Aberrant DNA methylation patterns in malignant cells allow insight into tumor evolution and development and can be used for disease classification. Here, we describe the genome-wide DNA methylation ...signatures of NPM-ALK-positive (ALK+) and NPM-ALK-negative (ALK−) anaplastic large-cell lymphoma (ALCL). We find that ALK+ and ALK− ALCL share common DNA methylation changes for genes involved in T cell differentiation and immune response, including TCR and CTLA-4, without an ALK-specific impact on tumor DNA methylation in gene promoters. Furthermore, we uncover a close relationship between global ALCL DNA methylation patterns and those in distinct thymic developmental stages and observe tumor-specific DNA hypomethylation in regulatory regions that are enriched for conserved transcription factor binding motifs such as AP1. Our results indicate similarity between ALCL tumor cells and thymic T cell subsets and a direct relationship between ALCL oncogenic signaling and DNA methylation through transcription factor induction and occupancy.
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•ALK+ and ALK− ALCL show highly similar genome-wide DNA methylation•ALCL tumor cells closely resemble undifferentiated thymic progenitor cells•Differentially methylated genes are implicated in major T cell functions•Oncogenic transcription factors produce epigenetic footprints
Using genome-wide DNA methylation profiling, Hassler et al. find that DNA methylation patterns in ALCL are related to specific thymic stages in T cell development, suggesting a thymic progenitor cell of origin. Moreover, comparison of ALK+ ALCL to ALK− ALCL indicates no ALK-specific impact on DNA methylation.
Aside from genetic alterations, epigenetic tumor-specific changes including DNA methylation are measurable in ctDNA and CTCs and their potential as diagnostic, prognostic and predictive epigenetic ...biomarkers has been demonstrated in a large number of studies although only few have made it into clinical practice, yet 7. Next, the 92 analyzed marker candidates were used for prediction model calculations by inputting PMR values for class prediction models based on different algorithms including Diagonal Linear Discriminant Analysis (DLDA), Nearest Centroid Predictor, k-Nearest-Neighbor Predictor, Support Vector Machines and (Bayesian) Compound Covariate Predictor (BCCP/CCP). Together, these data suggest that mCRPC can be identified based on methylation signatures with high accuracy, whereas organ-confined PCa with Gleason scores lower than 9 cannot be differentiated from benign samples, most likely due to limited amounts of ctDNA, which was also described in other studies analyzing DNA methylation in localized PCa patients using digital droplet PCR 11, 12. When performing fragment analysis of a subset of benign, localized PCa and mCRPC plasma samples (n=20 per group), we observed a significant shift of the mean cfDNA fragment size from 175 bp in benign and localized PCa (range 168 - 183bp) to 168 bp in mCRPC (range 145 – 179 bp) samples (Figure S2I). ...our markers might be suitable to identify high risk patients, who have already developed micrometastases, which cannot be detected by regular computed tomography (CT).
To detect uterine cancer, simpler and more specific index tests are needed to triage women with abnormal uterine bleeding to a reference histology test. We aimed to compare the performance of ...conventional index imaging tests with the novel WID-qEC DNA methylation test in terms of detecting the presence or absence of uterine cancers in women with abnormal uterine bleeding.
EPI-SURE was a prospective, observational study that invited all women aged 45 years and older with abnormal uterine bleeding attending a tertiary gynaecological diagnostic referral centre at University College London Hospital (London, UK) to participate. Women meeting these inclusion criteria who consented to participate were included. Pregnant women and those with previous hysterectomy were excluded. A cervicovaginal sample for the WID-qEC test was obtained before standard assessment using index imaging tests (ie, ultrasound) and, where applicable, reference histology (ie, biopsy, hysteroscopy, or both) was performed. Technicians performing the WID-qEC test were masked to the final clinical outcome. The result of the WID-qEC test is defined as the sum of the percentage of fully methylated reference (ΣPMR) of the ZSCAN12 and GYPC regions. Patients were followed until diagnostic resolution or until June 12, 2023. The primary outcome was to assess the real-world performance of the WID-qEC test in comparison with ultrasound with regard to the area under the receiver-operating-characteristic curve (AUC), sensitivity, specificity, and positive and negative predictive values. EPI-SURE is registered with ISRCTN (16815568).
From June 1, 2022, to Nov 24, 2022, 474 women were deemed eligible to participate. 74 did not accept the invitation to participate, and one woman withdrew after providing consent. 399 women were included in the primary analysis cohort. Based on 603 index imaging tests, 186 (47%) women were recommended for a reference histology test (ie, biopsy, hysteroscopy, or both). 12 women were diagnosed with cancer, 375 were not diagnosed with cancer, and 12 had inconclusive clinical outcomes and were considered study dropouts. 198 reference histology test procedures detected nine cases of cancer and missed two; one further cancer was directly diagnosed at hysterectomy without a previous reference test. The AUC for detection of uterine cancer based on endometrial thickness in mm was 87·2% (95% CI 71·1–100·0) versus 94·3% (84·7–100·0) based on WID-qEC (p=0·48). Endometrial thickness assessment on ultrasound scan was possible in 379 (95%) of the 399 women and a prespecified cut-off of 4·5 mm or more showed a sensitivity of 90·9% (95% CI 62·3–98·4), a specificity of 79·1% (74·5–82·9), a positive predictive value of 11·8% (6·5–20·3), and a negative predictive value of 99·6% (98·0–99·9). The WID-qEC test was possible in 390 (98%) of the 399 patients with a sensitivity of 90·9% (95% CI 62·3–98·4), a specificity of 92·1% (88·9–94·4), a positive predictive value of 25·6% (14·6–41·1), and a negative predictive value of 99·7% (98·3–99·9), when the prespecified threshold of 0·03 ΣPMR or more was applied. When a higher threshold (≥0·3 ΣPMR) was applied the specificity increased to 97·3% (95% CI 95·1–98·5) without a change in sensitivity.
The WID-qEC test delivers fast results and shows improved performance compared with a combination of imaging index tests. Triage of women with abnormal uterine bleeding using the WID-qEC test could reduce the number of women requiring histological assessments for identification of potential malignancy and specifically reduce the false positive rate.
The Eve Appeal, Land Tirol, and the European Research Council under the European Union's Horizon 2020 Research and Innovation Programme
The majority of endometrial and cervical cancers present with abnormal vaginal bleeding but only a small proportion of women suffering from vaginal bleeding actually have such a cancer. A simple, ...operator‐independent and accurate test to correctly identify women presenting with abnormal bleeding as a consequence of endometrial or cervical cancer is urgently required. We have recently developed and validated the WID‐qEC test, which assesses DNA methylation of ZSCAN12 and GYPC via real‐time PCR, to triage women with symptoms suggestive of endometrial cancer using ThinPrep‐based liquid cytology samples. Here, we investigated whether the WID‐qEC test can additionally identify women with cervical cancer. Moreover, we evaluate the test's applicability in a SurePath‐based hospital‐cohort by comparing its ability to detect endometrial and cervical cancer to cytology. In a set of 23 cervical cancer cases and 28 matched controls the receiver operating characteristic (ROC) area under the curve (AUC) is 0.99 (95% confidence interval CI: 0.97‐1.00) with a sensitivity and specificity of 100% and 92.9%, respectively. Amongst the hospital‐cohort (n = 330), the ROC AUC is 0.99 (95% CI: 0.98‐1) with a sensitivity and specificity of 100% and 82.5% for the WID‐qEC test, respectively, and 33.3% and 96.9% for cytology (considering PAP IV/V as positive). Our data suggest that the WID‐qEC test detects both endometrial and cervical cancer with high accuracy.
What's new?
While abnormal vaginal bleeding is a presenting symptom of endometrial and cervical cancers, only a small proportion of women who present with vaginal bleeding have endometrial or cervical cancer. Currently, the tests used to triage women with abnormal bleeding, such as ultrasound or cytology, are subjective and have modest accuracy. Here, the authors demonstrate that a real‐time PCR‐based test, which assesses DNA methylation at three gene regions using a cervical or vaginal sample, is able to identify 100% of women who have cervical or endometrial cancer with a high specificity (>80%), irrespective of the sample collection system.
Endometrial cancer (EC) is the most prevalent gynaecological cancer in high‐income countries and its incidence is continuing to rise sharply. Simple and objective tools to reliably detect women with ...EC are urgently needed. We recently developed and validated the DNA methylation (DNAme)‐based women's cancer risk identification—quantitative polymerase chain reaction test for endometrial cancer (WID‐qEC) test that could address this need. Here, we demonstrate that the stability of the WID‐qEC test remains consistent regardless of: (i) the cervicovaginal collection device and sample media used (Cervex brush and PreservCyt or FLOQSwab and eNAT), (ii) the collector of the specimen (gynaecologist‐ or patient‐based), and (iii) the precise sampling site (cervical, cervicovaginal and vaginal). Furthermore, we demonstrate sample stability in eNAT medium for 7 days at room temperature, greatly facilitating the implementation of the test into diagnostic laboratory workflows. When applying FLOQSwabs (Copan) in combination with the eNAT (Copan) sample collection media, the sensitivity and specificity of the WID‐qEC test to detect uterine (i.e., endometrial and cervical) cancers in gynaecologist‐taken samples was 92.9% (95% confidence interval CI = 75.0%–98.8%) and 98.6% (95% CI = 91.7%–99.9%), respectively, whilst the sensitivity and specificity in patient collected self‐samples was 75.0% (95% CI = 47.4%–91.7%) and 100.0% (95% CI = 93.9%–100.0%), respectively. Taken together these data confirm the robustness and clinical potential of the WID‐qEC test.
What's new?
Subjective diagnostic tests with modest accuracy, such as cytology or ultrasound, are currently used to assess the likelihood of uterine cancer in women with abnormal bleeding. Here, the authors show that the DNA methylation‐based women's cancer risk identification—quantitative polymerase chain reaction test for endometrial cancer (WID‐qEC) test they have previously developed has high sensitivity and specificity in detecting uterine cancers in symptomatic women irrespective of the sample collection device and medium, sample collector and precise sampling site. Furthermore, they demonstrate the compatibility of the WID‐qEC test used with the Copan sampling system with established diagnostic laboratory workflows, confirming the robustness and clinical potential of the WID‐qEC test.
Prostate cancer (PCa) is a common and fatal type of cancer in men. Metastatic PCa (mPCa) is a major factor contributing to its lethality, although the mechanisms remain poorly understood. PTEN is one ...of the most frequently deleted genes in mPCa. Here we show a frequent genomic co-deletion of PTEN and STAT3 in liquid biopsies of patients with mPCa. Loss of Stat3 in a Pten-null mouse prostate model leads to a reduction of LKB1/pAMPK with simultaneous activation of mTOR/CREB, resulting in metastatic disease. However, constitutive activation of Stat3 led to high LKB1/pAMPK levels and suppressed mTORC1/CREB pathway, preventing mPCa development. Metformin, one of the most widely prescribed therapeutics against type 2 diabetes, inhibits mTORC1 in liver and requires LKB1 to mediate glucose homeostasis. We find that metformin treatment of STAT3/AR-expressing PCa xenografts resulted in significantly reduced tumor growth accompanied by diminished mTORC1/CREB, AR and PSA levels. PCa xenografts with deletion of STAT3/AR nearly completely abrogated mTORC1/CREB inhibition mediated by metformin. Moreover, metformin treatment of PCa patients with high Gleason grade and type 2 diabetes resulted in undetectable mTORC1 levels and upregulated STAT3 expression. Furthermore, PCa patients with high CREB expression have worse clinical outcomes and a significantly increased risk of PCa relapse and metastatic recurrence. In summary, we have shown that STAT3 controls mPCa via LKB1/pAMPK/mTORC1/CREB signaling, which we have identified as a promising novel downstream target for the treatment of lethal mPCa.
Cervical screening using primary human papilloma virus (HPV) testing and cytology is being implemented in several countries. Cytology as triage for colposcopy referral suffers from several ...shortcomings. HPV testing overcomes some of these but lacks specificity in women under 30. Here, we aimed to develop and validate an automatable triage test that is highly sensitive and specific independently of age and sample heterogeneity, and predicts progression to CIN3+ in HPV+ patients.
The WID™-qCIN, assessing three regions in human genes DPP6, RALYL, and GSX1, was validated in both a diagnostic (case-control) and predictive setting (nested case-control), in a total of 761 samples. Using a predefined threshold, the sensitivity of the WID™-qCIN test was 100% and 78% to detect invasive cancer and CIN3, respectively. Sensitivity to detect CIN3+ was 65% and 83% for women < and ≥ 30 years of age. The specificity was 90%. Importantly, the WID™-qCIN test identified 52% of ≥ 30-year-old women with a cytology negative (cyt-) index sample who were diagnosed with CIN3 1-4 years after sample donation.
We identified suitable DNAme regions in an epigenome-wide discovery using HPV+ controls and CIN3+ cases and established the WID™-qCIN, a PCR-based DNAme test. The WID™-qCIN test has a high sensitivity and specificity that may outperform conventional cervical triage tests and can in an objective, cheap, and scalable fashion identify most women with and at risk of (pre-)invasive cervical cancer. However, evaluation was limited to case-control settings and future studies will assess performance and generalisability in a randomised controlled trial.
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