Cutting out the middleman: measuring nuclear area in histopathology slides without segmentation

The size of nuclei in histological preparations from excised breast tumors is predictive of patient outcome (large nuclei indicate poor outcome). Pathologists take into account nuclear size when performing breast cancer grading. In addition, the mean nuclear area (MNA) has been shown to have independent prognostic value. The straightforward approach to measuring nuclear size is by performing nuclei segmentation. We hypothesize that given an image of a tumor region with known nuclei locations, the area of the individual nuclei and region statistics such as the MNA can be reliably computed directly from the image data by employing a machine learning model, without the intermediate step of nuclei segmentation. Towards this goal, we train a deep convolutional neural network model that is applied locally at each nucleus location, and can reliably measure the area of the individual nuclei and the MNA. Furthermore, we show how such an approach can be extended to perform combined nuclei detection and measurement, which is reminiscent of granulometry.Comment: Conditionally accepted for MICCAI 201

Proteomic maps of breast cancer subtypes

Systems-wide profiling of breast cancer has almost always entailed RNA and DNA analysis by microarray and sequencing techniques. Marked developments in proteomic technologies now enable very deep profiling of clinical samples, with high identification and quantification accuracy. We analysed 40 oestrogen receptor positive (luminal), Her2 positive and triple negative breast tumours and reached a quantitative depth of >10,000 proteins. These proteomic profiles identified functional differences between breast cancer subtypes, related to energy metabolism, cell growth, mRNA translation and cell-cell communication. Furthermore, we derived a signature of 19 proteins, which differ between the breast cancer subtypes, through support vector machine (SVM)-based classification and feature selection. Remarkably, only three proteins of the signature were associated with gene copy number variations and eleven were also reflected on the mRNA level. These breast cancer features revealed by our work provide novel insights that may ultimately translate to development of subtype-specific therapeutics

A randomized study on the effect of extended voluntary waiting period in primiparous dairy cows on milk yield during first and second lactation

Extending the voluntary waiting period (VWP) for primiparous cows can have a positive impact on fertil-ity without a negative impact on milk production per day in the calving interval (CInt). We investigated the effect of extended VWP during first lactation on milk yield (MY) during 2 consecutive lactations in primipa-rous cows. The study involved 16 commercial herds in southern Sweden. A total of 533 Holstein and Red dairy cattle (Swedish Red, Danish Red, Ayrshire) dairy cows were randomly assigned to a conventional 25 to 95 d VWP (n = 252) or extended 145 to 215 d VWP (n = 281). Data on calvings, inseminations, and test-day yields were retrieved from the Swedish Milk Record -ing System. Cows with VWP according to plan and completing 1 or 2 CInt with a second or third calving were included in the data analysis. Whole lactation and 305-d energy-corrected milk (ECM) yield were higher for the extended VWP group than the conventional VWP group in both the first lactation (12,307 vs. 9,587 and 9,653 vs. 9,127 kg ECM) and second lactation (12,817 vs. 11,986 and 11,957 vs. 11,304 kg ECM). We found no difference between the VWP groups in MY per day during the first CInt or during the first and second CInt combined, although MY per day during the second CInt was around 1.5 kg higher for cows with extended VWP than for cows with conventional VWP. Thus extended VWP for primiparous cows can be used as a management tool without compromising MY

Morphometrical malignancy grading is a valuable prognostic factor in invasive ductal breast cancer

The aim of the present study is to augment the prognostic power of breast cancer grading by elaboration of quantitative histopathological methods. We focus on the recently introduced morphometrical grading system in which the three grading sub-features of the WHO grading system are evaluated with the help of computerised nuclear morphometry, and quantitative methods for assessing mitotic activity and tubular differentiation. The prognostic value of the morphometrical grading system is now confirmed in a material of 159 cases of invasive ductal breast cancer. In the current material the morphometrical grading system very efficiently predicted the prognosis of breast cancer by dividing the patients into favourable (grade I), intermediate (grade II), and unfavourable (grade III) outcome (P<0.0001). The morphometrical grading system was especially efficient in identifying patients with the most unfavourable outcome. In our material the morphometrical grade III was associated with a 5.4-fold risk of breast cancer death. In light of the present results, the morphometrical grading can be applied to clinical use as an aid in treatment decisions of patients with invasive ductal breast cancer

A randomized study on the effect of an extended voluntary waiting period in primiparous dairy cows on fertility, health, and culling during first and second lactation

When the voluntary waiting period (VWP), defined as the days between calving and when the cow is eligible to receive the first insemination, is extended, high-yielding dairy cows may have better opportunities to regain energy balance before first insemination. This study investigated the effect of an extended (145–215 days in milk [DIM], n = 280) or conventional (25–95 DIM, n = 251) VWP treatment on fertility, disease incidence, and culling rate in cows during their first lactation. The cows were also followed through a second lactation without intervention regarding VWP, during which the farmers could decide when they wished to start the inseminations. This was done in a randomized-controlled study on 16 high-yielding commercial herds in southern Sweden, containing a total of 531 primiparous cows of the Holstein and Red Dairy Cattle breeds. Data from the Swedish national dairy herd recording scheme collected between August 2018 and September 2021 were used in the analysis, including records on breed, calvings, estrus intensity, inseminations, disease, somatic cell count, culling date, and culling reason. During first lactation, more cows receiving the extended VWP treatment showed strong estrus intensity (score 4–5, 55% vs. 48%) and fewer showed moderate estrus intensity (score 3, 35% vs. 43%) at first insemination, compared with cows receiving the conventional VWP treatment. First service conception rate (FSCR) was higher (67% vs. 51%) and number of inseminations per conception (NINS) was lower (1.6 vs. 2.0) during the first lactation for cows receiving the extended compared with the conventional VWP treatment. For disease incidence rate or culling rate expressed as number of events per cow-time in the study, we found no differences between the cows receiving the 2 VWP treatments in any lactation. Calving to first service interval during second lactation was longer (86 vs. 74 d) for cows with extended compared with conventional VWP. In conclusion, primiparous cows with extended VWP showed improved reproductive functions, in the form of higher estrus intensity, greater FSCR, and lower NINS, during the first lactation. However, we observed no apparent effect on these fertility measures during the following lactation (without VWP intervention) and no differences in disease prevalence or culling between cows receiving the 2 different VWP treatments in either lactation. Compliance with the planned VWP treatment was lower for cows with planned extended compared with planned conventional VWP treatment. We studied the “intention-to-treat” effect (i.e., the results for all cows randomized to each treatment regardless of whether the planned VWP was achieved or not) to identify any bias arising due to degree of compliance. However, we found no difference in culling rate between cows randomized to an extended VWP compared with those randomized to a conventional VWP. These findings can be used to support management decisions on VWP length in high-yielding dairy herds

Proteomic maps of breast cancer subtypes

Systems-wide profiling of breast cancer has almost always entailed RNA and DNA analysis by microarray and sequencing techniques. Marked developments in proteomic technologies now enable very deep profiling of clinical samples, with high identification and quantification accuracy. We analysed 40 oestrogen receptor positive (luminal), Her2 positive and triple negative breast tumours and reached a quantitative depth of >10,000 proteins. These proteomic profiles identified functional differences between breast cancer subtypes, related to energy metabolism, cell growth, mRNA translation and cell-cell communication. Furthermore, we derived a signature of 19 proteins, which differ between the breast cancer subtypes, through support vector machine (SVM)-based classification and feature selection. Remarkably, only three proteins of the signature were associated with gene copy number variations and eleven were also reflected on the mRNA level. These breast cancer features revealed by our work provide novel insights that may ultimately translate to development of subtype-specific therapeutics.</p

Correlation of computed tomography with carotid plaque transcriptomes associates calcification with lesion-stabilization

Background and aims: Unstable carotid atherosclerosis causes stroke, but methods to identify patients and lesions at risk are lacking. We recently found enrichment of genes associated with calcification in carotid plaques from asymptomatic patients. Here, we hypothesized that calcification represents a stabilising feature of plaques and investigated how macro-calcification, as estimated by computed tomography (CT), correlates with gene expression profiles in lesions. Methods: Plaque calcification was measured in pre-operative CT angiographies. Plaques were sorted into high- and lowcalcified, profiled with microarrays, followed by bioinformatic analyses. Immunohistochemistry and qPCR were performed to evaluate the findings in plaques and arteries with medial calcification from chronic kidney disease patients. Results: Smooth muscle cell (SMC) markers were upregulated in high-calcified plaques and calcified plaques from symptomatic patients, whereas macrophage markers were downregulated. The most enriched processes in high-calcified plaques were related to SMCs and extracellular matrix (ECM) organization, while inflammation, lipid transport and chemokine signaling were repressed. These findings were confirmed in arteries with high medial calcification. Proteoglycan 4 (PRG4) was identified as the most upregulated gene in association with plaque calcification and found in the ECM, SMA+ and CD68+/TRAP + cells. Conclusions: Macro-calcification in carotid lesions correlated with a transcriptional profile typical for stable plaques, with altered SMC phenotype and ECM composition and repressed inflammation. PRG4, previously not described in atherosclerosis, was enriched in the calcified ECM and localized to activated macrophages and smooth muscle-like cells. This study strengthens the notion that assessment of calcification may aid evaluation of plaque phenotype and stroke risk.The European Union’s Horizon 2020/Marie Sklodowska-Curie grant agreement No 722609 (INTRICARE);Swedish Heart and Lung FoundationSwedish Research Council (K2009-65X-2233-01-3, K2013- 65X-06816-30-4, 349-2007-8703)Uppdrag Besegra Stroke (P581/ 2011-123)Stockholm County Council (ALF2011-0260, ALF-2011- 0279)Swedish Society for Medical ResearchTore Nilsson’s FoundationMagnus Bergvall’s FoundationKarolinska Institutet FoundationEuropean Commission (722609)Publishe

PTTG1-interacting protein (PTTG1IP/PBF) predicts breast cancer survival

Background: PTTG1-interacting protein (PTTG1IP) is an oncogenic protein, which participates in metaphase-anaphase transition of the cell cycle through activation of securin (PTTG1). PTTG1IP promotes the shift of securin from the cell cytoplasm to the nucleus, allowing the interaction between separase and securin. PTTG1IP overexpression has been previously observed in malignant disease, e.g. in breast carcinoma. However, the prognostic value of PTTG1IP in breast carcinoma patients has not previously been revealed.Methods: A total of 497 breast carcinoma patients with up to 22-year follow-up were analysed for PTTG1IP and securin immunoexpression. The results were evaluated for correlations with the clinical prognosticators and patient survival.Results: In our material, negative PTTG1IP immunoexpression predicted a 1.5-fold risk of breast cancer death (p = 0.02). However, adding securin immunoexpression to the analysis indicated an even stronger and independent prognostic power in the patient material (HR = 2.5, p < 0.0001). The subcellular location of securin was found with potential prognostic value also among the triple-negative breast carcinomas (n = 96, p = 0.052).Conclusions: PTTG1IP-negativity alone and in combination with high securin immunoexpression indicates a high risk of breast cancer death, resulting in up to 14-year survival difference in our material