Bone marrow-derived mesenchymal stromal cells obstruct AML-targeting CD8+ clonal effector and CAR T-cell function while promoting a senescence-associated phenotype

Bone marrow mesenchymal stromal cells (MSCs) have been described as potent regulators of T-cell function, though whether they could impede the effectiveness of immunotherapy against acute myeloid leukemia (AML) is still under investigation. We examine whether they could interfere with the activity of leukemia-specific clonal cytotoxic T-lymphocytes (CTLs) and chimeric antigen receptor (CAR) T cells, as well as whether the immunomodulatory properties of MSCs could be associated with the induction of T-cell senescence. Co-cultures of leukemia-associated Wilm's tumor protein 1 (WT1) and tyrosine-protein kinase transmembrane receptor 1 (ROR1)-reactive CTLs and of CD123-redirected switchable CAR T cells were prepared in the presence of MSCs and assessed for cytotoxic potential, cytokine secretion, and expansion. T-cell senescence within functional memory sub-compartments was investigated for the senescence-associated phenotype CD28-CD57+ using unmodified peripheral blood mononuclear cells. We describe inhibition of expansion of AML-redirected switchable CAR T cells by MSCs via indoleamine 2,3-dioxygenase 1 (IDO-1) activity, as well as reduction of interferon gamma (IFNγ) and interleukin-2 (IL-2) release. In addition, MSCs interfered with the secretory potential of leukemia-associated WT1- and ROR1-targeting CTL clones, inhibiting the release of IFNγ, tumor necrosis factor alpha, and IL-2. Abrogated T cells were shown to retain their cytolytic activity. Moreover, we demonstrate induction of a CD28loCD27loCD57+KLRG1+ senescent T-cell phenotype by MSCs. In summary, we show that MSCs are potent modulators of anti-leukemic T cells, and targeting their modes of action would likely be beneficial in a combinatorial approach with AML-directed immunotherapy.

A chemically defined biomimetic surface for enhanced isolation efficiency of high-quality human mesenchymal stromal cells under xenogeneic/serum-free conditions

BACKGROUND AIMS

Mesenchymal stromal cells (MSCs) are one of the most frequently used cell types in regenerative medicine and cell therapy. Generating sufficient cell numbers for MSC-based therapies is constrained by (i) their low abundance in tissues of origin, which imposes the need for significant ex vivo cell expansion; (ii) donor-specific characteristics, including MSC frequency/quality, that decline with disease state and increasing age; and (iii) cellular senescence, which is promoted by extensive cell expansion and results in decreased therapeutic functionality. The final yield of a manufacturing process is therefore primarily determined by the applied isolation procedure and its efficiency in isolating therapeutically active cells from donor tissue. To date, MSCs are predominantly isolated using media supplemented with either serum or its derivatives, which poses safety and consistency issues.

METHODS

To overcome these limitations while enabling robust MSC production with constant high yield and quality, the authors developed a chemically defined biomimetic surface coating called isoMATRIX (denovoMATRIX GmbH, Dresden, Germany) and tested its performance during isolation of MSCs.

RESULTS

The isoMATRIX facilitates the isolation of significantly higher numbers of MSCs in xenogeneic (xeno)/serum-free and chemically defined conditions. The isolated cells display a smaller cell size and higher proliferation rate than those derived from a serum-containing isolation procedure and a strong immunomodulatory capacity. The high proliferation rates can be maintained up to 5 passages after isolation and cells even benefit from a switch towards a proliferation-specific MSC matrix (myMATRIX MSC) (denovoMATRIX GmbH, Dresden, Germany).

CONCLUSION

In sum, isoMATRIX promotes enhanced xeno/serum-free and chemically defined isolation of human MSCs and supports consistent and reliable cell performance for improved stem cell-based therapies.

Immunomodulatory Properties of Mesenchymal Stromal Cells: An Update

Mesenchymal stromal cells (MSCs) are characterized by an extraordinary capacity to modulate the phenotype and functional properties of various immune cells that play an essential role in the pathogenesis of inflammatory disorders. Thus, MSCs efficiently impair the phagocytic and antigen-presenting capacity of monocytes/macrophages and promote the expression of immunosuppressive molecules such as interleukin (IL)-10 and programmed cell death 1 ligand 1 by these cells. They also effectively inhibit the maturation of dendritic cells and their ability to produce proinflammatory cytokines and to stimulate potent T-cell responses. Furthermore, MSCs inhibit the generation and proinflammatory properties of CD4⁺ T helper (Th)1 and Th17 cells, while they promote the proliferation of regulatory T cells and their inhibitory capabilities. MSCs also impair the expansion, cytokine secretion, and cytotoxic activity of proinflammatory CD8⁺ T cells. Moreover, MSCs inhibit the differentiation, proliferation, and antibody secretion of B cells, and foster the generation of IL-10-producing regulatory B cells. Various cell membrane-associated and soluble molecules essentially contribute to these MSC-mediated effects on important cellular components of innate and adaptive immunity. Due to their immunosuppressive properties, MSCs have emerged as promising tools for the treatment of inflammatory disorders such as acute graft-versus-host disease, graft rejection in patients undergoing organ/cell transplantation, and autoimmune diseases.

Lobular Carcinomas In Situ Display Intralesion Genetic Heterogeneity and Clonal Evolution in the Progression to Invasive Lobular Carcinoma

PURPOSE

Lobular carcinoma in situ (LCIS) is a preinvasive lesion of the breast. We sought to define its genomic landscape, whether intralesion genetic heterogeneity is present in LCIS, and the clonal relatedness between LCIS and invasive breast cancers.Experimental Design: We reanalyzed whole-exome sequencing (WES) data and performed a targeted amplicon sequencing validation of mutations identified in 43 LCIS and 27 synchronous more clinically advanced lesions from 24 patients [9 ductal carcinomas in situ (DCIS), 13 invasive lobular carcinomas (ILC), and 5 invasive ductal carcinomas (IDC)]. Somatic genetic alterations, mutational signatures, clonal composition, and phylogenetic trees were defined using validated computational methods.

RESULTS

WES of 43 LCIS lesions revealed a genomic profile similar to that previously reported for ILCs, with CDH1 mutations present in 81% of the lesions. Forty-two percent (18/43) of LCIS were found to be clonally related to synchronous DCIS and/or ILCs, with clonal evolutionary patterns indicative of clonal selection and/or parallel/branched progression. Intralesion genetic heterogeneity was higher among LCIS clonally related to DCIS/ILC than in those nonclonally related to DCIS/ILC. A shift from aging to APOBEC-related mutational processes was observed in the progression from LCIS to DCIS and/or ILC in a subset of cases.

CONCLUSIONS

Our findings support the contention that LCIS has a repertoire of somatic genetic alterations similar to that of ILCs, and likely constitutes a nonobligate precursor of breast cancer. Intralesion genetic heterogeneity is observed in LCIS and should be considered in studies aiming to develop biomarkers of progression from LCIS to more advanced lesions.

Bi-allelic alterations in DNA repair genes underpin homologous recombination DNA repair defects in breast cancer

Homologous recombination (HR) DNA repair-deficient (HRD) breast cancers have been shown to be sensitive to DNA repair targeted therapies. Burgeoning evidence suggests that sporadic breast cancers, lacking germline BRCA1/BRCA2 mutations, may also be HRD. We developed a functional ex vivo RAD51-based test to identify HRD primary breast cancers. An integrated approach examining methylation, gene expression, and whole-exome sequencing was employed to ascertain the aetiology of HRD. Functional HRD breast cancers displayed genomic features of lack of competent HR, including large-scale state transitions and specific mutational signatures. Somatic and/or germline genetic alterations resulting in bi-allelic loss-of-function of HR genes underpinned functional HRD in 89% of cases, and were observed in only one of the 15 HR-proficient samples tested. These findings indicate the importance of a comprehensive genetic assessment of bi-allelic alterations in the HR pathway to deliver a precision medicine-based approach to select patients for therapies targeting tumour-specific DNA repair defects. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Clonal relationships between lobular carcinoma in situ and other breast malignancies

Background

Recent evidence suggests that lobular carcinoma in situ (LCIS) can be a clonal precursor of invasive breast cancers of both the ductal and lobular phenotypes. We sought to confirm these findings with an extensive study of fresh frozen breast specimens from women undergoing mastectomy.

Methods

Patients with a history of LCIS presenting for therapeutic mastectomy were identified prospectively. Frozen tissue blocks were collected, screened for lesions of interest, and subjected to microdissection and DNA extraction. Copy number profiling, whole-exome sequencing, or both were performed. Clonal relatedness was assessed using specialized statistical techniques developed for this purpose.

Results

After exclusions for genotyping failure, a total of 84 lesions from 30 patients were evaluated successfully. Strong evidence of clonal relatedness was observed between an LCIS lesion and the invasive cancer for the preponderance of cases with lobular carcinoma. Anatomically distinct in situ lesions of both ductal and lobular histology were also shown to be frequently clonally related.

Conclusions

These data derived from women with LCIS with or without invasive cancer confirm that LCIS is commonly the clonal precursor of invasive lobular carcinoma and that distinct foci of LCIS frequently share a clonal origin, as do foci of LCIS and ductal carcinoma in situ.

Electronic supplementary material

The online version of this article (doi:10.1186/s13058-016-0727-z) contains supplementary material, which is available to authorized users.

Abstract S4-04: Lobular carcinoma in situ displays intra-lesion genetic heterogeneity and its progression to invasive disease involves clonal selection and variations in mutational processes

Introduction: Lobular carcinoma in situ (LCIS) is considered both a risk factor and non-obligate precursor of invasive breast cancer. We sought to determine the genomic landscape of LCIS and the mutational processes involved in the clonal evolution and progression from LCIS to ductal carcinoma in situ (DCIS) and invasive lobular carcinoma (ILC).

Methods: Patients with a history of LCIS undergoing therapeutic or prophylactic mastectomy were prospectively enrolled in an IRB approved protocol. Frozen tissue blocks were collected, screened for lesions of interest (LCIS, DCIS, ILC, invasive ductal carcinomas (IDC)) and subjected to microdissection and DNA/RNA extraction. Matched germline DNA was available for all cases. Whole exome sequencing was performed on a HiSeq2000 and data were aligned to the reference human genome and processed using GATK. Single nucleotide variants (SNVs) and small insertions/deletions were identified using MuTect and Varscan, respectively. Purity and ploidy estimates were calculated using ABSOLUTE. Clonal frequencies were estimated using Pyclone and the clonal structure of each sample was reconstructed using SubcloneSeeker. Shannon index and Simpson index metrics were used to calculate heterogeneity levels. Mutational signatures were defined according to their mutational trinucleotide context, and the expression levels of APOBEC gene family members were assessed by quantitative reverse transcription (qRT)-PCR.

Results: 30 LCIS, 10 ILCs, 7 DCIS and 5 IDCs from 15 patients qualified for data analysis. CDH1 was the most frequently mutated gene and found to be targeted by mutations in 26 LCIS samples (23 somatic, 3 germline). The repertoire of somatic mutations in LCIS was similar to that of luminal A breast cancers, with the exception of the significantly higher frequency of CDH1 mutations and the lower prevalence of TP53 mutations. ILCs were clonally related to at least one LCIS in 10 patients, and in 3/7 patients, DCIS was clonally related to at least one LCIS. Clonal composition analysis revealed that the presence of a minor clone(s) in LCIS, and the levels of intra-tumor genetic heterogeneity were significantly higher in LCIS clonally related with DCIS/ILC than in LCIS unrelated to DCIS/ILC. In two cases, a minor LCIS subclone constituted the major clone in the associated DCIS/ILC. A comparative analysis of the mutational signatures in the truncal and branch mutations of these cases revealed that whilst the truncal mutations displayed an aging signature, branch mutations were enriched for the APOBEC signature. qRT-PCR analysis demonstrated that cases displaying the APOBEC signature also harbored significantly higher levels of APOBEC3B expression than samples with the aging signature.

Conclusions: LCIS displays intra-lesion genetic heterogeneity, and the progression from LCIS to DCIS or ILC may involve the selection of clones resulting from distinct mutational processes during clonal evolution. Our findings also suggest that cytodine deamination driven by the overexpression of APOBEC3B may drive the progression of LCIS to DCIS/ILC in a subset of cases.

Citation Format: Reis-Filho JS, Schizas M, Piscuoglio S, Sakr RA, Ng CKY, Lim RS, Carniello JVS, Towers R, Martelotto L, Giri DD, de Andrade VP, Viale A, Solit DB, Weigelt B, King TA. Lobular carcinoma in situ displays intra-lesion genetic heterogeneity and its progression to invasive disease involves clonal selection and variations in mutational processes. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr S4-04.

Abstract P6-06-02: Germline CDH1 mutations in lobular carcinoma in situ

BACKGROUND: Germline CDH1 mutations are responsible for the increased risk of both gastric cancer and invasive lobular breast cancer (ILC) in families with hereditary diffuse gastric cancer syndrome; yet germline CDH1 mutations in women with ILC without a family history (FH) of gastric cancer are rare. Lobular carcinoma in situ (LCIS) is both a risk factor and non-obligate precursor of ILC and recent data suggest that germline CDH1 mutations may be present in up to 8% of patients with bilateral LCIS +/- ILC; raising questions about the role of genetic testing in this context. The purpose of this study was to determine the frequency of germline CDH1 mutations in a large prospectively followed cohort of patients with pathologically confirmed bilateral LCIS.

METHODS: Patients with a biopsy proven history of LCIS, entering surveillance or presenting for surgery (prophylactic or therapeutic mastectomy), between 2005 and 2013 were prospectively identified and enrolled in IRB approved protocols at Memorial Sloan-Kettering Cancer Center for the collection of tissue and/or germline DNA (IRB 01-135, 99-030). All biopsies were reviewed to confirm LCIS and mastectomy specimens were subject to extensive sampling of all quadrants. Cases with confirmed bilateral LCIS were chosen for the primary analysis. Cases where bilateral mastectomy tissue sampling confirmed only unilateral LCIS were included for comparison. Germline DNA was anonymized and analyzed for CDH1 mutations using targeted capture sequencing with baits for all exons of CDH1 on HiSeq2000. Germline single nucleotide variants were called using GATK HaplotypeCaller and insertions/deletions by Varscan and Scalpel. Mutations were manually inspected using the Integrative Genomics Viewer (IGV). Clinical data were abstracted prior to anonymization.

RESULTS: Germline DNA was available for 114 patients; 78 underwent bilateral mastectomy for breast cancer (BC), 8 chose prophylactic mastectomy and 28 patients with biopsy proven bilateral LCIS were identified in surveillance. Following mastectomy, tissue sampling confirmed bilateral LCIS in 67/86 (78%) patients, and ruled out bilateral LCIS in 19 patients; yielding 95 patients with bilateral LCIS for the primary analysis. Median age at LCIS diagnosis for bilateral and unilateral cases respectively was 48yrs (range 36-70) and 44 yrs (range 38-63). One patient with bilateral LCIS also reported a FH of gastric cancer. Pathogenic germline CDH1 mutations (D72N (missense) and E35* (nonsense)) were identified in 2/95 (2%) patients with bilateral LCIS, one of whom also had invasive breast cancer (ILC). A germline CDH1 mutation was not identified in the patient with bilateral LCIS and a FH of gastric cancer, nor were CDH1 mutations identified among the 19 patients with unilateral LCIS.

CONCLUSIONS: In this cohort of 95 patients with pathologically documented bilateral LCIS +/- BC, the overall frequency of CDH1 germline mutations was 2%; considerably lower than previously reported. To our knowledge this is the largest series to address this question and these findings do not support germline testing for CDH1 mutations in women with bilateral LCIS.

Citation Format: Reyes SA, Sakr RA, Schizas M, Towers R, Park AY, Ng CKY, Weigelt B, Reis-Filho JS, King TA. Germline CDH1 mutations in lobular carcinoma in situ. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-06-02.

Biomarkers That Predict Sensitivity to Heat Shock Protein 90 Inhibitors

INTRODUCTION

Heat shock protein (HSP) 90, a viable target for cancer treatment, mediates the maturation and stabilization of client oncoproteins. HSP90 inhibitors (HSP90i) are potentially active in a variety of tumors, but therapeutic benefit is confirmed in only a small subset. We explored potential biomarkers across multiple studies of HSP90i in advanced solid tumors.

PATIENTS AND METHODS

Archived tumor specimens from patients treated with HSP90i in 7 different phase I/II trials at Memorial Sloan Kettering Cancer Center were identified. Tumor tissue was tested using immunohistochemistry; estrogen, progesterone, and androgen receptors ≥ 1% positive and < 1% negative; HSP90 and HSP70: 0, 1 + negative, and 2+, 3 + positive; phosphatase and tensin homolog: 0 negative, 1 reduced, and 2 positive; HER2: 0, 1 + negative, 2 + equivocal, 3 + positive; and epidermal growth factor receptor: 0 negative, and 1+, 2+, 3 + positive. The expression of the biomarker panel was correlated with clinical benefit (CB) (defined by overall response [ORR] or CB by the "8-week" scan) using Fisher exact test.

RESULTS

Adequate tissue was available for 51 of 158 patients (32%), including 10 different solid tumors. Of these, 71% (36 of 51) and 51% (26 of 51) patients met the criteria to assess CB by best ORR or by the "8-week scan" assessment, respectively. Breast was the most frequent tumor. The mean duration of HSP90i therapy was 55 days (range, 16-411 days). There were 16 responses (4 partial response; 12 stable disease); 13 of 16 responses strongly correlated with HER2-positive status (P = .001).

CONCLUSION

Our findings suggest HER2 as a sensitive client and perhaps the only effective biomarker for sensitivity to these HSP90i.

Targeted capture massively parallel sequencing analysis of LCIS and invasive lobular cancer: Repertoire of somatic genetic alterations and clonal relationships

PURPOSE

Lobular carcinoma in situ (LCIS) has been proposed as a non-obligate precursor of invasive lobular carcinoma (ILC). Here we sought to define the repertoire of somatic genetic alterations in pure LCIS and in synchronous LCIS and ILC using targeted massively parallel sequencing.

METHODS

DNA samples extracted from microdissected LCIS, ILC and matched normal breast tissue or peripheral blood from 30 patients were subjected to massively parallel sequencing targeting all exons of 273 genes, including the genes most frequently mutated in breast cancer and DNA repair-related genes. Single nucleotide variants and insertions and deletions were identified using state-of-the-art bioinformatics approaches.

RESULTS

The constellation of somatic mutations found in LCIS (n = 34) and ILC (n = 21) were similar, with the most frequently mutated genes being CDH1 (56% and 66%, respectively), PIK3CA (41% and 52%, respectively) and CBFB (12% and 19%, respectively). Among 19 LCIS and ILC synchronous pairs, 14 (74%) had at least one identical mutation in common, including identical PIK3CA and CDH1 mutations. Paired analysis of independent foci of LCIS from 3 breasts revealed at least one common mutation in each of the 3 pairs (CDH1, PIK3CA, CBFB and PKHD1L1).

CONCLUSION

LCIS and ILC have a similar repertoire of somatic mutations, with PIK3CA and CDH1 being the most frequently mutated genes. The presence of identical mutations between LCIS-LCIS and LCIS-ILC pairs demonstrates that LCIS is a clonal neoplastic lesion, and provides additional evidence that at least some LCIS are non-obligate precursors of ILC.

Abstract 2971: Whole exome sequencing reveals heterogeneity within lobular carcinoma in situ (LCIS) and clonal selection in the progression to malignant lesions

INTRODUCTION: Lobular carcinoma in situ (LCIS) is considered both a risk factor and non-obligate precursor of low-grade estrogen receptor-positive breast cancer. We sought to define the mutational repertoire, subclone complexity and heterogeneity of LCIS, and whether invasive lobular carcinomas (ILCs) would stem from specific subclones within a LCIS.

METHODS: Patients with a history of LCIS undergoing therapeutic or prophylactic mastectomy were prospectively enrolled in an IRB approved protocol. Frozen tissue blocks were collected, screened for lesions of interest (LCIS, ductal carcinoma in situ (DCIS), ILC, invasive ductal carcinoma (IDC)) and subject to microdissection and DNA extraction. Matched germline DNA was available for all cases. Whole exome sequencing was performed on a HiSeq2000 (Illumina) and data were aligned to the reference human genome hg19 and processed using GATK. SNVs were called using MuTect, and indels were called using a combination of Varscan and Strelka. Purity and ploidy estimates were calculated by ABSOLUTE. Clonal frequencies were estimated using Pyclone.

RESULTS: 30 LCIS, 10 ILCs, 6 IDCs and 7 DCIS from 15 patients qualified for data analysis, resulting in 18 LCIS-ILC pairs, 22 LCIS-LCIS pairs, 12 LCIS-DCIS pairs, and 14 LCIS-IDC pairs for comparison. 9/18 (50%) LCIS-ILC pairs and 8/22 (36%) LCIS-LCIS pairs were clonally related, supported by several shared mutations (median 18, range 7-81 for LCIS-ILC; median 14, range 5-22 for LCIS-LCIS). All related LCIS-ILC pairs and 6/8 related LCIS-LCIS pairs shared a pathogenic CDH1 mutation; 75% of related LCIS-ILC pairs also shared a PIK3CA hotspot mutation. 7/12 (58%) LCIS-DCIS pairs were found to be clonally related but the number of shared mutations was generally lower than that found in LCIS-ILC pairs (median 9, range 2-11). No evidence of a clonal relationship was found in any of the LCIS-IDC pairs tested. Clonal composition analysis revealed that samples of LCIS display intra-lesion genetic heterogeneity in the form of the presence of a minor clone in 70% of cases. In one case, the LCIS minor subclone (∼15%) constituted the major clone in the ILC and in another case the LCIS minor subclone constituted the major clone in the associated DCIS. The majority of the clonally related lesions were located in the same quadrant of the breast, however evidence of clonality was found in 5 LCIS-LCIS and 3 LCIS-DCIS pairs located in separate quadrants of the breast.

CONCLUSIONS: Intra-lesion genetic heterogeneity is a common phenomenon in LCIS. The dominant clone of a LCIS may not always be the clone directly involved in the progression to malignancy. The spatial relationships of clonally related lesions in this study suggest that anatomy does not always infer clonality, as lesions located in separate quadrants of the breast may be clonally related.

Citation Format: Michail Schizas, Rita A. Sakr, Britta Weigelt, Charlotte KY Ng, Jose Victor S. Carniello, Dilip Giri, Salvatore Piscuoglio, Luciano G. Martelotto, Russell Towers, Victor P. Andrade, Raymond Lim, David B. Solit, Jorge S. Reis-Filho, Tari A. King. Whole exome sequencing reveals heterogeneity within lobular carcinoma in situ (LCIS) and clonal selection in the progression to malignant lesions. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2971. doi:10.1158/1538-7445.AM2015-2971

Abstract 930: Analysis of cell-free tumor DNA in cerebrospinal fluid to characterize and monitor the genetic alterations of brain tumors

Background: Genetic characterization and monitoring of brain tumors is challenging given the restricted sampling of tumors and the limited abundance of brain tumor-derived circulating tumor DNA (ctDNA) in the plasma. Here, we sought to define whether cerebrospinal fluid (CSF) could serve as a ‘liquid biopsy’ for the genetic characterization of tumor DNA originated from the central nervous system (CNS) of patients (pts) with brain tumors.

Methods: CSF, plasma and tumor tissue were obtained from pts with glioblastoma (GBM), brain metastases from breast (BMBC) and lung cancers (BMLC) and leptomeningeal carcinomatosis (LC). Whole exome sequencing was done in CSF and tumor (n = 3) and was coupled with digital PCR for monitoring CSF and plasma ctDNA (n = 6). Targeted capture massively parallel sequencing of 39 samples from 4 BMBC pts, including samples from CSF, plasma and matched metastatic sites obtained at autopsy was performed using two independent platforms (MSK-IMPACT (341 genes) and BC panel (254 genes most frequently mutated in BC)) comprising 488 unique genes. Sequencing was performed on an Illumina HiSeq2000. Single nucleotide variants were defined using MuTect, and indels using Varscan. Copy number alterations were assessed using Varscan2 and GISTIC.

Results: Whole exome sequencing of tumor and CSF DNA revealed a high proportion of tumor-derived cell-free DNA in the CSF of 3 pts (1 GBM, 2 BMBC). We identified actionable somatic mutations (EGFR L858R, IDH1 R132H) and also IDH1 mutations associated with molecular diagnosis of proneural GBM. In CSF and plasma ctDNA of 6 pts with GBM, BMBC, BMLC, we observed that the mutations present in the CSF ctDNA, but not plasma ctDNA, and their mutant allele fractions (MAFs) correlated with brain tumor burden. In 3 pts with suspected LC, we compared the results of cytopathologic analysis and CSF ctDNA obtained from samples used for cytopathologic diagnosis, and observed that CSF ctDNA was more robust and sensitive for the diagnosis of LC. The analysis of synchronous CSF ctDNA, plasma ctDNA and intra- and extra-cranial metastases from 4 autopsied BMBC pts showed that CSF ctDNA recapitulated the somatic genetic alterations present in the intra-cranial lesions. We detected similar MAFs for the truncal mutations (RB1, KMT2D, AHNAK2) in both CSF and plasma DNA of BMBC3, a pt with Li-Fraumeni syndrome and a diagnosis of concurrent BMBC and esthesioneuroblastoma; however, mutations in PIK3CB, PAK7, MSH5 found only in the CNS implant of each disease were only detected in the CSF but not in the plasma DNA.

Conclusions: Brain tumor-derived ctDNA is abundantly present in the CSF of brain cancer pts and compared to plasma ctDNA, CSF ctDNA is more representative of the brain lesions. Our results demonstrate that massively parallel sequencing can be performed using CSF DNA, allowing for the non-invasive genomic characterization and monitoring of brain lesions.

Citation Format: Leticia De Mattos-Arruda, Regina Mayor, Charlotte K. Y. Ng, Britta Weigelt, Francisco Martínez-Ricarte, Davis Torrejon, Mafalda Oliveira, Carolina Raventos, Alexandra Arias, Elena Guerini-Rocco, Elena Martínez-Sáez, Sergio Lois, Oscar Marín, Xavier de la Cruz, Salvatore Piscuoglio, Russell Towers, Ana Vivancos, Vicente Peg, Santiago Ramon y Cajal, Jordi Rodon, Enriqueta Felip, Joan Sahuquillo, Josep Tabernero, Javier Cortes, Jorge S. Reis-Filho, Joan Seoane. Analysis of cell-free tumor DNA in cerebrospinal fluid to characterize and monitor the genetic alterations of brain tumors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 930. doi:10.1158/1538-7445.AM2015-930

Biomarkers that predict sensitivity to heat shock protein 90 inhibitors (HSP90i)

10618

Background: HSP90 is an attractive target in tumors as it mediates the maturation and stabilization of client oncoproteins. HSP90i are potentially active in a variety of tumors, but therapeutic benefit is confirmed in only a small subset to date. Predictive biomarkers could identify patients (pts) and/or tumors with sensitivity to HSP90i improving the therapeutic index. We explored potential biomarkers across multiple studies of HSP90i. Methods: Archived pre-treatment tumor specimens from pts treated with any of several HSP90i (17-AAG, 17-DMAG, CNF2024, retaspimycin & ganetespib) on 8 phase I/II trials at MSKCC from 1999 to 2011 were identified. The following antibodies were validated at MSKCC and tumor tissue was tested by immunohistochemistry (IHC) with results defined for each as: ER, PR & AR: >1% pos & <1% neg; HSP90 & HSP70: 0, 1+ neg & 2+, 3+ pos; PTEN: 0, 1+ neg & 2+ pos; HER2: 0, 1+ neg, 2+ equivocal, 3+ pos; EGFR: 0 neg & 1+, 2+, 3+ pos. Clinical response was correlated with IHC using Fisher’s exact test. Results: Of the 164 pts identified, adequate tissue was available for 51, including 11 different solid tumors & 1 CML. Breast (N=31), melanoma & prostate (N=4 each) were most frequent. The mean age at primary diagnosis was 50 yrs (24-81). The median no. of lines of prior chemotherapy for metastatic disease was 2 (0-8). The mean duration of HSP90i therapy was 79 days (0-411). There were 19 responses (5 PR; 14 SD); 14/19 responses strongly correlated with HER2+ status (p = 0.001); 1 pt with ER+/HER2-/EGFR- & 4 with EGFR +/HER2-/ER- disease also responded. A correlation for ER & EGFR with response was not excluded (p=0.07 & p=0.086 respectively). Conclusions: Our findings confirm HER2 as a sensitive client and an effective biomarker for sensitivity to HSP90 inhibitors. ER & EGFR did not meet statistical significance but may warrant further exploration in prospective settings.

Alpha1-adrenergic receptor mRNA and inflammatory mediator expression in circulating leucocytes after cardiac surgery

Vasodilation after coronary artery bypass surgery is a common complication. Inflammatory mediators influence the expression of alpha1-adrenergic receptors. Do patients requiring high doses of postoperative inotropic support have down-regulated alpha-adrenergic receptors? Is there a characteristic pattern of preoperative inflammatory mediator expression that could predict a complicated course after the operation? Forty-four patients undergoing cardiac bypass surgery with extracorporeal circulation were prospectively investigated. Five perioperative blood samples were taken (preoperative, two hours, 12 hours, 36 hours and 72 hours postoperative). The leucocyte mRNA-expression of the three alpha1-adrenergic receptor subtypes (A, B and D) and 11 different pro-inflammatory mediators were investigated with the real-time reverse transcriptase polymerase chain reaction. The patients were divided into three groups (No-noradrenaline [No-NA]= 0 microg/min, Low-noradrenaline [Low-NA]=0.1-7 microg/min, High-noradrenaline [High-NA] >7 microg/min), according to their postoperative noradrenaline requirements. Preoperatively, alpha1(A)-receptor expression was 4.9-fold (High-NA) and 18.7-fold (Low-NA) higher than the No-NA group (P=0.005) and plasma noradrenaline levels were higher in the High-NA group (P=0.005). Across all groups at 12 hours after the operation, alpha1(A) -receptor expression decreased to approximately one-fifth of preoperative levels (P=0.01); but with greater duration and magnitude of relative decrease in the High-NA group. Patients in the No-NA group had significant postoperative increases in leucocyte inflammatory mediator expression for IL-1beta, TLR4, TREM, MPO, MMP9 and TNF genes, whereas the changes in the Low-NA and High-NA groups were not significant. Low preoperative levels of noradrenaline and low expression of alpha1(A)-adrenoreceptors in leucocytes was associated with less probability of requiring noradrenaline support after cardiac surgery.

High levels of glucocorticoid receptors in patients with active Crohn's disease may predict steroid resistance

Up to 20% of Crohn's disease (CD) patients respond poorly to glucocorticoids (GC). A product of an alternative splicing of the glucocorticoid receptor (GR) premRNA, GRbeta, may play a role as a dominant inhibitor of the glucocorticoid response. Increasing evidence suggests that inflammatory cytokines such as interleukin (IL)-18 alternate the splicing of the primary transcript between the two isoforms GRbeta and GRalpha in hGR gene of CD patients. The aim of this study is to assess the expression of GRalpha and GRbeta in patients with CD and to look for a possible correlation between these receptors and the response to glucocorticoid treatment. Forty-two CD patients and 17 healthy volunteers were studied. Quantitative reverse transcription-polymerase chain reaction (RT-PCR) was performed using real-time PCR techniques. Serum IL-18 protein levels were measured by enzyme-linked immunosorbent assay (ELISA). The amount of hGRalpha-mRNA in patients in remission was significantly lower than in controls (P < 0.05). The amount of hGRbeta-mRNA was significantly higher in GC-resistant patients in the active stage of disease compared with all other groups (P < 0.05). Patients in the active stage of the disease had higher levels of IL-18 than patients in remission and both had higher levels than controls (P < 0.05). The amounts of IL-18 were directly correlated with the amount of hGRbeta mRNA in GC-resistant patients with an active disease. High levels of hGRbeta might be connected to GC resistance. IL-18 might participate in the alternative splicing of the hGR preliminary mRNA of CD patients. The results support the theory that augmented hGRbeta mRNA expression level in PBMC is connected with GC-resistance of CD patients.

Two distinct genotypes of prtF2, encoding a fibronectin binding protein, and evolution of the gene family in Streptococcus pyogenes

The group A Streptococcus (GAS) is an important pathogen that is responsible for a wide range of human diseases. Fibronectin binding proteins (FBPs) play an important role in promoting GAS adherence and invasion of host cells. The prtF2 gene encodes an FBP and is present in approximately 60% of GAS strains. In the present study we examined 51 prtF2-positive GAS strains isolated from the Northern Territory of Australia, and here we describe two genotypes of prtF2 which are mutually exclusive. The two genotypes have been identified previously as pfbp and fbaB. We show that these genotypes map to the same chromosomal location within the highly recombinatorial fibronectin-collagen-T antigen (FCT) locus, indicating that they arose from a common ancestor, and in this study these genotypes were designated the pfbp type and the fbaB type. Phylogenetic analysis of seven pfbp types, 14 fbaB types, and 11 prtF2-negative GAS strains by pulsed-field gel electrophoresis (PFGE) produced 32 distinct PFGE patterns. Interpretation of evolution based on the PFGE dendrogram by parsimony suggested that the pfbp type had a recent origin compared to the fbaB type. A comparison of multiple DNA sequences of the pfbp and fbaB types revealed a mosaic pattern for the amino-terminal region of the pfbp types. The fbaB type is generally conserved at the amino terminus but varies in the number of fibronectin binding repeats in the carboxy terminus. Our data also suggest that there is a possible association of the pfbp genotype with sof (84.2%), while the fbaB genotype was found in a majority of the GAS strains negative for sof (90.6%), indicating that these two prtF2 subtypes may be under different selective pressures.

Mild familial goitrous hypothyroidism associated with prolonged 131-iodine retention: possible defect in thyroglobulin synthesis

Four male siblings presented with goitrous hypothyroidism which had been present from the first few years of life. Serum total thyroxine (T4), free T4 index and free T4 levels were low or in the low-normal range while TSH levels were elevated; triiodothyronine (T3) levels were normal. The 131-I-uptake was elevated at 4 and 24 h, 76-93% and 69-82% respectively (normal less than 50%), and remained elevated 96 h after the administration of radioiodine. Administration of potassium perchlorate did not cause a reduction in thyroidal radioiodine. These findings, therefore, were not consistent with defects affecting iodine trapping, iodine organification or iodotyrosine deiodinase. If a coupling defect was the cause of the disorder, iodotyrosines would have to cycle between the thyroid cell and thyroglobulin in the follicular lumen undergoing deiodination, and reorganification continually. To examine this possibility carbimazole, which inhibits organification of iodine was taken orally following administration of 131-I; potassium perchlorate was given to discharge any accumulating nonorganified radioiodine. 131-I uptake changed only from 50 to 48% and from 68 to 71% in the 2 subjects studied. These findings do not support a coupling defect. The possibility of abnormal thyroglobulin synthesis was supported by the finding of inappropriately low serum thyroglobulin levels. A specimen of thyroid tissue demonstrated a 40-fold reduction in normal thyroglobulin content. These findings suggest that our sibship have a rare partial defect in thyroglobulin synthesis and that iodine is incorporated into an alternative complex which is resistant to mobilization.