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  1. Article: Current and Future Horizons of Patient-Derived Xenograft Models in Colorectal Cancer Translational Research.

    Inoue, Akira / Deem, Angela K / Kopetz, Scott / Heffernan, Timothy P / Draetta, Giulio F / Carugo, Alessandro

    Cancers

    2019  Volume 11, Issue 9

    Abstract: Our poor understanding of the intricate biology of cancer and the limited availability of preclinical models that faithfully recapitulate the complexity of tumors are primary contributors to the high failure rate of novel therapeutics in oncology ... ...

    Abstract Our poor understanding of the intricate biology of cancer and the limited availability of preclinical models that faithfully recapitulate the complexity of tumors are primary contributors to the high failure rate of novel therapeutics in oncology clinical studies. To address this need, patient-derived xenograft (PDX) platforms have been widely deployed and have reached a point of development where we can critically review their utility to model and interrogate relevant clinical scenarios, including tumor heterogeneity and clonal evolution, contributions of the tumor microenvironment, identification of novel drugs and biomarkers, and mechanisms of drug resistance. Colorectal cancer (CRC) constitutes a unique case to illustrate clinical perspectives revealed by PDX studies, as they overcome limitations intrinsic to conventional ex vivo models. Furthermore, the success of molecularly annotated "Avatar" models for co-clinical trials in other diseases suggests that this approach may provide an additional opportunity to improve clinical decisions, including opportunities for precision targeted therapeutics, for patients with CRC in real time. Although critical weaknesses have been identified with regard to the ability of PDX models to predict clinical outcomes, for now, they are certainly the model of choice for preclinical studies in CRC. Ongoing multi-institutional efforts to develop and share large-scale, well-annotated PDX resources aim to maximize their translational potential. This review comprehensively surveys the current status of PDX models in translational CRC research and discusses the opportunities and considerations for future PDX development.
    Language English
    Publishing date 2019-09-06
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers11091321
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A systems biology approach to personalizing therapeutic combinations.

    Kwong, Lawrence N / Heffernan, Timothy P / Chin, Lynda

    Cancer discovery

    2013  Volume 3, Issue 12, Page(s) 1339–1344

    Abstract: The identification of evidence-based, efficacious drug combinations for each cancer, among thousands of potential permutations, is a daunting task. In this perspective, we propose a systematic approach to defining such combinations by molecularly ... ...

    Abstract The identification of evidence-based, efficacious drug combinations for each cancer, among thousands of potential permutations, is a daunting task. In this perspective, we propose a systematic approach to defining such combinations by molecularly benchmarking a drug against a desired state of efficacy using model systems.
    MeSH term(s) Antineoplastic Combined Chemotherapy Protocols ; Computer Simulation ; Databases, Factual ; Evidence-Based Medicine ; Humans ; Molecular Targeted Therapy/methods ; Neoplasms/drug therapy ; Neoplasms/genetics ; Precision Medicine ; Systems Biology/methods
    Language English
    Publishing date 2013-12-10
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2625242-9
    ISSN 2159-8290 ; 2159-8274
    ISSN (online) 2159-8290
    ISSN 2159-8274
    DOI 10.1158/2159-8290.CD-13-0394
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Combined inhibition of DDR1 and CDK4/6 induces synergistic effects in ER-positive, HER2-negative breast cancer with PIK3CA/AKT1 mutations.

    Shariati, Maryam / Evans, Kurt W / Zheng, Xiaofeng / Bristow, Christopher A / Ng, Patrick Kwok-Shing / Rizvi, Yasmeen Q / Tapia, Coya / Yang, Fei / Carugo, Alessandro / Heffernan, Timothy P / Peoples, Michael D / Tripathy, Debu / Meric-Bernstam, Funda

    Oncogene

    2021  Volume 40, Issue 26, Page(s) 4425–4439

    Abstract: Molecular alterations in the PI3K/AKT pathway occur frequently in hormone receptor-positive breast tumors. Patients with ER-positive, HER2-negative metastatic breast cancer are often treated with CDK4/6 inhibitors such as palbociclib in combination with ... ...

    Abstract Molecular alterations in the PI3K/AKT pathway occur frequently in hormone receptor-positive breast tumors. Patients with ER-positive, HER2-negative metastatic breast cancer are often treated with CDK4/6 inhibitors such as palbociclib in combination with endocrine therapy. Although this is an effective regimen, most patients ultimately progress. The purpose of this study was identifying synthetic lethality partners that can enhance palbociclib's antitumor efficacy in the presence of PIK3CA/AKT1 mutations. We utilized a barcoded shRNA library to determine critical targets for survival in isogenic MCF7 cells with PIK3CA/AKT1 mutations. We demonstrated that the efficacy of palbociclib is reduced in the presence of PIK3CA/AKT1 mutations. We also identified that the downregulation of discoidin domain receptor 1 (DDR1) is synthetically lethal with palbociclib. DDR1 knockdown and DDR1 pharmacological inhibitor decreased cell growth and inhibited cell cycle progression in all cell lines, while enhanced the sensitivity of PIK3CA/AKT1 mutant cells to palbociclib. Combined treatment of palbociclib and 7rh further induced cell cycle arrest in PIK3CA/AKT1 mutant cell lines. In vivo, 7rh significantly enhanced palbociclib's antitumor efficacy. Our data indicates that DDR1 inhibition can augment cell cycle suppressive effect of palbociclib and could be effective strategy for targeted therapy of ER-positive, HER2-negative breast cancers with PI3K pathway activation.
    MeSH term(s) Animals ; Antineoplastic Combined Chemotherapy Protocols/pharmacology ; Breast Neoplasms/drug therapy ; Breast Neoplasms/genetics ; Cell Cycle Checkpoints/drug effects ; Cell Cycle Checkpoints/genetics ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Cell Proliferation/genetics ; Class I Phosphatidylinositol 3-Kinases/genetics ; Cyclin-Dependent Kinases/antagonists & inhibitors ; Discoidin Domain Receptor 1/antagonists & inhibitors ; Female ; Humans ; MCF-7 Cells ; Mutation/genetics ; Protein Kinase Inhibitors/pharmacology ; Proto-Oncogene Proteins c-akt/genetics ; Receptor, ErbB-2/genetics ; Receptors, Estrogen/genetics ; Signal Transduction/drug effects ; Signal Transduction/genetics
    Chemical Substances Protein Kinase Inhibitors ; Receptors, Estrogen ; Class I Phosphatidylinositol 3-Kinases (EC 2.7.1.137) ; PIK3CA protein, human (EC 2.7.1.137) ; DDR1 protein, human (EC 2.7.10.1) ; Discoidin Domain Receptor 1 (EC 2.7.10.1) ; Receptor, ErbB-2 (EC 2.7.10.1) ; AKT1 protein, human (EC 2.7.11.1) ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1) ; Cyclin-Dependent Kinases (EC 2.7.11.22)
    Language English
    Publishing date 2021-06-09
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 639046-8
    ISSN 1476-5594 ; 0950-9232
    ISSN (online) 1476-5594
    ISSN 0950-9232
    DOI 10.1038/s41388-021-01819-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: The cytosolic iron-sulfur cluster assembly (CIA) pathway is required for replication stress tolerance of cancer cells to Chk1 and ATR inhibitors.

    Redwood, Abena B / Zhang, Xiaomei / Seth, Sahil B / Ge, Zhongqi / Bindeman, Wendy E / Zhou, Xinhui / Sinha, Vidya C / Heffernan, Timothy P / Piwnica-Worms, Helen

    NPJ breast cancer

    2021  Volume 7, Issue 1, Page(s) 152

    Abstract: The relationship between ATR/Chk1 activity and replication stress, coupled with the development of potent and tolerable inhibitors of this pathway, has led to the clinical exploration of ATR and Chk1 inhibitors (ATRi/Chk1i) as anticancer therapies for ... ...

    Abstract The relationship between ATR/Chk1 activity and replication stress, coupled with the development of potent and tolerable inhibitors of this pathway, has led to the clinical exploration of ATR and Chk1 inhibitors (ATRi/Chk1i) as anticancer therapies for single-agent or combinatorial application. The clinical efficacy of these therapies relies on the ability to ascertain which patient populations are most likely to benefit, so there is intense interest in identifying predictive biomarkers of response. To comprehensively evaluate the components that modulate cancer cell sensitivity to replication stress induced by Chk1i, we performed a synthetic-lethal drop-out screen in a cell line derived from a patient with triple-negative breast cancer (TNBC), using a pooled barcoded shRNA library targeting ~350 genes involved in DNA replication, DNA damage repair, and cycle progression. In addition, we sought to compare the relative requirement of these genes when DNA fidelity is challenged by clinically relevant anticancer breast cancer drugs, including cisplatin and PARP1/2 inhibitors, that have different mechanisms of action. This global comparison is critical for understanding not only which agents should be used together for combinatorial therapies in breast cancer patients, but also the genetic context in which these therapies will be most effective, and when a single-agent therapy will be sufficient to provide maximum therapeutic benefit to the patient. We identified unique potentiators of response to ATRi/Chk1i and describe a new role for components of the cytosolic iron-sulfur assembly (CIA) pathway, MMS19 and CIA2B-FAM96B, in replication stress tolerance of TNBC.
    Language English
    Publishing date 2021-12-02
    Publishing country United States
    Document type Journal Article
    ISSN 2374-4677
    ISSN 2374-4677
    DOI 10.1038/s41523-021-00353-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Oncogenic Kras

    Mahadevan, Krishnan K / McAndrews, Kathleen M / LeBleu, Valerie S / Yang, Sujuan / Lyu, Hengyu / Li, Bingrui / Sockwell, Amari M / Kirtley, Michelle L / Morse, Sami J / Moreno Diaz, Barbara A / Kim, Michael P / Feng, Ningping / Lopez, Anastasia M / Guerrero, Paola A / Sugimoto, Hikaru / Arian, Kent A / Ying, Haoqiang / Barekatain, Yasaman / Kelly, Patience J /
    Maitra, Anirban / Heffernan, Timothy P / Kalluri, Raghu

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Pancreatic ductal adenocarcinoma (PDAC) is associated with mutations in Kras, a known oncogenic driver of PDAC; and ... ...

    Abstract Pancreatic ductal adenocarcinoma (PDAC) is associated with mutations in Kras, a known oncogenic driver of PDAC; and the
    Language English
    Publishing date 2023-02-18
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.02.15.528757
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Neddylation inhibition sensitises renal medullary carcinoma tumours to platinum chemotherapy.

    Shapiro, Daniel D / Zacharias, Niki Millward / Tripathi, Durga N / Karki, Menuka / Bertocchio, Jean-Philippe / Soeung, Melinda / He, Rong / Westerman, Mary E / Gao, Jianjun / Rao, Priya / Lam, Truong N A / Jonasch, Eric / Perelli, Luigi / Cheng, Emily H / Carugo, Alessandro / Heffernan, Timothy P / Walker, Cheryl L / Genovese, Giannicola / Tannir, Nizar M /
    Karam, Jose A / Msaouel, Pavlos

    Clinical and translational medicine

    2023  Volume 13, Issue 5, Page(s) e1267

    Abstract: Background: Renal medullary carcinoma (RMC) is a highly aggressive cancer in need of new therapeutic strategies. The neddylation pathway can protect cells from DNA damage induced by the platinum-based chemotherapy used in RMC. We investigated if ... ...

    Abstract Background: Renal medullary carcinoma (RMC) is a highly aggressive cancer in need of new therapeutic strategies. The neddylation pathway can protect cells from DNA damage induced by the platinum-based chemotherapy used in RMC. We investigated if neddylation inhibition with pevonedistat will synergistically enhance antitumour effects of platinum-based chemotherapy in RMC.
    Methods: We evaluated the IC
    Results: The RMC cell lines demonstrated IC
    Conclusions: Our results suggest that pevonedistat synergises with carboplatin to inhibit RMC cell and tumour growth through inhibition of DNA damage repair. These findings support the development of a clinical trial combining pevonedistat with platinum-based chemotherapy for RMC.
    MeSH term(s) Humans ; Carboplatin/pharmacology ; Carboplatin/therapeutic use ; Carcinoma, Medullary ; Carcinoma, Renal Cell/drug therapy ; Kidney Neoplasms/drug therapy
    Chemical Substances pevonedistat (S3AZD8D215) ; Carboplatin (BG3F62OND5)
    Language English
    Publishing date 2023-05-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2697013-2
    ISSN 2001-1326 ; 2001-1326
    ISSN (online) 2001-1326
    ISSN 2001-1326
    DOI 10.1002/ctm2.1267
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Targeting Glucose Metabolism Sensitizes Pancreatic Cancer to MEK Inhibition.

    Yan, Liang / Tu, Bo / Yao, Jun / Gong, Jing / Carugo, Alessandro / Bristow, Christopher A / Wang, Qiuyun / Zhu, Cihui / Dai, Bingbing / Kang, Ya'an / Han, Leng / Feng, Ningping / Jin, Yanqing / Fleming, Jason / Heffernan, Timothy P / Yao, Wantong / Ying, Haoqiang

    Cancer research

    2021  Volume 81, Issue 15, Page(s) 4054–4065

    Abstract: Pancreatic ductal adenocarcinoma (PDAC) is almost universally lethal. A critical unmet need exists to explore essential susceptibilities in PDAC and to identify druggable targets to improve PDAC treatment. KRAS mutations dominate the genetic landscape of ...

    Abstract Pancreatic ductal adenocarcinoma (PDAC) is almost universally lethal. A critical unmet need exists to explore essential susceptibilities in PDAC and to identify druggable targets to improve PDAC treatment. KRAS mutations dominate the genetic landscape of PDAC and lead to activation of multiple downstream pathways and cellular processes. Here, we investigated the requirement of these pathways for tumor maintenance using an inducible
    MeSH term(s) Adenocarcinoma/drug therapy ; Animals ; Carcinoma, Pancreatic Ductal/drug therapy ; Glucose/metabolism ; Humans ; Mice ; Protein Kinase Inhibitors/pharmacology ; Protein Kinase Inhibitors/therapeutic use
    Chemical Substances Protein Kinase Inhibitors ; Glucose (IY9XDZ35W2)
    Language English
    Publishing date 2021-06-11
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1432-1
    ISSN 1538-7445 ; 0008-5472
    ISSN (online) 1538-7445
    ISSN 0008-5472
    DOI 10.1158/0008-5472.CAN-20-3792
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Evolutionary fingerprints of EMT in pancreatic cancers.

    Perelli, Luigi / Zhang, Li / Mangiameli, Sarah / Russell, Andrew J C / Giannese, Francesca / Peng, Fuduan / Carbone, Federica / Le, Courtney / Khan, Hania / Citron, Francesca / Soeung, Melinda / Lam, Truong Nguyen Anh / Lundgren, Sebastian / Zhu, Cihui / Catania, Desiree / Feng, Ningping / Gurreri, Enrico / Sgambato, Alessandro / Tortora, Giampaolo /
    Draetta, Giulio F / Tonon, Giovanni / Futreal, Andrew / Giuliani, Virginia / Carugo, Alessandro / Viale, Andrea / Heffernan, Timothy P / Wang, Linghua / Cittaro, Davide / Chen, Fei / Genovese, Giannicola

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Mesenchymal plasticity has been extensively described in advanced and metastatic epithelial cancers; however, its functional role in malignant progression, metastatic dissemination and therapy response is controversial. More importantly, the role of ... ...

    Abstract Mesenchymal plasticity has been extensively described in advanced and metastatic epithelial cancers; however, its functional role in malignant progression, metastatic dissemination and therapy response is controversial. More importantly, the role of epithelial mesenchymal transition (EMT) and cell plasticity in tumor heterogeneity, clonal selection and clonal evolution is poorly understood. Functionally, our work clarifies the contribution of EMT to malignant progression and metastasis in pancreatic cancer. We leveraged
    Language English
    Publishing date 2023-09-19
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.09.18.558231
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Combined KRAS

    Thatikonda, Venu / Lu, Hengyu / Jurado, Sabine / Kostyrko, Kaja / Bristow, Christopher A / Bosch, Karin / Feng, Ningping / Gao, Sisi / Gerlach, Daniel / Gmachl, Michael / Lieb, Simone / Jeschko, Astrid / Machado, Annette A / Marszalek, Ethan D / Mahendra, Mikhila / Jaeger, Philipp A / Sorokin, Alexey / Strauss, Sandra / Trapani, Francesca /
    Kopetz, Scott / Vellano, Christopher P / Petronczki, Mark / Kraut, Norbert / Heffernan, Timothy P / Marszalek, Joseph R / Pearson, Mark / Waizenegger, Irene / Hofmann, Marco H

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Efforts to improve the anti-tumor response to ... ...

    Abstract Efforts to improve the anti-tumor response to KRAS
    Language English
    Publishing date 2023-01-23
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.01.23.525210
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: SMARCB1 regulates the hypoxic stress response in sickle cell trait.

    Soeung, Melinda / Perelli, Luigi / Chen, Ziheng / Dondossola, Eleonora / Ho, I-Lin / Carbone, Federica / Zhang, Li / Khan, Hania / Le, Courtney N / Zhu, Cihui / Peoples, Michael D / Feng, Ningping / Jiang, Shan / Zacharias, Niki Millward / Minelli, Rosalba / Shapiro, Daniel D / Deem, Angela K / Gao, Sisi / Cheng, Emily H /
    Lucchetti, Donatella / Walker, Cheryl L / Carugo, Alessandro / Giuliani, Virginia / Heffernan, Timothy P / Viale, Andrea / Tannir, Nizar M / Draetta, Giulio F / Msaouel, Pavlos / Genovese, Giannicola

    Proceedings of the National Academy of Sciences of the United States of America

    2023  Volume 120, Issue 21, Page(s) e2209639120

    Abstract: Renal medullary carcinoma (RMC) is an aggressive kidney cancer that almost exclusively develops in individuals with sickle cell trait (SCT) and is always characterized by loss of the tumor ... ...

    Abstract Renal medullary carcinoma (RMC) is an aggressive kidney cancer that almost exclusively develops in individuals with sickle cell trait (SCT) and is always characterized by loss of the tumor suppressor
    MeSH term(s) Animals ; Humans ; Mice ; Carcinoma, Renal Cell/pathology ; Hypoxia/genetics ; Hypoxia/metabolism ; Kidney/metabolism ; Kidney Neoplasms/pathology ; Sickle Cell Trait/genetics ; Sickle Cell Trait/metabolism ; SMARCB1 Protein/genetics ; SMARCB1 Protein/metabolism
    Chemical Substances SMARCB1 Protein
    Language English
    Publishing date 2023-05-15
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2209639120
    Database MEDical Literature Analysis and Retrieval System OnLINE

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