RET fusions in a small subset of advanced colorectal cancers at risk of being neglected

Background

Recognition of rare molecular subgroups is a challenge for precision oncology and may lead to tissue-agnostic approval of targeted agents. Here we aimed to comprehensively characterize the clinical, pathological and molecular landscape of RET rearranged metastatic colorectal cancer (mCRC).

Patients and methods

In this case series, we compared clinical, pathological and molecular characteristics of 24 RET rearranged mCRC patients with those of a control group of 291 patients with RET negative tumors. RET rearranged and RET negative mCRCs were retrieved by systematic literature review and by taking advantage of three screening sources: (i) Ignyta's phase 1/1b study on RXDX-105 (NCT01877811), (ii) cohorts screened at two Italian and one South Korean Institutions and (iii) Foundation Medicine Inc. database. Next-generation sequencing data were analyzed for RET rearranged cases.

Results

RET fusions were more frequent in older patients (median age of 66 versus 60 years, P = 0.052), with ECOG PS 1-2 (90% versus 50%, P = 0.02), right-sided (55% versus 32%, P = 0.013), previously unresected primary tumors (58% versus 21%, P < 0.001), RAS and BRAF wild-type (100% versus 40%, P < 0.001) and MSI-high (48% versus 7%, P < 0.001). Notably, 11 (26%) out of 43 patients with right-sided, RAS and BRAF wild-type tumors harbored a RET rearrangement. At a median follow-up of 45.8 months, patients with RET fusion-positive tumors showed a significantly worse OS when compared with RET-negative ones (median OS 14.0 versus 38.0 months, HR: 4.59; 95% CI, 3.64-32.66; P < 0.001). In the multivariable model, RET rearrangements were still associated with shorter OS (HR: 2.97; 95% CI, 1.25-7.07; P = 0.014), while primary tumor location, RAS and BRAF mutations and MSI status were not.

Conclusions

Though very rare, RET rearrangements define a new subtype of mCRC that shows poor prognosis with conventional treatments and is therefore worth of a specific management.

Comprehensive genomic profiles of metastatic and relapsed salivary gland carcinomas are associated with tumor type and reveal new routes to targeted therapies

Background

Relapsed/metastatic salivary gland carcinomas (SGCs) have a wide diversity of histologic subtypes associated with variable clinical aggressiveness and response to local and systemic therapies. We queried whether comprehensive genomic profiling could define the tumor subtypes and uncover clinically relevant genomic alterations, revealing new routes to targeted therapies for patients with relapsed and metastatic disease.

Patients and methods

From a series of 85 686 clinical cases, DNA was extracted from 40 µm of formalin-fixed paraffin embedded (FFPE) sections for 623 consecutive SGC. CGP was carried out on hybridization-captured, adaptor ligation-based libraries (mean coverage depth, >500×) for up to 315 cancer-related genes. Tumor mutational burden was determined on 1.1 Mb of sequenced DNA. All classes of alterations, base substitutions, short insertions/deletions, copy number changes, and rearrangements/fusions were determined simultaneously.

Results

The clinically more indolent SGC including adenoid cystic carcinoma, acinic cell carcinoma, polymorphous low-grade adenocarcinoma, mammary analog secretory carcinoma, and epithelial-myoepithelial carcinomas have significantly fewer genomic alterations, TP53 mutations, and lower tumor mutational burden than the typically more aggressive SGCs including mucoepidermoid carcinoma, salivary duct carcinoma, adenocarcinoma, not otherwise specified, carcinoma NOS, and carcinoma ex pleomorphic adenoma. The more aggressive SGCs are commonly driven by ERBB2 PI3K pathway genomic alterations. Additional targetable GAs are frequently seen.

Conclusions

Genomic profiling of SGCs demonstrates important differences between traditionally indolent and aggressive cancers. These differences may provide therapeutic options in the future.

Emergence of EGFR G724S mutation in EGFR-mutant lung adenocarcinoma post progression on osimertinib

Mutations in the epidermal growth factor receptor (EGFR) are drivers for a subset of lung cancers. Osimertinib is a third-generation tyrosine kinase inhibitor (TKI) recently approved for the treatment of T790M-positive non-small cell lung cancer (NSCLC); however, acquired resistance to osimertinib is evident and resistance mechanisms remain incompletely defined. The EGFR G724S mutation was detected using hybrid-capture based comprehensive genomic profiling (CGP) and a hybrid-capture based circulating tumor DNA (ctDNA) assays in two cases of EGFR-driven lung adenocarcinoma in patients who had progressed on osimertinib treatment. This study demonstrates the importance of both tissue and blood based hybrid-capture based genomic profiling at disease progression to identifying novel resistance mechanisms in the clinic.

Management of mixed type congenital mesoblastic nephroma: Case series and review of the literature

Congenital mesoblastic nephroma (CMN) is the most common renal tumor of infancy; however, it occurs infrequently with an incidence of 1 : 125,000. The cellular and classical variants are the most common subtypes of tumors, with a mixed variant occurring infrequently. We describe two cases of mixed variant CMN, which presented within days of each other differing in their clinical behavior. The first case followed a typical course, previously described in the literature, while the other deviated significantly. Traditionally, CMN presents as large abdominal mass in the neonatal period associated with a paraneoplastic syndrome, which can result in hypertension or hypercalcemia. Surgical resection is curative in most cases and long-term prognosis is excellent. Hypertension rarely persists after removal of the tumor, but remained in one of our two patients.

Microsecond-pulsed dielectric barrier discharge plasma stimulation of tissue macrophages for treatment of peripheral vascular disease

Angiogenesis is the formation of new blood vessels from pre-existing vessels and normally occurs during the process of inflammatory reactions, wound healing, tissue repair, and restoration of blood flow after injury or insult. Stimulation of angiogenesis is a promising and an important step in the treatment of peripheral artery disease. Reactive oxygen species have been shown to be involved in stimulation of this process. For this reason, we have developed and validated a non-equilibrium atmospheric temperature and pressure short-pulsed dielectric barrier discharge plasma system, which can non-destructively generate reactive oxygen species and other active species at the surface of the tissue being treated. We show that this plasma treatment stimulates the production of vascular endothelial growth factor, matrix metalloproteinase-9, and CXCL 1 that in turn induces angiogenesis in mouse aortic rings in vitro. This effect may be mediated by the direct effect of plasma generated reactive oxygen species on tissue.

Self-hypnosis for intrapartum pain management in pregnant nulliparous women: a randomised controlled trial of clinical effectiveness

Objective

(Primary) To establish the effect of antenatal group self-hypnosis for nulliparous women on intra-partum epidural use.

Design

Multi-method randomised control trial (RCT).

Setting

Three NHS Trusts.

Population

Nulliparous women not planning elective caesarean, without medication for hypertension and without psychological illness.

Methods

Randomisation at 28–32 weeks’ gestation to usual care, or to usual care plus brief self-hypnosis training (two × 90-minute groups at around 32 and 35 weeks’ gestation; daily audio self-hypnosis CD). Follow up at 2 and 6 weeks postnatal.

Main outcome measures

Primary: epidural analgesia. Secondary: associated clinical and psychological outcomes; cost analysis.

Results

Six hundred and eighty women were randomised. There was no statistically significant difference in epidural use: 27.9% (intervention), 30.3% (control), odds ratio (OR) 0.89 [95% confidence interval (CI): 0.64–1.24], or in 27 of 29 pre-specified secondary clinical and psychological outcomes. Women in the intervention group had lower actual than anticipated levels of fear and anxiety between baseline and 2 weeks post natal (anxiety: mean difference −0.72, 95% CI −1.16 to −0.28, P = 0.001); fear (mean difference −0.62, 95% CI −1.08 to −0.16, P = 0.009) [Correction added on 7 July 2015, after first online publication: ‘Mean difference’ replaced ‘Odds ratio (OR)’ in the preceding sentence.]. Postnatal response rates were 67% overall at 2 weeks. The additional cost in the intervention arm per woman was £4.83 (CI −£257.93 to £267.59).

Conclusions

Allocation to two-third-trimester group self-hypnosis training sessions did not significantly reduce intra-partum epidural analgesia use or a range of other clinical and psychological variables. The impact of women's anxiety and fear about childbirth needs further investigation.

Tweetable abstract

Going to 2 prenatal self-hypnosis groups didn't reduce labour epidural use but did reduce birth fear & anxiety postnatally at < £5 per woman.

Hypnotherapy for irritable bowel syndrome: an audit of one thousand adult patients

BACKGROUND

Gut-focused hypnotherapy improves the symptoms of irritable bowel syndrome (IBS) with benefits being sustained for many years. Despite this, the technique has not been widely adopted by healthcare systems, possibly due to relatively small numbers in published studies and uncertainty about how it should be provided.

AIM

To review the effect of hypnotherapy in a large cohort of refractory IBS patients.

METHODS

One thousand IBS patients fulfilling Rome II criteria, mean age 51.6 years (range 17-91 years), 80% female, receiving 12 sessions of hypnotherapy over 3 months, were studied. The primary outcome was a 50 point reduction in the IBS Symptom Severity Score. The fall in scores for Noncolonic Symptoms, Quality of Life and Anxiety or Depression, were secondary outcomes. The Federal Drug Administration's recommended outcome of a 30% or more reduction in abdominal pain was also recorded.

RESULTS

Overall, 76% met the primary outcome which was higher in females (females: 80%, males: 62%, P < 0.001) and those with anxiety (anxious: 79%, non-anxious: 71%, P = 0.010). The mean reduction in other scores was: IBS Symptom Severity Score, 129 points (P < 0.001), Noncolonic Symptom Score, 65 (P < 0.001) and Quality of Life Score, 66 (P < 0.001). Sixty-seven per cent reported a 30% or more reduction in abdominal pain scores. Pain days fell from 18 to 9 per month. Patients with anxiety and depression fell from 63% to 34% and 25% to 12% respectively (P < 0.001). Outcome was unaffected by bowel habit subtype.

CONCLUSION

These results provide further evidence that gut-focused hypnotherapy is an effective intervention for refractory IBS.

Improving evidence developed from population-level experience with targeted agents

Off-label drug use is common in oncology, due in part to significant unmet medical need, the rarity of many cancers, and the difficulty of conducting randomized controlled trials (RCTs) to support labeling of every drug in every disease setting. As new drugs are developed for use in tumors defined by genomic aberrations, it may be scientifically reasonable to expect that a targeted anti-cancer agent with efficacy in a biomarker-defined population within one tumor type may also have activity in another tumor type expressing the same biomarker. Such expectations also fuel off-label prescribing. However, the current approach to prescribing targeted agents off-label does not capture patient outcomes, thus missing an opportunity to gather data that could validate this approach. We explore the potential for collecting such data, highlight two proposals for oncology-specific patient registries, and put forward considerations that should be addressed to move toward better evidence development around off-label use.

Goal setting with mothers in child development services

AIM

The aim of this grounded theory study was to explore mothers' perspectives of the processes of collaborative goal setting in multidisciplinary child development services involving follow-up home therapy.

METHODS

Semi-structured interviews were conducted in South East Queensland, Australia with 14 mothers of children aged 3-6 years who were accessing multidisciplinary child development services. Interviews were focussed around the process of goal setting.

RESULTS

A grounded theory of Maternal Roles in Goal Setting (The M-RIGS Model) was developed from analysis of data. Mothers assumed Dependent, Active Participator and Collaborator roles when engaging with the therapist in goal-setting processes. These roles were characterized by the mother's level of dependence on the therapist and insight into their child's needs and therapy processes. Goal Factors, Parent Factors and Therapist Factors influenced and added complexity to the goal-setting process.

CONCLUSION

The M-RIGS Model highlights that mothers take on a range of roles in the goal-setting process. Although family-centred practice encourages negotiation and collaborative goal setting, parents may not always be ready to take on highly collaborative roles. Better understanding of parent roles, goal-setting processes and influencing factors will inform better engagement with families accessing multidisciplinary child development services.

Abstract PD3-1: Serial next generation sequencing (NGS) of poor prognosis luminal tumors across treatment history reveals both de novo and acquired alterations potentially associated with endocrine resistance

Cancer therapies exert selective pressure on genomically heterogeneous breast cancers and may select for alterations in genes associated with drug resistance or metastasis. We evaluated this hypothesis by comparing sequential primary, post-neoadjuvant chemotherapy, and recurrent metastatic tumor samples from 5 patients with aggressive hormone receptor positive (HR+) breast cancer.

Triplet samples (primary untreated, primary post-neoadjuvant chemotherapy, metastatic recurrence) were assessed in 5 patients with HR+ breast cancer. All patients were treated with cyclophosphamide and doxorubicin followed by paclitaxel or docetaxel, and adjuvant radiation and hormonal therapy. They all recurred during adjuvant antiestrogen treatment (12-43 months post-surgery). Metastatic sites included liver (2), ovary, brain, and pleural fluid. In these 5 tumor sets, we queried genomic alterations across 3,769 exons from 236 cancer genes using the FoundationOne™ NGS assay.

Gene amplifications were frequently discordant among the triplet biopsies; all patients showed copy number alterations and 3 of 5 patients had two or more additional gene amplifications confirmed only in the biopsy of the metastasis. ESR1 (ERa) mutations were identified in the metastatic lesions of 2/5 patients but not in the diagnostic biopsy or the post-neoadjuvant therapy mastectomy specimen; both also harbored de novo and concurrent GATA3 truncations. One of the ESR1 mutations, Y537S, is known to result in an estrogen-independent, transcriptionally active receptor. The same patient showed amplification of 11q13 genes CCND1, EMSY, and FGF19, an amplicon known to be associated with endocrine resistance. Concordant FGFR1 and ZNF703 amplifications, both at 8p12, were observed de novo in 2 other patients; these alterations have beenassociated with the luminal B subtype and resistance to antiestrogens. FGFR1/ZNF703 alterations were mutually exclusive with ESR1 mutations. The 5th tumor contained a PIK3CA ‘hot spot’ mutation in all 3 sequential biopsies. This tumor also exhibited IGF1R, IRS2, MYC and MCL1 gene amplification only in the metastasis. Overall, IGF1R amplifications were observed in 3/5 patients. In addition, amplification of ZNF217 at 20q13.2, an amplicon with known association with poor prognosis, was observed de novo in 2 patients that exhibited rapid recurrence on adjuvant therapy (12 and 17 months).

Acquired somatic alterations that deregulate ERα signaling may allow for escape from estrogen deprivation leading to treatment resistance. We speculate ESR1 mutations, rarely observed in primary breast tumors, are selected for during adjuvant hormonal treatment in aggressive HR+ breast cancer. Testing for de novo and acquired alterations throughout the clinical course of patients with ER+ cancers may identify targetable alterations, such as FGFR1 and IGF1R gene amplifications and others, against which targeted drugs are available. Studies are underway to validate these findings in additional patients with sequential samples and to investigate the function and therapeutic implications of ESR1 mutations.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr PD3-1.

Abstract PD02-07: Next-generation sequencing of FFPE breast cancers demonstrates high concordance with FISH in calling HER2 amplifications and commonly detects other clinically relevant genomic alterations

Background: As more therapies targeting genomic alterations become available, next-generation sequencing (NGS) is increasingly performed in tumor types where mutational status may drive treatment choice. In addition to its ability to identify base substitutions, insertions and deletions across entire exons, NGS can detect relevant copy number changes such as amplification of HER2 in breast tumors. However, for NGS to be clinically applicable, it must reliably analyze FFPE tumor samples and show concordance with the best current diagnostic methods.

Methods: To confirm a clinical role for NGS in detecting copy number alterations, we identified 35 FFPE invasive breast carcinomas previously tested for HER2 status by FISH, including 15 HER2 positives (≥7 copies) and 20 HER2 negatives (&lt;4 copies) and sequenced 3,230 exons of 182 cancer genes including HER2, in a CLIA certified lab (Foundation Medicine). Average coverage depth of &gt;900X uniquely-mapping reads was obtained. Sequence data were analyzed for HER2 copy number (blinded to FISH results) based on a statistical model using allele frequencies and coverage depth of HER2 exons versus a process-matched normal control, classifying cases as HER2 positive (≥6 average copies), HER2 negative (&lt;4 copies), intermediate (4–5 copies) or unknown (&lt;20% tumor purity). The data were also analyzed for additional clinically relevant genomic alterations.

Results: High concordance was noted between HER2 copy number status determined by FISH and NGS: 30 of the 35 samples were classified as positive or negative by NGS, 1 was classified as intermediate and 4 as unknown due to low purity. Using FISH as a gold standard, NGS HER2 calls demonstrated an accuracy of 97% (29/30, 95% CI 83–99%), 93% sensitivity (13/14, 95% CI 69–99%) and 100% specificity (16/16, 95% CI 81–100%). One discordant case was noted (FISH positive, NGS negative). Furthermore, NGS revealed 70 additional alterations (38 base substitutions, 10 insertions/deletions, 22 copy number alterations) in 23 cancer genes (an average of 2.0 alterations per sample). Genomic alterations that predict sensitivity or resistance to approved or experimental targeted therapies and thus plausibly guide treatment decisions were found in 69% of patients. These include PIK3CA (16 cases, PI3 kinase/mTOR inhibitors), PTEN (3 cases, PI3K/AKT/mTOR inhibitors), KRAS (1 case, resistance to cetuximab and panitumumab), and NF1 (1 case, mTOR/MAPK inhibitors) plus amplifications of CCND1 (4 cases, CDK4 inhibitors), FGFR1 (3 cases, FGF inhibitors) and MCL1 (3 cases, BCL-2 inhibitors, resistance to anti-tubulin therapies). Four cases included co-amplification of RARA with HER2.

Conclusions: We conclude that HER2 status can be reliably determined by NGS on FFPE breast cancers and that NGS uncovers additional actionable genomic alterations that could impact disease management in a high proportion of patients. Further evaluation of NGS as a guide to therapy in breast cancer is warranted.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr PD02-07.