Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments.

Plasma consists of DNA released from multiple tissues within the body. Using genome-wide bisulfite sequencing of plasma DNA and deconvolution of the sequencing data with reference to methylation profiles of different tissues, we developed a general approach for studying the major tissue contributors to the circulating DNA pool. We tested this method in pregnant women, patients with hepatocellular carcinoma, and subjects following bone marrow and liver transplantation. In most subjects, white blood cells were the predominant contributors to the circulating DNA pool. The placental contributions in the plasma of pregnant women correlated with the proportional contributions as revealed by fetal-specific genetic markers. The graft-derived contributions to the plasma in the transplant recipients correlated with those determined using donor-specific genetic markers. Patients with hepatocellular carcinoma showed elevated plasma DNA contributions from the liver, which correlated with measurements made using tumor-associated copy number aberrations. In hepatocellular carcinoma patients and in pregnant women exhibiting copy number aberrations in plasma, comparison of methylation deconvolution results using genomic regions with different copy number status pinpointed the tissue type responsible for the aberrations. In a pregnant woman diagnosed as having follicular lymphoma during pregnancy, methylation deconvolution indicated a grossly elevated contribution from B cells into the plasma DNA pool and localized B cells as the origin of the copy number aberrations observed in plasma. This method may serve as a powerful tool for assessing a wide range of physiological and pathological conditions based on the identification of perturbed proportional contributions of different tissues into plasma.

Application of droplet digital PCR in minimal residual disease monitoring of rare fusion transcripts and mutations in haematological malignancies.

Leukaemia of various subtypes are driven by distinct chromosomal rearrangement or genetic abnormalities. The leukaemogenic fusion transcripts or genetic mutations serve as molecular markers for minimal residual disease (MRD) monitoring. The current study evaluated the applicability of several droplet digital PCR assays for the detection of these targets at RNA and DNA levels (atypical BCR::ABL1 e19a2, e23a2ins52, e13a2ins74, rare types of CBFB::MYH11 (G and I), PCM1::JAK2, KMT2A::ELL2, PICALM::MLLT10 fusion transcripts and CEBPA frame-shift and insertion/duplication mutations) with high sensitivity. The analytical performances were assessed by the limit of blanks, limit of detection, limit of quantification and linear regression. Our data demonstrated serial MRD monitoring for patients at molecular level could become "digitalized", which was deemed important to guide clinicians in treatment decision for better patient care.

CD44 activation in mature B-cell malignancies by a novel recurrent IGH translocation.

Using inverse polymerase chain reaction, we identified CD44, located on chromosome 11p13, as a novel translocation partner of IGH in 9 of 114 cases of gastric, nongastric extranodal, follicular, and nodal diffuse large B-cell lymphoma (DLBCL). Notably, these translocations involving IGHSmu were detected in follicular lymphomas and exclusively in germinal center B cell-ike (GCB)-DLBCLs. CD44 is not expressed in reactive GC B cells. The IGHSmu/CD44 translocations substitute Smu for the CD44 promoter and remove exon 1 of CD44, resulting in the overexpression of Imu-CD44 hybrid mRNA transcripts activated from derivative 11 that encode a new CD44 variant lacking the leader peptide and with a unique C-terminus (CD44DeltaEx1). When overexpressed in vitro in the CD44(-) GCB-DLBCL cell line BJAB, CD44DeltaEx1-green fluorescent protein localized to the cytoplasm and nucleus, whereas CD44s-green fluorescent protein (standard form) localized to the plasma membrane. The ectopic expression of CD44DeltaEx1 in BJAB cells enhanced their proliferation rate and clonogenic ability, indicating a possible pathogenic role of the translocation.

Use of Rasch analysis in the evaluation of the Oropharyngeal Mucositis Quality Of Life Scale.

BACKGROUND: Oropharyngeal mucositis (OM) is a significant clinical problem causing profound impairment of health-related quality of life (HQoL) for patients undergoing cancer therapy. The Oropharyngeal Mucositis-Specific Health-Related Quality of Life Measure (OMQoL) was developed using classical test theory to measure the self-perceived HQoL of patients with mucositis. OBJECTIVES: The aim of this study was to analyze the OMQoL according to the Rasch model and, on the basis of results, determine whether improvements could be made. METHOD: A multicenter approach was used, and 210 patients treated with stomatotoxic chemotherapy (36%), high-dose myeloablative chemotherapy ± total body irradiation (10%), or head and neck irradiation ± chemotherapy (54%) completed the OMQoL. The Partial Credit Model of Rasch analysis was applied to evaluate the 31-item OMQoL using WINSTEPS and R software. Unidimensionality (measurement of a single construct), item fit, response category performance, person separation reliability, targeting of item difficulty to person ability, and differential item functioning (DIF) were examined. RESULTS: Of 31 items, 5 were removed due to misfit; the OMQoL was reduced to 26 items with acceptable information weighted fit/outlier-sensitive fit indices (within 0.7-1.3) and eigenvalue units (≤2.0), confirming the unidimensionality of the reduced OMQoL. The OMQoL and its four subscales showed ordered category thresholds, and the person separation reliability was high (person separation index >0.2 with reliability >.8). Nevertheless, some of the items in the OMQoL might not be targeted effectively to patients with low levels of OM. Significant uniform and nonuniform DIFs were not found for gender (uniform DIF, p = .26; nonuniform DIF, p= .24) and age (uniform DIF, p = .95; nonuniform DIF, p = .65). DISCUSSION: Rasch analysis reveals that the reduced 26-item OMQoL is unidimensional and is adequate to measure HQoL for patients with OM regardless of gender and age group. This improved version can provide a common platform for nurses to use in their assessment, caring, and treatment of patients with OM.

Severe oral mucositis associated with cancer therapy: impact on oral functional status and quality of life.

GOALS OF WORK: This study determined the incidence of severe oral mucositis (OM), patients' self-reported moderate and severe oral symptoms, and change of quality of life (QoL), as well as examined whether OM severity and pain scores predicted the impairment of oral function and QoL. PATIENTS AND METHODS: A multicenter approach was used and 137 patients treated with stomatotoxic chemotherapy (45%), high-dose myeloablative chemotherapy with or without concomitant total body irradiation (12%), head and neck irradiation with or without concomitant chemotherapy (44%) completed the OM-specific QoL measure (OMQoL) once or twice weekly over a 4- or 10-week period, along with concurrent measures of OM using WHO Mucositis Grading System and oral symptoms using 10 cm visual analog scale. MAIN RESULTS: The incidence of severe OM was 50% (n = 68). About 77-80% of patients with severe OM reported moderate or severe mouth or throat pain, and 66-78% reported moderate or severe oral functional problems. The oral symptoms peak and area-under-the-curve (AUC) scores of patients with severe OM (peak 5.6 to 6.8; AUC 3.8 to 5.2) were significantly higher than those without OM and those with mild OM (p < 0.01). The OMQoL subscales peak and AUC scores of patients with severe OM (peak 47.9 to 62.1; AUC -40.1 to -25.8) were significantly lower than those without OM and those with mild OM (p < 0.01). Of those with severe OM, 88-94% had a drop in the OMQoL subscale scores to at least 10 points from the baseline. Pain resulting from OM, in particular throat pain, is most predictive of oral functional impairment (standardized ß = 0.53-0.83). CONCLUSIONS: Severe OM can cause profound pain and oral functional incapability and clinical significant impairment of QoL.

Outbreak of intestinal infection due to Rhizopus microsporus.

Sinopulmonary and rhinocerebral zygomycosis has been increasingly found in patients with hematological malignancies and bone marrow transplantation, but intestinal zygomycosis remains very rare in the literature. We investigated an outbreak of intestinal infection due to Rhizopus microsporus in 12 patients on treatment for hematological malignancies over a period of 6 months in a teaching hospital. The intake of allopurinol during hospitalization (P < 0.001) and that of commercially packaged ready-to-eat food items in the preceding 2 weeks (P < 0.001) were found to be independently significant risk factors for the development of intestinal zygomycosis. A total of 709 specimens, including 378 environmental and air samples, 181 food samples, and 150 drug samples, were taken for fungal culture. Among them, 16 samples of allopurinol tablets, 3 prepackaged ready-to-eat food items, and 1 pair of wooden chopsticks were positive for Rhizopus microsporus, which was confirmed by ITS1-5.8S-ITS2 rRNA gene cluster (internal transcribed spacer [ITS]) sequencing. The mean viable fungal counts of allopurinol obtained from wards and pharmacy were 4.22 x 10(3) CFU/g of tablet (range, 3.07 x 10(3) to 5.48 x 10(3)) and 3.24 x 10(3) CFU/g of tablet (range, 2.68 x 10(3) to 3.72 x 10(3)), respectively, which were much higher than the mean count of 2 x 10(2) CFU/g of food. Phylogenetic analysis by ITS sequencing showed multiple clones from isolates of contaminated allopurinol tablets and ready-to-eat food, of which some were identical to patients' isolates, and with one isolate in the cornstarch used as an excipient for manufacture of this drug. We attempted to type the isolates by random amplification of polymorphic DNA analysis, with limited evidence of clonal distribution. The primary source of the contaminating fungus was likely to be the cornstarch used in the manufacturing of allopurinol tablets or ready-to-eat food. Rhizopus microsporus is thermotolerant and can multiply even at 50 degrees C. The long holding time of the intermediates during the manufacturing process of allopurinol amplified the fungal load. Microbiological monitoring of drugs manufactured for highly immunosuppressed patients should be considered.

A patient-reported outcome instrument to assess the impact of oropharyngeal mucositis on health-related quality of life: a longitudinal psychometric evaluation.

GOALS OF WORK: An oropharyngeal mucositis (OM)-specific health-related quality of life measure (OMQoL) has been developed to assess the impact of OM from the perspective of patients. The current paper describes the convergent, concurrent, and known-group validities and responsiveness in relation to clinical and health outcomes. MATERIALS AND METHODS: A multicenter approach was used, and 137 patients treated with different cancer therapies completed the OMQoL and the European Organization for Research and Treatment of Cancer Quality of Life questionnaire [EORTC QLQ-C30 (Ch)] twice over a 4-week period or weekly over a 7-week period, along with concurrent measures of OM and its related symptoms. MAIN RESULTS: The OM-related symptom scores correlated highly with the OMQoL, confirming its convergent validity (r = -0.724--0.971, p < 0.01). Moderate correlations between the subscales of the OMQoL and EORTC QLQ-C30 (Ch) were indicative of good concurrent validity (r = 0.450-0.724, p < 0.01). The OMQoL was able to distinguish between patients with different severities of OM (p < 0.01) and types of cancer therapy (p < 0.01), providing evidence of good known-group validity. The changes in effects sizes corresponding to changes in OM curves indicate that the OMQoL is responsive to changes in OM status. CONCLUSIONS: These findings suggest that the OMQoL has very good psychometric properties and can be used as a health-related quality of life assessment for cancer patients with OM. Much work is still needed in strengthening the psychometric qualities and interpretability of the OMQoL by demonstrating its ability to detect outcome changes over time.

Role of liver biopsy in the management of liver dysfunction after hematopoietic stem-cell transplantation in a hepatitis B virus-prevalent patient population.

BACKGROUND: Derangement of liver function tests (LFT) is common after hematopoietic stem-cell transplantation (HSCT). The role of liver biopsy in such cases has not been defined in hepatitis B virus (HBV)-prevalent patients. The impact of liver biopsy in the management of LFT derangement after HSCT in an HBV-prevalent population was examined. METHODS: Seventy-five liver biopsies, performed for 323 patients with LFT derangement post-HSCT (263 allogeneic, 60 autologous), were analyzed. The HBV carrier rate was 13.6%. RESULTS: Significantly more LFT derangements and therefore liver biopsies occurred in allogeneic versus autologous HSCT. Before biopsy, graft-versus-host disease (GVHD) and HBV reactivation were clinically diagnosed in 70.6% and 25.3% of cases, respectively. A definite histopathologic diagnosis was obtained after biopsy in 53 cases, with GVHD, HBV hepatitis, and concomitant GVHD-HBV hepatitis found in 33%, 21%, and 8% of cases, respectively. The clinical and histopathologic diagnoses were concordant in 43 cases and discordant in 9 cases. Clinical management was altered in six of nine discordant cases, five of which were caused by HBV or hepatitis C virus (HCV) reactivation. Twenty-two biopsy specimens showed nondiagnostic histopathologic features. Twenty of these cases were successfully managed on the basis of clinical diagnoses. The clinical-biochemical features of patients clinically diagnosed to have GVHD did not differ significantly whether or not they were HBV-HCV carriers. However, liver biopsies in HBV-HCV carriers resulted in significantly more treatment alterations as compared with noncarriers. CONCLUSIONS: Clinical diagnoses of LFT derangements post-HSCT might be adequate for initiation of treatment, but liver biopsies in HBV-HCV carriers were needed, as this might impact on management.

Natural killer cell neoplasms.

Lymphoid neoplasms that are derived from natural killer (NK) cells are uncommon but distinct clinicopathologic disease entities. Three types have been recognized and categorized in the latest World Health Organization classification: extranodal NK cell lymphoma, nasal-type; aggressive NK cell leukemia; and blastic NK cell lymphoma. All NK tumor cells express the NK cell marker CD56, but they lack the expression of surface CD3 and the rearrangement of T-cell receptor genes, which distinguish them from T-lymphoid neoplasms. There is also a strong association with the Epstein-Barr virus, except in blastic NK cell lymphoma. Extranodal involvement by the NK cell tumor is common, especially in the nasal cavity, the skin, and the gastrointestinal tract. All 3 NK cell neoplasms are characterized by aggressive clinical course and poor response to treatment. Although the optimal treatment modality remains to be determined, good initial response to combined radiation therapy and chemotherapy has been observed in localized disease. Further studies in the basic biology of the NK cell and the pathology of NK cell neoplasms may shed light on the development of newer and more effective therapy.

Postgraduate training and assessment in Hong Kong.

The Hong Kong Academy of Medicine, established in 1993, is the only statutory body in Hong Kong to train, assess and accredit medical and dental specialists. According to the law in Hong Kong, a doctor or dentist who wishes to have his name included in the Specialist Register of Medical Council or Dental Council must either be a Fellow of the Academy or be assessed and certified by the Academy to have qualifications and training comparable to that required of an Academy Fellow. Once a doctor or dentist is on the Specialist Register, he must fulfil the continuing medical education requirements as determined by the Academy to maintain his specialist status. The Hospital Authority of Hong Kong has implemented the Doctor Work Reform (DWR) since 2006 which involves reduction of doctors' work hours and may affect training. The long-term strategy of the Academy with regards to the issue of DWR is to modernise postgraduate medical education and closely monitor the process to ensure that the quality of training would not be affected.

Extranodal natural-killer/t-cell lymphoma, nasal type.

The World Health Organization (WHO) classification recognizes 2 main categories of natural killer (NK) cell-derived neoplasms, namely, extranodal NK/T-cell lymphoma, nasal type, and aggressive NK-cell leukaemia. Extranodal nasal NK/T-cell lymphoma is more frequent in the Far East and Latin America. Histopathological and immunophenotypical hallmarks include angiocentricity, angiodestruction, expression of cytoplasmic CD3 epsilon (ε), CD56, and cytotoxic molecules and evidence of Epstein-Barr virus (EBV) infection. Early stage disease, in particular for localized lesion in the nasal region, is treated with chemotherapy and involved-field radiotherapy. On the other hand, multiagent chemotherapy is the mainstay of treatment for advanced or disseminated disease. L-asparaginase-containing regimens have shown promise in treating this condition. The role of autologous hematopoietic stem cell transplantation is yet to be clearly defined. Allogeneic hematopoietic stem cell transplantation, with the putative graft-versus-lymphoma effect, offers a potentially curative option in patients with advanced disease.

New measure of health-related quality of life for patients with oropharyngeal mucositis: development and preliminary psychometric evaluation.

BACKGROUND: Oropharyngeal mucositis (OM) causes profound impairment of patients' health-related quality of life (HQoL). The aim of the article is to describe the development and preliminary validation of an HQoL instrument, OMQoL, specifically for patients with OM. METHODS: First, a qualitative phase was conducted to generate items (n = 23). Face validity was assessed by focus group interviews (n = 13). Expert content review (n = 7) was used to ensure content validity. The second step was a quantitative validation phase comprised a multicenter study (n = 210) to help identify subscales of the instrument addressing different dimensions of OM and to measure reliability. RESULTS: The qualitative interview generated 171 items. Using focus group discussion and expert content review, items were reduced to 41 items. Factor and scaling analyses of these 41 items resulted in 4 subscales, contributed by 31 items, depicting problems with symptoms, diet, social function, and swallowing. The floor effect was modest. The factorial structure was satisfactory with loading >0.40 on each subscale for all items. All corrected item-total corrections were higher than 0.40 (r = 0.457-0.874). The internal consistency reliability of each subscale was high, with Cronbach alpha coefficients ranging from 0.906 to 0.934. The test-retest reliability of the individual items using weighted kappa was good (kappa values 0.610-0.895). The intraclass correlation results for the subscale totals were all in excess of 0.70 (0.864-0.934). CONCLUSIONS: An initial psychometric analysis of the OMQoL was encouraging. The OMQoL could provide a valuable tool for the assessment of HQoL of patients with OM.

Frequent deletion of Fas gene sequences encoding death and transmembrane domains in nasal natural killer/T-cell lymphoma.

Nasal natural killer (NK)/T-cell lymphoma (NL) frequently co-expresses Fas (Apo-1/CD95) and Fas ligand (FasL), but the tumor cells seldom undergo apoptosis. To determine the reason for failure of apoptosis, we examined Fas mRNA expression in 23 NL cases by reverse transcriptase-polymerase chain reaction and sequenced the entire coding region of the Fas gene in 15 of these cases for which the full-length Fas cDNA could be amplified. The reverse transcriptase-polymerase chain reaction analysis revealed that all of the 23 cases expressed Fas mRNA and the sequencing results showed that in addition to the commonly expressed wild-type Fas mRNA and four alternative splice variants detected in 7 cases, mutant Fas transcripts were present in 9 of the 15 (60%) cases sequenced. With confirmation of some Fas mutations at the gene level, 12 deletions in nine cases and one insertion in one case were eventually identified. To rule out any potential polymerase chain reaction artifacts, the same protocol was used to examine 10 reactive tonsils as a control. No aberrant transcripts associated with deletions were detected in these tonsils except for three alternative splice variants. All of the deletion variants detected in NL contained N-terminal preligand assembly domain but not C-terminal death domain and/or transmembrane domain. Co-detection of the wild-type allele and the mutated Fas alleles without the death domain suggested that a dominant-negative mechanism could block the apoptosis signaling. Moreover, loss of the transmembrane domain could protect the tumor cells from apo-ptosis by producing a soluble form of the Fas receptor. The actuarial 3-year survivals leveled off at 15% for patients carrying the Fas mutations and/or splice variants in the lesions and 49% for those carrying the wild type only, but the difference did not reach statistical significance on the univariate analysis (P = 0.396). Taken together, the findings in this study suggest that frequent Fas gene mutations in NL can result in resistance to apoptosis and may contribute to the pathogenesis of NL by adding to the tumor immune privilege.