| Title: |
ImmuneLENS characterizes systemic immune dysregulation in aging and cancer |
| Authors: |
Bentham, R.; Jones, T.P.; Black, J.R.M.; Martinez-Ruiz, C.; Dietzen, M.; Litovchenko, M.; Thol, K.; Watkins, T.B.K.; Bailey, C.; Pich, O.; Zhang, Z.; Van Loo, P.; Jamal-Hanjani, M.; Martínez-Ruiz, C.; Karasaki, T.; Bunkum, A.; Hessey, S.; Liu, W.K.; Birkbak, N.J.; Frankell, A.M.; Huebner, A.; Puttick, C.; Hiley, C.T.; Moore, D.A.; Biswas, D.; Lim, E.L.; Grigoriadis, K.; Bakir, M.A.; Lucas, O.; Vendramin, R.; Ward, S.; Harries, S.; Zaccaria, S.; Zaidi, R.; Patruno, L.; Karagianni, D.; Quezada, S.A.; Bola, S.K.; Forster, M.D.; Lee, S.M.; Richard, C.; Naceur-Lombardelli, C.; Gimeno-Valiente, F.; Thakkar, K.; Sivakumar, M.; Kanu, N.; Usaite, I.; Saghafinia, S.; Veeriah, S.; Vanloo, S.; Toncheva, A.; Prymas, P.; Mussa, B.; Magala, M.; Keene, E.; Leung, M.M.; Wilson, G.A.; Rosenthal, R.; Rowan, A.; Lee, C.; Colliver, E.; Enfield, K.S.S.; Angelova, M.; Murphy, C.; Zagorulya, M.; Marafioti, T.; Borg, E.; Falzon, M.; Khiroya, R.; Wong, Y.N.S.; Hoogenboom, E.M.; Monk, F.; Holding, J.W.; Choudhary, J.; Bhakhri, K.; Gorman, P.; Stephens, R.C.M.; Pisciella, M.C.; Bandula, S.; Nicod, J.; Dwornik, A.; Karamani, A.; Chain, B.; Pearce, D.R.; Stavrou, G.; Mastrokalos, G.-T.; Lowe, H.L.; Reading, J.L.; Hartley, J.A.; Selvaraju, K.; Ensell, L.; Shah, M.; Pawlik, P.; Gamble, S.; Ung, S.K.A.; Spanswick, V.; Wu, Y.; Lester, J.F.; Dulloo, S.; Fennell, D.A.; Bajaj, A.; Nakas, A.; Sodha-Ramdeen, A.; Tufail, M.; Scotland, M.; Boyles, R.; Rathinam, S.; Wilson, C.; Matharu, G.; Shaw, J.A.; Boleti, E.; Cheyne, H.; Khalil, M.; Richardson, S.; Cruickshank, T.; Price, G.; Kerr, K.M.; Benafif, S.; Papadatos-Pastos, D.; Wilson, J.; Ahmad, T.; French, J.; Gilbert, K.; Naidu, B.; Patel, A.J.; Middleton, G.; Osman, A.; Sangha, M.; Langman, G.; Shackleford, H.; Djearaman, M.; Leek, A.; Hodgkinson, J.D.; Totton, N.; Crosbie, P.; Fontaine, E.; Granato, F.; Novasio, J.; Rammohan, K.; Joseph, L.; Bishop, P.; Joshi, V.; Waplington, S.; Atkin, A.; Brown, K.D.; Carter, M.; Chaturvedi, A.; Oliveira, P.; Lindsay, C.R.; Blackhall, F.H.; Summers, Y.; Krebs, M.G.; Paiva-Correia, A.; Tugwood, J.; Dive, C.; Aerts, H.J.W.L.; Schwarz, R.F.; Kaufmann, T.L.; Szallasi, Z.; Diossy, M.; Salgado, R.; Demeulemeester, J.; Castignani, C.; Beck, S.; Kassiotis, G.; Noorani, I.; Weeden, C.E.; Grönroos, E.; Goldman, J.; Escudero, M.; Hobson, P.; Boeing, S.; Denner, T.; Barbè, V.; Lu, W.-T.; Hill, W.; Naito, Y.; Sahai, E.; Ramsden, Z.; Nye, E.; Stone, R.K.; Rane, J.K.; Kittel, J.; Haase, K.; Koh, K.; Scott, R.; Peggs, K.S.; Veiga, C.; Royle, G.; Collins-Fekete, C.-A.; Fraioli, F.; Ashford, P.; Nair, A.; Procter, A.J.; Ahmed, A.; Taylor, M.N.; Lawrence, D.; Patrini, D.; Navani, N.; Thakrar, R.M.; Janes, S.M.; Kaplar, Z.; Hackshaw, A.; Pilotti, C.; Leslie, R.; Hacker, A.-M.; Smith, S.; Walker, A.; Grapa, A.; Zhang, H.; AbdulJabbar, K.; Pan, X.; Yuan, Y.; Chuter, D.; MacKenzie, M.; Chee, S.; Georg, P.; Alzetani, A.; Cave, J.; Lim, E.; Nicholson, A.G.; De Sousa, P.; Jordan, S.; Rice, A.; Raubenheimer, H.; Bhayani, H.; Ambrose, L.; Devaraj, A.; Chavan, H.; Begum, S.; Buderi, S.I.; Kaniu, D.; Malima, M.; Booth, S.; Fernandes, N.; Shah, P.; Proli, C.; Hewish, M.; Danson, S.; Shackcloth, M.J.; Robinson, L.; Russell, P.; Blyth, K.G.; Kidd, A.; Dick, C.; Le Quesne, J.; Kirk, A.; Asif, M.; Bilancia, R.; Kostoulas, N.; Whiteley, J.; Thomas, M.; Ambrose, J.C.; Arumugam, P.; Baple, E.L.; Bleda, M.; Boardman-Pretty, F.; Boissiere, J.M.; Boustred, C.R.; Brittain, H.; Caulfield, M.J.; Chan, G.C.; Craig, C.E.H.; Daugherty, L.C.; de Burca, A.; Devereau, A.; Elgar, G.; Foulger, R.E.; Fowler, T.; Furió-Tarí, P.; Hackett, J.M.; Halai, D.; Hamblin, A.; Henderson, S.; Holman, J.E.; Hubbard, T.J.P.; Ibáñez, K.; Jackson, R.; Jones, L.J.; Kasperaviciute, D.; Kayikci, M.; Lahnstein, L.; Lawson, L.; Leigh, S.E.A.; Leong, I.U.S.; Lopez, F.J.; Maleady-Crowe, F.; Mason, J.; McDonagh, E.M.; Moutsianas, L.; Mueller, M.; Murugaesu, N.; Need, A.C.; Odhams, C.A.; Patch, C.; Perez-Gil, D.; Polychronopoulos, D.; Pullinger, J.; Rahim, T.; Rendon, A.; Riesgo-Ferreiro, P.; Rogers, T.; Ryten, M.; Savage, K.; Sawant, K.; Scott, R.H.; Siddiq, A.; Sieghart, A.; Smedley, D.; Smith, K.R.; Sosinsky, A.; Spooner, W.; Stevens, H.E.; Stuckey, A.; Sultana, R.; Thomas, E.R.A.; Thompson, S.R.; Tregidgo, C.; Tucci, A.; Walsh, E.; Watters, S.A.; Welland, M.J.; Williams, E.; Witkowska, K.; Wood, S.M.; Zarowiecki, M.; Swanton, C.; McGranahan, N. |
| Publisher Information: |
Springer Science and Business Media LLC |
| Publication Year: |
2025 |
| Collection: |
White Rose Research Online (Universities of Leeds, Sheffield & York) |
| Description: |
Recognition and elimination of pathogens and cancer cells depend on the adaptive immune system. Thus, accurate quantification of immune subsets is vital for precision medicine. We present immune lymphocyte estimation from nucleotide sequencing (ImmuneLENS), which estimates T cell and B cell fractions, class switching and clonotype diversity from whole-genome sequencing data at depths as low as 5× coverage. By applying ImmuneLENS to the 100,000 Genomes Project, we identify genes enriched with somatic mutations in T cell-rich tumors, significant sex-based differences in circulating T cell fraction and demonstrated that the circulating T cell fraction in patients with cancer is significantly lower than in healthy individuals. Low circulating B cell fraction was linked to increased cancer incidence. Finally, circulating T cell abundance was more prognostic of 5-year cancer survival than infiltrating T cells. |
| Document Type: |
article in journal/newspaper |
| File Description: |
text |
| Language: |
English |
| ISSN: |
1061-4036 |
| Relation: |
https://eprints.whiterose.ac.uk/id/eprint/224142/1/s41588-025-02086-5.pdf; Bentham, R., Jones, T.P. orcid.org/0000-0003-2748-0780 , Black, J.R.M. orcid.org/0000-0001-5598-7752 et al. (327 more authors) (2025) ImmuneLENS characterizes systemic immune dysregulation in aging and cancer. Nature Genetics, 57. pp. 694-705. ISSN: 1061-4036 |
| Availability: |
https://eprints.whiterose.ac.uk/id/eprint/224142/ |
| Rights: |
cc_by_4 |
| Accession Number: |
edsbas.DCF4EA6A |
| Database: |
BASE |