"Threshold-crossing": A Useful Way to Establish the Counterfactual in Clinical Trials?

A central question in the assessment of benefit/harm of new treatments is: how does the average outcome on the new treatment (the factual) compare to the average outcome had patients received no treatment or a different treatment known to be effective (the counterfactual)? Randomized controlled trials (RCTs) are the standard for comparing the factual with the counterfactual. Recent developments necessitate and enable a new way of determining the counterfactual for some new medicines. For select situations, we propose a new framework for evidence generation, which we call "threshold-crossing." This framework leverages the wealth of information that is becoming available from completed RCTs and from real world data sources. Relying on formalized procedures, information gleaned from these data is used to estimate the counterfactual, enabling efficacy assessment of new drugs. We propose future (research) activities to enable "threshold-crossing" for carefully selected products and indications in which RCTs are not feasible.

Adaptive Biomedical Innovation: Evolving Our Global System to Sustainably and Safely Bring New Medicines to Patients in Need

The current system of biomedical innovation is unable to keep pace with scientific advancements. We propose to address this gap by reengineering innovation processes to accelerate reliable delivery of products that address unmet medical needs. Adaptive biomedical innovation (ABI) provides an integrative, strategic approach for process innovation. Although the term "ABI" is new, it encompasses fragmented "tools" that have been developed across the global pharmaceutical industry, and could accelerate the evolution of the system through more coordinated application. ABI involves bringing stakeholders together to set shared objectives, foster trust, structure decision-making, and manage expectations through rapid-cycle feedback loops that maximize product knowledge and reduce uncertainty in a continuous, adaptive, and sustainable learning healthcare system. Adaptive decision-making, a core element of ABI, provides a framework for structuring decision-making designed to manage two types of uncertainty - the maturity of scientific and clinical knowledge, and the behaviors of other critical stakeholders.

Rationale and design of a randomized trial of automated hovering for post-myocardial infarction patients: The HeartStrong program

BACKGROUND

Coronary artery disease is the single leading cause of death in the United States, and medications can significantly reduce the rate of repeat cardiovascular events and treatment procedures. Adherence to these medications, however, is very low.

METHODS

HeartStrong is a national randomized trial offering 3 innovations. First, the intervention is built on concepts from behavioral economics that we expect to enhance its effectiveness. Second, the implementation of the trial takes advantage of new technology, including wireless pill bottles and remote feedback, to substantially automate procedures. Third, the trial's design includes an enhancement of the standard randomized clinical trial that allows rapid-cycle innovation and ongoing program enhancement.

RESULTS

Using a system involving direct data feeds from 6 insurance partners followed by mail, telephone, and email contact, we enrolled 1,509 patients discharged from the hospital with acute myocardial infarction in a 2:1 ratio of intervention:usual care. The intervention period lasts 1 year; the primary outcome is time to first fatal or nonfatal acute vascular event or revascularization, including acute myocardial infarction, unstable angina, stroke, acute coronary syndrome admission, or death.

CONCLUSIONS

Our randomized controlled trial of the HeartStrong program will provide an evaluation of a state-of-the-art behavioral economic intervention with a number of important pragmatic features. These include a tailored intervention responding to patient activity, streamlining of consent and implementation processes using new technologies, outcomes centrally important to patients, and the ability to implement rapid-cycle innovation.

IFPA meeting 2015 workshop report IV: placenta and obesity; stem cells of the feto-maternal interface; placental immunobiology and infection

Workshops are an important part of the IFPA annual meeting as they allow for discussion of specialised topics. At the 2015 IFPA annual meeting there were 12 themed workshops, three of which are summarized in this report. These workshops related to various aspects of placental biology and collectively covered areas of obesity and the placenta, stem cells of the feto-maternal interface, and placental immunobiology and infection.

Venous thromboembolism rates in patients undergoing major hip and knee joint surgery at Waitemata District Health Board: a retrospective audit

BACKGROUND/AIM

Symptomatic venous thromboembolism (VTE) complicates approximately 4% of major orthopaedic surgical procedures performed without thromboprophylaxis. Randomised clinical trials demonstrate primary thromboprophylaxis reduces VTE rates to <1%, with low rates of clinically important bleeding, using low molecular weight heparin (LMWH), oral FXa inhibitors or thrombin inhibitors. We reviewed the rates of VTE in patients undergoing major hip/knee joint surgery at Waitemata District Health Board (WDHB).

METHODS

Cases of VTE within 90 days of orthopaedic surgery were identified by retrospective audit of data from the haematology VTE database. The number of major hip/knee joint surgeries at WDHB from January 2006 to December 2010 was obtained from clinical coding data.

RESULTS

The cumulative incidence of VTE within 90 days of surgery was 3.29%. The median time from surgery to diagnosis was 7 days. Deep vein thrombosis comprised 75% of cases, 77.6% distal and 23.2% proximal. Pulmonary embolism comprised 26.5% of VTE; 47.7% had right heart strain on computed tomography/echocardiography. Hip fracture surgery comprised one-third of patients. Of patients developing VTE, 85.5% had chemical thromboprophylaxis - aspirin 73%, LMWH 20 mg 16%, LMWH 40 mg 16%, therapeutic LMWH 3%, unfractionated heparin twice daily 1%, and warfarin 4%; 75.6% received mechanical prophylaxis, while 4% of patients received no prophylaxis.

CONCLUSION

VTE incidence after major hip/knee joint surgery at WDHB is high, with pulmonary embolism comprising almost one-third of all VTE in this study, indicating the prophylaxis given is suboptimal. Implementation of appropriate, extended duration prophylaxis as per evidence-based guidelines is required to reduce these rates.

A more stable transition matrix for acoustic target scattering by elongated objects

The transition (T) matrix of Waterman has been very useful for computing fast, accurate acoustic scattering predictions for axisymmetric elastic objects, but this technique is usually limited to fairly smooth objects that are not too aspherical unless complex basis functions or stabilization schemes are used. To ease this limitation, a spherical-basis formulation adapted from approaches proposed recently by Waterman [J. Acoust. Soc. Am. 125(1), 42-51 (2009)] and Doicu, Eremin, and Wriedt [Acoustic and Electromagnetic Scattering Analysis Using Discrete Sources (Academic, London, 2000)] is suggested. This is implemented by simply transforming the high-order outgoing spherical basis functions within standard T-matrix formulations to low-order functions distributed along the object's symmetry axis. A free-field T matrix is produced in a nonstandard form, but computations with it become much more stable for elongated aspherical elastic shapes. Some advantages of this approach over the approaches of Waterman and Doicu, Eremin, and Wriedt are noted, and sample calculations for a 10:1 Al prolate spheroid and a 10:1 Al superspheroid of order 10 are given to demonstrate the enhanced stability.

Electrical maturation of spinal neurons in the human fetus: comparison of ventral and dorsal horn

The spinal cord is critical for modifying and relaying sensory information to, and motor commands from, higher centers in the central nervous system to initiate and maintain contextually relevant locomotor responses. Our understanding of how spinal sensorimotor circuits are established during in utero development is based largely on studies in rodents. In contrast, there is little functional data on the development of sensory and motor systems in humans. Here, we use patch-clamp electrophysiology to examine the development of neuronal excitability in human fetal spinal cords (10-18 wk gestation; WG). Transverse spinal cord slices (300 μm thick) were prepared, and recordings were made, from visualized neurons in either the ventral (VH) or dorsal horn (DH) at 32°C. Action potentials (APs) could be elicited in VH neurons throughout the period examined, but only after 16 WG in DH neurons. At this age, VH neurons discharged multiple APs, whereas most DH neurons discharged single APs. In addition, at 16-18 WG, VH neurons also displayed larger AP and after-hyperpolarization amplitudes than DH neurons. Between 10 and 18 WG, the intrinsic properties of VH neurons changed markedly, with input resistance decreasing and AP and after-hyperpolarization amplitudes increasing. These findings are consistent with the hypothesis that VH motor circuitry matures more rapidly than the DH circuits that are involved in processing tactile and nociceptive information.

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

High-resolution genomic profiling of thyroid lesions uncovers preferential copy number gains affecting mitochondrial biogenesis loci in the oncocytic variants

Oncocytic change is the result of aberrant mitochondrial hyperplasia, which may occur in both neoplastic and non-neoplastic cells and is not infrequent in the thyroid. Despite being a well-characterized histologic phenotype, the molecular causes underlying such a distinctive cellular change are poorly understood. To identify potential genetic causes for the oncocytic phenotype in thyroid, we analyzed copy number alterations in a set of oncocytic (n=21) and non-oncocytic (n=20) thyroid lesions by high-resolution microarray-based comparative genomic hybridization (aCGH). Each group comprised lesions of diverse histologic types, including hyperplastic nodules, adenomas and carcinomas. Unsupervised hierarchical clustering of categorical aCGH data resulted in two distinct branches, one of which was significantly enriched for samples with the oncocytic phenotype, regardless of histologic type. Analysis of aCGH events showed that the oncocytic group harbored a significantly higher number of genes involved in copy number gains, when compared to that of conventional thyroid lesions. Functional annotation demonstrated an enrichment for copy number gains that affect genes encoding activators of mitochondrial biogenesis in oncocytic cases but not in their non-oncocytic counterparts. Taken together, our data suggest that genomic alterations may represent additional/alternative mechanisms underlying the development of the oncocytic phenotype in the thyroid.

Response to dual HER2 blockade in a patient with HER3-mutant metastatic breast cancer

BACKGROUND

HER3 activating mutations have been shown in preclinical models to be oncogenic and ligand-independent, but to depend on kinase-active HER2.

PATIENTS AND METHODS

Whole-exome sequencing of the primary HER2-negative breast cancer and its HER2-negative synchronous liver metastasis from a 46-year-old female revealed the presence of an activating and clonal HER3 G284R mutation.

RESULTS

HER2 dual blockade with trastuzumab and lapatinib as third-line therapy led to complete metabolic response in 2 weeks and confirmed radiological partial response after 8 weeks. Following the resection of the liver metastasis, the patient remains disease-free 40 weeks after initiation of the HER2 dual blockade therapy. Immunohistochemical analysis demonstrated a substantial reduction of phospho-rpS6 and phospho-AKT in the post-therapy biopsy of the liver metastasis.

DISCUSSION

This is the first-in-man evidence that anti-HER2 therapies are likely effective in breast cancers harboring HER3 activating mutations.

Abstract P2-03-08: Mutational landscape of metaplastic breast carcinomas

Introduction: Metaplastic breast carcinoma (MBC) is an aggressive histologic type of breast cancer, which preferentially displays a triple-negative phenotype. These tumors are characterized by the presence of malignant cells exhibiting differentiation towards squamous epithelium or mesenchymal elements, including spindle, chondroid, osseous and rhabdoid differentiation. Unlike other rare histologic types of breast cancer such as adenoid cystic and secretory carcinomas, which are underpinned by the MYB-NFIB and ETV6-NTRK3 fusion genes respectively, pathognomonic genetic alterations have not been identified in MBC. It has been suggested, however, that the frequency of PIK3CA somatic mutations would be significantly higher in MBCs than in other forms of triple-negative disease. Here we sought to characterize the mutational landscape of MBCs by means of high-depth whole exome sequencing analysis.

Material and Methods: Twenty-one triple-negative MBCs were retrieved from the authors’ institutions. Representative sections from frozen blocks were microdissected to ensure tumor cell content greater than 50%. DNA samples extracted from microdissected tumor and matched peripheral blood leukocytes were subjected to high-depth (250x) whole exome sequencing on an Illumina GAIIx or HiSeq2000. Somatic point mutations were called using MuTect and somatic insertions and deletions (indels) were called using Strelka, Varscan2 and Haplotype Caller. Potentially pathogenic mutations were predicted using computational algorithms including PolyPhen-2, Mutation Taster, Mutation Assessor, CHASM and FATHMM. Significantly mutated genes were identified using MutSigCV. Pathway and network enrichment analysis of mutations was performed with Ingenuity Pathway Analysis and HOTNET. The genomic landscape of MBCs was compared with that of triple-negative breast cancers (TNBCs) analyzed as part of The Cancer Genome Atlas project.

Results: A mean of 135 somatic non-synonymous point mutations and indels were identified per MBC. The most frequently mutated gene was TP53, found in 12/21 cases (57%), and the only significantly mutated gene as defined by MutSigCV (q&lt;0.01). The repertoire of somatic mutations found in MBCs was qualitatively similar to that of TNBCs of no special type, and recurrently mutated genes were altered at similar frequencies in MBCs and TNBCs of no special type. When somatic mutations were annotated in pathways and networks, MBCs were found to have potentially pathogenic mutations affecting genes directly related to the PI3K pathway, including pathogenic non-synonymous mutations affecting PIK3CA, PIK3R1, PIK3R2, PIK3C2B, PIK3C2G and PTEN, significantly more frequently than TNBCs of no special type (10 out of 21 MBCs vs. 11 out of 62 TNBCs; Fisher's exact test p-value=0.0099).

Conclusion: The majority (57%) of MBCs harbored non-synonymous mutations affecting TP53. While the frequencies of mutations affecting recurrently mutated genes in MBCs are similar to those found in other forms of TNBCs, MBCs significantly more frequently harbor mutations affecting PI3K pathway-related genes than TNBCs of no special type.

Citation Format: Charlotte KY Ng, Britta Weigelt, Salvatore Piscuoglio, Y Hannah Wen, Maria R De Filippo, Luciano G Martelotto, Rachael Natrajan, Raymond Lim, Edi Brogi, Larry Norton, Anne Vincent-Salomon, Jorge S Reis-Filho. Mutational landscape of metaplastic breast carcinomas [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P2-03-08.