Nature MedicinePub Date : 2024-11-17DOI: 10.1038/s41591-024-03374-z
Barry A. Borlaug, Michael R. Zile, Christopher M. Kramer, Seth J. Baum, Karla Hurt, Sheldon E. Litwin, Masahiro Murakami, Yang Ou, Navneet Upadhyay, Milton Packer
{"title":"Effects of tirzepatide on circulatory overload and end-organ damage in heart failure with preserved ejection fraction and obesity: a secondary analysis of the SUMMIT trial","authors":"Barry A. Borlaug, Michael R. Zile, Christopher M. Kramer, Seth J. Baum, Karla Hurt, Sheldon E. Litwin, Masahiro Murakami, Yang Ou, Navneet Upadhyay, Milton Packer","doi":"10.1038/s41591-024-03374-z","DOIUrl":"https://doi.org/10.1038/s41591-024-03374-z","url":null,"abstract":"<p>Patients with obesity-related heart failure with preserved ejection fraction (HFpEF) display circulatory volume expansion and pressure overload contributing to cardiovascular–kidney end-organ damage. In the SUMMIT trial, patients with HFpEF and obesity were randomized to the long-acting glucose-dependent insulinotropic polypeptide receptor and glucagon-like peptide-1 receptor agonist tirzepatide (<i>n</i> = 364, 200 women) or placebo (<i>n</i> = 367, 193 women). As reported separately, tirzepatide decreased cardiovascular death or worsening heart failure. Here, in this mechanistic secondary analysis of the SUMMIT trial, tirzepatide treatment at 52 weeks, as compared with placebo, reduced systolic blood pressure (estimated treatment difference (ETD) −5 mmHg, 95% confidence interval (CI) −7 to −3; <i>P</i> < 0.001), decreased estimated blood volume (ETD −0.58 l, 95% CI −0.63 to −0.52; <i>P</i> < 0.001) and reduced C-reactive protein levels (ETD −37.2%, 95% CI −45.7 to −27.3; <i>P</i> < 0.001). These changes were coupled with an increase in estimated glomerular filtration rate (ETD 2.90 ml min<sup>−1</sup> 1.73 m<sup>−2</sup> yr<sup>−1</sup>, 95% CI 0.94 to 4.86; <i>P</i> = 0.004), a decrease in urine albumin–creatinine ratio (ETD 24 weeks, −25.0%, 95% CI −36 to −13%; <i>P</i> < 0.001; 52 weeks, −15%, 95% CI −28 to 0.1; <i>P</i> = 0.051), a reduction in N-terminal prohormone B-type natriuretic peptide levels (ETD 52 weeks −10.5%, 95% CI −20.7 to 1.0%; <i>P</i> = 0.07) and a reduction in troponin T levels (ETD 52 weeks −10.4%, 95% CI −16.7 to −3.6; <i>P</i> = 0.003). In post hoc exploratory analyses, decreased estimated blood volume with tirzepatide treatment was significantly correlated with decreased blood pressure, reduced microalbuminuria, improved Kansas City Cardiomyopathy Questionnaire Clinical Summary Score and increased 6-min walk distance. Moreover, decreased C-reactive protein levels were correlated with reduced troponin T levels and improved 6-min walk distance. In conclusion, tirzepatide reduced circulatory volume–pressure overload and systemic inflammation and mitigated cardiovascular–kidney end-organ injury in patients with HFpEF and obesity, providing new insights into the mechanisms of benefit from tirzepatide. ClinicalTrials.gov registration: NCT04847557.</p>","PeriodicalId":19037,"journal":{"name":"Nature Medicine","volume":"84 1","pages":""},"PeriodicalIF":82.9,"publicationDate":"2024-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142645864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature MedicinePub Date : 2024-11-15DOI: 10.1038/s41591-024-03404-w
Steven M Horwitz, Ajit J Nirmal, Jahan Rahman, Ran Xu, Esther Drill, Natasha Galasso, Nivetha Ganesan, Theresa Davey, Helen Hancock, Leslie Perez, Catherine Maccaro, Alexandra Bahgat, Evan Marzouk, Elizabeth Cathcart, Alison Moskowitz, Ariela Noy, Anita Kumar, Eric Jacobsen, David C Fisher, Neha Mehta-Shah, Youn H Kim, Michael Khodadoust, Nikita Kotlov, Anastasia Nikitina, Olga Kudryashova, Valeria Zubareva, Ksenia Zornikova, Nara Shin, Maria Sorokina, Sandrine Degryse, Ekaterina Postovalova, Aleksander Bagaev, Kinga Hosszu, Devin McAvoy, Jaap J Boelens, Wenchao Wu, Zoe Ciantra, Jackson W Appelt, Christopher Trevisani, Sam Amaka, David M Weinstock, Santosha A Vardhana
{"title":"Author Correction: Duvelisib plus romidepsin in relapsed/refractory T cell lymphomas: a phase 1b/2a trial.","authors":"Steven M Horwitz, Ajit J Nirmal, Jahan Rahman, Ran Xu, Esther Drill, Natasha Galasso, Nivetha Ganesan, Theresa Davey, Helen Hancock, Leslie Perez, Catherine Maccaro, Alexandra Bahgat, Evan Marzouk, Elizabeth Cathcart, Alison Moskowitz, Ariela Noy, Anita Kumar, Eric Jacobsen, David C Fisher, Neha Mehta-Shah, Youn H Kim, Michael Khodadoust, Nikita Kotlov, Anastasia Nikitina, Olga Kudryashova, Valeria Zubareva, Ksenia Zornikova, Nara Shin, Maria Sorokina, Sandrine Degryse, Ekaterina Postovalova, Aleksander Bagaev, Kinga Hosszu, Devin McAvoy, Jaap J Boelens, Wenchao Wu, Zoe Ciantra, Jackson W Appelt, Christopher Trevisani, Sam Amaka, David M Weinstock, Santosha A Vardhana","doi":"10.1038/s41591-024-03404-w","DOIUrl":"https://doi.org/10.1038/s41591-024-03404-w","url":null,"abstract":"","PeriodicalId":19037,"journal":{"name":"Nature Medicine","volume":" ","pages":""},"PeriodicalIF":58.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142639387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature MedicinePub Date : 2024-11-14DOI: 10.1038/s41591-024-03382-z
{"title":"Are GLP-1 drugs really for everybody?","authors":"","doi":"10.1038/s41591-024-03382-z","DOIUrl":"10.1038/s41591-024-03382-z","url":null,"abstract":"As GLP-1 receptor agonists emerge as treatment options for conditions beyond diabetes and obesity, it becomes critical to understand how genetic, clinical and sociodemographic differences impact their effects on weight loss.","PeriodicalId":19037,"journal":{"name":"Nature Medicine","volume":"30 11","pages":"3029-3029"},"PeriodicalIF":58.7,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41591-024-03382-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142624366","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"ctDNA-based molecular residual disease and survival in resectable colorectal cancer","authors":"Yoshiaki Nakamura, Jun Watanabe, Naoya Akazawa, Keiji Hirata, Kozo Kataoka, Mitsuru Yokota, Kentaro Kato, Masahito Kotaka, Yoshinori Kagawa, Kun-Huei Yeh, Saori Mishima, Hiroki Yukami, Koji Ando, Masaaki Miyo, Toshihiro Misumi, Kentaro Yamazaki, Hiromichi Ebi, Kenji Okita, Atsushi Hamabe, Hiroki Sokuoka, Satoshi Kobayashi, George Laliotis, Vasily N. Aushev, Shruti Sharma, Adham Jurdi, Minetta C. Liu, Alexey Aleshin, Matthew Rabinowitz, Hideaki Bando, Hiroya Taniguchi, Ichiro Takemasa, Takeshi Kato, Daisuke Kotani, Masaki Mori, Takayuki Yoshino, Eiji Oki","doi":"10.1038/s41591-024-03254-6","DOIUrl":"10.1038/s41591-024-03254-6","url":null,"abstract":"The interim analysis of the CIRCULATE-Japan GALAXY observational study demonstrated the association of circulating tumor DNA (ctDNA)-based molecular residual disease (MRD) detection with recurrence risk and benefit from adjuvant chemotherapy (ACT) in resectable colorectal cancer (CRC). This updated analysis with a 23-month median follow-up, including 2,240 patients with stage II–III colon cancer or stage IV CRC, reinforces the prognostic value of ctDNA positivity during the MRD window with significantly inferior disease-free survival (DFS; hazard ratio (HR): 11.99, P < 0.0001) and overall survival (OS; HR: 9.68, P < 0.0001). In patients who experienced recurrence, ctDNA positivity correlated with shorter OS (HR: 2.71, P < 0.0001). The significantly shorter DFS in MRD-positive patients was consistent across actionable biomarker subsets. Sustained ctDNA clearance in response to ACT was an indicator of favorable DFS and OS compared to transient clearance (24-month DFS: 89.0% versus 3.3%; 24-month OS: 100.0% versus 82.3%). True spontaneous clearance rate with no clinical recurrence was 1.9% (2/105). Overall, our findings provide evidence for the utility of ctDNA monitoring for post-resection recurrence and mortality risk stratification that could be used for guiding adjuvant therapy. In a large cohort with a 23-month median follow-up of the CIRCULATE-Japan GALAXY observational study, ctDNA-based detection of molecular residual disease was predictive of survival outcomes and benefit of adjuvant chemotherapy in patients with resectable colorectal cancer.","PeriodicalId":19037,"journal":{"name":"Nature Medicine","volume":"30 11","pages":"3272-3283"},"PeriodicalIF":58.7,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41591-024-03254-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142234481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature MedicinePub Date : 2024-09-16DOI: 10.1038/s41591-024-03249-3
Iris Nederlof, Olga I. Isaeva, Manon de Graaf, Robbert C. A. M. Gielen, Noor A. M. Bakker, Adrianne L. Rolfes, Hannah Garner, Bram Boeckx, Joleen J. H. Traets, Ingrid A. M. Mandjes, Michiel de Maaker, Thomas van Brussel, Maksim Chelushkin, Elisa Champanhet, Marta Lopez-Yurda, Koen van de Vijver, José G. van den Berg, Ingrid Hofland, Natasja Klioueva, Ritse M. Mann, Claudette E. Loo, Frederieke H. van Duijnhoven, Victoria Skinner, Sylvia Luykx, Emile Kerver, Ekaterina Kalashnikova, Marloes G. J. van Dongen, Gabe S. Sonke, Sabine C. Linn, Christian U. Blank, Karin E. de Visser, Roberto Salgado, Lodewyk F. A. Wessels, Caroline A. Drukker, Ton N. Schumacher, Hugo M. Horlings, Diether Lambrechts, Marleen Kok
{"title":"Neoadjuvant nivolumab or nivolumab plus ipilimumab in early-stage triple-negative breast cancer: a phase 2 adaptive trial","authors":"Iris Nederlof, Olga I. Isaeva, Manon de Graaf, Robbert C. A. M. Gielen, Noor A. M. Bakker, Adrianne L. Rolfes, Hannah Garner, Bram Boeckx, Joleen J. H. Traets, Ingrid A. M. Mandjes, Michiel de Maaker, Thomas van Brussel, Maksim Chelushkin, Elisa Champanhet, Marta Lopez-Yurda, Koen van de Vijver, José G. van den Berg, Ingrid Hofland, Natasja Klioueva, Ritse M. Mann, Claudette E. Loo, Frederieke H. van Duijnhoven, Victoria Skinner, Sylvia Luykx, Emile Kerver, Ekaterina Kalashnikova, Marloes G. J. van Dongen, Gabe S. Sonke, Sabine C. Linn, Christian U. Blank, Karin E. de Visser, Roberto Salgado, Lodewyk F. A. Wessels, Caroline A. Drukker, Ton N. Schumacher, Hugo M. Horlings, Diether Lambrechts, Marleen Kok","doi":"10.1038/s41591-024-03249-3","DOIUrl":"10.1038/s41591-024-03249-3","url":null,"abstract":"Immune checkpoint inhibition (ICI) with chemotherapy is now the standard of care for stage II–III triple-negative breast cancer; however, it is largely unknown for which patients ICI without chemotherapy could be an option and what the benefit of combination ICI could be. The adaptive BELLINI trial explored whether short combination ICI induces immune activation (primary end point, twofold increase in CD8+ T cells or IFNG), providing a rationale for neoadjuvant ICI without chemotherapy. Here, in window-of-opportunity cohorts A (4 weeks of anti-PD-1) and B (4 weeks of anti-PD-1 + anti-CTLA4), we observed immune activation in 53% (8 of 15) and 60% (9 of 15) of patients, respectively. High levels of tumor-infiltrating lymphocytes correlated with response. Single-cell RNA sequencing revealed that higher pretreatment tumor-reactive CD8+ T cells, follicular helper T cells and shorter distances between tumor and CD8+ T cells correlated with response. Higher levels of regulatory T cells after treatment were associated with nonresponse. Based on these data, we opened cohort C for patients with high levels of tumor-infiltrating lymphocytes (≥50%) who received 6 weeks of neoadjuvant anti-PD-1 + anti-CTLA4 followed by surgery (primary end point, pathological complete response). Overall, 53% (8 of 15) of patients had a major pathological response (<10% viable tumor) at resection, with 33% (5 of 15) having a pathological complete response. All cohorts met Simon’s two-stage threshold for expansion to stage II. We observed grade ≥3 adverse events for 17% of patients and a high rate (57%) of immune-mediated endocrinopathies. In conclusion, neoadjuvant immunotherapy without chemotherapy demonstrates potential efficacy and warrants further investigation in patients with early triple-negative breast cancer. ClinicalTrials.gov registration: NCT03815890 . In the phase 2 adaptive BELLINI trial, patients with early-stage triple-negative breast cancer received neoadjuvant nivolumab with or without ipilimumab, showing immune activation, clearance of circulating tumor DNA and promising clinical response rates, especially in patients preselected based on high levels of tumor-infiltrating lymphocytes.","PeriodicalId":19037,"journal":{"name":"Nature Medicine","volume":"30 11","pages":"3223-3235"},"PeriodicalIF":58.7,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41591-024-03249-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142234487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature MedicinePub Date : 2024-09-15DOI: 10.1038/s41591-024-03250-w
Peter G. M. de Gooyer, Yara L. Verschoor, Lauren D. W. van den Dungen, Sara Balduzzi, Hendrik A. Marsman, Marnix H. Geukes Foppen, Cecile Grootscholten, Simone Dokter, Anne G. den Hartog, Wieke H. M. Verbeek, Karlijn Woensdregt, Joris J. van den Broek, Steven J. Oosterling, Ton N. Schumacher, Koert F. D. Kuhlmann, Regina G. H. Beets-Tan, John B. A. G. Haanen, Monique E. van Leerdam, Jose G. van den Berg, Myriam Chalabi
{"title":"Neoadjuvant nivolumab and relatlimab in locally advanced MMR-deficient colon cancer: a phase 2 trial","authors":"Peter G. M. de Gooyer, Yara L. Verschoor, Lauren D. W. van den Dungen, Sara Balduzzi, Hendrik A. Marsman, Marnix H. Geukes Foppen, Cecile Grootscholten, Simone Dokter, Anne G. den Hartog, Wieke H. M. Verbeek, Karlijn Woensdregt, Joris J. van den Broek, Steven J. Oosterling, Ton N. Schumacher, Koert F. D. Kuhlmann, Regina G. H. Beets-Tan, John B. A. G. Haanen, Monique E. van Leerdam, Jose G. van den Berg, Myriam Chalabi","doi":"10.1038/s41591-024-03250-w","DOIUrl":"10.1038/s41591-024-03250-w","url":null,"abstract":"Mismatch repair deficiency (dMMR) is found in approximately 15% of non-metastatic colon cancers (CCs) and is characterized by a defective DNA mismatch repair system, resulting in hypermutated and highly immunogenic tumors. Although patients with dMMR CC have limited benefit from chemotherapy, these tumors have been shown to respond exceptionally well to neoadjuvant anti-PD-1 plus anti-CTLA-4, with high rates of pathologic responses. Here, based on data from melanoma studies, we postulated a high efficacy and favorable toxicity profile of anti-PD-1 plus anti-LAG-3. In the NICHE-3 study, a total of 59 patients with locally advanced dMMR CC were treated with two 4-weekly cycles of nivolumab (480 mg) plus relatlimab (480 mg) before surgery. Pathologic response was observed in 57 of 59 (97%; 95% confidence interval (CI): 88–100%) patients, meeting the primary endpoint. Responses included 54 (92%; 95% CI: 81–97%) major pathologic responses (≤10% residual viable tumor) and 40 (68%; 95% CI: 54–79%) pathologic complete responses. With a median follow-up of 8 months (range, 2–19), one patient had recurrence of disease. The treatment displayed an acceptable safety profile, with all-grade and grade 3–4 immune-related adverse events (irAEs) occurring in 80% and 10% of patients, respectively. The most common irAEs were infusion-related reactions (29%), thyroid dysfunction (22%) and fatigue (20%). In conclusion, our results show that neoadjuvant nivolumab/relatlimab induces high rates of pathologic responses and that further investigation of this treatment in larger studies is warranted. These data add to the body of evidence in support of neoadjuvant immunotherapy regimens in dMMR CC. ClinicalTrials.gov identifier: NCT03026140 . In the phase 2 NICHE-3 trial, patients with locally advanced mismatch repair-deficient colon cancer who were treated with neoadjuvant anti-PD1 and anti-LAG3 agents showed high rates of pathological responses, requiring validation in larger trials.","PeriodicalId":19037,"journal":{"name":"Nature Medicine","volume":"30 11","pages":"3284-3290"},"PeriodicalIF":58.7,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41591-024-03250-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142233351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature MedicinePub Date : 2024-09-13DOI: 10.1038/s41591-024-03241-x
Ali Abbasi, Donna Rivera, Lesley H. Curtis, Robert M. Califf
{"title":"Post-approval evidence generation: a shared responsibility for healthcare","authors":"Ali Abbasi, Donna Rivera, Lesley H. Curtis, Robert M. Califf","doi":"10.1038/s41591-024-03241-x","DOIUrl":"10.1038/s41591-024-03241-x","url":null,"abstract":"Post-approval evidence generation is essential for high-quality clinical care and should be a shared priority for clinicians, health systems, payors, and the medical products industry, as well as the FDA and federal agencies.","PeriodicalId":19037,"journal":{"name":"Nature Medicine","volume":"30 11","pages":"3046-3049"},"PeriodicalIF":58.7,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142174944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature MedicinePub Date : 2024-09-12DOI: 10.1038/s41591-024-03246-6
Andrea Ganna, Angel Carracedo, Christian F. Christiansen, Emanuele Di Angelantonio, Pearl A. Dykstra, Angel M. Dzhambov, Roland Eils, Sara Green, Katharina L. Schneider, Tibor V. Varga, Anna-Leena Vuorinen, Luisa Zuccolo, Naja Hulvej Rod, Klaus Hoeyer
{"title":"The European Health Data Space can be a boost for research beyond borders","authors":"Andrea Ganna, Angel Carracedo, Christian F. Christiansen, Emanuele Di Angelantonio, Pearl A. Dykstra, Angel M. Dzhambov, Roland Eils, Sara Green, Katharina L. Schneider, Tibor V. Varga, Anna-Leena Vuorinen, Luisa Zuccolo, Naja Hulvej Rod, Klaus Hoeyer","doi":"10.1038/s41591-024-03246-6","DOIUrl":"10.1038/s41591-024-03246-6","url":null,"abstract":"The European Health Data Space provides an opportunity to benefit patients and the public.","PeriodicalId":19037,"journal":{"name":"Nature Medicine","volume":"30 11","pages":"3053-3056"},"PeriodicalIF":58.7,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142171027","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature MedicinePub Date : 2024-09-12DOI: 10.1038/s41591-024-03214-0
Lukas Heumos, Philipp Ehmele, Tim Treis, Julius Upmeier zu Belzen, Eljas Roellin, Lilly May, Altana Namsaraeva, Nastassya Horlava, Vladimir A. Shitov, Xinyue Zhang, Luke Zappia, Rainer Knoll, Niklas J. Lang, Leon Hetzel, Isaac Virshup, Lisa Sikkema, Fabiola Curion, Roland Eils, Herbert B. Schiller, Anne Hilgendorff, Fabian J. Theis
{"title":"An open-source framework for end-to-end analysis of electronic health record data","authors":"Lukas Heumos, Philipp Ehmele, Tim Treis, Julius Upmeier zu Belzen, Eljas Roellin, Lilly May, Altana Namsaraeva, Nastassya Horlava, Vladimir A. Shitov, Xinyue Zhang, Luke Zappia, Rainer Knoll, Niklas J. Lang, Leon Hetzel, Isaac Virshup, Lisa Sikkema, Fabiola Curion, Roland Eils, Herbert B. Schiller, Anne Hilgendorff, Fabian J. Theis","doi":"10.1038/s41591-024-03214-0","DOIUrl":"10.1038/s41591-024-03214-0","url":null,"abstract":"With progressive digitalization of healthcare systems worldwide, large-scale collection of electronic health records (EHRs) has become commonplace. However, an extensible framework for comprehensive exploratory analysis that accounts for data heterogeneity is missing. Here we introduce ehrapy, a modular open-source Python framework designed for exploratory analysis of heterogeneous epidemiology and EHR data. ehrapy incorporates a series of analytical steps, from data extraction and quality control to the generation of low-dimensional representations. Complemented by rich statistical modules, ehrapy facilitates associating patients with disease states, differential comparison between patient clusters, survival analysis, trajectory inference, causal inference and more. Leveraging ontologies, ehrapy further enables data sharing and training EHR deep learning models, paving the way for foundational models in biomedical research. We demonstrate ehrapy’s features in six distinct examples. We applied ehrapy to stratify patients affected by unspecified pneumonia into finer-grained phenotypes. Furthermore, we reveal biomarkers for significant differences in survival among these groups. Additionally, we quantify medication-class effects of pneumonia medications on length of stay. We further leveraged ehrapy to analyze cardiovascular risks across different data modalities. We reconstructed disease state trajectories in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) based on imaging data. Finally, we conducted a case study to demonstrate how ehrapy can detect and mitigate biases in EHR data. ehrapy, thus, provides a framework that we envision will standardize analysis pipelines on EHR data and serve as a cornerstone for the community. Incorporating a series of analytical steps, from data extraction and quality control to the generation of low-dimensional representations and to longitudinal analyses, an open-source software is proposed to standardize current electronic health record data processing and analysis pipelines.","PeriodicalId":19037,"journal":{"name":"Nature Medicine","volume":"30 11","pages":"3369-3380"},"PeriodicalIF":58.7,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41591-024-03214-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142170724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature MedicinePub Date : 2024-09-05DOI: 10.1038/s41591-024-03237-7
Sarah E. Hughes, Nicola E. Anderson, Eleanor Hathaway, Christel McMullan, Benjamin M. A. Hughes, Philip Collis, John Devin Peipert, Shamil Haroon, Melanie Calvert
{"title":"Opportunities and challenges for patient-reported outcome assessment in multimorbidity research and practice","authors":"Sarah E. Hughes, Nicola E. Anderson, Eleanor Hathaway, Christel McMullan, Benjamin M. A. Hughes, Philip Collis, John Devin Peipert, Shamil Haroon, Melanie Calvert","doi":"10.1038/s41591-024-03237-7","DOIUrl":"10.1038/s41591-024-03237-7","url":null,"abstract":"","PeriodicalId":19037,"journal":{"name":"Nature Medicine","volume":"30 11","pages":"3042-3043"},"PeriodicalIF":58.7,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142140605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}