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1. Coordinated Health Care Interventions for Childhood Asthma Gaps in Outcomes (CHICAGO) plan

Author

Ali, Sana, Flores, Janet, Gantiwala, Shahina, Goralski, Carmen, Kumar, Rajesh, Ortega, Jacqueline, Pittsenbarger, Zachary, Wilson, Isabelle, Lohff, Cortland, McDermott, Michael, Erwin, Kim, MacTavish, Thomas, Norell, Sarah, Damitz, Maureen, Massaquoi, David, Soyemi, Kenneth, Senko, Thomas, Thompson, Trevonne, McMahon, Kate, Africk, Joel, O’Rourke, Amy, Codispoti, Christopher, Kramer, Jane, Malik, Rabia, Manning, Pamela, Mosnaim, Giselle, Avila, Jeanette, Margellos-Anast, Helen, Padron, Fatima, Ramsay, Jessica, Saiyed, Nazia, Schwindt, Tala, Seals, Gloria, Zun, Leslie, Butters, Susannah, Hull, Ashley, Kim, John, Paik, S. Margaret, Press, Valerie, Stevenson, Crystal, Twu, Nicole, Woodrick, Nicole, Berbaum, Michael, Bracken, Nina, Buenrostro, Jennifer, Castro, Lauren, Chen, Yi-Fan, DeLisa, Julie, De La Torre-Dorado, David, Edwards, Dameka, Frye, Alexander, Grabarek, Maciej, Illendula, Sai Dheeraj, Kim, Hajwa, Krishnan, Jerry, Martin, Molly, Perez, Melissa Morales, Nguyen, Hannah, Nyenhuis, Sharmilee, Sculley, Jennifer, Bender, Bruce, Ducharme, Francine, Hurdle, Sheri, Li, Xue, Okelo, Sande, Krishnan, Jerry A., Africk, Joel J., Ignoffo, Stacy, MacTavish, Tom, Martin, Molly A., Mosnaim, Giselle S., Nyenhuis, Sharmilee M., Press, Valerie G., Thompson, Trevonne M., and Gerald, Lynn B.

Published
2023
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2. A long-term optical and X-ray ephemeris of the polar EK Ursae Majoris

Author

Beuermann, K., Diese, J., Paik, S., Ploch, A., Zachmann, J., Schwope, A. D., and Hessman, F. V.

Subjects
Astrophysics - Solar and Stellar Astrophysics
Abstract

We searched for long-term period changes in the polar EK UMa using new optical data and archival X-ray/EUV data. An optical ephemeris was derived from data taken remotely with the MONET/N telescope and compared with the X-ray ephemeris based on Einstein, Rosat, and EUVE data. A three-parameter fit to the combined data sets yields the epoch, the period, and the phase offset between the optical minima and the X-ray absorption dips. An added quadratic term is insignificant and sets a limit to the period change. The derived linear ephemeris is valid over 30 years and the common optical and X-ray period is P=0.0795440225(24) days. There is no evidence of long-term O-C variations or a period change over the past 17 years Delta P = -0.14+-0.50 ms. We suggest that the observed period is the orbital period and that the system is tightly synchronized. The limit on Delta P and the phase constancy of the bright part of the light curve indicate that O-C variations of the type seen in the polars DP Leo and HU Aqr or the pre-CV NN Ser do not seem to occur in EK UMa. The X-ray dips lag the optical minima by 9.5+-0.7 deg in azimuth, providing some insight into the accretion geometry., Comment: 4 pages, 2 Postscript figures, accepted for publication in Astronomy & Astrophysics

Published
2009
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3. $T_1$- and $T_2$-spin relaxation time limitations of phosphorous donor electrons near crystalline silicon to silicon dioxide interface defects

Author

Paik, S. -Y., Lee, S. -Y., Baker, W. J., and Boehme, D. R. McCamey. C.

Subjects
Condensed Matter - Materials Science
Abstract

A study of donor electron spins and spin--dependent electronic transitions involving phosphorous ($^{31}$P) atoms in proximity of the (111) oriented crystalline silicon (c-Si) to silicon dioxide (SiO$_{2}$) interface is presented for [$^{31}$P] = 10$^{15}$ $\mathrm{cm}^{-3}$ and [$^{31}$P] = 10$^{16}$ $\mathrm{cm}^{-3}$ at about liquid $^4$He temperatures ($T = 5$ $\mathrm{K} - 15$ $\mathrm{K}$). Using pulsed electrically detected magnetic resonance (pEDMR), spin--dependent transitions between the \Phos donor state and two distinguishable interface states are observed, namely (i) \Pb centers which can be identified by their characteristic anisotropy and (ii) a more isotropic center which is attributed to E$^\prime$ defects of the \sio bulk close to the interface. Correlation measurements of the dynamics of spin--dependent recombination confirm that previously proposed transitions between \Phos and the interface defects take place. The influence of these electronic near--interface transitions on the \Phos donor spin coherence time $T_2$ as well as the donor spin--lattice relaxation time $T_1$ is then investigated by comparison of spin Hahn--echo decay measurements obtained from conventional bulk sensitive pulsed electron paramagnetic resonance and surface sensitive pEDMR, as well as surface sensitive electrically detected inversion recovery experiments. The measurements reveal that both $T_2$ and $T_1$ of \Phos donor electrons spins in proximity of energetically lower interface states at $T\leq 13$ K are reduced by several orders of magnitude.

Published
2009
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4. Coordinated Health Care Interventions for Childhood Asthma Gaps in Outcomes (CHICAGO) plan

Author

Krishnan, Jerry A., primary, Margellos-Anast, Helen, additional, Kumar, Rajesh, additional, Africk, Joel J., additional, Berbaum, Michael, additional, Bracken, Nina, additional, Chen, Yi-Fan, additional, DeLisa, Julie, additional, Erwin, Kim, additional, Ignoffo, Stacy, additional, Illendula, Sai Dheeraj, additional, Kim, Hajwa, additional, Lohff, Cortland, additional, MacTavish, Tom, additional, Martin, Molly A., additional, Mosnaim, Giselle S., additional, Nguyen, Hannah, additional, Norell, Sarah, additional, Nyenhuis, Sharmilee M., additional, Paik, S. Margaret, additional, Pittsenbarger, Zachary, additional, Press, Valerie G., additional, Sculley, Jennifer, additional, Thompson, Trevonne M., additional, Zun, Leslie, additional, Gerald, Lynn B., additional, McDermott, Michael, additional, Ali, Sana, additional, Flores, Janet, additional, Gantiwala, Shahina, additional, Goralski, Carmen, additional, Ortega, Jacqueline, additional, Wilson, Isabelle, additional, MacTavish, Thomas, additional, Damitz, Maureen, additional, Massaquoi, David, additional, Soyemi, Kenneth, additional, Senko, Thomas, additional, Thompson, Trevonne, additional, McMahon, Kate, additional, Africk, Joel, additional, O’Rourke, Amy, additional, Codispoti, Christopher, additional, Kramer, Jane, additional, Malik, Rabia, additional, Manning, Pamela, additional, Mosnaim, Giselle, additional, Avila, Jeanette, additional, Padron, Fatima, additional, Ramsay, Jessica, additional, Saiyed, Nazia, additional, Schwindt, Tala, additional, Seals, Gloria, additional, Butters, Susannah, additional, Hull, Ashley, additional, Kim, John, additional, Press, Valerie, additional, Stevenson, Crystal, additional, Twu, Nicole, additional, Woodrick, Nicole, additional, Buenrostro, Jennifer, additional, Castro, Lauren, additional, De La Torre-Dorado, David, additional, Edwards, Dameka, additional, Frye, Alexander, additional, Grabarek, Maciej, additional, Krishnan, Jerry, additional, Martin, Molly, additional, Perez, Melissa Morales-, additional, Nyenhuis, Sharmilee, additional, Bender, Bruce, additional, Ducharme, Francine, additional, Hurdle, Sheri, additional, Li, Xue, additional, and Okelo, Sande, additional

Published
2023
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14. On measuring social biases in prompt-based multi-task learning

Author

Runyun, Şerife Leman, Akyürek; A.F.; Paik, S.; Koçyiğit, M.Y.; Akbıyık, S.; Wijaya, D., Graduate School of Social Sciences and Humanities, Department of Psychology, Runyun, Şerife Leman, Akyürek; A.F.; Paik, S.; Koçyiğit, M.Y.; Akbıyık, S.; Wijaya, D., Graduate School of Social Sciences and Humanities, and Department of Psychology

Abstract

Large language models trained on a mixture of NLP tasks that are converted into a textto- text format using prompts, can generalize into novel forms of language and handle novel tasks. A large body of work within prompt engineering attempts to understand the effects of input forms and prompts in achieving superior performance. We consider an alternative measure and inquire whether the way in which an input is encoded affects social biases promoted in outputs. In this paper, we study T0, a large-scale multi-task text-to-text language model trained using prompt-based learning. We consider two different forms of semantically equivalent inputs: question-answer format and premise-hypothesis format. We use an existing bias benchmark for the former BBQ (Parrish et al., 2021) and create the first bias benchmark in natural language inference BBNLI with hand-written hypotheses while also converting each benchmark into the other form. The results on two benchmarks suggest that given two different formulations of essentially the same input, T0 conspicuously acts more biased in question answering form, which is seen during training, compared to premisehypothesis form which is unlike its training examples., This work is supported in part by Google Research Scholar Award, DARPA HR001118S0044 (the LwLL program), and the U.S. NSF grant 1838193. The U.S. Government is authorized to reproduce and distribute reprints for Governmental purposes. The views and conclusions contained in this publication are those of the authors and should not be interpreted as representing official policies or endorsements of Google, DARPA, or the U.S. Government.

Published
2022

16. Rufomycin targets ClpC1 proteolysis in Mycobacterium tuberculosis and M. abscessus

Author

Cho, Sang Hyun, Choules, MP, Wolf, NM, Lee, H, Anderson, JR, Grzelak, EM, Wang, Y, Ma, R, Gao, W, McAlpine, JB, Jin, Y, Cheng, J, Suh, J, Duc, NM, Paik, S, Choe, JH, Jo, E, Chang, CH, Lee, JS, Jaki, Birgit, Pauli, Guido, and Franzblau, Scott

Subjects
FOS: Biological sciences, Microbiology
Abstract

ClpC1 is an emerging new target for the treatment of Mycobacterium tuberculosis infections, and several cyclic peptides (ecumicin, cyclomarin A, and lassomycin) are known to act on this target. This study identified another group of peptides, the rufomycins (RUFs), as bactericidal to M. tuberculosis through the inhibition of ClpC1 and subsequent modulation of protein degradation of intracellular proteins. Rufomycin I (RUFI) was found to be a potent and selective lead compound for both M. tuberculosis (MIC, 0.02 ��M) and Mycobacterium abscessus (MIC, 0.4 ��M). Spontaneously generated mutants resistant to RUFI involved seven unique single nucleotide polymorphism (SNP) mutations at three distinct codons within the N-terminal domain of clpC1 (V13, H77, and F80). RUFI also significantly decreased the proteolytic capabilities of the ClpC1/P1/P2 complex to degrade casein, while having no significant effect on the ATPase activity of ClpC1. This represents a marked difference from ecumicin, which inhibits ClpC1 proteolysis but stimulates the ATPase activity, thereby providing evidence that although these peptides share ClpC1 as a macromolecular target, their downstream effects are distinct, likely due to differences in binding.

Published
2022
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17. The tale of TILs in breast cancer: A report from The International Immuno-Oncology Biomarker Working Group

Author

El Bairi, K., Haynes, H. R., Blackley, E., Fineberg, S., Shear, J., Turner, S., de Freitas, J. R., Sur, D., Amendola, L. C., Gharib, M., Kallala, A., Arun, I., Azmoudeh-Ardalan, F., Fujimoto, L., Sua, L. F., Liu, S. -W., Lien, H. -C., Kirtani, P., Balancin, M., El Attar, H., Guleria, P., Yang, W., Shash, E., Chen, I. -C., Bautista, V., Do Prado Moura, J. F., Rapoport, B. L., Castaneda, C., Spengler, E., Acosta-Haab, G., Frahm, I., Sanchez, J., Castillo, M., Bouchmaa, N., Md Zin, R. R., Shui, R., Onyuma, T., Husain, Z., Willard-Gallo, K., Coosemans, A., Perez, E. A., Provenzano, E., Ericsson, P. G., Richardet, E., Mehrotra, R., Sarancone, S., Ehinger, A., Rimm, D. L., Bartlett, J. M. S., Viale, G., Denkert, C., Hida, A. I., Sotiriou, C., Loibl, S., Hewitt, S. M., Badve, S., Symmans, W. F., Kim, R. S., Pruneri, G., Goel, S., Francis, P. A., Inurrigarro, G., Yamaguchi, R., Garcia-Rivello, H., Horlings, H., Afqir, S., Salgado, R., Adams, S., Kok, M., Dieci, M. V., Michiels, S., Demaria, S., Loi, S., Schelfhout, V., Arbzadeh, E., Bondanar, A., Reyes, S. A. G., Ruz, J. R., Kang, J., Xiang, L., Zimovjanova, M., Togores, P., Ozturk, T., Patil, A., Corpa, M., Whitehouse, A., Tan, B., de Paula, A., Rossetti, C., Lang-Schwarz, C., Mahon, S., Giacometti, C., Linderholm, B., Deman, F., Montagna, G., Gong, G., Pavcovich, M., Chaer, Y., Cabrero, I. A., de Brito, M. L., Ilieva, N., Fulop, A., Souza, M., Bilancia, D., Idowu, M., Johri, R., Szpor, J., Bachani, L., Schmitt, F., Giannotti, M., Kurebayashi, Y., Ramirez, B. E. A., Salido, E., Bortesi, L., Bonetto, S., Elomina, K., Lopez, P., Sharma, V., Edirisinghe, A., Mathur, D., Sahay, A., Mouloud, M. A., Giang, C. H., Mukolwe, E., Kiruka, E., Samberg, N., Abe, N., Brown, M., Millar, E., X. B., Li, Yuan, Z., Pasupathy, A., Miele, R., Luff, R., e Porfirio, M. M. A., Ajemba, O., Soni, R., Orvieto, E., Dimaio, M., Thomas, J., Merard, R., Subramaniam, M. M., Apolinario, T., Preda, O., Preda, R., Makanga, A., Maior, M. S., Li, L., Saghatchian, M., Saurine, T., Janssen, E., Cochran, J., Vlada, N., Cappellesso, R., Elfer, K., Hollick, M., Desai, S., Oner, G., Schreurs, A., Liu, S., Perera, R., Mercurio, P., Garcia, F., Hosny, K., Matsumoto, H., van Deurzen, C., Bianchini, G., Coban, I., Jahangir, A., Rahman, A., Stover, D., Luz, P., Martel, A., Waumans, Y., Stenzinger, A., Cortes, J., Dimitrova, P., Nauwelaers, I., Velasco, M., Fan, F., Akturk, G., Firer, M., Roxanis, I., Schneck, M., Wen, H., Cockenpot, V., Konstantinov, A., Calatrava, A., Vidya, M. N., Choi, H. J., Jank, P., Ciinen, A. H., Sabanathan, D., Floris, G., Hoeflmayer, D., Hamada, T., Laudus, N., Grigoriadis, A., Porcellato, I., Acs, B., Miglietta, F., Parrodi, J., Clunie, D., Calhoun, B., F. -I., Lu, Lefevre, A., Tabbarah, S., Tran, W., Garcia-murillas, I., Jelinic, P., Boeckx, C., Souza, S., Cebollero, M. C., Felip, E., Rendon, J. L. S., El Gabry, E., Saltz, J., Bria, E., Garufi, G., Hartman, J., Sebastian, M., Olofsson, H., Kooreman, L., Cucherousset, J., Mathieu, M. -C., Ballesteros-Merino, C., Siziopikou, P., Fong, J., Klein, M., Qulis, I. R. I., Wesseling, J., Bellolio, E., Araya, J. C., Naber, S., Cheang, M., Castellano, I., Ales, A., Laenkholm, A. -V., Kulka, J., Quinn, C., Sapino, A., Amendoeira, I., Marchio, C., Braybrooke, J., Vincent-Salomon, A., Korski, K. P., Sofopoulos, M., Stovgaard, E. I. S., Bianchi, S., Bago-Horvath, Z., Yu, C., Regitnig, P., Hall, S., Kos, Z., Sant, S., Tille, J. -C., Gallas, B., Bethmann, D., Savas, P., Mendes, L., Soler, T., van Seijen, M., Gruosso, T., Quintana, A., Giltnane, J., Van den Eynden, G., Duregon, E., de Cabo, R., Recamo, P. C., Gaboury, L., Zimmerman, J., Pop, C. S., Wernicke, A., Williams, D., Gill, A., Solomon, B., Thapa, B., Farshid, G., Gilham, L., Christie, M., O'Toole, S., Hendry, S., Fox, S. B., Luen, S. J., Lakhani, S. R., Fuchs, T., John, T., Brcic, I., Hainfellner, J., Sigurd, L., Preusser, M., Poortmans, P., Decaluwe, A., Carey, C., Colpaert, C., Larsimont, D., Peeters, D., Broeckx, G., van de Vijver, K., Buisseret, L., Dirix, L., Hertoghs, M., Piccart, M., Ignatiadis, M., Van Bockstal, M., Sirtaine, N., Vermeulen, P., de Wind, R., Declercq, S., Gevaert, T., Haibe-Kans, B., Nelson, B. H., Watson, P. H., Leung, S., Nielsen, T., Shi, L., Balslev, E., Thagaard, J., Almangush, A., Makitie, A., Joensuu, H., Lundin, J., Drubay, D., Roblin, E., Andre, F., Penault-Llorca, F., Lemonnier, J., Adam, J., Lacroix-Triki, M., Ternes, N., Radosevic-Robin, N., Klaushen, F., Weber, K., Harbeck, N., Gluz, O., Wienert, S., Cserni, G., Vingiani, A., Criscitiello, C., Solinas, C., Curigliano, G., Konishi, E., Suzuki, E., Yoshikawa, K., Kawaguchi, K., Takada, M., Toi, M., Ishida, M., Shibata, N., Saji, S., Kogawa, T., Sakatani, T., Okamoto, T., Moriya, T., Kataoka, T., Shimoi, T., Sugie, T., Mukohara, T., Shu, Y., Kikawa, Y., Kozuka, Y., Sayed, S., Rahayu, R., Ramsaroop, R., Senkus-Konefka, E., Chmielik, E., Cardoso, F., Ribeiro, J., Chan, J., Dent, R., Martin, M., Hagen, C., Guerrero, A., Rojo, F., Comerma, L., Nuciforo, P., Serrano, V. V., Camaea, V. P., Steenbruggen, T., Ciompi, F., Nederlof, I., Jan, Hudecek, van der Laak, J., van den Berg, J., Voorwerk, L., van de Vijver, M., de Maaker, M., Linn, S., Mckenzie, H., Somaiah, N., Tutt, A., Swanton, C., Hiley, C., Moore, D. A., Hall, J. A., Le Quesne, J., Jabbar, K. A., al Bakir, M., Hills, R., Irshad, S., Yuan, Y., Li, Z., Liu, M., Klein, J., Fadare, O., Thompson, A., Lazar, A. J., Gown, A., Lo, A., Garrido Castro, A. C., Madabhushi, A., Moreira, A., Richardson, A., Beck, A. H., Bellizzi, A. M., Wolff, A., Harbhajanka, A., Sharma, A., Cimino-Mathews, A., Srinivasan, A., Singh, B., Chennubhotla, C. S., Chauhan, C., Dillon, D. A., Zardavas, D., Johnson, D. B., Thompson, A. E., Brogi, E., Reisenbichler, E., Huang, E., Hirsch, F. R., Mcarthur, H., Ziai, J., Brock, J., Kerner, J., Zha, J., Lennerz, J. K., Carter, J. M., Reis-Filho, J., Sparano, J., Balko, J. M., Pogue-Geile, K., Steele, K. E., Blenman, K. R. M., Allison, K. H., Pusztai, L., Cooper, L., Estrada, V. M., Flowers, M., Robson, M., Rebelatto, M. C., Hanna, M. G., Goetz, M. P., Khojasteh, M., Sanders, M. E., Regan, M. M., Misialek, M., Amgad, M., Tung, N., Singh, R., Huang, R., Pierce, R. H., Leon-Ferre, R., Swain, S., Ely, S., Kim, S. -R., Bedri, S., Paik, S., Schnitt, S., D'Alfons, T., Kurkure, U., Bossuyt, V., Tong, W., Wang, Y., Dos Anjos, C. H., Gaire, F., Van Diest, P. J., El Bairi, Khalid [0000-0002-8414-4145], de Freitas, Juliana Ribeiro [0000-0003-4978-7273], Sur, Daniel [0000-0002-0926-4614], Amendola, Luis Claudio [0000-0002-6404-450X], Azmoudeh-Ardalan, Farid [0000-0003-4701-0532], Kirtani, Pawan [0000-0002-2343-7016], Yang, Wenxian [0000-0002-5349-9680], Castillo, Miluska [0000-0002-0111-3176], Provenzano, Elena [0000-0003-3345-3965], Mehrotra, Ravi [0000-0001-9453-1408], Ehinger, Anna [0000-0001-9225-7396], Rimm, David L [0000-0001-5820-4397], Bartlett, John MS [0000-0002-0347-3888], Denkert, Carsten [0000-0002-2249-0982], Hida, Akira I [0000-0002-4486-8819], Sotiriou, Christos [0000-0002-5745-9977], Hewitt, Stephen M [0000-0001-8283-1788], Badve, Sunil [0000-0001-8861-9980], Symmans, William Fraser [0000-0002-1526-184X], Goel, Shom [0000-0001-8329-9084], Francis, Prudence A [0000-0002-7207-9286], Horlings, Hugo [0000-0003-4782-8828], Salgado, Roberto [0000-0002-1110-3801], Demaria, Sandra [0000-0003-4426-0499], Loi, Sherene [0000-0001-6137-9171], Apollo - University of Cambridge Repository, UCL - SSS/IREC/SLUC - Pôle St.-Luc, UCL - (SLuc) Service d'anatomie pathologique, Imagerie Moléculaire et Stratégies Théranostiques (IMoST), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA), Centre Jean Perrin [Clermont-Ferrand] (UNICANCER/CJP), and UNICANCER

Subjects
Oncology, medicine.medical_treatment, [SDV]Life Sciences [q-bio], TRASTUZUMAB, Improved survival, MICROENVIRONMENT, Review Article, SUBTYPES, NEOADJUVANT CHEMOTHERAPY, 0302 clinical medicine, Breast cancer, Ecology,Evolution & Ethology, PROGNOSTIC-SIGNIFICANCE, Medicine and Health Sciences, Pharmacology (medical), TUMOR-INFILTRATING LYMPHOCYTES, Stage (cooking), RC254-282, Chemical Biology & High Throughput, 0303 health sciences, Human Biology & Physiology, Genome Integrity & Repair, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, ASSOCIATION, 3. Good health, 030220 oncology & carcinogenesis, Biomarker (medicine), Life Sciences & Biomedicine, Genetics & Genomics, medicine.medical_specialty, chemical and pharmacologic phenomena, International Immuno-Oncology Biomarker Working Group, Predictive markers, 03 medical and health sciences, Signalling & Oncogenes, SDG 3 - Good Health and Well-being, Internal medicine, 692/53/2423, medicine, Radiology, Nuclear Medicine and imaging, In patient, 030304 developmental biology, Computational & Systems Biology, Science & Technology, IDENTIFICATION, business.industry, review-article, Cancer, 03.01. Általános orvostudomány, Immunotherapy, Tumour Biology, medicine.disease, PREDICTIVE-VALUE, 692/4028/67/1347, Programmed death 1, business, FREE SURVIVAL
Abstract

The advent of immune-checkpoint inhibitors (ICI) in modern oncology has significantly improved survival in several cancer settings. A subgroup of women with breast cancer (BC) has immunogenic infiltration of lymphocytes with expression of programmed death-ligand 1 (PD-L1). These patients may potentially benefit from ICI targeting the programmed death 1 (PD-1)/PD-L1 signaling axis. The use of tumor-infiltrating lymphocytes (TILs) as predictive and prognostic biomarkers has been under intense examination. Emerging data suggest that TILs are associated with response to both cytotoxic treatments and immunotherapy, particularly for patients with triple-negative BC. In this review from The International Immuno-Oncology Biomarker Working Group, we discuss (a) the biological understanding of TILs, (b) their analytical and clinical validity and efforts toward the clinical utility in BC, and (c) the current status of PD-L1 and TIL testing across different continents, including experiences from low-to-middle-income countries, incorporating also the view of a patient advocate. This information will help set the stage for future approaches to optimize the understanding and clinical utilization of TIL analysis in patients with BC. ispartof: NPJ BREAST CANCER vol:7 issue:1 ispartof: location:United States status: published

Published
2021

19. NSABP FB-7: A phase II randomized neoadjuvant trial with paclitaxel + trastuzumab and/or neratinib followed by chemotherapy and postoperative trastuzumab in HER2+ breast cancer

Author

Jacobs, S, Robidoux, A, Abraham, J, Perez-Garcia, J, La Verde, N, Orcutt, J, Cazzaniga, M, Piette, F, Antolin, S, Aguirre, E, Cortes, J, Llombart-Cussac, A, Di Cosimo, S, Kim, R, Feng, H, Lipchik, C, Lucas, P, Srinivasan, A, Wang, Y, Song, N, Gavin, P, Balousek, A, Paik, S, Allegra, C, Wolmark, N, Pogue-Geile, K, Jacobs S. A., Robidoux A., Abraham J., Perez-Garcia J. M., La Verde N., Orcutt J. M., Cazzaniga M. E., Piette F., Antolin S., Aguirre E., Cortes J., Llombart-Cussac A., Di Cosimo S., Kim R. S., Feng H., Lipchik C., Lucas P. C., Srinivasan A., Wang Y., Song N., Gavin P. G., Balousek A. D., Paik S., Allegra C. J., Wolmark N., Pogue-Geile K. L., Jacobs, S, Robidoux, A, Abraham, J, Perez-Garcia, J, La Verde, N, Orcutt, J, Cazzaniga, M, Piette, F, Antolin, S, Aguirre, E, Cortes, J, Llombart-Cussac, A, Di Cosimo, S, Kim, R, Feng, H, Lipchik, C, Lucas, P, Srinivasan, A, Wang, Y, Song, N, Gavin, P, Balousek, A, Paik, S, Allegra, C, Wolmark, N, Pogue-Geile, K, Jacobs S. A., Robidoux A., Abraham J., Perez-Garcia J. M., La Verde N., Orcutt J. M., Cazzaniga M. E., Piette F., Antolin S., Aguirre E., Cortes J., Llombart-Cussac A., Di Cosimo S., Kim R. S., Feng H., Lipchik C., Lucas P. C., Srinivasan A., Wang Y., Song N., Gavin P. G., Balousek A. D., Paik S., Allegra C. J., Wolmark N., and Pogue-Geile K. L.

Abstract

Purpose: The primary aim of NSABP FB-7 was to determine the pathologic complete response (pCR) rate in locally advanced HER2-positive (HER2+) breast cancer patients treated with neoadjuvant trastuzumab or neratinib or the combination and weekly paclitaxel followed by standard doxorubicin plus cyclophosphamide. The secondary aims include biomarker analyses. Experimental design: pCR was tested for association with treatment, gene expression, and a single nucleotide polymorphism (SNP) in the Fc fragment of the IgG receptor IIIa-158V/F (FCGR3A). Pre-treatment biopsies and residual tumors were also compared to identify molecular changes. Results: The numerical pCR rate in the trastuzumab plus neratinib arm (50% [95%CI 34-66%]) was greater than that for single-targeted therapies with trastuzumab (38% [95%CI 24-54]) or neratinib (33% [95%CI 20-50]) in the overall cohort but was not statistically significant. Hormone receptor-negative (HR-) tumors had a higher pCR rate than HR+ tumors in all three treatment arms, with the highest pCR rate in the combination arm. Diarrhea was the most frequent adverse event and occurred in virtually all patients who received neratinib-based therapy. Grade 3 diarrhea was reported in 31% of patients; there were no grade 4 events. Our 8-gene signature, previously validated for trastuzumab benefit in two different clinical trials in the adjuvant setting, was correlated with pCR across all arms of NSABP FB-7. Specifically, patients predicted to receive no trastuzumab benefit had a significantly lower pCR rate than did patients predicted to receive the most benefit (P = 0.03). FCGR genotyping showed that patients who were homozygous for the Fc low-binding phenylalanine (F) allele for FCGR3A-158V/F were less likely to achieve pCR. Conclusions: Combining trastuzumab plus neratinib with paclitaxel increased the absolute pCR rate in the overall cohort and in HR- patients. The 8-gene signature, which is validated for predicting trastuzumab benefit in t

Published
2019

23. Glecaprevir-pibrentasvir for 8 or 12 weeks in HCV genotype 1 or 3 infection

Author

Zeuzem, S, Foster, G, Wang, S, Asatryan, A, Gane, E, Feld, J, Asselah, T, Bourliere, M, Ruane, P, Wedemeyer, H, Pol, S, Flisiak, R, Poordad, F, Chuang, W, Stedman, C, Flamm, S, Kwo, P, Dore, G, Sepulveda-Arzola, G, Roberts, S, Soto-Malave, R, Kaita, K, Puoti, M, Vierling, J, Tam, E, Vargas, H, Bruck, R, Fuster, F, Paik, S, Felizarta, F, Kort, J, Fu, B, Liu, R, Ng, T, Pilot-Matias, T, Lin, C, Trinh, R, Mensa, F, Zeuzem S., Foster G. R., Wang S., Asatryan A., Gane E., Feld J. J., Asselah T., Bourliere M., Ruane P. J., Wedemeyer H., Pol S., Flisiak R., Poordad F., Chuang W. -L., Stedman C. A., Flamm S., Kwo P., Dore G. J., Sepulveda-Arzola G., Roberts S. K., Soto-Malave R., Kaita K., Puoti M., Vierling J., Tam E., Vargas H. E., Bruck R., Fuster F., Paik S. -W., Felizarta F., Kort J., Fu B., Liu R., Ng T. I., Pilot-Matias T., Lin C. -W., Trinh R., Mensa F. J., Zeuzem, S, Foster, G, Wang, S, Asatryan, A, Gane, E, Feld, J, Asselah, T, Bourliere, M, Ruane, P, Wedemeyer, H, Pol, S, Flisiak, R, Poordad, F, Chuang, W, Stedman, C, Flamm, S, Kwo, P, Dore, G, Sepulveda-Arzola, G, Roberts, S, Soto-Malave, R, Kaita, K, Puoti, M, Vierling, J, Tam, E, Vargas, H, Bruck, R, Fuster, F, Paik, S, Felizarta, F, Kort, J, Fu, B, Liu, R, Ng, T, Pilot-Matias, T, Lin, C, Trinh, R, Mensa, F, Zeuzem S., Foster G. R., Wang S., Asatryan A., Gane E., Feld J. J., Asselah T., Bourliere M., Ruane P. J., Wedemeyer H., Pol S., Flisiak R., Poordad F., Chuang W. -L., Stedman C. A., Flamm S., Kwo P., Dore G. J., Sepulveda-Arzola G., Roberts S. K., Soto-Malave R., Kaita K., Puoti M., Vierling J., Tam E., Vargas H. E., Bruck R., Fuster F., Paik S. -W., Felizarta F., Kort J., Fu B., Liu R., Ng T. I., Pilot-Matias T., Lin C. -W., Trinh R., and Mensa F. J.

Abstract

BACKGROUND Glecaprevir and pibrentasvir are direct-acting antiviral agents with pangenotypic activity and a high barrier to resistance. We evaluated the efficacy and safety of 8-week and 12-week courses of treatment with 300 mg of glecaprevir plus 120 mg of pibrentasvir in patients without cirrhosis who had hepatitis C virus (HCV) genotype 1 or 3 infection. METHODS We conducted two phase 3, randomized, open-label, multicenter trials. Patients with genotype 1 infection were randomly assigned in a 1:1 ratio to receive oncedaily glecaprevir-pibrentasvir for either 8 or 12 weeks. Patients with genotype 3 infection were randomly assigned in a 2:1 ratio to receive 12 weeks of treatment with either glecaprevir-pibrentasvir or sofosbuvir-daclatasvir. Additional patients with genotype 3 infection were subsequently enrolled and nonrandomly assigned to receive 8 weeks of treatment with glecaprevir-pibrentasvir. The primary end point was the rate of sustained virologic response 12 weeks after the end of treatment. RESULTS In total, 1208 patients were treated. The rate of sustained virologic response at 12 weeks among genotype 1-infected patients was 99.1% (95% confidence interval [CI], 98 to 100) in the 8-week group and 99.7% (95% CI, 99 to 100) in the 12-week group. Genotype 3-infected patients who were treated for 12 weeks had a rate of sustained virologic response at 12 weeks of 95% (95% CI, 93 to 98; 222 of 233 patients) with glecaprevir-pibrentasvir and 97% (95% CI, 93 to 99.9; 111 of 115) with sofosbuvir-daclatasvir; 8 weeks of treatment with glecaprevir-pibrentasvir yielded a rate of 95% (95% CI, 91 to 98; 149 of 157 patients). Adverse events led to discontinuation of treatment in no more than 1% of patients in any treatment group. CONCLUSIONS Once-daily treatment with glecaprevir-pibrentasvir for either 8 weeks or 12 weeks achieved high rates of sustained virologic response among patients with HCV genotype 1 or 3 infection who did not have cirrhosis. (Funded by AbbVie

Published
2018

24. Pitfalls in assessing stromal tumor infiltrating lymphocytes (sTILs) in breast cancer

Author

Kos, Z., Roblin, E., Kim, R. S., Michiels, S., Gallas, B. D., Chen, W., van de Vijver, K. K., Goel, S., Adams, S., Demaria, S., Viale, G., Nielsen, T. O., Badve, S. S., Symmans, W. F., Sotiriou, C., Rimm, D. L., Hewitt, S., Denkert, C., Loibl, S., Luen, S. J., Bartlett, J. M. S., Savas, P., Pruneri, G., Dillon, D. A., Cheang, M. C. U., Tutt, A., Hall, J. A., Kok, M., Horlings, H. M., Madabhushi, A., van der Laak, J., Ciompi, F., Laenkholm, A. -V., Bellolio, E., Gruosso, T., Fox, S. B., Araya, J. C., Floris, G., Hudecek, J., Voorwerk, L., Beck, A. H., Kerner, J., Larsimont, D., Declercq, S., Van den Eynden, G., Pusztai, L., Ehinger, A., Yang, W., Abduljabbar, K., Yuan, Y., Singh, R., Hiley, C., Bakir, M., Lazar, A. J., Naber, S., Wienert, S., Castillo, M., Curigliano, G., Dieci, M. -V., Andre, F., Swanton, C., Reis-Filho, J., Sparano, J., Balslev, E., Chen, I. -C., Stovgaard, E. I. S., Pogue-Geile, K., Blenman, K. R. M., Penault-Llorca, F., Schnitt, S., Lakhani, S. R., Vincent-Salomon, A., Rojo, F., Braybrooke, J. P., Hanna, M. G., Soler-Monso, M. T., Bethmann, D., Castaneda, C. A., Willard-Gallo, K., Sharma, A., Lien, H. -C., Fineberg, S., Thagaard, J., Comerma, L., Gonzalez-Ericsson, P., Brogi, E., Loi, S., Saltz, J., Klaushen, F., Cooper, L., Amgad, M., Moore, D. A., Salgado, R., Hyytiainen, A., Hida, A. I., Thompson, A., Lefevre, A., Gown, A., Lo, A., Sapino, A., Moreira, A. M., Richardson, A., Vingiani, A., Bellizzi, A. M., Guerrero, A., Grigoriadis, A., Garrido-Castro, A. C., Cimino-Mathews, A., Srinivasan, A., Acs, B., Singh, B., Calhoun, B., Haibe-Kans, B., Solomon, B., Thapa, B., Nelson, B. H., Ballesteroes-Merino, C., Criscitiello, C., Boeckx, C., Colpaert, C., Quinn, C., Chennubhotla, C. S., Solinas, C., Drubay, D., Sabanathan, D., Peeters, D., Zardavas, D., Hoflmayer, D., Johnson, D. B., Thompson, E. A., Perez, E., Elgabry, E. A., Blackley, E. F., Reisenbichler, E., Chmielik, E., Gaire, F., F. -I., Lu, Azmoudeh-Ardalan, F., Peale, F., Hirsch, F. R., Acosta-Haab, G., Farshid, G., Broeckx, G., Koeppen, H., Haynes, H. R., Mcarthur, H., Joensuu, H., Olofsson, H., Cree, I., Nederlof, I., Frahm, I., Brcic, I., Chan, J., Ziai, J., Brock, J., Weseling, J., Giltnane, J., Lemonnier, J., Zha, J., Ribeiro, J., Lennerz, J. K., Carter, J. M., Hartman, J., Hainfellner, J., Le Quesne, J., Juco, J. W., van den Berg, J., Sanchez, J., Cucherousset, J., Adam, J., Balko, J. M., Saeger, K., Siziopikou, K., Sikorska, K., Weber, K., Steele, K. E., Emancipator, K., El Bairi, K., Allison, K. H., Korski, K., Buisseret, L., Shi, L., Kooreman, L. F. S., Molinero, L., Estrada, M. V., Van Seijen, M., Lacroix-Triki, M., Sebastian, M. M., Balancin, M. L., Mathieu, M. -C., van de Vijver, M., Rebelatto, M. C., Piccart, M., Goetz, M. P., Preusser, M., Khojasteh, M., Sanders, M. E., Regan, M. M., Barnes, M., Christie, M., Misialek, M., Ignatiadis, M., de Maaker, M., Van Bockstal, M., Harbeck, N., Tung, N., Laudus, N., Sirtaine, N., Burchardi, N., Ternes, N., Radosevic-Robin, N., Gluz, O., Grimm, O., Nuciforo, P., Jank, P., Kirtani, P., Watson, P. H., Jelinic, P., Francis, P. A., Russell, P. A., Pierce, R. H., Hills, R., Leon-Ferre, R., de Wind, R., Shui, R., Leung, S., Tabbarah, S., Souza, S. C., O'Toole, S., Swain, S., Dudgeon, S., Willis, S., Ely, S., Bedri, S., Irshad, S., Liu, S., Hendry, S., Bianchi, S., Braganca, S., Paik, S., Luz, S., Gevaert, T., D'Alfons, T., John, T., Sugie, T., Kurkure, U., Bossuyt, V., Manem, V., Camaea, V. P., Tong, W., Tran, W. T., Wang, Y., Allory, Y., Husain, Z., Bago-Horvath, Z., Service de biostatistique et d'épidémiologie (SBE), Direction de la recherche clinique [Gustave Roussy], Institut Gustave Roussy (IGR)-Institut Gustave Roussy (IGR), Institut Gustave Roussy (IGR), Division of Pathology and Laboratory Medicine, Università degli Studi di Milano [Milano] (UNIMI)-European Institute of Oncology [Milan] (ESMO), Institut Jules Bordet [Bruxelles], Faculté de Médecine [Bruxelles] (ULB), Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB), Charité, Institute of Pathology, Translational Tumorpathology Unit, German Breast Group, University of the Sunshine Coast (USC), European Institute of Oncology [Milan] (ESMO), Breakthrough Breast Cancer Centre, London Institute of Cancer, Department of Pathology, The Netherlands Cancer Institute, Division of Experimental Therapy, The Netherlands Cancer Institute NKI/AvL, Odense University Hospital, Unité de génétique et biologie des cancers (U830), Université Paris Descartes - Paris 5 (UPD5)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Breast Medical Oncology [Houston], The University of Texas M.D. Anderson Cancer Center [Houston], Helsingborg Hospital, Division of Experimental Therapeutics [Milan, Italy], Département de médecine oncologique [Gustave Roussy], Cancer Research UK Lung Cancer Centre of Excellence [Londres, Royaume-Uni], University College of London [London] (UCL), Memorial Sloane Kettering Cancer Center [New York], Herlev and Gentofte Hospital, Centre Jean Perrin [Clermont-Ferrand] (UNICANCER/CJP), UNICANCER, Imagerie Moléculaire et Stratégies Théranostiques (IMoST), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Southern Queensland (USQ), Pharmacogenomics Unit [Paris], Department of Genetics [Paris], Institut Curie [Paris]-Institut Curie [Paris], Instituto de Física Teórica UAM/CSIC (IFT), Universidad Autonoma de Madrid (UAM)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Ctr Biomol Struct & Org, University of Maryland [College Park], University of Maryland System-University of Maryland System, The University of Sydney, Breast Cancer Translational Research Laboratory, Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB)-Faculté de Médecine [Bruxelles] (ULB), Innovation North - Faculty of Information and Technology, Leeds Metropolitan University, Int Immuno-Oncology Biomarker, Graduate School, CCA - Cancer biology and immunology, Pathology, Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Oncostat (U1018 (Équipe 2)), Institut Gustave Roussy (IGR)-Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Università degli Studi di Milano = University of Milan (UNIMI)-European Institute of Oncology [Milan] (ESMO), German Breast Group (GBG), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Universidad Autónoma de Madrid (UAM)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Gallas, Brandon D [0000-0001-7332-1620], van de Vijver, Koen K [0000-0002-2026-9790], Demaria, Sandra [0000-0003-4426-0499], Badve, Sunil S [0000-0001-8861-9980], Symmans, W Fraser [0000-0002-1526-184X], Rimm, David L [0000-0001-5820-4397], Savas, Peter [0000-0001-5999-428X], Hall, Jacqueline A [0000-0003-0708-1360], Horlings, Hugo M [0000-0003-4782-8828], van der Laak, Jeroen [0000-0001-7982-0754], Bellolio, Enrique [0000-0003-0079-5264], Araya, Juan Carlos [0000-0003-3501-8203], Floris, Giuseppe [0000-0003-2391-5425], Hudeček, Jan [0000-0003-1071-5686], Ehinger, Anna [0000-0001-9225-7396], Lazar, Alexander J [0000-0002-6395-4499], Castillo, Miluska [0000-0002-0111-3176], Curigliano, Giuseppe [0000-0003-1781-2518], Sparano, Joseph [0000-0002-9031-2010], Braybrooke, Jeremy P [0000-0003-1943-7360], Hanna, Matthew G [0000-0002-7536-1746], Willard-Gallo, Karen [0000-0002-1150-1295], Sharma, Ashish [0000-0002-1011-6504], Comerma, Laura [0000-0002-0249-4636], Gonzalez-Ericsson, Paula [0000-0002-6292-6963], Loi, Sherene [0000-0001-6137-9171], Cooper, Lee [0000-0002-3504-4965], Apollo - University of Cambridge Repository, Research Programs Unit, Heikki Joensuu / Principal Investigator, HUS Comprehensive Cancer Center, Department of Oncology, Medicum, Gallas, Brandon D. [0000-0001-7332-1620], van de Vijver, Koen K. [0000-0002-2026-9790], Badve, Sunil S. [0000-0001-8861-9980], Symmans, W. Fraser [0000-0002-1526-184X], Rimm, David L. [0000-0001-5820-4397], Hall, Jacqueline A. [0000-0003-0708-1360], Horlings, Hugo M. [0000-0003-4782-8828], Lazar, Alexander J. [0000-0002-6395-4499], Braybrooke, Jeremy P. [0000-0003-1943-7360], and Hanna, Matthew G. [0000-0002-7536-1746]

Subjects
Oncology, [SDV]Life Sciences [q-bio], THERAPY, Tumours of the digestive tract Radboud Institute for Health Sciences [Radboudumc 14], Prognostic markers, 0302 clinical medicine, Breast cancer, Medicine and Health Sciences, Pharmacology (medical), Lymphocytes, Stromal tumor, health care economics and organizations, 0303 health sciences, CHEMOTHERAPY, Sciences bio-médicales et agricoles, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, 3. Good health, Women's cancers Radboud Institute for Health Sciences [Radboudumc 17], PROGNOSTIC VALUE, Clinical Practice, 030220 oncology & carcinogenesis, Educational resources, Immunosurveillance, medicine.medical_specialty, 3122 Cancers, [SDV.CAN]Life Sciences [q-bio]/Cancer, IMMUNITY, lcsh:RC254-282, Article, Limfòcits, Càncer de mama, 03 medical and health sciences, Gastrointestinal cancer, SDG 3 - Good Health and Well-being, Internal medicine, 692/53/2422, medicine, Radiology, Nuclear Medicine and imaging, Càncer gastrointestinal, 030304 developmental biology, Predictive biomarker, Tumor-infiltrating lymphocytes, business.industry, Médecine pathologie humaine, medicine.disease, Cancérologie, Human medicine, business, SYSTEM, 631/67/580/1884
Abstract

Stromal tumor-infiltrating lymphocytes (sTILs) are important prognostic and predictive biomarkers in triple-negative (TNBC) and HER2-positive breast cancer. Incorporating sTILs into clinical practice necessitates reproducible assessment. Previously developed standardized scoring guidelines have been widely embraced by the clinical and research communities. We evaluated sources of variability in sTIL assessment by pathologists in three previous sTIL ring studies. We identify common challenges and evaluate impact of discrepancies on outcome estimates in early TNBC using a newly-developed prognostic tool. Discordant sTIL assessment is driven by heterogeneity in lymphocyte distribution. Additional factors include: technical slide-related issues; scoring outside the tumor boundary; tumors with minimal assessable stroma; including lymphocytes associated with other structures; and including other inflammatory cells. Small variations in sTIL assessment modestly alter risk estimation in early TNBC but have the potential to affect treatment selection if cutpoints are employed. Scoring and averaging multiple areas, as well as use of reference images, improve consistency of sTIL evaluation. Moreover, to assist in avoiding the pitfalls identified in this analysis, we developed an educational resource available at www.tilsinbreastcancer.org/pitfalls., info:eu-repo/semantics/published

Published
2020

25. Application of a risk-management framework for integration of stromal tumor-infiltrating lymphocytes in clinical trials

Author

Hudecek, J., Voorwerk, L., van Seijen, M., Nederlof, I., de Maaker, M., van den Berg, J., van de Vijver, K. K., Sikorska, K., Adams, S., Demaria, S., Viale, G., Nielsen, T. O., Badve, S. S., Michiels, S., Symmans, W. F., Sotiriou, C., Rimm, D. L., Hewitt, S. M., Denkert, C., Loibl, S., Loi, S., Bartlett, J. M. S., Pruneri, G., Dillon, D. A., Cheang, M. C. U., Tutt, A., Hall, J. A., Kos, Z., Salgado, R., Kok, M., Horlings, H. M., Hyytiainen, A., Hida, A. I., Thompson, A., Lefevre, A., Lazar, A. J., Gown, A., Lo, A., Sapino, A., Madabhushi, A., Moreira, A., Richardson, A., Vingiani, A., Beck, A. H., Bellizzi, A. M., Guerrero, A., Grigoriadis, A., Ehinger, A., Garrido-Castro, A., Vincent-Salomon, A., Laenkholm, A. -V., Sharma, A., Cimino-Mathews, A., Srinivasan, A., Acs, B., Singh, B., Calhoun, B., Haibe-Kans, B., Solomon, B., Thapa, B., Nelson, B. H., Gallas, B. D., Castaneda, C., Ballesteros-Merino, C., Criscitiello, C., Boeckx, C., Colpaert, C., Quinn, C., Chennubhotla, C. S., Swanton, C., Solinas, C., Hiley, C., Drubay, D., Bethmann, D., Moore, D. A., Larsimont, D., Sabanathan, D., Peeters, D., Zardavas, D., Hoflmayer, D., Johnson, D. B., Thompson, E. A., Brogi, E., Perez, E., Elgabry, E. A., Stovgaard, E. S., Blackley, E. F., Roblin, E., Reisenbichler, E., Bellolio, E., Balslev, E., Chmielik, E., Gaire, F., Andre, F., F. -I., Lu, Azmoudeh-Ardalan, F., Rojo, F., Gruosso, T., Ciompi, F., Peale, F., Hirsch, F. R., Klauschen, F., Penault-Llorca, F., Acosta Haab, G., Farshid, G., van den Eynden, G., Curigliano, G., Floris, G., Broeckx, G., Gonzalez-Ericsson, Koeppen, H., Haynes, H. R., Mcarthur, H., Joensuu, H., Olofsson, H., Lien, H. -C., Chen, I. -C., Cree, I., Frahm, I., Brcic, I., Chan, J., Ziai, J., Brock, J., Wesseling, J., Giltnane, J., Kerner, J. K., Thagaard, J., Braybrooke, J. P., van der Laak, J. A. W. M., Lemonnier, J., Zha, J., Ribeiro, J., Lennerz, J. K., Carter, J. M., Saltz, J., Hartman, J., Hainfellner, J., Quesne, J. L., Juco, J. W., Reis-Filho, J., Sanchez, J., Sparano, J., Cucherousset, J., Araya, J. C., Adam, J., Balko, J. M., Saeger, K., Siziopikou, K., Willard-Gallo, K., Weber, K., Pogue-Geile, K. L., Steele, K. E., Emancipator, K., Abduljabbar, K., El Bairi, K., Blenman, K. R. M., Allison, K. H., Korski, K., Pusztai, L., Comerma, L., Buisseret, L., Cooper, L. A. D., Shi, L., Kooreman, L. F. S., Molinero, L., Estrada, M. V., Lacroix-Triki, M., Al Bakir, M., Sebastian, M. M., van de Vijver, M., Balancin, M. L., Dieci, M. V., Mathieu, M. -C., Rebelatto, M. C., Piccart, M., Hanna, M. G., Goetz, M. P., Preusser, M., Khojasteh, M., Sanders, M. E., Regan, M. M., Barnes, M., Christie, M., Misialek, M., Ignatiadis, M., van Bockstal, M., Castillo, M., Amgad, M., Harbeck, N., Tung, N., Laudus, N., Sirtaine, N., Burchardi, N., Ternes, N., Radosevic-Robin, N., Gluz, O., Grimm, O., Nuciforo, P., Jank, P., Gonzalez-Ericsson, P., Kirtani, P., Jelinic, P., Watson, P. H., Savas, P., Francis, P. A., Russell, P. A., Singh, R., Kim, R. S., Pierce, R. H., Hills, R., Leon-Ferre, R., de Wind, R., Shui, R., De Clercq, S., Leung, S., Tabbarah, S., Souza, S. C., O'Toole, S., Swain, S., Dudgeon, S., Willis, S., Ely, S., Kim, S. -R., Bedri, S., Irshad, S., Liu, S. -W., Goel, S., Hendry, S., Bianchi, S., Braganca, S., Paik, S., Wienert, S., Fox, S. B., Luen, S. J., Naber, S., Schnitt, S. J., Sua, L. F., Lakhani, S. R., Fineberg, S., Soler, T., Gevaert, T., D'Alfonso, T., John, T., Sugie, T., Kurkure, U., Bossuyt, V., Manem, V., Camara, V. P., Tong, W., Chen, W., Yang, W., Tran, W. T., Wang, Y., Yuan, Y., Allory, Y., Husain, Z., Bago-Horvath, Z., Division of Pathology and Laboratory Medicine, Università degli Studi di Milano [Milano] (UNIMI)-European Institute of Oncology [Milan] (ESMO), Service de biostatistique et d'épidémiologie (SBE), Direction de la recherche clinique [Gustave Roussy], Institut Gustave Roussy (IGR)-Institut Gustave Roussy (IGR), Institut Gustave Roussy (IGR), Institut Jules Bordet [Bruxelles], Faculté de Médecine [Bruxelles] (ULB), Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB), Charité, Institute of Pathology, Translational Tumorpathology Unit, German Breast Group, Breast Cancer Translational Research Laboratory, Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB)-Faculté de Médecine [Bruxelles] (ULB), University of the Sunshine Coast (USC), European Institute of Oncology [Milan] (ESMO), Breakthrough Breast Cancer Centre, London Institute of Cancer, Department of Pathology, The Netherlands Cancer Institute, Division of Experimental Therapy, The Netherlands Cancer Institute NKI/AvL, Imagerie Moléculaire et Stratégies Théranostiques (IMoST), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Jean Perrin [Clermont-Ferrand] (UNICANCER/CJP), UNICANCER, Hudeček, Jan [0000-0003-1071-5686], van de Vijver, Koen K [0000-0002-2026-9790], Demaria, Sandra [0000-0003-4426-0499], Badve, Sunil S [0000-0001-8861-9980], Symmans, William Fraser [0000-0002-1526-184X], Rimm, David L [0000-0001-5820-4397], Loi, Sherene [0000-0001-6137-9171], Hall, Jacqueline A [0000-0003-0708-1360], Horlings, Hugo M [0000-0003-4782-8828], Apollo - University of Cambridge Repository, van de Vijver, Koen K. [0000-0002-2026-9790], Badve, Sunil S. [0000-0001-8861-9980], Rimm, David L. [0000-0001-5820-4397], Hall, Jacqueline A. [0000-0003-0708-1360], Horlings, Hugo M. [0000-0003-4782-8828], Università degli Studi di Milano = University of Milan (UNIMI)-European Institute of Oncology [Milan] (ESMO), Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Oncostat (U1018 (Équipe 2)), Institut Gustave Roussy (IGR)-Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, German Breast Group (GBG), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])

Subjects
0301 basic medicine, Oncology, medicine.medical_specialty, [SDV]Life Sciences [q-bio], medicine.medical_treatment, MEDLINE, [SDV.CAN]Life Sciences [q-bio]/Cancer, Review Article, lcsh:RC254-282, 631/67/1857, Tumour biomarkers, Tumours of the digestive tract Radboud Institute for Health Sciences [Radboudumc 14], 03 medical and health sciences, 0302 clinical medicine, Breast cancer, 692/53, Internal medicine, Medicine and Health Sciences, medicine, Pharmacology (medical), Radiology, Nuclear Medicine and imaging, 692/4028/67/580, Stromal tumor, Biomarkers, Tumour immunology, business.industry, Risk management framework, review-article, Médecine pathologie humaine, 631/67/1347, Immunotherapy, Sciences bio-médicales et agricoles, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, medicine.disease, Women's cancers Radboud Institute for Health Sciences [Radboudumc 17], 3. Good health, Review article, Clinical trial, Cancérologie, 030104 developmental biology, 030220 oncology & carcinogenesis, Biomarker (medicine), business
Abstract

Stromal tumor-infiltrating lymphocytes (sTILs) are a potential predictive biomarker for immunotherapy response in metastatic triple-negative breast cancer (TNBC). To incorporate sTILs into clinical trials and diagnostics, reliable assessment is essential. In this review, we propose a new concept, namely the implementation of a risk-management framework that enables the use of sTILs as a stratification factor in clinical trials. We present the design of a biomarker risk-mitigation workflow that can be applied to any biomarker incorporation in clinical trials. We demonstrate the implementation of this concept using sTILs as an integral biomarker in a single-center phase II immunotherapy trial for metastatic TNBC (TONIC trial, NCT02499367), using this workflow to mitigate risks of suboptimal inclusion of sTILs in this specific trial. In this review, we demonstrate that a web-based scoring platform can mitigate potential risk factors when including sTILs in clinical trials, and we argue that this framework can be applied for any future biomarker-driven clinical trial setting., info:eu-repo/semantics/published

Published
2020

26. NSABP FB-7: a phase II randomized neoadjuvant trial with paclitaxel + trastuzumab and/or neratinib followed by chemotherapy and postoperative trastuzumab in HER2+ breast cancer (vol 21, 133, 2019)

Author

Jacobs, S, Robidoux, A, Abraham, J, Perez-Garcia, J, La Verde, N, Orcutt, J, Cazzaniga, M, Piette, F, Antolin, S, Aguirre, E, Cortes, J, Llombart-Cussac, A, Di Cosimo, S, Kim, R, Feng, H, Lipchik, C, Lucas, P, Srinivasan, A, Wang, Y, Song, N, Gavin, P, Balousek, A, Paik, S, Allegra, C, Wolmark, N, and Pogue-Geile, K

Published
2020

27. Determining the Anthropogenic Greenhouse Gas Contribution to the Observed Intensification of Extreme Precipitation

Author

Paik, S, Min, S-K, Zhang, X, Donat, MG, King, AD, Sun, Q, Paik, S, Min, S-K, Zhang, X, Donat, MG, King, AD, and Sun, Q

Abstract

This study conducts a detection and attribution analysis of the observed changes in extreme precipitation during 1951–2015. Observed and CMIP6 multimodel simulated changes in annual maximum daily and consecutive 5-day precipitation are compared using an optimal fingerprinting technique for different spatial scales from global land, Northern Hemisphere extratropics, tropics, three continental regions (North America and western and eastern Eurasia), and global “dry” and “wet” land areas (as defined by their average extreme precipitation intensities). Results indicate that anthropogenic greenhouse gas influence is robustly detected in the observed intensification of extreme precipitation over the global land and most of the subregions considered, all with clear separation from natural and anthropogenic aerosol forcings. Also, the human-induced greenhouse gas increases are found to be a dominant contributor to the observed increase in extreme precipitation intensity, which largely follows the increased moisture availability under global warming.

Published
2020

28. Correction to: NSABP FB-7: a phase II randomized neoadjuvant trial with paclitaxel + trastuzumab and/or neratinib followed by chemotherapy and postoperative trastuzumab in HER2+ breast cancer

Author

Jacobs, S, Robidoux, A, Abraham, J, Pérez-Garcia, J, La Verde, N, Orcutt, J, Cazzaniga, M, Piette, F, Antolín, S, Aguirre, E, Cortes, J, Llombart-Cussac, A, Di Cosimo, S, Kim, R, Feng, H, Lipchik, C, Lucas, P, Srinivasan, A, Wang, Y, Song, N, Gavin, P, Balousek, A, Paik, S, Allegra, C, Wolmark, N, Pogue-Geile, K, Jacobs, Samuel A, Robidoux, André, Abraham, Jame, Pérez-Garcia, José Manuel, La Verde, Nicla, Orcutt, James M, Cazzaniga, Marina E, Piette, Fanny, Antolín, Silvia, Aguirre, Elena, Cortes, Javier, Llombart-Cussac, Antonio, Di Cosimo, Serena, Kim, Rim S, Feng, Huichen, Lipchik, Corey, Lucas, Peter C, Srinivasan, Ashok, Wang, Ying, Song, Nan, Gavin, Patrick G, Balousek, April D, Paik, Soonmyung, Allegra, Carmen J, Wolmark, Norman, Pogue-Geile, Katherine L, Jacobs, S, Robidoux, A, Abraham, J, Pérez-Garcia, J, La Verde, N, Orcutt, J, Cazzaniga, M, Piette, F, Antolín, S, Aguirre, E, Cortes, J, Llombart-Cussac, A, Di Cosimo, S, Kim, R, Feng, H, Lipchik, C, Lucas, P, Srinivasan, A, Wang, Y, Song, N, Gavin, P, Balousek, A, Paik, S, Allegra, C, Wolmark, N, Pogue-Geile, K, Jacobs, Samuel A, Robidoux, André, Abraham, Jame, Pérez-Garcia, José Manuel, La Verde, Nicla, Orcutt, James M, Cazzaniga, Marina E, Piette, Fanny, Antolín, Silvia, Aguirre, Elena, Cortes, Javier, Llombart-Cussac, Antonio, Di Cosimo, Serena, Kim, Rim S, Feng, Huichen, Lipchik, Corey, Lucas, Peter C, Srinivasan, Ashok, Wang, Ying, Song, Nan, Gavin, Patrick G, Balousek, April D, Paik, Soonmyung, Allegra, Carmen J, Wolmark, Norman, and Pogue-Geile, Katherine L

Abstract

After the publication [1] the authors report corrections for Table 3, for the headers of columns 5 and 7, which should read as follows: Column 5 Header: P-value for pCR, T vs Other Arms in HR+, and Column 7 Header: P-value for pCR, T vs Other Arms in HR-. The correct version of the table can be found below. (Table presented).

Published
2020

29. Correction: NSABP FB-7: A phase II randomized neoadjuvant trial with paclitaxel + trastuzumab and/or neratinib followed by chemotherapy and postoperative trastuzumab in HER2+ breast cancer (Breast Cancer Research (2019) 21 (133) DOI: 10.1186/s13058-019-1196-y)

Author

Jacobs, Samuel A, Jacobs, S, Robidoux, A, Abraham, J, Pérez-Garcia, J, La Verde, N, Orcutt, J, Cazzaniga, M, Piette, F, Antolín, S, Aguirre, E, Cortes, J, Llombart-Cussac, A, Di Cosimo, S, Kim, R, Feng, H, Lipchik, C, Lucas, P, Srinivasan, A, Wang, Y, Song, N, Gavin, P, Balousek, A, Paik, S, Allegra, C, Wolmark, N, Pogue-Geile, K, Jacobs, Samuel A, Robidoux, André, Abraham, Jame, Pérez-Garcia, José Manuel, La Verde, Nicla, Orcutt, James M, Cazzaniga, Marina E, Piette, Fanny, Antolín, Silvia, Aguirre, Elena, Cortes, Javier, Llombart-Cussac, Antonio, Di Cosimo, Serena, Kim, Rim S, Feng, Huichen, Lipchik, Corey, Lucas, Peter C, Srinivasan, Ashok, Wang, Ying, Song, Nan, Gavin, Patrick G, Balousek, April D, Paik, Soonmyung, Allegra, Carmen J, Wolmark, Norman, Pogue-Geile, Katherine L, Jacobs, Samuel A, Jacobs, S, Robidoux, A, Abraham, J, Pérez-Garcia, J, La Verde, N, Orcutt, J, Cazzaniga, M, Piette, F, Antolín, S, Aguirre, E, Cortes, J, Llombart-Cussac, A, Di Cosimo, S, Kim, R, Feng, H, Lipchik, C, Lucas, P, Srinivasan, A, Wang, Y, Song, N, Gavin, P, Balousek, A, Paik, S, Allegra, C, Wolmark, N, Pogue-Geile, K, Jacobs, Samuel A, Robidoux, André, Abraham, Jame, Pérez-Garcia, José Manuel, La Verde, Nicla, Orcutt, James M, Cazzaniga, Marina E, Piette, Fanny, Antolín, Silvia, Aguirre, Elena, Cortes, Javier, Llombart-Cussac, Antonio, Di Cosimo, Serena, Kim, Rim S, Feng, Huichen, Lipchik, Corey, Lucas, Peter C, Srinivasan, Ashok, Wang, Ying, Song, Nan, Gavin, Patrick G, Balousek, April D, Paik, Soonmyung, Allegra, Carmen J, Wolmark, Norman, and Pogue-Geile, Katherine L

Abstract

After the publication [1] the authors report corrections for Table 3, for the headers of columns 5 and 7, which should read as follows: Column 5 Header: P-value for pCR, T vs Other Arms in HR+, and Column 7 Header: P-value for pCR, T vs Other Arms in HR-. The correct version of the table can be found below. (Table presented).

Published
2020

48. NSABP FB-7: a phase II randomized neoadjuvant trial with paclitaxel plus trastuzumab and/or neratinib followed by chemotherapy and postoperative trastuzumab in HER2(+) breast cancer

Author

Jacobs, S, Robidoux, A, Abraham, J, Perez-Garcia, J, La Verde, N, Orcutt, J, Cazzaniga, M, Piette, F, Antolin, S, Aguirre, E, Cortes, J, Llombart-Cussac, A, Di Cosimo, S, Kim, R, Feng, H, Lipchik, C, Lucas, P, Srinivasan, A, Wang, Y, Song, N, Gavin, P, Balousek, A, Paik, S, Allegra, C, Wolmark, N, and Pogue-Geile, K

Subjects
Breast cancer, Neratinib, Neoadjuvant, skin and connective tissue diseases
Abstract

Purpose: The primary aim of NSABP FB-7 was to determine the pathologic complete response (pCR) rate in locally advanced HER2-positive (HER2(+)) breast cancer patients treated with neoadjuvant trastuzumab or neratinib or the combination and weekly paclitaxel followed by standard doxorubicin plus cyclophosphamide. The secondary aims include biomarker analyses. Experimental design: pCR was tested for association with treatment, gene expression, and a single nucleotide polymorphism (SNP) in the Fc fragment of the IgG receptor IIIa-158V/F (FCGR3A). Pre-treatment biopsies and residual tumors were also compared to identify molecular changes. Results: The numerical pCR rate in the trastuzumab plus neratinib arm (50% [95%CI 34-66%]) was greater than that for single-targeted therapies with trastuzumab (38% [95%CI 24-54]) or neratinib (33% [95%CI 20-50]) in the overall cohort but was not statistically significant. Hormone receptor-negative (HR-) tumors had a higher pCR rate than HR+ tumors in all three treatment arms, with the highest pCR rate in the combination arm. Diarrhea was the most frequent adverse event and occurred in virtually all patients who received neratinib-based therapy. Grade 3 diarrhea was reported in 31% of patients; there were no grade 4 events. Our 8-gene signature, previously validated for trastuzumab benefit in two different clinical trials in the adjuvant setting, was correlated with pCR across all arms of NSABP FB-7. Specifically, patients predicted to receive no trastuzumab benefit had a significantly lower pCR rate than did patients predicted to receive the most benefit (P = 0.03). FCGR genotyping showed that patients who were homozygous for the Fc low-binding phenylalanine (F) allele for FCGR3A-158V/F were less likely to achieve pCR. Conclusions: Combining trastuzumab plus neratinib with paclitaxel increased the absolute pCR rate in the overall cohort and in HR- patients. The 8-gene signature, which is validated for predicting trastuzumab benefit in the adjuvant setting, was associated with pCR in the neoadjuvant setting, but remains to be validated as a predictive marker in a larger neoadjuvant clinical trial. HR status, and the FCGR3A-158V/F genotype, also warrant further investigation to identify HER2(+) patients who may benefit from additional anti-HER2 therapies beyond trastuzumab. All of these markers will require further validation in the neoadjuvant setting.

Published
2019

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