAL could be used to predict continuous renal replacement therapy (CRRT) and mortality in critical coronavirus disease 2019 (COVID-19). This prospective multicenter cohort study included adult COVID-19 patients in six intensive care units (ICUs) in Sweden between May 11, 2020 and May 10, 2021. Blood was sampled at admission, days two and seven in the ICU. The samples were batch analyzed for NGAL, creatinine, and cystatin c after the end of the study period. Initiation of CRRT and 90-day survival were used as dependent variables in regression models. Of 498 included patients, 494 were analyzed regarding CRRT and 399 were analyzed regarding survival. Seventy patients received CRRT and 154 patients did not survive past 90 days. NGAL, in combination with creatinine and cystatin c, predicted the subsequent initiation of CRRT with an area under the curve (AUC) of 0.95. For mortality, NGAL, in combination with age and sex, had an AUC of 0.83. In conclusion, NGAL is a valuable biomarker for predicting subsequent initiation of CRRT and 90-day mortality in critical COVID-19. NGAL should be considered when developing future clinical scoring systems.
Collapse
Affiliation(s)
- Jonas Engström
- Department of Clinical Sciences, Lund University, Anesthesiology and Intensive Care, Lund, 221 00, Sweden.
- Department of Anesthesia and Intensive Care, Kristianstad Hospital, Kristianstad, 291 85, Sweden.
| | - Hazem Koozi
- Department of Clinical Sciences, Lund University, Anesthesiology and Intensive Care, Lund, 221 00, Sweden
- Department of Anesthesia and Intensive Care, Kristianstad Hospital, Kristianstad, 291 85, Sweden
| | - Ingrid Didriksson
- Department of Clinical Sciences, Lund University, Anesthesiology and Intensive Care, Lund, 221 00, Sweden
- Department of Intensive and Perioperative Care, Skåne University Hospital, Malmö, 205 02, Sweden
| | - Anders Larsson
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala, 751 05, Sweden
| | - Hans Friberg
- Department of Clinical Sciences, Lund University, Anesthesiology and Intensive Care, Lund, 221 00, Sweden
- Department of Intensive and Perioperative Care, Skåne University Hospital, Malmö, 205 02, Sweden
| | - Attila Frigyesi
- Department of Clinical Sciences, Lund University, Anesthesiology and Intensive Care, Lund, 221 00, Sweden
- Department of Intensive and Perioperative Care, Skåne University Hospital, Lund, 221 85, Sweden
| | - Martin Spångfors
- Department of Clinical Sciences, Lund University, Anesthesiology and Intensive Care, Lund, 221 00, Sweden
- Department of Anesthesia and Intensive Care, Kristianstad Hospital, Kristianstad, 291 85, Sweden
| |
Collapse
|
26
|
Xu J, Huang X, Gou S, Luo H, Zeng S, Zhang Q, Wu Q, Chi H, Yang G. Unraveling the role of the circadian clock genes in cervical squamous cell carcinoma and endocervical adenocarcinoma: A prognostic indicator for prognostic, immunotherapy response, and chemotherapy sensitivity. J Cancer 2024; 15:2788-2804. [PMID: 38577592 PMCID: PMC10988312 DOI: 10.7150/jca.94063] [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: 01/09/2024] [Accepted: 02/27/2024] [Indexed: 04/06/2024] Open
Abstract
Background: Cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) account for a significant proportion of gynecological malignancies and represent a major global health concern. Globally, CESC is ranked as the fourth most common cancer among women. Conventional treatment of this disease has a less favorable prognosis for most patients. However, the discovery of early molecular biomarkers is therefore important for the diagnosis of CESC, as well as for slowing down their progression process. Methods: To identify differentially expressed genes strongly associated with prognosis, univariate Cox proportional hazard analysis and least absolute shrinkage and selection operator (LASSO) regression analysis were used. Using multiple Cox proportional hazard regression, a multifactorial model for prognostic risk assessment was then created. Results: The expression of biological clock-related genes, which varied considerably among distinct subtypes and were associated with significantly diverse prognoses, was used to categorize CESC patients. These findings demonstrate how the nomogram developed based on the 7-CRGs signature may assist physicians in creating more precise, accurate, and successful treatment plans that can aid CESC patients at 1, 3, and 5 years. Conclusions: By using machine learning techniques, we thoroughly investigated the impact of CRGs on the prognosis of CESC patients in this study. By creating a unique nomogram, we were able to accurately predict patient prognosis. At the same time, we showed new perspectives on the development of CESC and its treatment by analyzing the associations of the prognostic model with immunity, enrichment pathways, chemotherapy sensitivity, and so on. This research provides a new direction for clinical treatment.
Collapse
Affiliation(s)
- Jiayu Xu
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, and University Hospital, Macau University of Science and Technology, Macao, Macao SAR, China
- School of Science, Minzu University of China, Beijing, China
| | - Xueyuan Huang
- School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Siqi Gou
- School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Huanyu Luo
- School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Shicheng Zeng
- Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Qinhong Zhang
- Heilongjiang University of Chinese Medicine, Harbin, China
| | - Qibiao Wu
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, and University Hospital, Macau University of Science and Technology, Macao, Macao SAR, China
| | - Hao Chi
- School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Guanhu Yang
- Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicine, and University Hospital, Macau University of Science and Technology, Macao, Macao SAR, China
- Department of Specialty Medicine, Ohio University, Athens, OH, United States
| |
Collapse
|
27
|
Singh K, Armstrong SC, Wagner BE, Counts J, Skinner A, Kay M, Li JS, Shah S, Zucker N, Neshteruk C, Story M, Suarez L, Kraus WE, Zizzi AR, Dunn J. Physical activity and sleep changes among children during the COVID-19 pandemic. NPJ Digit Med 2024; 7:70. [PMID: 38493216 PMCID: PMC10944532 DOI: 10.1038/s41746-024-01041-8] [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: 08/24/2023] [Accepted: 02/14/2024] [Indexed: 03/18/2024] Open
Abstract
Daily routines, including in-person school and extracurricular activities, are important for maintaining healthy physical activity and sleep habits in children. The COVID-19 pandemic significantly disrupted daily routines as in-person school and activities closed to prevent spread of SARS-CoV-2. We aimed to examine and assess differences in objectively measured physical activity levels and sleep patterns from wearable sensors in children with obesity before, during, and after a period of school and extracurricular activity closures associated with the COVID-19 pandemic. We compared average step count and sleep patterns (using the Mann-Whitney U Test) before and during the pandemic-associated school closures by using data from activity tracker wristbands (Garmin VivoFit 3). Data were collected from 94 children (aged 5-17) with obesity, who were enrolled in a randomized controlled trial testing a community-based lifestyle intervention for a duration of 12-months. During the period that in-person school and extracurricular activities were closed due to the COVID-19 pandemic, children with obesity experienced objectively-measured decreases in physical activity, and sleep duration. From March 15, 2020 to March 31, 2021, corresponding with local school closures, average daily step count decreased by 1655 steps. Sleep onset and wake time were delayed by about an hour and 45 min, respectively, while sleep duration decreased by over 12 min as compared with the pre-closure period. Step counts increased with the resumption of in-person activities. These findings provide objective evidence for parents, clinicians, and public health professionals on the importance of in-person daily activities and routines on health behaviors, particularly for children with pre-existing obesity. Trial Registration: Clinical trial registration: NCT03339440.
Collapse
Affiliation(s)
- Karnika Singh
- Duke University Department of Biomedical Engineering, Durham, NC, USA
- Duke Center for Childhood Obesity Research, Durham, NC, USA
| | - Sarah C Armstrong
- Duke Center for Childhood Obesity Research, Durham, NC, USA
- Duke University Department of Pediatrics, Durham, NC, USA
- Duke University Department of Population Health Sciences, Durham, NC, USA
- Duke Global Health Institute, Durham, NC, USA
| | - Brooke E Wagner
- Duke Center for Childhood Obesity Research, Durham, NC, USA
- Duke University Department of Pediatrics, Durham, NC, USA
- Duke University Department of Population Health Sciences, Durham, NC, USA
| | - Julie Counts
- Duke Center for Childhood Obesity Research, Durham, NC, USA
- Duke University Molecular Physiology Institute, Durham, NC, USA
| | - Asheley Skinner
- Duke Center for Childhood Obesity Research, Durham, NC, USA
- Duke University Department of Population Health Sciences, Durham, NC, USA
| | - Melissa Kay
- Duke Center for Childhood Obesity Research, Durham, NC, USA
- Duke University Department of Pediatrics, Durham, NC, USA
| | - Jennifer S Li
- Duke Center for Childhood Obesity Research, Durham, NC, USA
- Duke University Department of Pediatrics, Durham, NC, USA
| | - Svati Shah
- Duke Center for Childhood Obesity Research, Durham, NC, USA
- Duke University Molecular Physiology Institute, Durham, NC, USA
| | - Nancy Zucker
- Duke Center for Childhood Obesity Research, Durham, NC, USA
- Duke University Department of Psychiatry and Behavioral Science, Durham, NC, USA
| | - Cody Neshteruk
- Duke Center for Childhood Obesity Research, Durham, NC, USA
- Duke University Department of Population Health Sciences, Durham, NC, USA
| | - Mary Story
- Duke Center for Childhood Obesity Research, Durham, NC, USA
- Duke Global Health Institute, Durham, NC, USA
| | - Lilianna Suarez
- Duke Center for Childhood Obesity Research, Durham, NC, USA
- Duke University Department of Pediatrics, Durham, NC, USA
| | - William E Kraus
- Duke Center for Childhood Obesity Research, Durham, NC, USA
- Duke University Molecular Physiology Institute, Durham, NC, USA
| | - Alexandra R Zizzi
- Duke Center for Childhood Obesity Research, Durham, NC, USA
- Duke University Department of Pediatrics, Durham, NC, USA
| | - Jessilyn Dunn
- Duke University Department of Biomedical Engineering, Durham, NC, USA.
- Duke Center for Childhood Obesity Research, Durham, NC, USA.
- Duke University Department of Biostatistics, Durham, NC, USA.
| |
Collapse
|
28
|
Guan Z, Liu J, Zheng L. Effect of radiotherapy on head and neck cancer tissues in patients receiving radiotherapy: a bioinformatics analysis-based study. Sci Rep 2024; 14:6304. [PMID: 38491080 PMCID: PMC10943217 DOI: 10.1038/s41598-024-56753-4] [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: 12/02/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024] Open
Abstract
Radiotherapy is pivotal in treating head and neck cancers including nasopharyngeal, tongue, hypopharyngeal, larynx, maxillary sinus, parotid gland, and oral cancers. It holds the potential for curative effects and finds application in conjunction with chemotherapy, either as a radical method to preserve organ function or as an adjuvant postoperative treatment. We used bioinformatics analysis to investigate the effects of radiotherapy on head and neck cancer tissues in patients who had received radiotherapy. In this study, the expression and mutation profiles of The Cancer Genome Atlas-Head-Neck Squamous Cell Carcinoma were downloaded from the UCSC-Xena database, categorizing patients into two groups-those receiving radiotherapy and those not receiving radiotherapy. Subsequently, differential expression analysis and gene set enrichment analysis (GSEA) were performed. Following this, single-sample GSEA (ssGSEA) scores related to glucose and lipid metabolism were compared between the two groups. Additionally, immune cell infiltration analysis and single-cell verification were performed. Finally, the mutation profiles of the two groups were compared. The analyses revealed that patients receiving radiotherapy exhibited prolonged survival, enhanced apoptosis in head and neck cancer tissue, and diminished keratinocyte proliferation and migration. A comparison of ssGSEA scores related to glucose and lipid metabolism between the two groups indicated a reduction in glycolysis, tricarboxylic acid cycle activity, and fat synthesis in tissues treated with radiotherapy, suggesting that radiotherapy can effectively inhibit tumour cell energy metabolism. Analyses of immune cell infiltration and single-cell verification suggested decreased infiltration of immune cells post-radiotherapy in head and neck cancer tissues. A comparison of mutation profiles revealed a higher frequency of TP53, TTN, and CDKN2A mutations in patients receiving radiotherapy for head and neck cancer. In conclusion, the bioinformatics analyses delved into the effect of radiotherapy on patients with head and neck carcinoma. This study provides a theoretical framework elucidating the molecular mechanisms underlying radiotherapy's efficacy in treating head and neck cancer and presents scientific recommendations for drug therapy following radiotherapy.
Collapse
Affiliation(s)
- Zhenjie Guan
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Jie Liu
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Zhengzhou University, NO.1 Jianshedong Road, Zhengzhou, 450052, Henan, China
| | - Lian Zheng
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Zhengzhou University, NO.1 Jianshedong Road, Zhengzhou, 450052, Henan, China.
| |
Collapse
|
29
|
Brum WS, Cullen NC, Therriault J, Janelidze S, Rahmouni N, Stevenson J, Servaes S, Benedet AL, Zimmer ER, Stomrud E, Palmqvist S, Zetterberg H, Frisoni GB, Ashton NJ, Blennow K, Mattsson-Carlgren N, Rosa-Neto P, Hansson O. A blood-based biomarker workflow for optimal tau-PET referral in memory clinic settings. Nat Commun 2024; 15:2311. [PMID: 38486040 PMCID: PMC10940585 DOI: 10.1038/s41467-024-46603-2] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
Blood-based biomarkers for screening may guide tau positrion emissition tomography (PET) scan referrals to optimize prognostic evaluation in Alzheimer's disease. Plasma Aβ42/Aβ40, pTau181, pTau217, pTau231, NfL, and GFAP were measured along with tau-PET in memory clinic patients with subjective cognitive decline, mild cognitive impairment or dementia, in the Swedish BioFINDER-2 study (n = 548) and in the TRIAD study (n = 179). For each plasma biomarker, cutoffs were determined for 90%, 95%, or 97.5% sensitivity to detect tau-PET-positivity. We calculated the percentage of patients below the cutoffs (who would not undergo tau-PET; "saved scans") and the tau-PET-positivity rate among participants above the cutoffs (who would undergo tau-PET; "positive predictive value"). Generally, plasma pTau217 performed best. At the 95% sensitivity cutoff in both cohorts, pTau217 resulted in avoiding nearly half tau-PET scans, with a tau-PET-positivity rate among those who would be referred for a scan around 70%. And although tau-PET was strongly associated with subsequent cognitive decline, in BioFINDER-2 it predicted cognitive decline only among individuals above the referral cutoff on plasma pTau217, supporting that this workflow could reduce prognostically uninformative tau-PET scans. In conclusion, plasma pTau217 may guide selection of patients for tau-PET, when accurate prognostic information is of clinical value.
Collapse
Affiliation(s)
- Wagner S Brum
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Graduate Program in Biological Sciences: Biochemistry, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Nicholas C Cullen
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Faculty of Medicine, Lund University, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
| | - Joseph Therriault
- McGill Centre for Studies in Aging, McGill University, Verdun, Quebec, QC, Canada
- Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Quebec, QC, Canada
| | - Shorena Janelidze
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Faculty of Medicine, Lund University, Lund, Sweden
| | - Nesrine Rahmouni
- McGill Centre for Studies in Aging, McGill University, Verdun, Quebec, QC, Canada
- Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Quebec, QC, Canada
| | - Jenna Stevenson
- McGill Centre for Studies in Aging, McGill University, Verdun, Quebec, QC, Canada
- Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Quebec, QC, Canada
| | - Stijn Servaes
- McGill Centre for Studies in Aging, McGill University, Verdun, Quebec, QC, Canada
- Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Quebec, QC, Canada
| | - Andrea L Benedet
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Eduardo R Zimmer
- Graduate Program in Biological Sciences: Biochemistry, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- McGill Centre for Studies in Aging, McGill University, Verdun, Quebec, QC, Canada
- Department of Pharmacology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Graduate Program in Biological Sciences: Pharmacology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Erik Stomrud
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Faculty of Medicine, Lund University, Lund, Sweden
- Memory Clinic, Skåne University Hospital, Lund, Sweden
| | - Sebastian Palmqvist
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Faculty of Medicine, Lund University, Lund, Sweden
- Memory Clinic, Skåne University Hospital, Lund, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK
- UK Dementia Research Institute at UCL, London, United Kingdom
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
- Wisconsin Alzheimer's Disease Research Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Giovanni B Frisoni
- Memory Center, Geneva University and University Hospital, Geneva, Switzerland
| | - Nicholas J Ashton
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- King's College London, Institute of Psychiatry, Psychology and Neuroscience Maurice Wohl Institute Clinical Neuroscience Institute, London, UK
- NIHR Biomedical Research Centre for Mental Health and Biomedical Research Unit for Dementia at South London and Maudsley NHS Foundation, London, UK
- Centre for Age-Related Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Niklas Mattsson-Carlgren
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Faculty of Medicine, Lund University, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
- Department of Neurology, Skåne University Hospital, Lund, Sweden
| | - Pedro Rosa-Neto
- McGill Centre for Studies in Aging, McGill University, Verdun, Quebec, QC, Canada
- Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Quebec, QC, Canada
| | - Oskar Hansson
- Clinical Memory Research Unit, Department of Clinical Sciences Malmö, Faculty of Medicine, Lund University, Lund, Sweden.
| |
Collapse
|
30
|
Foldyna B, Hadzic I, Zeleznik R, Langenbach MC, Raghu VK, Mayrhofer T, Lu MT, Aerts HJWL. Deep learning analysis of epicardial adipose tissue to predict cardiovascular risk in heavy smokers. Commun Med (Lond) 2024; 4:44. [PMID: 38480863 PMCID: PMC10937640 DOI: 10.1038/s43856-024-00475-1] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 03/04/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Heavy smokers are at increased risk for cardiovascular disease and may benefit from individualized risk quantification using routine lung cancer screening chest computed tomography. We investigated the prognostic value of deep learning-based automated epicardial adipose tissue quantification and compared it to established cardiovascular risk factors and coronary artery calcium. METHODS We investigated the prognostic value of automated epicardial adipose tissue quantification in heavy smokers enrolled in the National Lung Screening Trial and followed for 12.3 (11.9-12.8) years. The epicardial adipose tissue was segmented and quantified on non-ECG-synchronized, non-contrast low-dose chest computed tomography scans using a validated deep-learning algorithm. Multivariable survival regression analyses were then utilized to determine the associations of epicardial adipose tissue volume and density with all-cause and cardiovascular mortality (myocardial infarction and stroke). RESULTS Here we show in 24,090 adult heavy smokers (59% men; 61 ± 5 years) that epicardial adipose tissue volume and density are independently associated with all-cause (adjusted hazard ratios: 1.10 and 1.38; P < 0.001) and cardiovascular mortality (adjusted hazard ratios: 1.14 and 1.78; P < 0.001) beyond demographics, clinical risk factors, body habitus, level of education, and coronary artery calcium score. CONCLUSIONS Our findings suggest that automated assessment of epicardial adipose tissue from low-dose lung cancer screening images offers prognostic value in heavy smokers, with potential implications for cardiovascular risk stratification in this high-risk population.
Collapse
Affiliation(s)
- Borek Foldyna
- Cardiovascular Imaging Research Center (CIRC), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Ibrahim Hadzic
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Radiology and Nuclear Medicine, CARIM & GROW, Maastricht University, Maastricht, The Netherlands
| | - Roman Zeleznik
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Marcel C Langenbach
- Cardiovascular Imaging Research Center (CIRC), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Institute for Diagnostic and Interventional Radiology, University Hospital Cologne, Cologne, Germany
| | - Vineet K Raghu
- Cardiovascular Imaging Research Center (CIRC), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Thomas Mayrhofer
- Cardiovascular Imaging Research Center (CIRC), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- School of Business Studies, Stralsund University of Applied Sciences, Stralsund, Germany
| | - Michael T Lu
- Cardiovascular Imaging Research Center (CIRC), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hugo J W L Aerts
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Radiology and Nuclear Medicine, CARIM & GROW, Maastricht University, Maastricht, The Netherlands
| |
Collapse
|
31
|
Rydzewski NR, Shi Y, Li C, Chrostek MR, Bakhtiar H, Helzer KT, Bootsma ML, Berg TJ, Harari PM, Floberg JM, Blitzer GC, Kosoff D, Taylor AK, Sharifi MN, Yu M, Lang JM, Patel KR, Citrin DE, Sundling KE, Zhao SG. A platform-independent AI tumor lineage and site (ATLAS) classifier. Commun Biol 2024; 7:314. [PMID: 38480799 PMCID: PMC10937974 DOI: 10.1038/s42003-024-05981-5] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
Histopathologic diagnosis and classification of cancer plays a critical role in guiding treatment. Advances in next-generation sequencing have ushered in new complementary molecular frameworks. However, existing approaches do not independently assess both site-of-origin (e.g. prostate) and lineage (e.g. adenocarcinoma) and have minimal validation in metastatic disease, where classification is more difficult. Utilizing gradient-boosted machine learning, we developed ATLAS, a pair of separate AI Tumor Lineage and Site-of-origin models from RNA expression data on 8249 tumor samples. We assessed performance independently in 10,376 total tumor samples, including 1490 metastatic samples, achieving an accuracy of 91.4% for cancer site-of-origin and 97.1% for cancer lineage. High confidence predictions (encompassing the majority of cases) were accurate 98-99% of the time in both localized and remarkably even in metastatic samples. We also identified emergent properties of our lineage scores for tumor types on which the model was never trained (zero-shot learning). Adenocarcinoma/sarcoma lineage scores differentiated epithelioid from biphasic/sarcomatoid mesothelioma. Also, predicted lineage de-differentiation identified neuroendocrine/small cell tumors and was associated with poor outcomes across tumor types. Our platform-independent single-sample approach can be easily translated to existing RNA-seq platforms. ATLAS can complement and guide traditional histopathologic assessment in challenging situations and tumors of unknown primary.
Collapse
Affiliation(s)
- Nicholas R Rydzewski
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - Yue Shi
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - Chenxuan Li
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | | | - Hamza Bakhtiar
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - Kyle T Helzer
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - Matthew L Bootsma
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - Tracy J Berg
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - Paul M Harari
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
| | - John M Floberg
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
| | - Grace C Blitzer
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
| | - David Kosoff
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Amy K Taylor
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Marina N Sharifi
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Menggang Yu
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - Joshua M Lang
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Krishnan R Patel
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Deborah E Citrin
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kaitlin E Sundling
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, USA
- Wisconsin State Laboratory of Hygiene, University of Wisconsin, Madison, WI, USA
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA.
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA.
- William S. Middleton Veterans Hospital, Madison, WI, USA.
| |
Collapse
|
32
|
Jawad BN, Shaker SM, Altintas I, Eugen-Olsen J, Nehlin JO, Andersen O, Kallemose T. Development and validation of prognostic machine learning models for short- and long-term mortality among acutely admitted patients based on blood tests. Sci Rep 2024; 14:5942. [PMID: 38467752 PMCID: PMC10928126 DOI: 10.1038/s41598-024-56638-6] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 03/08/2024] [Indexed: 03/13/2024] Open
Abstract
Several scores predicting mortality at the emergency department have been developed. However, all with shortcomings either simple and applicable in a clinical setting, with poor performance, or advanced, with high performance, but clinically difficult to implement. This study aimed to explore if machine learning algorithms could predict all-cause short- and long-term mortality based on the routine blood test collected at admission. METHODS We analyzed data from a retrospective cohort study, including patients > 18 years admitted to the Emergency Department (ED) of Copenhagen University Hospital Hvidovre, Denmark between November 2013 and March 2017. The primary outcomes were 3-, 10-, 30-, and 365-day mortality after admission. PyCaret, an automated machine learning library, was used to evaluate the predictive performance of fifteen machine learning algorithms using the area under the receiver operating characteristic curve (AUC). RESULTS Data from 48,841 admissions were analyzed, of these 34,190 (70%) were randomly divided into training data, and 14,651 (30%) were in test data. Eight machine learning algorithms achieved very good to excellent results of AUC on test data in a of range 0.85-0.93. In prediction of short-term mortality, lactate dehydrogenase (LDH), leukocyte counts and differentials, Blood urea nitrogen (BUN) and mean corpuscular hemoglobin concentration (MCHC) were the best predictors, whereas prediction of long-term mortality was favored by age, LDH, soluble urokinase plasminogen activator receptor (suPAR), albumin, and blood urea nitrogen (BUN). CONCLUSION The findings suggest that measures of biomarkers taken from one blood sample during admission to the ED can identify patients at high risk of short-and long-term mortality following emergency admissions.
Collapse
Affiliation(s)
- Baker Nawfal Jawad
- Department of Clinical Research, Copenhagen University Hospital Amager and Hvidovre, Hvidovre, Denmark.
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
| | | | - Izzet Altintas
- Department of Clinical Research, Copenhagen University Hospital Amager and Hvidovre, Hvidovre, Denmark
- Emergency Department, Copenhagen University Hospital Amager and Hvidovre, Hvidovre, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Eugen-Olsen
- Department of Clinical Research, Copenhagen University Hospital Amager and Hvidovre, Hvidovre, Denmark
| | - Jan O Nehlin
- Department of Clinical Research, Copenhagen University Hospital Amager and Hvidovre, Hvidovre, Denmark
| | - Ove Andersen
- Department of Clinical Research, Copenhagen University Hospital Amager and Hvidovre, Hvidovre, Denmark
- Emergency Department, Copenhagen University Hospital Amager and Hvidovre, Hvidovre, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Kallemose
- Department of Clinical Research, Copenhagen University Hospital Amager and Hvidovre, Hvidovre, Denmark
| |
Collapse
|
33
|
Zhang M, Ma Z, Yi Z, Wang H, Zhu J, Wen G, Jin H, An J, Deng Z, Tuo B, Li T, Liu X. SLC26A9 promotes colorectal tumorigenesis by modulating Wnt/β-catenin signaling. Cell Death Discov 2024; 10:123. [PMID: 38461207 PMCID: PMC10925040 DOI: 10.1038/s41420-024-01888-6] [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: 10/22/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/11/2024] Open
Abstract
Solute carrier family 26 member 9 (SLC26A9) is a member of the Slc26a family of multifunctional anion transporters that functions as a Cl- channel in parietal cells during acid secretion. We explored the role of SLC26A9 in colorectal cancer (CRC) and its related mechanisms through clinical samples from CRC patients, CRC cell lines and mouse models. We observed that SLC26A9 was expressed at low levels in the cytoplasm of adjacent tissues, polyps and adenomas but was significantly increased in colorectal adenocarcinoma. Moreover, increased levels of SLC26A9 were associated with a high risk of disease and poor prognosis. In addition, downregulation of SLC26A9 in CRC cells induced cell cycle arrest and apoptosis but inhibited cell proliferation and xenograft tumor growth both in vitro and in vivo. Mechanistic analysis revealed that SLC26A9 was colocalized with β-catenin in the nucleus of CRC cells. The translocation of these two proteins from the cytoplasm to the nucleus reflected the activation of Wnt/β-catenin signaling, and promoted the transcription of downstream target proteins, including CyclinD1, c-Myc and Snail, but inhibited the expression of cytochrome C (Cyt-c), cleaved Caspase9, cleaved Caspase3 and apoptosis-inducing factor (AIF). CRC is accompanied by alteration of epithelial mesenchymal transition (EMT) markers. Meanwhile, further studies showed that in SW48 cells, overexpressing SLC26A9 was cocultured with the β-catenin inhibitor XAV-939, β-catenin was downregulated, and EMT was reversed. Our study demonstrated SLC26A9 may be responsible for alterations in the proliferative ability and aggressive potential of CRC by regulating the Wnt/β-catenin signaling pathway.
Collapse
Affiliation(s)
- Minglin Zhang
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zhiyuan Ma
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zhiqiang Yi
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Hu Wang
- Department of General Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Jiaxing Zhu
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Guorong Wen
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Hai Jin
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Jiaxing An
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zilin Deng
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Biguang Tuo
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China.
| | - Taolang Li
- Department of General Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China.
| | - Xuemei Liu
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China.
| |
Collapse
|
34
|
Torii Y, Suzuki T, Fukuda Y, Haruta K, Yamaguchi M, Horiba K, Kawada JI, Ito Y. MicroRNA expression profiling of urine exosomes in children with congenital cytomegalovirus infection. Sci Rep 2024; 14:5475. [PMID: 38443656 PMCID: PMC10914720 DOI: 10.1038/s41598-024-56106-1] [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: 12/28/2023] [Accepted: 03/01/2024] [Indexed: 03/07/2024] Open
Abstract
Congenital cytomegalovirus (cCMV) infection can damage the central nervous system in infants; however, its prognosis cannot be predicted from clinical evaluations at the time of birth. Urinary exosomes can be used to analyze neuronal damage in neuronal diseases. To investigate the extent of neuronal damage in patients with cCMV, exosomal miRNA expression in the urine was investigated in cCMV-infected infants and controls. Microarray analysis of miRNA was performed in a cohort of 30 infants, including 11 symptomatic cCMV (ScCMV), 7 asymptomatic cCMV (AScCMV), and one late-onset ScCMV cases, and 11 healthy controls (HC). Hierarchical clustering analysis revealed the distinct expression profile of ScCMV. The patient with late-onset ScCMV was grouped into the ScCMV cluster. Pathway enrichment analysis of the target mRNAs differed significantly between the ScCMV and HC groups; this analysis also revealed that pathways related to brain development were linked to upregulated pathways. Six miRNAs that significantly different between groups (ScCMV vs. HC and ScCMV vs. AScCMV) were selected for digital PCR in another cohort for further validation. Although these six miRNAs seemed insufficient for predicting ScCMV, expression profiles of urine exosomal miRNAs can reveal neurological damage in patients with ScCMV compared to those with AcCMV or healthy infants.
Collapse
Affiliation(s)
- Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Yuto Fukuda
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Kazunori Haruta
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Makoto Yamaguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Kazuhiro Horiba
- Pathogen Genomics Center, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-Ku, Tokyo, 162-8640, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Aichi Medical University, 1-1 Yazakokarimata, Nagakute, 480-1195, Japan.
| |
Collapse
|
35
|
Shitara K, Muro K, Watanabe J, Yamazaki K, Ohori H, Shiozawa M, Takashima A, Yokota M, Makiyama A, Akazawa N, Ojima H, Yuasa Y, Miwa K, Yasui H, Oki E, Sato T, Naitoh T, Komatsu Y, Kato T, Mori I, Yamanaka K, Hihara M, Soeda J, Misumi T, Yamamoto K, Yamashita R, Akagi K, Ochiai A, Uetake H, Tsuchihara K, Yoshino T. Baseline ctDNA gene alterations as a biomarker of survival after panitumumab and chemotherapy in metastatic colorectal cancer. Nat Med 2024; 30:730-739. [PMID: 38347302 PMCID: PMC10957476 DOI: 10.1038/s41591-023-02791-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 09/29/2023] [Accepted: 12/21/2023] [Indexed: 03/23/2024]
Abstract
Certain genetic alterations and right-sided primary tumor location are associated with resistance to anti-epidermal growth factor (EGFR) treatment in metastatic colorectal cancer (mCRC). The phase 3 PARADIGM trial (n = 802) demonstrated longer overall survival with first-line anti-EGFR (panitumumab) versus antivascular endothelial growth factor (bevacizumab) plus modified FOLFOX6 in patients with RAS wild-type mCRC with left-sided primary tumors. This prespecified exploratory biomarker analysis of PARADIGM (n = 733) evaluated the association between circulating tumor DNA (ctDNA) gene alterations and efficacy outcomes, focusing on a broad panel of gene alterations associated with resistance to EGFR inhibition, including KRAS, NRAS, PTEN and extracellular domain EGFR mutations, HER2 and MET amplifications, and ALK, RET and NTRK1 fusions. Overall survival was prolonged with panitumumab plus modified FOLFOX6 versus bevacizumab plus modified FOLFOX6 in patients with ctDNA that lacked gene alterations in the panel (that is, negative hyperselected; median in the overall population: 40.7 versus 34.4 months; hazard ratio, 0.76; 95% confidence interval, 0.62-0.92) but was similar or inferior with panitumumab in patients with ctDNA that contained any gene alteration in the panel (19.2 versus 22.2 months; hazard ratio, 1.13; 95% confidence interval, 0.83-1.53), regardless of tumor sidedness. Negative hyperselection using ctDNA may guide optimal treatment selection in patients with mCRC. ClinicalTrials.gov registrations: NCT02394834 and NCT02394795 .
Collapse
Affiliation(s)
- Kohei Shitara
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan.
- Department of Immunology, Nagoya University Graduate School of Medicine, Aichi, Japan.
| | - Kei Muro
- Department of Clinical Oncology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Jun Watanabe
- Department of Surgery, Gastroenterological Center, Yokohama City University Medical Center, Yokohama, Japan
| | - Kentaro Yamazaki
- Division of Gastrointestinal Oncology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Hisatsugu Ohori
- Division of Medical Oncology, Japanese Red Cross Ishinomaki Hospital, Miyagi, Japan
| | - Manabu Shiozawa
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Kanagawa, Japan
| | - Atsuo Takashima
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Mitsuru Yokota
- Department of General Surgery, Kurashiki Central Hospital, Okayama, Japan
| | - Akitaka Makiyama
- Department of Hematology/Oncology, Japan Community Healthcare Organization, Fukuoka, Japan
- Cancer Center, Gifu University Hospital, Gifu, Japan
- Division of Animal Medical Science, Center for One Medicine Innovative Translational Research, Gifu, Japan
| | - Naoya Akazawa
- Department of Gastroenterological Surgery, Sendai City Medical Center, Sendai Open Hospital, Miyagi, Japan
| | - Hitoshi Ojima
- Department of Gastroenterological Surgery, Gunma Prefectural Cancer Center, Gunma, Japan
| | - Yasuhiro Yuasa
- Department of Gastroenterological Surgery, Japanese Red Cross Tokushima Hospital, Tokushima, Japan
| | - Keisuke Miwa
- Multidisciplinary Treatment Cancer Center, Kurume University Hospital, Kurume, Japan
| | - Hirofumi Yasui
- Division of Gastrointestinal Oncology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takeo Sato
- Research and Development Center for Medical Education, Department of Clinical Skills Education, Kitasato University School of Medicine, Sagamihara, Japan
| | - Takeshi Naitoh
- Department of Lower Gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Japan
| | - Yoshito Komatsu
- Division of Cancer Chemotherapy, Hokkaido University Hospital Cancer Center, Sapporo, Japan
| | - Takeshi Kato
- Department of Surgery, National Hospital Organization Osaka National Hospital, Osaka, Japan
| | - Ikuo Mori
- Japan Medical Affairs, Japan Oncology Business Unit, Takeda Pharmaceutical Company Ltd, Tokyo, Japan
| | - Kazunori Yamanaka
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, Kanagawa, Japan
| | - Masamitsu Hihara
- Japan Medical Affairs, Japan Oncology Business Unit, Takeda Pharmaceutical Company Ltd, Tokyo, Japan
| | - Junpei Soeda
- Japan Medical Affairs, Japan Oncology Business Unit, Takeda Pharmaceutical Company Ltd, Tokyo, Japan
| | - Toshihiro Misumi
- Department of Biostatistics, Yokohama City University School of Medicine, Yokohama, Japan
| | - Kouji Yamamoto
- Department of Biostatistics, Yokohama City University School of Medicine, Yokohama, Japan
| | - Riu Yamashita
- Division of Translational Informatics, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Kiwamu Akagi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | - Atsushi Ochiai
- Research Institute for Biomedical Sciences, Tokyo University of Science, Tokyo, Japan
| | - Hiroyuki Uetake
- National Hospital Organization, Disaster Medical Center, Tokyo, Japan
| | - Katsuya Tsuchihara
- Division of Translational Informatics, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| |
Collapse
|
36
|
Luna Santamaría M, Andersson D, Parris TZ, Helou K, Österlund T, Ståhlberg A. Digital RNA sequencing using unique molecular identifiers enables ultrasensitive RNA mutation analysis. Commun Biol 2024; 7:249. [PMID: 38429519 PMCID: PMC10907754 DOI: 10.1038/s42003-024-05955-7] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 02/22/2024] [Indexed: 03/03/2024] Open
Abstract
Mutation analysis is typically performed at the DNA level since most technical approaches are developed for DNA analysis. However, some applications, like transcriptional mutagenesis, RNA editing and gene expression analysis, require RNA analysis. Here, we combine reverse transcription and digital DNA sequencing to enable low error digital RNA sequencing. We evaluate yield, reproducibility, dynamic range and error correction rate for seven different reverse transcription conditions using multiplexed assays. The yield, reproducibility and error rate vary substantially between the specific conditions, where the yield differs 9.9-fold between the best and worst performing condition. Next, we show that error rates similar to DNA sequencing can be achieved for RNA using appropriate reverse transcription conditions, enabling detection of mutant allele frequencies <0.1% at RNA level. We also detect mutations at both DNA and RNA levels in tumor tissue using a breast cancer panel. Finally, we demonstrate that digital RNA sequencing can be applied to liquid biopsies, analyzing cell-free gene transcripts. In conclusion, we demonstrate that digital RNA sequencing is suitable for ultrasensitive RNA mutation analysis, enabling several basic research and clinical applications.
Collapse
Affiliation(s)
- Manuel Luna Santamaría
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Daniel Andersson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Toshima Z Parris
- Sahlgrenska Center for Cancer Research, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Khalil Helou
- Sahlgrenska Center for Cancer Research, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tobias Österlund
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden.
| |
Collapse
|
37
|
Beunk L, Nijenhuis M, Soree B, de Boer-Veger NJ, Buunk AM, Guchelaar HJ, Houwink EJF, Risselada A, Rongen GAPJM, van Schaik RHN, Swen JJ, Touw D, van Westrhenen R, Deneer VHM, van der Weide J. Dutch Pharmacogenetics Working Group (DPWG) guideline for the gene-drug interaction between CYP2D6, CYP3A4 and CYP1A2 and antipsychotics. Eur J Hum Genet 2024; 32:278-285. [PMID: 37002327 PMCID: PMC10923774 DOI: 10.1038/s41431-023-01347-3] [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: 04/13/2022] [Revised: 02/22/2023] [Accepted: 03/13/2023] [Indexed: 04/03/2023] Open
Abstract
The Dutch Pharmacogenetics Working Group (DPWG) aims to facilitate pharmacogenetics implementation in clinical practice by developing evidence-based guidelines to optimize pharmacotherapy. A guideline describing the gene-drug interaction between the genes CYP2D6, CYP3A4 and CYP1A2 and antipsychotics is presented here. The DPWG identified gene-drug interactions that require therapy adjustments when respective genotype is known for CYP2D6 with aripiprazole, brexpiprazole, haloperidol, pimozide, risperidone and zuclopenthixol, and for CYP3A4 with quetiapine. Evidence-based dose recommendations were obtained based on a systematic review of published literature. Reduction of the normal dose is recommended for aripiprazole, brexpiprazole, haloperidol, pimozide, risperidone and zuclopenthixol for CYP2D6-predicted PMs, and for pimozide and zuclopenthixol also for CYP2D6 IMs. For CYP2D6 UMs, a dose increase or an alternative drug is recommended for haloperidol and an alternative drug or titration of the dose for risperidone. In addition, in case of no or limited clinical effect, a dose increase is recommended for zuclopenthixol for CYP2D6 UMs. Even though evidence is limited, the DPWG recommends choosing an alternative drug to treat symptoms of depression or a dose reduction for other indications for quetiapine and CYP3A4 PMs. No therapy adjustments are recommended for the other CYP2D6 and CYP3A4 predicted phenotypes. In addition, no action is required for the gene-drug combinations CYP2D6 and clozapine, flupentixol, olanzapine or quetiapine and also not for CYP1A2 and clozapine or olanzapine. For identified gene-drug interactions requiring therapy adjustments, genotyping of CYP2D6 or CYP3A4 prior to treatment should not be considered for all patients, but on an individual patient basis only.
Collapse
Affiliation(s)
- Lianne Beunk
- Department of Clinical Chemistry, St Jansdal Hospital, Harderwijk, the Netherlands
| | - Marga Nijenhuis
- Royal Dutch Pharmacists Association (KNMP), The Hague, the Netherlands.
| | - Bianca Soree
- Royal Dutch Pharmacists Association (KNMP), The Hague, the Netherlands
| | | | | | - Henk Jan Guchelaar
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, the Netherlands
| | - Elisa J F Houwink
- Department of Public Health and Primary Care (PHEG), Leiden University Medical Center, Leiden, the Netherlands
- National eHealth Living Lab (NELL), Leiden, the Netherlands
| | - Arne Risselada
- Department of Clinical Pharmacy, Wilhelmina Hospital, Assen, the Netherlands
| | - Gerard A P J M Rongen
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Pharmacology and Toxicology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ron H N van Schaik
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jesse J Swen
- Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, the Netherlands
| | - Daan Touw
- Department of Pharmaceutical Analysis, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, the Netherlands
- Department of Clinical Pharmacy & Pharmacology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Roos van Westrhenen
- Department of Psychiatry, Parnassia Group, Amsterdam, the Netherlands
- Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, the Netherlands
- Institute of Psychiatry, Psychology&Neuroscience (IoPPN), King's College London, London, UK
| | - Vera H M Deneer
- Department of Clinical Pharmacy, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences (UIPS), Department of Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands
| | - Jan van der Weide
- Department of Clinical Chemistry, St Jansdal Hospital, Harderwijk, the Netherlands
| |
Collapse
|
38
|
Sottile ML, Gómez LC, Redondo A, Ibarra J, García MB, Gonzalez L, Vargas-Roig LM, Nadin SB. Relevance of Comet Assay and Phosphorylated-Hsp90α in Cancer Patients' Peripheral Blood Leukocytes as Tools to Assess Cisplatin-based Chemotherapy Clinical Response and Disease Outcome. J Histochem Cytochem 2024; 72:173-188. [PMID: 38439738 PMCID: PMC10956442 DOI: 10.1369/00221554241236241] [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: 08/07/2023] [Accepted: 02/12/2024] [Indexed: 03/06/2024] Open
Abstract
Cisplatin (cPt) is a commonly used treatment for solid tumors. The main target of its cytotoxicity is the DNA molecule, which makes the DNA damage response (DDR) crucial for cPt-based chemotherapy. Therefore, it is essential to identify biomarkers that can accurately predict the individual clinical response and prognosis. Our goal was to assess the usefulness of alkaline comet assay and immunocytochemical staining of phosphorylated Hsp90α (p-Hsp90α), γH2AX, and 53BP1 as predictive/prognostic markers. Pre-chemotherapy peripheral blood leukocytes were exposed to cPt in vitro and collected at 0, 24 (T24), and 48 (T48) hr post-drug removal. Healthy subjects were also included. Baseline DNA damage was elevated in cancer patients (variability between individuals was observed). After cPt, patients showed increased γH2AX foci/nucleus (T24 and T48). Both in healthy persons and patients, the nuclear p-Hsp90α and N/C (nuclear/cytoplasmic) ratio augmented (T24), decreasing at T48. Favorable clinical response was associated with high DNA damage and p-Hsp90α N/C ratio following cPt. For the first time, p-Hsp90α significance as a predictive marker is highlighted. Post-cPt-DNA damage was associated with longer disease-free survival and overall survival. Our findings indicate that comet assay and p-Hsp90α (a marker of DDR) would be promising prognostic/predictive tools in cP-treated cancer patients.
Collapse
Affiliation(s)
- Mayra L. Sottile
- Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, National Scientific and Technical Research Council, National University of Cuyo, Mendoza, Argentina
- Medical Sciences School, Mendoza University, Mendoza, Argentina
| | - Laura C. Gómez
- Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, National Scientific and Technical Research Council, National University of Cuyo, Mendoza, Argentina
- Medical Sciences School, Mendoza University, Mendoza, Argentina
| | - Analía Redondo
- Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, National Scientific and Technical Research Council, National University of Cuyo, Mendoza, Argentina
| | - Jorge Ibarra
- Regional Integration Cancer Center, Mendoza, Argentina
| | | | | | - Laura M. Vargas-Roig
- Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, National Scientific and Technical Research Council, National University of Cuyo, Mendoza, Argentina
| | - Silvina B. Nadin
- Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, National Scientific and Technical Research Council, National University of Cuyo, Mendoza, Argentina
| |
Collapse
|
39
|
Le Teuff G, Cozic N, Boyer JC, Boige V, Diasio RB, Taieb J, Meulendijks D, Palles C, Schwab M, Deenen M, Largiadèr CR, Marinaki A, Jennings BA, Wettergren Y, Di Paolo A, Gross E, Budai B, Ackland SP, van Kuilenburg ABP, McLeod HL, Milano G, Thomas F, Loriot MA, Kerr D, Schellens JHM, Laurent-Puig P, Shi Q, Pignon JP, Etienne-Grimaldi MC. Dihydropyrimidine dehydrogenase gene variants for predicting grade 4-5 fluoropyrimidine-induced toxicity: FUSAFE individual patient data meta-analysis. Br J Cancer 2024; 130:808-818. [PMID: 38225422 PMCID: PMC10912560 DOI: 10.1038/s41416-023-02517-2] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/30/2023] [Accepted: 11/23/2023] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND Dihydropyrimidine dehydrogenase (DPD) deficiency is the main known cause of life-threatening fluoropyrimidine (FP)-induced toxicities. We conducted a meta-analysis on individual patient data to assess the contribution of deleterious DPYD variants *2A/D949V/*13/HapB3 (recommended by EMA) and clinical factors, for predicting G4-5 toxicity. METHODS Study eligibility criteria included recruitment of Caucasian patients without DPD-based FP-dose adjustment. Main endpoint was 12-week haematological or digestive G4-5 toxicity. The value of DPYD variants *2A/p.D949V/*13 merged, HapB3, and MIR27A rs895819 was evaluated using multivariable logistic models (AUC). RESULTS Among 25 eligible studies, complete clinical variables and primary endpoint were available in 15 studies (8733 patients). Twelve-week G4-5 toxicity prevalence was 7.3% (641 events). The clinical model included age, sex, body mass index, schedule of FP-administration, concomitant anticancer drugs. Adding *2A/p.D949V/*13 variants (at least one allele, prevalence 2.2%, OR 9.5 [95%CI 6.7-13.5]) significantly improved the model (p < 0.0001). The addition of HapB3 (prevalence 4.0%, 98.6% heterozygous), in spite of significant association with toxicity (OR 1.8 [95%CI 1.2-2.7]), did not improve the model. MIR27A rs895819 was not associated with toxicity, irrespective of DPYD variants. CONCLUSIONS FUSAFE meta-analysis highlights the major relevance of DPYD *2A/p.D949V/*13 combined with clinical variables to identify patients at risk of very severe FP-related toxicity.
Collapse
Affiliation(s)
- Gwénaël Le Teuff
- Service de Biostatistique et d'Epidémiologie, Gustave Roussy, Oncostat U1018 INSERM, labeled Ligue Contre le Cancer, Université Paris-Saclay, Villejuif, France.
| | - Nathalie Cozic
- Service de Biostatistique et d'Epidémiologie, Gustave Roussy, Oncostat U1018 INSERM, labeled Ligue Contre le Cancer, Université Paris-Saclay, Villejuif, France
| | | | - Valérie Boige
- Department of cancer medicine, Gustave-Roussy Cancer Campus, Paris-Saclay and Paris-Sud Universities, Villejuif, France
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Equipe Labellisée Ligue Nationale Contre le Cancer, CNRS SNC, 5096, Paris, France
| | - Robert B Diasio
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic Cancer Center, Rochester, MN, USA
| | - Julien Taieb
- Université Paris-Cité, SIRIC CARPEM, Department of Gastroenterology and Digestive Oncology, Georges Pompidou European Hospital, AP-HP, Paris, France
| | - Didier Meulendijks
- Department of Clinical Pharmacology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Claire Palles
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- Departments of Clinical Pharmacology, and of Biochemistry and Pharmacy, University of Tuebingen, Tuebingen, Germany
- Cluster of Excellence IFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72074, Tübingen, Germany
| | - Maarten Deenen
- Department of Clinical Pharmacy, Catharina Hospital, Eindhoven, the Netherlands
| | - Carlo R Largiadèr
- Department of Clinical Chemistry, Bern University Hospital, University of Bern, Inselspital, Bern, Switzerland
| | | | | | | | - Antonello Di Paolo
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Eva Gross
- LMU Munich, University Hospital, Campus Grosshadern, Munich, Germany
| | - Barna Budai
- National Institute of Oncology, Budapest, Hungary
| | - Stephen P Ackland
- College of Heath, Medicine and Wellbeing, University of Newcastle, Newcastle, NSW, Australia
| | - André B P van Kuilenburg
- Amsterdam UMC, location University of Amsterdam, Laboratory Genetic Metabolic Diseases, Meibergdreef 9, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Imaging and biomarkers, Amsterdam, The Netherlands
| | - Howard L McLeod
- Intermountain Precision Genomics, Intermountain Healthcare, St George, UT, USA
| | - Gérard Milano
- Oncopharmacology Laboratory, Centre Antoine Lacassagne, Nice, France
| | - Fabienne Thomas
- Institut Claudius Regaud, IUCT-Oncopôle and CRCT, University of Toulouse, Inserm, Toulouse, France
| | - Marie-Anne Loriot
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Equipe Labellisée Ligue Nationale Contre le Cancer, CNRS SNC, 5096, Paris, France
- Hôpital Européen Georges Pompidou, Hôpitaux Universitaires Paris Ouest, Paris, France
| | - David Kerr
- Nuffield Division of Clinical and Laboratory Sciences and University of Oxford, Oxford, UK
| | - Jan H M Schellens
- Department of Clinical Pharmacology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Equipe Labellisée Ligue Nationale Contre le Cancer, CNRS SNC, 5096, Paris, France
- Hôpital Européen Georges Pompidou, Hôpitaux Universitaires Paris Ouest, Paris, France
| | - Qian Shi
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Jean-Pierre Pignon
- Service de Biostatistique et d'Epidémiologie, Gustave Roussy, Oncostat U1018 INSERM, labeled Ligue Contre le Cancer, Université Paris-Saclay, Villejuif, France
| | | |
Collapse
|
40
|
Decker NS, Johnson T, Le Cornet C, Behrens S, Obi N, Kaaks R, Chang-Claude J, Fortner RT. Associations between lifestyle, health, and clinical characteristics and circulating oxysterols and cholesterol precursors in women diagnosed with breast cancer: a cross-sectional study. Sci Rep 2024; 14:4977. [PMID: 38424253 PMCID: PMC10904394 DOI: 10.1038/s41598-024-55316-x] [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: 10/25/2023] [Accepted: 02/22/2024] [Indexed: 03/02/2024] Open
Abstract
Despite increasing evidence that cholesterol precursors and oxysterols, oxidized cholesterol metabolites, play a role in numerous pathological processes and diseases including breast cancer, little is known about correlates of these sterols in women with breast cancer. In this study, 2282 women with breast cancer and blood draw post diagnosis were included and cross-sectional associations between circulating levels of 15 sterols/oxysterols and (a) lifestyle, anthropometric, reproductive characteristics, (b) comorbidities and medication use, and (c) breast cancer tumor and treatment characteristics were calculated using generalized linear models. Obesity was strongly associated with circulating levels of 7-dehydrocholesterol (DC) (body mass index ≥ 30 vs. 18.5-24.9 kg/m2: 51.7% difference) and 7-ketocholesterol (KC) (40.0% difference). After adjustment for BMI, comorbidities such as cardiovascular disease were associated with higher levels of 7-DC (26.1% difference) and lower levels of desmosterol (- 16.4% difference). Breast cancer tumor characteristics including hormone receptor status, tumor stage, and endocrine therapy were associated with lanosterol, 24-DHLan, 7b-HC, and THC (e.g., THC; tumor stage IIIa vs. I: 36.9% difference). Weaker associations were observed for lifestyle characteristics and for any of the other oxysterols. The findings of this study suggest that cholesterol precursors are strongly associated with metabolic factors, while oxysterols are associated with breast cancer tumor characteristics, warranting further investigation into the role of cholesterol precursors and oxysterols in women with breast cancer and other populations.
Collapse
Affiliation(s)
- Nina Sophia Decker
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Theron Johnson
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Charlotte Le Cornet
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nadia Obi
- Institute for Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute for Occupational and Maritime Medicine Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- University Cancer Center Hamburg, Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Renée Turzanski Fortner
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Department of Research, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway.
| |
Collapse
|
41
|
Tan L, Brown C, Mersiades A, Lee CK, John T, Kao S, Newnham G, O'Byrne K, Parakh S, Bray V, Jasas K, Yip S, Wong SQ, Ftouni S, Guinto J, Chandrashekar S, Clarke S, Pavlakis N, Stockler MR, Dawson SJ, Solomon BJ. A Phase II trial of alternating osimertinib and gefitinib therapy in advanced EGFR-T790M positive non-small cell lung cancer: OSCILLATE. Nat Commun 2024; 15:1823. [PMID: 38418463 PMCID: PMC10902357 DOI: 10.1038/s41467-024-46008-1] [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: 07/06/2023] [Accepted: 02/07/2024] [Indexed: 03/01/2024] Open
Abstract
In this phase II, single arm trial (ACTRN12617000720314), we investigate if alternating osimertinib and gefitinib would delay the development of resistance to osimertinib in advanced, non-small cell lung cancer (NSCLC) with the epidermal growth factor receptor (EGFR) T790M mutation (n = 47) by modulating selective pressure on resistant clones. The primary endpoint is progression free-survival (PFS) rate at 12 months, and secondary endpoints include: feasibility of alternating therapy, overall response rate (ORR), overall survival (OS), and safety. The 12-month PFS rate is 38% (95% CI 27.5-55), not meeting the pre-specified primary endpoint. Serial circulating tumor DNA (ctDNA) analysis reveals decrease and clearance of the original activating EGFR and EGFR-T790M mutations which are prognostic of clinical outcomes. In 73% of participants, loss of T790M ctDNA is observed at progression and no participants have evidence of the EGFR C797S resistance mutation following the alternating regimen. These findings highlight the challenges of treatment strategies designed to modulate clonal evolution and the clinical importance of resistance mechanisms beyond suppression of selected genetic mutations in driving therapeutic escape to highly potent targeted therapies.
Collapse
Affiliation(s)
- Lavinia Tan
- Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Chris Brown
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - Antony Mersiades
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - Chee Khoon Lee
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
- St George Hospital, Sydney, NSW, Australia
| | - Thomas John
- Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Steven Kao
- Chris O'Brien Lifehouse, Sydney, NSW, Australia
| | | | | | - Sagun Parakh
- Austin Hospital, Olivia Newton John Cancer and Wellness and Research Centre, Melbourne, VIC, Australia
| | | | - Kevin Jasas
- Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Sonia Yip
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - Stephen Q Wong
- Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Sarah Ftouni
- Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Jerick Guinto
- Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | | | - Stephen Clarke
- Royal North Shore Hospital, Sydney, NSW, Australia
- University of Sydney, Sydney, NSW, Australia
| | - Nick Pavlakis
- Royal North Shore Hospital, Sydney, NSW, Australia
- University of Sydney, Sydney, NSW, Australia
| | - Martin R Stockler
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, Australia
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Melbourne, Vic, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia.
- Centre for Cancer Research, The University of Melbourne, Melbourne, VIC, Australia.
| | - Benjamin J Solomon
- Peter MacCallum Cancer Centre, Melbourne, Vic, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia.
| |
Collapse
|
42
|
Núñez-Carpintero I, Rigau M, Bosio M, O'Connor E, Spendiff S, Azuma Y, Topf A, Thompson R, 't Hoen PAC, Chamova T, Tournev I, Guergueltcheva V, Laurie S, Beltran S, Capella-Gutiérrez S, Cirillo D, Lochmüller H, Valencia A. Rare disease research workflow using multilayer networks elucidates the molecular determinants of severity in Congenital Myasthenic Syndromes. Nat Commun 2024; 15:1227. [PMID: 38418480 PMCID: PMC10902324 DOI: 10.1038/s41467-024-45099-0] [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: 12/21/2022] [Accepted: 01/15/2024] [Indexed: 03/01/2024] Open
Abstract
Exploring the molecular basis of disease severity in rare disease scenarios is a challenging task provided the limitations on data availability. Causative genes have been described for Congenital Myasthenic Syndromes (CMS), a group of diverse minority neuromuscular junction (NMJ) disorders; yet a molecular explanation for the phenotypic severity differences remains unclear. Here, we present a workflow to explore the functional relationships between CMS causal genes and altered genes from each patient, based on multilayer network community detection analysis of complementary biomedical information provided by relevant data sources, namely protein-protein interactions, pathways and metabolomics. Our results show that CMS severity can be ascribed to the personalized impairment of extracellular matrix components and postsynaptic modulators of acetylcholine receptor (AChR) clustering. This work showcases how coupling multilayer network analysis with personalized -omics information provides molecular explanations to the varying severity of rare diseases; paving the way for sorting out similar cases in other rare diseases.
Collapse
Affiliation(s)
- Iker Núñez-Carpintero
- Barcelona Supercomputing Center (BSC), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain
| | - Maria Rigau
- Barcelona Supercomputing Center (BSC), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Mattia Bosio
- Barcelona Supercomputing Center (BSC), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain
- Coordination Unit Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Barcelona Supercomputing Center, Barcelona, Spain
| | - Emily O'Connor
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
- Brain and Mind Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Sally Spendiff
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Yoshiteru Azuma
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Pediatrics, Aichi Medical University, Nagakute, Japan
| | - Ana Topf
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Rachel Thompson
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Peter A C 't Hoen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, The Netherlands
| | - Teodora Chamova
- Department of Neurology, Expert Centre for Hereditary Neurologic and Metabolic Disorders, Alexandrovska University Hospital, Medical University-Sofia, Sofia, Bulgaria
| | - Ivailo Tournev
- Department of Neurology, Expert Centre for Hereditary Neurologic and Metabolic Disorders, Alexandrovska University Hospital, Medical University-Sofia, Sofia, Bulgaria
- Department of Cognitive Science and Psychology, New Bulgarian University, Sofia, 1618, Bulgaria
| | - Velina Guergueltcheva
- Clinic of Neurology, University Hospital Sofiamed, Sofia University St. Kliment Ohridski, Sofia, Bulgaria
| | - Steven Laurie
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Sergi Beltran
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain
| | - Salvador Capella-Gutiérrez
- Barcelona Supercomputing Center (BSC), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain
- Coordination Unit Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Barcelona Supercomputing Center, Barcelona, Spain
| | - Davide Cirillo
- Barcelona Supercomputing Center (BSC), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain.
| | - Hanns Lochmüller
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
- Brain and Mind Research Institute, University of Ottawa, Ottawa, ON, Canada
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, ON, Canada
- Department of Neuropediatrics and Muscle Disorders, Medical Center - University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain
- Coordination Unit Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Barcelona Supercomputing Center, Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| |
Collapse
|
43
|
Fonseca NM, Maurice-Dror C, Herberts C, Tu W, Fan W, Murtha AJ, Kollmannsberger C, Kwan EM, Parekh K, Schönlau E, Bernales CQ, Donnellan G, Ng SWS, Sumiyoshi T, Vergidis J, Noonan K, Finch DL, Zulfiqar M, Miller S, Parimi S, Lavoie JM, Hardy E, Soleimani M, Nappi L, Eigl BJ, Kollmannsberger C, Taavitsainen S, Nykter M, Tolmeijer SH, Boerrigter E, Mehra N, van Erp NP, De Laere B, Lindberg J, Grönberg H, Khalaf DJ, Annala M, Chi KN, Wyatt AW. Prediction of plasma ctDNA fraction and prognostic implications of liquid biopsy in advanced prostate cancer. Nat Commun 2024; 15:1828. [PMID: 38418825 PMCID: PMC10902374 DOI: 10.1038/s41467-024-45475-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: 07/21/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
No consensus strategies exist for prognosticating metastatic castration-resistant prostate cancer (mCRPC). Circulating tumor DNA fraction (ctDNA%) is increasingly reported by commercial and laboratory tests but its utility for risk stratification is unclear. Here, we intersect ctDNA%, treatment outcomes, and clinical characteristics across 738 plasma samples from 491 male mCRPC patients from two randomized multicentre phase II trials and a prospective province-wide blood biobanking program. ctDNA% correlates with serum and radiographic metrics of disease burden and is highest in patients with liver metastases. ctDNA% strongly predicts overall survival, progression-free survival, and treatment response independent of therapeutic context and outperformed established prognostic clinical factors. Recognizing that ctDNA-based biomarker genotyping is limited by low ctDNA% in some patients, we leverage the relationship between clinical prognostic factors and ctDNA% to develop a clinically-interpretable machine-learning tool that predicts whether a patient has sufficient ctDNA% for informative ctDNA genotyping (available online: https://www.ctDNA.org ). Our results affirm ctDNA% as an actionable tool for patient risk stratification and provide a practical framework for optimized biomarker testing.
Collapse
Affiliation(s)
- Nicolette M Fonseca
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | - Cameron Herberts
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Wilson Tu
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - William Fan
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Andrew J Murtha
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | - Edmond M Kwan
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
- Department of Medicine, School of Clinical Sciences; Monash University, Melbourne, VIC, Australia
| | - Karan Parekh
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Elena Schönlau
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Cecily Q Bernales
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Gráinne Donnellan
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Sarah W S Ng
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Takayuki Sumiyoshi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Joanna Vergidis
- Department of Medical Oncology, BC Cancer, Victoria, BC, Canada
| | - Krista Noonan
- Department of Medical Oncology, BC Cancer, Surrey, BC, Canada
| | - Daygen L Finch
- Department of Medical Oncology, BC Cancer, Kelowna, BC, Canada
| | | | - Stacy Miller
- Department of Radiation Oncology, BC Cancer, Prince George, BC, Canada
| | - Sunil Parimi
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | | | - Edward Hardy
- Tom McMurtry & Peter Baerg Cancer Centre, Vernon Jubilee Hospital, Vernon, BC, Canada
| | - Maryam Soleimani
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Lucia Nappi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Bernhard J Eigl
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | | | - Sinja Taavitsainen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Sofie H Tolmeijer
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Oncology, Research Institute for Medical Innovation, Radboud University, Nijmegen, The Netherlands
| | - Emmy Boerrigter
- Department of Pharmacy, Research Institute for Medical Innovation, Radboud University, Nijmegen, The Netherlands
| | - Niven Mehra
- Department of Medical Oncology, Research Institute for Medical Innovation, Radboud University, Nijmegen, The Netherlands
| | - Nielka P van Erp
- Department of Pharmacy, Research Institute for Medical Innovation, Radboud University, Nijmegen, The Netherlands
| | - Bram De Laere
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Daniel J Khalaf
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Matti Annala
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland.
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada.
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.
| |
Collapse
|
44
|
Lindahl G, Fjellander S, Selvaraj K, Vildeval M, Ali Z, Almter R, Erkstam A, Rodriguez GV, Abrahamsson A, Kersley ÅR, Fahlgren A, Kjølhede P, Linder S, Dabrosin C, Jensen L. Zebrafish tumour xenograft models: a prognostic approach to epithelial ovarian cancer. NPJ Precis Oncol 2024; 8:53. [PMID: 38413842 PMCID: PMC10899227 DOI: 10.1038/s41698-024-00550-9] [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: 06/27/2023] [Accepted: 02/16/2024] [Indexed: 02/29/2024] Open
Abstract
Epithelial ovarian cancer (EOC) is the gynaecological malignancy with highest mortality. Although adjuvant treatment with carboplatin and paclitaxel leads to an objective response in ~80% of these patients, a majority will relapse within two years. Better methods for assessing long-term treatment outcomes are needed. To address this, we established safe and efficacious doses of carboplatin and paclitaxel using IGROV-1 zebrafish-CDX models. Then fluorescently-labelled cell suspensions from 83 tumour biopsies collected at exploratory laparotomy of women with suspected EOC were generated and 37 (45%) were successfully implanted in zebrafish larvae. Among these 19 of 27 pathology-confirmed EOC samples (70%) engrafted. These zebrafish patient-derived tumour xenograft (ZTX) models were treated with carboplatin or paclitaxel and tumour growth/regression and metastatic dissemination were recorded. In a subgroup of nine patients, four ZTX models regressed during carboplatin treatment. All four corresponding patients had >24 months PFS. Furthermore, both ZTX models established from two patients having <24 months PFS failed to regress during carboplatin treatment. Seven of eight models seeding <6 metastatic cells were established from patients having >24 months PFS. In eleven of fourteen patients, FIGO stage I + II or III tumours gave rise to ZTX models seeding <4 or >4 metastatic cells, respectively. In conclusion, ZTX models predicted patients having >24 or <24 months PFS, based on response/no response to carboplatin. Furthermore, high metastatic dissemination in ZTX models correlated to shorter PFS and more advanced disease at diagnosis. These preliminary results suggest that ZTX models could become a useful prognostic tool in EOC treatment planning.
Collapse
Affiliation(s)
- Gabriel Lindahl
- Department of Oncology and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Sebastian Fjellander
- BioReperia AB, Linköping, Sweden
- Linköping University, Department of Health, Medicine and Care, Division of Diagnostics and Specialist Medicine, Linköping, Sweden
| | - Karthik Selvaraj
- Linköping University, Department of Biomedical and Clinical Sciences, Linköping, Sweden
| | | | | | | | | | | | - Annelie Abrahamsson
- Linköping University, Department of Biomedical and Clinical Sciences, Linköping, Sweden
| | - Åsa Rydmark Kersley
- Department of Obstetrics and Gynecology and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Anna Fahlgren
- BioReperia AB, Linköping, Sweden
- Linköping University, Department of Biomedical and Clinical Sciences, Linköping, Sweden
| | - Preben Kjølhede
- Department of Obstetrics and Gynecology and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Stig Linder
- Linköping University, Department of Biomedical and Clinical Sciences, Linköping, Sweden
| | - Charlotta Dabrosin
- Department of Oncology and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Lasse Jensen
- BioReperia AB, Linköping, Sweden.
- Linköping University, Department of Health, Medicine and Care, Division of Diagnostics and Specialist Medicine, Linköping, Sweden.
| |
Collapse
|
45
|
Wang S, Wang R, Hu D, Zhang C, Cao P, Huang J. Machine learning reveals diverse cell death patterns in lung adenocarcinoma prognosis and therapy. NPJ Precis Oncol 2024; 8:49. [PMID: 38409471 PMCID: PMC10897292 DOI: 10.1038/s41698-024-00538-5] [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: 07/13/2023] [Accepted: 02/08/2024] [Indexed: 02/28/2024] Open
Abstract
Cancer cell growth, metastasis, and drug resistance pose significant challenges in the management of lung adenocarcinoma (LUAD). However, there is a deficiency in optimal predictive models capable of accurately forecasting patient prognoses and guiding the selection of targeted treatments. Programmed cell death (PCD) pathways play a pivotal role in the development and progression of various cancers, offering potential as prognostic indicators and drug sensitivity markers for LUAD patients. The development and validation of predictive models were conducted by integrating 13 PCD patterns with comprehensive analysis of bulk RNA, single-cell RNA transcriptomics, and pertinent clinicopathological details derived from TCGA-LUAD and six GEO datasets. Utilizing the machine learning algorithms, we identified ten critical differentially expressed genes associated with PCD in LUAD, namely CHEK2, KRT18, RRM2, GAPDH, MMP1, CHRNA5, TMPRSS4, ITGB4, CD79A, and CTLA4. Subsequently, we conducted a programmed cell death index (PCDI) based on these genes across the aforementioned cohorts and integrated this index with relevant clinical features to develop several prognostic nomograms. Furthermore, we observed a significant correlation between the PCDI and immune features in LUAD, including immune cell infiltration and the expression of immune checkpoint molecules. Additionally, we found that patients with a high PCDI score may exhibit resistance to immunotherapy and standard adjuvant chemotherapy regimens; however, they may benefit from other FDA-supported drugs such as docetaxel and dasatinib. In conclusion, the PCDI holds potential as a prognostic signature and can facilitate personalized treatment for LUAD patients.
Collapse
Affiliation(s)
- Shun Wang
- Department of Respiratory Medicine, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, 200031, China
| | - Ruohuang Wang
- Department of Otolaryngology, the Second Affiliated Hospital of the Naval Military Medical University (Shanghai Changzheng Hospital), Shanghai, 200003, China
| | - Dingtao Hu
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, 200433, China
| | - Caoxu Zhang
- Department of Molecular Diagnostics, The Core Laboratory in Medical Center of Clinical Research, Department of Endocrinology, Shanghai Ninth People's Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiaotong University School of Medicine, Shanghai, 200011, China
| | - Peng Cao
- Department of Interventional Pulmonology, Anhui Chest Hospital, Hefei, Anhui, 230022, China
| | - Jie Huang
- Department of Respiratory Medicine, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, 200031, China.
| |
Collapse
|
46
|
Piątkowska D, Klimaszewska-Wiśniewska A, Kosińska A, Wujec R, Grzanka D, Durślewicz J. Ubiquitin B, Ubiquitin C, and β-Catenin as Promising Diagnostic and Prognostic Tools in Prostate Cancer. Cancers (Basel) 2024; 16:902. [PMID: 38473264 DOI: 10.3390/cancers16050902] [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: 01/13/2024] [Revised: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Prostate cancer (PC) is a major global public health concern, imposing a significant burden on men and ranking as the second most prevalent malignancy. This study delves into the intricate world of ubiquitination processes and expression regulation, with a specific focus on understanding the roles of ubiquitin B (UBB), ubiquitin C (UBC), and β-Catenin in PC development. We thoroughly analyze the expression profiles of UBB, UBC, and β-Catenin, investigating their interactions and associations with clinical and histopathological data. These findings offer valuable insights into their potential as robust prognostic markers and their significance for patient survival. Our research uncovers the upregulation of UBB and UBC expression in PC tissues, and an even more pronounced expression in lymph node metastases, highlighting their pivotal roles in PC progression. Moreover, we identify a compelling correlation between high UBB and UBC levels and diminished overall survival in PC patients, emphasizing their clinical relevance. Additionally, we observe a significant reduction in membranous β-Catenin expression in PC tissues. Importantly, abnormal β-Catenin expression is strongly associated with shorter survival in PC patients and serves as a significant, independent prognostic factor for patient outcomes. Kaplan-Meier survival analysis indicates that patients with tumors characterized by simultaneous UBB and aberrant β-Catenin expression exhibit the poorest overall survival. These collective insights underline the clinical importance of evaluating UBB, UBC, and β-Catenin as combined prognostic markers in PC.
Collapse
Affiliation(s)
- Daria Piątkowska
- Department of Clinical Pathomorphology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-094 Bydgoszcz, Poland
| | - Anna Klimaszewska-Wiśniewska
- Department of Clinical Pathomorphology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-094 Bydgoszcz, Poland
| | - Alicja Kosińska
- Department of Clinical Pathomorphology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-094 Bydgoszcz, Poland
| | - Radosław Wujec
- Department of Clinical Pathomorphology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-094 Bydgoszcz, Poland
| | - Dariusz Grzanka
- Department of Clinical Pathomorphology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-094 Bydgoszcz, Poland
| | - Justyna Durślewicz
- Department of Clinical Pathomorphology, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-094 Bydgoszcz, Poland
| |
Collapse
|
47
|
Tran A, Wang A, Mickaill J, Strbenac D, Larance M, Vernon ST, Grieve SM, Figtree GA, Patrick E, Yang JYH. Construction and optimization of multi-platform precision pathways for precision medicine. Sci Rep 2024; 14:4248. [PMID: 38378802 PMCID: PMC10879206 DOI: 10.1038/s41598-024-54517-8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 02/13/2024] [Indexed: 02/22/2024] Open
Abstract
In the enduring challenge against disease, advancements in medical technology have empowered clinicians with novel diagnostic platforms. Whilst in some cases, a single test may provide a confident diagnosis, often additional tests are required. However, to strike a balance between diagnostic accuracy and cost-effectiveness, one must rigorously construct the clinical pathways. Here, we developed a framework to build multi-platform precision pathways in an automated, unbiased way, recommending the key steps a clinician would take to reach a diagnosis. We achieve this by developing a confidence score, used to simulate a clinical scenario, where at each stage, either a confident diagnosis is made, or another test is performed. Our framework provides a range of tools to interpret, visualize and compare the pathways, improving communication and enabling their evaluation on accuracy and cost, specific to different contexts. This framework will guide the development of novel diagnostic pathways for different diseases, accelerating the implementation of precision medicine into clinical practice.
Collapse
Affiliation(s)
- Andy Tran
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia
| | - Andy Wang
- Westmead Medical Institute, Westmead, NSW, Australia
| | - Jamie Mickaill
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia
- School of Computer Science, The University of Sydney, Camperdown, NSW, Australia
| | - Dario Strbenac
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia
| | - Mark Larance
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
| | - Stephen T Vernon
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Kolling Institute of Medical Research, St Leonards, NSW, Australia
| | - Stuart M Grieve
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Department of Radiology, Royal Prince Alfred Hospital, Camperdown, Australia
| | - Gemma A Figtree
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Kolling Institute of Medical Research, St Leonards, NSW, Australia
| | - Ellis Patrick
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
| | - Jean Yee Hwa Yang
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia.
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia.
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia.
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China.
| |
Collapse
|
48
|
Begg LR, Orriols AM, Zannikou M, Yeh C, Vadlamani P, Kanojia D, Bolin R, Dunne SF, Balakrishnan S, Camarda R, Roth D, Zielinski-Mozny NA, Yau C, Vassilopoulos A, Huang TH, Kim KYA, Horiuchi D. S100A8/A9 predicts response to PIM kinase and PD-1/PD-L1 inhibition in triple-negative breast cancer mouse models. Commun Med (Lond) 2024; 4:22. [PMID: 38378783 PMCID: PMC10879183 DOI: 10.1038/s43856-024-00444-8] [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: 05/23/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Understanding why some triple-negative breast cancer (TNBC) patients respond poorly to existing therapies while others respond well remains a challenge. This study aims to understand the potential underlying mechanisms distinguishing early-stage TNBC tumors that respond to clinical intervention from non-responders, as well as to identify clinically viable therapeutic strategies, specifically for TNBC patients who may not benefit from existing therapies. METHODS We conducted retrospective bioinformatics analysis of historical gene expression datasets to identify a group of genes whose expression levels in early-stage tumors predict poor clinical outcomes in TNBC. In vitro small-molecule screening, genetic manipulation, and drug treatment in syngeneic mouse models of TNBC were utilized to investigate potential therapeutic strategies and elucidate mechanisms of drug action. RESULTS Our bioinformatics analysis reveals a robust association between increased expression of immunosuppressive cytokine S100A8/A9 in early-stage tumors and subsequent disease progression in TNBC. A targeted small-molecule screen identifies PIM kinase inhibitors as capable of decreasing S100A8/A9 expression in multiple cell types, including TNBC and immunosuppressive myeloid cells. Combining PIM inhibition and immune checkpoint blockade induces significant antitumor responses, especially in otherwise resistant S100A8/A9-high PD-1/PD-L1-positive tumors. Notably, serum S100A8/A9 levels mirror those of tumor S100A8/A9 in a syngeneic mouse model of TNBC. CONCLUSIONS Our data propose S100A8/A9 as a potential predictive and pharmacodynamic biomarker in clinical trials evaluating combination therapy targeting PIM and immune checkpoints in TNBC. This work encourages the development of S100A8/A9-based liquid biopsy tests for treatment guidance.
Collapse
Affiliation(s)
- Lauren R Begg
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Adrienne M Orriols
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- University of Florida College of Medicine, Gainesville, FL, USA
| | - Markella Zannikou
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chen Yeh
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Biostatistics Collaboration Center, Northwestern University, Chicago, IL, USA
- Rush University Medical Center, Chicago, IL, USA
| | | | - Deepak Kanojia
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Mythic Therapeutics, Waltham, MA, USA
| | - Rosemary Bolin
- Center for Comparative Medicine, Northwestern University, Chicago, IL, USA
- Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Sara F Dunne
- High Throughput Analysis Laboratory, Northwestern University, Evanston, IL, USA
| | - Sanjeev Balakrishnan
- University of California, San Francisco, San Francisco, CA, USA
- Pulze.ai, San Francisco, CA, USA
| | - Roman Camarda
- University of California, San Francisco, San Francisco, CA, USA
- Novo Ventures US, Inc., San Francisco, CA, USA
| | - Diane Roth
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Nicolette A Zielinski-Mozny
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Comparative Medicine, Northwestern University, Chicago, IL, USA
| | - Christina Yau
- University of California, San Francisco, San Francisco, CA, USA
| | - Athanassios Vassilopoulos
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
- AbbVie, Inc., North Chicago, IL, USA
| | - Tzu-Hsuan Huang
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Kwang-Youn A Kim
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Biostatistics Collaboration Center, Northwestern University, Chicago, IL, USA
| | - Dai Horiuchi
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
- Center for Human Immunobiology, Northwestern University, Chicago, IL, USA.
| |
Collapse
|
49
|
Schoenrock B, Muckelt PE, Hastermann M, Albracht K, MacGregor R, Martin D, Gunga HC, Salanova M, Stokes MJ, Warner MB, Blottner D. Muscle stiffness indicating mission crew health in space. Sci Rep 2024; 14:4196. [PMID: 38378866 PMCID: PMC10879143 DOI: 10.1038/s41598-024-54759-6] [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: 11/07/2023] [Accepted: 02/16/2024] [Indexed: 02/22/2024] Open
Abstract
Muscle function is compromised by gravitational unloading in space affecting overall musculoskeletal health. Astronauts perform daily exercise programmes to mitigate these effects but knowing which muscles to target would optimise effectiveness. Accurate inflight assessment to inform exercise programmes is critical due to lack of technologies suitable for spaceflight. Changes in mechanical properties indicate muscle health status and can be measured rapidly and non-invasively using novel technology. A hand-held MyotonPRO device enabled monitoring of muscle health for the first time in spaceflight (> 180 days). Greater/maintained stiffness indicated countermeasures were effective. Tissue stiffness was preserved in the majority of muscles (neck, shoulder, back, thigh) but Tibialis Anterior (foot lever muscle) stiffness decreased inflight vs. preflight (p < 0.0001; mean difference 149 N/m) in all 12 crewmembers. The calf muscles showed opposing effects, Gastrocnemius increasing in stiffness Soleus decreasing. Selective stiffness decrements indicate lack of preservation despite daily inflight countermeasures. This calls for more targeted exercises for lower leg muscles with vital roles as ankle joint stabilizers and in gait. Muscle stiffness is a digital biomarker for risk monitoring during future planetary explorations (Moon, Mars), for healthcare management in challenging environments or clinical disorders in people on Earth, to enable effective tailored exercise programmes.
Collapse
Affiliation(s)
- Britt Schoenrock
- NeuroMuscular System & Signaling Group, Berlin Center of Space Medicine and Extreme Environments, 10115 Berlin, Germany, Institute of Integrative Neuroanatomy, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10115 Berlin, Germany, 10115, Berlin, Germany
| | - Paul E Muckelt
- School of Health Sciences, University of Southampton, Southampton, UK
| | - Maria Hastermann
- Experimental and Clinical Research Center (ECRC) and NeuroCure Clinical Research Center (NCRC), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | | | | | - Hans-Christian Gunga
- Institute of Physiology, Berlin Center of Space Medicine and Extreme Environments, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10115 Berlin, Germany, Berlin, Germany
| | - Michele Salanova
- NeuroMuscular System & Signaling Group, Berlin Center of Space Medicine and Extreme Environments, 10115 Berlin, Germany, Institute of Integrative Neuroanatomy, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10115 Berlin, Germany, 10115, Berlin, Germany
| | - Maria J Stokes
- School of Health Sciences, University of Southampton, Southampton, UK
| | - Martin B Warner
- School of Health Sciences, University of Southampton, Southampton, UK
| | - Dieter Blottner
- NeuroMuscular System & Signaling Group, Berlin Center of Space Medicine and Extreme Environments, 10115 Berlin, Germany, Institute of Integrative Neuroanatomy, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10115 Berlin, Germany, 10115, Berlin, Germany.
| |
Collapse
|
50
|
Terragna C, Poletti A, Solli V, Martello M, Zamagni E, Pantani L, Borsi E, Vigliotta I, Mazzocchetti G, Armuzzi S, Taurisano B, Testoni N, Marzocchi G, Kanapari A, Pistis I, Tacchetti P, Mancuso K, Rocchi S, Rizzello I, Cavo M. Multi-dimensional scaling techniques unveiled gain1q&loss13q co-occurrence in Multiple Myeloma patients with specific genomic, transcriptional and adverse clinical features. Nat Commun 2024; 15:1551. [PMID: 38378709 PMCID: PMC10879136 DOI: 10.1038/s41467-024-45000-z] [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: 04/28/2023] [Accepted: 01/11/2024] [Indexed: 02/22/2024] Open
Abstract
The complexity of Multiple Myeloma (MM) is driven by several genomic aberrations, interacting with disease-related and/or -unrelated factors and conditioning patients' clinical outcome. Patient's prognosis is hardly predictable, as commonly employed MM risk models do not precisely partition high- from low-risk patients, preventing the reliable recognition of early relapsing/refractory patients. By a dimensionality reduction approach, here we dissect the genomic landscape of a large cohort of newly diagnosed MM patients, modelling all the possible interactions between any MM chromosomal alterations. We highlight the presence of a distinguished cluster of patients in the low-dimensionality space, with unfavorable clinical behavior, whose biology was driven by the co-occurrence of chromosomes 1q CN gain and 13 CN loss. Presence or absence of these alterations define MM patients overexpressing either CCND2 or CCND1, fostering the implementation of biology-based patients' classification models to describe the different MM clinical behaviors.
Collapse
Affiliation(s)
- Carolina Terragna
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy.
| | - Andrea Poletti
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Vincenza Solli
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Marina Martello
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Elena Zamagni
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Lucia Pantani
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Enrica Borsi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Ilaria Vigliotta
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Gaia Mazzocchetti
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Silvia Armuzzi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Barbara Taurisano
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Nicoletta Testoni
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Giulia Marzocchi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Ajsi Kanapari
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Ignazia Pistis
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Paola Tacchetti
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
| | - Katia Mancuso
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Serena Rocchi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Ilaria Rizzello
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Michele Cavo
- IRCCS Azienda Ospedaliero-Universitaria di Bologna-Istituto di Ematologia "Seràgnoli", Bologna, Italy
- DIMEC-Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| |
Collapse
|