Department Metrics

• Mathematical Model-Guided Adoptive Immunotherapy in Bladder Cancer
  Sponsor: Nat Institutes of Health
  PI (Contact):Rejniak, K.,PI (MPI):Pilon-Thomas, S.
• Characterizing Cytotoxic Therapy Induced Shifts in the Cost-to-Benefit Ratio of High Ploidy
  Sponsor: Nat Institutes of Health
  PI:Andor, N.
• A framework to integrate live-cell imaging with single-cell sequencing and learn how cells adapt to new environments
  Sponsor: Nat Institutes of Health
  PI:Andor, N.
• Engineering Model-Based Systems to Monitor and Steer Subclonal Dynamics
  Sponsor: Nat Institutes of Health
  PI:Andor, N.
• IMAT-ITCR Collaboration: Engineering model-based systems to monitor and steer subclonal dynamics
  Sponsor: Nat Institutes of Health
  PI:Andor, N.
• Development of Adoptive T-Cell Therapy in Bladder Cancer Incorporating Patient-Specific Tumor Microenvironment
  Sponsor: US Army
  PI:Rejniak, K.
• The Polyaneuploid Cancer Cell State Mediates Multitherapy Resistance in Cancer
  Sponsor: US Army
  PI:Brown, J.
• Modeling the Role and Regulation of Reactive Stroma in Breast Ductal Carcinoma Microinvasions
  Sponsor: Nat Institutes of Health
  PI:Rejniak, K.
• The Delta Ecology of NSCLC Treatment
  Sponsor: Nat Institutes of Health
  PI (Contact):Anderson, A.,PI (MPI):Gatenby, R.,Project PI:Marusyk, A.
• Using Patient-Reported Outcome Dynamics to Predict Response to Immunotherapy in Non-Small Cell Lung Cancer
  Sponsor: Moffitt Cancer Center
  PI:Brady, R.
• Evolutionary Therapy in ER+ Breast Cancer Guided by Second-Order Reasoning
  Sponsor: Moffitt Cancer Center
  PI:West, J.
• Effects of anesthetic agents on immune function and breast cancer progression
  Sponsor: Florida Breast Cancer Foundation
  PI:Brown, J.
• AR-agonist pre-treatment enables evolutionary steering in metastatic ER+ breast cancer
  Sponsor: Moffitt Cancer Center
  PI (Contact):West, J.

CLINICAL TRIAL 21559
A Phase 1/2 Study of EPI-7386 in Combination with Enzalutamide Compared with Enzalutamide Alone in Subjects with Metastatic Castration-Resistant Prostate Cancer
Condition: Genitourinary
Intervention: EPI-7386 (); Enzalutamide (Xtandi); Not Applicable ()

CLINICAL TRIAL 22344
A Phase I Clinical Trial of an Infusion of Autologous gamma delta T cells Genetically Engineered with a Chimeric Receptor to Target the Prostate Stem Cell Antigen in Patients with Metastatic Castration Resistant Prostate Cancer
Condition: Genitourinary
Intervention: MSGV1-PSCA-8T28Z (); cyclophosphamide (); cytoxan (cyclophosphamide); fludarabine (Fludarabine phosphate)

• Weitz P, Valkonen M, Solorzano L, Carr C, Kartasalo K, Boissin C, Koivukoski S, Kuusela A, Rasic D, Feng Y, Pouplier SS, Sharma A, Eriksson KL, Robertson S, Marzahl C, Gatenbee CD, Anderson ARA, Wodzinski M, Jurgas A, Marini N, Atzori M, Müller H, Budelmann D, Weiss N, Heldmann S, Lotz J, Wolterink JM, De Santi B, Patil A, Sethi A, Kondo S, Kasai S, Hirasawa K, Farrokh M, Kumar N, Greiner R, Latonen L, Laenkholm AV, Hartman J, Ruusuvuori P, Rantalainen M. The ACROBAT 2022 challenge: Automatic registration of breast cancer tissue. Med Image Anal. 2024 Oct.97:103257. Pubmedid: 38981282.
• Emond R, West J, Grolmusz V, Cosgrove P, Nath A, Anderson ARA, Bild AH. A novel combination therapy for ER+ breast cancer suppresses drug resistance via an evolutionary double-bind. bioRxiv. 2024 Sep. Pubmedid: 39282402. Pmcid: PMC11398327.
• Alahmari S, Schultz A, Albrecht J, Tagal V, Siddiqui Z, Prabhakaran S, El Naqa I, Anderson A, Heiser L, Andor N. Cell identity revealed by precise cell cycle state mapping links data modalities. bioRxiv. 2024 Sep. Pubmedid: 39282313. Pmcid: PMC11398313.
• Aguadé-Gorgorió G, Anderson ARA, Solé R. Modeling tumors as complex ecosystems. iScience. 2024 Sep.27(9):110699. Pubmedid: 39280631. Pmcid: PMC11402243.
• Marzban S, Srivastava S, Kartika S, Bravo R, Safriel R, Zarski A, Anderson ARA, Chung CH, Amelio AL, West J. Spatial interactions modulate tumor growth and immune infiltration. NPJ Syst Biol Appl. 2024 Sep.10(1):106. Pubmedid: 39349537. Pmcid: PMC11442770.
• Reed DR, Tulpule A, Metts J, Trucco M, Robertson-Tessi M, O'Donohue TJ, Iglesias-Cardenas F, Isakoff MS, Mauguen A, Shukla N, Dela Cruz FS, Tap W, Kentsis A, Morris CD, Hameed M, Honeyman JN, Behr GG, Sulis ML, Ortiz MV, Slotkin E. Pediatric Leukemia Roadmaps Are a Guide for Positive Metastatic Bone Sarcoma Trials. J Clin Oncol. 2024 Sep.42(25):2955-2960. Pubmedid: 38843482.
• Carrillo-Perez F, Cramer EM, Pizurica M, Andor N, Gevaert O. Towards Digital Quantification of Ploidy from Pan-Cancer Digital Pathology Slides using Deep Learning. bioRxiv. 2024 Aug. Pubmedid: 39229200. Pmcid: PMC11370345.
• Bhattacharya R, Brown JS, Gatenby RA, Ibrahim-Hashim A. A gene for all seasons: The evolutionary consequences of HIF-1 in carcinogenesis, tumor growth and metastasis. Semin Cancer Biol. 2024 Jul.102-103:17-24. Pubmedid: 38969311.
• Metts JL, Aye JM, Crane JN, Oberoi S, Balis FM, Bhatia S, Bona K, Carleton B, Dasgupta R, Dela Cruz FS, Greenzang KA, Kaufman JL, Linardic CM, Parsons SK, Robertson-Tessi M, Rudzinski ER, Soragni A, Stewart E, Weigel BJ, Wolden SL, Weiss AR, Venkatramani R, Heske CM. Roadmap for the next generation of Children's Oncology Group rhabdomyosarcoma trials. Cancer. 2024 Jun. Pubmedid: 38941509.
• Miti T, Desai B, Miroshnychenko D, Basanta D, Marusyk A. Dissecting the Spatially Restricted Effects of Microenvironment-Mediated Resistance on Targeted Therapy Responses. Cancers (Basel). 2024 Jun.16(13). Pubmedid: 39001467. Pmcid: PMC11240540.
• Park MA, Whelan CJ, Ahmed S, Boeringer T, Brown J, Crowder SL, Gage K, Gregg C, Jeong DK, Jim HSL, Judge AR, Mason TM, Parker N, Pillai S, Qayyum A, Rajasekhara S, Rasool G, Tinsley SM, Schabath MB, Stewart P, West J, McDonald P, Permuth JB. Defining and Addressing Research Priorities in Cancer Cachexia through Transdisciplinary Collaboration. Cancers (Basel). 2024 Jun.16(13). Pubmedid: 39001427. Pmcid: PMC11240731.
• Gallagher K, Strobl MA, Park DS, Spoendlin FC, Gatenby RA, Maini PK, Anderson AR. Mathematical Model-Driven Deep Learning Enables Personalized Adaptive Therapy. Cancer Res. 2024 Jun.84(11):1929-1941. Pubmedid: 38569183. Pmcid: PMC11148552.
• Strobl MAR, Martin AL, West J, Gallaher J, Robertson-Tessi M, Gatenby R, Wenham R, Maini PK, Damaghi M, Anderson ARA. To modulate or to skip: De-escalating PARP inhibitor maintenance therapy in ovarian cancer using adaptive therapy. Cell Syst. 2024 Jun.15(6):510-525.e6. Pubmedid: 38772367. Pmcid: PMC11190943.
• Gatenby RA, Luddy KA, Teer JK, Berglund A, Freischel AR, Carr RM, Lam AE, Pienta KJ, Amend SR, Austin RH, Hammarlund EU, Cleveland JL, Tsai KY, Brown JS. Lung adenocarcinomas without driver genes converge to common adaptive strategies through diverse genetic, epigenetic, and niche construction evolutionary pathways. Med Oncol. 2024 May.41(6):135. Pubmedid: 38704802. Pmcid: PMC11070398.
• Colyer B, Bak M, Basanta D, Noble R. A seven-step guide to spatial, agent-based modelling of tumour evolution. Evol Appl. 2024 May.17(5):e13687. Pubmedid: 38707992. Pmcid: PMC11064804.
• Hu A, Ojwang' AME, Olumoyin KD, Rejniak KA. LinG3D: visualizing the spatio-temporal dynamics of clonal evolution. BMC Bioinformatics. 2024 May.25(1):201. Pubmedid: 38802748. Pmcid: PMC11131251.
• Onubogu U, Gatenbee CD, Prabhakaran S, Wolfe K, Oakes B, Salatino R, Vaubel R, Szentirmai O, Anderson ARA, Janiszewska M. Spatial analysis of recurrent glioblastoma reveals perivascular niche organization. JCI Insight. 2024 May.9(12). Pubmedid: 38805346.
• West J, Marzban S, Srivast S, Kartika S, Bravo R, Safriel R, Zarski A, Anderson A, Chung C, Amelio A. Spatial interactions modulate tumor growth and immune infiltration. Res Sq. 2024 May. Pubmedid: 38826398. Pmcid: PMC11142313.
• Aguadé-Gorgorió G, Anderson ARA, Solé R. Modeling tumors as species-rich ecological communities. bioRxiv. 2024 Apr. Pubmedid: 38712062. Pmcid: PMC11071393.
• Ojwang' AME, Bazargan S, Johnson JO, Pilon-Thomas S, Rejniak KA. Histology-guided mathematical model of tumor oxygenation: sensitivity analysis of physical and computational parameters. bioRxiv. 2024 Mar. Pubmedid: 38496532. Pmcid: PMC10942376.
• Hu A, Ojwang' AME, Olumoyin KD, Rejniak KA. Visualizing the Spatio-Temporal Dynamics of Clonal Evolution with LinG3D software. bioRxiv. 2024 Mar. Pubmedid: 38496472. Pmcid: PMC10942425.
• Bishop RT, Miller AK, Froid M, Nerlakanti N, Li T, Frieling JS, Nasr MM, Nyman KJ, Sudalagunta PR, Canevarolo RR, Silva AS, Shain KH, Lynch CC, Basanta D. The bone ecosystem facilitates multiple myeloma relapse and the evolution of heterogeneous drug resistant disease. Nat Commun. 2024 Mar.15(1):2458. Pubmedid: 38503736. Pmcid: PMC10951361.
• Pierik L, McDonald P, Anderson ARA, West J. Second-Order Effects of Chemotherapy Pharmacodynamics and Pharmacokinetics on Tumor Regression and Cachexia. Bull Math Biol. 2024 Mar.86(5):47. Pubmedid: 38546759.
• Marzban S, Srivastava S, Kartika S, Bravo R, Safriel R, Zarski A, Anderson A, Chung CH, Amelio AL, West J. Spatial interactions modulate tumor growth and immune infiltration. bioRxiv. 2024 Mar. Pubmedid: 38370722. Pmcid: PMC10871273.
• West J, Rentzeperis F, Adam C, Bravo R, Luddy KA, Robertson-Tessi M, Anderson ARA. Tumor-immune metaphenotypes orchestrate an evolutionary bottleneck that promotes metabolic transformation. Front Immunol. 2024 Feb.15:1323319. Pubmedid: 38426105. Pmcid: PMC10902449.
• Mathur S, Chen S, Rejniak KA. Exploring chronic and transient tumor hypoxia for predicting the efficacy of hypoxia-activated pro-drugs. NPJ Syst Biol Appl. 2024 Jan.10(1):1. Pubmedid: 38182612. Pmcid: PMC10770176.
• Seyedi S, Teo R, Foster L, Saha D, Mina L, Northfelt D, Anderson KS, Shibata D, Gatenby R, Cisneros LH, Troan B, Anderson ARA, Maley CC. Testing Adaptive Therapy Protocols Using Gemcitabine and Capecitabine in a Preclinical Model of Endocrine-Resistant Breast Cancer. Cancers (Basel). 2024 Jan.16(2). Pubmedid: 38254748. Pmcid: PMC10813385.
• Mohsin N, Enderling H, Brady-Nicholls R, Zahid MU. Simulating tumor volume dynamics in response to radiotherapy: Implications of model selection. J Theor Biol. 2024 Jan.576:111656. Pubmedid: 37952611.
• Axenie C, López-Corona O, Makridis MA, Akbarzadeh M, Saveriano M, Stancu A, West J. Antifragility as a complex system's response to perturbations, volatility, and time. ArXiv. 2023 Dec. Pubmedid: 38196741. Pmcid: PMC10775345.
• Poonja S, Forero Pinto A, Lloyd MC, Damaghi M, Rejniak KA. Dynamics of Fibril Collagen Remodeling by Tumor Cells: A Model of Tumor-Associated Collagen Signatures. Cells. 2023 Nov.12(23). Pubmedid: 38067116. Pmcid: PMC10705683.
• Welch DL, Fridley BL, Cen L, Teer JK, Yoder SJ, Pettersson F, Xu L, Cheng CH, Zhang Y, Alexandrow MG, Xiang S, Robertson-Tessi M, Brown JS, Metts J, Brohl AS, Reed DR. Modeling phenotypic heterogeneity towards evolutionarily inspired osteosarcoma therapy. Sci Rep. 2023 Nov.13(1):20125. Pubmedid: 37978271. Pmcid: PMC10656496.
• Miroshnychenko D, Miti T, Kumar P, Miller A, Laurie M, Giraldo N, Bui MM, Altrock PM, Basanta D, Marusyk A. Stroma-Mediated Breast Cancer Cell Proliferation Indirectly Drives Chemoresistance by Accelerating Tumor Recovery between Chemotherapy Cycles. Cancer Res. 2023 Nov.83(22):3681-3692. Pubmedid: 37791818. Pmcid: PMC10646478.
• Brown JS, Amend SR, Austin RH, Gatenby RA, Hammarlund EU, Pienta KJ. Updating the Definition of Cancer. Mol Cancer Res. 2023 Nov.21(11):1142-1147. Pubmedid: 37409952. Pmcid: PMC10618731.
• Pradeu T, Daignan-Fornier B, Ewald A, Germain PL, Okasha S, Plutynski A, Benzekry S, Bertolaso M, Bissell M, Brown JS, Chin-Yee B, Chin-Yee I, Clevers H, Cognet L, Darrason M, Farge E, Feunteun J, Galon J, Giroux E, Green S, Gross F, Jaulin F, Knight R, Laconi E, Larmonier N, Maley C, Mantovani A, Moreau V, Nassoy P, Rondeau E, Santamaria D, Sawai CM, Seluanov A, Sepich-Poore GD, Sisirak V, Solary E, Yvonnet S, Laplane L. Reuniting philosophy and science to advance cancer research. Biol Rev Camb Philos Soc. 2023 Oct.98(5):1668-1686. Pubmedid: 37157910.
• Chahoud J, Anderson ARA, Zhang J, Brown J, Gatenby RA. Evolutionary Dynamics and Intermittent Therapy for Metastatic Cancers. J Clin Oncol. 2023 Oct.41(28):4469-4471. Pubmedid: 37418680. Pmcid: PMC10553063.
• Bazargan S, Bunch B, Ojwang' AME, Blauvelt J, Landin A, Ali J, Abrahams D, Cox C, Hall AM, Beatty MS, Poch M, Rejniak KA, Pilon-Thomas S. Targeting myeloid-derived suppressor cells with gemcitabine to enhance efficacy of adoptive cell therapy in bladder cancer. Front Immunol. 2023 Oct.14:1275375. Pubmedid: 37901214. Pmcid: PMC10602731.
• Nowicka Z, Rentzeperis F, Beck R, Tagal V, Pinto AF, Scanu E, Veith T, Cole J, Ilter D, Viqueira WD, Teer JK, Maksin K, Pasetto S, Abdalah MA, Fiandaca G, Prabhakaran S, Schultz A, Ojwang M, Barnholtz-Sloan JS, Farinhas JM, Gomes AP, Katira P, Andor N. Interactions between ploidy and resource availability shape clonal interference at initiation and recurrence of glioblastoma. bioRxiv. 2023 Oct. Pubmedid: 37905142. Pmcid: PMC10614845.
• Strobl MAR, Gallaher J, Robertson-Tessi M, West J, Anderson ARA. Treatment of evolving cancers will require dynamic decision support. Ann Oncol. 2023 Oct.34(10):867-884. Pubmedid: 37777307.
• Bukkuri A, Pienta KJ, Amend SR, Austin RH, Hammarlund EU, Brown JS. The contribution of evolvability to the eco-evolutionary dynamics of competing species. Ecol Evol. 2023 Oct.13(10):e10591. Pubmedid: 37829179. Pmcid: PMC10565728.
• Chancellor S, Grasse B, Sakmar T, Scheel D, Brown JS, Santymire RM. Exploring the Effect of Age on the Reproductive and Stress Physiology of Octopus bimaculoides Using Dermal Hormones. Animals (Basel). 2023 Oct.13(19). Pubmedid: 37835721. Pmcid: PMC10571824.
• Gillis N, Padron E, Wang T, Chen K, DeVos JD, Spellman SR, Lee SJ, Kitko CL, MacMillan ML, West J, Tang YH, Teng M, McNulty S, Druley TE, Pidala JA, Lazaryan A. Pilot Study of Donor-Engrafted Clonal Hematopoiesis Evolution and Clinical Outcomes in Allogeneic Hematopoietic Cell Transplantation Recipients Using a National Registry. Transplant Cell Ther. 2023 Oct.29(10):640.e1-640.e8. Pubmedid: 37517612. Pmcid: PMC10592088.