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3043 citation(s) found for "Ha, Patrick K".

Development of a standard definition of ‘no-option’ and ‘poor-option’ for revascularization in chronic limb-threatening ischemia
Fabiani, Mario Alejandro , Berg, Jos C van den, Torre, Oscar A De la, Verastegui, Alfredo , Dua, Anahita, Alexandrescu, Vlad Adrian, Baadh, Amanjit S. , Bahaa, Nasr, Carvajal, Juan Guillermo Barrera, Beasley, Robert , Bisdas, Theodosios, Blessing, Erwin , Bonvini, Stefano, Brodmann, Marianne, Cabral, Gonçalo, Cancellieri, Roberto, Casini, Andrea , Chandra, Venita , Chisci, Emiliano, Chohan, Omar, Choke, Edward, Chong, Patrick, Clerici, Giacomo , Coscas, Raphaël, Costantino, Del Giudice, D'Oria, Mario, Davies, Robert, Donato, Gianmarco de , Vries, Jean-Paul de , Río-Solá, M.L. del, Deloose, Koen , Dhand, Sabeen , Díaz-Sandoval, Larry J, Falcone, Gianmarco , Fanelli, Fabrizio , Cardona, Lucas Ferrer, Garg, Karan, Giuffrida, Stefania, Gouëffic, Yann, Goverde, Peter , Henao, Esteban, Vegas, Diego Jorge Herrera, Hinchliffe, Robert, Hoballah, Jamal J. , Howard, Dominic, Huasen, Bella , Iida, Osamu, Katsanos, Konstantinos, Kolh, Philippe, Korosoglou, Grigorios, Lecis, Alexandre, Leopoldo, Marine, Lessne, Mark L. , Lichtenberg, Michael, Lobato, Marta , Loreni, Giorgio, Madassery, Kumar, Manzi, Marco, Maene, Lieven, Maresch, Martin, Trabal, Jorge Martinez, Mathews, S Jay, Michael, Siah, J, Bosiers Michel, Migliara, Bruno , Mills, Joseph, Miserlis, Dimitrios , Montero-Baker, Miguel, Alvarez, Luis Morelli, Morgan, Robert Anthony, Mouawad, Nicolas, Moxey, Paul, Antonio, Jose, Nakama, Tatsuya , Neville, Richard, Noronen, Katariina , Palena, Mariano, Parikh, Sahil, Parlani, Gianbattista, Pasqui, Edoardo , Patel, Rafiuddin, Patel, Ashish, Perkov, Dražen , Portou, Mark James, Langhoff, Ralf , Reijnen, Michel Marinus Petrus Johannes, Roy, Trisha , Ruffino, Maria Antonella , Gúzman, Tania Sáez, Sakr, Ahmed, Santini-Domínguez, Rafael , Schmidt, Andrej, Schneider, Peter, Sheorain, Virendersingh K, Siracuse, Jeffrey, Sirvent, Marc , Sommerset, Jill , Spiliopoulos, Stavros, Spinelli, Alessio , Stavroulakis, Konstantinos, Taneva, Gergana T, Teso, Desarom , Thomas, Shannon, Torsello, Giovanni, Tummala, Venkat, Tummala, Srinivas, Twine, Christopher, Uberoi, Raman, Heuvel, Daniel Van den, Varcoe, Ramon Lee, Serrano, José Francisco Vargas, Céniga, Melina Vega de, Venermo, Maarit, Vijaynagar, Badri, Stempel, Conrad von , Voûte, Michiel Thomas, Watts, Mine, Zaefferer, Patricio, Zayed, Hany , Zeebregts, Clark J, Zola, N'Dandu, Mills, Joseph L. , Torre, O. , Verastegui, Alfredo , de la Torre, Oscar , Fabiani, Mario Alejandro , Berg, Jos C. van den , Dua, Anahita , Nasr, Bahaa , Biasi, Lukla , Bisdas, Theodosios , Brodmann, Marianne , Cabral, Gonçalo , Caradu, Caroline , Casini, Andrea , Chisci, Emiliano , Choke, E, Chong, Patrick L.E., Cioppa, Angelo , Coscas, Raphaël , Giudice, Costantino Del , D'Oria, Mario , Peruyera, Pablo Del Canto , Διαμαντόπουλος, Αθανάσιος , Díaz‐Sandoval, Larry J. , Dick, Florian , Fazzini, Stefano , Ferrer, Lucas M. , Fujihara, Masahiko , Garg, Karan , Garriboli, Luca , Genovese, Elizabeth A. , Gifford, Edward D. , Gouëffic, Yann , Gupta, Prem Chand , Vegas, Diego Herrera , Hinchliffe, Robert J. , Holden, Andrew Hugh , Isernia, Giacomo , Kolh, Philippe H. , Korosoglou, Grigorios , Krokidis, Miltiadis E. , Lichtenberg, Michael, Loureiro, Luís , Mathews, S. Jay , Bosiers, Michel Joseph , Morosetti, Daniele , Mouawad, Nicolas J. , Moxey, Paul, Neville, Richard, Palena, Luis Mariano , Parikh, Sahil, Parlani, Gianbattista, Patel, Rafiuddin, Patrone, Lorenzo , Portou, Mark J. , Pratesi, Giovanni , Rammos, Christos , Reijnen, Michel M.P.J. , Sakr, Ahmed , Schneider, Peter A. , Secemsky, Eric A. , Sheorain, Virendersingh K, Simonte, Gioele , Spiliοpoulos, Stavros , Stavroulakis, Konstantinos , Steiner, Sabine , Taneva, Gergana T. , Torsello, Giovanni , Troisi, Nicola , Twine, Christopher P. , Uberoi, Raman , Ucci, Alessandro , Heuvel, Daniel van den, Varcoe, Ramon Lee , Venermo, Maarit A. , Voûte, Michiel T., Ysa, August , Zeebregts, Clark J. , Zeller, Thomas , N'Dandu, Zola M.

British Journal of Surgery | April 3, 2026 | Volume: 113 | Issue: 4 | Pages: No page available

10.1093/bjs/znag040 | PMID 41941595 Get It

Abstract Introduction Revascularization to prevent limb loss is not feasible or represents a very high risk in a significant proportion of patients with chronic limb-threatening ischaemia (CLTI). No standard definition currently exists to define this population of patients. The aim of this study was to develop a consensus-based, multidomain definition to improve clinical assessment and reporting of studies in people with ‘no option’ (NO) or ‘poor option’ (PO) CLTI. Methods A modified Delphi process was conducted with 164 specialists from 30 countries. Two iterative survey rounds were used to reach consensus, defined as ≥70% agreement with a score of ≥7 on a nine-point scale. Results Some 164 international vascular specialists participated in the study, averaging 19 years of experience. A multidomain framework including arterial disease anatomy, biology, risk, function, and context (ABRFC) achieved 83% consensus. A ‘desert foot’ was defined as the absence of distal arterial revascularization targets on advanced non-invasive imaging, invasive digital subtraction angiography, and at least one failed endovascular revascularization attempt (81.6% agreement). Inadequate autogenous bypass conduit was defined as the lack of usable autologous vein across all four limbs (85% agreement). Patients were classified as NO for revascularization if they present with ‘desert foot’, prohibitive medical risk, a non-functional limb, or in those patients who refused arterial revascularization. PO revascularization patients combined factors such as severe infection, lack of autologous vein, or treatment non-compliance (72.1% agreement). Conclusion This consensus study established a structured, expert-validated definition of no option or poor option for revascularisation of patients with CLTI. The multidomain ABRFC framework provides a foundation for standardized clinical assessment, trial design, and future guideline development.
Abstract 2740: Applications of large language models to CAR-T cell therapy clinical data using Google cloud computing.
Jankowski, Matthew, Corraes, Andre de Menezes Silva, Gupta, Malvika , Shaw, Monica, Iqbal, Madiha , Chhabra, Saurabh, McLean, Jody, Riester, Kim R., Joseph, Kayla, Tan, Melinda, Ross, Holly, Barnett, Cleyonia, Carter, Sylvia L., Girmay, Semy, Wolan, Rachel M., Ramsey, Milana, Downhour, Christian, Morgan, Kristy, Sibley, Shae, Rushing, Erica C., Holmes, Lucy , Burgstahler, Allison R., Ansell, Stephen M., Hathcock, Matthew, Bruno, Ramona L., Johnston, Patrick B., Paludo, J., Lin, Yi, Guzman, Emmanuel Contreras , Jankowski, Matthew, Corraes, Andre De Menezes Silva , Hilal, Talal , Chhabra, Saurabh , Parrondo, Ricardo D , Riester, Kimberly, Tan, Melinda, Holmes, Lucy, Ansell, Stephen M. , Alkhateeb, Hassan B. , Hathcock, Matthew , Rosenthal, Allison , Murthy, Hemant S. , Johnston, Patrick B, Paludo, Jonas

Cancer Research | April 3, 2026 | Volume: 86 | Issue: 7_Supplement | Pages: 2740-2740

10.1158/1538-7445.am2026-2740 Get It

Abstract Large Language Models (LLM) are being widely adopted into the medical field for their impressive ability to analyze and summarize large amounts of text data. These models enable clinicians and researchers to extract meaningful insights from complex datasets and may assist with decision making. Here we present our workflows and application of LLM for the interpretation and summarization of clinical data related to CAR-T cell therapy. Using an LLM (Gemini 2.5 pro) in the Google Cloud Computing (GCP) environment, two applications were developed to analyze CAR-T cell therapy clinical data: 1) extracting and summarizing CRS and ICANS event-related data to streamline the compliance team workflow, and 2) identifying features available at time of CAR-T infusion able to classify patients into high- or low-monitoring needs 14 days post CAR-T. Patient data (vitals, labs, hematology notes, and EKGs) were extracted from the electronic medical record (EMR) using Google BigQuery into SQL tables in GCP. For each application, relevant data fields were retrieved, formatted into JSON objects, and embedded in the LLM prompt for context-aware processing. Both applications have undergone iterative prompt engineering after analyzing the LLM output against ground truth data in the EMR. For the application extracting and summarizing CRS and ICANS events, the LLM was optimized on Mayo Clinic Rochester data. When compared to the IEC compliance database, the LLM achieved 100% accuracy and F1 score for CRS events, and 96% accuracy and 82% F1 score for ICANS events. The match rate for CRS and ICANS grades were 83% and 89% respectively. We applied the same LLM to Mayo Clinic Arizona (MCA) and Mayo Clinic Florida (MCF) cases, who document clinical notes and toxicity flowsheet differently, and achieved an accuracy (MCA: 93%, MCF:93%) and F1 score (MCA: 96%, MCF: 96%) for CRS and accuracy (MCA: 81%, MCF:82%) and F1 score (MCA: 76%, MCF: 75%) for ICANS. LLM was able to capture events missed by manual reviews. For most of the discrepancies where compliance team final adjudication is needed, LLM will be updated to flag discrepancies for review by the compliance team. For the application related to the monitoring needs 14 days post CAR-T, the LLM identified 5 categories predictive of high or low monitoring needs post CAR-T infusion (disease status, inflammatory and tumor burden markers, hematologic status, renal function and performance status). Our model achieved a sensitivity of 85.7%, specificity of 23.8%, and F1 score of 65.5% for our first cohort, compared with data extracted by the LLM from the EMR. For our second cohort, with demographics statistically similar to cohort 1 and using the same 5 categories, the LLM achieved a sensitivity of 83.3%, a specificity of 28.6%, and F1 score of 65.4%. Our workflow and applications of LLM’s provide examples and guidance to others interested in applying LLM’s for clinical and research applications. Citation Format: Emmanuel Contreras Guzman, Matthew Jankowski, Andre De Menezes Silva Corraes, Malvika Gupta, Monica L. Shaw, Madiha Iqbal, Talal Hilal, Saurabh Chhabra, Ricardo Daniel Parrondo, Jody K. Mclean, Kim R. Riester, Kayla Joseph, Melinda Tan, Holly Ross, Cleyonia Barnett, Sylvia Carter, Semy Girmay, Rachel Wolan, Milana Ramsey, Christian Downhour, Kristy Morgan, Shae Sibley, Erica Rushing, Lucy Holmes, Allison Burgstahler, Stephen M. Ansell, Hassan Alkhateeb, Matthew Hathcock, Ramona Bruno, Allison C. Rosenthal, Hemant Murthy, Patrick B. Johnston, Jonas Paludo, Yi Lin. Applications of large language models to CAR-T cell therapy clinical data using Google cloud computing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 2740.
Abstract 3278: Metabolic pathway signatures defining response to CD19 CAR T-Cell therapy in aggressive B-cell non-hodgkin lymphoma
Tan, Melinda S.Y., Wang, Panwen , Corraes, Andre de Menezes Silva, Wu, Chen , Shao, Zuoyi, Regan, Kevin M., Audrey, Ma, Khurana, Arushi , Benanni, Nora N, Wang, Y., Hampel, P., Paludo, J., Kenderian, Saad J., Johnston, Patrick B., Villasboas, Jose Caetano, Ansell, Stephen M., Li, Ying , dong, Haidong, Zeng, Hu, Lin, Yi, Mondello, Patrizia , Turner, Jacqueline A. , Corraes, Andre De Menezes Silva , Ma, Audrey, Wang, Yucai , Hampel, Paul J. , Paludo, Jonas , Durani, Urshila , Johnston, Patrick B, Ansell, Stephen M. , Dong, Haidong , Zeng, Hu

Cancer Research | April 3, 2026 | Volume: 86 | Issue: 7_Supplement | Pages: 3278-3278

10.1158/1538-7445.am2026-3278 Get It

Abstract Chimeric antigen receptor (CAR) T-cell therapy achieves high response rates in relapsed/refractory aggressive B-cell non-Hodgkin lymphoma, yet only 40% of patients achieve durable remission. Identifying biological programs linked to long-term response remains critical. As metabolic fitness underlies T-cell persistence and effector function, we profiled metabolic pathways associated with clinical outcomes following commercial CD19 CAR T-cell therapy. Single-cell RNA sequencing of peripheral blood mononuclear cells collected at baseline (BL), peak CAR-T expansion (PK), and one-month post-infusion (M1) was analyzed using CellRanger v7.0.1, immunopipe. Seurat v4.3.0 was applied for unsupervised clustering to delineate cell subsets based on top differentially expressed genes. Patients were categorized as durable complete remission (CR ≥6 months; n = 16), primary refractory (PD1; n = 4), or relapse after initial response (PD2; n = 12). Gene-set enrichment analysis defined metabolic pathway activity across T-cell, monocyte, dendritic cell (DC), and natural killer (NK) subsets. Oxidative phosphorylation (OXPHOS) emerged as the dominant metabolic program distinguishing clinical outcomes. At BL and PK, OXPHOS was consistently enriched in PD1 relative to CR across T-cell, monocyte, and DC subsets, suggesting early oxidative activation in non-responders. By M1, this pattern inverted, with higher OXPHOS activity in CR. PD2 largely paralleled PD1, but several subsets including CD8 T central memory, classical monocytes TGFβ, intermediate monocytes CD38, monocytic myeloid-derived suppressor cell (mMDSC) HIF1A, and mMDSC SIRPA, showed OXPHOS enrichment in CR at BL and/or PK that persisted through M1. In contrast, DC and NK subsets exhibited the opposite pattern: OXPHOS was enriched in CR at PK (conventional DC 2 (cDC2), plasmacytoid DC (pDC), NK, proliferating NK), but shifted toward enrichment in PD2 at M1 (cDC2, NK, NK CD56bright). Glycolysis (GLY) followed a similar trajectory in monocytes and NK cells, with enrichment in PD1/PD2 at BL and PK, followed by enrichment in CR at M1. In T-cells, PD1 maintained GLY enrichment from BL through PK, with no significant differences observed at M1. The inositol-phosphate metabolism pathway showed a more static pattern and was consistently enriched in multiple PD2 effector and memory T-cell subsets without reversal at M1. Taken together, these data reveal distinct, lineage-specific metabolic signatures that differentiate durable remission from early and late progression. Dynamic OXPHOS and GLY programming, characterized by lower activity early and enhanced activity at M1 in CR, may reflect adaptive metabolic programming that supports sustained antitumor immunity. Immune-metabolic profiling may therefore serve as a biomarker of response and highlight actionable metabolic pathways to enhance CAR T-cell durability. Citation Format: Melinda S.Y. Tan, Panwen Wang, Patrizia Mondello, Jacqueline Turner, Andre de Menezes Silva Corraes, Chen Wu, Zuoyi Shao, Kevin Regan, Ma Audrey, Arushi Khurana, Nora N. Benanni, Yucai Wang, Paul Hampel, Jonas Paludo, Saad J. Kenderian, Urshila Durani, Patrick B. Johnston, Jose Caetano Villasboas, Stephen M. Ansell, Ying Li, Haidong Dong, Hu Zeng, Yi Lin. Metabolic pathway signatures defining response to CD19 CAR T-Cell therapy in aggressive B-cell non-hodgkin lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 3278.
Abstract 7656: Comprehensive investigation of stool metaproteomes among patients with precancerous lesions and colorectal cancer.
Northrop-Albrecht, Emmalee J., Gupta, Vinod K., Taylor, Walt, Mahoney, Doug, Burger, Kelli N. , Northrop‐Albrecht, Emmalee J. , Gupta, Vinod K. , Sinnwell, Jason P. , Foote, Patrick H. , Sung, Jaeyun , Kisiel, John B.

Cancer Research | April 3, 2026 | Volume: 86 | Issue: 7_Supplement | Pages: 7656-7656

10.1158/1538-7445.am2026-7656 Get It

Abstract INTRODUCTION: Colorectal cancer (CRC) is the 2nd most fatal cancer in the U.S.; most benefits of CRC screening are from detection of advanced pre-cancerous lesions (APLs). With a goal to improve non-invasive stool test APL sensitivity, we sought novel APL signatures in stool metaproteomes (host- and gut microbiome-derived proteins) among cancer-free controls (CTRL), APL, and CRC patients. Since dysbiosis in gut microbiota is associated with CRC initiation, we also examined the microbial source of differentially expressed proteins (DEPs). METHODS: Mass spectrometry was performed on archival stool supernatants (n=63 patients; 15 CTRL, 32 APL [16 adenomas & 16 sessile serrated lesions], 16 CRC). A sectioning and database-enrichment strategy was applied for peptide-spectrum matching. Microbial and human-derived proteins were searched against the Integrated Gene Catalogue (IGC) and UniProt human reference proteome. DEPs were identified using thresholds of P < 0.05 and fold-change ≥ 1.5. Pathway annotation of human DEPs was performed with the REVIGO webserver, while gut microbial DEPs were functionally categorized using the KEGG Automatic Annotation Server (KAAS). To assess the taxonomic distribution of microbial DEPs, sequences were aligned against the NCBI non-redundant database using BLASTP. RESULTS: Mass spectrometry detected 879 human and 32,514 microbiome-derived proteins. When limiting detection to proteins present in ≥ 75% of patients, only 117 human and 204 microbial proteins remained. There were 17 (4,875), 288 (9,638), and 63 (3,053) unique human (microbial) proteins detected in CTRL, APL, and CRC groups, respectively. When the protein presence cutoff was set at >30% of patients, there were 52 (13 human [11 upregulated, 2 downregulated], 39 microbial [28 upregulated, 11 downregulated]) DEPs detected for the CRC + APL vs CTRL comparison. Some pathways associated with upregulated human DEPs included: inflammatory response, cellular response to iron, and endothelial cell migration. The top upregulated microbial DEPs were derived from the Phocaeicola, Lachnospiraceae, and Oscillospiraceae genera. The top downregulated microbial DEPs belonged to the Bacteroides, Eubacterium, Agathobacter, Coprococcus, and Blautia genera. CONCLUSION: This work highlights the biological diversity and molecular heterogeneity of the stool proteome. We identified several host and microbial protein markers that differentiate APLs and early CRC from controls. These results provide a foundation for future validation studies, which are necessary to determine the clinical utility of these protein biomarkers prior to their integration into a noninvasive stool test. Citation Format: Emmalee J. Northrop-Albrecht, Vinod K. Gupta, William R. Taylor, Jason P. Sinnwell, Doug W. Mahoney, Patrick H. Foote, Kelli N. Burger, Jaeyun Sung, John B. Kisiel, . Comprehensive investigation of stool metaproteomes among patients with precancerous lesions and colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 7656.
Abstract 1213: Mitochondrial transcriptome profiles associated with clinical responses to CAR-T therapy in aggressive lymphoma.
Wang, Panwen , Tan, Melinda, Schaefers, Christoph, Wu, Chen , Corraes, Andre de Menezes Silva, Regan, Kevin M., Shao, Zuoyi, Audrey, Ma, Khurana, Arushi , Benanni, Nora N, Wang, Y., Hampel, P., Kenderian, Saad J., Paludo, J., Johnston, Patrick B., Villasboas, Jose Caetano, Ansell, Stephen M., dong, Haidong, Li, Ying, Hu, Zeng , Lin, Yi, Turner, Jacqueline A. , Mondello, Patrizia , Tan, Melinda, Schaefers, Christoph , Corraes, Andre De Menezes Silva , Ma, Audrey, Wang, Yucai , Hampel, Paul J. , Paludo, Jonas , Durani, Urshila , Johnston, Patrick B, Ansell, Stephen M. , Dong, Haidong

Cancer Research | April 3, 2026 | Volume: 86 | Issue: 7_Supplement | Pages: 1213-1213

10.1158/1538-7445.am2026-1213 Get It

Abstract Introduction: Therapeutic outcomes in B-cell non-Hodgkin’s lymphoma (B-NHL) have substantially improved with the introduction of chimeric antigen receptor T-cell (CAR-T) therapy. Yet, persistent immune dysfunction and underlying metabolic dysregulation remain major obstacles to achieving durable clinical responses in B-NHL. We hypothesize that mitochondrial pathways play a critical role in mediating anti-tumor immunity during CAR-T therapy. Methods: Peripheral blood mononuclear cells were collected from healthy controls (CNTRL, n=5) and patients with advanced stage lymphoma (LYM) who received FDA approved CAR-T (n=32). Samples were collected before lymphodepletion (BL), at peak CAR-T expansion (PK) and one-month post-infusion (M1). Single-cell RNA sequencing was used to interrogate differential mitochondrial gene expression. Samples were obtained from LYM patients with complete remission for >6 months (CR), primary refractory (PD1), or relapsed (PD2) disease. Results: Compared to CNTRLs, LYM patients exhibited reduced expression of cytochrome c oxidase. At BL, CR patients demonstrated broader mitochondrial differential gene expression across all T-cell subsets relative to PD1 and PD2 and showed higher expression of MT-ATP-6, MT-ATP-8, and MT-CO3. Following CAR-T infusion, global mitochondrial gene expression increased across patients corresponding with expansion of CD8 effector T cells (Tem tumor circulating) and activated peripheral memory T cells (Tpm). Certain mitochondrial genes, such as MT-CO1, were durably expressed across LYM patients at BL, PK, and M1 in peripheral and central memory T cells (Tpm, Tcm). At PK, cytochrome c oxidase and ATP synthase genes were upregulated in CR Tpm and Tcm. At M1, MT-ATP-6, MT-ATP-8, MT-CO3 were significantly upregulated in CD8 memory precursor effector T-cells (MPECs) of CR patients compared to both PD1 and PD2. While CR and PD2 patients appeared clinically responsive at M1, CR samples maintained significantly higher MT-ATP-8 expression across T cell subsets (CD8 MPECS, Tpm, Tcm) compared to PD2 (p values 0.008; <0.0001; <0.0001). Conclusions: We report a temporal shift in immunometabolism with CAR-T therapy in LYM. Clinical responders exhibited sustained mitochondrial activity characterized by persistent expression of ATP synthase in CD8 MPECs and cytochrome c oxidase in Tpm and Tcm. In sum, mitochondrial programming may distinguish effective versus dysfunctional T cells and identify targets for therapeutic development. Citation Format: Jacqueline Turner, Panwen Wang, Patrizia Mondello, Melinda Tan, Christoph Schaefers, Chen Wu, Andre de Menezes Silva Corraes, Kevin Regan, Zuoyi Shao, Ma Audrey, Arushi Khurana, Nora N. Benanni, Yucai Wang, Paul Hampel, Saad J. Kenderian, Jonas Paludo, Urshila Durani, Patrick B. Johnston, Jose Caetano Villasboas, Stephen M. Ansell, Haidong Dong, Ying Li, Zeng Hu, Yi Lin. Mitochondrial transcriptome profiles associated with clinical responses to CAR-T therapy in aggressive lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 1213.
Abstract 643: The Sean Karl Cohort: An international single-cell RNAseq study of paired patient Ewing sarcoma specimens.
Pannucci, Abbe , Mukherjee, Elina , Daley, Jessica, Ganapathi, Shireen Sita, Surrey, Lea F. , Gutstein, Lauren, Azar, Patrick, Neyaz, Azfar, John, Ivy, Tanaka, Yutaro , Butaney, Byron, Janeway, Katherine A. , Taroni, Jaclyln, Davis, Jade, Laetsch, Theodore W. , Mody, Rajen , Henon, Clémence , Grünewald, Thomas G., Lawlor, Elizabeth R. , Cruz, Filemon S. Dela, Grohar, Patrick J. , Pavisic, Jovana , Hawkins, Ally, Ganapathi, Shireen S. , Boguslawski, Elissa A. , Azar, Patrick, Stockfisch, Emily , Neyaz, Azfar , John, Ivy , Picarsic, Jennifer , Gillani, Riaz , Crompton, Brian D. , Reed, Damon R. , Shlien, Adam , Grünewald, Thomas G. P. , Cruz, Filemon S. Dela , Cillo, Anthony Richard , Bailey, Kelly M.

Cancer Research | April 3, 2026 | Volume: 86 | Issue: 7_Supplement | Pages: 643-643

10.1158/1538-7445.am2026-643 Get It

Abstract Introduction: Ewing sarcoma (EwS) is a FET::ETS family member-driven primary bone cancer demonstrating vast heterogeneity. Between a patient’s primary diagnosis and disease progression, tumor cell state adaptation, microenvironment changes, and the landscape of evolving therapeutic vulnerabilities remain poorly understood. To address these gaps, the Sean Karl Cohort was established in 2025 to conduct the largest single-cell transcriptomic analysis of retrospective paired tumor samples from patients with EwS. Here, we present data from the five analytic teams, and through shared SOPs now expand this cohort to Europe. Methods: Common sample processing SOPs were established to isolate cells from FFPE material from paired patient EwS samples. Single-cell (sc) RNAseq was generated using the GEM-X Flex Gene Expression protocol (10x Genomics). Alex’s Lemonade Stand Foundation (ALSF) Data Lab established a common data processing and integration pipeline with an EwS-specific cell annotation workflow to create a harmonized dataset for downstream analyses. Analytic teams were created to define tumor cell subpopulations and their therapeutic vulnerabilities and to characterize the tumor microenvironment. Data: We demonstrate the feasibility of generating high-quality scRNAseq profiles from retrospective FFPE-preserved EwS tumors. To date, 116 samples have yielded ∼800,000 cells. Integrated analysis reveals reproducible EwS tumor cell states shared across patients with regulatory network analyses nominating candidate therapeutic vulnerabilities. The scale of this international cohort enables saturation analysis for rare cell populations. Paired and longitudinal samples further allow correlation of emergent cell states with therapy resistance and metastatic progression. For example, immune-focused analyses show increases in T cell and macrophage populations in post-therapy samples. A novel, standardized EwS-specific cell annotation workflow has been developed to harmonize analyses and findings. These data will be openly shared with the community through the ALSF Single-cell Pediatric Cancer Atlas Portal. Conclusion: Large-scale international collaborative sample sharing, standardized processing pipelines, and harmonized EwS-specific annotations now enable deep single-cell analyses to characterize tumor heterogeneity in this rare pediatric and adolescent cancer. An in vivo expansion of the Sean Karl Cohort is underway to assess conservation of EwS tumor cell states and regulatory vulnerabilities identified in human tumors pre- and post-therapy in preclinical models, further supporting translation of these findings toward therapeutic strategies. Citation Format: Abbe Pannucci, Elina Mukherjee, Jessica D. Daley, Shireen Sita Ganapathi, Elissa Boguslawski, Lea Surrey, Lauren Gutstein, Patrick Azar, Emily Stockfisch, Azfar Neyaz, Ivy John, Jennifer Picarsic, Yutaro Tanaka, Byron Butaney, Riaz Gillani, Brian D. Crompton, Katherine A. Janeway, Jaclyln Taroni, Jessica Davis, Damon Reed, Adam Shlien, Theodore W. Laetsch, Rajen Mody, Clémence Henon, Thomas G. Grünewald, Elizabeth R. Lawlor, Filemon Dela Cruz, Patrick J. Grohar, Jovana Pavisic, Ally Hawkins, Anthony R. Cillo, Kelly M. Bailey. The Sean Karl Cohort: An international single-cell RNAseq study of paired patient Ewing sarcoma specimens [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 643.
Show Me the “Mino:” In Vitro Efficacy of Minocycline on Clinical Gram-Negative Bacterial Isolates
Streck, Nicholas , Saleh, O. Abu, Crowley, Patrick D , Mira, Portia , Challener, Douglas W. , Abu Saleh, Omar , Crowley, Patrick D., Ranganath, Nischal , Rivera, Christina G. , AbuSaleh, Omar

Microbial Drug Resistance | March 31, 2026 | Volume: 32 | Issue: 4 | Pages: 128-134

10.1177/10766294261424485 | PMID 41677880 Get It

Background: There are limited oral treatment options available for resistant Gram-negative bacterial (GNB) infections. Minocycline, a second-generation tetracycline antibiotic, offers good bioavailability and broad-spectrum coverage that may be an option for GNB infections. Methods: We conducted a retrospective review of minocycline susceptibility testing performed on GNB isolates at the Mayo Clinic reference lab between 2013 and 2022. Minocycline susceptibility was evaluated with a focus on difficult-to-treat organisms and relevant anatomic source. Organisms included resistant isolates of Escherichia coli and Klebsiella pneumoniae ; high-risk ampC-derepressors, including Citrobacter freundii, Enterobacter cloacae, and K. aerogenes; and clinically challenging non-Enterobacterales, Acinetobacter species, Achromobacter species, and Stenotrophomonas maltophilia . Results: Of 217,206 GNB isolates, 18,148 Enterobacterales (EB) and 8,190 non- Enterobacter isolates were tested for minocycline susceptibility. Of these, 80% of all EB and 92% of non-EB isolates were susceptible. Among E. coli isolates with ceftriaxone, ciprofloxacin, meropenem, or multidrug resistance, minocycline susceptibility was 78%, 76%, 70%, and 70.9%, respectively. Among the K. pneumoniae isolates with ceftriaxone, ciprofloxacin, meropenem, or multidrug resistance, minocycline susceptibility was 46%, 38%, 37%, and 39.3%, respectively. 85% of C. freundii , 81% of E. cloacae, and 85% of K. aerogenes isolates were susceptible to Minocycline. 83.5% of Achromobacter species isolates, 66% of Acinetobacter species isolates, and 99.1% of S. maltophilia isolates were susceptible. Conclusions: Our study reports the largest collection of minocycline susceptibility findings in GNB. Minocycline showed in vitro activity against many difficult-to-treat GNB isolates, including ceftriaxone- and multidrug-resistant E. coli and some K. pneumoniae isolates, common Amp-C-producing species, and non-fermenting GNB, including Stenotrophomonas , Acinetobacter , and Achromobacter .
Inflammatory Myofibroblastic Tumor of the Lung: A Rare Find in an Elderly Female
VALLABHANENI, MAITHRI, Boyapati, Renu Bhargavi , Balliahgari, Sai Samhitha Avula, Ezeani, Chukwunonso , Dahiya, Ashish , LeBlanc, N.L. , Stagg, Marshall Patrick, LeBlanc, Nicholas, Stagg, M. Patrick

Journal of Investigative Medicine High Impact Case Reports | March 31, 2026 | Volume: 14 | Issue: No issue available | Pages: No page available

10.1177/23247096261435539 | PMID 41914218 Get It

Inflammatory myofibroblastic tumors (IMTs), originating from mesenchymal cells, are rare neoplasms with intermediate biological potential. Despite being predominantly benign, they can progress to locally aggressive disease and may recur over time. IMTs are predominantly seen in the pediatric population, making our case of IMT in an older adult even rarer. A 67-year-old female with a 42-pack-year smoking history presented with cough, fever, and progressively worsening exertional dyspnea. Imaging studies, including chest X-ray followed by chest computed tomography, identified a right lower lobe lung nodule without evidence of metastasis. Subsequent evaluation with robotic bronchoscopy and endobronchial ultrasound revealed densely cellular reactive lung tissue on lymph node biopsy. Ultimately, the patient underwent a robotic-assisted right lower lobectomy. Final pathology confirmed the diagnosis of an IMT. IMTs are characterized by the presence of spindle cells associated with dense monomorphic inflammatory cells. It has been found that IMT arises from chromosomal rearrangements that aberrantly activate various kinase signaling pathways. This understanding of the molecular mechanisms underlying IMT development has elucidated the neoplastic nature of the disease and has also been pivotal in distinguishing IMT from other inflammatory pseudotumors. Surgical resection remains the cornerstone of treatment, with targeted therapies offering promising results for unresectable or advanced cases. IMTs pose a multifaceted challenge in clinical practice due to their diverse clinical manifestations, histopathological variability, and unclear etiopathogenesis, underscoring the need for continued research and a multidisciplinary approach to optimize patient outcomes.
BASECAMP-1 screening study: a model for efficient enrolment in precision oncology clinical trials
Hecht, J Randolph , Molina, Julian R , Liechty, Kirstin B., Welling, Theodore H., Grierson, Patrick , Patel, Sandip Pravin , Kirtane, Kedar , Morelli, M Pia, Locke, Frederick L, Maloney, David G. , Nikiforow, Sarah, Lin, Yi, Ulrickson, Matthew, Specht, J. M., Lozac’hmeur, Ariane, Garde, Ryan J., Rangel, Gena A, Ng, Eric W, Welch, John S. , Tebbets, Jessica , Go, William Y., Specht, Jennifer M. , Tebbets, Jessica C , Specht, Jennifer , Molina, Julian R. , Morelli, Maria Pia , Locke, Frederick L. , Punekar, Salman R. , Nikiforow, Sarah , Ulrickson, Matthew L. , Osterman, Chelsea Kendall , Ng, Eric W., Simeone, Diane M.

BMJ Oncology | March 27, 2026 | Volume: 5 | Issue: 1 | Pages: e001033

10.1136/bmjonc-2025-001033 | PMID 41918932 Get It

Objective Identifying eligible patients for precision oncology clinical trials is challenging, particularly for rare molecular subpopulations. To address this challenge, A2 Biotherapeutics developed BASECAMP-1 ( NCT04981119 ), a non-interventional master screening study to identify patients eligible for interventional studies of logic-gated Tmod chimeric antigen receptor T-cell therapies. Eligible patients for these interventional trials have an advanced solid malignancy and are germline human leucocyte antigen (HLA)-A*02 heterozygous, with tumour-associated HLA-A loss of heterozygosity (LOH). HLA-A LOH occurs in ~16% of advanced solid malignancies; therefore, an efficient screening strategy is required. This report describes BASECAMP-1; compares the efficiency of two screening methods; and discusses the broader advantages of BASECAMP-1 beyond efficient enrolment. Methods and analysis Patients are identified for BASECAMP-1 using two approaches. In the traditional approach, common for clinical trials, investigators consent and screen all patients who might be good candidates for cell therapy trials, with no prior knowledge of patient HLA-A type or LOH status. To further optimise our approach, we co-developed with Tempus AI (Tempus) the bioinformatic programme Aware, which identifies potentially eligible patients with tumour-associated HLA-A*02 LOH within a clinico-genomic database that includes linked genomic and transcriptomic sequencing and clinical data collected during routine care. Results Over 42 months of using a traditional approach to identify eligible patients, 1918 patients at 13 study sites were consented and screened for BASECAMP-1; of these, 30 patients with tumour-associated HLA-A*02 LOH were enrolled (~0.7 participants per month). Over the last 30 months of that same period, Tempus Aware screening was implemented and 55 patients with tumour-associated HLA-A*02 LOH were enrolled (~1.8 participants per month). The bioinformatic approach identified more patients than the traditional approach and used sequencing results produced as part of the standard clinical tumour sequencing workflow, reducing resource use and study staff burden. Additional advantages of using a screening study, such as BASECAMP-1, include manufacturing efficiencies and collection of a large dataset of molecular and clinical parameters that can be used to supplement trial analyses. Conclusions The BASECAMP-1 study demonstrates a clinico-genomic screening approach can more efficiently identify patients for precision oncology trials. Furthermore, precision oncology can be enhanced through collaborative data-sharing. Trial registration number NCT04981119 .
Clinical Criteria for the Definition of Refractory Septic Shock: A Joint Delphi Consensus from the Society of Critical Care Medicine (SCCM) and European Society of Intensive Care Medicine (ESICM)
Myatra, Sheila Nainan , Dugar, Siddharth , Russell, Lene , Delamarre, Louis , Sharif, Sameer , Chew, Michelle S. , Gong, Michelle N. , Hernández, Glenn , Martín‐Loeches, Ignacio , Dünser, Martin W., Einav, Sharon , Hamzaoui, Olfa, Frazee, Erin N. , Busse, Laurence W. , Deutschman, Clifford S. , Holder, Andre L. , Nazer, Lama , Nunnally, Mark , Rincon, Teresa , Seymour, Christopher W. , Besen, Bruno Adler Maccagnan Pinheiro , Finfer, Simon , Machado, Flávia Ribeiro , Mer, Mervyn , Young, Paul J. , Khanna, Ashish , Dugar, Siddharth , Wieruszewski, Patrick M , Russell, Lene , Evans, Laura , Delamarre, Louis , Sharif, Sameer , Chew, Michelle S , Gong, Michelle Ng , Hernández, Glenn , Schorr, Christa , Lakbar, Ines , Smith, Susan E , Martin-Loeches, Ignacio , Annane, Djillali , Balik, Martin , Cecconi, Maurizio , De Backer, Daniel , Donadello, Katia , Einav, Sharon , Ferrer, Ricard , Juffermans, Nicole , Hamzaoui, Olfa , Landoni, Giovanni , Levy, Bruno , McKenzie, Cathrine , Monnet, Xavier , Ostermann, Marlies , Spies, Claudia D , Singer, Mervyn , Theodorakopulou, Maria , Topeli, Arzu , Frazee, Erin N , Bauer, Seth R , Busse, Laurence W , Coopersmith, Craig M , Deutschman, Clifford , Holder, Andre L , Kamaleswaran, Rishikesan , Legrand, Matthieu , Martin, Greg S , Maves, Ryan C , Nazer, Lama , Nunnally, Mark E , Prescott, Hallie C , Rincon, Teresa , Sacha, Gretchen , Seymour, Chris W , Arabi, Yaseen M , Besen, Bruno Amp , Cavalcanti, Alexandre Biasi , Deane, Adam M , Finfer, Simon , Hammond, Naomi , Ibarra-Estrada, Miguel , Kattan, Eduardo , Kotani, Yuki , Machado, Flavia R , Ospina-Tascón, Gustavo A , Mer, Mervyn , Young, Paul J , Rochwerg, Bram , Khanna, Ashish K , Léone, Marc , Wieruszewski, Patrick M. , Smith, Susan , Backer, Daniel De , Dünser, Martin W. , Lévy, Bruno , McKenzie, Cathrine , Ostermann, Marlies , Spies, Claudia , Kamaleswaran, Rishikesan , Legrand, Matthieu , Martin, Greg S. , Maves, Ryan C. , Prescott, Hallie C. , Arabi, Yaseen M. , Deane, Adam M. , Hammond, Naomi

Critical Care Medicine | March 24, 2026 | Volume: 54 | Issue: 5 | Pages: 1073-1091

10.1097/ccm.0000000000007124 | PMID 41873857 Get It

OBJECTIVE: A definition of refractory septic shock is necessary to guide diagnosis, management, prognostication, research, and future guidelines for this most severe form of the disease. We sought to achieve consensus on clinical criteria that would be used to define refractory septic shock. DESIGN: Review of literature, expert panel position statements, and Delphi rounds with an international expert group. SETTING: Consensus was defined as having at least 75% of panellists in agreement or disagreement on the three highest or lowest levels of a 7-point Likert scale or based on responses to single- or multiple-choice questions, respectively. SUBJECTS: A panel of multinational, multiprofessional and multidisciplinary critical care experts assembled by the Society of Critical Care Medicine and the European Society of Intensive Care Medicine (57 invitations and 56 participants). MEASUREMENTS AND MAIN RESULTS: A five-round Delphi process was conducted for consensus and stability. The steering committee proposed 34 statements, and five of them were rejected by panel experts after round 2. Among 29 statements selected from eight domains, consensus was reached for 13. The panel agreed on the need for a comprehensive consensus set of clinical criteria for refractory septic shock. Markers of organ dysfunction (75%, 2 rounds), tissue perfusion (91.1%, 2 rounds) including lactate (94.6%, 2 rounds) and capillary refill time (76.8%, 2 rounds), assessment of fluid-responsiveness after initial resuscitation (92.9%, 5 rounds), and use of vasoactive drugs at norepinephrine equivalents greater than 0.5 µg/kg/min (75.0%, 3 rounds), were selected as clinical criteria of refractory septic shock. The use of critical care ultrasound (CCUS) (92.9%, 3 rounds) was the single diagnostic modality that reached a consensus-based agreement. CONCLUSIONS: A consensus for 13 criteria to frame the definition of refractory septic shock was reached. Refractory septic shock is characterised by persistently elevated lactate concentrations and or prolonged capillary refill time in patients with septic shock who are fluid unresponsive, require a norepinephrine base equivalent dose greater than 0.5 micrograms per kilogram per minute, and undergo CCUS assessment when mixed shock is suspected.