Consensus clustering methodology to improve molecular stratification of non-small cell lung cancer.

Recent advances in machine learning research, combined with the reduced sequencing costs enabled by modern next-generation sequencing, paved the way to the implementation of precision medicine through routine multi-omics molecular profiling of tumours. Thus, there is an emerging need of reliable models exploiting such data to retrieve clinically useful information. Here, we introduce an original consensus clustering approach, overcoming the intrinsic instability of common clustering methods based on molecular data. This approach is applied to the case of non-small cell lung cancer (NSCLC), integrating data of an ongoing clinical study (PROMOLE) with those made available by The Cancer Genome Atlas, to define a molecular-based stratification of the patients beyond, but still preserving, histological subtyping. The resulting subgroups are biologically characterized by well-defined mutational and gene-expression profiles and are significantly related to disease-free survival (DFS). Interestingly, it was observed that (1) cluster B, characterized by a short DFS, is enriched in KEAP1 and SKP2 mutations, that makes it an ideal candidate for further studies with inhibitors, and (2) over- and under-representation of inflammation and immune systems pathways in squamous-cell carcinomas subgroups could be potentially exploited to stratify patients treated with immunotherapy.

Biological versus Clinical Risk Factors in Acute Myeloid Leukemia: Is There a Winner?

We present a case of a patient with a three-month history of peripheral blood cytopenia without a confirmed diagnosis of myelodysplastic syndrome, who developed a favourable-risk acute myeloid leukemia (AML), according to the European Leukemia Net (ELN) criteria. The patient achieved a complete remission with incomplete platelet recovery (CRi) after induction. The patient achieved the morphological CR after the first consolidation and completed the first-line treatment with a syngeneic stem cell transplantation (SCT). A disease relapse occurred after one year of CR (blast cell count in the bone marrow 15%), and the patient was offered a haplo-SCT, which he refused due to personal reasons. In this paper, we discuss the interplay between clinical and biological risk factors in non-high-risk AML patients and speculate that some old clinical risk factors (e.g., age of the patient, achievement of CR after induction, and previous history of myelodysplastic syndrome) may still impact on the treatment decision algorithm of some of these patients.

Short-course R-CHOP followed by (90)Y-Ibritumomab tiuxetan in previously untreated high-risk elderly diffuse large B-cell lymphoma patients: 7-year long-term results.

An update at 7 years was conceived for our multicenter phase II study in which 55 elderly high-risk untreated diffuse large B-cell lymphoma patients were treated with (90)Y-ibritumomab tiuxetan after a short course of rituximab, cyclophosphamide, doxorubicin, vincristine and prednisolone (R-CHOP) as long-term follow-up analyses of this combined therapeutic modality are lacking. The overall response rate to the entire regimen was 80%, including 73% (40/55) of complete response (CR) rate and 7% (4/55) of partial response rate. At the time of writing, 24/55 (43.6%) patients experienced a progression disease and 20 of 40 (50%) patients who obtained a CR are still alive in continuous CR. With a median follow-up of 7 years, the disease-free survival was 43.3% and the progression-free survival was 36.1%. The overall survival at 7.9 years was 38.9% (27 deaths mainly because of lymphoma). Two patients developed secondary hematological malignancies, an acute myeloid leukemia and a myelodysplastic syndrome, at 4 and 3 years from radioimmunotherapy, respectively. Our data confirm the feasibility, efficacy and safety of four cycles of R-CHOP followed by radioimmunotherapy consolidation even in the long term: this combination allows dispensing less chemotherapy in a frail group of patients without invalidating response quality and duration.

Gluten-free dietary compliance in Brazilian celiac patients: questionnaire versus serological test

This study assessed the adherence to treatment of celiac disease (CD) patients being followed at Brasilia’s University Hospital. Forty-six CD patients underwent structural interviews. Their answers were compared with their IgA-tTG test results to determine their level of compliance with a gluten-free diet (GDF). The serological test results showed that 56.5% of the patients did not follow a GFD. Consumption of processed gluten-free foods (GFF) was significantly associated with IgA-tTG test result. Eighteen patients had other diseases in addition to CD and 77.8% of these had positive IgA-tTG results. 90.0% of the patients who presented negative serological test results attended the follow-up visits regularly. Adherence to treatment by this group of CD patients is low although most of them report complying with the diet. Compliance is affected by consumption of GFF, follow-up attendance and presence of other diseases. Awareness of these factors allows the establishment of actions that are beneficial to the celiac‘s treatment (AU)

O presente estudo avaliou a adesão ao tratamento da doença celíaca (DC) por pacientes em acompanhamento no Hospital Universitário de Brasília. 46 pacientes foram submetidos a entrevistas com questionário estruturado e suas respostas foram comparadas aos resultados do teste IgA-tTG para determinar seu nível de cumprimento de uma dieta livre de glúten (DLG). Os resultados dos testes sorológicos mostraram que 56,5% dos pacientes não seguem um DLG. O consumo de alimentos industrializados sem glúten (AISG) foi significativamente associada com o resultado do teste IgA-tTG. 18 pacientes tinham outras doenças, além da DC e 77,8% deles tiveram resultados IgA-tTG positivos. 90,0% dos pacientes que apresentaram os resultados dos testes sorológicos negativos participaram das visitas de acompanhamento regularmente. A adesão ao tratamento por este grupo de pacientes com DC é baixa, embora a maioria deles relatam cumprimento da dieta. A adesão ao tratamento é afetada pelo consumo de AISG, pela frequência de acompanhamento e pela presença de outras doenças. A consciência destes fatores permite o estabelecimento de ações que são benéficas para o tratamento do paciente (AU)

A phase II trial of short course fludarabine, mitoxantrone, rituximab followed by 9°Y-ibritumomab tiuxetan in untreated intermediate/high-risk follicular lymphoma.

BACKGROUND: A prospective, single-arm, open-label, multicenter, nonrandomised phase II trial to evaluate efficacy and safety of short fludarabine, mitoxantrone, and rituximab (FMR) induction followed by radioimmunotherapy, in untreated, intermediate/high-risk follicular non-Hodgkin's lymphoma (NHL) patients. PATIENTS AND METHODS: Fifty-five patients were treated using a sequential treatment schedule of four induction cycles of FMR chemoimmunotherapy, and a subsequent consolidating single administration of (90)Y-ibritumomab tiuxetan ((90)Y-IT), 8-14 weeks later. Patients were eligible for radioimmunotherapy if at least in partial response (PR) after induction, with normal platelet and granulocyte counts and a bone marrow infiltration ≤ 25%. Primary study end points were response rate and hematologic toxic effects; secondary end points were overall survival (OS) and progression-free survival (PFS). RESULTS: All the 55 patients received four induction cycles with an overall response rate of 96% (38 complete responses [CR] and 15 PR). Fifty-one patients (38 in CR and 13 in PR) received (90)Y-IT. By the end of the treatment, 49/55 patients achieved a CR. With a median follow-up of 21 months, the estimated 3-year PFS was 81% and the 3-year OS 100%. CONCLUSIONS: This study has established feasibility, tolerability, and efficacy of a regimen composed by short FMR induction with (90)Y-IT consolidation in untreated intermediate/high-risk follicular NHL patients.

MACOP-B regimen in the treatment of adult Langerhans cell histiocytosis: experience on seven patients.

BACKGROUND: Adult Langerhans cell histiocytosis (LCH) is a rare disease. The combination of vinblastine and prednisone, given in a 6-month course, is the standard of care but prospective randomized trials are lacking. PATIENTS AND METHODS: We report our monocentric experience in the treatment of seven adult patients with multisystem (MS) LCH (n = 3) or single-system multifocal (SS-m) LCH (n = 4) with the short-course intensive chemotherapy regimen methotrexate, doxorubicin, cyclophosphamide, vincristine, prednisone and bleomicin (MACOP-B). RESULTS: The overall response rate was 100% [five complete response (CR), two partial response (PR)]. After a median follow-up of 6.5 years, four patients are in first continuous CR and three patients relapsed after 5, 8 and 62 months, respectively. Four patients were evaluated with positron emission tomography (PET) scan: all three PET-negative patients at the end of treatment had a long-lasting response with only one patient relapsing after 5 years. PET scan detected additional bone lesions at diagnosis in two of four patients, changing the treatment program in one of them. CONCLUSIONS: MACOP-B regimen seems to be very active in the treatment of adult MS or SS-m LCH, with long-lasting responses in five of seven patients. PET scan merits further evaluation in the initial staging and in the evaluation of the response to chemotherapy.

Gemcitabine as single agent in pretreated T-cell lymphoma patients: evaluation of the long-term outcome.

BACKGROUND: Peripheral T-cell lymphoma unspecified (PTCLU) and mycosis fungoides (MF) often show resistance to conventional chemotherapy. Gemcitabine should be considered a suitable option. We report the long-term update of 39 pretreated T-cell lymphoma patients treated with gemcitabine. PATIENTS AND METHODS: From May 1997 to September 2007, 39 pretreated MF and PTCLU patients received gemcitabine. Inclusion criteria were as follows: histologic diagnosis of MF or PTCLU; relapsed/refractory disease; age > or =18 years; and World Health Organization performance status of two or less. Nineteen patients had MF and 20 PTCLU. All patients with MF had a T3-T4, N0, and M0 disease and patients with PTCLU had stage III-IV disease. Gemcitabine was given on days 1, 8, and 15 on a 28-day schedule (1200 mg/m(2)/day) for a total of three to six cycles. RESULTS: Overall response rate was 51% (20 of 39 patients); complete response (CR) and partial response (PR) rates were 23% (9 of 39 patients) and 28% (11 of 39 patients), respectively. Patients with MF had a CR rate of 16% and a PR rate of 32% compared with a CR rate of 30% and a PR rate of 25% of PTCLU patients. Among the CR patients, 7 of 9 are in continuous complete response with a variable disease-free interval (15-120 months). CONCLUSION: In our experience, gemcitabine proved to be effective in pretreated MF and PTCLU patients, even in the long term.

Possible role of everolimus in improving renal function in long-term heart transplantation.

Patient survival after heart transplantation has improved dramatically since the availability of calcineurine inhibitor (CNIs); the number of long-term patients is progressively increasing. However, in these patients, nephrotoxicity of CNIs has been largely responsible for the progressive development of renal dysfunction. Since impaired renal function is an important issue that reduces long-term patient survival, it is important to develop strategies to improve renal function while maintaining immunologic safety to preserve graft function. Everolimus is an mTOR inhibitor sirolimus analogue, that has proved, to be highly efficacious to prevent acute myocardial rejection and reduce the severity of cardiac allograft vasculopathy in de novo HTx patients. There is reasonable evidence that, in long term heart transplanted patients, renal function may improve when everolimus is administered associated with a progressive reduction of CNIs. So far there is no evidence to identify which patient may benefit from this therapeutic approach. Indeed everolimus alone may be equally effective to prevent rejection and improve renal function when CNIs are completely discontinued, but data are still lacking on the risks, dosages and side effects of this type of immunosuppression. Ongoing clinical studies will provide further guidance about the possibility to halt or reduce the progression of renal impairment in long term heart transplant patients.

Celiac disease and epilepsy: favorable outcome in a child with difficult to control seizures.

We report the case of a child with difficulties to control epilepsy and celiac disease, diagnosed soon after the onset of the seizure disorder. Seizure frequency and pattern, in addition to electroencephalogram record were suggestive of Lennox-Gastaut syndrome. Diagnosis of celiac disease was determined by positive anti-endomysium and anti-transglutaminase tests, and abnormal jejunal biopsy. Gluten-free diet, started soon after the diagnosis, led to progressive seizure control, allowing significant decrease in dosage of anti-epileptic drugs. This case corroborates the importance of serological screening tests for celiac disease, at least in patients with difficult to control epilepsy.

Prevalence of coeliac disease: unexplained age-related variation in the same population.

BACKGROUND: The aims of this work were (a) to evaluate the prevalence of coeliac disease (CD) in a large sample of the Brazilian general population and (b) to compare CD prevalence between children and adults. METHODS: The study group comprised 4405 subjects (2629 F and 1776 M). Age distributions were 2034 (1-14 years), 848 (15-29), 584 (30-44), 667 (45-59) and 272 above 60. The immunoglobulin A antiendomysial antibody (IgA-EMA) test was used as the serological screening tool. All sera were submitted to turbidimetric measurement of IgA levels and those with IgA deficiency to the IgG antigliadin (IgG-AGA) test. The small intestinal biopsy was recommended for subjects showing either (a) IgA-EMA positivity or (b) selective IgA deficiency (SigAD) and IgG-AGA positivity. RESULTS: There were 16 EMA positive out of 4405 sera tested. SigAD was found in five cases (one adult and four children). Two of these children tested positive for IgG-AGA and underwent jejunal biopsy that, in both cases, disclosed a normal mucosa. Overall, 17 out of 18 eligible subjects performed the small intestinal biopsy. The prevalence of biopsy-proven CD in this study group was 3.41 per 1000 individuals. If all 18 EMA-positive patients were included, the overall prevalence would become 3.63 per 1000. The prevalence in adults and children was 2.11 per 1000 and 5.44 per 1000, respectively. CONCLUSION: This work supports previous findings showing that CD is not a rare disorder in Brazil and that there is an unexplained difference in the prevalence of CD between adults and children.

Antiendomysial antibody test reliability in children with frequent diarrhea and malnutrition: is it celiac disease?

BACKGROUND: The aim of this study was to evaluate the specificity of the immunoglobulin A (IgA) antiendomysial antibody test in the diagnosis of celiac disease in a group of malnourished children with acute diarrhea, chronic diarrhea, or parasitosis, because the reliability of this test has been questioned when applied to this specific group of patients. METHODS: Serum IgA level, IgA antiendomysial antibody (EMA) test, and stool examination were performed in 315 children, ranging in age 6 months to 13 years (range, 41 +/- 2.9 months), affected by malnutrition, isolated or in association with diarrhea or parasitosis. Independent of results, 33 children with a strong suspicion of celiac disease, also underwent IgA antitransglutaminase antibody test and jejunal biopsy. RESULTS: The EMA test was negative in 313 children, including the 43 with parasitosis, being positive in two patients in whom biopsy disclosed typical celiac mucosal abnormalities (1:157). The 31 children with negative EMA test who underwent biopsy also showed negative antitransglutaminase antibody results. Their biopsies disclosed normal mucosa in 1 patient, variable degree of jejunal atrophy (grade 1 and 2) in 27 patients, and grade 3 abnormalities in 3 patients. One of these three children, showing severe jejunal atrophy, died. The diagnosis of celiac disease was apparently not confirmed by a protracted gluten challenge in the other two children. CONCLUSIONS: The specificity of the EMA test seems to be high also in children with chronic malnutrition and diarrhea. However, the possibility of false-negative tests among immunologically compromised children cannot be excluded. In doubtful cases, the gluten challenge is required in malnourished children with clinical picture, biopsy finding, and evolution suggestive of celiac disease.

Prevalence of celiac disease among blood donors in Brazil.

OBJECTIVE: There are no studies on the prevalence of celiac disease (CD) in either Brazil or, as far as we know, South America. The aim of this study was to determine the prevalence of CD in healthy blood donors in the city of Brasilia, Brazil. METHODS: Sera were obtained, independently of age and gender, from an unselected group of 2045 blood donors attending the Hematological Center of Brasilia. An IgG antigliadin antibody (AGA) test was used as a first-level screening step, followed by IgA-AGA test, serum IgA antiendomysium (EMA), and total serum IgA determination performed in all sera showing abnormally high IgG-AGA results. Jejunal biopsy was suggested for all subjects showing at least one of the following: IgA-EMA positivity; IgG-AGA and IgA-AGA positivity; IgG-AGA positivity and selective IgA deficiency. AGA was determined by an enzyme-linked immunosorbent assay (ELISA) technique and IgA-EMA was ascertained by indirect immunofluorescence on cryostat sections of monkey esophagus. Jejunal mucosa samples were obtained with a Watson capsule. RESULTS: Sixty-two (3.03%) blood donors had IgG-AGA above the cut-off values. Fifty-eight individuals showed isolated high values of IgG-AGA, whereas four had simultaneously increased IgG and IgA-AGA. Three patients had positive IgA-EMA test (one with both IgG- and IgA-AGA and two with only IgG-AGA) and underwent jejunal biopsies that disclosed complete villous atrophy associated with an increased number of intraepithelial lymphocytes and hypertrophic criptae. In this study group, the prevalence of biopsy-proven celiac disease was 1.47 +/- 1.66 in 1000 subjects. CONCLUSIONS: We found a prevalence of undiagnosed CD of 1:681 among apparently healthy blood donors. These preliminary results support the view that CD is not a rare disease in Brazil.

Why is coeliac disease endemic in the people of the Sahara?

The prevalence of antiendomysial antibody (AEA) in 989 Saharawi children was 5.6%. Intestinal biopsies in a subsample confirmed that AEA is a marker of coellac disease in people living in a developing country.

Measuring quality of life in dyspeptic patients: development and validation of a new specific health status questionnaire: final report from the Italian QPD project involving 4000 patients.

OBJECTIVE: Despite the fact that gastrointestinal disorders represent one of the most common reasons for medical consultations, formal assessment of patients' health-related quality of life (HRQOL) has been carried out only in a few studies, and in most cases generic questionnaires have been adopted. Because the specific issue of living with dyspeptic problems has been addressed in very few cases and no questionnaire has been shown to be appropriate for the Italian setting, a prospective project was launched to develop a specific HRQOL questionnaire for dyspepsia sufferers tailored to Italian patients but also appropriate in other cultural settings. METHODS: The project consisted in a 3-yr, three-phase survey, in which different versions of the quality of life in peptic disease questionnaire (QPD) were developed through expert and patient focus groups and empiric field studies and then administered to patients recruited in five multicenter studies. Standard psychometric techniques were used to evaluate the validity, reliability, responsiveness, and patient acceptability of the QPD. RESULTS: Three different versions of the QPD questionnaire were self-administered to more than 4000 patients. The final 30-item version, measuring three health concepts related to dyspeptic disease (anxiety induced by pain, social restriction, symptom perception), fulfilled the recommended psychometric criteria in terms of reliability and validity, correlated with health concepts measured with a well-known independent generic HRQOL instrument (the SF-36 Health Survey questionnaire) and was relatively invariant to diagnosis and sociodemographic variables; it also correlated with a measure of gastric pain frequency and was able to detect meaningful differences over time. CONCLUSIONS: Although further validation studies in different cultural and linguistic settings are mandatory before any firm conclusions can be drawn regarding the cross-cultural validity of the QPD, the data obtained provide evidence of the psychometric validity and robustness of the questionnaire when used in a fairly large, well-characterized population of Italian dyspeptic patients.

Synthesis of beta-D-Galf-(1-3)-D-GlcNAc by the trichloroacetamidate method and of beta-D-Galf-(1-6)-D-GlcNAc by SnCl4-promoted glycosylation.

In a continuation of our studies on the characterization of the glycoproteins of T. cruzi new galactofuranosyl disaccharides were synthesized. Beta-D-Galf-(1-3)-D-GlcNAc was prepared by employing the trichloroacetamidate procedure for the glycosylation step. The mild conditions of this reaction are appropriate for condensation of 2,3,5,6-tetra-O-benzoyl-beta-D-galactofuranosyl trichloroacetamidate with acid-labile benzyl 2-acetamido-4,6-O-benzylidene-2-deoxy-alpha-D-glucopyranoside. On the other hand, tin(IV) chloride promoted condensation of benzyl 2-acetamido-3-O-benzoyl-2-deoxy-alpha-D-glucopyranoside with penta-O-benzoyl-alpha-beta-D-galactofuranose gave the derivative of beta-D-Galf-(1-6)-D-GlcNAc in 78% yield.

Serum IgA antibodies from patients with coeliac disease react strongly with human brain blood-vessel structures.

BACKGROUND: Our objective was to determine the possible presence of IgA antibodies directed against human central nervous system (CNS) structures in sera from coeliac disease (CD) patients. METHODS: Serum samples were collected from 4 patients with active CD on a gluten-containing diet, 11 biopsy-proven CD patients on a gluten-free diet (GFD), and 52 non-coeliac gastrointestinal controls. In all patients IgA antigliadin antibody (AGA) titres were determined with enzyme-linked immunoassay (ELISA), and IgA antiendomysium antibodies (EMA) with indirect immunofluorescence on human umbilical cord. Cryostat sections of human brain occipital cortex were incubated with the patients' sera and subsequently labelled with anti-human IgA fluorescein conjugate. RESULTS: All sera from patients with active CD on a gluten-containing diet yielded positive results in both the IgG-AGA and EMA test and in indirect immunofluorescence on brain tissue, disclosing a strong fluorescence over blood-vessels structures. All sera from CD patients on a GFD and from non-coeliac gastrointestinal controls gave a negative result on both the EMA test and the immunofluorescence reaction on human brain. CONCLUSIONS: Sera from patients with active CD contain IgA antibodies that react with human brain vessel structures, giving intense fluorescence. These antibodies are not present in sera from coeliac patients on a GFD or non-coeliac controls. This finding might be involved in the abnormal nervous system manifestations frequently described in association with coeliac disease.