Digital Histopathology of Cancer

Syöpä on merkittävä ja yleistyvä kansansairaus. Maailman terveysjärjestön mukaan syöpä on maailmanlaajuisesti toiseksi yleisin kuolinsyy sydän- ja verisuonitautien jälkeen. Jos ei-melanoottisia ihosyöpiä ei oteta huomioon, ovat tavallisimmat syöpätyypit naisilla rintasyöpä ja miehillä keuhkosyöpä ja eturauhassyöpä. Sitä mukaa kun syövän biologisten syntymekanismien ymmärrys on lisääntynyt, ovat myös hoitovaihtoehdot lisääntyneet. Useampi kuin joka neljäs uusi lääke, joka lanseerattiin vuosina 2010-2018, oli tarkoitettu syövän hoitoon. Jotta potilas voisi hyötyä tarjolla olevasta laajasta syöpälääkevalikoimasta ja minimoida lääkkeiden haittavaikutukset, tulee hoito kohdistaa hänen yksilölliseen syöpäänsä. Tätä varten syöpä on sekä diagnosoitava luotettavasti että luokiteltava yksityiskohtaisesti. Vaikka kajoamattomat kuvantamistutkimukset kuten magneettikuvaus ovat viime vuosina kehittyneet huomattavasti, on syöpädiagnostiikan perusta edelleen histopatologiassa eli leikkauksessa tai neulanäytteenotossa poistetun kudoksen mikroskooppisessa tutkimuksessa. Valomikroskooppi on pysynyt patologin pääasiallisena työvälineenä yli puolentoista vuosisadan ajan. Se on sallinut kudoksen tarkastelun aina solutasolle saakka ja jopa sitä pienempiin rakenteisiin. Tärkeitä lisätutkimuksia tavallisen valomikroskooppisen tutkimuksen lisäksi ovat proteiiniantigeenien osoittamistutkimukset, kuten immunohistokemia ja in situ - hybridisaatio, joita voidaan käyttää syöpäkudoksen luokittelemiseen. Syövän tarkalla diagnosoimisella ja luokittelulla on haasteensa. Yksi sellainen on Suomessa ja ulkomailla vallitseva pula patologeista. Toinen haaste liittyy kasvainten välisen vaihtelun arviointiin, joka on tärkeää kasvainten kasvutaipumuksen luokittelussa (esim. eturauhassyövän Gleason-luokitus) ja tiettyjen värjäysten tulkinnassa (esim. rintasyövän HER2-värjäytyminen). Todellisen biologisen vaihtelun lisäksi vaihtelua esiintyy patologien välisissä arvioissa (interobserver variation) sekä saman patologin luokitteluissa eri ajan hetkellä (intraobserver variation). Kolmas haaste on itse valomikroskooppi. Vaikka se on luotettava, halpa ja helppokäyttöinen diagnostiikkalaite, on sillä omat puutteensa modernin patologian laboratorion työnkulussa. Digitaalihistopatologia edustaa uutta tapaa toteuttaa patologin pääasiallinen työtehtävä syöpäpotilaan hoidossa: asettaa diagnoosi ja luokitella syöpä yksityiskohtaisesti. Siirtyminen valomikroskoopista tietokoneympäristöön tarjoaa monia etuja, joista muutamia on tutkittu tässä väitöskirjassa. Tämän tutkimuksen tarkoituksena oli kehittää ja testata digitaalipatologian sovelluksia syöpädiagnostiikan parantamiseksi. Osatöissä tutkittiin eturauhassyövän Gleason-luokituksen opettamista ja standardointia, rinta- ja eturauhassyövän immunohistokemiallisten värjäysten tulkintaa, digitaalinäytteille kehitettyä kuvanpakkausmenetelmää, sekä näyteskannerin optimaalisen kuvausresoluution määrittämistä. Väitöskirjassa osoitetaan, että digitaalinäytteitä voi käyttää eturauhaskoepalan Gleason-luokituksen tekemiseen ja että internet-pohjainen ohjelma voi edistää tulkitsijoiden välisen vaihtelun määrittämistä sekä Gleason-luokituksen opettamista ja standardisointia. Gleason-luokituksen ohella toinen tärkeä osa eturauhassyövän histopatologiaa on immunohistokemiallisten värjäysten tulkinta. Tässä väitöskirjassa esitetään menetelmä, jolla kahta digitaalinäytettä voidaan tutkia yhtäaikaisesti ja synkronoidusti. Menetelmää testattiin eturauhassyövän immunohistokemiallisella AMACR–p63-kaksoisvärjäyksellä yhdessä rutiininomaisen hematoksyliini–eosiini- värjäyksen kanssa. Tutkimuksessa osoitettiin, että tekniikkaa voidaan käyttää hyväksi histopatologian opetuksessa ja valikoiduissa tapauksissa kliinisessä diagnostiikassa. Keskeinen asia rintasyövän diagnostiikassa on HER2-statuksen tutkiminen, koska kasvaimia, joissa HER2 on yli-ilmentynyt, voidaan hoitaa anti-HER2- lääkkeillä. Yhdessä osatöistä tutkittiin digitaalisen kuva-analyysin käyttöä niin valomikroskooppikuvilla kuin digitaalinäytteillä tarkoituksena auttaa patologia määrittämään kirurgisesti poistetun kasvainkudoksen HER2-status. Työssä osoitettiin, että ilmaista ja kaikille avointa ohjelmistoa käyttämällä voitiin vähentää HER2-statuksen suhteen vaikeatulkintaisten tapausten määrää. Digitaalihistopatologian käyttöönotto rutiinidiagnostiikkaan on laajentumassa nopeasti. Yksi tekninen haaste on digitaalinäytteiden vaatiman suuren tallennuskapasiteetin hallinta. Tarve tallentaa suuria määriä tietoa edellyttää digitaalinäytteiden kuvanlaadun ja tiedostokoon yhteensovittamista. Yhdessä tämän väitöskirjan osatöistä tutkittiin skannerimikroskoopin optimaalisen kuvausresoluution määrittämistä. Menetelmää voidaan hyödyntää esimerkiksi vertailtaessa skannereita ennen hankintaa. Toisessa osatyössä esiteltiin uusi kuvanpakkausmenetelmä, joka suunniteltiin varta vasten histopatologisia digitaalinäytteitä varten niiden tiedostokoon minimoimiseksi ja siten tallennuskustannusten pienentämiseksi. Tämän väitöskirjan kaksi ensimmäistä osatyötä edustavat digitaalipatologian alkutaivalta ja tutkimuskenttä on kehittynyt sittemmin, mahdollisesti pieneltä osin edellä mainittujen tutkimusten löydösten myötä. Yhteenvetona osatyöt toivottavasti vievät digitaalipatologian alaa eteenpäin ja siten edesauttavat syöpäpotilaiden hoitoa.Cancer is a significant and growing public health concern. According to the World Health Organisation's estimates it is – after cardiovascular diseases – the second leading cause of death worldwide. Excluding non-melanoma skin cancers the most common types of cancer are for women breast cancer and for men lung cancer followed by prostate cancer. While the biological understanding of cancer has expanded, so too has the selection of available treatments. More than one fourth of all new medicines entering the market during 2010-2018 were for treating cancer. In order for a patient to benefit from the wide variety of cancer treatments, and avoid adverse effects, their unique cancer has to be matched with the appropriate treatment. For this the cancer needs to be both diagnosed accurately and classified in detail. Although non-invasive imaging methods, such as magnetic resonance imaging, have evolved substantially in recent years, the basis of cancer diagnosis is still in histopathology, that is, the pathological evaluation of tissue removed through surgery or needle biopsy. The light microscope has remained the pathologist's main diagnostic tool for a century and a half allowing for the examination of tissue down to cellular – and even subcellular – level. Important adjuncts to routine histopathological staining of tissue, needed for light microscopy, are techniques allowing for the visualization of protein antigens and nucleic acid in the tissue. These techniques, among which are immunohistochemistry and in situ hybridization, respectively, can be used for instance in the molecular characterization of cancer. There are challenges in meeting the need for accurate diagnosing and characterization of cancer. One such challenge is posed by the shortage of pathologists observed in Finland and elsewhere. Another challenge is the variability in the interpretation of the tumor growth pattern (grading, such as Gleason grading in prostate cancer) and in the interpretation of certain tissue staining patterns (such as the immunohistochemical staining of the HER2 molecule in breast cancer). This variability manifests itself both between pathologists (interobserver variation) and also in the same pathologist's work over time (intraobserver variation). A third challenge is presented by the fact that the light microscope – although a reliable, cheap, and easy-to-use diagnostic tool – has shortcomings in the modern day pathology service. Digital histopathology presents a new way of carrying out the central task of a pathologist in managing cancer patients, namely making the diagnosis and characterising the tumor in detail. Making the shift from a light microscope to a computer environment offers many benefits, some of which have been examined in this dissertation. The present study was carried out with the purpose of developing and testing applications of digital pathology in order to improve the histopathological diagnosis of cancer. The individual studies looked at advancing the teaching and standardization of Gleason grading or prostate cancer, aiding in the interpretation of immunohistochemical staining of prostate and breast cancer, as well as facilitating the implementation of digital pathology by way of a novel whole slide image optimised image compression algorithm and mapping the determinants of an optimal imaging resolution for a whole slide scanner. We demonstrated that whole slide images can be used to assess the Gleason grade of a prostate biopsy and that the use of an internet based platform can be beneficial in assessing interobserver variation in the grading and teaching and standardising the grading. Besides Gleason grading another important aspect of prostate histopathology is the interpretation of immunohistochemistry. We created a method of viewing two whole slide images simultaneously and synchronously and tested this method in visualising the AMACR-p63 double stain along with normal hematoxylin and eosin staining of prostate biopsies. We showed that this technique can be used for histopathology education as well as in clinical diagnostics in selected cases. A key issue in breast cancer diagnostics is defining the HER2 status of a tumor, that is, whether the tumor overexpresses the molecule and can then be treated with HER2 antibody based drugs. We studied the use of digital image analysis, using both photomicrographs and whole slide images, in aiding the pathologist in defining the HER2 status on a breast cancer surgical resection specimen. We showed that using a free and publicly available image analysis software can help to resolve cases otherwise deemed equivocal by conventional light microscopy. The introduction of digital histopathology into routine diagnostic work is underway. One technical challenge is managing the large amounts of image data generated by whole slide images. When there is a need to store large numbers of whole slide images it is essential to strike a balance between image fidelity and file size. To deal with this issue we studied the optimal imaging resolution of a whole slide scanner using a methodology that can be utilised for instance in comparing whole slide scanners before acquiring one. In addition we introduced a novel way of image compression suited for whole slide images in order to reduce the storage footprint, and cost, of whole slide images. The first two studies in this dissertation represent the very beginnings of whole slide imaging in pathology, and the field has advanced since then, perhaps in small part due to the findings in these studies. Taken together, the findings in this dissertation can hopefully advance the use of digital pathology in cancer diagnostics and thereby improve the care of cancer patients

Fallstudie för utveckling av två gårdar

Syftet med detta arbete att hjälpa ägarna till ett utvalt fallföretag att hitta en eller flera lönsamma produktionsgrenar som är lämpliga för gårdarnas förutsättningar och göra relevanta kalkyler så att ägarna ska kunna fatta ett beslut och bygga upp en produktion inom de närmsta åren. De aktuella gårdarna ligger i Västergötland respektive Värmland. Efter sondering av tänkbara produktionsgrenar koncentrerade vi oss på mjölkproduktion och hjortköttsproduktion. Arbete går ut på att hitta en intressant och lönsam produktion för framtiden. I Sverige finns det en del hjorthägn men marknaden för förädling av köttet är liten. Produktionen är väldigt dyr och osäker om man inte kan förädla och slakta sina egna djur. Kan man bygga upp ett slakteri för förädling ökar chanserna för en bra vinst. Mjölkproduktion däremot en säkrare investering, produktionen är stabil då efterfrågan är konstant. Uppstartskostnaderna för dessa två produktioner skiljer sig mycket åt. Mjölkproduktion kräver nya byggnader med inventarier och maskiner för produktionen. Hjortproduktionen kräver ett hägn på befintlig mark. Möjligheten finns att produktionerna kan kombineras då fodret och betet från korna kan utnyttjas för hjortar. Vi har gjort intervjuer med personer i branscherna för att få en uppfattning om möjligheter och nackdelar med de utvalda produktionsgrenarna. Areal och möjligheten till byggnation för mjölkproduktion passar bäst på gården i Västergötland och biotopen i Värmland kan passa hjortproduktionen bättre.The purpose of this work is to help the owners of a selected case company to find one or more profitable branches of production that are suitable for farm conditions and make relevant calculations so that the owners should be able to make a decision and build a production within the next few years. The current farms are situated in Västergötland and Värmland. After probing the possible branches of production, we concentrated on dairy farming and deer meat production. This work is to find an interesting and profitable production for the future. In Sweden, there are some deer companies, but the market for processing of meat is small. The production is very expensive and not sure if you can’t refine and slaughter your own animals. Can you build a slaughterhouse for processing it will increase the chances of a good profit. Milk production, however is a safer investment, with stable production when demand is constant. Start-up costs for these two productions are very different. Milk production requires new buildings with equipment and machinery for production. Deer production requires a shelter on existing track. The possibility exists that the productions can be combined with feed and bait from the cows can be used for deer. We have done interviews with people in industries to get an idea of the possibilities and disadvantages of the selected branches of production. Area and the possibility of building for milk is best for the farm in Västergötland and the biotope of Värmland can fit deer production better

Free digital image analysis software helps to resolve equivocal scores in HER2 immunohistochemistry

Evaluation of human epidermal growth factor receptor 2 (HER2) immunohistochemistry (IHC) is subject to interobserver variation and lack of reproducibility. Digital image analysis (DIA) has been shown to improve the consistency and accuracy of the evaluation and its use is encouraged in current testing guidelines. We studied whether digital image analysis using a free software application (ImmunoMembrane) can assist in interpreting HER2 IHC in equivocal 2+ cases. We also compared digital photomicrographs with whole-slide images (WSI) as material for ImmunoMembrane DIA. We stained 750 surgical resection specimens of invasive breast cancers immunohistochemically for HER2 and analysed staining with ImmunoMembrane. The ImmunoMembrane DIA scores were compared with the originally responsible pathologists' visual scores, a researcher's visual scores and in situ hybridisation (ISH) results. The originally responsible pathologists reported 9.1 % positive 3+ IHC scores, for the researcher this was 8.4 % and for ImmunoMembrane 9.5 %. Equivocal 2+ scores were 34 % for the pathologists, 43.7 % for the researcher and 10.1 % for ImmunoMembrane. Negative 0/1+ scores were 57.6 % for the pathologists, 46.8 % for the researcher and 80.8 % for ImmunoMembrane. There were six false positive cases, which were classified as 3+ by ImmunoMembrane and negative by ISH. Six cases were false negative defined as 0/1+ by IHC and positive by ISH. ImmunoMembrane DIA using digital photomicrographs and WSI showed almost perfect agreement. In conclusion, digital image analysis by ImmunoMembrane can help to resolve a majority of equivocal 2+ cases in HER2 IHC, which reduces the need for ISH testing.Peer reviewe

Head-to-head comparison of plasma p-tau181, p-tau231 and glial fibrillary acidic protein in clinically unimpaired elderly with three levels of APOE4-related risk for Alzheimer's disease

Plasma phosphorylated tau (p-tau) and glial fibrillary acidic protein (GFAP) both reflect early changes in Alzheimer's disease (AD) pathology. Here, we compared the biomarker levels and their association with regional β-amyloid (Aβ) pathology and cognitive performance head-to-head in clinically unimpaired elderly (n = 88) at three levels of APOE4-related genetic risk for sporadic AD (APOE4/4 n = 19, APOE3/4 n = 32 or non-carriers n = 37). Concentrations of plasma p-tau181, p-tau231 and GFAP were measured using Single molecule array (Simoa), regional Aβ deposition with 11C-PiB positron emission tomography (PET), and cognitive performance with a preclinical composite. Significant differences in plasma p-tau181 and p-tau231, but not plasma GFAP concentrations were present between the APOE4 gene doses, explained solely by brain Aβ load. All plasma biomarkers correlated positively with Aβ PET in the total study population. This correlation was driven by APOE3/3 carriers for plasma p-tau markers and APOE4/4 carriers for plasma GFAP. Voxel-wise associations with amyloid-PET revealed different spatial patterns for plasma p-tau markers and plasma GFAP. Only higher plasma GFAP correlated with lower cognitive scores. Our observations suggest that plasma p-tau and plasma GFAP are both early AD markers reflecting different Aβ-related processes

Association of Early β-Amyloid Accumulation and Neuroinflammation Measured With [11C]PBR28 in Elderly Individuals Without Dementia

OBJECTIVE: To examine whether early β-amyloid (Aβ) accumulation and metabolic risk factors are associated with neuroinflammation in elderly individuals without dementia. METHODS: We examined 54 volunteers (mean age 70.0 years, 56% women, 51% APOE ɛ4 carriers) with the translocator protein (TSPO) tracer [11C]PBR28 to assess neuroinflammation and with [11C] Pittsburgh compound B (PiB) to assess cerebral Aβ accumulation. [11C]PBR28 and [11C]PiB standardized uptake value ratios (SUVRs) were quantified in 6 regions of interests by using the cerebellar cortex as a pseudo-reference and reference region, respectively. Fasting venous glucose, insulin, and high-sensitivity C-reactive protein (hs-CRP) values were determined. Homeostatic model assessment of insulin resistance (HOMA-IR) was calculated. A subset of individuals (n = 11) underwent CSF sampling, and Aβ40, Aβ42, total tau, phospho-tau, soluble TREM2, and YKL-40 levels were measured. RESULTS: Among the whole study group, no significant association was found between [11C]PiB and [11C]PBR28 SUVR composite scores (slope 0.02, p = 0.30). However, higher [11C]PiB binding was associated with higher [11C]PBR28 binding among amyloid-negative ([11C]PiB composite score ≤1.5) (TSPO genotype-, age- and sex-adjusted slope 0.26, p = 0.008) but not among amyloid-positive (slope -0.004, p = 0.88) participants. Higher CSF soluble TREM2 (rs = 0.72, p = 0.01) and YKL-40 (rs = 0.63, p = 0.04) concentrations were associated with a higher [11C]PBR28 composite score. Higher body mass index, HOMA-IR, and hs-CRP were associated with higher [11C]PBR28 binding in brain regions where Aβ accumulation is first detected in Alzheimer disease. CONCLUSIONS: While there was no association between amyloid and neuroinflammation in the overall study group, neuroinflammation was associated with amyloid among the subgroup at early stages of amyloid pathology. Copyright © 2021 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology.</p

The calcium-binding protein S100P in normal and malignant human tissues

<p>Abstract</p> <p>Background</p> <p>S100P is a Ca²⁺binding protein overexpressed in a variety of cancers, and thus, has been considered a potential tumor biomarker. Very little has been studied about its normal expression and functions.</p> <p>Methods</p> <p>We examined S100P expression in normal human tissues by quantitative reverse transcription polymerase chain reaction and immunohistochemistry. S100P protein expression was also studied in a series of tumors, consisting of 74 ovarian, 11 pancreatic, 56 gastric, 57 colorectal, 89 breast and 193 prostate carcinomas using a novel anti-S100P monoclonal antibody.</p> <p>Results</p> <p>Among the normal tissues, the highest S100P mRNA levels were observed in the placenta and esophagus. Moderate signals were also detected in the stomach, duodenum, large intestine, prostate and leukocytes. At the protein level, the highest reactions for S100P were seen in the placenta and stomach. Immunostaining of tumor specimens showed that S100P protein is expressed in all the tumor categories included in the study, being most prevalent in gastric tumors.</p> <p>Conclusion</p> <p>Based on our observations, S100P is widely expressed in both normal and malignant tissues. The high expression in some tumors suggests that it may represent a potential target molecule for future diagnostic and therapeutic applications.</p

PPM - Passive Placement for Many

Introduction: In 1998, the pension system was changed and the so called PPM system was introduced. The PPM system is partly fund-based, partly distribution-based. There are approximately 700 different investment funds to choose between, at a maximum five for each individual. For persons who are not familiar with the financial market, the choice might be difficult. The lions’ part of the investors do not seem to have an active strategy. Are the reasons for that the complexity of the system or which factors do influence the choice between different fund strategies? Problem area: The problem area of this thesis was to clarify the following questions: Why do not more peoples entitled to the Swedish PPM system make active investments and changes between different fund options? On the individual level, which factors influence how actively placements and changes are made within the PPM system? Propose: Our mission was to investigate the reasons for the lack of activity of the individuals entitled to the benefits of the Swedish PPM system. Methods: Our main approach was to quantitatively analyse the relations and to draw conclusion based on the questionnaire answers from a cohort of 100 respondents living in the city of Stockholm. The results were statistically analysed by using the computerised program SPSS. Results: The lack of knowledge, experience and interest seem to be the factors most positively associated with the lack of initiative to actively make use of the possibilities offered by the PPM system. Conclusions: The quantitative analysis performed indicates that a large majority of the Swedish population lack the qualities needed to manage the money obtainable within the Premium Pension System. It is evident that there are individual differences depending on educational level, income, age and risk attitude.Inledning: 1998 reformerades det svenska pensionssystemet och det så kallade premiepensionssystemet infördes, som dels är fondbaserat, dels distributionsbaserat. I systemet finns omkring 700 olika fonder emellan spararen kan välja, maximalt fem. För en individ som inte är hemma på den finansiella marknaden kan valet av fonder vara ett svårt beslut. Är systemets komplexitet orsaken till att merparten av spararna inte har en aktiv strategi för sin premiepension eller vilka faktorer är det som styr detta? Problemområde: De problemområden som avsågs klargöras genom denna studie var: Varför väljer inte fler svenska premiepensionssparare att aktivt placera och byta fonder? Vilka individuella faktorer styr hur aktiv individen är i sitt placerande av premiepensionsmedlen? Syfte: Syftet var att undersöka orsakerna till varför merparten av de svenska premiepensionsspararna inte agerar aktivt i valet av fonder samt vilka individuella faktorer som är nav betydelse för graden av aktivitet i premiepensionssparandet. Metodval: En kvantitativ ansats har huvudsakligen använts i denna uppsats då syftet var att uppdaga samband och dra slutsatser baserat på enkätsvar från en stor urvalsgrupp. Urvalet utgjordes av ett bekvämlighetsurval med 100 deltagande respondenter i stockholmsregionen. Det empiriska materialet bearbetades statistiskt i dataprogrammet SPSS. Resultat: De faktorer författarna funnit haft störst inverkan för aktiviteten i premiepensionsvalet är kunskap, erfarenhet samt intresse. Avsaknaden av dessa antas vara vad som resulterar i många av de svenska premiepensionsspararnas passivitet i premiepensionsvalet. Slutsatser: Den kvantitativa undersökning som genomförts indikerar att stora delar av den svenska befolkningen saknar de egenskaper som krävs för förvaltande av premiepensionen. Det framgår även att det föreligger skillnader beroende på bland annat individens utbildning, inkomst, ålder, kön samt åsikter kring risktagande

Assessing landscape experiences as a cultural ecosystem service in public infrastructure projects : From concept to practice

Undesirable landscape changes, especially from large infrastructure projects, may give rise to large welfare losses due to degraded landscape experiences. These losses are largely unaccounted for in Nordic countries’ planning processes. There is a need to develop practical methods of including people’s preferences and the value of landscape impacts in policy assessments and decision-making. The project aims to explore how the ecosystem service approach and values of landscape experiences can be better incorporated in actual cases. The project developed a two-step approach to assess, value and incorporate landscape impacts and tested these in case studies based on EIA documentation. We found that despite the lack of information generated in the EIAs, the step-wise method significantly improved upon evidence and conclusions of how people are impacted due to landscape changes