Differences In Somatic Mutations Research Articles

Genomic Landscape of Pancreatic Adenocarcinoma in Younger versus Older Patients: Does Age Matter?

State-of-the-art genomic analyses of pancreatic adenocarcinoma (PDAC) have yielded insight into signaling pathways underlying carcinogenesis. PDAC is characterized by substantial genomic heterogeneity. We aimed to determine whether early-onset PDAC (EOPC; ≤55 years) displays a distinctive molecular landscape from average-age onset PDAC (AOPC; ≥70 years). Three distinct datasets for PDAC were analyzed. In the first, patients undergoing treatment at Memorial Sloan Kettering (MSK) were consented for MSK-IMPACT next-generation sequencing. The second cohort analyzed was The Cancer Genome Atlas (TCGA) dataset for differences in somatic mutations, gene expression, and protein expression. The third dataset was an Australian cohort of PDAC. Clinical data were correlated with genomic analyses. A total of 293 samples were analyzed, yielding 90 patients aged ≤55 years and 203 patients aged ≥70 years. Among the genes known to be associated with carcinogenesis, SMAD4 displayed higher mutation rates in younger patients. Comprehensive transcriptomic analysis of cellular pathways indicated that the TGFβ pathway has increased activation, and the expression levels of phospho-GSK3 were higher in EOPC. Survival outcomes revealed no differences between age groups. These exploratory analyses suggest that there may be somatic gene alterations within the population of patients with early-onset PDAC that involve unique cellular pathways compared with average-onset PDAC. Former studies imply these cellular pathways may play a role in smoking-related PDAC carcinogenesis. Larger genomic datasets are warranted for future evaluation to extend these observations.

Comparative Effectiveness of Busulfan/Cyclophosphamide Versus Busulfan/Fludarabine Myeloablative Conditioning for Allogeneic Hematopoietic Cell Transplantation in Acute Myeloid Leukemia

BackgroundMyeloablative conditioning (MAC) is a standard approach for allogeneic hematopoietic cell transplantation (alloHCT), but is associated with risks of morbidity and mortality. As regimen intensity affects post-transplant outcomes, assessment of pre-transplant cytogenetics and somatic mutations may refine which acute myeloid leukemia (AML) patients benefit the most. We compared the effectiveness of two approaches: busulfan/cyclophosphamide (Bu/Cy) and the MAC, but reduced toxicity regimen busulfan/fludarabine (Bu/Flu). Moreover, it is unclear whether somatic mutations in AML may differentially affect post-transplant outcomes between these regimens. We hypothesized that despite relative differences with these regimens, they may result in comparable outcomes.MethodsWe conducted a single center, retrospective analysis of adult AML patients in CR1 or CR2 who underwent a first T-cell replete HLA-8/8 matched related or unrelated donor alloHCT. Patients received either parenteral Bu (12.8 mg/kg total over 4 days) with Cy (120 mg/kg total over 2 days) or parenteral Bu (400 mg/m2 total over 4 days) with Flu (160 mg/m2 total over 4 days). Bu dose adjustment was not used in either cohort. In addition to cytogenetic risk group stratification by European LeukemiaNet criteria (Döhner H, et al, Blood 2016), a subset of patients had a 36-gene somatic mutation panel assessed prior to alloHCT by next-generation sequencing. Pre-transplant characteristics were compared between regimens with Chi-square, Fisher's exact, or Wilcoxon rank sum tests. Differing characteristics were included in a multivariable Fine and Gray regression model with results as hazard ratios (HR) and 95% confidence intervals (CI).ResultsFrom 2008 - 2017, 76 AML patients receiving Bu/Cy and 50 receiving Bu/Flu were identified meeting inclusion criteria (Bu/Flu used starting in 2010). Median age at transplant was 51 (21-61) years for Bu/Cy vs. 64 (34-74) for Bu/Flu (P<0.001). The cohorts were otherwise comparable in regards to gender, race, performance status, HCT-CI, and disease status at alloHCT. Bu/Cy vs. Bu/Flu patients had 16% vs. 10% favorable, 66% vs. 50% intermediate, and 18% vs. 40% adverse-risk cytogenetics (P=0.033). The most common somatic mutations in the Bu/Cy cohort were FLT3 (20%), NPM1 (18%), DNMT3A (16%), TET2 (9%), CEBPA (5%), and IDH1 (5%). In the Bu/Flu cohort, these were FLT3 (20%), NPM1 (18%), NRAS (12%), TET2 (12%), and DNMT3A (10%). There were no significant differences in somatic mutations between the cohorts, except for a higher incidence of NRAS in the Bu/Flu cohort (12% vs. 4%, P=0.029). Bu/Flu patients were more likely to have an unrelated donor (70% vs. 47%, P=0.012) and receive a peripheral blood stem cell (PBSC) graft (94% vs. 17%, P<0.001). As such, Bu/Flu patients had more rapid neutrophil (median 13 vs. 14 days, P=0.009) and platelet (median 15 vs. 20 days, P<0.001) recovery and a shorter length of hospital stay (LOS) (median 22 vs. 27 days, P<0.001). In multivariable analysis, Bu/Flu patients trended towards more chronic graft-versus-host-disease (GvHD; any stage) (HR 0.42, CI 0.16-1.11, P=0.08), but there were no other differences in CMV infections, other infections, acute GvHD, relapse, relapse mortality (RM), non-relapse mortality (NRM), relapse-free (RFS), and overall survival (OS). 58% of Bu/Cy and 56% of Bu/Flu patients remain alive with median follow-up of 59 and 22 months, respectively (P=0.003). The most common causes of death for these respective cohorts were relapse (50% vs. 41%) and infection (16% vs. 27%).ConclusionBu/Cy and Bu/Flu in alloHCT for AML results in comparable incidences of infection, GvHD, RM, NRM, RFS, and OS. This was despite Bu/Flu patients being older and more likely to have adverse cytogenetics and an unrelated donor. Bu/Flu is better tolerated with less toxicity. Faster hematopoietic recovery and shorter LOS with Bu/Flu reflects PBSC graft use and has implications for health care resource utilization. Future prospective studies with larger cohorts and cost-effectiveness analyses comparing these conditioning strategies are warranted. In this analysis, no mutations appeared to be sensitive to use of the more intensive regimen, Bu/Cy. Further investigation of pre-transplant or post-transplant persistence of somatic mutations may risk stratify those who may benefit from more intensive or innovative approaches to prevent relapse after transplant. DisclosuresGerds:Apexx Oncology: Consultancy; Celgene: Consultancy; CTI Biopharma: Consultancy; Incyte: Consultancy. Majhail:Incyte: Honoraria; Atara: Honoraria; Anthem, Inc.: Consultancy.

Abstract 5364: Somatic mutations in African American and non-Hispanic White young-onset colorectal cancers

Abstract The proportion of colorectal cancers (CRCs) diagnosed at age &amp;lt;50 years is two-fold higher among African-Americans (AAs) compared to non-Hispanic Whites (NHW). Additionally, despite the rising incidence of young-onset CRC, little is known about the molecular characteristics of these as only 23 young-onset tumors were profiled in the TCGA cohort. Studies of CRC diagnosed in older individuals (age &amp;gt;50) demonstrate that CRC tumors in AAs are more often right-sided and MMR proficient, with higher prevalence of KRAS mutations. Risk of death from CRC among AAs with MMR proficient tumors is 73% higher than for NHW, after adjusting for treatment and known prognostic factors. We analyzed archival FFPE CRC tumors diagnosed in individuals age &amp;lt;50 (NHW enrolled in the UM Cancer Genetics Registry N=38 and African American subjects ascertained through the Wayne State University EpiCore N=13) for somatic mutations. Mutation profiling of tumor DNA from 51 CRCs diagnosed age &amp;lt;50 was performed using NGS sequencing with multigene panels in 2 sets (Qiagen GeneRead Cancer panel of 124 genes [N=36 tumors], Qiagen Qiaseq Comprehensive Cancer Panel of 275 genes [15 tumors]). We observed differences in CRC somatic mutations by race and by age. There was marked heterogeneity among tumors with regard to numbers of somatic mutations, with an average of 659 (range 39-10,267) variants detected per tumor, with 19/51 (37%) tumors classified as hypermutated. Among the most frequently mutated genes in young CRC tumors were APC (98% of tumors), PIK3CA (92% of tumors), NOTCH2 (86% of tumors), PTCH1 (82%), BRCA2 (67%), BRCA1 (84%), HNF1A (100%), RAD50 (29%), POLE (27%), MSH6 (39%), and FGFR3 (39%). These mutation profiles differ markedly from those of TCGA older-onset, nonhypermutated tumors. We identified differences in somatic mutations by race, including mutations in PTEN (NHW: 21% vs. AA: 8%), TGFBR2 (NHW: 32% vs. AA: 15%), FBXW7 (NHW: 47% vs. AA: 8%), and KRAS (NHW: 45% vs. AA: 31%). The relatively high prevalence of hypermutated tumors in this racially diverse cohort highlights the critical gaps in knowledge about pathways involved in pathogenesis of young-onset CRCs and how genomic information could guide precision therapies. Citation Format: Laura S. Rozek, Tingting Qin, Erika Koeppe, Peter Ulintz, Joel K. Greenson, Michele L. Cote, Elean M. Stoffel. Somatic mutations in African American and non-Hispanic White young-onset colorectal cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5364.

Abstract LB-121: Exploring the germ-line contribution to exceptional response to PD-1/PD-L1 inhibition in patients with metastatic non-small-cell lung cancer by whole genome sequencing

Abstract Responses to immune checkpoint inhibitors (CPI) may vary between individuals because of differences in somatic mutations in the tumour and/or germ-line differences in immunological tolerance. To explore the latter, this ongoing study evaluates patients with metastatic non-small cell lung cancer treated with single agent PD-1 or PD-L1 inhibitors from an active treatment pool of over 200 patients. Rare and common germ-line DNA variants are analysed in exceptional responders and non-responders by whole genome sequencing (Illumina HiSeq X Ten). Exceptional responders are defined as individuals with sustained partial (&amp;gt;6 months) or complete response per RECIST criteria with concurrent autoimmune toxicity, implying systemic immune activation. In these individuals, the cumulative burden of rare and common variants in a curated list of immune tolerance genes is analysed and compared to the Medical Genome Reference Bank, comprising whole genome sequences of 1146 well-elderly individuals. Comparisons are made with Fisher Exact test. Recurrent rare variants (Exome Aggregation Consortium (ExAC) frequency &amp;lt;1%) were found within responders sequenced to date (n=10), including variant A, a frameshift mutation in a protein associated with autoimmunity, not present in ExAC with Genome Aggregation Database (GnomAD) frequency 0.0002% (P &amp;lt; 0.0001). Multiple common variants (ExAC &amp;gt;2%) are more frequent within this cohort compared with population standard, for example variant B, a missense mutation within a DNA-repair protein that has ExAC allelic frequency of 2.5% and is present in 30% of our cohort (P = .013). Polygenic risk scores for diseases of impaired immune tolerance within exceptional responders are distinct from control groups. Further analyses of immune-related variants within anti-PD-1/PD-L1 responders and control groups will be presented. Preliminary findings suggest individuals harbouring damaging variants in genes promoting immune tolerance are more responsive to PD-1/PD-L1 inhibitors because basal immune activation is higher, requiring greater reliance on inhibitory checkpoints to maintain homeostasis. Ordinarily, this would be clinically undetectable, however the addition of a pharmacological CPI may more effectively break immune tolerance in this primed environment. Citation Format: Megan B. Barnet, Katherine J. Jackson, Bo Gao, Adnan M. Nagrial, Michael J. Boyer, Wendy A. Cooper, Rina Hui, Anthony Linton, Martin H. Tattersall, Greg Gibson, Jonathan Cebon, Georgina V. Long, Alexander M. Menzies, Richard A. Scolyer, Paul Lacaze, Robert Brink, Timothy Peters, Mark Cowley, Velimir Gayevskiy, David M. Thomas, Mark Pinese, Prunella Blinman, Steven Kao, Christopher C. Goodnow. Exploring the germ-line contribution to exceptional response to PD-1/PD-L1 inhibition in patients with metastatic non-small-cell lung cancer by whole genome sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-121.

Increased Frequency of KRAS Mutations in African Americans Compared with Caucasians in Sporadic Colorectal Cancer.

Objectives:The basis for over-representation of colorectal cancer (CRC) in African-American (AA) populations compared with Caucasians are multifactorial and complex. Understanding the mechanisms for this racial disparity is critical for delivery of better care. Several studies have investigated sporadic CRC for differences in somatic mutations between AAs and Caucasians, but owing to small study sizes and conflicting results to date, no definitive conclusions have been reached.Methods:Here, we present the first systematic literature review and meta-analysis investigating the mutational differences in sporadic CRC between AAs and Caucasians focused on frequent driver mutations (APC,TP53, KRAS,PI3CA, FBXW7,SMAD4, and BRAF). Publication inclusion criteria comprised sporadic CRC, human subjects, English language, information on ethnicity (AA, Caucasian, or both), total subject number >20, and information on mutation frequencies.Results:We identified 6,234 publications. Meta-analysis for APC, TP54, FBXW7, or SMAD4 was not possible owing to paucity of data. KRAS mutations were statistically less frequent in non-Hispanic Whites when compared with AAs (odds ratio, 0.640; 95% confidence interval (CI): 0.5342–0.7666; P=0.0001), while the mutational differences observed in BRAF and PI3CA did not reach statistical significance.Conclusions:Here, we report the mutational patterns for KRAS, BRAF, and PI3CA in sporadic CRC of AAs and Caucasians in a systematic meta-analysis of previously published data. We identified an increase in KRAS mutations in sporadic CRC in AAs, which may contribute to worse prognosis and increased mortality of CRC in AAs. Future studies investigating health-care disparities in CRC in AAs should control for KRAS mutational frequency.

Genomic Profile of Chronic Lymphocytic Leukemia in Korea Identified by Targeted Sequencing.

Chronic lymphocytic leukemia (CLL) is extremely rare in Asian countries and there has been one report on genetic changes for 5 genes (TP53, SF3B1, NOTCH1, MYD88, and BIRC3) by Sanger sequencing in Chinese CLL. Yet studies of CLL in Asian countries using Next generation sequencing have not been reported. We aimed to characterize the genomic profiles of Korean CLL and to find out ethnic differences in somatic mutations with prognostic implications. We performed targeted sequencing for 87 gene panel using next-generation sequencing along with G-banding and fluorescent in situ hybridization (FISH) for chromosome 12, 13q14.3 deletion, 17p13 deletion, and 11q22 deletion. Overall, 36 out of 48 patients (75%) harbored at least one mutation and mean number of mutation per patient was 1.6 (range 0–6). Aberrant karyotypes were observed in 30.4% by G-banding and 66.7% by FISH. Most recurrent mutation (>10% frequency) was ATM (20.8%) followed by TP53 (14.6%), SF3B1 (10.4%), KLHL6 (8.3%), and BCOR (6.25%). Mutations of MYD88 was associated with moderate adverse prognosis by multiple comparisons (P = 0.055). Mutation frequencies of MYD88, SAMHD1, EGR2, DDX3X, ZMYM3, and MED12 showed similar incidence with Caucasians, while mutation frequencies of ATM, TP53, KLHL6, BCOR and CDKN2A tend to be higher in Koreans than in Caucasians. Especially, ATM mutation showed 1.5 fold higher incidence than Caucasians, while mutation frequencies of SF3B1, NOTCH1, CHD2 and POT1 tend to be lower in Koreans than in Caucasians. However, mutation frequencies between Caucasians and Koreans were not significantly different statistically, probably due to low number of patients. Collectively, mutational profile and adverse prognostic genes in Korean CLL were different from those of Caucasians, suggesting an ethnic difference, while profile of cytogenetic aberrations was similar to those of Caucasians.

Genomic landscape of pancreatic adenocarcinoma: Does age matter?

250 Background: State-of the art genomic analyses of pancreatic adenocarcinoma (PDAC) has yielded insights into signaling pathways underlying carcinogenesis. PDAC is characterized by substantial genomic heterogeneity. We aimed to determine if early-onset PDAC ( ≤ 55 yrs) displays a distinctive molecular landscape from average-age onset PDAC ( ≥ 70 yrs). Methods: Three distinct datasets of PDAC in age groups ≤ 55 and ≥ 70 years old were analyzed. In the first, patients undergoing treatment at MSKCC were consented for MSK-IMPACT (Integrated Mutation Profiling of Actionable Cancer Targets) next generation sequencing. The second cohort analyzed was The Cancer Genome Atlas (TCGA) dataset for differences in somatic mutations, gene expression and protein expression. The third dataset was the Australian cohort of PDAC (Waddell et al, Nature, 2015). Clinical data were correlated with genomic analyses. Results: One hundred and eighty-three samples were analyzed, yielding N = 56 patients (pts) aged ≤ 55 years and N = 127 pts aged ≥ 70 years. Several genes known to be associated with carcinogenesis differed in mutation frequency across age groups: SMAD4, MYC and PIK3CA displayed higher mutation rates in younger patients (p &lt; 0.05, table below). Comprehensive analysis by cellular pathways indicated that the PI3Kpathway is further altered in the younger population. Protein expression had different patterns in younger versus older patients. Smoking was more prevalent in the early-onset group in all three cohorts (59% vs. 47%). Survival outcomes revealed no differences between the age groups. Conclusions: This exploratory analysis suggests that there may be somatic gene alterations within the population of early onset PDAC patients that involve unique cellular pathways compared with average onset PDAC. Former studies imply these cellular pathways may play a role in smoking-related PDAC carcinogenesis. Larger genomic datasets are warranted for future analysis to support this observation. [Table: see text]

Tumor and Host Factors Controlling Antitumor Immunity and Efficacy of Cancer Immunotherapy.

Despite recent clinical advances in immunotherapy, a fraction of cancer patients fails to respond to these interventions. Evidence from preclinical mouse models as well as clinical samples has provided evidence that the extent of activated T cell infiltration within the tumor microenvironment is associated with clinical response to immunotherapies including checkpoint blockade. Therefore, understanding the molecular mechanisms mediating the lack of T cell infiltration into the tumor microenvironment will be instrumental for the development of new therapeutic strategies to render those patients immunotherapy responsive. Recent data have suggested that major sources of intersubject heterogeneity include differences in somatic mutations in specific oncogene pathways between cancers of individual subjects and also environmental factors including commensal microbial composition. Successful identification of such causal factors should lead to new therapeutic approaches that may facilitate T cell entry into noninflamed tumors and expand the fraction of patients capable of responding to novel immunotherapies.