Machine learning for rhabdomyosarcoma histopathology

Correctly diagnosing a rare childhood cancer such as sarcoma can be critical to assigning the correct treatment regimen. With a finite number of pathologists worldwide specializing in pediatric/young adult sarcoma histopathology, access to expert differential diagnosis early in case assessment is limited for many global regions. The lack of highly-trained sarcoma pathologists is especially pronounced in low to middle-income countries, where pathology expertise may be limited despite a similar rate of sarcoma incidence. To address this issue in part, we developed a deep learning convolutional neural network (CNN)-based differential diagnosis system to act as a pre-pathologist screening tool that quantifies diagnosis likelihood amongst trained soft-tissue sarcoma subtypes based on whole histopathology tissue slides. The CNN model is trained on a cohort of 424 centrally-reviewed histopathology tissue slides of alveolar rhabdomyosarcoma, embryonal rhabdomyosarcoma and clear-cell sarcoma tumors, all initially diagnosed at the originating institution and subsequently validated by central review. This CNN model was able to accurately classify the withheld testing cohort with resulting receiver operating characteristic (ROC) area under curve (AUC) values above 0.889 for all tested sarcoma subtypes. We subsequently used the CNN model to classify an externally-sourced cohort of human alveolar and embryonal rhabdomyosarcoma samples and a cohort of 318 histopathology tissue sections from genetically engineered mouse models of rhabdomyosarcoma. Finally, we investigated the overall robustness of the trained CNN model with respect to histopathological variations such as anaplasia, and classification outcomes on histopathology slides from untrained disease models. Overall positive results from our validation studies coupled with the limited worldwide availability of sarcoma pathology expertise suggests the potential of machine learning to assist local pathologists in quickly narrowing the differential diagnosis of sarcoma subtype in children, adolescents, and young adults.

Treatment of Urethral Intercourse and Impact on Female Sexual Function

Background

Urethral intercourse is a very rare entity which usually presents as urinary incontinence during and after intercourse and is most commonly seen in patients with vaginal agenesis (Mayer–Rokitansky–Hauser Syndrome) or hypoplasia, or other rear vaginal anomalies.

Aim

To evaluate management and outcomes for vaginal and urethral consequences of urethral intercourse, including urinary incontinence.

Methods

Between February 2006 and March 2021, 8 women aged from 17 to 22 years underwent genital and urethral reconstruction due to consequences of urethral sexual intercourse. Vaginal reconstruction included sigmoid vaginoplasty and introitoplasty with division of the vaginal septum in cases of vaginal agenesis (5 cases) and vaginal duplication (3 cases), respectively. Incontinence was treated by sling procedures in 5 women with longer history of urethral coitus and evident bladder neck prolapse.

Outcomes

Sexual and psychosexual outcomes assessment was based on the Female Sexual Function Index and standardized questionnaires.

Results

Follow-up ranged from 9 to 188 months (mean 78 months). Good esthetical and functional results were achieved in all 8 women. All patients reported satisfactory sexual intercourse. All 5 incontinent women who had underwent sling procedure were continent. In one of 3 nontreated cases, additional sling treatment was indicated 6 months after vaginal reconstruction with satisfactory outcome. One patient with vaginal duplication reported a successful pregnancy with a Caesarean section delivery.

Clinical Implications

Urinary incontinence with megalourethra in young women, along with the presence of Mullerian anomalies should raise suspicion of urethral coitus. Surgical treatment includes correction of vaginal anomalies and management of consequences.

Strengths and Limitations

This study represents one of the largest series for urethral intercourse, with assessment of psychosexual outcome. The limitation is the lack of statistical analysis due to small sample size.

Conclusion

Urethral intercourse is very rare, but it can cause severe consequences. It is important to recognize this occurrence and treat it by well-known vaginal or urethral reconstructive procedures.

Djordjevic ML, Bizic M, Stojanovic B, et al. Treatment of Urethral Intercourse and Impact on Female Sexual Function. Sex Med 2022;10:100534.

SMARCA4 biology in alveolar rhabdomyosarcoma

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children and phenocopies a muscle precursor that fails to undergo terminal differentiation. The alveolar subtype (ARMS) has the poorest prognosis and represents the greatest unmet medical need for RMS. Emerging evidence supports the role of epigenetic dysregulation in RMS. Here we show that SMARCA4/BRG1, an ATP-dependent chromatin remodeling enzyme of the SWI/SNF complex, is prominently expressed in primary tumors from ARMS patients and cell cultures. Our validation studies for a CRISPR screen of 400 epigenetic targets identified SMARCA4 as a unique factor for long-term (but not short-term) tumor cell survival in ARMS. A SMARCA4/SMARCA2 protein degrader (ACBI-1) demonstrated similar long-term tumor cell dependence in vitro and in vivo. These results credential SMARCA4 as a tumor cell dependency factor and a therapeutic target in ARMS.

Bromodomain 4 inhibition leads to MYCN downregulation in Wilms tumor

BACKGROUND

Wilms tumor is the most common childhood kidney cancer. Two distinct histological subtypes of Wilms tumor have been described: tumors lacking anaplasia (the favorable subtype) and tumors displaying anaplastic features (the unfavorable subtype). Children with favorable disease generally have a very good prognosis, whereas those with anaplasia are oftentimes refractory to standard treatments and suffer poor outcomes, leading to an unmet clinical need. MYCN dysregulation has been associated with a number of pediatric cancers including Wilms tumor.

PROCEDURES

In this context, we undertook a functional genomics approach to uncover novel therapeutic strategies for those patients with anaplastic Wilms tumor. Genomic analysis and in vitro experimentation demonstrate that cell growth can be reduced by modulating MYCN overexpression via bromodomain 4 (BRD4) inhibition in both anaplastic and nonanaplastic Wilms tumor models.

RESULTS

We observed a time-dependent reduction of MYCN and MYCC protein levels upon BRD4 inhibition in Wilms tumor cell lines, which led to cell death and proliferation suppression. BRD4 inhibition significantly reduced tumor volumes in Wilms tumor patient-derived xenograft (PDX) mouse models.

CONCLUSIONS

We suggest that AZD5153, a novel dual-BRD4 inhibitor, can reduce MYCN levels in both anaplastic and nonanaplastic Wilms tumor cell lines, reduces tumor volume in Wilms tumor PDXs, and should be further explored for its therapeutic potential.

Metastatic Pediatric Sclerosing Epithelioid Fibrosarcoma

Sclerosing epithelioid fibrosarcoma (SEF) is a rare and aggressive soft-tissue sarcoma thought to originate in fibroblasts of the tissues comprising tendons, ligaments, and muscles. Minimally responsive to conventional cytotoxic chemotherapies, >50% of SEF patients experience local recurrence and/or metastatic disease. SEF is most commonly discovered in middle-aged and elderly adults, but also rarely in children. A common gene fusion occurring between the EWSR1 and CREB3L1 genes has been observed in 80%–90% of SEF cases. We describe here the youngest SEF patient reported to date (a 3-yr-old Caucasian male) who presented with numerous bony and lung metastases. Additionally, we perform a comprehensive literature review of all SEF-related articles published since the disease was first characterized. Finally, we describe the generation of an SEF primary cell line, the first such culture to be reported. The patient described here experienced persistent disease progression despite aggressive treatment including multiple resections, radiotherapy, and numerous chemotherapies and targeted therapeutics. Untreated and locally recurrent tumor and metastatic tissue were sequenced by whole-genome, whole-exome, and deep-transcriptome next-generation sequencing with comparison to a patient-matched normal blood sample. Consistent across all sequencing analyses was the disease-defining EWSR1–CREB3L1 fusion as a single feature consensus. We provide an analysis of our genomic findings and discuss potential therapeutic strategies for SEF.

Nanoscale petrographic and geochemical insights on the origin of the Palaeoproterozoic stromatolitic phosphorites from Aravalli Supergroup, India

Stromatolites composed of apatite occur in post-Lomagundi-Jatuli successions (late Palaeoproterozoic) and suggest the emergence of novel types of biomineralization at that time. The microscopic and nanoscopic petrology of organic matter in stromatolitic phosphorites might provide insights into the suite of diagenetic processes that formed these types of stromatolites. Correlated geochemical micro-analyses of the organic matter could also yield molecular, elemental and isotopic compositions and thus insights into the role of specific micro-organisms among these communities. Here, we report on the occurrence of nanoscopic disseminated organic matter in the Palaeoproterozoic stromatolitic phosphorite from the Aravalli Supergroup of north-west India. Organic petrography by micro-Raman and Transmission Electron Microscopy demonstrates syngeneity of the organic matter. Total organic carbon contents of these stromatolitic phosphorite columns are between 0.05 and 3.0 wt% and have a large range of δ(13) Corg values with an average of -18.5‰ (1σ = 4.5‰). δ(15) N values of decarbonated rock powders are between -1.2 and +2.7‰. These isotopic compositions point to the important role of biological N2 -fixation and CO2 -fixation by the pentose phosphate pathway consistent with a population of cyanobacteria. Microscopic spheroidal grains of apatite (MSGA) occur in association with calcite microspar in microbial mats from stromatolite columns and with chert in the core of diagenetic apatite rosettes. Organic matter extracted from the stromatolitic phosphorites contains a range of molecular functional group (e.g. carboxylic acid, alcohol, and aliphatic hydrocarbons) as well as nitrile and nitro groups as determined from C- and N-XANES spectra. The presence of organic nitrogen was independently confirmed by a CN(-) peak detected by ToF-SIMS. Nanoscale petrography and geochemistry allow for a refinement of the formation model for the accretion and phototrophic growth of stromatolites. The original microbial biomass is inferred to have been dominated by cyanobacteria, which might be an important contributor of organic matter in shallow-marine phosphorites.

Palaeosol control on groundwater flow and pollutant distribution: the example of arsenic

The consumption of groundwater polluted by arsenic (As) has a severe and adverse effect on human health, particularly where, as happens in parts of SE Asia, groundwater is supplied largely from fluvial/deltaic aquifers. The lateral distribution of the As-pollution in such aquifers is heterogeneous. The cause of the heterogeneity is obscure. The location and severity of the As-pollution is therefore difficult to predict, despite the importance of such predictions to the protection of consumer health, aquifer remediation, and aquifer development. To explain the heterogeneity, we mapped As-pollution in groundwater using 659 wells across 102 km(2) of West Bengal, and logged 43 boreholes, to reveal that the distribution of As-pollution is governed by subsurface sedimentology. Across 47 km(2) of contiguous palaeo-interfluve, we found that the shallow aquifer (<70 mbgl) is unpolluted by As (<10 μg/L) because it is capped by an impermeable palaeosol of red clay (the last glacial maximum palaeosol, or LGMP, of ref 1 ) at depths between 16 and 24 mbgl. The LGMP protects the aquifer from vertical recharge that might carry As-rich water or dissolved organic matter that might drive reduction of sedimentary iron oxides and so release As to groundwater. In 55 km(2) of flanking palaeo-channels, the palaeosol is absent, so invasion of the aquifer by As and dissolved organic matter can occur, so palaeo-channel groundwater is mostly polluted by As (>50 μg/L). The role of palaeosols and, in particular, the LGMP, has been overlooked as a control on groundwater flow and pollutant movement in deltaic and coastal aquifers worldwide. Models of pollutant infiltration in such environments must include the appreciation that, where the LGMP (or other palaeosols) are present, recharge moves downward in palaeo-channel regions that are separated by palaeo-interfluvial regions where vertical recharge to underlying aquifers cannot occur and where horizontal flow occurs above the LGMP and any aquifer it caps.

A novel computational and structural analysis of nsSNPs in CFTR gene

Single Nucleotide Polymorphisms (SNPs) are being intensively studied to understand the biological basis of complex traits and diseases. The Genetics of human phenotype variation could be understood by knowing the functions of SNPs. In this study using computational methods, we analyzed the genetic variations that can alter the expression and function of the CFTR gene responsible candidate for causing cystic fibrosis. We applied an evolutionary perspective to screen the SNPs using a sequence homology-based SIFT tool, which suggested that 17 nsSNPs (44%) were found to be deleterious. The structure-based approach PolyPhen server suggested that 26 nsSNPS (66%) may disrupt protein function and structure. The PupaSuite tool predicted the phenotypic effect of SNPs on the structure and function of the affected protein. Structure analysis was carried out with the major mutation that occurred in the native protein coded by CFTR gene, and which is at amino acid position F508C for nsSNP with id (rs1800093). The amino acid residues in the native and mutant modeled protein were further analyzed for solvent accessibility, secondary structure and stabilizing residues to check the stability of the proteins. The SNPs were further subjected to iHAP analysis to identify htSNPs, and we report potential candidates for future studies on CFTR mutations.

Linear mRNA amplification from as little as 5 ng total RNA for global gene expression analysis

Gene expression analysis has become an invaluable tool for understanding gene function and regulation. However, global expression analysis requires large RNA quantities or RNA preamplification. We describe an isothermal messenger RNA (mRNA) amplification method, Ribo-SPIA™, which generates micrograms of labeled cDNA from 5 ng of total RNA in 1 day for analysis on arrays or by PCR quantification. Highly reproducible GeneChip® array performance (R2 > 0.95) was achieved with independent reactions starting with 5–100 ng Universal Human Reference total RNA. Targets prepared by the Ribo-SPIA procedure (20 ng total RNA input) or the Affymetrix Standard Protocol (10 µg total RNA) perform similarly, as indicated by gene call concordance (86%) and good correlation of differential gene expression determination (R2 = 0.82). Accuracy of transcript representation in cDNA generated by the Ribo-SPIA procedure was also demonstrated by PCR quantification of 33 transcripts, comparing differential expression in amplified and nonamplified cDNA (R2 = 0.97 over a range of nearly 106 in fold change). Thus Ribo-SPIA amplification of mRNA is rapid, robust, highly accurate and reproducible, and sensitive enough to allow quantification of very low abundance transcripts.

Cure of undifferentiated small cell carcinoma of the urinary bladder with M-VAC chemotherapy

Small cell carcinoma (SCC) of the urinary bladder is a rare, aggressive malignancy with approximately 135 cases reported in the literature. Treatments have included chemotherapy, radical surgery, radiotherapy, and combinations of these. We present the apparent cure of a 73-year-old man who presented with clinical stage T2 SCC of the urinary bladder. He was treated with three cycles of methotrexate, vinblastine, Adriamycin (doxorubicin), and cisplatin (M-VAC) chemotherapy. Subsequent radical cystoprostatectomy revealed no pathologic evidence of tumor. The patient is alive and well with no evidence of recurrence 3 years post cystectomy. A brief review of the literature is also presented.

Coccygeal muscle injury in English Pointers (limber tail)

A condition colloquially referred to as "limber tail" and "cold tail" is familiar to people working with hunting dogs, primarily Pointers and Labrador Retrievers. The typical case consists of an adult dog that suddenly develops a flaccid tail. The tail either hangs down from the tail base or is held out horizontally for several inches from the tail base and then hangs straight down or at some degree below horizontal. Initially, the hair on the dorsal aspect of the proximal tail may be raised and dogs may resent palpation of the area 3-4 inches (8-10 cm) from the tail base. Most dogs recover spontaneously within a few days to weeks. Anecdotal reports suggest that anti-inflammatory drugs administered within 24 hours after onset hasten recovery. Less than one half of affected dogs experience a recurrence. Affected Pointers almost always have a history of prolonged cage transport, a hard workout the previous day, or exposure to cold or wet weather Most owners and trainers familiar with the condition do not seek veterinary assistance. In cases where people are not familiar with this disease, other conditions such as a fracture, spinal cord disease, impacted anal glands, or prostatic disease have been incorrectly diagnosed. We examined 4 affected Pointers and found evidence of coccygeal muscle damage, which included mild elevation of creatine kinase early after onset of clinical signs, needle electromyographic examination showing abnormal spontaneous discharges restricted to the coccygeal muscles several days after onset, and histopathologic evidence of muscle fiber damage. Specific muscle groups, namely the laterally positioned intertransversarius ventralis caudalis muscles, were affected most severely. Abnormal findings on thermography and scintigraphy further supported the diagnosis.

Characterization of a recent retroposon insertion on mouse chromosome 2 and localization of the cognate parental gene to chromosome 11

The genomic sequence on mouse Chromosome (Chr) 2 corresponding to a previously identified novel cDNA has been characterized. The genomic organization of this locus, adjacent to the beta 2 microglobulin gene, has the properties of a processed gene or retroposon including the presence of a short flanking direct repeat, a polyadenylation signal/poly A tract, and the absence of introns. Analysis of inbred and wild-derived Mus DNAs reveals the retroposon to be a feature only of M. m. domesticus subspecies, suggesting that the insertion event is relatively recent. This notion is supported by the presence of an open reading frame and the lack of sequence divergence in the flanking direct repeats. The complex chromatin configuration characteristic of this region in mouse and human is not, therefore, related to this cDNA. The cognate parental gene encoding the cDNA was mapped to Chr 11. A further, more ancient retroposon present in many Mus species localizes to Chr 17.

Platelet function testing in the pony

Platelet isolation techniques and platelet function were evaluated in 35 adult ponies. Platelet recovery from whole blood was consistent and the preparation of platelet rich plasma was facilitated by an enhanced erythrocyte sedimentation rate. All platelet samples aggregated in response to 10 microM ADP. However, concentrations of ADP as high as 100 microM did not elicit significant 14C-serotonin release. Collagen induced irreversible platelet aggregation and 14C-serotonin release in all samples. The threshold dose for collagen in most ponies was 1.5 micrograms. Arachidonic acid (500 microM) failed to induce irreversible platelet aggregation or 14C-serotonin release in any of the samples evaluated. Pony platelets were nonresponsive to epinephrine (5.5 microM).

Carcinoma of the urinary bladder in Zambia. A quantitative estimation of Schistosoma haematobium infection

The incidence and intensity of schistosomal infection in 50 African malignant bladders determined by quantitative analysis have been compared with a matched control group of nonmalignant cadaver bladders, and the incidence of radiological calcification in the former has been compared with that of 50 adult urinary bilharziasis patients without associated malignancy. Compared with 45% in the non-malignant group, schistosomal infection was present in an overwhelming 94% of the malignant cases. Radiological calcification in the malignant bladders (38%) was slightly more than in patients with urinary bilharziasis (35%). In the majority of the malignant bladders (55.3%) the parasitic infection was noted to be of moderate to low intensity. It has been suggested that the overall severity of schistosomal infection is unlikely to be the sole factor in the pathogenesis of carcinoma of the urinary bladder.

The pharmacokinetics and pharmacodynamics of the diuretic bumetanide in hepatic and renal disease

1 Bumetanide (1 mg) was given orally and intravenously to a group of patients with chronic renal failure (n = 6) and to another group with cirrhosis of the liver (n = 8). 2 The pharmacokinetics, using a two-compartment model, and the pharmacodynamics of the drug in these patients were compared with those previously obtained for normal subjects. 3 In the renal group serum bumetanide concentrations were higher than for the normal subjects and the terminal half-lives were significantly prolonged (P less than 0.001). A decreased whole body clearance was attributable to a low renal clearance of drug, the non-renal clearance being significantly increased (P less than 0.01). 4 For the patients with liver disease, serum bumetanide concentrations were higher than for the renal group, and the terminal half-lives were significantly further prolonged (P less than 0.001). Both non-renal and renal clearances were significantly reduced (P less than 0.001). 5 Absorption rates were not significantly altered in either group and the values of F (bioavailability) were 0.82 and 0.95 for the patients with renal disease and hepatic disease, respectively. 6 A poor pharmacodynamic response and a reduced bumetanide excretion rate were observed for the patients with chronic renal failure, whereas with hepatic disease normal bumetanide excretion rates were observed with an impaired diuretic response.

The pharmacokinetics and pharmacodynamics of bumetanide in normal subjects

The pharmacokinetics and pharmacodynamics of bumetanide (1 mg) administered either orally or intravenously were studied in a group of normal subjects using high-pressure liquid chromatography. A two-compartment model adequately fitted the intravenous data. Renal clearance (85 ml min-1) contributed 65% to the total elimination of bumetanide irrespective of whether a model-dependent or model-independent method was used. Oral administration of bumetanide elicited a greater and a more prolonged pharmacological response than did intravenous bumetanide. An attempt is made to relate the pharmacokinetics of the drug to its pharmacodynamics.