Deep Learning Applied to Raman Spectroscopy for the Detection of Microsatellite Instability/MMR Deficient Colorectal Cancer

Defective DNA mismatch repair is one pathogenic pathway to colorectal cancer. It is characterised by microsatellite instability which provides a molecular biomarker for its detection. Clinical guidelines for universal testing of this biomarker are not met due to resource limitations; thus, there is interest in developing novel methods for its detection. Raman spectroscopy (RS) is an analytical tool able to interrogate the molecular vibrations of a sample to provide a unique biochemical fingerprint. The resulting datasets are complex and high-dimensional, making them an ideal candidate for deep learning, though this may be limited by small sample sizes. This study investigates the potential of using RS to distinguish between normal, microsatellite stable (MSS) and microsatellite unstable (MSI-H) adenocarcinoma in human colorectal samples and whether deep learning provides any benefit to this end over traditional machine learning models. A 1D convolutional neural network (CNN) was developed to discriminate between healthy, MSI-H and MSS in human tissue and compared to a principal component analysis-linear discriminant analysis (PCA-LDA) and a support vector machine (SVM) model. A nested cross-validation strategy was used to train 30 samples, 10 from each group, with a total of 1490 Raman spectra. The CNN achieved a sensitivity and specificity of 83% and 45% compared to PCA-LDA, which achieved a sensitivity and specificity of 82% and 51%, respectively. These are competitive with existing guidelines, despite the low sample size, speaking to the molecular discriminative power of RS combined with deep learning. A number of biochemical antecedents responsible for this discrimination are also explored, with Raman peaks associated with nucleic acids and collagen being implicated

Scale-up in PEM electro-ozonizers for the degradation of organics

This work focuses on the scale-up of electro-ozonizers by evaluating the production of ozone and the degradation of clopyralid synthetic wastes using three commercial PEM electrolyzers. The mechanical concept of the three cells is similar: a single compartment cell equipped with a MEA (consisting of a polymer exchange membrane and two pressed diamond coatings electrodes), powered with monopolar electric connection and where water flows on the surface of the electrodes, although the main electrolyte is the Nafion proton exchange membrane. However, their size and recommended operating conditions are not as similar, and their comparison becomes a good scaleup case study. The CabECO® cell consists of 2 MEAs with a total surface area of 24 cm2, a maximum operating current density of 2. 0A. The Mikrozom® cell consists of only one MEA with a net surface electrodic area of 112 mm2 and a maximum operation current density of 1.0 A. Finally, the CONDIAPURE® cell consists of a single MEA with a total surface area of 146 cm2 and a maximum operation current density of 10.0 A. The performance under mild and extreme operating conditions was compared and the results show that, although the cell concept is similar, the results obtained differ very significantly. The three PEM electrolyzers tested can produce ozone efficiently and mineralize completely clopyralid. The only intermediates measured come from the cathodic hydrodechlorination of clopyralid and oxidative intermediates were only detected at trace concentrations. CabECO® cell demonstrates an outstanding performance with very high current efficiencies in the production of ozone. However, the highest mineralization efficiencies are obtained with the Microzon®, which, although it is the PEM electrolyzer with the smallest active area, is the most efficient because can reach high ozone concentrations and achieve the best clopyralid mineralization. Efficiencies as high as 0.47 mg O3 Wh−1 can be obtained with this cell. Slightly lower values are reached by the CabECO® cell (0.38 mg O3 Wh−1). Enlarging electrode surface area does not seem to be a good strategy from the viewpoint of efficiency and it seems to promote side reactions that compete with ozone production and with the degradation of organics. This means that stacking rather than electrode enlarging should be the strategy more advisable for scaling up the electro-ozonation technology.Este trabajo se centra en la ampliación de los electro-ozonizadores mediante la evaluación de la producción de ozono y la degradación de los desechos sintéticos de clopiralida utilizando tres electrolizadores PEM comerciales. El concepto mecánico de las tres celdas es similar: una celda de un solo compartimiento equipada con un MEA (compuesto por una membrana de intercambio de polímero y dos electrodos de revestimiento de diamante prensado), alimentada con conexión eléctrica monopolar y donde el agua fluye en la superficie de los electrodos, aunque el electrolito principal es la membrana de intercambio de protones Nafion. Sin embargo, su tamaño y las condiciones operativas recomendadas no son tan similares, y su comparación se convierte en un buen caso de estudio de ampliación. La celda CabECO® consta de 2 MEA con una superficie total de 24 cm 2, una densidad de corriente operativa máxima de 2. 0A. La celda Mikrozom® consta de un solo MEA con un área superficial neta de electrodos de 112 mm 2 y una densidad de corriente máxima de operación de 1,0 A. Finalmente, la celda CONDIAPURE® consta de un solo MEA con un área superficial total de 146 cm 2y una densidad de corriente máxima de operación de 10.0 A. Se comparó el desempeño en condiciones de operación suaves y extremas y los resultados muestran que, aunque el concepto de celda es similar, los resultados obtenidos difieren muy significativamente. Los tres electrolizadores PEM probados pueden producir ozono de manera eficiente y mineralizar completamente la clopiralida. Los únicos intermedios medidos provienen de la hidrodecloración catódica de clopiralida y los intermedios oxidativos solo se detectaron en concentraciones mínimas. La celda CabECO® demuestra un desempeño sobresaliente con eficiencias de corriente muy altas en la producción de ozono. Sin embargo, las mayores eficiencias de mineralización se obtienen con el Microzon® que, si bien es el electrolizador PEM con menor área activa, es el más eficiente porque puede alcanzar altas concentraciones de ozono y lograr la mejor mineralización de clopiralida. Eficiencias de hasta 0,47 mg OCon esta celda se pueden obtener 3 Wh −1 . La celda CabECO® alcanza valores ligeramente inferiores (0,38 mg O 3 Wh −1 ). Ampliar el área de la superficie del electrodo no parece ser una buena estrategia desde el punto de vista de la eficiencia y parece promover reacciones secundarias que compiten con la producción de ozono y con la degradación de compuestos orgánicos. Esto significa que el apilamiento en lugar de la ampliación de electrodos debería ser la estrategia más recomendable para escalar la tecnología de electro-ozonización

Deep learning enables spatial mapping of the mosaic microenvironment of myeloma bone marrow trephine biopsies

Bone marrow trephine biopsy is crucial for the diagnosis of multiple myeloma. However, the complexity of bone marrow cellular, morphological, and spatial architecture preserved in trephine samples hinders comprehensive evaluation. To dissect the diverse cellular communities and mosaic tissue habitats, we developed a superpixel-inspired deep learning method (MoSaicNet) that adapts to complex tissue architectures and a cell imbalance aware deep learning pipeline (AwareNet) to enable accurate detection and classification of rare cell types in multiplex immunohistochemistry images. MoSaicNet and AwareNet achieved an area under the curve of >0.98 for tissue and cellular classification on separate test datasets. Application of MoSaicNet and AwareNet enabled investigation of bone heterogeneity and thickness as well as spatial histology analysis of bone marrow trephine samples from monoclonal gammopathies of undetermined significance (MGUS) and from paired newly diagnosed and post-treatment multiple myeloma. The most significant difference between MGUS and newly diagnosed multiple myeloma (NDMM) samples was not related to cell density but to spatial heterogeneity, with reduced spatial proximity of BLIMP1+ tumor cells to CD8+ cells in MGUS compared with NDMM samples. Following treatment of multiple myeloma patients, there was a reduction in the density of BLIMP1+ tumor cells, effector CD8+ T cells, and T regulatory cells, indicative of an altered immune microenvironment. Finally, bone heterogeneity decreased following treatment of MM patients. In summary, deep-learning based spatial mapping of bone marrow trephine biopsies can provide insights into the cellular topography of the myeloma marrow microenvironment and complement aspirate-based techniques

Crypt fusion as a homeostatic mechanism in the human colon.

OBJECTIVE: The crypt population in the human intestine is dynamic: crypts can divide to produce two new daughter crypts through a process termed crypt fission, but whether this is balanced by a second process to remove crypts, as recently shown in mouse models, is uncertain. We examined whether crypt fusion (the process of two neighbouring crypts fusing into a single daughter crypt) occurs in the human colon. DESIGN: We used somatic alterations in the gene cytochrome c oxidase (CCO) as lineage tracing markers to assess the clonality of bifurcating colon crypts (n=309 bifurcating crypts from 13 patients). Mathematical modelling was used to determine whether the existence of crypt fusion can explain the experimental data, and how the process of fusion influences the rate of crypt fission. RESULTS: In 55% (21/38) of bifurcating crypts in which clonality could be assessed, we observed perfect segregation of clonal lineages to the respective crypt arms. Mathematical modelling showed that this frequency of perfect segregation could not be explained by fission alone (p<10-20). With the rates of fission and fusion taken to be approximately equal, we then used the distribution of CCO-deficient patch size to estimate the rate of crypt fission, finding a value of around 0.011 divisions/crypt/year. CONCLUSIONS: We have provided the evidence that human colonic crypts undergo fusion, a potential homeostatic process to regulate total crypt number. The existence of crypt fusion in the human colon adds a new facet to our understanding of the highly dynamic and plastic phenotype of the colonic epithelium.wellcome trust royal societ

The ReIMAGINE prostate cancer risk study protocol: A prospective cohort study in men with a suspicion of prostate cancer who are referred onto an MRI-based diagnostic pathway with donation of tissue, blood and urine for biomarker analyses

INTRODUCTION: The ReIMAGINE Consortium was conceived to develop risk-stratification models that might incorporate the full range of novel prostate cancer (PCa) diagnostics (both commercial and academic). METHODS: ReIMAGINE Risk is an ethics approved (19/LO/1128) multicentre, prospective, observational cohort study which will recruit 1000 treatment-naive men undergoing a multi-parametric MRI (mpMRI) due to an elevated PSA (≤20ng/ml) or abnormal prostate examination who subsequently had a suspicious mpMRI (score≥3, stage ≤T3bN0M0). Primary outcomes include the detection of ≥Gleason 7 PCa at baseline and time to clinical progression, metastasis and death. Baseline blood, urine, and biopsy cores for fresh prostate tissue samples (2 targeted and 1 non-targeted) will be biobanked for future analysis. High-resolution scanning of pathology whole-slide imaging and MRI-DICOM images will be collected. Consortium partners will be granted access to data and biobanks to develop and validate biomarkers using correlation to mpMRI, biopsy-based disease status and long-term clinical outcomes. RESULTS: Recruitment began in September 2019(n = 533). A first site opened in September 2019 (n = 296), a second in November 2019 (n = 210) and a third in December 2020 (n = 27). Acceptance to the study has been 65% and a mean of 36.5ml(SD+/-10.0), 12.9ml(SD+/-3.7) and 2.8ml(SD+/-0.7) urine, plasma and serum donated for research, respectively. There are currently 4 academic and 15 commercial partners spanning imaging (~9 radiomics, artificial intelligence/machine learning), fluidic (~3 blood-based and ~2urine-based) and tissue-based (~1) biomarkers. CONCLUSION: The consortium will develop, or adjust, risk models for PCa, and provide a platform for evaluating the role of novel diagnostics in the era of pre-biopsy MRI and targeted biopsy

HER2-HER3 heterodimer quantification by FRET-FILM and patient subclass analysis of the COIN colorectal trial

BACKGROUND: The phase 3 MRC COIN trial showed no statistically significant benefit from adding the EGFR-target cetuximab to oxaliplatin-based chemotherapy in first-line treatment of advanced colorectal cancer. This study exploits additional information on HER2-HER3 dimerization to achieve patient stratification and reveal previously hidden subgroups of patients who had differing disease progression and treatment response. METHODS: HER2-HER3 dimerization was quantified by 'FLIM Histology' in primary tumor samples from 550 COIN trial patients receiving oxaliplatin and fluoropyrimidine chemotherapy +/-cetuximab. Bayesian latent class analysis (LCA) and covariate reduction was performed to analyze the effects of HER2-HER3 dimer, RAS mutation and cetuximab on progression-free survival (PFS) and overall survival (OS). All statistical tests were two-sided. RESULTS: LCA on a cohort of 398 patients revealed two patient subclasses with differing prognoses (median OS: 1624 days [95%CI=1466-1816] vs 461 [95%CI=431-504]): Class 1 (15.6%) showed a benefit from cetuximab in OS (HR = 0.43 [95%CI=0.25-0.76]; p = 0.004). Class 2 showed an association of increased HER2-HER3 with better OS (HR = 0.64 [95%CI=0.44-0.94]; p = 0.02). A class prediction signature was formed and tested on an independent validation cohort (N = 152) validating the prognostic utility of the dimer assay. Similar subclasses were also discovered in full trial dataset (N = 1,630) based on 10 baseline clinicopathological and genetic covariates. CONCLUSIONS: Our work suggests that the combined use of HER dimer imaging and conventional mutation analyses will be able to identify a small subclass of patients (>10%) who will have better prognosis following chemotherapy. A larger prospective cohort will be required to confirm its utility in predicting the outcome of anti-EGFR treatment

Immunosuppressive niche engineering at the onset of human colorectal cancer

The evolutionary dynamics of tumor initiation remain undetermined, and the interplay between neoplastic cells and the immune system is hypothesized to be critical in transformation. Colorectal cancer (CRC) presents a unique opportunity to study the transition to malignancy as pre-cancers (adenomas) and early-stage cancers are frequently resected. Here, we examine tumor-immune eco-evolutionary dynamics from pre-cancer to carcinoma using a computational model, ecological analysis of digital pathology data, and neoantigen prediction in 62 patient samples. Modeling predicted recruitment of immunosuppressive cells would be the most common driver of transformation. As predicted, ecological analysis reveals that progressed adenomas co-localized with immunosuppressive cells and cytokines, while benign adenomas co-localized with a mixed immune response. Carcinomas converge to a common immune “cold” ecology, relaxing selection against immunogenicity and high neoantigen burdens, with little evidence for PD-L1 overexpression driving tumor initiation. These findings suggest re-engineering the immunosuppressive niche may prove an effective immunotherapy in CRC

The stem cell organisation, and the proliferative and gene expression profile of Barrett's epithelium, replicates pyloric-type gastric glands

Objective: Barrett's oesophagus shows appearances described as ‘intestinal metaplasia’, in structures called ‘crypts’ but do not typically display crypt architecture. Here, we investigate their relationship to gastric glands. Methods: Cell proliferation and migration within Barrett's glands was assessed by Ki67 and iododeoxyuridine (IdU) labelling. Expression of mucin core proteins (MUC), trefoil family factor (TFF) peptides and LGR5 mRNA was determined by immunohistochemistry or by in situ hybridisation, and clonality was elucidated using mitochondrial DNA (mtDNA) mutations combined with mucin histochemistry. Results: Proliferation predominantly occurs in the middle of Barrett's glands, diminishing towards the surface and the base: IdU dynamics demonstrate bidirectional migration, similar to gastric glands. Distribution of MUC5AC, TFF1, MUC6 and TFF2 in Barrett's mirrors pyloric glands and is preserved in Barrett's dysplasia. MUC2-positive goblet cells are localised above the neck in Barrett's glands, and TFF3 is concentrated in the same region. LGR5 mRNA is detected in the middle of Barrett's glands suggesting a stem cell niche in this locale, similar to that in the gastric pylorus, and distinct from gastric intestinal metaplasia. Gastric and intestinal cell lineages within Barrett's glands are clonal, indicating derivation from a single stem cell. Conclusions: Barrett's shows the proliferative and stem cell architecture, and pattern of gene expression of pyloric gastric glands, maintained by stem cells showing gastric and intestinal differentiation: neutral drift may suggest that intestinal differentiation advances with time, a concept critical for the understanding of the origin and development of Barrett's oesophagus

Accuracy of endoscopic staging and targeted biopsies for routine gastric intestinal metaplasia and gastric atrophy evaluation study protocol of a prospective, cohort study: The estimate study

Introduction Patients with chronic atrophic gastritis (CAG) and intestinal metaplasia (IM) are at risk of developing gastric adenocarcinoma. Their diagnosis and management currently rely on histopathological guidance after random endoscopic biopsy sampling (Sydney biopsy strategy). This approach has significant flaws such as under-diagnosis, poor reproducibility and poor correlation between endoscopy and histology. This prospective, international multicentre study aims to establish whether endoscopy-led risk stratification accurately and reproducibly predicts CAG and IM extent and disease stage. Methods and analysis Patients with CAG and/or IM on standard white light endoscopy (WLE) will be prospectively identified and invited to undergo a second endoscopy performed by an expert endoscopist using enhanced endoscopic imaging techniques with virtual chromoendoscopy. Extent of CAG/IM will be endoscopically staged with enhanced imaging and compared with standard WLE. Histopathological risk stratification through targeted biopsies will be compared with endoscopic disease staging and to random biopsy staging on WLE as a reference. At least 234 patients are required to show a 10% difference in sensitivity and accuracy between enhanced imaging endoscopy-led staging and the current biopsy-led staging protocol of gastric atrophy with a power (beta) of 80% and a 0.05 probability of a type I error (alpha). Ethics and dissemination The study was approved by the respective Institutional Review Boards (Netherlands: MEC-2018-078; UK: 19/LO/0089). The findings will be published in peer-reviewed journals and presented at scientific meetings. Trial registration number NTR7661; Pre-results

Clonal transitions and phenotypic evolution in Barrett esophagus

BACKGROUND & AIMS: Barrett's esophagus (BE) is a risk factor for esophageal adenocarcinoma but our understanding of how it evolves is poorly understood. We investigated BE gland phenotype distribution, the clonal nature of phenotypic change, and how phenotypic diversity plays a role in progression. METHODS: Using immunohistochemistry and histology, we analyzed the distribution and the diversity of gland phenotype between and within biopsy specimens from patients with nondysplastic BE and those who had progressed to dysplasia or had developed postesophagectomy BE. Clonal relationships were determined by the presence of shared mutations between distinct gland types using laser capture microdissection sequencing of the mitochondrial genome. RESULTS: We identified 5 different gland phenotypes in a cohort of 51 nondysplastic patients where biopsy specimens were taken at the same anatomic site (1.0-2.0 cm superior to the gastroesophageal junction. Here, we observed the same number of glands with 1 and 2 phenotypes, but 3 phenotypes were rare. We showed a common ancestor between parietal cell-containing, mature gastric (oxyntocardiac) and goblet cell-containing, intestinal (specialized) gland phenotypes. Similarly, we have shown a clonal relationship between cardiac-type glands and specialized and mature intestinal glands. Using the Shannon diversity index as a marker of gland diversity, we observed significantly increased phenotypic diversity in patients with BE adjacent to dysplasia and predysplasia compared to nondysplastic BE and postesophagectomy BE, suggesting that diversity develops over time. CONCLUSIONS: We showed that the range of BE phenotypes represents an evolutionary process and that changes in gland diversity may play a role in progression. Furthermore, we showed a common ancestry between gastric and intestinal-type glands in BE