Braggio, Esteban

Key Points Pembrolizumab was first shown to be clinically active in CLL patients with RT. PD-1 and PD-L1 expression in tumor microenvironment are promising biomarkers to select RT patients for PD-1 blockade.

Abstract Cancer development is a complex process driven by inherited and acquired molecular and cellular alterations. Prevention is the holy grail of cancer elimination, but making this a reality will take a fundamental rethinking and deep understanding of premalignant biology. In this Perspective, we propose a national concerted effort to create a Precancer Atlas (PCA), integrating multi-omics and immunity – basic tenets of the neoplastic process. The biology of neoplasia caused by germline mutations has led to paradigm-changing precision prevention efforts, including: tumor testing for mismatch repair (MMR) deficiency in Lynch syndrome establishing a new paradigm, combinatorial chemoprevention efficacy in familial adenomatous polyposis (FAP), signal of benefit from imaging-based early detection research in high-germline risk for pancreatic neoplasia, elucidating early ontogeny in BRCA1-mutation carriers leading to an international breast cancer prevention trial, and insights into the intricate germline-somatic-immunity interaction landscape. Emerging genetic and pharmacologic (metformin) disruption of mitochondrial (mt) respiration increased autophagy to prevent cancer in a Li-Fraumeni mouse model (biology reproduced in clinical pilot) and revealed profound influences of subtle changes in mt DNA background variation on obesity, aging, and cancer risk. The elaborate communication between the immune system and neoplasia includes an increasingly complex cellular microenvironment and dynamic interactions between host genetics, environmental factors, and microbes in shaping the immune response. Cancer vaccines are in early murine and clinical precancer studies, building on the recent successes of immunotherapy and HPV vaccine immune prevention. Molecular monitoring in Barrett's esophagus to avoid overdiagnosis/treatment highlights an important PCA theme. Next generation sequencing (NGS) discovered age-related clonal hematopoiesis of indeterminate potential (CHIP). Ultra-deep NGS reports over the past year have redefined the premalignant landscape remarkably identifying tiny clones in the blood of up to 95% of women in their 50s, suggesting that potentially premalignant clones are ubiquitous. Similar data from eyelid skin and peritoneal and uterine lavage fluid provide unprecedented opportunities to dissect the earliest phases of stem/progenitor clonal (and microenvironment) evolution/diversity with new single-cell and liquid biopsy technologies. Cancer mutational signatures reflect exogenous or endogenous processes imprinted over time in precursors. Accelerating the prevention of cancer will require a large-scale, longitudinal effort, leveraging diverse disciplines (from genetics, biochemistry, and immunology to mathematics, computational biology, and engineering), initiatives, technologies, and models in developing an integrated multi-omics and immunity PCA – an immense national resource to interrogate, target, and intercept events that drive oncogenesis. Cancer Res; 77(7); 1510–41. ©2017 AACR.

Key Points IMiDs inhibit TrxR-mediated intracellular decomposition of H2O2 and caused oxidative stress in MM cells. MM cells with lower antioxidative capacity were more vulnerable to lenalidomide-induced H2O2 accumulation and its associated cytotoxicity.

Key Points The incidence of mutations within the MAPK pathway, the CRBN pathway, and TP53 is significantly increased in drug-refractory MM. Mutations in CRBN might contribute to IMiD resistance in drug-refractory MM.

Abstract Background: It has been shown that t(14;18), a translocation involving IgH and BCL-2 genes that is present in over 80% of all cases of follicular lymphomas, is detectable in the peripheral blood of up to 52% of normal Caucasian patients from Germany and up to 16% of normal individuals from Japan (Yasukawa et al, Blood 2001). The fact that follicular lymphoma is one of the two most common lymphomas in the USA and Germany and much less common in Japan, demonstrates that this molecular alteration is perhaps an early event in the development of this malignancy which is not sufficient for its causation. There have not been any studies evaluating the prevalence of this translocation in healthy African American (AA) subjects. We speculated that the prevalence of this translocation will be lower in healthy AA subjects given the findings of lower prevalence of IgH translocations in AA patients with multiple myeloma compared with Caucasian patients, which may explain the better outcome of myeloma in AA subjects (Baker et al, Blood 2013). This effort to evaluate the prevalence of t (14; 18) in AA subjects, was part of a pilot study in which we brought an educational program on the importance of cancer research together with concomitant access to a translational research project to AA churches utilizing a mobile research unit in an attempt to overcome some of the known barriers to AA subject participation in clinical research (Colon-Otero et al, Cancer2008; Colon-Otero et al, J Cancer Educ 2012). Methods: IRB approval of the project was obtained and peripheral blood samples collected from consented subjects during educational sessions in Northeast Florida AA Churches. Caucasian subjects were identified from the Mayo Clinic Bio-bank. DNA was isolated from the buffy coat fractions and a PCR quality control assay targeting a 293bp fragment of an HLA class II gene was used to determine acceptable DNA quality and quantity. Next, a two-step semi-nested PCR was performed on the t (14;18) major and minor breakpoint cluster regions using ~500ng of DNA for each assay. A consensus JH primer was used in combination with primers complementary to BCL-2 sequences for both, the major and minor breakpoint cluster regions. PCR products were run on a 1% agarose gel. In order to confirm the positive results, positive PCR products were analyzed by direct sequence by Sanger method and subsequently assembled to the human genome using BLAST tool. Results: A total of 110 blood samples from AA subjects were analyzed for the presence of t (14;18). A total of 13 of the samples were positive for the major breakpoint site (12%) and 4 were positive for the minor breakpoint site (4%), for a total of 17 positive samples (15%). In 167 Caucasian patients samples, a total of 22 (13%) were positive for the major breakpoint site and 5 (3%) were positive for the minor breakpoint site for a total of 27 positive samples (16%). All cases were confirmed by Sanger sequencing. Conclusions: The prevalence of t(14;18) is not significantly different among African American and Caucasian subjects from the USA based on our findings. This represents the first report of the prevalence of t(14;18) in an African American population. The prevalence found in our Caucasian subjects is significantly lower than what had been described in previous population series. A plausible explanation is the high heterogeneity of approaches used across studies, significantly affecting the assay sensitivity. Additional studies with larger series may reveal minor differences in the prevalence of t(14;18) among these populations. Citation Format: Scott Van Wier, Gerardo Colon-Otero, Gregory Ahmann, Esteban Braggio, Monica Albertie, Sikander Ailawadhi, Rafael Fonseca. Similar prevalence of t(14,18) in African American and Caucasian subjects. [abstract]. In: Proceedings of the Eighth AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 13-16, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2016;25(3 Suppl):Abstract nr B48.

Abstract Purpose: Primary central nervous system lymphoma (PCNSL) is an aggressive non-Hodgkin lymphoma confined to the central nervous system. Whether there is a PCNSL-specific genomic signature and, if so, how it differs from systemic diffuse large B-cell lymphoma (DLBCL) is uncertain. Experimental Design: We performed a comprehensive genomic study of tumor samples from 19 immunocompetent PCNSL patients. Testing comprised array-comparative genomic hybridization and whole exome sequencing. Results: Biallelic inactivation of TOX and PRKCD was recurrently found in PCNSL but not in systemic DLBCL, suggesting a specific role in PCNSL pathogenesis. In addition, we found a high prevalence of MYD88 mutations (79%) and CDKN2A biallelic loss (60%). Several genes recurrently affected in PCNSL were common with systemic DLBCL, including loss of TNFAIP3, PRDM1, GNA13, TMEM30A, TBL1XR1, B2M, CD58, activating mutations of CD79B, CARD11, and translocations IgH-BCL6. Overall, B-cell receptor/Toll-like receptor/NF-κB pathways were altered in >90% of PNCSL, highlighting its value for targeted therapeutic approaches. Furthermore, integrated analysis showed enrichment of pathways associated with immune response, proliferation, apoptosis, and lymphocyte differentiation. Conclusions: In summary, genome-wide analysis uncovered novel recurrent alterations, including TOX and PRKCD, helping to differentiate PCNSL from systemic DLBCL and related lymphomas. Clin Cancer Res; 21(17); 3986–94. ©2015 AACR.

Abstract Introduction: Identification of causal DNA copy number variations (CNVs) is critical to the understanding of cancer development and progression, and is important clinically for accurate prognosis and efficient treatment. T-cell lymphomas are replete with amplifications and deletions that result in over- and under-expression of genes. Array comparative genomic hybridization (aCGH) has been the technology of choice to detect CNVs but recently, it has been proposed that mate-pair Next Generation Sequencing (mpNGS) can produce similar results. Here, we report a comparison between the two techniques. Methods: We have developed an algorithm based on extreme value theory to identify CNVs across the genome at high resolution from mate-pair NGS data. The algorithm is based on plotting the distribution of read-counts in windows across the genome, and detecting deletions and gains by finding the windows that differ significantly from the distribution of the normal part of the genome. We compared this algorithm with aCGH data to detect CNVs. We ran five cases of T-cell lymphoma with both techniques and compared the results using concordance statistics. Results: With 50kb lower cutoff for a CNV, mpNGS detected 98% of the cumulative deleted genome and 94% of the amplified/gained genome that were called by aCGH. Most of the discordant CNVs that were detected by only aCGH were in regions of repetitive areas where mapping fails. Conversely, aCGH detected 75% of the cumulative deleted genome and 74% of the amplified/gained genome that were called by mpNGS. Conclusion: A detailed comparison of these techniques showed that both have pros and cons. In general, mpNGS can detect most CNVs detected by aCGH, as long as they are more than 50KB. Additionally, mpNGS offers confirmatory data, particularly for deletions, based on detection of aberrant mate pairs that map to the rejoined ends of deleted regional. Finally, the mate-pair technology can also detect balanced translocations and can also predict fusion genes. Citation Format: George Vasmatzis, Andrew L. Feldman, Sarah H. Johnson, Erik C. Thorland, Rafael Fonseca, Esteban Braggio, Troy J. Gliem. Copy number detection using genomics technologies: A comparison between aCGH and NGS. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3572. doi:10.1158/1538-7445.AM2014-3572