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[cat] La leucèmia limfoblàstica aguda (LLA) és l’expansió clonal de cèl·lules malignes originades a partir de progenitors hematopoètics i és el càncer pediàtric més freqüent. La supervivència dels pacients pediàtrics afectes de LLA ha augmentat de forma important en les últimes dècades, actualment supera el 90% en països de renda alta. La intensitat terapèutica dels règims quimioteràpics actuals ha arribat al límit de la tolerància. D’aquesta manera, per a millorar el pronòstic és més important disminuir-ne la toxicitat, més que incrementar-ne la intensitat. L’asparaginasa (ASP) és un quimioteràpic essencial en el tractament de la LLA però s’associa a toxicitats freqüents i a vegades greus, com hipersensibilitat i pancreatitis, que poden tenir un impacte en la supervivència. En la pràctica clínica s’utilitzen 3 formulacions d’ASP, dues derivades d’E. coli (una nativa i una pegilada: E. coli-ASP nativa, PEG-ASP) i una d’Erwinia chrysanthemi (Erwinia-ASP), amb un patró similar de toxicitat excepte una potencial menor immunogenicitat de PEG-ASP respecte E. coli-ASP nativa. La hipersensibilitat és la toxicitat més freqüent i pot manifestar-se com al·lèrgia real (clínica d’al·lèrgia amb inactivació del fàrmac), pseudoal·lèrgia (clínica d’al·lèrgia sense inactivació del fàrmac) i inactivació silent (IS) (inactivació del fàrmac sense cap simptomatologia associada). S’han relacionat certs polimorfismes genètics amb la pancreatitis i la hipersensibilitat associades a ASP. Per a avaluar l’efectivitat de l’ASP, la tècnica gold stantard és la determinació d’activitat d’asparaginasa en sèrum (AAS). Un nivell ≥ 100 UI/L defineix una AAS en rang terapèutic. Partint d’aquest context, en aquest treball de tesi vam plantejar les següents hipòtesis: l’anàlisi de polimorfismes genètics relacionats amb toxicitat a ASP podria identificar els pacients amb major risc de pancreatitis o al·lèrgia; la incidència d'al·lèrgia en pacients pediàtrics que reben un esquema seqüencial d’ASP (E. coli nativa-ASP seguida de PEG-ASP) podria ser major a la dels que reben únicament PEG-ASP dins del mateix protocol i, finalment; que amb la dosi més baixa de PEG-ASP (1.000 UI/m2) es podrien aconseguir nivells d’AAS suficients per a una correcta efectivitat clínica. Per a donar resposta a aquestes hipòtesis, vam enfocar els següents objectius: estudiar la correlació entre els polimorfismes en el gen de l’asparagin-sintetasa (ASNS) relacionats amb toxicitat a ASP en una sèrie de pacients pediàtrics afectes de LLA i comparar la incidència d’al·lèrgia clínica en pacients pediàtrics amb LLA que han rebut diferents esquemes d'administració d’ASP dins el mateix protocol terapèutic. En la nostra població d’estudi, els polimorfismes rs3757676 i rs3832526, descrits prèviament com a haplotip de risc i protector del gen ASNS enfront al·lèrgia i pancreatitis, no van tenir una relació clara amb l’aparició d’aquestes toxicitats. El risc de presentar al·lèrgia a ASP es va associar tant amb el fet de rebre un protocol d’alt risc de recaiguda com el fet de pertànyer a l’ètnia llatinoamericana. El risc de presentar pancreatitis secundària a ASP es va associar amb el fet de tenir una edat ≥ 10 anys en el moment del diagnòstic. En el nostre protocol de tractament LAL/SEHOP-PETHEMA 2013, l’ús de PEG-ASP en primera línia es va associar amb una menor incidència d'al·lèrgia clínica que l'observada en l’ús seqüencial d’E. coli-ASP nativa seguida de PEG-ASP. PEG-ASP a una dosi de 1.000 UI/m2 intramuscular va ser eficaç per assolir una AAS suficient en més del 90% dels pacients. La incidència d'inactivació silent en els pacients tractats amb PEG-ASP en primera línia va ser molt baixa. Vam detectar una associació significativa entre els nivells d’AAS i l’increment dels nivells d’amoni sèric, la disminució dels nivells d’albúmina, i l’increment dels nivells de triglicèrids. No es van observar diferències significatives en la incidència de pancreatitis en funció de la formulació d’ASP utilitzada., [eng] Acute lymphoblastic leukaemia (ALL) is the clonal expansion of malignant cells originating from haematopoietic progenitors and is the most common paediatric cancer. Survival of paediatric ALL patients has increased significantly in recent decades, now exceeding 90% in high-income countries. The therapeutic intensity of current chemotherapy regimens has reached the limit of tolerance. Thus, to improve prognosis, it is more important to decrease toxicity than to increase intensity. Asparaginase (ASP) is an essential chemotherapy drug in the treatment of ALL but is associated with frequent and sometimes severe toxicities, such as hypersensitivity and pancreatitis, which can impact survival. In clinical practice, 3 ASP formulations are used, two derived from E. coli (one native and one pegylated: native E. coli-ASP, PEG-ASP) and one from Erwinia chrysanthemi (Erwinia-ASP), with a similar pattern of toxicity except for a potential lower immunogenicity of PEG-ASP compared to native E. coli-ASP. Hypersensitivity is the most common toxicity and can manifest as allergy (clinical allergy with drug inactivation), allergic-like reaction (clinical allergy without drug inactivation) and silent inactivation (SI) (drug inactivation without any associated symptoms). Certain genetic polymorphisms have been linked to ASP-associated pancreatitis and hypersensitivity. To assess the effectiveness of ASP, the gold standard technique is the determination of serum asparaginase activity (SAA). A level ≥ 100 IU/L defines a SAA in therapeutic range. Against this background, we hypothesise that: the analysis of genetic polymorphisms related to ASP toxicity could identify patients at higher risk of pancreatitis or allergy; the incidence of allergy in paediatric patients receiving a sequential ASP scheme (native E. coli-ASP followed by PEG-ASP) could be higher than those receiving only PEG-ASP within the same clinical protocol and, finally, that the lowest dose of PEG-ASP (1,000 IU/m2) could achieve sufficient SAA levels for clinical effectiveness. To answer these hypotheses, we focused on the following objectives: to study the correlation between polymorphisms in the asparagin synthetase gene (ASNS) related to ASP toxicity in a series of paediatric patients with ALL and to compare the incidence of clinical allergy in paediatric patients with ALL who have received different ASP administration schemes in the same therapeutic protocol. In our study population, the rs3757676 and rs3832526 polymorphisms, previously described as risk and protective haplotypes of the ASNS gene for allergy and pancreatitis, were not clearly associated with the occurrence of these toxicities. The risk of ASP allergy was associated with both receiving a high-risk relapse protocol and being of Latin American ethnicity. The risk of pancreatitis was associated with age ≥ 10 years at diagnosis. In our LAL/SEHOP-PETHEMA 2013 treatment protocol, first-line use of PEG-ASP was associated with lower incidence of clinical allergy than that observed with sequential use of native E. coli-ASP followed by PEG-ASP. PEG-ASP at a dose of 1,000 IU/m2 intramuscularly was effective in achieving sufficient SAA in more than 90% of patients. The incidence of silent inactivation in patients treated with PEG-ASP first-line was very low. We detected a significant association between SAA levels and increased serum ammonium levels, decreased albumin levels, and increased triglyceride levels. No significant differences in the incidence of pancreatitis were observed depending on the ASP formulation used.

[eng] Next-generation sequencing (NGS) has revolutionized biomedical sciences, especially in the area of cancer. It has nourished genomic research with extensive collections of sequenced genomes that are investigated to untangle the molecular bases of disease, as well as to identify potential targets for the design of new treatments. To exploit all this information, several initiatives have emerged worldwide, among which the Pan-Cancer project of the ICGC (International Cancer Genome Consortium) stands out. This project has jointly analyzed thousands of tumor genomes of different cancer types in order to elucidate the molecular bases of the origin and progression of cancer. To accomplish this task, new emerging technologies, including virtualization systems such as virtual machines or software containers, were used and had to be adapted to various computing centers. The portability of this system to the supercomputing infrastructure of the BSC (Barcelona Supercomputing Center) has been carried out during the first phase of the thesis. In parallel, other projects promote the application of genomics discoveries into the clinics. This is the case of MedPerCan, a national initiative to design a pilot project for the implementation of personalized medicine in oncology in Catalonia. In this context, we have centered our efforts on the methodological side, focusing on the detection and characterization of somatic variants in tumors. This step is a challenging action, due to the heterogeneity of the different methods, and an essential part, as it lays at the basis of all downstream analyses. On top of the methodological section of the thesis, we got into the biological interpretation of the results to study the evolution of chronic lymphocytic leukemia (CLL) in a close collaboration with the group of Dr. Elías Campo from the Hospital Clínic/IDIBAPS. In the first study, we have focused on the Richter transformation (RT), a transformation of CLL into a high-grade lymphoma that leads to a very poor prognosis and with unmet clinical needs. We found that RT has greater genomic, epigenomic and transcriptomic complexity than CLL. Its genome may reflect the imprint of therapies that the patients received prior to RT, indicating the presence of cells exposed to these mutagenic treatments which later expand giving rise to the clinical manifestation of the disease. Multiple NGS- based techniques, including whole-genome sequencing and single-cell DNA and RNA sequencing, among others, confirmed the pre-existence of cells with the RT characteristics years before their manifestation, up to the time of CLL diagnosis. The transcriptomic profile of RT is remarkably different from that of CLL. Of particular importance is the overexpression of the OXPHOS pathway, which could be used as a therapeutic vulnerability. Finally, in a second study, the analysis of a case of CLL in a young adult, based on whole genome and single-cell sequencing at different times of the disease, revealed that the founder clone of CLL did not present any somatic driver mutations and was characterized by germline variants in ATM, suggesting its role in the origin of the disease, and highlighting the possible contribution of germline variants or other non-genetic mechanisms in the initiation of CLL.

The authors thank the Hematopathology Collection registered at the Biobank of Hospital Clínic—Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) as well as Sílvia Martín for the technical support. This study was supported by the “la Caixa” Foundation (CLLEvolution-LCF/PR/HR17/52150017, Health Research 2017 Program HR17-00221, to EC), the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (810287, BCLLatlas, to EC, and HH), CERCA Program/Generalitat de Catalunya, Generalitat de Catalunya Suport Grups de Recerca AGAUR 2017-SGR-1142 (to EC), CIBERONC (CB16/12/00225 to EC), Ministerio de Ciencia e Innovación PID2020-117185RB-I00 (to XSP), FEDER: European Regional Development Fund “Una manera de hacer Europa”, and Fundación Asociación Española Contra el Cáncer FUNCAR-PRYGN211258SUÁR (to XSP). The authors thankfully acknowledge the computer resources at MareNostrum4 and the technical support provided by Barcelona Supercomputing Center (RES activity BCV-2018-3-0001). FN acknowledge research support from the American Association for Cancer Research (2021 AACR-Amgen Fellowship in Clinical/Translational Cancer Research, Grant Number 21-40-11-NADE), the European Hematology Association (EHA Junior Research Grant 2021, Grant Number RG-202012-00245), and the Lady Tata Memorial Trust (International Award for Research in Leukemia 2021–2022, Grant Number LADY_TATA_21_3223). EC is an Academia Researcher of the “Institució Catalana de Recerca i Estudis Avançats” (ICREA) of the Generalitat de Catalunya. This work was partially developed at the Centre Esther Koplowitz (CEK, Barcelona, Spain). Peer Reviewed "Article signat per 11 autors/es: Romina Royo, Laura Magnano, Julio Delgado, Sara Ruiz-Gil, Josep Ll. Gelpí, Holger Heyn, Malcom A. Taylor, Tatjana Stankovic, Xose S. Puente, Ferran Nadeu & Elías Campo"

This work was partially supported by the European Union's Horizon 2020 research and innovation program (grant No 856620); grants from the Instituto de Salud Carlos III (Madrid, Spain; PI17/02256 and PI20/01845); Consejeria de Economia, Conocimiento, Empresas y Universidad (Granada, Spain; A-CTS-448-UGR18); Consejeria de Transformacion Economica, Industria, Conocimiento y Universidades (Sevilla, Spain; PY20/01282); Generalitat de Catalunya (17SGR437); Gilead Sciences Fellowship (GLD17/00282); the "Xarxa de Bancs de tumors" sponsored by Pla Director d'Oncologia de Catalunya (XBTC); the Associazione Italiana per la Ricerca sul Cancro and Fondazione Cariplo (TRIDEO 16923 and AIRC IG21436); the Spanish Association Against Cancer (AECC) Scientific Foundation grant GCTRA18022MORE; and the Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), action Genrisk. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., In conclusion, this study confirmed the association of 31 GWASidentified SNPs with CLL risk and shed some light on the function of some of these biomarkers in the modulation of TReg, B, and T cell differentiation and proliferation, blood concentrations of B cell-related proteins, cell survival, and the expression of immuneand non-immune-related loci. Though outside the scope of the current study, it is important to mention that additional functional studies using blood samples from CLL patients are still required to validate our findings and to decipher the exact biological mechanisms behind the observed associations. A potential limitation of this work was the relatively small population size of the CRuCIAL cohort that hampered the validation of the SNPs showing modest associations., European Union's Horizon 2020 research and innovation program 856620, Instituto de Salud Carlos III PI17/02256 PI20/01845, Consejeria de Economia, Conocimiento, Empresas y Universidad (Granada, Spain) A-CTS-448-UGR18 Consejeria de Transformacion Economica, Industria, Conocimiento y Universidades (Sevilla, Spain) PY20/01282, Generalitat de Catalunya, General Electric 17SGR437, Gilead Sciences GLD17/00282, "Xarxa de Bancs de tumors" - Pla Director d'Oncologia de Catalunya (XBTC), Fondazione AIRC per la ricerca sul cancro Fondazione Cariplo TRIDEO 16923 AIRC IG21436, Spanish Association Against Cancer (AECC) Scientific Foundation grant GCTRA18022MORE, Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), action Genrisk

The authors would like to thank the patients who participated in the study and their families, friends, caregivers and referring physicians. The authors are very grateful to Drs. Miguel Ángel Perales (Memorial Sloan Kettering Cancer Center, New York), Shannon Maude (Children's Hospital of Philadelphia), Juan José Lasarte (Centro de Investigación Médica Aplicada, Navarra) and Michael Schmitt (Universitäts Klinikum Heidelberg), members of the CART19-BE-01 trial DSMB. The authors are also indebted to the study staff and health care providers at Hospital Clínic, specifically to Anna Boronat, Raquel Martín-Ibáñez, Unai Perpiñá, Josep M. Canals, Vanina Rodríguez, Guillermo Suñé, Esteve Trias and Jordi Yagüe who participated in the development of the CART19 construct; Sara Varea, Judit Pich, Gabriela Recalde, Leticia Pereira and Joan Albert Arnáiz, from the Clinical Trials Unit; Gonzalo Calvo, Andrea Scalise, Joaquín Sáez-Peñataro, Ferran Torres and Sandra Castaño, from the Department of Pharmacology; and Josep Maria Campistol, Antoni Castells, Aurea Mira and Marc Roda as the main representatives from the institution. This study was funded by CatSalut, Projecte ARI and grants co-financed by the Instituto de Salud Carlos III-Subdirección General de Evaluación y Fomento de la Investigación Sanitaria-and Fondo Europeo de Desarrollo Regional (FEDER) PICI14/122, PI13/676, PIE13/33, PI18/775; and Fundació La Caixa CP042702/LCF/PR/GN18/50310007. VO-M and JD were recipients of research grants from FEHH and Generalitat de Catalunya (PERIS IPFE SLT006/17/301), respectively. CART19 cells are emerging as an alternative therapy for patients with chronic lymphocytic leukemia (CLL). Here we report the outcome of nine consecutive patients with CLL treated with ARI-0001 CART19 cells, six of them with Richter's transformation (RT). One patient with RT never received therapy. The cytokine release syndrome rate was 87.5% (12.5% grade ≥3). Neurotoxicity was not observed in any patient. All patients experienced absolute B-cell aplasia, and seven (87.5%) responded to therapy. With a median follow-up of 5.6 months, two patients with RT experienced a CD19-negative relapse. In conclusion, ARI-0001 cell therapy was feasible, safe, and effective in patients with high-risk CLL or RT.

The integration of multi-omics data can greatly facilitate the advancement of research in Life Sciences by highlighting new interactions. However, there is currently no widespread procedure for meaningful multi-omics data integration. Here, we present a robust framework, called InterTADs, for integrating multi-omics data derived from the same sample, and considering the chromatin configuration of the genome, i.e. the topologically associating domains (TADs). Following the integration process, statistical analysis highlights the differences between the groups of interest (normal versus cancer cells) relating to (i) independent and (ii) integrated events through TADs. Finally, enrichment analysis using KEGG database, Gene Ontology and transcription factor binding sites and visualization approaches are available. We applied InterTADs to multi-omics datasets from 135 patients with chronic lymphocytic leukemia (CLL) and found that the integration through TADs resulted in a dramatic reduction of heterogeneity compared to individual events. Significant differences for individual events and on TADs level were identified between patients differing in the somatic hypermutation status of the clonotypic immunoglobulin genes, the core biological stratifier in CLL, attesting to the biomedical relevance of InterTADs. In conclusion, our approach suggests a new perspective towards analyzing multi-omics data, by offering reasonable execution time, biological benchmarking and potentially contributing to pattern discovery through TADs. ‘Hellenic Network for Precision Medicine’ in the framework of the Hellenic Republic – Siemens Settlement Agreement; European Regional Development Fund of the European Union and Greek national funds through the Operational Program Competitiveness, Entrepreneurship and Innovation, under the call RESEARCH – CREATE – INNOVATE [GenOptics, project code: T2E1DK-00407]

Several gene expression profiles with a strong correlation with patient outcomes have been previously described in chronic lymphocytic leukemia (CLL), although their applicability as biomarkers in clinical practice has been particularly limited. Here we describe the training and validation of a gene expression signature for predicting early progression in patients with CLL based on the analysis of 200 genes related to microenvironment signaling on the NanoString platform. In the training cohort (n = 154), the CLL15 assay containing a 15-gene signature was associated with the time to first treatment (TtFT) (hazard ratio [HR], 2.83; 95% CI, 2.17-3.68; P < .001). The prognostic value of the CLL15 score (HR, 1.71; 95% CI, 1.15-2.52; P = .007) was further confirmed in an external independent validation cohort (n = 112). Notably, the CLL15 score improved the prognostic capacity over IGHV mutational status and the International Prognostic Score for asymptomatic early-stage (IPS-E) CLL. In multivariate analysis, the CLL15 score (HR, 1.83; 95% CI, 1.32-2.56; P < .001) and the IPS-E CLL (HR, 2.23; 95% CI, 1.59-3.12; P < .001) were independently associated with TtFT. The newly developed and validated CLL15 assay successfully translated previous gene signatures such as the microenvironment signaling into a new gene expression–based assay with prognostic implications in CLL., This work was supported by research funding from the Asociacion Espa ´ nola Contra el C ˜ ancer grant [5U01CA157581- 05, ECRIN-M3 - A29370] and in part by the Instituto de Salud Carlos III, Fondo de Investigaciones Sanitarias [PI17/00950, M.C., PI17/00943, F.B, PI18/01392, P.A.], and the Spanish Ministry of Economy and Competitiveness [CIBERONC-CB16/12/00233], the Education Council or Health Council of the Junta de Castilla y Leon [GRS 2036/A/19], and Gilead Sciences [GLD15/00348]. ´ This work was supported by research funding from the Asociacion´ Espanola Contra el C ˜ ancer grant [5U01CA157581-05, ECRIN-M3 ´ - A29370] and in part by the Instituto de Salud Carlos III, Fondo de Investigaciones Sanitarias [PI17/00950, M.C., PI17/00943, F.B, PI18/01392, P.A.], and the Spanish Ministry of Economy and Competitiveness [CIBERONC-CB16/12/00233], the Education Council or Health Council of the Junta de Castilla y Leon [GRS ´ 2036/A/19], Gilead Sciences [GLD15/00348] and Gilead Fellowships [GLD16/00144, GLD18/00047, F.B.], and Fundacio la ´Marato de TV3 [201905-30-31 F.B]. All Spanish funding was ´ cosponsored by the European Union FEDER program “Una manera de hacer Europa”. M.C. holds a contract from Ministerio de Ciencia, Innovacion y Universidades [RYC-2012-2018].