ALK upregulates POSTN and WNT signaling to drive neuroblastoma

Neuroblastoma is the most common extracranial solid tumor of childhood. While MYCN and mutant anaplastic lymphoma kinase (ALKF1174L) cooperate in tumorigenesis, how ALK contributes to tumor formation remains unclear. Here, we used a human stem cell-based model of neuroblastoma. Mis-expression of ALKF1174L and MYCN resulted in shorter latency compared to MYCN alone. MYCN tumors resembled adrenergic, while ALK/MYCN tumors resembled mesenchymal, neuroblastoma. Transcriptomic analysis revealed enrichment in focal adhesion signaling, particularly the extracellular matrix genes POSTN and FN1 in ALK/MYCN tumors. Patients with ALK-mutant tumors similarly demonstrated elevated levels of POSTN and FN1. Knockdown of POSTN, but not FN1, delayed adhesion and suppressed proliferation of ALK/MYCN tumors. Furthermore, loss of POSTN reduced ALK-dependent activation of WNT signaling. Reciprocally, inhibition of the WNT pathway reduced expression of POSTN and growth of ALK/MYCN tumor cells. Thus, ALK drives neuroblastoma in part through a feedforward loop between POSTN and WNT signaling.

Fibroblasts and macrophages cooperate to create a pro-tumorigenic and immune resistant environment via activation of TGF-β/IL-6 pathway in neuroblastoma

Tumor-associated macrophages (TAM) and cancer-associated fibroblasts (CAF) and their precursor mesenchymal stromal cells (MSC) are often detected together in tumors, but how they cooperate is not well understood. Here, we show that TAM and CAF are the most abundant nonmalignant cells and are present together in untreated human neuroblastoma (NB) tumors that are also poorly infiltrated with T and natural killer (NK) cells. We then show that MSC and CAF-MSC harvested from NB tumors protected human monocytes (MN) from spontaneous apoptosis in an interleukin (IL)-6 dependent mechanism. The interactions of MN and MSC with NB cells resulted in a significant induction or increase in the expression of several pro-tumorigenic cytokines/chemokines (TGF-β1, MCP-1, IL-6, IL-8, and IL-4) but not of anti-tumorigenic cytokines (TNF-α, IL-12) by MN or MSC, while also inducing cytokine expression in quiescent NB cells. We then identified a TGF-β1/IL-6 pathway where TGF-β1 stimulated the expression of IL-6 in NB cells and MSC, promoting TAM survival. Evidence for the contribution of TAM and MSC to the activation of this pathway was then provided in xenotransplanted NB tumors and patients with primary tumors by demonstrating a direct correlation between the presence of CAF and p-SMAD2 and p-STAT3. The data highlight a new mechanism of interaction between TAM and CAF supporting their pro-tumorigenic function in cancer.

Abstract 3123: Cancer-associated fibroblasts and tumor-associated macrophages cooperate to promote TGF-β1-dependent NFkB activation and IL6 production and immune escape

The individual contribution of tumor-associated macrophages (TAM) and cancer-associated fibroblasts (CAF), and their precursors mesenchymal stromal cells (MSC) to a pro-tumorigenic and immune-suppressive tumor microenvironment (TME) in neuroblastoma (NB) is well known. However, whether and how they could cooperate has not been studied in this cancer. This important question, in the context of current immunotherapies for NB, has been addressed here in complementary studies evaluating the TME landscape in primary human NB tumors and examining the production of cytokines/chemokines and the activation of signaling pathways in NB cells in the presence of human monocytes and MSC-CAF in vitro and in vivo. A multiplex immunohistochemistry evaluation of 17 untreated human NB tumors demonstrated the presence of MSC-CAF and TAM representing between 0.5% to 7.4% and 0.4% to 8.4% of the total cell population respectively. MSC-CAF were predominantly present in the stroma around NB cells, while TAM diffusely infiltrated tumors. There was a paucity of infiltrating T cells and NK cells (0.7% and 0.1% of total cells, respectively) in all tumors. MSC-CAF promoted in vitro the survival of human monocytes and TAM through their production of IL6 and soluble IL6 receptor. When co-cultured with NB cells, MSC-CAF and monocytes increased the production of pro-tumorigenic cytokines/chemokines like TGFβ1, IL6, IL8, IL10, CCL2/MCP-1 and induced a high expression in MYCN amplified NB cells and TME cells. In contrast they did not stimulate the production of anti-tumorigenic cytokines like IFNγ, TNFα and IL12. Among these multiple cytokines, we demonstrated the central role of TGFβ1 which induced the expression of IL6 in NB cells and in MSC-CAF. Mechanistically, we demonstrated that production of IL6 in NB cells was dependent on the activation of NFκB by TGFβ1 via TAK1 and SMAD2 signaling pathways. In contrast, in MSC, the production of IL6 was dependent on the transcriptional activity of SMAD2/SMAD4 but independent of NFκB. Moreover, the significant increase in TGFβ1 production and secretion to a level only observed in co-cultures of MSC-CAF, TAM and NB cells led to inhibition of NK cell-mediated NB cytotoxicity. Increased TGFβ1, NFκB and IL6 activities were also detected in NB tumors implanted in immunodeficient mice in the presence of human MSC-CAF and monocytes and in primary human NB tumors where we observed a direct correlation between pSMAD2, pSTAT3, and the presence of α-SMA positive MSC-CAF. Our results emphasize the importance of the synergistic role of TAM and CAF in promoting immune escape and resistance to immunotherapies, and the need to define the TME of tumors in patients with NB in order to improve immunotherapies.

Citation Format: Kevin Louault, Tania Porras, Meng-Hua Lee, Sakunthala Muthugounder, Rebekah Kennedy, Laurence Sarte, Gerardo E. Fernandez, Bruce Pawel, Hiroyuki Shimada, Shahab Asgharzadeh, Yves A. Declerck. Cancer-associated fibroblasts and tumor-associated macrophages cooperate to promote TGF-β1-dependent NFkB activation and IL6 production and immune escape [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3123.

RNA-Seq of Circulating Tumor Cells in Stage II-III Breast Cancer

BACKGROUND

We characterized the whole transcriptome of circulating tumor cells (CTCs) in stage II-III breast cancer to evaluate correlations with primary tumor biology.

METHODS

CTCs were isolated from peripheral blood (PB) via immunomagnetic enrichment followed by fluorescence-activated cell sorting (IE/FACS). CTCs, PB, and fresh tumors were profiled using RNA-seq. Formalin-fixed, paraffin-embedded (FFPE) tumors were subjected to RNA-seq and NanoString PAM50 assays with risk of recurrence (ROR) scores.

RESULTS

CTCs were detected in 29/33 (88%) patients. We selected 21 cases to attempt RNA-seq (median number of CTCs = 9). Sixteen CTC samples yielded results that passed quality-control metrics, and these samples had a median of 4,311,255 uniquely mapped reads (less than PB or tumors). Intrinsic subtype predicted by comparing estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) versus PAM50 for FFPE tumors was 85% concordant. However, CTC RNA-seq subtype assessed by the PAM50 classification genes was highly discordant, both with the subtype predicted by ER/PR/HER2 and by PAM50 tumors. Two patients died of metastatic disease, both of whom had high ROR scores and high CTC counts. We identified significant genes, canonical pathways, upstream regulators, and molecular interaction networks comparing CTCs by various clinical factors. We also identified a 75-gene signature with highest expression in CTCs and tumors taken together that was prognostic in The Cancer Genome Atlas and Molecular Taxonomy of Breast Cancer International Consortium datasets.

CONCLUSION

It is feasible to use RNA-seq of CTCs in non-metastatic patients to discover novel tumor biology characteristics.

Abstract P2-01-04: The whole transcriptional landscape of circulating tumor cells compared to metastases in stage IV breast cancer

Background: Metastatic breast cancer (MBC) and the circulating cells (CTCs) leading to macrometastasis are inherently different than primary breast cancer, evolving under the selection pressure of systemic therapy. A better understanding of the tumor biology of CTCs compared to metastasis may shed light on treatment opportunities.

Methods: We performed whole transcriptome sequencing (RNA Seq) on fresh metastatic tumor biopsies (mets), CTCs, and peripheral blood (PB) from 21 newly diagnosed MBC patients. CTCs were harvested using the ANGLE Parsortix to isolate cells based on size and deformability. Data were analyzed for differential expression, pathways, single nucleotide variants (SNV), fusions, intrinsic subtype, and a CTC-mets shared gene signature was validated using data from The Cancer Genome Atlas (TCGA). Detailed clinical-pathological and treatment data was evaluated.

Results: CTCs as a group showed much stronger gene expression of oncogenes, stem cell genes, keratins and mesenchymal markers than did mets from the same patients. Matched patient comparisons for 66 potentially clinically actionable genes for 8/9 pathways showed no significant difference in gene expression targets between CTCs and mets on ANOVA, although fold-change did vary. Eight SNVs in the ESR1 gene (n=5 patients) and 5 SNVs in the HER2 gene (n=2 patients) were shared between CTCs and distant metastases.

Differential gene expression analysis identified a signature of 8870 genes that were statistically significantly correlated between CTCs and mets (FDR adjusted p<0.05). Ingenuity pathway analysis was applied to the list of genes shared between CTCs and mets, with analysis of canonical pathways and upstream regulators revealing numerous oncogenes and breast cancer related genes. The top upstream regulators of CTCs-mets were beta-estradiol, progesterone, FOXA1, HNRPA2B1 and HNF1A. The top 50 genes of this CTC-mets shared signature were prognostic of worse overall survival in the TCGA breast cancer dataset (p<0.001), which included 817 patients with a median follow-up of 59.5 months. Second time-point data for n=5 patients with subsequent PB draws 6 months after baseline is currently pending. Intrinsic subtyping of mets by either NanoString assays or RNA Seq were not concordant with intrinsic subtyping of CTCs by RNA Seq.

Four of 21 CTC samples showed strong whole transcriptome RPKM correlation with PB (R2)>0.9, however, 3/21 CTC samples showed strong whole transcriptome RPKM correlation with mets (R2)>0.8. The remainder showed low correlation with both. Coverage was 91.4X for CTCs, 140.2X for mets and 138.5X for PB.

Conclusions: We present the transcriptomic landscape of CTCs with comparison to metastases and peripheral blood all acquired prior to treatment of newly diagnosed Stage IV breast cancer. Multiple genes, including oncogenes and stem cell genes, were found with higher expression in CTCs versus metastases. When focusing on 66 known potentially clinically actionable genes in breast cancer, CTCs did not show significantly different patterns of expression than mets in terms of up-regulation versus down-regulation compared to PB. RNA Seq of CTCs may be utilized to identify molecular alterations that are potentially clinically actionable.

Citation Format: Ring A, Porras T, Campo D, Kaur P, Forte VA, Tripathy D, Lu J, Zada G, Wagle N, Wecsler JS, Lang JE. The whole transcriptional landscape of circulating tumor cells compared to metastases in stage IV breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-01-04.

Abstract 1549: Molecular profiling of circulating tumor cells as a surrogate for distant metastasis in stage IV breast cancer

Background: Metastasis is responsible for virtually all breast cancer related deaths. While circulating tumor cells (CTCs) have been shown to be prognostic in metastatic breast cancer (MBC), their use as a biomarker to date has been limited. While initial treatment recommendations are based on primary tumor biology, ASCO guidelines call for biopsy of a metastatic site to guide decision making for systemic therapy. The ANGLE Parsortix system is a microfluidics device that separates CTCs based on size and deformability, without the need for cell-surface marker selection. We hypothesize that the ANGLE Parsortix system permits isolation and gene expression profiling of pure CTCs and allows comparison of the biopsied metastatic site, thereby acting as a surrogate for macrometastases.

Methods: We are currently enrolling metastatic breast cancer patients to a prospective, observational clinical study in which CTCs are enumerated and captured from 10-20 mL peripheral blood (PB) via the ANGLE Parsortix system. CTCs, peripheral blood (PB), and metastatic sites were profiled with RNA Seq via the Illumina HiSeq (primary predictor). We received fresh frozen tissue biopsies from the following metastatic sites: skin, brain, pleural effusion, pericardial effusion, breast, cerebrospinal fluid and bone tissue. Bioinformatics analysis was then performed. NanoString PAM50 and real-time polymerase chain reaction will be used as validation studies.

Results: To date we have successfully isolated and molecularly profiled CTCs and metastatic tissue (MT) from 9/9 stage IV breast cancer patients. Final bioinformatics analysis on the last five patients is underway. Principal component analysis demonstrated clustering of MT and CTCs, with clear separation from PB. These results demonstrated high purity of CTCs, eliminating the need for subtraction of PB background signal, and demonstrated common gene expression between CTCs and MT. Differential gene expression analysis (FDR p<0.05) identified a 214 gene-expression signature that statistically significantly correlated (R>0.98) between CTCs and MT. Gene Set Enrichment Analysis (GSEA) analysis of 214-gene signature identified biological pathways related to metastasis in CTCs and MT. Individual intra-patient analysis confirmed gene-expression correlation between CTCs and MT, but not PB.

Conclusion and outlook: Cell surface marker independent CTC isolation is feasible for RNA Seq analysis without background subtraction. Furthermore, RNA Seq of CTCs can identify gene expression signatures that correlate with distant macrometastatic sites. The gene-expression patterns revealed biological relevant information that could be used as biomarkers or identify potential therapeutic targets.

Citation Format: Alexander Ring, Victoria Forte, Dany Barrak, Tania Porras, Vasu Punj, Steven Carrasco, Min Yu, Debu Tripathy, Julie Lang. Molecular profiling of circulating tumor cells as a surrogate for distant metastasis in stage IV breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1549.

Role of embB codon 306 mutations in Mycobacterium tuberculosis revisited: a novel association with broad drug resistance and IS6110 clustering rather than ethambutol resistance

Mutations at position 306 of embB (embB306) have been proposed as a marker for ethambutol resistance in Mycobacterium tuberculosis; however, recent reports of embB306 mutations in ethambutol-susceptible isolates caused us to question the biological role of this mutation. We tested 1,020 clinical M. tuberculosis isolates with different drug susceptibility patterns and of different geographical origins for associations between embB306 mutations, drug resistance patterns, and major genetic group. One hundred isolates (10%) contained a mutation in embB306; however, only 55 of these mutants were ethambutol resistant. Mutations in embB306 could not be uniquely associated with any particular type of drug resistance and were found in all three major genetic groups. A striking association was observed between these mutations and resistance to any drug (P < 0.001), and the association between embB306 mutations and resistance to increasing numbers of drugs was highly significant (P < 0.001 for trend). We examined the association between embB306 mutations and IS6110 clustering (as a proxy for transmission) among all drug-resistant isolates. Mutations in embB306 were significantly associated with clustering by univariate analysis (odds ratio, 2.44; P = 0.004). In a multivariate model that also included mutations in katG315, katG463, gyrA95, and kasA269, only mutations in embB306 (odds ratio, 2.14; P = 0.008) and katG315 (odds ratio, 1.99; P = 0.015) were found to be independently associated with clustering. In conclusion, embB306 mutations do not cause classical ethambutol resistance but may predispose M. tuberculosis isolates to the development of resistance to increasing numbers of antibiotics and may increase the ability of drug-resistant isolates to be transmitted between subjects.

Multicenter study of MTT and resazurin assays for testing susceptibility to first-line anti-tuberculosis drugs

OBJECTIVE

A multicentre evaluation was performed to assess two rapid low-cost methods, MTT (3-[4.5-dimethylthiazol-2-yl]-2.5-diphenyltetrazolium bromide) and resazurin assays, for testing the susceptibility of Mycobacterium tuberculosis to the first-line anti-tuberculosis drugs rifampicin (RMP), isoniazid (INH), ethambutol (EMB) and streptomycin (SM).

METHODS

Thirty coded M. tuberculosis strains were sent to seven laboratories located in Latin America, representing six countries. Each site performed the colorimetric assays, MTT and resazurin, blind for the first-line drugs RMP, INH, EMB and SM. The minimum inhibitory concentration results obtained were compared to the conventional proportion method on Lowenstein-Jensen medium.

RESULTS

After establishing the breakpoint concentrations, excellent results were obtained for RMP, INH and EMB, with levels of specificity and sensitivity of between 96% and 99%.

CONCLUSION

MTT and resazurin assays are promising, accessible new alternative methods for middle- and low-resource countries that need low-cost methods to perform rapid susceptibility testing of M. tuberculosis to key anti-tuberculosis drugs.

Cyclic nucleotides modulate store-mediated calcium entry through the activation of protein-tyrosine phosphatases and altered actin polymerization in human platelets

Agonists elevate the cytosolic calcium concentration in human platelets via a receptor-operated mechanism, involving both Ca(2+) release from intracellular stores and subsequent Ca(2+) entry, which can be inhibited by platelet inhibitors, such as prostaglandin E(1) and nitroprusside which elevate cAMP and cGMP, respectively. In the present study we investigated the mechanisms by which cAMP and cGMP modulate store-mediated Ca(2+) entry. Both prostaglandin E(1) and sodium nitroprusside inhibited thapsigargin-evoked store-mediated Ca(2+) entry and actin polymerization. However, addition of these agents after induction of store-mediated Ca(2+) entry did not affect either Ca(2+) entry or actin polymerization. Furthermore, prostaglandin E(1) and sodium nitroprusside dramatically inhibited the tyrosine phosphorylation induced by depletion of the internal Ca(2+) stores or agonist stimulation without affecting the activation of Ras or the Ras-activated phosphatidylinositol 3-kinase or extracellular signal-related kinase (ERK) pathways. Inhibition of cyclic nucleotide-dependent protein kinases prevented inhibition of agonist-evoked Ca(2+) release but it did not have any effect on the inhibition of Ca(2+) entry or actin polymerization. Phenylarsine oxide and vanadate, inhibitors of protein-tyrosine phosphatases prevented the inhibitory effects of the cGMP and cAMP elevating agents on Ca(2+) entry and actin polymerization. These results suggest that Ca(2+) entry in human platelets is directly down-regulated by cGMP and cAMP by a mechanism involving the inhibition of cytoskeletal reorganization via the activation of protein tyrosine phosphatases.