Assessing Tumor-infiltrating Lymphocytes in Solid Tumors: A Practical Review for Pathologists and Proposal for a Standardized Method From the International Immunooncology Biomarkers Working Group: Part 1: Assessing the Host Immune Response, TILs in Invasive Breast Carcinoma and Ductal Carcinoma In Situ, Metastatic Tumor Deposits and Areas for Further Research.

Assessment of tumor-infiltrating lymphocytes (TILs) in histopathologic specimens can provide important prognostic information in diverse solid tumor types, and may also be of value in predicting response to treatments. However, implementation as a routine clinical biomarker has not yet been achieved. As successful use of immune checkpoint inhibitors and other forms of immunotherapy become a clinical reality, the need for widely applicable, accessible, and reliable immunooncology biomarkers is clear. In part 1 of this review we briefly discuss the host immune response to tumors and different approaches to TIL assessment. We propose a standardized methodology to assess TILs in solid tumors on hematoxylin and eosin sections, in both primary and metastatic settings, based on the International Immuno-Oncology Biomarker Working Group guidelines for TIL assessment in invasive breast carcinoma. A review of the literature regarding the value of TIL assessment in different solid tumor types follows in part 2. The method we propose is reproducible, affordable, easily applied, and has demonstrated prognostic and predictive significance in invasive breast carcinoma. This standardized methodology may be used as a reference against which other methods are compared, and should be evaluated for clinical validity and utility. Standardization of TIL assessment will help to improve consistency and reproducibility in this field, enrich both the quality and quantity of comparable evidence, and help to thoroughly evaluate the utility of TILs assessment in this era of immunotherapy.

Assessing Tumor-Infiltrating Lymphocytes in Solid Tumors: A Practical Review for Pathologists and Proposal for a Standardized Method from the International Immuno-Oncology Biomarkers Working Group: Part 2: TILs in Melanoma, Gastrointestinal Tract Carcinomas, Non-Small Cell Lung Carcinoma and Mesothelioma, Endometrial and Ovarian Carcinomas, Squamous Cell Carcinoma of the Head and Neck, Genitourinary Carcinomas, and Primary Brain Tumors.

Assessment of the immune response to tumors is growing in importance as the prognostic implications of this response are increasingly recognized, and as immunotherapies are evaluated and implemented in different tumor types. However, many different approaches can be used to assess and describe the immune response, which limits efforts at implementation as a routine clinical biomarker. In part 1 of this review, we have proposed a standardized methodology to assess tumor-infiltrating lymphocytes (TILs) in solid tumors, based on the International Immuno-Oncology Biomarkers Working Group guidelines for invasive breast carcinoma. In part 2 of this review, we discuss the available evidence for the prognostic and predictive value of TILs in common solid tumors, including carcinomas of the lung, gastrointestinal tract, genitourinary system, gynecologic system, and head and neck, as well as primary brain tumors, mesothelioma and melanoma. The particularities and different emphases in TIL assessment in different tumor types are discussed. The standardized methodology we propose can be adapted to different tumor types and may be used as a standard against which other approaches can be compared. Standardization of TIL assessment will help clinicians, researchers and pathologists to conclusively evaluate the utility of this simple biomarker in the current era of immunotherapy.

The evaluation of tumor-infiltrating lymphocytes (TILs) in breast cancer: recommendations by an International TILs Working Group 2014.

BACKGROUND: The morphological evaluation of tumor-infiltrating lymphocytes (TILs) in breast cancer (BC) is gaining momentum as evidence strengthens for the clinical relevance of this immunological biomarker. Accumulating evidence suggests that the extent of lymphocytic infiltration in tumor tissue can be assessed as a major parameter by evaluation of hematoxylin and eosin (H&E)-stained tumor sections. TILs have been shown to provide prognostic and potentially predictive value, particularly in triple-negative and human epidermal growth factor receptor 2-overexpressing BC. DESIGN: A standardized methodology for evaluating TILs is now needed as a prerequisite for integrating this parameter in standard histopathological practice, in a research setting as well as in clinical trials. This article reviews current data on the clinical validity and utility of TILs in BC in an effort to foster better knowledge and insight in this rapidly evolving field, and to develop a standardized methodology for visual assessment on H&E sections, acknowledging the future potential of molecular/multiplexed approaches. CONCLUSIONS: The methodology provided is sufficiently detailed to offer a uniformly applied, pragmatic starting point and improve consistency and reproducibility in the measurement of TILs for future studies.

Inferring coancestry in population samples in the presence of linkage disequilibrium.

In both pedigree linkage studies and in population-based association studies there has been much interest in the use of modern dense genetic marker data to infer segments of gene identity by descent (ibd) among individuals not known to be related, to increase power and resolution in localizing genes affecting complex traits. In this article, we present a hidden Markov model (HMM) for ibd among a set of chromosomes and describe methods and software for inference of ibd among the four chromosomes of pairs of individuals, using either phased (haplotypic) or unphased (genotypic) data. The model allows for missing data and typing error, but does not model linkage disequilibrium (LD), because fitting an accurate LD model requires large samples from well-studied populations. However, LD remains a major confounding factor, since LD is itself a reflection of coancestry at the population level. To study the impact of LD, we have developed a novel simulation approach to generate realistic dense marker data for the same set of markers but at varying levels of LD. Using this approach, we present results of a study of the impact of LD on the sensitivity and specificity of our HMM model in estimating segments of ibd among sets of four chromosomes and between genotype pairs. We show that, despite not incorporating LD, our model has been quite successful in detecting segments as small as 10(6) bp (1 Mpb); we present also comparisons with fastIBD which uses an LD model in estimating ibd.

The use of Complementary and Alternative Medicine in pregnancy: data from the Avon Longitudinal Study of Parents and Children (ALSPAC).

OBJECTIVES: To report the frequency of Complementary and Alternative Medicine (CAM) use by a population of pregnant women in the UK. DESIGN: Four postal self-completion questionnaires completed at 8, 12, 18 and 32 weeks' gestation provided the source of CAMs used. Questions asked for written descriptions about the use of any treatments, pills, medicines, ointments, homeopathic medicines, herbal medicines, supplements, drinks and herbal teas. SETTING: An observational, population-based, cohort study of parents and children of 14,541 pregnant women residing within the former county of Avon in south-west England. Data was available for 14,115 women. RESULTS: Over a quarter (26.7%; n=3774) of women had used a CAM at least once in pregnancy, the use rising from 6% in the 1st trimester to 12.4% in the 2nd to 26.3% in the 3rd. Herbal teas were the most commonly reported CAM at any time in pregnancy (17.7%; n=2499) followed by homeopathic medicine (14.4%; n=2038) and then herbal medicine (5.8%; n=813). The most commonly used herbal product was chamomile used by 14.6% of women, the most commonly used homeopathic product was Arnica used by 3.1% of women. Other CAMs (osteopathy, aromatherapy, acupuncture/acupressure, Chinese herbal medicine, chiropractic, cranial sacral therapy, hypnosis, non-specific massage and reflexology) accounted for less than 1% of users. CONCLUSIONS: CAM use in pregnancy, where a wide range of CAMs has been assessed, has not been widely reported. Studies that have been conducted report varying results to this study (26.7%) by between 13.3% and 87% of pregnant women. Survey results will be affected by a number of factors namely the inclusion/exclusion of vitamins and minerals, the timing of data collection, the country of source, the number of women surveyed, and the different selection criteria of either recruiting women to the study or of categorising and identifying a CAM treatment or product.

The feasibility of a pragmatic randomised controlled trial to compare usual care with usual care plus individualised homeopathy, in children requiring secondary care for asthma.

OBJECTIVE: To test the feasibility of a pragmatic trial design with economic evaluation and nested qualitative study, comparing usual care (UC) with UC plus individualised homeopathy, in children requiring secondary care for asthma. This included recruitment and retention, acceptability of outcome measures patients' and health professionals' views and experiences and a power calculation for a definitive trial. METHODS: In a pragmatic parallel group randomised controlled trial (RCT) design, children on step 2 or above of the British Thoracic Society Asthma Guidelines (BTG) were randomly allocated to UC or UC plus a five visit package of homeopathic care (HC). Outcome measures included the Juniper Asthma Control Questionnaire, Quality of Life Questionnaire and a resource use questionnaire. Qualitative interviews were used to gain families' and health professionals' views and experiences. RESULTS: 226 children were identified from hospital clinics and related patient databases. 67 showed an interest in participating, 39 children were randomised, 18 to HC and 21 to UC. Evidence in favour of adjunctive homeopathic treatment was lacking. Economic evaluation suggests that the cost of additional consultations was not offset by the reduced cost of homeopathic remedies and the lower use of primary care by children in the homeopathic group. Qualitative data gave insights into the differing perspectives of families and health care professionals within the research process. CONCLUSIONS: A future study using this design is not feasible, further investigation of a potential role for homeopathy in asthma management might be better conducted in primary care with children with less severe asthma.

A likelihood-based trait-model-free approach for linkage detection of binary trait.

Trait-model-free (or "allele-sharing") approach to linkage analysis is a popular tool in genetic mapping of complex traits, because of the absence of explicit assumptions about the underlying mode of inheritance of the trait. The likelihood framework introduced by Kong and Cox (1997, American Journal of Human Genetics 61, 1179-1188) allows calculation of accurate p-values and LOD scores to test for linkage between a genomic region and a trait. Their method relies on the specification of a model for the trait-dependent segregation of marker alleles at a genomic region linked to the trait. Here we propose a new such model that is motivated by the desire to extract as much information as possible from extended pedigrees containing data from individuals related over several generations. However, our model is also applicable to smaller pedigrees, and has some attractive features compared with existing models (Kong and Cox, 1997), including the fact that it incorporates information on both affected and unaffected individuals. We illustrate the proposed model on simulated and real data, and compare its performance with the existing approach (Kong and Cox, 1997). The proposed approach is implemented in the program lm_ibdtests within the framework of MORGAN 2.8 (http://www.stat.washington.edu/thompson/Genepi/MORGAN/Morgan.shtml).

C/EBPalpha expression is partially regulated by C/EBPbeta in response to DNA damage and C/EBPalpha-deficient fibroblasts display an impaired G1 checkpoint.

We observed that CCAAT/enhancer-binding protein (C/EBP)alpha is highly inducible in primary fibroblasts by DNA-damaging agents that induce strand breaks, alkylate and crosslink DNA as well as those that produce bulky DNA lesions. Fibroblasts deficient in C/EBPalpha (C/EBPalpha(-/-)) display an impaired G1 checkpoint as evidenced by an inappropriate entry into the S-phase in response to DNA damage, and these cells also display an enhanced G1/S transition in response to mitogens. The induction of C/EBPalpha by DNA damage in fibroblasts does not require p53. Electrophoretic mobility shift assay (EMSA) analysis of nuclear extracts prepared from ultraviolet B (UVB)- and N-methyl-N'-nitro-N-nitrosoguanidine (MNNG)-treated fibroblasts showed increased binding of C/EBPbeta to a C/EBP consensus sequence and chromatin immunoprecipitation (ChIP) analysis also showed increased C/EBPbeta binding to the C/EBPalpha promoter. To determine whether C/EBPbeta has a function in the regulation of C/EBPalpha, we treated C/EBPbeta(-/-) fibroblasts with UVB or MNNG. We observed that C/EBPalpha induction was impaired in both UVB- and MNNG-treated C/EBPbeta(-/-) fibroblasts. Our study shows a novel function for C/EBPbeta in the regulation of C/EBPalpha in response to DNA damage and provides definitive genetic evidence that C/EBPalpha has a critical role in the DNA damage G1 checkpoint.

The SWI/SNF complex and cancer.

The mammalian SWI/SNF complexes mediate ATP-dependent chromatin remodeling processes that are critical for differentiation and proliferation. Not surprisingly, loss of SWI/SNF function has been associated with malignant transformation, and a substantial body of evidence indicates that several components of the SWI/SNF complexes function as tumor suppressors. This review summarizes the evidence that underlies this conclusion, with particular emphasis upon the two catalytic subunits of the SWI/SNF complexes, BRM, the mammalian ortholog of SWI2/SNF2 in yeast and brahma in Drosophila, and Brahma-related gene-1 (BRG1).

TGF-beta repression of Id2 induces apoptosis in gut epithelial cells.

Transforming growth factor-beta (TGF-beta) regulates epithelial tissue homeostasis by activating processes that control cell cycle arrest, differentiation and apoptosis. Disruption of the TGF-beta signaling pathway often occurs in colorectal cancers. Earlier, we have shown that TGF-beta induces apoptosis through the transcription factor Smad3. Affymetrix oligonucleotide microarrays were used to identify TGF-beta/Smad3 target genes that regulate apoptosis in rat intestinal epithelial cells (RIE-1). We found that TGF-beta repressed the expression of the inhibitor of differentiation (Id) gene family. Knockdown of Id1 and Id2 gene expression induced apoptosis in RIE-1 cells, whereas overexpression of Id2 attenuated TGF-beta-induced apoptosis. TranSignal Protein/DNA arrays were used to identify the hypoxia-inducing factor-1 (HIF-1) as a downstream target of TGF-beta. HIF-1 is a basic helix-loop-helix protein, and overexpression of Id2 blocked HIF-1 activation by TGF-beta. Furthermore, knockdown of HIF-1 blocked TGF-beta-induced apoptosis. Thus, we have identified HIF-1 as a novel mediator downstream of Id2 in the pathway of TGF-beta-induced apoptosis.

Exact trait-model-free tests for linkage detection in pedigrees.

A number of trait-model-free tests have been proposed for linkage detection between a genomic region and a trait. These tests involve testing the dependence in segregation between a trait and marker alleles by assigning a score to every possible identity-by-descent configuration of the pedigree members without modeling the trait, and then averaging the scores over all such configurations compatible with the observed marker genotypes and genealogical relationship of the pedigree members. In this paper we propose a permutation test as an alternative to the existing exact trait-model-free tests for linkage detection. The proposed test is computationally efficient and is applicable on complex multigeneration pedigree structures. In this paper, we have compared the performance of the permutation test with two other exact trait-model-free tests for linkage detection on simulated datasets. We have demonstrated that the proposed permutation test is fully robust against mispecification of marker allele frequencies and has very good power for linkage detection. The permutation test is implemented in the program lm_ibdtests within the framework of MORGAN 2.8 (http://www.stat.washington.edu/thompson/Genepi/MORGAN/Morgan.shtml).

Matrix metalloproteinase-10 is a critical effector of protein kinase Ciota-Par6alpha-mediated lung cancer.

Protein kinase Ciota (PKCiota) drives transformed growth of non-small cell lung cancer (NSCLC) cells through the Rho family GTPase Rac1. We show here that PKCiota activates Rac1 in NSCLC cells by formation of a PKCiota-Par6alpha complex that drives anchorage-independent growth and invasion through activation of matrix metalloproteinase-10 (MMP-10) expression. RNAi-mediated knockdown of PKCiota, Par6alpha or Rac1 expression inhibits NSCLC transformation and MMP-10 expression in vitro. Expression of wild-type Par6alpha in Par6alpha-deficient cells restores transformation and MMP-10 expression, whereas expression of Par6alpha mutants that either cannot bind PKCiota (Par6alpha-K19A) or couple to Rac1 (Par6alpha-DeltaCRIB) do not. Knockdown of MMP-10 expression blocks anchorage-independent growth and invasion of NSCLC cells and addition of catalytically active MMP-10 to PKCiota- or Par6alpha-deficient cells restores anchorage-independent growth and invasion. Dominant-negative PKCiota inhibits tumorigenicity and MMP-10 expression in subcutaneous NSCLC tumors. MMP-10 and PKCiota are coordinately overexpressed in primary NSCLC tumors, and tumor MMP-10 expression predicts poor survival in NSCLC patients. Our data define a PKCiota-Par6alpha-Rac1 signaling axis that drives anchorage-independent growth and invasion of NSCLC cells through induction of MMP-10 expression.

Capturing the value of complementary and alternative medicine: including patient preferences in economic evaluation.

Complementary and alternative medicine (CAM) is growing in popularity among patients, for an increasing range of conditions. However, current provision of CAM in the National Health Service in the UK is limited, patchy and disparate, which results in considerable inequity and patient unease. This has led to an escalation in the debate about the role of CAM within the NHS. Lack of evidence about the cost effectiveness of CAM therapies compared with other forms of care is often cited as the main reason for the reluctance of funders to integrate CAM into mainstream service provision. Cost-effectiveness relies on evidence about costs and benefits. Cost data are relatively straightforward to collect but it has proved difficult to value the complete package of benefits offered by CAM, likely to be both process and outcome based, in a way that can be compared with alternatives. Stated preference discrete choice modelling (SPDCM), a method of healthcare evaluation growing in popularity, uses information about patient preferences to identify the important characteristics of an intervention or method of delivering care and how patients value these. SPDCM is a method that could be used to evaluate the 'added value' provided by CAM and thus supply evidence on cost-effectiveness that policy makers could use in configuring service provision.

The IBD process along four chromosomes.

In this note, we present the continuous-time Markov rate matrix that models identity by descent (ibd) patterns among four chromosomes in a population. The equilibrium distribution of this Markov process along a chromosome is the set of 4-gene state probabilities given by the Ewens sampling formula. This model will facilitate inference of identity by descent among the four chromosomes of a pair of individuals, using data at dense SNP loci among which there may be linkage disequilibrium.

Men with cancer: is their use of complementary and alternative medicine a response to needs unmet by conventional care?

This qualitative study aims to investigate why men with cancer choose to use complementary and alternative medicine (CAM), and whether CAM is used to fill 'gaps' in conventional cancer care or as an 'alternative' to conventional treatment. Interviews were carried out with 34 CAM users recruited from a National Health Service (NHS) oncology department, an NHS homeopathic hospital and a private cancer charity offering CAM. Participants used therapies to improve quality of life, to actively 'fight' the disease and possibly prolong life, but rarely as an alternative to conventional treatment. Many were initially sceptical about CAM, but took a 'pragmatic' and 'consumerist' approach to getting their needs met. Gaps in conventional care included: lack of empathy and support during and after treatment, poor continuity of care, and lack of advice on self-help, diet and lifestyle. The skills of CAM therapists may enable them to tap into the underlying needs of men in a way that health professionals do not always have the time or the skills to achieve.

Setting standards in homeopathic practice--a pre-audit exploring motivation and expectation for patients attending the Bristol Homeopathic Hospital.

OBJECTIVE: To set a standard of routine goal setting with patients within their package of care at the Bristol Homeopathic Hospital. We hope goal setting will improve communication with our patients and health professional colleagues, focus outcome and improve targeting of problems. We therefore explored motivation for and expectation of hospital attendance from a patient perspective. MATERIALS AND METHODS: Questionnaire based pre-audit survey. The questionnaire was administered to 110 consecutive patients attending outpatients and 20 parents of children attending with asthma and eczema to gain understanding of motivation and expectation and more specific information for two of the commonest conditions. RESULTS: Seventy percent of patients had used some form of complementary and alternative medicine (CAM), 35% had used homeopathy and only 10% had specialist homeopathic care, the majority of use being over the counter. The majority of patients had been encouraged by their General Practitioners, themselves and by word of mouth with family and friends. Few patients cited the media as a major influence. "Pull" factors such as "treating the whole person" were given greater emphasis except for parents of children with asthma and eczema for whom "push" factors such as fear of steroid side effects predominated. In the main patient expectations were reasonable with the majority hoping to see improvements in their conditions. A fifth of patients hoped to reduce conventional medications. CONCLUSIONS: Patients had used CAM in general but not homeopathy in particular. Encouragement from doctors, self motivation and word of mouth most motivated patients to come and might suggest more direct communication with General Practitioners would be worthwhile. Being treated as a whole person was the most significant motivating factor, with a significant number of patients wishing to reduce medication. Goal setting and direct communication with other healthcare professionals is essential for safety, to focus outcome, and to value the role of homeopathy in a patient's healthcare. As a result we have set a standard whereby treatment goals are agreed with patients and communicated to referring health care professionals at each outpatient visit. This could be audited.

The vital sensation of the minerals: reducing uncertainty in homeopathic prescribing.

We illustrate the 'vital sensation' of mineral-based homeopathic medicines as revealed by an interview style based on a synthesis of the Bombay method and Scholten's, understanding derived from the periodic table. The 'Bombay method', described by Rajan Sankaran, builds on homeopathic teaching giving a structure to guide the gathering and synthesising homeopathic data. The concept of 'levels' gives a route to the deepest reflection of the vital disturbance, the vital sensation. Moving through the levels of fact, symptom, emotion, delusion and finally vital sensation provides valuable prescribing information. These aspects are discussed in conjunction with the kingdoms: plant, mineral and animal, focusing on the mineral kingdom. By synthesizing information relating to the concepts of vital sensation and kingdom we can reduce uncertainly in homeopathic prescribing.

Evi1 is a survival factor which conveys resistance to both TGFbeta- and taxol-mediated cell death via PI3K/AKT.

In hematopoietic cells the transforming potential of the ecotropic viral integration site 1 (Evi1) oncogene is thought to be dependent upon the ability to inhibit TGFbeta signaling. Although Evi1 has recently been implicated in certain epithelial cancers, the effects of Evi1 on transformation and TGFbeta signaling in epithelial cells are not completely understood. Herein, we have determined the effects of Evi1 on TGFbeta signaling in intestinal epithelial cells. Stable expression of Evi1 in non-transformed intestinal epithelial cells inhibited induction of some Smad3-dependent TGFbeta target genes, such as PAI1. However, TGFbeta-mediated induction of cellular adhesion signaling components such as integrin1 and paxillin was not inhibited by Evi1; nor did Evi1 inhibit TGFbeta-mediated epithelial to mesenchymal transition. Likewise, Evi1 did not inhibit TGFbeta-mediated downregulation of cyclin D1 or block TGFbeta-mediated growth inhibition. However, Evi1 did inhibit TGFbeta-mediated apoptosis by a process that involves phosphoinositide-3-kinase (PI3K) and its downstream effector AKT. The ability of Evi1 to suppress apoptosis is not restricted to TGFbeta-mediated cell death, since Evi1 also protects intestinal epithelial cells from taxol-mediated apoptosis. Evi1 is overexpressed in some human colon cancer cell lines, and overexpression is associated with amplification of the Evi1 gene. Knockdown of Evi1 by siRNA inhibited AKT phosphorylation in HT-29 human colon cancer cells and increased their sensitivity to taxol-mediated apoptosis. These data indicate that Evi1 functions as a survival gene in intestinal epithelial cells and colon cancer cells, activating PI3K/AKT and conveying resistance to both physiological and therapeutic apoptotic stimuli.

The placebo-controlled trial as a test of complementary and alternative medicine: observations from research experience of individualised homeopathic treatment.

The authors' experience of conducting clinical trials in homeopathy and analysing data from these has drawn attention to a fundamental problem with the interpretation of results from placebo controlled trials in homeopathy: It is not reasonable to assume that the specific effects of homeopathic medicine and the non-specific effects of consultations are independent of each other-specific effects of the medicine (as manifested by patients' reactions) may influence the nature of subsequent consultations and the non-specific effects of the consultation may enhance or diminish the effects of the medicine. For clinical trials of homeopathy to be accurate representations of practice, we need modified designs that take into account the complexity of the homeopathic intervention. Only with such trials will the results be generalisable to homeopathic practice in the real world. The authors propose that comparative trials are a meaningful way of evaluating the effectiveness of homeopathic treatment.

A model for the length of tracts of identity by descent in finite random mating populations.

Linkage disequilibrium (LD) reflects coinheritance of an ancestral segment by chromosomes in a population. To begin to understand the effects of population history on the extent of LD, we model the length of a tract of identity-by-descent (IBD) between two chromosomes in a finite, random mating population. The variance of an IBD tract is large: a model described by (Genet. Res. Cambridge 35 (1980) 131) underestimates this variance. Using Fisher's concept of junctions, we predict the mean length of an IBD tract, given the age of the population and the population sizes over time. We derive results also for subdivided populations, given times of subdivision events and sizes of the resulting subpopulations. The model demonstrates that population growth and subdivision strongly affect the expected length of an IBD tract in small populations. These effects are less dramatic in large populations.