Duplex Sequencing Uncovers Recurrent Low-frequency Cancer-associated Mutations in Infant and Childhood KMT2A-rearranged Acute Leukemia

Infant acute lymphoblastic leukemia (ALL) with KMT2A-gene rearrangements (KMT2A-r) have few mutations and a poor prognosis. To uncover mutations that are below the detection of standard next-generation sequencing (NGS), a combination of targeted duplex sequencing and NGS was applied on 20 infants and 7 children with KMT2A-r ALL, 5 longitudinal and 6 paired relapse samples. Of identified nonsynonymous mutations, 87 had been previously implicated in cancer and targeted genes recurrently altered in KMT2A-r leukemia and included mutations in KRAS, NRAS, FLT3, TP53, PIK3CA, PAX5, PIK3R1, and PTPN11, with infants having fewer such mutations. Of identified cancer-associated mutations, 62% were below the resolution of standard NGS. Only 33 of 87 mutations exceeded 2% of cellular prevalence and most-targeted PI3K/RAS genes (31/33) and typically KRAS/NRAS. Five patients only had low-frequency PI3K/RAS mutations without a higher-frequency signaling mutation. Further, drug-resistant clones with FLT3 D835H or NRAS G13D/G12S mutations that comprised only 0.06% to 0.34% of diagnostic cells, expanded at relapse. Finally, in longitudinal samples, the relapse clone persisted as a minor subclone from diagnosis and through treatment before expanding during the last month of disease. Together, we demonstrate that infant and childhood KMT2A-r ALL harbor low-frequency cancer-associated mutations, implying a vast subclonal genetic landscape.publishedVersionPeer reviewe

”Hur tar vi oss upp igen från källaren?” – en fallstudie på Bong AB´s turnaround under 2000-talet

SYFTE: Syftet med studien är att beskriva och analysera en turnaround. METOD: Undersökningen har gjorts utifrån en kvalitativ metodansats med en fallstudie som angreppssätt. Datainsamlingen består främst av semistrukturerade intervjuer samt olika former av interna dokument från fallföretaget. TEORETISKA PERSPEKTIV: Det teoretiska kapitlet beskriver i ett första skede grundläggande teorier, tidigare forskning och begrepp inom turnaround. Vidare skalas teorin ner till processnivå för att fokusera på arbetsprocessen i turnaround management och implementeringen av ny strategi. Avsnittet avslutas med en sammanfattande teoretisk referensram med tillhörande figur. EMPIRI: Empirin bygger huvudsakligen på information från intervjuer med nyckelpersoner från fallföretaget. Annan information är hämtad från artiklar, protokoll, powerpoints samt en utgiven bok om fallföretaget. RESULTAT: Anledningen till fallföretagets turnaround var huvudsakligen ett misslyckat företagsförvärv men även en lågkonjunktur som resulterade i överkapacitet. Företagets huvudåtgärd var att byta ledning, effektivisera samt att växa genom en ny produktgren; ProPac. Uppsatsens teoretiska referensram stämmer relativt väl överens med vårt empiriska resultat. Fallföretagets förändringsprocess tenderar dock att mer kunna liknas vid en kontinuerlig förändringsprocess.PURPOSE: The purpose of this essay is to describe and analyze a turnaround. METHODOLOGY: The study was conducted by a qualitative method with a case study approach. The data collection consists mainly by semi-structured interviews and different kind of internal documents from the case company. THEORETICAL PERSPECTIVES: The theoretical chapter describes in a first stage, basic theories, previous research and concepts in turnaround. Furthermore, the theory is scaled down to process level to focus on the work in turnaround management and implementation of a new strategy. The section ends with a comprehensive theoretical framework. EMPIRICAL FOUNDATION: Empirical data are based on information mainly from interviews with key individuals from the case company. Other information is taken from articles, protocols and a published book about the case company. CONCLUSIONS: The reason for the case company’s turnaround was mainly due to an unsuccessful acquisition, but also because of a recession in the economy which led to excess capacity. The company solved the problems primarily by switching management, rationalize and grow through a new product line; ProPac. Our theoretical framework match relatively well with our empirical results. The case company’s transformation, however, tend to be more like a continuous process of change

Obesity associates with increased all-cause and cardiovascular mortality in adults with asthma

Background: Asthma and obesity are prevalent conditions that are increasing worldwide. Asthma is characterized by airway inflammation and bronchial variability, while obesity is a complex metabolic disorder that poses significant morbidity and mortality risks. Obesity is a risk factor for asthma and a plethora of other non-communicable diseases. Objective: To compare all-cause and cause-specific mortality between obese, overweight and normal weight adults with asthma in a cohort with long-term follow-up. Methods: Individuals from a population-based adult asthma cohort recruited in Norrbotten county, Sweden, were clinically examined between 1986 and 2001 and grouped into body mass index (BMI) categories. Underlying causes of death until December 31st, 2020 were categorized as cardiovascular, respiratory, cancer and other mortality by linking cohort data to the Swedish National Board of Health and Welfare's National Cause of Death register. Hazard ratios (HR) with 95% confidence intervals (CI) for all-cause and cause-specific mortality associated with overweight and obesity were calculated via Cox proportional hazard models. Results: In total, 940 individuals were normal weight, 689 overweight and 328 obese while only 13 were underweight. Obesity increased the hazard for all-cause (HR 1.26, 95% CI 1.03–1.54) and cardiovascular mortality (HR 1.43, 95% CI 1.03–1.97). Obesity was not significantly associated with respiratory or cancer mortality. Overweight did not increase the hazard of all-cause or any cause-specific mortality category. Conclusion: Obesity, but not overweight, was significantly associated with increased hazard of all-cause and cardiovascular mortality in adults with asthma. Neither obesity nor overweight were associated with increased hazard of respiratory mortality

Activating mutations remodeled the chromatin accessibility landscape to drive distinct regulatory networks in <i>KMT2A</i>-rearranged acute leukemia associated with immune evasion

This dataset includes ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) of five infants with acute lymphoblastic leukemia. All patients had an underlying rearrangement of the KMT2A genes, either KMT2A::MLLT1 (n=1), KMT2A::AFF1 (n=3), or KMT2A::MLLT10 (n=1). Three patients also had activating mutations of NRAS G13D and/or KRAS G12D. The median age of the cohort was 2 months 7 days. Diagnostic sample from bone marrow underwent the ATAC-seq library preparation and sequenced on the NextSeq 500 platform (Illumina, San Diego, CA, USA).</p

De novo activating mutations drive clonal evolution and enhance clonal fitness in KMT2A-rearranged leukemia

Activating signaling mutations are common in acute leukemia with KMT2A (previously MLL) rearrangements (KMT2A-R). These mutations are often subclonal and their biological impact remains unclear. Using a retroviral acute myeloid mouse leukemia model, we demonstrate that FLT3 ITD, FLT3 N676K, and NRAS G12D accelerate KMT2A-MLLT3 leukemia onset. Further, also subclonal FLT3 N676K mutations accelerate disease, possibly by providing stimulatory factors. Herein, we show that one such factor, MIF, promotes survival of mouse KMT2A-MLLT3 leukemia initiating cells. We identify acquired de novo mutations in Braf, Cbl, Kras, and Ptpn11 in KMT2A-MLLT3 leukemia cells that favored clonal expansion. During clonal evolution, we observe serial genetic changes at the Kras G12D locus, consistent with a strong selective advantage of additional Kras G12D . KMT2A-MLLT3 leukemias with signaling mutations enforce Myc and Myb transcriptional modules. Our results provide new insight into the biology of KMT2A-R leukemia with subclonal signaling mutations and highlight the importance of activated signaling as a contributing driver