A Partially Supervised Bayesian Image Classification Model with Applications in Diagnosis of Sentinel Lymph Node Metastases in Breast Cancer

A method has been developed for the analysis of images of sentinel lymph nodes generated by a spectral scanning device. The aim is to classify the nodes, excised during surgery for breast cancer, as normal or metastatic. The data from one node constitute spectra at 86 wavelengths for each pixel of a 20*20 grid. For the analysis, the spectra are reduced to scores on two factors, one derived externally from a linear discriminant analysis using spectra taken manually from known normal and metastatic tissue, and one derived from the node under investigation to capture variability orthogonal to the external factor. Then a three-group mixture model (normal, metastatic, non-nodal background) using multivariate t distributions is fitted to the scores, with external data being used to specify informative prior distributions for the parameters of the three distributions. A Markov random field prior imposes smoothness on the image generated by the model. Finally, the node is classified as metastatic if any one pixel in this smoothed image is classified as metastatic. The model parameters were tuned on a training set of nodes, and then the tuned model was tested on a separate validation set of nodes, achieving satisfactory sensitivity and specificity. The aim in developing the analysis was to allow flexibility in the way each node is modelled whilst still using external information. The Bayesian framework employed is ideal for this.Comment: 31 pages, 7 figure

PBEF1/NAmPRTase/Visfatin: a potential malignant astrocytoma/glioblastoma serum marker with prognostic value

Malignant astrocytomas comprise anaplastic astrocytoma (AA; grade III) and Glioblastoma (GBM; grade IV). GBM is the most malignant with a median survival of 10-12 months in patients. Using cDNA microarray based expression profiling of different grades of astrocytomas, we identified several fold increased levels of PBEF1 transcripts in GBM samples. Pre-B-cell colony enhancing factor 1 gene (PBEF1) encodes Nicotinamide phosphoribosyltransferase (NAmPRTase), which catalyses the rate limiting step in the salvage pathway of NAD metabolism in mammalian cells. Further validation using real time RT-qPCR on an independent set of tumor samples (n=91) and normal brain samples (n=9), GBM specific higher expression of PBEF1 was confirmed. Immunohistochemical staining for PBEF1 on a subset of the above samples largely reinforced our finding. We carried out ELISA analysis on serum samples of astrocytoma patients to determine whether this protein levels would correlate with the presence of tumor and tumor grade. PBEF1 serum levels were substantially elevated in many of the AA and GBM patients. Statistical analysis of these data indicates that in patients with astrocytoma, serum PBEF1 levels correlate with tumor grade and is highest in GBM. Immunohistochemical analysis of an independent set of 51 retrospective GBM cases with known survival data revealed that PBEF1 expression in the tumor tissue along with its co-expression with p53 was associated with poor survival. Thus, we have identified PBEF1 as a potential malignant astrocytoma serum marker and prognostic indicator among GBMs

Identification of potential serum biomarkers of glioblastoma: serum osteopontin levels correlate with poor prognosis

Background: The aim of this study is to identify serum biomarkers with classification and prognosis utility for astrocytoma, in particular glioblastoma (GBM). Methods: Our previous glioma microarray database was mined to identify genes that encode secreted or membrane-localized proteins. Subsequent analysis was done using significant analysis of microarrays, followed by reverse transcription-quantitative PCR (RT-qPCR) and immunohistochemical validation in tumor tissues, ELISA and Western blot validation in sera, and correlation with survival of GBM patients. Results: Significant analysis of microarrays identified 31 upregulated and 3 downregulated genes specifically in GBMs. RT-qPCR validation on an independent set of samples confirmed the GBM-specific differential expression of several genes, including three upregulated (CALU, CXCL9, and TIMP1) and two downregulated (GPX3 and TIMP3) novel genes. With respect to osteopontin (OPN), we show the GBM-specific upregulation by RT-qPCR and immunohistochemical staining of tumor tissues. Elevated serum OPN levels in GBM patients were also shown by ELISA and Western blot. GBM patients with high serum OPN levels had poorer survival than those with low serum OPN levels (median survival 9 versus 22 months respectively; P = 0.0001). Further, we also show high serum TIMP1 levels in GBM patients compared with grade II/III patients by ELISA and downregulation of serum GPX3 and TIMP3 proteins in GBMs compared with normal control by Western blot analysis. Conclusions: Several novel potential serum biomarkers of GBM are identified and validated. High serum OPN level is found as a poor prognostic indicator in GBMs. Impact: Identified serum biomarkers may have potential utility in astrocytoma classification and GBM prognosis

Upregulation of ASCL1 and inhibition of Notch signaling pathway characterize progressive astrocytoma

Astrocytoma is the most common type of brain cancer constituting more than half of all brain tumors. With an aim to identify markers describing astrocytoma progression, we have carried out microarray analysis of astrocytoma samples of different grades using cDNA microarray containing 1152 cancer-specific genes. Data analysis identified several differentially regulated genes between normal brain tissue and astrocytoma as well as between grades II/III astrocytoma and glioblastoma multiforme (GBM; grade IV). We found several genes known to be involved in malignancy including Achaete-scute complex-like 1 (Drosophila) (ASCL1; Hash 1). As ASCL has been implicated in neuroendocrine, medullary thyroid and small-cell lung cancers, we chose to examine the role of ASCL1 in the astrocytoma development. Our data revealed that ASCL1 is overexpressed in progressive astrocytoma as evidenced by increased levels of ASCL1 transcripts in 85.71% (6/7) of grade II diffuse astrocytoma (DA), 90% (9/10) of grade III anaplastic astrocytoma (AA) and 87.5% (7/8) of secondary GBMs, while the majority of primary de novo GBMs expressed similar to or less than normal brain levels (66.67%; 8/12). ASCL1 upregulation in progressive astrocytoma is accompanied by inhibition of Notch signaling as seen by uninduced levels of HES1, a transcriptional target of Notch1, increased levels of HES6, a dominant-negative inhibitor of HES1-mediated repression of ASCL1, and increased levels of Notch ligand Delta1, which is capable of inhibiting Notch signaling by forming intracellular Notch ligand autonomous complexes. Our results imply that inhibition of Notch signaling may be an important early event in the development of grade II DA and subsequent progression to grade III AA and secondary GBM. Furthermore, ASCL1 appears to be a putative marker to distinguish primary GBM from secondary GBM

Novel glioblastoma markers with diagnostic and prognostic value identified through transcriptome analysis

Purpose: Current methods of classification of astrocytoma based on histopathologic methods are often subjective and less accurate. Although patients with glioblastoma have grave prognosis, significant variability in patient outcome is observed. Therefore, the aim of this study was to identify glioblastoma diagnostic and prognostic markers through microarray analysis. Experimental Design: We carried out transcriptome analysis of 25 diffusely infiltrating astrocytoma samples [WHO grade II - diffuse astrocytoma, grade III - anaplastic astrocytoma, and grade IV - glioblastoma (GBM)] using cDNA microarrays containing 18,981 genes. Several of the markers identified were also validated by real-time reverse transcription quantitative PCR and immunohistochemical analysis on an independent set of tumor samples (n = 100). Survival analysis was carried out for two markers on another independent set of retrospective cases (n = 51). Results: We identified several differentially regulated grade-specific genes. Independent validation by real-time reverse transcription quantitative PCR analysis found growth arrest and DNA-damage-inducible α (GADD45α) and follistatin-like 1 (FSTL1) to be up-regulated in most GBMs (both primary and secondary), whereas superoxide dismutase 2 and adipocyte enhancer binding protein 1 were up-regulated in the majority of primary GBM. Further, identification of the grade-specific expression of GADD45α and FSTL1 by immunohistochemical staining reinforced our findings. Analysis of retrospective GBM cases with known survival data revealed that cytoplasmic overexpression of GADD45α conferred better survival while the coexpression of FSTL1 with p53 was associated with poor survival. Conclusions: Our study reveals that GADD45α and FSTLI are GBM-specific whereas superoxide dismutase 2 and adipocyte enhancer binding protein 1 are primary GBM-specific diagnostic markers. Whereas GADD45α overexpression confers a favorable prognosis, FSTL1 overexpression is a hallmark of poor prognosis in GBM patients

Breast cancer management pathways during the COVID-19 pandemic: outcomes from the UK ‘Alert Level 4’ phase of the B-MaP-C study

Abstract: Background: The B-MaP-C study aimed to determine alterations to breast cancer (BC) management during the peak transmission period of the UK COVID-19 pandemic and the potential impact of these treatment decisions. Methods: This was a national cohort study of patients with early BC undergoing multidisciplinary team (MDT)-guided treatment recommendations during the pandemic, designated ‘standard’ or ‘COVID-altered’, in the preoperative, operative and post-operative setting. Findings: Of 3776 patients (from 64 UK units) in the study, 2246 (59%) had ‘COVID-altered’ management. ‘Bridging’ endocrine therapy was used (n = 951) where theatre capacity was reduced. There was increasing access to COVID-19 low-risk theatres during the study period (59%). In line with national guidance, immediate breast reconstruction was avoided (n = 299). Where adjuvant chemotherapy was omitted (n = 81), the median benefit was only 3% (IQR 2–9%) using ‘NHS Predict’. There was the rapid adoption of new evidence-based hypofractionated radiotherapy (n = 781, from 46 units). Only 14 patients (1%) tested positive for SARS-CoV-2 during their treatment journey. Conclusions: The majority of ‘COVID-altered’ management decisions were largely in line with pre-COVID evidence-based guidelines, implying that breast cancer survival outcomes are unlikely to be negatively impacted by the pandemic. However, in this study, the potential impact of delays to BC presentation or diagnosis remains unknown

Preperitoneal mesh repair of incisional hernias: A seven-year retrospective study

Background : Incisional hernia is a common surgical condition with a reported incidence of 2-11% following all laparotomies. Results of repair have been disappointing. Aim : To evaluate our technique of preperitoneal mesh repair of incisional hernias. Materials and Methods : A seven-year retrospective study was done from January 1994 to December 2000 using a computerized database. Follow-up was initiated by a postal questionnaire on a response card. Our repair was evaluated by clinical examination, response card and telephone. Results were documented and statistically analyzed. Results : In our series of 105 patients, clinical details of 95 (90.5%) patients were available. Females (90.5%, n = 90) outnumbered males (9.5%, n = 10) and the highest incidence was in the 5 th decade of life in females and the 6 th decade of life in males ( P = 0.028). Gynecological operations accounted for 68.4% ( n = 65) of the index operations, with lower midline incisions resulting in 63% ( n = 60) of the incisional hernias. The polypropylene mesh placed preperitoneally varied from 15 ´ 7.5 cm to 30 ´ 20 cm. Sixty-five patients (62%) attended our follow-up, ranging from 14 months to eight years. Method of follow-up in outpatients department (OPD): 44.6% ( n = 29), postal: 40% ( n = 26), telephone: 15.3% ( n = 10). No recurrence was noted in the follow-up group. Conclusions : Based on our analyses, we believe that preperitoneal mesh repair is the ideal operation for incisional hernias. There are however, very few publications covering this technique of repair

Preperitoneal mesh repair of incisional hernias: A seven-year retrospective study

Background : Incisional hernia is a common surgical condition with a reported incidence of 2-11% following all laparotomies. Results of repair have been disappointing. Aim : To evaluate our technique of preperitoneal mesh repair of incisional hernias. Materials and Methods : A seven-year retrospective study was done from January 1994 to December 2000 using a computerized database. Follow-up was initiated by a postal questionnaire on a response card. Our repair was evaluated by clinical examination, response card and telephone. Results were documented and statistically analyzed. Results : In our series of 105 patients, clinical details of 95 (90.5%) patients were available. Females (90.5%, n = 90) outnumbered males (9.5%, n = 10) and the highest incidence was in the 5 th decade of life in females and the 6 th decade of life in males ( P = 0.028). Gynecological operations accounted for 68.4% ( n = 65) of the index operations, with lower midline incisions resulting in 63% ( n = 60) of the incisional hernias. The polypropylene mesh placed preperitoneally varied from 15 \ub4 7.5 cm to 30 \ub4 20 cm. Sixty-five patients (62%) attended our follow-up, ranging from 14 months to eight years. Method of follow-up in outpatients department (OPD): 44.6% ( n = 29), postal: 40% ( n = 26), telephone: 15.3% ( n = 10). No recurrence was noted in the follow-up group. Conclusions : Based on our analyses, we believe that preperitoneal mesh repair is the ideal operation for incisional hernias. There are however, very few publications covering this technique of repair