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1. Forimtamig, a novel GPRC5D-targeting T-cell bispecific antibody with a 2+1 format, for the treatment of multiple myeloma

Author

Eckmann, Jan, Fauti, Tanja, Biehl, Marlene, Zabaleta, Aintzane, Blanco, Laura, Lelios, Iva, Gottwald, Stefan, Rae, Richard, Lechner, Stefanie, Bayer, Christa, Dekempe, Quincy, Osl, Franz, Carrié, Nadege, Kassem, Sahar, Lorenz, Stefan, Christopeit, Tony, Carpy, Alejandro, Bujotzek, Alexander, Bröske, Ann-Marie, Dekhtiarenko, Iryna, Attig, Jan, Kunz, Leo, Cremasco, Floriana, Adelfio, Roberto, Fertig, Georg, Dengl, Stefan, Gassner, Christian, Bormann, Felix, Kirstenpfad, Claudia, Kraft, Thomas, Diggelmann, Sarah, Knobloch, Melanie, Hage, Carina, Feddersen, Romi, Heidkamp, Gordon, Pöschinger, Thomas, Mayoux, Maud, Bernasconi, Luise, Prosper, Felipe, Dumontet, Charles, Martinet, Ludovic, Leclair, Stéphane, Xu, Wei, Paiva, Bruno, Klein, Christian, and Umaña, Pablo

Published
2025
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2. Supersymmetry on the lattice: Geometry, Topology, and Flat Bands

Author

Roychowdhury, Krishanu, Attig, Jan, Trebst, Simon, and Lawler, Michael J.

Subjects
Condensed Matter - Strongly Correlated Electrons, Condensed Matter - Other Condensed Matter
Abstract

In quantum mechanics, supersymmetry (SUSY) posits an equivalence between two elementary degrees of freedom, bosons, and fermions defined by local rules. Here we apply it to find connections between bosonic and fermionic lattice models in the realm of condensed matter physics and uncover a novel 5-fold way topology it demands in these systems. At the single-particle level, our connections pair a bosonic and fermionic lattice model, either describing the hopping of number-conserving particles or local couplings between fermion parity-conserving particles. The pair are isospectral except for zero modes, such as flat bands, quadratic band touchings, and nexus points, whose existence is undergirded by the Witten index of the SUSY theory. We develop a unifying framework to formulate these SUSY connections in terms of general lattice graph correspondences. Notably, in this framework, the supercharge operator that generates SUSY is Hermitian and can itself be interpreted as a hopping Hamiltonian on a bipartite lattice, a feature that enables the discovery of materials or model lattices hosting the SUSY partners. To illustrate the power of SUSY, we present 16 use cases of SUSY, that span topics including frustrated magnets, Kitaev spin liquids, and topological superconductors, the majority of which turn out to provide insights into the discovery and design of flat bands and topological materials., Comment: 39 pages, 30 figures

Published
2022
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3. Universal principles of moir\'e band structures

Author

Attig, Jan, Park, Jinhong, Scherer, Michael M., Trebst, Simon, Altland, Alexander, and Rosch, Achim

Subjects
Condensed Matter - Mesoscale and Nanoscale Physics
Abstract

Moir\'e materials provide a highly tunable environment for the realization of band structures with engineered physical properties. Specifically, moir\'e structures with Fermi surface flat bands - a synthetic environment for the realization of correlated phases - have moir\'e unit cells containing thousands of atoms and tantalizingly complex bands structures. In this paper we show that statistical principles go a long way in explaining universal physical properties of these systems. Our approach builds on three conceptual elements: the presence of quantum chaos caused by the effective irregularity of the atomic configurations on short length scales, Anderson localization in momentum space, and the presence of approximate crystalline symmetries. Which of these principles dominates depends on material parameters such as the extension of the Fermi surface or the strength of the moir\'e lattice potential. The phenomenological consequences of this competition are predictions for the characteristic group velocity of moir\'e bands, a primary indicator for their average flatness. In addition to these generic features, we identify structures outside the statistical context, notably almost flat bands close to the extrema of the unperturbed spectra, and the celebrated zero energy `magic angle' flat bands, where the latter require exceptionally fine tuned material parameters., Comment: 15 pages, 10 figures

Published
2021
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4. Antibodies against endogenous retroviruses promote lung cancer immunotherapy

Author

Ng, Kevin W., Boumelha, Jesse, Enfield, Katey S. S., Almagro, Jorge, Cha, Hongui, Pich, Oriol, Karasaki, Takahiro, Moore, David A., Salgado, Roberto, Sivakumar, Monica, Young, George, Molina-Arcas, Miriam, de Carné Trécesson, Sophie, Anastasiou, Panayiotis, Fendler, Annika, Au, Lewis, Shepherd, Scott T. C., Martínez-Ruiz, Carlos, Puttick, Clare, Black, James R. M., Watkins, Thomas B. K., Kim, Hyemin, Shim, Seohee, Faulkner, Nikhil, Attig, Jan, Veeriah, Selvaraju, Magno, Neil, Ward, Sophia, Frankell, Alexander M., Al Bakir, Maise, Lim, Emilia L., Hill, Mark S., Wilson, Gareth A., Cook, Daniel E., Birkbak, Nicolai J., Behrens, Axel, Yousaf, Nadia, Popat, Sanjay, Hackshaw, Allan, Hiley, Crispin T., Litchfield, Kevin, McGranahan, Nicholas, Jamal-Hanjani, Mariam, Larkin, James, Lee, Se-Hoon, Turajlic, Samra, Swanton, Charles, Downward, Julian, and Kassiotis, George

Published
2023
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5. Topological Mechanics from Supersymmetry

Author

Attig, Jan, Roychowdhury, Krishanu, Lawler, Michael J., and Trebst, Simon

Subjects
Condensed Matter - Strongly Correlated Electrons, Condensed Matter - Mesoscale and Nanoscale Physics, Condensed Matter - Statistical Mechanics
Abstract

In topological mechanics, the identification of a mechanical system's rigidity matrix with an electronic tight-binding model allows to infer topological properties of the mechanical system, such as the occurrence of `floppy' boundary modes, from the associated electronic band structure. Here we introduce an approach to systematically construct topological mechanical systems by an exact supersymmetry (SUSY) that relates the bosonic (mechanical) and fermionic (e.g. electronic) degrees of freedom. As examples we discuss mechanical analogues of the Kitaev honeycomb model and of a second-order topological insulator with floppy corner modes. Our SUSY construction naturally defines hitherto unexplored topological invariants for bosonic (mechanical) systems, such as bosonic Wilson loop operators that are formulated in terms of a SUSY-related fermionic Berry curvature., Comment: 8 pages, 6 figures

Published
2018
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6. Two-stage multipolar ordering in Pr(TM)$_2$Al$_{20}$ Kondo materials

Author

Freyer, Frederic, Attig, Jan, Lee, SungBin, Paramekanti, Arun, Trebst, Simon, and Kim, Yong Baek

Subjects
Condensed Matter - Strongly Correlated Electrons
Abstract

Among heavy fermion materials, there is a set of rare-earth intermetallics with non-Kramers Pr$^{3+}$ $4f^2$ moments which exhibit a rich phase diagram with intertwined quadrupolar orders, superconductivity, and non-Fermi liquid behavior. However, more subtle broken symmetries such as multipolar orders in these Kondo materials remain poorly studied. Here, we argue that multi-spin interactions between local moments beyond the conventional two-spin exchange must play an important role in Kondo materials near the ordered to heavy Fermi liquid transition. We show that this drives a plethora of phases with coexisting multipolar orders and multiple thermal phase transitions, providing a natural framework for interpreting experiments on the Pr(TM)$_2$Al$_{20}$ class of compounds., Comment: 8 pages, 8 figures

Published
2017
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7. Classical Spin Spirals in Frustrated Magnets from Free-Fermion Band Topology

Author

Attig, Jan and Trebst, Simon

Subjects
Condensed Matter - Strongly Correlated Electrons, Condensed Matter - Statistical Mechanics
Abstract

The formation of coplanar spin spirals is a common motif in the magnetic ordering of many frustrated magnets. For classical antiferromagnets, geometric frustration can lead to a massively degenerate ground state manifold of spirals whose propagation vectors can be described, depending on the lattice geometry, by points (triangular), lines (fcc), surfaces (frustrated diamond) or completely flat bands (pyrochlore). Here we demonstrate an exact mathematical correspondence of these spiral manifolds of classical antiferromagnets with the Fermi surfaces of free-fermion band structures. We provide an explicit lattice construction relating the frustrated spin model to a corresponding free-fermion tight-binding model. Examples of this correspondence relate the 120$^\circ$ order of the triangular lattice antiferromagnet to the Dirac nodal structure of the honeycomb tight-binding model or the spiral line manifold of the fcc antiferromagnet to the Dirac nodal line of the diamond tight-binding model. We discuss implications of topological band structures in the fermionic system to the corresponding classical spin system., Comment: 16 pages, 20 figures

Published
2017
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8. Determinants of anti-PD-1 response and resistance in clear cell renal cell carcinoma

Author

Abbosh, Chris, Shiu, Kai-Keen, Bridgewater, John, Hochhauser, Daniel, Forster, Martin, Lee, Siow-Ming, Ahmad, Tanya, Papadatos-Pastos, Dionysis, Janes, Sam, Van Loo, Peter, Enfield, Katey, McGranahan, Nicholas, Huebner, Ariana, Beck, Stephan, Parker, Peter, Walczak, Henning, Enver, Tariq, Hynds, Rob, Sinclair, Ron, Lok, Chi-wah, Rhodes, Zoe, Moore, David, Khiroya, Reena, Trevisan, Giorgia, Ellery, Peter, Linch, Mark, Brandner, Sebastian, Hiley, Crispin, Veeriah, Selvaraju, Razaq, Maryam, Shaw, Heather, Attard, Gert, Akther, Mita Afroza, Naceur-Lombardelli, Cristina, Manzano, Lizi, Al-Bakir, Maise, Summan, Simranpreet, Kanu, Nnenna, Ward, Sophie, Asghar, Uzma, Lim, Emilia, Gishen, Faye, Tookman, Adrian, Stone, Paddy, Stirling, Caroline, Hunter, Nikki, Vaughan, Sarah, Mangwende, Mary, Spain, Lavinia, Yan, Haixi, Shum, Ben, Carlyle, Eleanor, Yousaf, Nadia, Popat, Sanjay, Curtis, Olivia, Stamp, Gordon, Toncheva, Antonia, Nye, Emma, Murra, Aida, Korteweg, Justine, Josephs, Debra, Chandra, Ashish, Spicer, James, Stewart, Ruby, Iredale, Lara-Rose, Mackay, Tina, Deakin, Ben, Enting, Debra, Rudman, Sarah, Ghosh, Sharmistha, Karapagniotou, Lena, Pintus, Elias, Tutt, Andrew, Howlett, Sarah, Michalarea, Vasiliki, Brenton, James, Caldas, Carlos, Fitzgerald, Rebecca, Jimenez-Linan, Merche, Provenzano, Elena, Cluroe, Alison, Stewart, Grant, Watts, Colin, Gilbertson, Richard, McDermott, Ultan, Tavare, Simon, Beddowes, Emma, Roxburgh, Patricia, Biankin, Andrew, Chalmers, Anthony, Fraser, Sioban, Oien, Karin, Kidd, Andrew, Blyth, Kevin, Krebs, Matt, Blackhall, Fiona, Summers, Yvonne, Dive, Caroline, Marais, Richard, Gomes, Fabio, Carter, Mat, Dransfield, Jo, Le Quesne, John, Fennell, Dean, Shaw, Jacqui, Naidu, Babu, Baijal, Shobhit, Tanchel, Bruce, Langman, Gerald, Robinson, Andrew, Collard, Martin, Cockcroft, Peter, Ferris, Charlotte, Bancroft, Hollie, Kerr, Amy, Middleton, Gary, Webb, Joanne, Kadiri, Salma, Colloby, Peter, Olisemeke, Bernard, Wilson, Rodelaine, Tomlinson, Ian, Jogai, Sanjay, Ottensmeier, Christian, Harrison, David, Loda, Massimo, Flanagan, Adrienne, McKenzie, Mairead, Hackshaw, Allan, Ledermann, Jonathan, Chan, Kitty, Sharp, Abby, Farrelly, Laura, Bridger, Hayley, Challacombe, Ben, Chowdhury, Simon, Drake, William, Fernando, Archana, Harrison-Phipps, Karen, Hazell, Steve, Hill, Peter, Horsfield, Catherine, O'Brien, Tim, Olsburgh, Jonathon, Polson, Alexander, Varia, Mary, Verma, Hema, Au, Lewis, Hatipoglu, Emine, Robert de Massy, Marc, Litchfield, Kevin, Beattie, Gordon, Rowan, Andrew, Schnidrig, Desiree, Thompson, Rachael, Byrne, Fiona, Horswell, Stuart, Fotiadis, Nicos, Nicol, David, Shepherd, Scott T.C., Fendler, Annika, Mason, Robert, Del Rosario, Lyra, Edmonds, Kim, Lingard, Karla, Sarker, Sarah, Attig, Jan, Joshi, Kroopa, Uddin, Imran, Becker, Pablo D., Sunderland, Mariana Werner, Akarca, Ayse, Puccio, Ignazio, Yang, William W., Lund, Tom, Dhillon, Kim, Vasquez, Marcos Duran, Ghorani, Ehsan, Xu, Hang, Spencer, Charlotte, López, José I., Green, Anna, Mahadeva, Ula, Borg, Elaine, Mitchison, Miriam, Moore, David A., Proctor, Ian, Falzon, Mary, Pickering, Lisa, Furness, Andrew J.S., Reading, James L., Salgado, Roberto, Marafioti, Teresa, Jamal-Hanjani, Mariam, Kassiotis, George, Chain, Benny, Larkin, James, Swanton, Charles, Quezada, Sergio A., and Turajlic, Samra

Published
2021
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9. Endogenous retroviruses promote homeostatic and inflammatory responses to the microbiota

Author

Lima-Junior, Djalma S., Krishnamurthy, Siddharth R., Bouladoux, Nicolas, Collins, Nicholas, Han, Seong-Ji, Chen, Erin Y., Constantinides, Michael G., Link, Verena M., Lim, Ai Ing, Enamorado, Michel, Cataisson, Christophe, Gil, Louis, Rao, Indira, Farley, Taylor K., Koroleva, Galina, Attig, Jan, Yuspa, Stuart H., Fischbach, Michael A., Kassiotis, George, and Belkaid, Yasmine

Published
2021
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16. Cap-binding protein 4EHP effects translation silencing by microRNAs

Author

Chapat, Clément, Jafarnejad, Seyed Mehdi, Matta-Camacho, Edna, Hesketh, Geoffrey G., Gelbart, Idit A., Attig, Jan, Gkogkas, Christos G., Alain, Tommy, Stern-Ginossar, Noam, Fabian, Marc R., Gingras, Anne-Claude, Duchaine, Thomas F., and Sonenberg, Nahum

Published
2017

17. P-006 SBCMA has utility for early response monitoring in the blood and is correlated with forimtamig pharmacodynamic activity, clinical response and MRD

Author

Dekhtiarenko, Iryna, primary, Attig, Jan, additional, Helms, Hans-Joachin, additional, Lelios, Iva, additional, Clausen, Inga, additional, Jacob, Wolfgang, additional, Schneider, Meike, additional, Weisser, Martin, additional, Carlo-Stella, Carmelo, additional, Manier, Salomon, additional, Harrison, Simon, additional, Popat, Rakesh, additional, Riley, Caroline Hasselbalch, additional, and Bröske, Ann-Marie, additional

Published
2023
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18. Tumor beta2-microglobulin and HLA-A expression is increased by immunotherapy and can predict response to CIT in association with other biomarkers.

Author

Reis, Bernhard, Attig, Jan, Dziadek, Sebastian, Graefe, Nico, Heller, Astrid, Rieder, Natascha, and Gomes, Bruno

Subjects
IMMUNOTHERAPY, BIOMARKERS, ANTIGEN presentation
Abstract

Background: Downregulation of MHC class I expression and/or defects in the antigen presentation pathways are commonly reported in human cancers. Numerous studies previously have explored extensively the molecular mechanisms that underlie HLA-class I and Beta2-Microglobulin (B2M) downregulation. However, the techniques presently available to detect expression of MHC class I proteins lack the robustness, specificity and sensitivity needed for systematic integration and analysis in clinical trials. Furthermore, the dynamics of HLA-class I and B2M expression have not been comprehensively studied as a potential biomarker for immunotherapy. Methods: Using novel, validated, immunohistochemistry (IHC)-based methods for quantifying B2M and HLA-A in tumor samples from diverse cancer types, we have determined loss of B2M and HLA-A proteins in 336 archived, primary specimens and 329 biopsies from metastatic patients collected during Roche-sponsored Phase 1 clinical trials investigating novel immunotherapy candidates as monotherapy or in combination with CPI. Results: Up to 56% of cases with B2M or HLA-A loss were noted in the investigated tumor types. The frequency of loss was dependent on indication and stage of disease and revealed heterogeneous expression patterns across patients. B2M and HLA-A loss was increased in metastatic lesions compared to primary tumors, indicating selection of MHC class I low clones in metastatic and refractory tumor cells. High on-treatment B2M expression correlated with successful clinical outcome (RECIST), while high baseline B2M did not. A treatment-induced increase of B2M expression was noted in most of the patients with low B2M levels at baseline. The triple biomarker combination of B2M, CD8 and PDL1 strongly improved response prediction to cancer immunotherapy. Conclusion: Our results indicate that B2M and HLA-A loss occurs frequently in tumors and is reversed in most instances following immunotherapy which supports the conclusion that MHC class I loss is not the dominant resistance mechanism to CPI treatment. This investigation reveals a highly dynamic expression of HLA-A and B2M in tumors affected by indication, metastatic status, immunophenotype and immunotherapy treatment. Baseline expression levels of B2M on tumors may be of utility as a constituent of a biomarker panel used for selecting patients for immunotherapy clinical trials. [ABSTRACT FROM AUTHOR]

Published
2024
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19. Human endogenous retrovirus onco-exaptation counters cancer cell senescence through calbindin

Author

Attig, Jan, primary, Pape, Judith, additional, Doglio, Laura, additional, Kazachenka, Anastasiya, additional, Ottina, Eleonora, additional, Young, George R., additional, Enfield, Katey S.S., additional, Aramburu, Iker Valle, additional, Ng, Kevin W., additional, Faulkner, Nikhil, additional, Bolland, William, additional, Papayannopoulos, Venizelos, additional, Swanton, Charles, additional, and Kassiotis, George, additional

Published
2023
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22. Antibodies against endogenous retroviruses promote lung cancer immunotherapy

Author

Ng, Kevin W, Boumelha, Jesse, Enfield, Katey S S; https://orcid.org/0000-0002-4551-6073, Almagro, Jorge; https://orcid.org/0000-0002-0652-6447, Cha, Hongui, Pich, Oriol; https://orcid.org/0000-0002-1956-1882, Karasaki, Takahiro; https://orcid.org/0000-0001-6863-2360, Moore, David A, Salgado, Roberto; https://orcid.org/0000-0002-1110-3801, Sivakumar, Monica, Young, George; https://orcid.org/0000-0002-1203-588X, Molina-Arcas, Miriam; https://orcid.org/0000-0002-8176-8948, de Carné Trécesson, Sophie, Anastasiou, Panayiotis, Fendler, Annika, Au, Lewis, Shepherd, Scott T C, Martínez-Ruiz, Carlos, Puttick, Clare, Black, James R M, Watkins, Thomas B K, Kim, Hyemin, Shim, Seohee, Faulkner, Nikhil, Attig, Jan; https://orcid.org/0000-0002-2159-2880, Veeriah, Selvaraju, Magno, Neil, Ward, Sophia; https://orcid.org/0000-0002-6777-5279, Frankell, Alexander M; https://orcid.org/0000-0002-0341-7878, Al Bakir, Maise; https://orcid.org/0000-0002-0846-8332, et al, Boos, Laura Amanda, Ng, Kevin W, Boumelha, Jesse, Enfield, Katey S S; https://orcid.org/0000-0002-4551-6073, Almagro, Jorge; https://orcid.org/0000-0002-0652-6447, Cha, Hongui, Pich, Oriol; https://orcid.org/0000-0002-1956-1882, Karasaki, Takahiro; https://orcid.org/0000-0001-6863-2360, Moore, David A, Salgado, Roberto; https://orcid.org/0000-0002-1110-3801, Sivakumar, Monica, Young, George; https://orcid.org/0000-0002-1203-588X, Molina-Arcas, Miriam; https://orcid.org/0000-0002-8176-8948, de Carné Trécesson, Sophie, Anastasiou, Panayiotis, Fendler, Annika, Au, Lewis, Shepherd, Scott T C, Martínez-Ruiz, Carlos, Puttick, Clare, Black, James R M, Watkins, Thomas B K, Kim, Hyemin, Shim, Seohee, Faulkner, Nikhil, Attig, Jan; https://orcid.org/0000-0002-2159-2880, Veeriah, Selvaraju, Magno, Neil, Ward, Sophia; https://orcid.org/0000-0002-6777-5279, Frankell, Alexander M; https://orcid.org/0000-0002-0341-7878, Al Bakir, Maise; https://orcid.org/0000-0002-0846-8332, et al, and Boos, Laura Amanda

Abstract

B cells are frequently found in the margins of solid tumours as organized follicles in ectopic lymphoid organs called tertiary lymphoid structures (TLS)$^{1,2}$. Although TLS have been found to correlate with improved patient survival and response to immune checkpoint blockade (ICB), the underlying mechanisms of this association remain elusive$^{1,2}$. Here we investigate lung-resident B cell responses in patients from the TRACERx 421 (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy) and other lung cancer cohorts, and in a recently established immunogenic mouse model for lung adenocarcinoma$^{3}$. We find that both human and mouse lung adenocarcinomas elicit local germinal centre responses and tumour-binding antibodies, and further identify endogenous retrovirus (ERV) envelope glycoproteins as a dominant anti-tumour antibody target. ERV-targeting B cell responses are amplified by ICB in both humans and mice, and by targeted inhibition of KRAS(G12C) in the mouse model. ERV-reactive antibodies exert anti-tumour activity that extends survival in the mouse model, and ERV expression predicts the outcome of ICB in human lung adenocarcinoma. Finally, we find that effective immunotherapy in the mouse model requires CXCL13-dependent TLS formation. Conversely, therapeutic CXCL13 treatment potentiates anti-tumour immunity and synergizes with ICB. Our findings provide a possible mechanistic basis for the association of TLS with immunotherapy response.

Published
2023

26. Intravenous and Subcutaneous Administration of RG6234, a Novel GPRC5DxCD3 T-Cell Engaging Bispecific Antibody, Is Highly Active in Patients with Relapsed/Refractory Multiple Myeloma (RRMM): Biomarker Results from a Phase I Study

Author

Dekhtiarenko, Iryna, primary, Lelios, Iva, additional, Attig, Jan, additional, Sleiman, Nassim, additional, Lazzaro, Domenico, additional, Schindler, Emilie, additional, Eckmann, Jan, additional, Umana, Pablo, additional, Jacob, Wolfgang, additional, Schneider, Meike, additional, Carlo-Stella, Carmelo, additional, Mazza, Rita, additional, Manier, Salomon, additional, Facon, Thierry, additional, Yoon, Sung-Soo, additional, Koh, Youngil, additional, Harrison, Simon J, additional, Er, Jeremy, additional, Pinto, Antonio, additional, Volzone, Francesco, additional, Perrone, Giulia, additional, Corradini, Paolo, additional, Cazaubiel, Titouan, additional, Hulin, Cyrille, additional, Touzeau, Cyrille, additional, Moreau, Philippe, additional, Ocio, Enrique M., additional, Montes Gaisan, Carmen Maria, additional, Popat, Rakesh, additional, Leong, Sarah, additional, Offner, Fritz, additional, Rodriguez Otero, Paula, additional, Alfonso-Pierola, Ana, additional, Hutchings, Martin, additional, Riley, Caroline Hasselbalch, additional, and Bröske, Ann-Marie E, additional

Published
2022
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27. Supersymmetry on the lattice: Geometry, Topology, and Spin Liquids

Author

Roychowdhury, Krishanu, Attig, Jan, Trebst, Simon, and Lawler, Michael J.

Subjects
Condensed Matter - Other Condensed Matter, Condensed Matter - Strongly Correlated Electrons, Strongly Correlated Electrons (cond-mat.str-el), FOS: Physical sciences, Other Condensed Matter (cond-mat.other)
Abstract

In quantum mechanics, supersymmetry (SUSY) posits an equivalence between two elementary degrees of freedom, bosons and fermions. Here we show how this fundamental concept can be applied to connect bosonic and fermionic lattice models in the realm of condensed matter physics, e.g., to identify a variety of (bosonic) phonon and magnon lattice models which admit topologically nontrivial free fermion models as superpartners. At the single-particle level, the bosonic and the fermionic models that are generated by the SUSY are isospectral except for zero modes, such as flat bands, whose existence is undergirded by the Witten index of the SUSY theory. We develop a unifying framework to formulate these SUSY connections in terms of general lattice graph correspondences and discuss further ramifications such as the definition of supersymmetric topological invariants for generic bosonic systems. Notably, a Hermitian form of the supercharge operator, the generator of the SUSY, can itself be interpreted as a hopping Hamiltonian on a bipartite lattice. This allows us to identify a wide class of interconnected lattices whose tight-binding Hamiltonians are superpartners of one another or can be derived via squaring or square-rooting their energy spectra all the while preserving band topology features. We introduce a five-fold way symmetry classification scheme of these SUSY lattice correspondences, including cases with a non-zero Witten index, based on a topological classification of the underlying Hermitian supercharge operator. These concepts are illustrated for various explicit examples including frustrated magnets, Kitaev spin liquids, and topological superconductors., 37 pages, 27 figures

Published
2022

31. Determinants of anti-PD-1 response and resistance in clear cell renal cell carcinoma

Author

Au, Lewis, Hatipoglu, Emine, Robert De Massy, Marc, Litchfield, Kevin, Beattie, Gordon, Rowan, Andrew, Schnidrig, Desiree, Thompson, Rachael, Byrne, Fiona, Horswell, Stuart, Fotiadis, Nicos, Hazell, Steve, Nicol, David, Shepherd, Scott TC, Fendler, Annika, Mason, Robert, Del Rosario, Lyra, Edmonds, Kim, Lingard, Karla, Sarker, Sarah, Mangwende, Mary, Carlyle, Eleanor, Attig, Jan, Joshi, Kroopa, Uddin, Imran, Becker, Pablo D, Sunderland, Mariana Werner, Akarca, Ayse, Puccio, Ignazio, Yang, William W, Lund, Tom, Dhillon, Kim, Vasquez, Marcos Duran, Ghorani, Ehsan, Xu, Hang, Spencer, Charlotte, López, José I, Green, Anna, Mahadeva, Ula, Borg, Elaine, Mitchison, Miriam, Moore, David A, Proctor, Ian, Falzon, Mary, Pickering, Lisa, Furness, Andrew JS, Reading, James L, Salgado, Roberto, Marafioti, Teresa, Jamal-Hanjani, Mariam, PEACE Consortium, Kassiotis, George, Chain, Benny, Larkin, James, Swanton, Charles, Quezada, Sergio A, Turajlic, Samra, TRACERx Renal Consortium, and Apollo - University of Cambridge Repository

Subjects
multiregion, Receptors, Antigen, T-Cell, clear cell renal cell carcinoma, CD8-Positive T-Lymphocytes, autopsy, Clinical Trials, Phase II as Topic, Exome Sequencing, Tumor Microenvironment, Humans, TCR clonal replacement, Prospective Studies, TCR clonal maintenance, Carcinoma, Renal Cell, Immune Checkpoint Inhibitors, nivolumab, Sequence Analysis, RNA, Gene Expression Profiling, Endogenous Retroviruses, Genomics, Kidney Neoplasms, human endogenous retrovirus, Drug Resistance, Neoplasm, anti-PD-1, Tumor Escape, T cell receptor, Single-Cell Analysis
Abstract

ADAPTeR is a prospective, phase II study of nivolumab (anti-PD-1) in 15 treatment-naive patients (115 multiregion tumor samples) with metastatic clear cell renal cell carcinoma (ccRCC) aiming to understand the mechanism underpinning therapeutic response. Genomic analyses show no correlation between tumor molecular features and response, whereas ccRCC-specific human endogenous retrovirus expression indirectly correlates with clinical response. T cell receptor (TCR) analysis reveals a significantly higher number of expanded TCR clones pre-treatment in responders suggesting pre-existing immunity. Maintenance of highly similar clusters of TCRs post-treatment predict response, suggesting ongoing antigen engagement and survival of families of T cells likely recognizing the same antigens. In responders, nivolumab-bound CD8+ T cells are expanded and express GZMK/B. Our data suggest nivolumab drives both maintenance and replacement of previously expanded T cell clones, but only maintenance correlates with response. We hypothesize that maintenance and boosting of a pre-existing response is a key element of anti-PD-1 mode of action.

Published
2021

32. Determinants of anti-PD-1 response and resistance in clear cell renal cell carcinoma

Author

Au, Lewis, primary, Hatipoglu, Emine, additional, Robert de Massy, Marc, additional, Litchfield, Kevin, additional, Beattie, Gordon, additional, Rowan, Andrew, additional, Schnidrig, Desiree, additional, Thompson, Rachael, additional, Byrne, Fiona, additional, Horswell, Stuart, additional, Fotiadis, Nicos, additional, Hazell, Steve, additional, Nicol, David, additional, Shepherd, Scott T.C., additional, Fendler, Annika, additional, Mason, Robert, additional, Del Rosario, Lyra, additional, Edmonds, Kim, additional, Lingard, Karla, additional, Sarker, Sarah, additional, Mangwende, Mary, additional, Carlyle, Eleanor, additional, Attig, Jan, additional, Joshi, Kroopa, additional, Uddin, Imran, additional, Becker, Pablo D., additional, Sunderland, Mariana Werner, additional, Akarca, Ayse, additional, Puccio, Ignazio, additional, Yang, William W., additional, Lund, Tom, additional, Dhillon, Kim, additional, Vasquez, Marcos Duran, additional, Ghorani, Ehsan, additional, Xu, Hang, additional, Spencer, Charlotte, additional, López, José I., additional, Green, Anna, additional, Mahadeva, Ula, additional, Borg, Elaine, additional, Mitchison, Miriam, additional, Moore, David A., additional, Proctor, Ian, additional, Falzon, Mary, additional, Pickering, Lisa, additional, Furness, Andrew J.S., additional, Reading, James L., additional, Salgado, Roberto, additional, Marafioti, Teresa, additional, Jamal-Hanjani, Mariam, additional, Kassiotis, George, additional, Chain, Benny, additional, Larkin, James, additional, Swanton, Charles, additional, Quezada, Sergio A., additional, Turajlic, Samra, additional, Abbosh, Chris, additional, Shiu, Kai-Keen, additional, Bridgewater, John, additional, Hochhauser, Daniel, additional, Forster, Martin, additional, Lee, Siow-Ming, additional, Ahmad, Tanya, additional, Papadatos-Pastos, Dionysis, additional, Janes, Sam, additional, Van Loo, Peter, additional, Enfield, Katey, additional, McGranahan, Nicholas, additional, Huebner, Ariana, additional, Beck, Stephan, additional, Parker, Peter, additional, Walczak, Henning, additional, Enver, Tariq, additional, Hynds, Rob, additional, Sinclair, Ron, additional, Lok, Chi-wah, additional, Rhodes, Zoe, additional, Moore, David, additional, Khiroya, Reena, additional, Trevisan, Giorgia, additional, Ellery, Peter, additional, Linch, Mark, additional, Brandner, Sebastian, additional, Hiley, Crispin, additional, Veeriah, Selvaraju, additional, Razaq, Maryam, additional, Shaw, Heather, additional, Attard, Gert, additional, Akther, Mita Afroza, additional, Naceur-Lombardelli, Cristina, additional, Manzano, Lizi, additional, Al-Bakir, Maise, additional, Summan, Simranpreet, additional, Kanu, Nnenna, additional, Ward, Sophie, additional, Asghar, Uzma, additional, Lim, Emilia, additional, Gishen, Faye, additional, Tookman, Adrian, additional, Stone, Paddy, additional, Stirling, Caroline, additional, Hunter, Nikki, additional, Vaughan, Sarah, additional, Spain, Lavinia, additional, Yan, Haixi, additional, Shum, Ben, additional, Yousaf, Nadia, additional, Popat, Sanjay, additional, Curtis, Olivia, additional, Stamp, Gordon, additional, Toncheva, Antonia, additional, Nye, Emma, additional, Murra, Aida, additional, Korteweg, Justine, additional, Josephs, Debra, additional, Chandra, Ashish, additional, Spicer, James, additional, Stewart, Ruby, additional, Iredale, Lara-Rose, additional, Mackay, Tina, additional, Deakin, Ben, additional, Enting, Debra, additional, Rudman, Sarah, additional, Ghosh, Sharmistha, additional, Karapagniotou, Lena, additional, Pintus, Elias, additional, Tutt, Andrew, additional, Howlett, Sarah, additional, Michalarea, Vasiliki, additional, Brenton, James, additional, Caldas, Carlos, additional, Fitzgerald, Rebecca, additional, Jimenez-Linan, Merche, additional, Provenzano, Elena, additional, Cluroe, Alison, additional, Stewart, Grant, additional, Watts, Colin, additional, Gilbertson, Richard, additional, McDermott, Ultan, additional, Tavare, Simon, additional, Beddowes, Emma, additional, Roxburgh, Patricia, additional, Biankin, Andrew, additional, Chalmers, Anthony, additional, Fraser, Sioban, additional, Oien, Karin, additional, Kidd, Andrew, additional, Blyth, Kevin, additional, Krebs, Matt, additional, Blackhall, Fiona, additional, Summers, Yvonne, additional, Dive, Caroline, additional, Marais, Richard, additional, Gomes, Fabio, additional, Carter, Mat, additional, Dransfield, Jo, additional, Le Quesne, John, additional, Fennell, Dean, additional, Shaw, Jacqui, additional, Naidu, Babu, additional, Baijal, Shobhit, additional, Tanchel, Bruce, additional, Langman, Gerald, additional, Robinson, Andrew, additional, Collard, Martin, additional, Cockcroft, Peter, additional, Ferris, Charlotte, additional, Bancroft, Hollie, additional, Kerr, Amy, additional, Middleton, Gary, additional, Webb, Joanne, additional, Kadiri, Salma, additional, Colloby, Peter, additional, Olisemeke, Bernard, additional, Wilson, Rodelaine, additional, Tomlinson, Ian, additional, Jogai, Sanjay, additional, Ottensmeier, Christian, additional, Harrison, David, additional, Loda, Massimo, additional, Flanagan, Adrienne, additional, McKenzie, Mairead, additional, Hackshaw, Allan, additional, Ledermann, Jonathan, additional, Chan, Kitty, additional, Sharp, Abby, additional, Farrelly, Laura, additional, Bridger, Hayley, additional, Challacombe, Ben, additional, Chowdhury, Simon, additional, Drake, William, additional, Fernando, Archana, additional, Harrison-Phipps, Karen, additional, Hill, Peter, additional, Horsfield, Catherine, additional, O'Brien, Tim, additional, Olsburgh, Jonathon, additional, Polson, Alexander, additional, Varia, Mary, additional, and Verma, Hema, additional

Published
2021
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36. Determinants of anti-PD1 response and resistance in clear cell renal cell carcinoma

Author

Au, Lewis, primary, Hatipoglu, Emine, additional, de Massy, Marc Robert, additional, Litchfield, Kevin, additional, Rowan, Andrew, additional, Thompson, Rachael, additional, Schnidrig, Desiree, additional, Byrne, Fiona, additional, Beattie, Gordon, additional, Horswell, Stuart, additional, Fotiadis, Nicos, additional, Hazell, Steve, additional, Nicol, David, additional, Shepherd, Scott Thomas Colville, additional, Fendler, Annika, additional, Mason, Robert, additional, Attig, Jan, additional, Joshi, Kroopa, additional, Uddin, Imran, additional, Becker, Pablo, additional, Sunderland, Mariana Werner, additional, Akarca, Ayse, additional, Puccio, Ignazio, additional, Yang, William, additional, Lund, Tom, additional, Dhillon, Kim, additional, Vasquez, Marcos Duran, additional, Ghorani, Ehsan, additional, Xu, Hang, additional, López, José Ignacio, additional, Green, Anna, additional, Mahadeva, Ula, additional, Borg, Elaine, additional, Mitchison, Miriam, additional, Moore, David, additional, Proctor, Ian, additional, Falzon, Mary, additional, Furness, Andrew, additional, Pickering, Lisa, additional, Reading, James L., additional, Salgado, Roberto, additional, Marafioti, Teresa, additional, Jamal-Hanjani, Mariam, additional, Kassiotis, George, additional, Chain, Benny, additional, Larkin, James, additional, Swanton, Charles, additional, Quezada, Sergio A, additional, and Turajlic, Samra, additional

Published
2021
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43. Topological mechanics from supersymmetry

Author

Attig, Jan, Roychowdhury, Krishanu, Lawler, Michael J., Trebst, Simon, Attig, Jan, Roychowdhury, Krishanu, Lawler, Michael J., and Trebst, Simon

Published
2019

47. Additional file 1: Figure S1. of Insights into the design and interpretation of iCLIP experiments

Author

Haberman, Nejc, Huppertz, Ina, Attig, Jan, König, Julian, Wang, Zhen, Hauer, Christian, Hentze, Matthias, Kulozik, Andreas, Hir, Hervé Le, Tomaž Curk, Sibley, Christopher, Zarnack, Kathi, and Ule, Jernej

Abstract

Quality control of the PTBP1 and eIF4A3 iCLIP. Figure S2. CL-motifs are enriched at cDNA deletions and cDNA-starts in U2AF2-iCLIP. Figure S3. Analysis of cDNA-starts and cDNA-ends at the start of Y-tracts. Figure S4. Constrained cDNA-ends in eIF4A3 iCLIP. Figure S5. The impact of cDNA-end constraints on cDNA-starts in eIF4A3 iCLIP. Figure S6. Distribution of cDNA sizes in the studied experiments. (PDF 5.42 mb)

Published
2017
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48. Translational control of ERK signaling through miRNA/4EHP-directed silencing

Author

Jafarnejad, Seyed Mehdi, primary, Chapat, Clément, additional, Matta-Camacho, Edna, additional, Gelbart, Idit Anna, additional, Hesketh, Geoffrey G, additional, Arguello, Meztli, additional, Garzia, Aitor, additional, Kim, Sung-Hoon, additional, Attig, Jan, additional, Shapiro, Maayan, additional, Morita, Masahiro, additional, Khoutorsky, Arkady, additional, Alain, Tommy, additional, Gkogkas, Christos, G, additional, Stern-Ginossar, Noam, additional, Tuschl, Thomas, additional, Gingras, Anne-Claude, additional, Duchaine, Thomas F, additional, and Sonenberg, Nahum, additional

Published
2018
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