3′RNA Sequencing Accurately Classifies Formalin-Fixed Paraffin-Embedded Uterine Leiomyomas

Mehine, Miika; Khamaiseh, Sara; Ahvenainen, Terhi; Heikkinen, Tuomas; Äyräväinen, Anna; Pakarinen, Päivi; Härkki, Päivi; Pasanen, Annukka; Bützow, Ralf; Vahteristo, Pia

doi:10.3390/cancers12123839

Cited by 10 publications

(13 citation statements)

References 39 publications

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“…We acknowledge that the archival age of our samples affects their RNA quality and therefore reduces the power to detect differential gene expression. We, however, used a method successfully applied on archival samples in several recent studies to be able to study our unique cohort with extended follow-up times [34,35]. Therefore, we believe that our results are still valid and in line with previous findings; a subset of AGCT patients gain secondary mutations, but they do not explain the diverse clinical behavior of this disease, and the FOXL2 C402G mutation remains the main driver of this disease [36].…”

Section: Discussionsupporting

confidence: 73%

Analysis of Non-Relapsed and Relapsed Adult Type Granulosa Cell Tumors Suggests Stable Transcriptomes during Tumor Progression

Andersson

Haltia

Färkkilä

et al. 2022

CIMB

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Adult-type granulosa cell tumor (AGCT) is a rare ovarian malignancy characterized by slow growth and hormonal activity. The prognosis of AGCT is generally favorable, but one-third of patients with low-stage disease experience a late relapse, and over half of them die of AGCT. To identify markers that would distinguish patients at risk for relapse, we performed Lexogen QuantSeq 3′ mRNA sequencing on formalin-fixed paraffin-embedded, archival AGCT tissue samples tested positive for the pathognomonic Forkhead Box L2 (FOXL2) mutation. We compared the transcriptomic profiles of 14 non-relapsed archival primary AGCTs (follow-up time 17–26 years after diagnosis) with 13 relapsed primary AGCTs (follow-up time 1.7–18 years) and eight relapsed tumors (follow-up time 2.8–18.9 years). Non-relapsed and relapsed primary AGCTs had similar transcriptomic profiles. In relapsed tumors three genes were differentially expressed: plasmalemma vesicle associated protein (PLVAP) was upregulated (p = 0.01), whereas argininosuccinate synthase 1 (ASS1) (p = 0.01) and perilipin 4 (PLIN4) (p = 0.02) were downregulated. PLVAP upregulation was validated using tissue microarray RNA in situ hybridization. In our patient cohort with extremely long follow-up, we observed similar gene expression patterns in both primary AGCT groups, suggesting that relapse is not driven by transcriptomic changes. These results reinforce earlier findings that molecular markers do not predict AGCT behavior or risk of relapse.

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Section: Discussionsupporting

confidence: 73%

Analysis of Non-Relapsed and Relapsed Adult Type Granulosa Cell Tumors Suggests Stable Transcriptomes during Tumor Progression

Andersson

Haltia

Färkkilä

et al. 2022

CIMB

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“…To explore the gene expression pattern of AKR1B10hi leiomyomas, we performed 3′RNA sequencing with thirteen AKR1B10hi leiomyomas and seven corresponding myometrium samples. We analyzed these samples together with a previously published dataset of 44 leiomyomas [ 16 ]. Principal component analysis revealed that the AKR1B10hi samples clustered separately from the other three established leiomyoma subtypes, but close to leiomyomas of the FH subtype (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…3′RNA sequencing was performed with 13 leiomyomas and 7 corresponding myometrium samples as previously described [ 16 ]. These 20 samples were analyzed together with a previously published dataset of 44 leiomyomas (13 leiomyomas with a MED12 mutation, 15 with significant HMGA2 overexpression, and 16 with FH- deficiency) and 5 myometrium samples [ 16 ].…”

Section: Methodsmentioning

confidence: 99%

“…We and others have shown that overexpression of AKR1B10 can function as a biomarker for FH-deficiency and NRF2 activation in uterine leiomyomas and renal cell cancer [ 9 ]. Indeed, we recently analyzed publicly available leiomyoma data and reclassified two leiomyomas as FH-deficient partly based on the expression of AKR1B10 [ 16 ]. Using FH-deficient tumors derived from HLRCC patients and sporadic leiomyomas with biallelic loss of FH , we recently showed that AKR1B10 immunohistochemistry can act as a biomarker on protein-level as well [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

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A novel uterine leiomyoma subtype exhibits NRF2 activation and mutations in genes associated with neddylation of the Cullin 3-RING E3 ligase

et al. 2022

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Uterine leiomyomas, or fibroids, are the most common tumors in women of reproductive age. Uterine leiomyomas can be classified into at least three main molecular subtypes according to mutations affecting MED12, HMGA2, or FH. FH-deficient leiomyomas are characterized by activation of the NRF2 pathway, including upregulation of the NRF2 target gene AKR1B10. Here, we have identified a novel leiomyoma subtype showing AKR1B10 expression but no alterations in FH or other known driver genes. Whole-exome and whole-genome sequencing revealed biallelic mutations in key genes involved in neddylation of the Cullin 3-RING E3 ligase, including UBE2M, NEDD8, CUL3, and NAE1. 3′RNA sequencing confirmed a distinct molecular subtype with activation of the NRF2 pathway. Most tumors displayed cellular histopathology, perivascular hypercellularity, and characteristics typically seen in FH-deficient leiomyomas. These results suggest a novel leiomyoma subtype that is characterized by distinct morphological features, genetic alterations disrupting neddylation of the Cullin 3-RING E3 ligase, and oncogenic NRF2 activation. They also present defective neddylation as a novel mechanism leading to aberrant NRF2 signaling. Molecular characterization of uterine leiomyomas provides novel opportunities for targeted treatment options.

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“…However these techniques have not emerged yet as optimal for prognostic determination in ACC. The 3' RNA sequencing recently emerged as an opportunity to study transcriptome signatures from FFPE material, as reported for several tumor types [37][38][39] . This technique was applied to samples from operated patients.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome in paraffin samples for the diagnosis and prognosis of adrenocortical carcinoma

Jouinot

Lippert²,

Sibony

et al. 2022

European Journal of Endocrinology

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Design: Molecular classification is important for diagnosis and prognosis of adrenocortical tumors (ACT). Transcriptome profiles separate adrenocortical adenomas “C2” from carcinomas, and identify two groups of carcinomas “C1A” and “C1B”, of poor and better prognosis respectively. However, many ACT cannot be profiled because of improper or absent freezing procedure, a mandatory requirement so far. The main aim was to determine transcriptome profiles on formalin-fixed paraffin-embedded (FFPE) samples, using the new 3’-end RNA-sequencing technology. A secondary aim was to demonstrate the ability of this technique to explore large FFPE archives, by focusing on the rare oncocytic ACT variants. Methods: We included 131 ACT: a training cohort from Cochin hospital and an independent validation cohort from Wuerzburg hospital. The 3’ transcriptome was generated from FFPE samples using QuantSeq (Lexogen) and NextSeq500 (Illumina). Results: In the training cohort, unsupervised clustering identified 3 groups: “C1A” aggressive carcinomas (N=28, 29%), “C1B” more indolent carcinomas (N=28, 29%), and “C2” adenomas (N=39, 41%). The prognostic value of FFPE transcriptome was confirmed in the validation cohort (5-year OS: 26% in “C1A” (N=26) and 100% in “C1B” (N=10), p=0.003). FFPE transcriptome was an independent prognostic factor in multivariable model including tumor stage and Ki-67 (OS HR 7.5, p=0.01). Oncocytic ACT (N=19) did not form any specific cluster. Oncocytic carcinomas (N=6) and oncocytic ACT of uncertain malignant potential (N=4) were all in “C1B”. Conclusions: The 3’ RNA-sequencing represents a convenient solution for determining ACT molecular class from FFPE samples. This technique should facilitate routine use and large retrospective studies.

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3′RNA Sequencing Accurately Classifies Formalin-Fixed Paraffin-Embedded Uterine Leiomyomas

Cited by 10 publications

References 39 publications

Analysis of Non-Relapsed and Relapsed Adult Type Granulosa Cell Tumors Suggests Stable Transcriptomes during Tumor Progression

Analysis of Non-Relapsed and Relapsed Adult Type Granulosa Cell Tumors Suggests Stable Transcriptomes during Tumor Progression

A novel uterine leiomyoma subtype exhibits NRF2 activation and mutations in genes associated with neddylation of the Cullin 3-RING E3 ligase

Transcriptome in paraffin samples for the diagnosis and prognosis of adrenocortical carcinoma

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