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

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

Essential role of METTL3-mediated m(6)A modification in glioma stem-like cells maintenance and radioresistance

Despite advances in biology and therapeutic modalities, existence of highly tumorigenic glioma stem-like cells (GSCs) makes glioblastomas (GBMs) invincible. N6-methyl adenosine (m(6)A), one of the abundant mRNA modifications catalyzed by methyltransferase-like 3 and 14 (METTL3/14), influences various events in RNA metabolism. Here, we report the crucial role of METTL3-mediated m(6)A modification in GSC (neurosphere) maintenance and dedifferentiation of glioma cells. METTL3 expression is elevated in GSC and attenuated during differentiation. RNA immunoprecipitation studies identified SOX2 as a bonafide m(6)A target of METTL3 and the m(6)A modification of SOX2 mRNA by METTL3 enhanced its stability. The exogenous overexpression of 3' UTR-less SOX2 significantly alleviated the inhibition of neurosphere formation observed in METTL3 silenced GSCs. METTL3 binding and m(6)A modification in vivo required intact three METTL3/m(6)A sites present in the SOX2-3' UTR. Further, we found that the recruitment of Human antigen R (HuR) to m(6)A-modified RNA is essential for SOX2 mRNA stabilization by METTL3. In addition, we found a preferential binding by HuR to the m(6)A-modified transcripts globally. METTL3 silenced GSCs showed enhanced sensitivity to gamma-irradiation and reduced DNA repair as evidenced from the accumulation of gamma-H2AX. Exogenous overexpression of 3' UTR-less SOX2 in METTL3 silenced GSCs showed efficient DNA repair and also resulted in the significant rescue of neurosphere formation from METTL3 silencing induced radiosensitivity. Silencing METTL3 inhibited RasV12 mediated transformation of mouse immortalized astrocytes. GBM tumors have elevated levels of METTL3 transcripts and silencing METTL3 in U87/TIC inhibited tumor growth in an intracranial orthotopic mouse model with prolonged mice survival. METTL3 transcript levels predicted poor survival in GBMs which are enriched for GSC-specific signature. Thus our study reports the importance of m(6)A modification in GSCs and uncovers METTL3 as a potential molecular target in GBM therapy

Integrative functional genomic analysis identifies epigenetically regulated fibromodulin as an essential gene for glioma cell migration

An integrative functional genomics study of multiple forms of data are vital for discovering molecular drivers of cancer development and progression. Here, we present an integrated genomic strategy utilizing DNA methylation and transcriptome profile data to discover epigenetically regulated genes implicated in cancer development and invasive progression. More specifically, this analysis identified fibromodulin (FMOD) as a glioblastoma (GBM) upregulated gene because of the loss of promoter methylation. Secreted FMOD promotes glioma cell migration through its ability to induce filamentous actin stress fiber formation. Treatment with cytochalasin D, an actin polymerization inhibitor, significantly reduced the FMOD-induced glioma cell migration. Small interfering RNA and small molecule inhibitor-based studies identified that FMOD-induced glioma cell migration is dependent on integrin-FAK-Src-Rho-ROCK signaling pathway. FMOD lacking C-terminus LRR11 domain (Delta FMOD), which does not bind collagen type I, failed to induce integrin and promote glioma cell migration. Further, FMOD-induced integrin activation and migration was abrogated by a 9-mer wild-type peptide from the FMOD C-terminus. However, the same peptide with mutation in two residues essential for FMOD interaction with collagen type I failed to compete with FMOD, thus signifying the importance of collagen type IFMOD interaction in integrin activation. Chromatin immunoprecipitation-PCR experiments revealed that transforming growth factor beta-1 (TGF-beta 1) regulates FMOD expression through epigenetic remodeling of FMOD promoter that involved demethylation and gain of active histone marks with a simultaneous loss of DNMT3A and EZH2 occupancy, but enrichment of Sma- and Mad related protein-2 (SMAD2) and CBP. FMOD silencing inhibited the TGF-beta 1-mediated glioma cell migration significantly. In univariate and multivariate Cox regression analysis, both FMOD promoter methylation and transcript levels predicted prognosis in GBM. Thus, this study identified several epigenetically regulated alterations responsible for cancer development and progression. Specifically, we found that secreted FMOD as an important regulator of glioma cell migration downstream of TGF-beta 1 pathway and forms a potential basis for therapeutic intervention in GBM

Serum biomarkers identification by iTRAQ and verification by MRM: S100A8/S100A9 levels predict tumor-stroma involvement and prognosis in Glioblastoma

Despite advances in biology and treatment modalities, the prognosis of glioblastoma (GBM) remains poor. Serum reflects disease macroenvironment and thus provides a less invasive means to diagnose and monitor a diseased condition. By employing 4-plex iTRAQ methodology, we identified 40 proteins with differential abundance in GBM sera. The high abundance of serum S100A8/S100A9 was verified by multiple reaction monitoring (MRM). ELISA and MRM-based quantitation showed a significant positive correlation. Further, an integrated investigation using stromal, tumor purity and cell type scores demonstrated an enrichment of myeloid cell lineage in the GBM tumor microenvironment. Transcript levels of S100A8/S100A9 were found to be independent poor prognostic indicators in GBM. Medium levels of pre-operative and three-month post-operative follow-up serum S100A8 levels predicted poor prognosis in GBM patients who lived beyond median survival. In vitro experiments showed that recombinant S100A8/S100A9 proteins promoted integrin signalling dependent glioma cell migration and invasion up to a threshold level of concentrations. Thus, we have discovered GBM serum marker by iTRAQ and verified by MRM. We also demonstrate interplay between tumor micro and macroenvironment and identified S100A8 as a potential marker with diagnostic and prognostic value in GBM. © 2019, The Author(s)