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Digitization of histologic slides brings with it the promise of enhanced toxicologic pathology practice through the increased application of computational methods. However, the development of these advanced methods requires access to substrate image data, that is, whole slide images (WSIs). Deep learning methods, in particular, rely on extensive training data to develop robust algorithms. As a result, pharmaceutical companies interested in leveraging computational methods in their digital pathology workflows must first invest in data infrastructure to enable data access for both data scientists and pathologists. The process of building robust image data resources is challenging and includes considerations of generation, curation, and storage of WSI files, and WSI access including via linked metadata. This opinion piece describes the collective experience of building resources for WSI data in the Roche group. We elaborate on the challenges encountered and solutions developed with the goal of providing examples of how to build a data resource for digital pathology analytics in the pharmaceutical industry.

Figure S1 shows that there are equivalent levels of CIN in p53-/- and CENP-E+/-;p53-/- lymphomas

PDF file - 30K, Relative gene expression is shown for three adenomas and three intramucosal carcinomas taken from the colons of DSS-treated F1 Min mice.

PDF file - 54K, Panel A illustrates the colonoscopic surveillance protocol. Panel B shows the serial biopsy protocol.

PDF file - 21K, Characteristics of F1 ApcMin/+ mice treated with 4% dextran sodium sulfate.

This file contains 5 supplemental figures and 1 supplemental table

Table S1 shows expected and observed birth frequencies.

PDF file - 42K, Complete list of differentially expressed genes between intramucosal carcinomas and adenomas.

Colorectal cancer often arises from adenomatous colonic polyps. Polyps can grow and progress to cancer, but may also remain static in size, regress, or resolve. Predicting which polyps progress and which remain benign is difficult. We developed a novel long-lived murine model of colorectal cancer with tumors that can be followed by colonoscopy. Our aim was to assess whether these tumors have similar growth patterns and histologic fates to human colorectal polyps to identify features to aid in risk stratification of colonic tumors. Long-lived ApcMin/+ mice were treated with dextran sodium sulfate to promote colonic tumorigenesis. Tumor growth patterns were characterized by serial colonoscopy with biopsies obtained for immunohistochemistry and gene expression profiling. Tumors grew, remained static, regressed, or resolved over time with different relative frequencies. Newly developed tumors demonstrated higher rates of growth and resolution than more established tumors that tended to remain static in size. Colonic tumors were hyperplastic lesions (3%), adenomas (73%), intramucosal carcinomas (20%), or adenocarcinomas (3%). Interestingly, the level of β-catenin was higher in adenomas that became intratumoral carcinomas than those that failed to progress. In addition, differentially expressed genes between adenomas and intramucosal carcinomas were identified. This novel murine model of intestinal tumorigenesis develops colonic tumors that can be monitored by serial colonoscopy, mirror growth patterns seen in human colorectal polyps, and progress to colorectal cancer. Further characterization of cellular and molecular features is needed to determine which features can be used to risk-stratify polyps for progression to colorectal cancer and potentially guide prevention strategies. Cancer Prev Res; 7(1); 105–13. ©2013 AACR.

PDF file - 28K, Differentially Expressed Gene Functional Categories between Adenomas and Intramucosal Carcinomas

Chromosomal instability (CIN) is a hallmark of cancer. While low levels of CIN can be tumor promoting, high levels of CIN cause cell death and tumor suppression. The widely used chemotherapeutic, paclitaxel (Taxol), exerts its anticancer effects by increasing CIN above a maximally tolerated threshold. One significant outstanding question is whether the p53 tumor suppressor is required for the cell death and tumor suppression caused by high CIN. Both p53 loss and reduction of the mitotic kinesin, centromere-associated protein-E, cause low CIN. Combining both genetic insults in the same cell leads to high CIN. Here, we test whether high CIN causes cell death and tumor suppression even in the absence p53. Despite a surprising sex-specific difference in tumor spectrum and latency in p53 heterozygous animals, these studies demonstrate that p53 is not required for high CIN to induce tumor suppression. Pharmacologic induction of high CIN results in equivalent levels of cell death due to loss of essential chromosomes in p53+/+ and p53−/− cells, further demonstrating that high CIN elicits cell death independently of p53 function.Implications:These results provide support for the efficacy of anticancer therapies that induce high CIN, even in tumors that lack functional p53.

PDF file - 7894K, Supplementary Figure 7. Xenograft models of aggressive prostate cancer.

PDF file - 3402K, Supplementary Figure 6. Additional PTEN/AKT Pathway models.

Supplementary Figures 1-2 from Inactivation of Apc in the Mouse Prostate Causes Prostate Carcinoma

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PDF file - 583K, Mice expressing activated PI3K were scanned to identify those bearing tumors. After sacrifice, the intestine was removed to characterize tissue morphology, cell signaling and cell proliferation within the epithelium and the associated neoplasms

WMP file - 834MB, The tumors in FC+ PIK3ca*+ mice exhibit high avidity for 124I-CLR1404. A mouse was injected with the imaging agent and then dual hybrid PET/CT colonography was performed. The agent was detected in all three tumors. This mouse is the same as shown in Figure 1, panels C and D. The agent was also detected in heart.

PDF file - 9226K, Supplementary Figure 1. Differentiating primary and metastatic lung lesions in GEM mouse models.

PDF file - 17933K, Supplementary Figure 4. Neuroendocrine carcinoma.

PDF file - 2509K, Supplementary Figure 3. Heterologous differentiation in prostate.

PDF file - 2674K, Supplementary Figure 2. Lung metastasis versus tumor embolism.

Alterations of the Wnt/β-catenin signaling pathway are positively associated with the development and progression of human cancer, including carcinoma of the prostate. To determine the role of activated Wnt/β-catenin signaling in mouse prostate carcinogenesis, we created a mouse prostate tumor model using probasin-Cre–mediated deletion of Apc. Prostate tumors induced by the deletion of Apc have elevated levels of β-catenin protein and are highly proliferative. Tumor formation is fully penetrant and follows a consistent pattern of progression. Hyperplasia is observed as early as 4.5 weeks of age, and adenocarcinoma is observed by 7 months. Continued tumor growth usually necessitated sacrifice between 12 and 15 months of age. Despite the high proliferation rate, we have not observed metastasis of these tumors to the lymph nodes or other organs. Surgical castration of 6-week-old mice inhibited tumor formation, and castration of mice with more advanced tumors resulted in the partial regression of specific prostate glands. However, significant areas of carcinoma remained 2 months postcastration, suggesting that tumors induced by Apc loss of function are capable of growth under conditions of androgen depletion. We conclude that the prostate-specific deletion of Apc and the increased expression of β-catenin associated with prostate carcinoma suggests a role for β-catenin in prostate cancer and offers an appropriate animal model to investigate the interaction of Wnt signaling with other genetic and epigenetic signals in prostate carcinogenesis. [Cancer Res 2007;67(6):2490–6]

PDF file - 4441K, Supplementary Figure 5. PTEN/AKT Pathway models.

Supplementary Figure Legends 1-2 from Inactivation of Apc in the Mouse Prostate Causes Prostate Carcinoma

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Animal models, particularly mouse models, play a central role in the study of the etiology, prevention, and treatment of human prostate cancer. While tissue culture models are extremely useful in understanding the biology of prostate cancer, they cannot recapitulate the complex cellular interactions within the tumor microenvironment that play a key role in cancer initiation and progression. The National Cancer Institute (NCI) Mouse Models of Human Cancers Consortium convened a group of human and veterinary pathologists to review the current animal models of prostate cancer and make recommendations about the pathologic analysis of these models. More than 40 different models with 439 samples were reviewed, including genetically engineered mouse models, xenograft, rat, and canine models. Numerous relevant models have been developed over the past 15 years, and each approach has strengths and weaknesses. Analysis of multiple genetically engineered models has shown that reactive stroma formation is present in all the models developing invasive carcinomas. In addition, numerous models with multiple genetic alterations display aggressive phenotypes characterized by sarcomatoid carcinomas and metastases, which is presumably a histologic manifestation of epithelial–mesenchymal transition. The significant progress in development of improved models of prostate cancer has already accelerated our understanding of the complex biology of prostate cancer and promises to enhance development of new approaches to prevention, detection, and treatment of this common malignancy. Cancer Res; 73(9); 2718–36. ©2013 AACR.

Although sexual transmission of Zika virus (ZIKV) is well-documented, the viral reservoir(s) in the male reproductive tract remains uncertain in humans and immune-intact animal models. We evaluated the presence of ZIKV in a rhesus macaque pilot study to determine persistence in semen, assess the impact of infection on sperm functional characteristics, and define the viral reservoir in the male reproductive tract. Five adult male rhesus monkeys were inoculated with 105 PFU of Asian-lineage ZIKV isolate PRVABC59, and two males were inoculated with the same dose of African-lineage ZIKV DAKAR41524. Viremia and viral RNA (vRNA) shedding in semen were monitored, and a cohort of animals were necropsied for tissue collection to assess tissue vRNA burden and histopathology. All animals exhibited viremia for limited periods (1–11 days); duration of shedding did not differ significantly between viral isolates. There were sporadic low levels of vRNA in the semen from some, but not all animals. Viral RNA levels in reproductive tract tissues were also modest and present in the epididymis in three of five cases, one case in the vas deferens, but not detected in testis, seminal vesicles or prostate. ZIKV infection did not impact semen motility parameters as assessed by computer-assisted sperm analysis. Despite some evidence of prolonged ZIKV RNA shedding in human semen and high tropism of ZIKV for male reproductive tract tissues in mice deficient in Type 1 interferon signaling, in the rhesus macaques assessed in this pilot study, we did not consistently find ZIKV RNA in the male reproductive tract.

Spinal cord stimulation (SCS) is a common treatment for neuropathic pain. There are 2 main categories of SCS leads: paddle leads and cylindrical leads. Paddle leads have reduced long-term complications and provide better coverage of target dermatomes when compared to cylindrical leads. However, insertion of a paddle lead requires invasive surgery that comes with significantly higher costs and more short-term complications, such as postoperative pain and infection. In contrast, cylindrical leads can be inserted minimally invasively using percutaneous techniques but provide less coverage of targeted dermatomes and have a higher tendency to migrate from intended neuronal targets.Our objective is to develop a novel improved cylindrical spinal cord stimulation device that can convert into an optimal geometry once exposed to the body's environment after minimally invasive surgery. Such a device would be able to reduce long-term complications, lead migration, and better cover targeted dermatomes.Biomaterial selection, medical intervention device design with an in-vitro lab-scale test, and cadaveric experimental study.A shape memory alloy nitinol-based cylindrical lead was designed, and its nitinol core material was processed and geometrically programmed for percutaneous insertion into the epidural space and morphing into an optimal geometry once exposed to the body's environment. Deployment of the nitinol component of the design was tested in the lab and human cadaveric models of the epidural space.Deployment of the nitinol component of the proposed cylindrical lead was successfully demonstrated in both a lab model of the epidural space and in the epidural space of a human cadaver in a minimally invasive fashion, indicating that a similar component could be used clinically in a full SCS electrode manufactured in a custom final geometry.The focus of this study was to test the deployment of a novel minimally invasive lead that provides optimal coverage of intended dermatomes using in-vitro methods. Our study does not include in vivo trials. We do not test the electrical components of the design proposed since our design does not make changes to the electrical components of current commercially used cylindrical leads.The unique shape memory property of nitinol shows promise in allowing cylindrical spinal cord stimulation leads to expand into a more optimal geometry within the epidural space. By having a body temperature-dependent geometry change, nitinol-based cylindrical leads could reduce lead migration, increase dermatomal coverage, and increase electrode density while maintaining the advantages of minimally invasive insertion.

Prolactin (PRL) cooperates with other factors to orchestrate mammary development and lactation, and is epidemiologically linked to higher risk for breast cancer. However, how PRL collaborates with oncogenes to foster tumorigenesis and influence breast cancer phenotype is not well understood. To understand its interactions with canonical Wnt signals, which elevate mammary stem cell activity, we crossed heterozygous NRL-PRL mice with Apc(Min/+) mice and treated pubertal females with a single dose of mutagen. PRL in the context of Apc(Min/+) fueled a dramatic increase in tumor incidence in nulliparous mice, compared to Apc(Min/+) alone. Although carcinomas in both NRL-PRL/Apc(Min/+) and Apc(Min/+) females acquired a mutation in the remaining wildtype Apc allele and expressed abundant β-catenin, PRL-promoted tumors displayed higher levels of Notch-driven target genes and Notch-dependent cancer stem cell activity, compared to β-catenin-driven activity in Apc(Min/+) tumors. This PRL-induced shift to dominant Notch signals was evident in preneoplastic epithelial hyperplasias at 120 days of age. In NRL-PRL/Apc(Min/+) females, rapidly proliferating hyperplasias, characterized by β-catenin at cell junctions and high NOTCH1 expression, contrasted with slower growing lesions with nuclear β-catenin in Apc(Min/+) females. These studies demonstrate that PRL can powerfully modulate the incidence and phenotype of mammary tumors, shedding light on mechanisms whereby PRL elevates risk of breast cancer.

Chromosomal instability (CIN) is a hallmark of cancer. While low levels of CIN can be tumor promoting, high levels of CIN cause cell death and tumor suppression. The widely used chemotherapeutic, paclitaxel (Taxol), exerts its anticancer effects by increasing CIN above a maximally tolerated threshold. One significant outstanding question is whether the p53 tumor suppressor is required for the cell death and tumor suppression caused by high CIN. Both p53 loss and reduction of the mitotic kinesin, centromere-associated protein-E, cause low CIN. Combining both genetic insults in the same cell leads to high CIN. Here, we test whether high CIN causes cell death and tumor suppression even in the absence p53. Despite a surprising sex-specific difference in tumor spectrum and latency in p53 heterozygous animals, these studies demonstrate that p53 is not required for high CIN to induce tumor suppression. Pharmacologic induction of high CIN results in equivalent levels of cell death due to loss of essential chromosomes in p53+/+ and p53−/− cells, further demonstrating that high CIN elicits cell death independently of p53 function. Implications: These results provide support for the efficacy of anticancer therapies that induce high CIN, even in tumors that lack functional p53.

Non-melanoma skin cancers (NMSCs) are the most diagnosed cancers in the US and occur more frequently in males. We previously demonstrated chemoprotective effects of dietary grape powder (GP) against UVB-mediated skin tumorigenesis in female SKH-1 mice. To expand on this, here, we determined the effects of GP in a short-term UVB exposure protocol (0 or 5% GP, followed by UVB every other day for 2 weeks) in male and female SKH-1 mice, as well as explored any sex-related differences in UVB carcinogenesis via male SKH-1 mice (0, 3, or 5% GP, UVB twice weekly for 28 weeks). In the short-term study, we found that GP protects against early-stage epithelial hyperplasia and mast cell infiltration in both sexes. In the long term, GP markedly reduced tumor counts and malignant conversion, along with significant decreases in mast cell infiltration, serum IgE and Eotaxin. We also found inhibition of P38 phosphorylation and reduced PCNA, Ki67 and BCL2 levels, suggesting that the anti-inflammatory effects of GP inhibits P38, acting as an upstream regulator to inhibit proliferation and reduce tumor cell survival. Together, GP appears to protect against UVB-mediated skin damage and carcinogenesis in SKH-1 mice and should be explored further as a supplement for NMSC prevention.

The membrane transporter AT‐1/SLC33A1 translocates cytosolic acetyl‐CoA into the lumen of the endoplasmic reticulum (ER), participating in quality control mechanisms within the secretory pathway. Mutations and duplication events in AT‐1/SLC33A1 are highly pleiotropic and have been linked to diseases such as spastic paraplegia, developmental delay, autism spectrum disorder, intellectual disability, propensity to seizures, and dysmorphism. Despite these known associations, the biology of this key transporter is only beginning to be uncovered. Here, we show that systemic overexpression of AT‐1 in the mouse leads to a segmental form of progeria with dysmorphism and metabolic alterations. The phenotype includes delayed growth, short lifespan, alopecia, skin lesions, rectal prolapse, osteoporosis, cardiomegaly, muscle atrophy, reduced fertility, and anemia. In terms of homeostasis, the AT‐1 overexpressing mouse displays hypocholesterolemia, altered glycemia, and increased indices of systemic inflammation. Mechanistically, the phenotype is caused by a block in Atg9a‐Fam134b‐LC3β and Atg9a‐Sec62‐LC3β interactions, and defective reticulophagy, the autophagic recycling of the ER. Inhibition of ATase1/ATase2 acetyltransferase enzymes downstream of AT‐1 restores reticulophagy and rescues the phenotype of the animals. These data suggest that inappropriately elevated acetyl‐CoA flux into the ER directly induces defects in autophagy and recycling of subcellular structures and that this diversion of acetyl‐CoA from cytosol to ER is causal in the progeria phenotype. Collectively, these data establish the cytosol‐to‐ER flux of acetyl‐CoA as a novel event that dictates the pace of aging phenotypes and identify intracellular acetyl‐CoA‐dependent homeostatic mechanisms linked to metabolism and inflammation.

Doxycycline (doxy) is used in treating intracellular and extracellular infections. Liposomal (LE) antibiotics allow low-frequency dosing and extended efficacy compared with standard (STD) formulations. We developed a novel sulfuric acid–loading method for doxycycline liposomes (LE-doxy). We hypothesized that a single s.c. injection of LE-doxy would be detectable in serum for at least 2 weeks at concentrations equal to or better than STD-doxy and would be bactericidal in an in vitro Mycobacterium smegmatis infection of J774A.1 macrophage cells. Liposomes were encapsulated by sulfuric acid gradient loading, and release kinetics were performed in vitro and in vivo. LE-doxy made using 8.25 mg/ml doxycycline loaded for 24 hours achieved 97.77% capture in 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 43.87% in sphingomyelin (sphing). Rats were injected s.c. with 50 mg/kg LE-doxy or 5 mg/kg STD-doxy, and serial blood samples were collected. Pharmacokinetics were analyzed using high-performance liquid chromatography. Liver and injection site skin samples were collected at euthanasia (4 weeks postinjection). Minimal histologic tissue reactions occurred after injection of STD (nonliposomal), DPPC, or sphing-doxy. DPPC-doxy had slightly faster in vitro leakage than sphing liposomes, although both were detectable at 264 hours. The mean residence time for DPPC was the highest (111.78 hours), followed by sphing (56.00 hours) and STD (6.86 hours). DPPC and sphing-doxy were detectable at 0.2 μg/ml in serum at 336 hours postadministration. LE-doxy was not toxic to J774A.1 cells in vitro and produced inhibition of viable Mycobacterium smegmatis at 24 and 48 hours. LE-doxy will require further testing in in vivo infection models.

Orofacial clefts (OFCs) of the lip and/or palate are among the most common human birth defects. Current treatment strategies focus on functional and cosmetic repair but even when this care is available, individuals born with OFCs are at high risk for persistent neurobehavioral problems. In addition to learning disabilities and reduced academic achievement, recent evidence associates OFCs with elevated risk for a constellation of psychiatric outcomes including anxiety disorders, autism spectrum disorder, and schizophrenia. The relationship between these outcomes and OFCs is poorly understood and controversial. Recent neuroimaging studies in humans and mice demonstrate subtle morphological brain abnormalities that co-occur with OFCs but specific molecular and cellular mechanisms have not been investigated. Here, we provide the first evidence directly linking OFC pathogenesis to abnormal development of GABAergic cortical interneurons (cINs). Lineage tracing revealed that the structures that form the upper lip and palate develop in molecular synchrony and spatiotemporal proximity to cINs, suggesting these populations may have shared sensitivity to genetic and/or teratogenic insult. Examination of cIN development in a mouse model of nonsyndromic OFCs revealed significant disruptions in cIN proliferation and migration, culminating in misspecification of the somatostatin-expressing subgroup. These findings reveal a unified developmental basis for orofacial clefting and disrupted cIN development, and may explain the significant overlap in neurobehavioral and psychiatric outcomes associated with OFCs and cIN dysfunction. This emerging mechanistic understanding for increased prevalence of adverse neurobehavioral outcomes in OFC patients is the entry-point for developing evidence-based therapies to improve patient outcomes.

Background There is limited availability of context-specific physical activity questionnaires in low and middle income countries. The aim of this study was to develop and examine the validity of a new Indian physical activity questionnaire, the Andhra Pradesh Children and Parent Study Physical Activity Questionnaire (APCAPS-PAQ). Methods The current study was conducted with the cohort from the Hyderabad DXA Study (n = 2321), recruited in 2009-2010. Criterion validity (n = 245) was examined by comparing the APCAPS-PAQ to a combined heart rate and motion sensor worn for 8 days. Construct validity (n = 2321) was assessed with linear regression, comparing APCAPS-PAQ against BMI, percent body fat, and pulse rate. Results The APCAPS-PAQ criterion validity was variable depending on the PA intensity groups (ρ = 0.26, 0.07, 0.39; к = 0.14, 0.04, 0.16 for sedentary, light, moderate/vigorous physical activity (MVPA) respectively). Sedentary and light intensity activities from the questionnaire were underestimated when compared to the criterion data while MVPA in APCAPS-PAQ was overestimated. Higher time spent in sedentary activity in APCAPS-PAQ was associated with higher BMI and percent body fat, suggesting construct validity. Conclusions The APCAPS-PAQ validity is comparable to other physical activity questionnaires. This tool is able to assess sedentary behavior, moderate/vigorous activity and physical activity energy expenditure on a group level with reasonable validity. This new questionnaire may be used for ranking individuals according to their sedentary time and physical activity in southern India. Electronic supplementary material The online version of this article (doi:10.1186/s12889-016-2706-9) contains supplementary material, which is available to authorized users.

Case comment on Supreme Court of Canada decisions between 1998 and 2015 related to statutory interpretation.