PATRI, a Genomics Data Integration Tool for Biomarker Discovery.

The availability of genomic datasets in association with clinical, phenotypic, and drug sensitivity information represents an invaluable source for potential therapeutic applications, supporting the identification of new drug sensitivity biomarkers and pharmacological targets. Drug discovery and precision oncology can largely benefit from the integration of treatment molecular discriminants obtained from cell line models and clinical tumor samples; however this task demands comprehensive analysis approaches for the discovery of underlying data connections. Here we introduce PATRI (Platform for the Analysis of TRanslational Integrated data), a standalone tool accessible through a user-friendly graphical interface, conceived for the identification of treatment sensitivity biomarkers from user-provided genomics data, associated with information on sample characteristics. PATRI streamlines a translational analysis workflow: first, baseline genomics signatures are statistically identified, differentiating treatment sensitive from resistant preclinical models; then, these signatures are used for the prediction of treatment sensitivity in clinical samples, via random forest categorization of clinical genomics datasets and statistical evaluation of the relative phenotypic features. The same workflow can also be applied across distinct clinical datasets. The ease of use of the PATRI tool is illustrated with validation analysis examples, performed with sensitivity data for drug treatments with known molecular discriminants.

The E3 ubiquitin ligase WWP1 sustains the growth of acute myeloid leukaemia.

The E3 ubiquitin ligase (E3) WWP1 is an oncogenic factor implicated in the maintenance of different types of epithelial cancers. The role of WW domain-containing E3 ubiquitin protein ligase 1 (WWP1) in haematological neoplasms remains unknown. Acute myeloid leukaemia (AML) is characterized by the expansion of malignant myeloid cells blocked at different stages of differentiation. Here we report that the expression of WWP1 is significantly augmented in a large cohort of primary AML patients and in AML cell lines, compared with haematopoietic cells from healthy donors. We show that WWP1 inactivation severely impairs the growth of primary AML blasts and cell lines in vitro. In vivo, we observed a reduced leukaemogenic potential of WWP1-depleted AML cells upon transplantation into immunocompromised mice. Mechanistically, WWP1 inactivation induces the accumulation of its protein substrate p27Kip1, which ultimately contributes to G0/G1 cell cycle arrest of AML blasts. In addition, WWP1 depletion triggers the autophagy signalling and reduces survival of leukaemic cells. Collectively, our findings provide molecular insights into the anti-cancer potential of WWP1 inhibition, suggesting that this E3 is a promising biomarker and druggable target in AML.

PML-RARA-associated cooperating mutations belong to a transcriptional network that is deregulated in myeloid leukemias.

It has been shown that individual acute myeloid leukemia (AML) patients are characterized by one of few initiating DNA mutations and 5-10 cooperating mutations not yet defined among hundreds identified by massive sequencing of AML genomes. We report an in vivo insertional-mutagenesis screen for genes cooperating with one AML initiating mutations (PML-RARA, oncogene of acute promyelocytic leukemia, APL), which allowed identification of hundreds of genetic cooperators. The cooperators are mutated at low frequency in APL or AML patients but are always abnormally expressed in a cohort of 182 APLs and AMLs analyzed. These deregulations appear non-randomly distributed and present in all samples, regardless of their associated genomic mutations. Reverse-engineering approaches showed that these cooperators belong to a single transcriptional gene network, enriched in genes mutated in AMLs, where perturbation of single genes modifies expression of others. Their gene-ontology analysis showed enrichment of genes directly involved in cell proliferation control. Therefore, the pool of PML-RARA cooperating mutations appears large and heterogeneous, but functionally equivalent and deregulated in the majority of APLs and AMLs. Our data suggest that the high heterogeneity of DNA mutations in APLs and AMLs can be reduced to patterns of gene expression deregulation of a single 'mutated' gene network.

Preoperative assessment in patients with postintubation tracheal stenosis : Rigid and flexible bronchoscopy versus spiral CT scan with multiplanar reconstructions.

BACKGROUND: Postintubation stenosis remains the most frequent indication for tracheal surgery. Rigid bronchoscopy has traditionally been considered the technique of choice for the preoperative diagnostic assessment. However, this technique is not routinely available, and new techniques such as flexible videobronchoscopy and spiral computed tomography (CT) scan with multiplanar reconstructions have been proposed as alternatives to rigid bronchoscopy. The aim of this study was to compare these techniques in the diagnostic assessment of patients with tracheal stenosis submitted to surgical treatment. METHODS: Twelve patients who underwent airway resection and reconstruction for postintubation tracheal and laryngotracheal stenosis were preoperatively evaluated with rigid and flexible bronchoscopy and with spiral CT scan with multiplanar reconstructions. The following parameters were examined: involvement of subglottic larynx, length of the stenosis, and associated lesions. The results were compared with the intraoperative findings. RESULTS: The accuracy of rigid bronchoscopy, flexible bronchoscopy, and CT scan in the evaluation of the involvement of subglottic larynx was, respectively, 92%, 83%, and 83%. The evaluation of the length of the stenosis was correct in 83%, 92%, and 25% of the patients, respectively, with rigid bronchoscopy, flexible bronchoscopy, and CT scan. A significant correlation was observed between the length of the stenosis measured intraoperatively and preoperatively with rigid (p < 0.001) and flexible bronchoscopy (p < 0.05) but not with CT scan (p = 0.08). The three techniques correctly showed the presence of an associated tracheoesophageal fistula in two patients, but CT scan did not correctly show the exact location of the fistula in relation to the airway. Flexible bronchoscopy was the only effective technique in the assessment of laryngeal function. CONCLUSIONS: Rigid bronchoscopy remains the procedure of choice in the evaluation of candidates for tracheal resection and reconstruction for postintubation stenosis, and it should be available in centers that perform surgery of the airway. Flexible bronchoscopy and CT scan have to be considered complementary techniques in the evaluation of laryngeal function and during follow-up.

Self-expanding stents in the treatment of tracheobronchial obstruction.

The self-expandable stainless steel stents (Gianturco, William Cook, Bjaeverskov, Denmark) used extensively in biliary ducts and the vascular system have recently been modified for use in the tracheobronchial tree. Between March 1991 and September 1992, six patients with unresectable tracheobronchial and mediastinal diseases were treated with the placement of one or more self-expanding stents under direct vision with a fiberoptic bronchoscope. All patients had been intubated for severe respiratory insufficiency. In all cases, immediate relief of respiratory symptoms was achieved and all patients were extubated 1 or 2 days after stent placement. Tolerance of the stents was excellent. No patient complained of pain, discomfort, or foreign body sensation. No infection or obstruction of the stents was observed. The chest roentgenogram and the bronchoscopies performed during follow-up have shown no change in the position of the stents. Our results seem promising since these devices provide effective palliation of airway obstructions and are well tolerated.

Therapeutic outcome according to histologic subtype in 121 patients with malignant pleural mesothelioma.

One-hundred and twenty-one cases of malignant pleural mesothelioma (MPM) seen between 1986 and 1999 at the authors' Institution were reviewed. Histotype was epithelial in 88 patients (73%), sarcomatous in 21 (17%) and mixed in 12 (10%). Ninety-one patients received a treatment (38 palliative pleurectomy and no further therapy, 16 palliative pleurectomy followed by chemotherapy, 37 chemotherapy alone), while 30 were referred to supportive care only. Median survival of the whole population was 10.5 months. The 1-, 2- and 3-year survival were 40, 17 and 8%, respectively. Univariate analysis of subgroups showed that poor performance status (PS), non-epithelial histotype, Butchart stage>I and International Mesothelioma Interest Group (IMIG) stage>I were individually associated with lower survival. Patients receiving any therapy survived longer than patients treated with supportive care only (P=0.0004). Treatment modality had an independent prognostic value (P=0.00005), with a survival advantage for patients receiving surgery and adjuvant chemotherapy. Multivariate analysis confirmed the independent prognostic value of PS (P=0.001; HR=2.48) and treatment modality (P=0.003; HR=1.38). The prognostic role of PS (P=0.02) and treatment modality (P=0.01) was confirmed in the subset of patients with epithelial histology. On the contrary, therapy had no impact on survival in patients with sarcomatoid MPM (P=0.74). Despite the predicted bias of a retrospective non-randomized evaluation of treatment-related factors, patients with good PS and epithelial histology seemed to have a survival benefit from surgery or multimodality therapy, as opposite to patients with poor PS or non-epithelial histotype. However, these results must be confirmed in a larger prospective trial with uniform treatment.

Electrostatic and electrophilic catalysis in the reductive cleavage of alkyl aryl ethers. The influence of ion pairing on the regioselectivity

Electrophilic and electrostatic catalysis have been identified as distinct contributions that affect the reactivity of radical anions in the reductive cleavage of alkyl aryl ethers. Two modes of mesolytic scission of these radical anions are possible: homolytic (dealkylation, a thermodynamically favored but kinetically forbidden process) and heterolytic (dealkoxylation). From our studies (alkali metal reductions, electrochemical studies, use of substrates with a preformed positive charge in certain positions of their structure) it can be concluded that the heterolytic scission is very much dependent on the electrophilic assistance by the counterion and it is only observed in contact ionic pairs with unsaturated cations (electrophilic catalysis). On the other hand, the homolytic scission is observed in solvent-separated ionic pairs, and it is especially efficient when the pair has a controlled topology with a tetralkylammonium cation (saturated cation) near the oxygen atom. The effect of the cation has, in this case, electrostatic origin (electrostatic catalysis), probably lowering the barrier of the intramolecular pi-sigma electron transfer process and thus reducing the kinetic control of the reaction in such a way that the thermodynamically more favorable process is produced.

Thoracoscopic treatment of a pericardial diverticulum.

A 35-year-old female patient presented with a history of recurrent chest pain. On chest x-ray, a regularly shaped lesion at the right cardiophrenic angle was observed. The lesion appeared smaller on a subsequent x-ray. Magnetic resonance imaging showed a cystic lesion that could be differentiated from the pericardium only in its lower part. Thoracoscopy revealed a pericardial diverticulum. Resection of the lesion was performed thoracoscopically, with complete remission of the symptoms.

18-FDG positron emission tomography in the evaluation of malignant pleural diseases - a pilot study.

OBJECTIVE: The diagnostic approach to pleural diseases may be difficult. The CT scan, which is the current diagnostic technique, has limited accuracy both in the differentiation between benign and malignant pleural diseases and in the diagnosis of primary and metastatic pleural neoplasms. Invasive procedures, such as thoracoscopy, are therefore frequently required to complete the diagnostic approach. The increasing incidence of malignant pleural mesothelioma has led to the development of new treatment strategies, which still need to be fully validated. There is, therefore, a need for new diagnostic techniques that can lead to a definite diagnosis and a satisfactory evaluation of the response to treatment. Encouraging results have been reported with the F-18-labeled analogue of 2-deoxyglucose (18-FDG) positron emission tomography (PET) in the evaluation of chest tumors such as lung cancer. The aim of this study was to evaluate the role of 18-FDG PET in the diagnostic assessment of pleural diseases. METHODS: Patients with CT scan evidence of pleural thickening, or fluid, entered a study to evaluate the accuracy of 18-FDG PET in diagnosing pleural diseases. Image analysis was performed both with visual interpretation and using a semiquantitative method, standardized uptake values (SUV), on coronal, sagittal and axial reconstructions. The results of PET imaging were compared to histological data. PET was also performed before and after treatment in patients who underwent chemotherapy to evaluate the accuracy of this technique in the assessment of the response. RESULTS: Fourteen patients entered the study. Histology demonstrated a malignant pleural disease in 13 patients; malignant pleural mesothelioma in ten patients, adenocarcinoma in two and liposarcoma in one. Benign pleural disease was diagnosed in the remaining patient. PET assessment demonstrated significant 18-FDG uptake in 12 of the 13 patients with a malignant disease, also revealing distant metastases in two of them. A false-negative result was observed in a patient with an epithelial mesothelioma. The overall accuracy was 92%. A benign pleural disease without significant uptake was correctly diagnosed in another patient. An aspecific uptake was observed in two patients who had undergone pleurectomy and intrapleural chemotherapy. A decreased tracer uptake was observed after chemotherapy in four patients. CONCLUSIONS: These preliminary results demonstrate that 18-FDG PET may have a great potential, both in the differential diagnosis of pleural diseases and in the evaluation of the response to treatment. At present, however, histological thoracoscopic diagnosis remains mandatory before planning treatment. Further studies in larger groups of patients are needed to draw definite conclusions on the role of PET in the assessment of pleural diseases.

Surgery following neoadjuvant MPV chemotherapy (mitomycin, cisplatin, vinblastine) in locally advanced (IIIa and IIIb) non-small cell lung cancer.

From November 1990 to August 1993, 32 patients with non-small cell lung cancer (NSCLC) entered a multimodality treatment study with neoadjuvant Mitomycin, Cisplatin and Vinblastine (MPV), surgery and radiotherapy at the San Raffaele Hospital in Milan, Italy. Neoadjuvant chemotherapy was performed on an outpatient basis. To date 23 patients (11 stage IIIa and 12 stage IIIb) have completed the chemotherapy treatment and are available for evaluation of response, toxicity, surgical eligibility and resection rate. The overall major response to MPV chemotherapy was 87%. The overall resection rate after major response to treatment was 60% (90% in stage IIIa and 17% in stage IIIb). After a median follow-up of 21 months (8-31) 17 patients are still alive (74%). Ten patients (83%) who had a complete resection are alive after a median follow-up of 23 months (21-30) and eight of them (66%) are in complete pathological remission. No treatment-related mortality was observed. The authors conclude that MPV is a highly effective neoadjuvant regimen for NSCLC and is feasible on an outpatient basis. Favorable resection rates can be obtained in stage IIIa patients. Stage IIIb patients can be downstaged and undergo complete resection. A longer follow-up is needed to assess the impact of this multimodality approach on long-term survival and to evaluate the role of adjuvant radiotherapy.

Surgical tracheostomy versus percutaneous dilatational tracheostomy. A prospective-randomized study with long-term follow-up.

BACKGROUND: To compare surgical tracheostomy (ST) versus percutaneous dilatational tracheostomy (PDT) in terms of complication rates. In particular we specifically studied the late tracheal complications of both methods by means of endoscopic controls of patients up to 6 months after the procedures. DESIGN: prospective-randomized clinical study. SETTING: University-affiliated tertiary care referral hospital. PATIENTS: 50 consecutive translaryngeally intubated patients with respiratory failure were randomized to undergo either ST (25 patients) or endoscopic guided PDT (25 patients). RESULTS: ST was performed in 41+/-14 min versus 14+/-6 min for PDT (p<0.0001). There was no procedure-related death. In the ST group there were no intraoperative complications. In the PDT group 2 intraoperative complications (minor hemorrhages) were observed. In the ST group 9 early postoperative complications occurred: one minor bleeding, 7 stomal infections and one accidental decannulation. In the PDT group only one early postoperative complication (minor bleeding) occurred. Early postoperative complication rates were 36% for ST and 4% for PDT. In the ST group there were no late tracheal complications. In the PDT group 2 late tracheal complications (one segmental malacia and one stenosis at the level of the stoma) were observed. CONCLUSIONS: This study confirms that PDT is a simpler and quicker procedure than ST and that it has a lower rate of early postoperative complications. Late tracheal complications were more frequent, although the difference was not statistically-significant, in the PDT group. Further investigations of long-term outcome following PDT are therefore necessary.

Imaging of bronchial carcinoid tumors associated to Cushing syndrome with 111In-Octreoscan scintigraphy and immunoscintigraphy with anti-chromogranin monoclonal antibodies. Report of two cases.

Bronchial carcinoid tumors are neuroendocrine neoplasms capable of expressing somatostatin receptors and of secreting neuromediators such as ACTH and chromogranins. Radiologic appearance is usually non-specific and has to be distinguished from benign pulmonary nodules and other malignant diseases. Standard radiological techniques have limited accuracy in the evaluation of such lesions. Radioisotopic imaging techniques may increase the specificity of diagnostic assessment. The role of immunoscintigraphy with anti-chromogranin A and B monoclonal antibodies (MoAbs) and of 111In-Octreoscan scintigraphy is evaluated in two cases of bronchial carcinoid tumors associated to Cushing syndrome.

Temporary main bronchial occlusion under bronchoscopic control in the evaluation of candidates for pneumonectomy.

BACKGROUND: In this study we report our experience with temporary main bronchial occlusion in the preoperative evaluation of candidates for pneumonectomy. METHODS: Between January 1991 and January 1994, 57 candidates for pneumonectomy underwent a 15-minute temporary main bronchial occlusion with an inflatable balloon during fiberoptic bronchoscopy. The following parameters were monitored during bronchial occlusion: general status, ECG, arterial pressure, heart rate and respiratory rate. Arterial blood gases were measured after 7 and 14 minutes. Values at 7 and at 14 minutes were compared with those obtained before the procedure. Patients were considered suitable surgical candidates for pneumonectomy if PaCO2 < 42 mmHg and pH > 7.35. RESULTS: Fifty-three patients were considered functionally operable. Three patients were considered functionally inoperable (PaCO2 > 42 mmHg, pH < 7.35 and appearance of dyspnea). One patient was excluded from the analysis because of balloon mispositioning due to a coughing fit. Sixteen of the operable patients underwent pneumonectomy and all did well without clinical evidence of respiratory insufficiency. At present 11 patients are alive, all without chronic respiratory insufficiency (mean follow-up 14 months). No postoperative mortality related to cardiorespiratory problems was observed. CONCLUSIONS: Temporary main bronchial occlusion is a simple and inexpensive test that can correctly predict functional resectability in candidates for pneumonectomy.

Efficacy of ketorolac tromethamine and extrapleural intercostal nerve block on post-thoracotomy pain. A prospective, randomized study.

BACKGROUND: Post-thoracotomy pain causes severe impairment of the respiratory function. Epidural analgesia is effective in the treatment of post-thoracotomy pain but may give rise to significant side-effects. Other low-risk and cost-effective analgesic treatments are therefore required. METHODS: Thirty male patients who had undergone pulmonary lobectomy entered a prospective, randomized trial to evaluate the efficacy of ketorolac tromethamine (Group 2) and extrapleural intercostal nerve block (Group 3) with intermittent low-dose bupivacaine. Objective and subjective assessment was carried out at 8, 16, 24 and 48 hours postoperatively. RESULTS: There were no significant differences between Groups 1 (control group) and 2. Vital capacity was significantly lower in Group 3 (p<0.05) than in Group 1 after 16 hours. Forced Vital Capacity was significantly higher in Group 2 than in Group 3 after 16 and 24 hours (p<0.05). Peak expiratory flow was also significantly better in Group 2 than in Group 3 after 16 hours (p<0.05). On-demand opioid consumption was significantly lower in Group 2 (p<0.001) and Group 3 (p<0.05). No side-effects were observed. CONCLUSIONS: Ketorolac tromethamine was effective in the treatment of post-thoracotomy pain. Extrapleural intercostal nerve block allowed a significant reduction in the consumption of opioids. These analgesic techniques could be useful as low-risk, cost-effective and reproducible treatments when more effective techniques, such as epidural analgesia, are contraindicated.

Surgical treatment of non-small cell lung cancer in patients 70 years of age or older.

BACKGROUND: Indications to surgical treatment of lung cancer in the elderly are still being discussed. The aim of this study was to evaluate postoperative complications and survival after surgery for non-small cell lung cancer (NSCLC) in patients 70 years of age or older. METHODS: During a 4 year and 6 month period, 76 patients (67 men and 9 women) entered the study. RESULTS: Postoperative complications occurred in 15 cases (19.7%) and the 30-day operative mortality was 1.3%. The overall 54 month actuarial survival was 53%. Mortality at 12 months wasn't related to stage of disease, histology or lobectomy versus wedge resection but was higher in those patients who had had postoperative cardiopulmonary complications. Results of preoperative spirometry, blood gas and cardiac status were predictive of mortality at twelve months (p < 0.05). CONCLUSIONS: Surgery for NSCLC in the elderly should not be denied on the basis of age alone. Postoperative outcome is mainly related to concomitant cardiopulmonary disease.

Single lung transplantation for emphysema. Lessons learned on the field. The Lung Transplant Group of the Ospedale Maggiore of Milan.

Emphysematous patients that were once treated with double lung transplantation can now also be treated with single lung transplantation. However, single lung transplantation in emphysematous patients presents problems in lung size matching, choice of side to transplant and post-operative assistance. Analysing their own experience of three single lung transplants performed on emphysematous patients, the Authors evaluate the effectiveness of the operation, the results and the difficulties encountered. Single lung transplantation is a good therapeutic option for end-stage emphysematous patients. In these patients right lung transplantation is preferable and the donor organ should be oversized. Positive and expiratory pressure in the native emphysematous lung should be applied with extreme caution.

[Transection of the popliteal artery caused by exostosis]. / Trans-sezione dell'arteria poplitea causata da esostosi.

Two cases of post-traumatic transection of the popliteal artery in patients with exostosis of the lower extremities are reported. This complication does not seem to have been previously described in the literature. The pathogenetic, clinical, diagnostic and therapeutic aspects are analysed.

[Endoscopic monitoring in lung transplantation. Transplantation Group of the Maggiore Policlinico Hospital of Milan]. / Il monitoraggio endoscopico nel trapianto di polmone. Gruppo Trapianto di Polmone dell'Ospedale Maggiore Policlinico di Milano.

During the period March 1991-June 1992 5 single lung transplantations were successfully performed at the Ospedale Maggiore Policlinico in Milan. All patients underwent regular fibrobronchoscopies within the context of a complex follow-up programme in order to monitor the resolution of the bronchial anastomosis and identify the onset of intercurrent lung infections and rejections using bronchioalveolar lavage (BAL) and transbronchial biopsies (TBB). Forty-four fibrobronchoscopies were performed of which 24 for anastomotic follow-up, BAL and TBB, and 20 for the simple monitoring of the anastomosis. Fibrobronchoscopies confirmed the optimal resolution of bronchial anastomosis in 4 patients, whereas one patient showed a granulomatous anastomotic reaction which was successfully treated using local steroid injections. Although recovery was normal in one patient, kinking appeared in the bronchus of the receiving lung which was successfully treated by the insertion of Gianturco prosthesis. BAL enabled the identification of 2 CMV infections, one Pseudomonas aeruginosa, one Haemophilus influenzae and one Pneumocystis carinii infection. TBB allowed 3 cases of CMW lung infection and 7 episodes of rejection to be diagnosed. The authors' personal experience confirms the decisive role played by bronchoscopy in the follow-up of lung transplant patients. This procedure allowed bronchial anastomosis to be closely monitored and was of vital importance in the diagnosis of lung infections and rejection.

[Endoscopic laser therapy in the palliative treatment of cancer of the esophagus]. / Laser-terapia endoscopica nel trattamento palliativo del cancro dell'esofago.

Frequently when dysphagia first becomes manifest, esophageal carcinoma is already unresectable. Endoscopic laser therapy is a recently introduced method which can be used for the palliative treatment of esophageal cancer. By using the method the tumour is destroyed and the esophagus is recanalized, there is low incidence of complications, and the patient can be fed naturally thus improving quality of life. The method has been perfected over the past years and now offers excellent results.

[Cardiorespiratory changes induced in man by the acute occlusion of the main bronchus]. / Modificazioni cardiorespiratorie indotte nell'uomo dall'occlusione acuta del bronco principale.

Following the exclusion of the ventilation of a lung, perfusion is arrested as a consequence of the Von Euler and Liljestrand vasoconstrictive reflex. However it is as yet unknown how long this phenomenon takes to manifest itself in human beings. In order to verify whether hypoxic pulmonary vasoconstriction follows immediately on the arrest of ventilation or whether there is one some delay, in 21 candidates for pneumonectomy a bronchial block was provoked during fibrobronchoscopy and the hemogasanalytic modifications induced by the acute occlusion of the main bronchus have been studied. The analysis of the resulting data allows for the hypothesis that the exclusion of lung ventilation for 14 minutes is not sufficient to cause the complete manifestation of the hypoxic vasoconstrictive reflex.