An investigation of the clinical impact and therapeutic relevance of a DNA damage immune response (DDIR) signature in patients with advanced gastroesophageal adenocarcinoma.

BACKGROUND: An improved understanding of which gastroesophageal adenocarcinoma (GOA) patients respond to both chemotherapy and immune checkpoint inhibitors (ICI) is needed. We investigated the predictive role and underlying biology of a 44-gene DNA damage immune response (DDIR) signature in patients with advanced GOA. MATERIALS AND METHODS: Transcriptional profiling was carried out on pretreatment tissue from 252 GOA patients treated with platinum-based chemotherapy (three dose levels) within the randomized phase III GO2 trial. Cross-validation was carried out in two independent GOA cohorts with transcriptional profiling, immune cell immunohistochemistry and epidermal growth factor receptor (EGFR) fluorescent in situ hybridization (FISH) (n = 430). RESULTS: In the GO2 trial, DDIR-positive tumours had a greater radiological response (51.7% versus 28.5%, P = 0.022) and improved overall survival in a dose-dependent manner (P = 0.028). DDIR positivity was associated with a pretreatment inflamed tumour microenvironment (TME) and increased expression of biomarkers associated with ICI response such as CD274 (programmed death-ligand 1, PD-L1) and a microsatellite instability RNA signature. Consensus pathway analysis identified EGFR as a potential key determinant of the DDIR signature. EGFR amplification was associated with DDIR negativity and an immune cold TME. CONCLUSIONS: Our results indicate the importance of the GOA TME in chemotherapy response, its relationship to DNA damage repair and EGFR as a targetable driver of an immune cold TME. Chemotherapy-sensitive inflamed GOAs could benefit from ICI delivered in combination with standard chemotherapy. Combining EGFR inhibitors and ICIs warrants further investigation in patients with EGFR-amplified tumours.

Machine learning to predict early recurrence after oesophageal cancer surgery.

BACKGROUND: Early cancer recurrence after oesophagectomy is a common problem, with an incidence of 20-30 per cent despite the widespread use of neoadjuvant treatment. Quantification of this risk is difficult and existing models perform poorly. This study aimed to develop a predictive model for early recurrence after surgery for oesophageal adenocarcinoma using a large multinational cohort and machine learning approaches. METHODS: Consecutive patients who underwent oesophagectomy for adenocarcinoma and had neoadjuvant treatment in one Dutch and six UK oesophagogastric units were analysed. Using clinical characteristics and postoperative histopathology, models were generated using elastic net regression (ELR) and the machine learning methods random forest (RF) and extreme gradient boosting (XGB). Finally, a combined (ensemble) model of these was generated. The relative importance of factors to outcome was calculated as a percentage contribution to the model. RESULTS: A total of 812 patients were included. The recurrence rate at less than 1 year was 29·1 per cent. All of the models demonstrated good discrimination. Internally validated areas under the receiver operating characteristic (ROC) curve (AUCs) were similar, with the ensemble model performing best (AUC 0·791 for ELR, 0·801 for RF, 0·804 for XGB, 0·805 for ensemble). Performance was similar when internal-external validation was used (validation across sites, AUC 0·804 for ensemble). In the final model, the most important variables were number of positive lymph nodes (25·7 per cent) and lymphovascular invasion (16·9 per cent). CONCLUSION: The model derived using machine learning approaches and an international data set provided excellent performance in quantifying the risk of early recurrence after surgery, and will be useful in prognostication for clinicians and patients.

ANTECEDENTES: la recidiva precoz del cáncer tras esofaguectomía es un problema frecuente con una incidencia del 20-30% a pesar del uso generalizado del tratamiento neoadyuvante. La cuantificación de este riesgo es difícil y los modelos actuales funcionan mal. Este estudio se propuso desarrollar un modelo predictivo para la recidiva precoz después de la cirugía para el adenocarcinoma de esófago utilizando una gran cohorte multinacional y enfoques con aprendizaje automático. MÉTODOS: Se analizaron pacientes consecutivos sometidos a esofaguectomía por adenocarcinoma y que recibieron tratamiento neoadyuvante en 6 unidades de cirugía esofagogástrica del Reino Unido y 1 de los Países Bajos. Con la utilización de características clínicas y la histopatología postoperatoria se generaron modelos mediante regresión de red elástica (elastic net regression, ELR) y métodos de aprendizaje automático Random Forest (RF) y XG boost (XGB). Finalmente, se generó un modelo combinado (Ensemble) de dichos métodos. La importancia relativa de los factores respecto al resultado se calculó como porcentaje de contribución al modelo. RESULTADOS: En total se incluyeron 812 pacientes. La tasa de recidiva a menos de 1 año fue del 29,1%. Todos los modelos demostraron una buena discriminación. Las áreas bajo la curva ROC (AUC) validadas internamente fueron similares, con el modelo Ensemble funcionando mejor (ELR = 0,791, RF = 0,801, XGB = 0,804, Ensemble = 0,805). El rendimiento fue similar cuando se utilizaba validación interna-externa (validación entre centros, Ensemble AUC = 0,804). En el modelo final, las variables más importantes fueron el número de ganglios linfáticos positivos (25,7%) y la invasión linfovascular (16,9%). CONCLUSIÓN: El modelo derivado con la utilización de aproximaciones con aprendizaje automático y un conjunto de datos internacional proporcionó un rendimiento excelente para cuantificar el riesgo de recidiva precoz tras la cirugía y será útil para clínicos y pacientes a la hora de establecer un pronóstico.

Multicentre cohort study to define and validate pathological assessment of response to neoadjuvant therapy in oesophagogastric adenocarcinoma.

BACKGROUND: This multicentre cohort study sought to define a robust pathological indicator of clinically meaningful response to neoadjuvant chemotherapy in oesophageal adenocarcinoma. METHODS: A questionnaire was distributed to 11 UK upper gastrointestinal cancer centres to determine the use of assessment of response to neoadjuvant chemotherapy. Records of consecutive patients undergoing oesophagogastric resection at seven centres between January 2000 and December 2013 were reviewed. Pathological response to neoadjuvant chemotherapy was assessed using the Mandard Tumour Regression Grade (TRG) and lymph node downstaging. RESULTS: TRG (8 of 11 centres) was the most widely used system to assess response to neoadjuvant chemotherapy, but there was discordance on how it was used in practice. Of 1392 patients, 1293 had TRG assessment; data were available for clinical and pathological nodal status (cN and pN) in 981 patients, and TRG, cN and pN in 885. There was a significant difference in survival between responders (TRG 1-2; median overall survival (OS) not reached) and non-responders (TRG 3-5; median OS 2·22 (95 per cent c.i. 1·94 to 2·51) years; P < 0·001); the hazard ratio was 2·46 (95 per cent c.i. 1·22 to 4·95; P = 0·012). Among local non-responders, the presence of lymph node downstaging was associated with significantly improved OS compared with that of patients without lymph node downstaging (median OS not reached versus 1·92 (1·68 to 2·16) years; P < 0·001). CONCLUSION: A clinically meaningful local response to neoadjuvant chemotherapy was restricted to the small minority of patients (14·8 per cent) with TRG 1-2. Among local non-responders, a subset of patients (21·3 per cent) derived benefit from neoadjuvant chemotherapy by lymph node downstaging and their survival mirrored that of local responders.

Fibroblast growth factor receptor 4 (FGFR4): a targetable regulator of drug resistance in colorectal cancer.

The discovery of underlying mechanisms of drug resistance, and the development of novel agents to target these pathways, is a priority for patients with advanced colorectal cancer (CRC). We previously undertook a systems biology approach to design a functional genomic screen and identified fibroblast growth factor receptor 4 (FGFR4) as a potential mediator of drug resistance. The aim of this study was to examine the role of FGFR4 in drug resistance using RNAi and the small-molecule inhibitor BGJ398 (Novartis). We found that FGFR4 is highly expressed at the RNA and protein levels in colon cancer tumour tissue compared with normal colonic mucosa and other tumours. Silencing of FGFR4 reduced cell viability in a panel of colon cancer cell lines and increased caspase-dependent apoptosis. A synergistic interaction was also observed between FGFR4 silencing and 5-fluorouracil (5-FU) and oxaliplatin chemotherapy in colon cancer cell lines. Mechanistically, FGFR4 silencing decreased activity of the pro-survival STAT3 transcription factor and expression of the anti-apoptotic protein c-FLIP. Furthermore, silencing of STAT3 resulted in downregulation of c-FLIP protein expression, suggesting that FGFR4 may regulate c-FLIP expression via STAT3. A similar phenotype and downstream pathway changes were observed following FGFR4 silencing in cell lines resistant to 5-FU, oxaliplatin and SN38 and upon exposure of parental cells to the FGFR small-molecule inhibitor BGJ398. Our results indicate that FGFR4 is a targetable regulator of chemo-resistance in CRC, and hence inhibiting FGFR4 in combination with 5-FU and oxaliplatin is a potential therapeutic strategy for this disease.

A phase I trial of bortezomib in combination with epirubicin, carboplatin and capecitabine (ECarboX) in advanced oesophagogastric adenocarcinoma.

PURPOSE: The protease inhibitor bortezomib attenuates the action of NF-κB and has shown preclinical activity alone and in combination with chemotherapy. DESIGN: A Phase I dose-escalation study was performed administering bortezomib (0.7, 1.0, 1.3 and 1.6 mg m(-2) on days 1 and 8 from cycle 2 onwards) in combination with Epirubicin 50 mg m(-2) intravenously on day 1, Carboplatin AUC 5 day 1 and Capecitabine 625 mg m(-2) BD days 1-21 every 21 days (VECarboX regimen), in patients with advanced oesophagogastric adenocarcinoma. The primary objective was to define the maximum tolerated dose (MTD) of Bortezomib when combined with ECarboX. RESULTS: 18 patients received bortezomib 0.7 (n = 6), 1.0 (n = 3), 1.3 (n = 6) and 1.6 mg m(-2) (n = 3) and a protocol amendment reducing the capecitabine dose to 500 mg m(-2) BD was enacted due to myelotoxicity. Common treatment-related non-haematological adverse events of any grade were fatigue (83.3 %), anorexia (55.6 %), constipation (55.6 %) and nausea (55.6 %). Common Grade 3/4 haematological toxicities were neutropenia (77.8 %) and thrombocytopenia (44.4 %). Objective responses were achieved in 6 patients (33.3 %) and a further 5 patients (27.8 %) had stable disease for >8 weeks. CONCLUSIONS: The addition of Bortezomib to ECarboX is well tolerated and response rates are comparable with standard chemotherapy.

Diversity loss with persistent human disturbance increases vulnerability to ecosystem collapse.

Long-term and persistent human disturbances have simultaneously altered the stability and diversity of ecological systems, with disturbances directly reducing functional attributes such as invasion resistance, while eliminating the buffering effects of high species diversity. Theory predicts that this combination of environmental change and diversity loss increases the risk of abrupt and potentially irreversible ecosystem collapse, but long-term empirical evidence from natural systems is lacking. Here we demonstrate this relationship in a degraded but species-rich pyrogenic grassland in which the combined effects of fire suppression, invasion and trophic collapse have created a species-poor grassland that is highly productive, resilient to yearly climatic fluctuations, and resistant to invasion, but vulnerable to rapid collapse after the re-introduction of fire. We initially show how human disturbance has created a negative relationship between diversity and function, contrary to theoretical predictions. Fire prevention since the mid-nineteenth century is associated with the loss of plant species but it has stabilized high-yield annual production and invasion resistance, comparable to a managed high-yield low-diversity agricultural system. In managing for fire suppression, however, a hidden vulnerability to sudden environmental change emerges that is explained by the elimination of the buffering effects of high species diversity. With the re-introduction of fire, grasslands only persist in areas with remnant concentrations of native species, in which a range of rare and mostly functionally redundant plants proliferate after burning and prevent extensive invasion including a rapid conversion towards woodland. This research shows how biodiversity can be crucial for ecosystem stability despite appearing functionally insignificant beforehand, a relationship probably applicable to many ecosystems given the globally prevalent combination of intensive long-term land management and species loss.

Medical record confidentiality law, scientific research, and data collection in the information age.

Author reviews U.S. federal and state laws on privacy and confidentiality on access and disclosure of health records governing government and private sector data bases. He also examines legislative proposals and recommendations for privacy and confidentiality now before the U.S. Congress.

Impact of food and predation on the snowshoe hare cycle.

Snowshoe hare populations in the boreal forests of North America go through 10-year cycles. Supplemental food and mammalian predator abundance were manipulated in a factorial design on 1-square-kilometer areas for 8 years in the Yukon. Two blocks of forest were fertilized to test for nutrient effects. Predator exclosure doubled and food addition tripled hare density during the cyclic peak and decline. Predator exclosure combined with food addition increased density 11-fold. Added nutrients increased plant growth but not hare density. Food and predation together had a more than additive effect, which suggests that a three-trophic-level interaction generates hare cycles.

Reversal of severe diabetic hyperlipidemia by prandial insulinization.

Severe hyperlipidemia was nearly completely corrected in 16 diabetic patients who were treated with regular insulin at breakfast and supper. Serum cholesterol levels fell from 572 +/- 52 mg/dl to 247 +/- 10 mg/dl, and serum triglycerides fell from 6,330 +/- 820 mg/dl to 354 +/- 40 mg/dl over a 4-month period of treatment. Establishment of comparable degrees of control of the fasting blood glucose and hemoglobin A1C levels by NPH insulin did not correct the hyperlipidemia. Regular insulin timed to act for the disposal of ingested substrates appears to provide physiologic actions important in the treatment of diabetic hyperlipidemia.

Secretion of insulin or connecting peptide: a predictor of insulin dependence of obese "diabetics".

Ninety obese "diabetic" patients, including 55 treated with insulin injection, were characterized by measurement of levels of insulin or connecting peptide of proinsulin (C peptide) induced during oral glucose tolerance testing. After reduction of body weight to ideal values, patients whose peak serum insulin levels were initially 64 microunits/mL or greater had reductions of blood glucose values from 227 +/- 24 to 122 +/- 10 mg/dL (fasting) and from 400 +/- 49 to 160 +/- 11 mg/dL (two hours postprandial); at C-peptide peaks of 6.0 ng/mL or greater, these blood glucose values fell from 244 +/- 30 to 118 +/- 12 mg/mL and from 400 +/- 51 to 160 +/- 16 mg/dL, respectively. Patients with peak values of less than 60 microunits/ml for insulin or less than 6.0 ng/mL for C peptide did not normalize the blood glucose concentration after weight loss. This critical level of insulin secretory reserve separating these groups was similar to that previously reported for avoidance of diabetic retinopathy and neuropathy. These results suggest that levels of insulin or C peptide induced during glucose tolerance testing distinguish between two types of hyperglycemic obesity-insulin-dependent diabetes mellitus and insulin-resistant obesity. Blood glucose levels alone did not identify these groups. Among consecutive hyperglycemic obese patients, 36% achieved normoglycemia by weight loss alone, including 33% of those previously treated with insulin injection.

Depression masquerading as diabetic neuropathy.

Fifty-nine patients referred for painful diabetic neuropathy of the lower extremities were evaluated for depression and response to antidepressant drug therapy in a double-blind controlled study. All patients were found to have substantial degrees of depression during psychiatric interview and by Kupfer-Detre test scores (8.1 +/- 0.6, as compared with control values of 4.0 to 4.3 +/- 0.2). Treatment with imipramine hydrochloride or amitriptyline hydrochloride resulted in complete remission of lower extremity pains in all patients in 10 +/- 2 weeks, with concomitant relief of depression and return of depression test scores to 3.8. These results suggest that the syndrome of painful diabetic neuropathy of the lower extremities represents a depressive equivalent in a large proportion of cases and that treatment with imipramine or amitriptyline is a successful mode of therapy for such persons.

Insulin secretion in the diagnosis of adult-onset diabetes mellitus.

The natural history of patients with glucose intolerance was observed in 334 patients during a period of 18 years. Glucose tolerance testing (100 g orally) was characterized by measurement of induced insulin secretion. Diabetic complications of retinopathy, sensory neuropathy, and renal disease developed only in the group of patients in whom the induced serum insulin peak fell below 60 mu U/ml. Preservation of an insulin secretory reserve that permitted serum insulin peaks of 60 muU/ml or greater was not associated with development of these complications or symptoms of insulin deficiency despite the presence of an equal degree of fasting hyperglycemia and glucose intolerance. A critical amount of insulin secretory reserve distinguishes between two qualitatively distinct clinical syndromes: true diabetes mellitus (the development of signs and symptoms of insulin deficiency) and the syndrome of pure resistance to insulin (signs and symptoms of hyperglycemia in the setting of adequate or excessive insulin secretion, frequently with obesity, but without diabetic complication).

Encephalopathy induced by oral hypoglycemic drugs.

Three patients experienced severe hypoglycemic encephalopathy during oral therapy of adult-onset diabetes mellitus. Disabling residual neurological deficits were observed in two of these patients. The insidious time course of drug-induced hypoglycemia appeared to prevent patient recognition of sustained hypoglycemia. These cases indicate the need for further caution in the administration of oral hypoglycemic agents.

Regulation by testosterone and serum protein of DNA synthesis in the developing epididymis of the rat.

Rates of DNA synthesis were measured as an index of cellular proliferation during the pubertal development of the rat epididymis. A highly reproducible pattern of DNA synthesis was defined by (1) a prepubertal, testosterone-insensitive peak of DNA synthesis at 25 days; (2) a dramatic decrease in DNA synthesis with the onset of puberty; (3) a major burst of testosterone-dependent synthesis peaking at 40 days in the head of the epididymis and at 40-60 days in the tail; (4) a fall to low levels as the adult organ weight was attained. An organ culture system was defined and utilized to analyse further the hormonal dependence of DNA synthesis in the epididymis. Testosterone and dihydrotestosterone failed to activate DNA synthesis at any stage of development in vitro. DNA synthesis was stimulated 100-300% by insulin at supra-physiological concentrations and by protein serum factor(s) at physiological concentrations. The serum activity was stable to heat treatment at 60 degrees C, destroyed by heating at 70 degrees C, and was present in the sera of hypophysectomized animals. These results indicate a primarily 'permissive' role for the action of testerone on DNA synthesis in the epididymis: testosterone acts to permit the expression of a developmental 'programme' of cell proliferation which is activated by specific protein(s) in serum.

Hormonal regulation of isoenzymes of N-acetyl-beta-glucosaminidase and beta-galactosidase during spermatogenesis in the rat.

Isoenzymes of beta-galactosidase and of N-acetyl-beta-glucosaminidase were assayed during development of rat testis and as a function of hormonal treatments. Isoenzyme 1 of beta-galactosidase was highest in specific activity in the 4-day-old testis, at a point when Sertoli cells and gonocytes were the predominant cell type. Beta-galactosidase II, previously shown to be associated with the sperm acrosome, was undetectable through the spermatocyte stage of development, but increased in specific activity during the formation of spermatids. The specific activities of isoenzymes I and II of N-acetyl-beta-glucosaminidase increased markedly in association with the formation of spermatogonia and spermatocytes, and then declined with the appearance of spermatids. Following hypophysectomy of rats at 26 days of age or in adulthood the specific activities of the lysosomal enzymes beta-galactosidase I and N-acetyl-beta-glucosaminidase I and II increased markedly, while the acrosomal beta-galactosidase II was undetectable. The normal patterns of isoenzyme distributed were restored completely by administration of LH and FSH or testosterone to hypophysectomized animals. These results thus demonstrate specific patterns of isoenzyme concentration during spermatogenesis. Formation of the acrosome in developing spermatids is associated with the induction of new forms of beta-galactosidase (isoenzyme II) and N-acetyl-beta-glucosaminidase (sperm isoenzyme). These molecules appear to be specialized forms which may participate in fertilization, and their induction is dependent upon the actions of gonadotropins or testosterone.

Gene activation during spermatogenesis.

Cell differentiation during spermatogenesis in the rat has been analyzed in terms of the formation of specific "marker" enzymes. Hyaluronidase and other acrosomal enzymes are formed in spermatids according to a highly predictable time schedule which may be termed a "molecular biological clock". The acrosomal enzymes beta-galactosidase and N-acetyl-beta-glucosaminidase exist as isoenzyme forms distinct from enzymes with similar substrate specificities in the lysosomes of precursor cells. Differentiation of spermatids thus involves the loss of gene expression for lysosomal enzymes and the activation of genes for acrosomal isoenzymes. Spermatogenesis is characterized by the sequential loss of expression of many genes, as evidenced by the loss of beta-glucuronidase in the differentiation of spermatogonia to spermatocytes, and the loss of uridine diphosphatase activity in the differentiation of spermatocytes to spermatids. The apparent absence of ornithine decarboxylase activity from spermatids suggests a dependence of these cells upon Sertoli cells for the provision of putrescine and/or spermidine. Such biochemical cooperativity among germinal cells may be necessary as the genes of spermatids are repressed and late spermatids become metabolically inactive. Spermatogenesis is also characterized by changes in the cellular content and rates of synthesis and phosphorylation of specific acidic chromatin proteins. It is hypothesized that these proteins may participate in the activation or repression of genes during spermatogenesis.