Genes, Chromosomes and Cancer

An update of molecular findings in uterine tumor resembling ovarian sex cord tumor and GREB1‐rearranged uterine sarcoma with variable sex‐cord differentiation

AbstractUterine tumor resembling ovarian sex cord tumor (UTROSCT) is a uterine mesenchymal tumor defined histologically by showing sex cord‐like growth patterns, such as sheets, nests, trabeculae, cords, or tubules, with/without Sertoli‐like or Leydig‐like components, and immunohistochemically by exhibiting variable sex cord markers in addition to epithelial, myogenic, and sex hormone markers. Recent years have seen the emergence in UTROSCT of novel fusion genes that involve key genes in sex hormone pathways, including ESR1 and GREB1 as the 5′ partner, and (co)activator oncogenes, particularly NCOA1‐3, as the 3′ partner. While the identification of similar fusions in the majority of cases serves as a strong argument for UTROSCT to be a distinct entity, there is no denying significant clinicopathologic heterogeneity within the disease spectrum, which might to some extent correlate with the different fusion types. The current review gives a summary of the recently identified fusions in UTROSCT, along with their possible clinicopathologic relevance. Also discussed are unsolved issues including the relationship between UTROSCT and so‐called GREB1‐rearranged uterine sarcoma as well as other uterine mesenchymal tumors harboring similar fusions.

Uterine Myxoid Mesenchymal Tumor With a Novel SS18::VEZF1 Gene Fusion, Lacking Worrisome Histological Features

ABSTRACTWe report a uterine myxoid mesenchymal tumor with a novel SS18::VEZF1 gene fusion. The current lesion was identified in a 53‐year‐old woman who presented with symptomatic “fibroids” showing accelerated growth and heterogeneous morphology on radiologic assessment. Microscopic examination revealed a well‐demarcated neoplasm, and the tumor exhibited alternating hypocellular/hyalinized and hypercellular areas, composed of a monomorphic proliferation of spindle, ovoid, and epithelioid cells arranged in sheets. These cells were embedded within either a hyalinized collagenous stroma or abundant myxoid stroma. Tumor cells were frequently located around blood vessels and exhibited amphophilic or eosinophilic cytoplasm and elongated or ovoid‐shaped nuclei with coarsely clumped chromatin. No mitoses, pleomorphism, or necrosis was identified. Immunohistochemically, the tumor was positive for CD10, CD34, TLE1, estrogen, and progesterone receptors. It was negative for h‐caldesmon, desmin, smooth muscle actin, smoothelin, myosin, cyclin D1, S100, ALK, EMA, panTRK, and SS18‐SSX. Targeted RNA sequencing revealed an SS18::VEZF1 gene fusion (breakpoint: exon 9–exon 2), which was confirmed by FISH (SS18). In conclusion, RNA sequencing was useful in identifying the fusion event, thereby excluding potential mimics with uncommon morphology or ambiguous immunophenotype.

Malignant Peripheral Nerve Sheath Tumor (MPNST) With Smooth Muscle Differentiation of the Uterus—A Case Report With Emphasis on Diagnostic Pitfalls and Value of DNA Methylation Analysis

ABSTRACTWith no more than two dozen cases reported in the literature, malignant peripheral nerve sheath tumor (MPNST) is a rare primary mesenchymal neoplasm arising in the female genital tract. Most cases occurred in middle‐aged adults with high grade histology, unfavorable clinical outcome, and no history of neurofibromatosis type 1. Its extreme rarity in this site no doubt poses a diagnostic challenge during routine clinical practice. In the following, we report an additional case of uterine MPNST occurring in a 49‐year‐old Chinese woman, which was initially misdiagnosed as a leiomyosarcoma. The primary tumor showed two distinctive components—a high‐grade poorly differentiated component with markedly pleomorphic spindle cells arranged in a peritheliomatous pattern; and a leiomyosarcoma‐like (LMS‐like) component with tumor cells displaying obvious myoid differentiation. The patient suffered a recurrence less than 2 years later with the recurrent tumor demonstrating similar features to the high‐grade component of the primary tumor. The patient eventually succumbed 46 months later after developing another recurrence despite receiving targeted therapy and chemotherapy. On retrospective molecular analysis, no clinically relevant fusion transcript was detected on RNA sequencing. Interestingly instead, DNA methylation analysis showed the tumor clustered with the “MPNST” group in the German Cancer Research Center (DKFZ) sarcoma classifier. The tumor was also found to have EED gene homozygous deletion, multiple copy number alterations and loss of H3K27me3 expression in both high‐grade and LMS‐like components. Combining histology with all the ancillary tests results, the diagnosis was most consistent with MPNST. Our case highlights the diagnostic pitfalls for MPNST arising in the female genital tract and the potential clinical utility of DNA methylation analysis.

Clonal origin and genomic diversity in Lynch syndrome‐associated endometrial cancer with multiple synchronous tumors: Identification of the pathogenicity of MLH1 p.L582H

AbstractLynch syndrome‐associated endometrial cancer patients often present multiple synchronous tumors and this assessment can affect treatment strategies. We present a case of a 27‐year‐old woman with tumors in the uterine corpus, cervix, and ovaries who was diagnosed with endometrial cancer and exhibited cervical invasion and ovarian metastasis. Her family history suggested Lynch syndrome, and genetic testing identified a variant of uncertain significance, MLH1 p.L582H. We conducted immunohistochemical staining, microsatellite instability analysis, and Sanger sequencing for Lynch syndrome‐associated cancers in three generations of the family and identified consistent MLH1 loss. Whole‐exome sequencing for the corpus, cervical, and ovarian tumors of the proband identified a copy‐neutral loss of heterozygosity (LOH) occurring at the MLH1 position in all tumors. This indicated that the germline variant and the copy‐neutral LOH led to biallelic loss of MLH1 and was the cause of cancer initiation. All tumors shared a portion of somatic mutations with high mutant allele frequencies, suggesting a common clonal origin. There were no mutations shared only between the cervix and ovary samples. The profiles of mutant allele frequencies shared between the corpus and cervix or ovary indicated that two different subclones originating from the corpus independently metastasized to the cervix or ovary. Additionally, all tumors presented unique mutations in endometrial cancer‐associated genes such as ARID1A and PIK3CA. In conclusion, we demonstrated clonal origin and genomic diversity in a Lynch syndrome‐associated endometrial cancer, suggesting the importance of evaluating multiple sites in Lynch syndrome patients with synchronous tumors.

Delineating genotype and parent‐of‐origin effect on the phenotype in MSH6‐associated Lynch syndrome

AbstractBackgroundThis study investigates the potential influence of genotype and parent‐of‐origin effects (POE) on the clinical manifestations of Lynch syndrome (LS) within families carrying (likely) disease‐causing MSH6 germline variants.Patients and MethodsA cohort of 1615 MSH6 variant carriers (310 LS families) was analyzed. Participants were categorized based on RNA expression and parental inheritance of the variant. Hazard ratios (HRs) were calculated using weighted Cox regression, considering external information to address ascertainment bias. The findings were cross‐validated using the Prospective Lynch Syndrome Database (PLSD) for endometrial cancer (EC).ResultsNo significant association was observed between genotype and colorectal cancer (CRC) risk (HR = 1.06, 95% confidence interval [CI]: 0.77–1.46). Patients lacking expected RNA expression exhibited a reduced risk of EC (Reference Cohort 1: HR = 0.68, 95% CI: 0.43–1.03; Reference Cohort 2: HR = 0.63, 95% CI: 0.46–0.87). However, these results could not be confirmed in the PLSD. Moreover, no association was found between POE and CRC risk (HR = 0.78, 95% CI: 0.52–1.17) or EC risk (Reference Cohort 1: HR = 0.93, 95% CI: 0.65–1.33; Reference Cohort 2: HR = 0.8, 95% CI: 0.64–1.19).Discussion and ConclusionNo evidence of POE was detected in MSH6 families. While RNA expression may be linked to varying risks of EC, further investigation is required to explore this observation.

Paratesticular Endometrial Stromal Sarcoma‐Like Sarcoma With EPC1‐SUZ12 Fusion

ABSTRACTEndometrial stromal sarcoma‐like (ESS‐like) sarcomas have rarely been described in male patients and represent a subset of “Mullerian analog” tumors. These ESS‐like sarcomas most commonly arise in the paratesticular or pelvic regions and often harbor the same signature molecular fusion events that are typical of endometrial stromal sarcoma (ESS) of the uterine corpus. Here we report and describe an ESS‐like sarcoma of the paratesticular soft tissue in an 85‐year‐old man with an EPC1‐SUZ12 t(10;17)(p11.22;q12) fusion. This fusion event has been described in a high‐grade uterine ESS one time previously where it displayed an aggressive clinical course. However, our patient showed no evidence of metastatic disease prior to surgery or in a short follow‐up period after resection.

COL1A1::PDGFB fusion uterine sarcoma with a TERT promoter mutation

AbstractCOL1A1::PDGFB fusion uterine sarcoma is a rare uterine mesenchymal tumor with some clinicopathological features that overlap with those of soft tissue dermatofibrosarcoma protuberans. However, the varied clinicopathologic and genetic characteristics have not been fully revealed, which may be a potential pitfall for diagnosis. Here, we present a case of COL1A1::PDGFB fusion‐positive uterine sarcoma in a 49‐years‐old female. Histologically, the tumor from the initial marginal excision predominantly exhibited high‐grade fibrosarcomatous and myxofibrosarcoma‐like appearances, while a low‐grade focal area displaying storiform growth was identified in the residual tumor after subsequently extended resection. Immunohistochemically, the high‐grade components mainly exhibited focal positivity for CD34 and mutated‐type p53 immunoreactivity, whereas the low‐grade component showed diffuse positivity for CD34 and wild‐type p53 staining. The COL1A1::PDGFB fusion was confirmed by fluorescence in situ hybridization and next‐generation sequencing. In addition, the TERT‐124 C > T mutation was further identified in this lesion's fibrosarcomatous and classic storiform components. To the best of our knowledge, this is the first described case of COL1A1::PDGFB fusion uterine sarcoma with a TERT promoter mutation, which might be a novel genetic finding associated with tumorigenesis of this rare tumor.

Single nucleotide polymorphism array and cytogenetic analyses of ovarian teratomas in children

AbstractTeratomas are the most common tumors in the ovary during childhood. Previous studies suggested that they may be derived from germ cells at any developmental stage from premeiotic oogonia through meiotic oocytes to post‐meiotic ova. The majority of mature teratomas reveal normal karyotypes and immature teratomas show higher frequency of chromosomal abnormalities. We analyzed fresh tissue samples from 25 primary ovarian teratomas and three extraovarian deposits using whole genome single nucleotide polymorphism (SNP) array and karyotype. SNP array detected five patterns of copy neutral loss of heterozygosity (CN‐LOH): failure of meiosis I (type I) in 12 tumors, failure of meiosis II (type II) in six tumors, endoreduplication of a haploid ovum (type III) in two tumors, premeiotic error (type IV) in four tumors, and both meiotic I and meiotic II errors in one tumor (type V). Three tumors with type I error had a single chromosome showing meiotic II error, and two tumors with type II error had a single chromosome showing premature sister‐chromatid separation in meiosis I. Lack of recombination in multiple chromosomes in meiosis I were common, chromosomes 17, 7, 8, 21, and 22 were most commonly involved. Abnormal karyotypes were observed in four teratomas including +3, del(3q), +7, +8, +12, and i(18q). The extraovarian deposits revealed the same CN‐LOH pattern as the primary teratoma. In summary, SNP array reveals the origin of ovarian teratoma and we propose a new mechanism that consecutive meiotic I and II errors occur frequently in ovarian teratomas.

PARP inhibitors in ovarian cancer: An overview of the practice‐changing trials

AbstractPoly (ADP‐ribose) polymerase (PARP) inhibitors have transformed the management of recurrent ovarian cancer in patients with BRCA‐mutations and beyond. Olaparib was the first PARP inhibitor to gain approval as maintenance therapy for patients with newly diagnosed, advanced BRCA‐mutated ovarian cancer establishing a new standard of care. At the end of 2020, as a result of the SOLO1, PRIMA, and PAOLA‐1 phase III trials, we are now in an era where three maintenance PARP inhibitor strategies have FDA and European Medicines Agency approval in the first‐line setting. In this review, we provide an overview of the key PARP inhibitor trials that have changed clinical practice, discuss directing therapy according to biomarker status (BRCA and homologous recombination deficiency) and future strategies in ovarian cancer and other gynecological malignancies.

Genomic profile analysis of leiomyomas with bizarre nuclei and fumarate hydratase deficient leiomyomas: Strengths, weaknesses, and limitations of array‐CGH interpretation

AbstractA close relationship has been demonstrated between genomic complexity and clinical outcome in uterine smooth muscle tumors. We studied the genomic profiles by array‐CGH of 28 fumarate hydratase deficient leiomyomas and 37 leiomyomas with bizarre nuclei (LMBN) from 64 patients. Follow‐up was available for 46 patients (from three to 249 months, mean 87.3 months). All patients were alive without evidence of disease. For 51 array‐CGH interpretable tumors the mean Genomic Index (GI) was 16.4 (median: 9.8; from 1 to 57.8), significantly lower than the mean GI in LMS (mean GI 51.8, p < 0.001). We described three groups: (1) a group with FH deletion (24/58) with low GI (mean GI: 11 vs. 22,4, p = 0.02), (2) a group with TP53 deletion (17/58) with higher GI (22.4 vs. 11 p = 0.02), and (3) a group without genomic events on FH or TP53 genes (17/58) (mean GI:18.3; from 1 to 57.8). Because none of these tumors recurred and none showed morphological features of LMS we concluded that GI at the cut‐off of 10 was not applicable in these subtypes of LM. By integration of all those findings, a GI <10 in LMBN remains a valuable argument for benignity. Conversely, in LMBN a GI >10 or alteration in tumor suppressor genes, should not alone warrant a diagnosis of malignancy. Nine tumors were tested with Nanocind CINSARC® signature and all were classified in low risk of recurrence. We propose, based on our observations, a diagnostic approach of these challenging lesions.

Single‐nucleotide polymorphism array and fluorescence in situ hybridization analysis to decode the cytogenetic profile of atypical partial hydatidiform moles diagnosed by short tandem repeat polymorphism analysis

AbstractAccurate diagnosis of partial hydatidiform moles (PHMs) is crucial for improving outcomes of gestational trophoblastic neoplasia. The use of short tandem repeat (STR) polymorphism analysis to distinguish between PHM and hydropic abortuses is instrumental; however, its diagnostic power has not been comprehensively assessed. Herein, we evaluated the diagnostic efficacy of STR in differentiating between PHM and hydropic abortus, thus providing an opportunity for early measurement of human chorionic gonadotropin for PHMs. We reviewed charts of STR polymorphism analysis performed on fresh villous specimens and patient blood samples using a commercial kit for 16 loci. The genetic classification of 79 PHMs was confirmed. STR was reliable in differentiating PHMs when at least 15 loci were available. Typically, PHMs are characterized by their triploidy, including two paternal and one maternal haploid contribution. In our sample, seven PHMs lacked the three‐allelic loci, requiring fluorescence in situ hybridization (FISH) analysis to investigate imbalanced biparental conceptus and single‐nucleotide polymorphism array analysis to reveal cytogenetic details. Of these PHMs, two, three, and one were identified as androgenetic/biparental mosaics (diploids), monospermic diandric monogynic triploids, and a typical dispermic diandric monogynic triploid, respectively. The remaining case was monospermic origin, but its ploidy details could not be available. Therefore, STR differentiated PHM from a biparental diploid abortus in most cases. However, PHM diagnosis may be compromised when STR is used as the sole method for cases displaying distinct cytogenetic patterns lacking the three‐allelic loci, including androgenetic/biparental mosaicism. Therefore, FISH should be considered to confirm the diagnosis.

Expanding the molecular spectrum of gene fusions in endometrial stromal sarcoma: Novel subunits of the chromatin remodeling complexes PRC2 and NuA4/TIP60 as alternative fusion partners

AbstractEndometrial stromal sarcomas (ESS) are morphologically and molecularly heterogeneous. We report novel gene fusions (EPC1::EED, EPC1::EZH2, ING3::PHF1) identified by targeted RNA sequencing in five cases. The ING3::PHF1‐fusion positive ESS presented in a 58‐year‐old female as extrauterine mesocolonic, ovarian masses, and displayed large, monomorphic ovoid‐to‐epithelioid cells arranged in solid sheets. The patient remained alive with disease 13 months after surgery. The three ESS with EPC1::EED occurred in the uterine corpus in patients with a median age of 58 years (range 27–62 years). One tumor showed a uniform epithelioid nested morphology, while the other two were composed of monomorphic spindle cells in fascicles with elevated mitotic figures, focal tumor cell necrosis, and lymphovascular invasion. At a median follow‐up of 20 months, two patients developed local recurrence, including one with concomitant distant metastasis, while one patient remained free of disease. All three patients were alive at the last follow‐up. The EPC1::EZH2‐fusion positive ESS presented in a 52‐year‐old female in the uterus, and displayed uniform spindled cells arranged in short fascicles, with focally elevated mitotic activity but without necrosis. The patient remained free of disease 3 months after surgery. All cases were diffusely positive for CD10; four diffusely express estrogen and progesterone receptors. Our study expands the molecular spectrum of EPC1 and PHF1‐related gene fusions in ESS to include additional novel subunits of the PRC2 and/or NuA4/TIP60 complexes. These cases displayed a monomorphic epithelioid or spindled phenotype, spanning low‐grade and high‐grade cytomorphology, all expressing CD10 and commonly ER and PR, and are prone to local and/or distant spread.

A novel WWTR1::AFF2 fusion in an intra‐abdominal soft tissue sarcoma with associated endometriosis

AbstractApplication of molecular testing in clinical practice has led to significant advances in the classification of soft tissue sarcomas. Despite remarkable progress, there are still challenging cases that remain unclassified. In this study, we present an unusual spindle cell sarcoma arising in the abdominal cavity of a 37‐year‐old female. An extensive panel of immunostains was nonspecific for a line of differentiation and the tumor was subjected to targeted RNA sequencing for further classification. The findings showed a novel WWTR1::AFF2 fusion, which was further confirmed by break‐apart FISH analysis for WWTR1 gene rearrangement. The tumor was attached to the wall of sigmoid colon and showed a highly cellular proliferation of plump spindle to epithelioid cells arranged in intersecting fascicles. Areas of extensive endometriosis were identified adjacent to the tumor. The immunoprofile was significant for reactivity with desmin, calponin, WT‐1, ER, and PR, while negative for CD10, SMA, caldesmon, pan‐keratin, ALK, CD117, and S100. The patient is alive and well after 11 months of follow‐up. The exact histogenesis of this sarcoma remains unclear, however, the presence of adjacent endometriosis and coexpression of WT1/ER/PR raises the possibility of an unusual endometrioid stromal sarcoma, occurring outside the GYN tract. Additional cases are needed to establish the recurrent potential of this fusion event and to better define its pathogenesis and clinical behavior.

NTRK and other recently described kinase fusion positive uterine sarcomas: A review of a group of rare neoplasms

AbstractThe landscape of uterine sarcomas has greatly expanded in recent years to include neoplasms with recurrent gene fusions, such as BCOR and YWHAE translocated high‐grade endometrial stromal sarcomas. Sophisticated molecular techniques have also resulted in the description of “new” entities associated with recurrent kinase fusions involving NTRK and RET as well as COL1A1‐PDGFB rearranged uterine sarcomas. These rare neoplasms will be discussed in this review, highlighting that some of the underlying molecular events are clinically actionable and potentially susceptible to targeted therapy. While relatively few of these neoplasms have been described to date, likely being previously lumped under the spectrum of undifferentiated uterine sarcoma, the number of cases will expand in the future given their recognition and the increasing availability of molecular testing. These neoplasms have overlapping morphology (often with a “fibrosarcoma‐like” appearance) and immunohistochemical features, and are characterized by variable clinical outcomes. Although immunohistochemistry may assist in some cases, a definitive subclassification requires confirmatory molecular studies. As these molecular assays may not be routinely available in most laboratories, referral to reference centers may be needed. In order to assist the pathologist, we suggest a diagnostic algorithm for routine practice when dealing with a malignant or potentially malignant uterine spindle cell neoplasm.

A novel MBTD1‐PHF1 gene fusion in endometrial stromal sarcoma: A case report and literature review

AbstractThe classification of endometrial stromal sarcoma (ESS) has been refined and aided by the discovery of various recurrent gene translocations. Low‐grade ESS (LG‐ESS) is most commonly characterized by JAZF1‐SUZ12 fusions followed by rearrangements involving PHD finger protein‐1 (PHF1) and multiple fusion partners, including JAZF1, EPC1, EPC2, and MEAF6. In the present study, integrating anchored polymerase chain reaction and paired‐end next‐generation ribonucleic acid sequencing, we identified the presence of a novel malignant brain tumor domain‐containing 1 (MBTD1)‐PHF1 gene fusion in a case of LG‐ESS. MBTD1 belongs to the Polycomb gene group, and its fusion with PHF1 is predicted to mediate tumorigenesis through aberrant transcriptional repression. Histology and immunohistochemical studies demonstrated conventional morphology for LG‐ESS and clinical follow‐up showed no progression of disease after 6 months. These findings help expand the current knowledge on the spectrum of gene rearrangements in the diagnosis of ESS.

Macroscopic Monozygotic Androgenetic/Biparental Mosaicism: Molecular Characterization and Clinical Implications

ABSTRACTHydatidiform moles represent abnormal pregnancies characterized by trophoblastic hyperproliferation. However, accurate diagnosis of partial hydatidiform moles (PHM) remains challenging. We present a rare case of a monozygotic androgenetic/biparental mosaic in a 26‐year‐old primigravida. The patient was referred to our institution for a suspected PHM, and ultrasonography revealed a nonviable embryo‐like structure alongside villous formations with focal cystic changes. Pathological examination of the evacuated tissue revealed the coexistence of normal and hydropic villi. Histological assessment with p57KIP2 immunohistochemistry initially suggested PHM; however, some cytotrophoblasts and villous stromal cells were negative for p57KIP2 immunoreactivity. Therefore, we conducted short tandem repeat analysis separately for normal villous tissue and cystic villous lesions to elucidate the genetic origin of this unusual presentation. The normal villous portion exhibited biparental diploidy, whereas the cystic villous portion exhibited androgenetic monospermic patterns. Comparisons across all 16 loci revealed concordance between the paternal alleles of biparental diploid villi and the androgenic molar alleles, indicating a single sperm origin. SNP array analysis with B allele frequency plotting confirmed these findings at the whole‐genome level; normal villi showed biparental diploid patterns, whereas cystic villi displayed uniparental disomic patterns. These results demonstrate that both components originated from a monozygotic conception rather than from dizygotic twinning. Therefore, we propose a clinical category based on the sequelae of endoduplication and the formation of a tripolar spindle apparatus through the first meiotic division, encompassing macroscopic androgenetic/biparental mosaicism, twin pregnancy with a hydatidiform mole, microscopic androgenetic/biparental mosaicism, and confined placental mosaicism. Given the presence of androgenetic elements and our institutional experience with gestational trophoblastic neoplasia development in a similar case, we recommend that such cases be managed according to complete hydatidiform mole surveillance protocols. This case highlights the diagnostic challenges posed by monozygotic androgenetic/biparental mosaic mechanisms and emphasizes the importance of molecular genetic analysis for the accurate diagnosis and appropriate clinical management of atypical hydatidiform moles.

High‐Grade Uterine Sarcoma: First Report of a MEIS2::FOXO4 Fusion

ABSTRACTUterine sarcomas are uncommon mesenchymal neoplasms ranging from low‐ to high‐grade or undifferentiated. High‐grade sarcomas are characterized by various morphologic, immunohistochemical, and molecular alterations. Here, we report the first description of a patient with uterine sarcoma with a MEIS2::FOXO4 fusion. This tumor showed alternating fascicular and diffuse architecture with a prominent nodular growth displaying striking hyalinization and less prominent myxoid background admixed with more cellular internodular areas. The neoplastic cells ranged from spindled to stellate to epithelioid and exhibited variable cytologic atypia and mitotic activity. Immunohistochemical stains showed diffuse expression of smooth muscle actin, preserved expression of PTEN, ATRX, and Rb1, wild‐type expression of p53, weak expression of PLAG1, multifocal expression of MDM2, and no reactivity for desmin. RNA sequencing detected a MEIS2::FOXO4 gene fusion with breakpoints at MEIS2 exon 6 and FOXO4 exon 2. Although this gene fusion has been described in other soft tissue neoplasms, it has not been previously reported in uterine sarcomas and highlights the significance of performing molecular analysis in uterine mesenchymal tumors with unusual morphology and/or immunophenotype.

Analysis of 11 candidate genes in 849 adult patients with suspected hereditary cancer predisposition

AbstractHereditary predisposition to cancer concerns between 5% and 10% of cancers. The main genes involved in the most frequent syndromes (hereditary breast and ovarian cancer syndrome, hereditary nonpolyposis colorectal cancer syndrome) were identified in the 1990s. Exploration of their functional pathways then identified novel genes for hereditary predisposition to cancer, and candidate genes whose involvement remains unclear. To determine the contribution of truncating variants in 11 candidate genes (BARD1, FAM175A, FANCM, MLH3, MRE11A, PMS1, RAD50, RAD51, RAD51B, RINT1, and XRCC2) to cancer predisposition in a population of interest, panel sequencing was performed in 849 patients with a suspected hereditary predisposition to cancer for whom a diagnostic panel of 38 genes identified no causal mutation. Sixteen truncating variants were found in FANCM (n = 7), RINT1 (n = 4), RAD50 (n = 2), BARD1, PMS1, and RAD51B. FANCM (adjusted P‐value: .03) and RINT1 (adjusted P‐value: .04) were significantly associated with hereditary breast and ovarian cancer. However, further studies are required to determinate the risk of cancer, including the segregation of the variants in the families of our cases. No mutation was identified in RAD51, MRE11A, FAM175A, XRCC2, or MLH3. The involvement of these genes in the hereditary predisposition to cancer cannot be ruled out, although if it exists it is rare or does not seem to involve truncating variants.

The landscape of BRCA1 and BRCA2 large rearrangements in an international cohort of over 20 000 ovarian tumors identified using next‐generation sequencing

AbstractBackgroundApproximately half of ovarian tumors have defects within the homologous recombination repair pathway. Tumors carrying pathogenic variants (PVs) in BRCA1/BRCA2 are more likely to respond to poly‐ADP ribose polymerase (PARP) inhibitor treatment. Large rearrangements (LRs) are a challenging class of variants to identify and characterize in tumor specimens and may therefore be underreported. This study describes the prevalence of pathogenic BRCA1/BRCA2 LRs in ovarian tumors and discusses the importance of their identification using a comprehensive testing strategy.MethodsSequencing and LR analyses of BRCA1/BRCA2 were conducted in 20 692 ovarian tumors received between March 18, 2016 and February 14, 2023 for MyChoice CDx testing. MyChoice CDx uses NGS dosage analysis to detect LRs in BRCA1/BRCA2 genes using dense tiling throughout the coding regions and limited flanking regions.ResultsOf the 2217 PVs detected, 6.3% (N = 140) were LRs. Overall, 0.67% of tumors analyzed carried a pathogenic LR. The majority of detected LRs were deletions (89.3%), followed by complex LRs (5.7%), duplications (4.3%), and retroelement insertions (0.7%). Notably, 25% of detected LRs encompassed a single or partial single exon. This study identified 84 unique LRs, 2 samples each carried 2 unique LRs in the same gene. We identified 17 LRs that occurred in multiple samples, some of which were specific to certain ancestries. Several cases presented here illustrate the intricacies involved in characterizing LRs, particularly when multiple events occur within the same gene.ConclusionsOver 6% of PVs detected in the ovarian tumors analyzed were LRs. It is imperative for laboratories to utilize testing methodologies that will accurately detect LRs at a single exon resolution to optimize the identification of patients who may benefit from PARP inhibitor treatment.

Segregation, immunohistochemical, molecular and functional analyses classify a novel missense variant in fumarate hydratase (FH) as pathogenic

AbstractHereditary leiomyomatosis and renal cell cancer (HLRCC) is an autosomal dominant cancer predisposition syndrome characterized by cutaneous leiomyomas, uterine leiomyomas, and aggressive renal cancer. Germline variants in the fumarate hydratase (FH) gene predispose to HLRCC. Identifying germline pathogenic FH variants enables lifetime renal cancer screening and genetic testing for family members. In this report, we present a FH missense variant (c.1039T>C (p.S347P)), initially classified as a variant of uncertain significance. Clinical assessment, histopathological findings, molecular genetic studies, and enzymatic activity studies support the re‐classification of the FH c.1039T>C variant to “pathogenic” based on ACMG/AMP criteria. Further insights into pathological recognition of FH‐deficient renal cancer are discussed and should be recognized. This study has shown how (a) detailed multi‐disciplinary analyses of a single variant can reclassify rare missense variants in FH and (b) careful pathological review of renal cancers is obligatory when HLRCC is suspected.

Update on SWI/SNF‐related gynecologic mesenchymal neoplasms: SMARCA4‐deficient uterine sarcoma and SMARCB1‐deficient vulvar neoplasms

AbstractOur knowledge regarding the role of genes encoding the chromatin remodeling switch/sucrose non‐fermenting (SWI/SNF) complex in the initiation and progression of gynecologic malignancies continues to evolve. This review focuses on gynecologic tumors in which the sole or primary genetic alteration is in SMARCA4 or SMARCB1, two members of the SWI/SNF chromatin remodeling complex. In this review, we present a brief overview of the classical example of such tumors, ovarian small cell carcinoma of hypercalcemic type, and then a detailed review and update of SMARCB1‐deficient and SMARCA4‐deficient tumors of the uterus and vulva.

Ovarian germ cell tumor/mastocytosis with KIT mutation: A unique clinicopathological entity

AbstractMost tumors are sporadic and originated from somatic mutations. Some rare germline mutations cause familial tumors, often involving multiple tissues or organs. Tumors from somatic mosaicism during embryonic development are extremely rare. We describe here a pediatric patient who developed both an ovarian germ cell tumor and systemic mastocytosis. Targeted DNA next‐generation sequencing analysis revealed similar genomic changes including the same KIT D816V mutation in both tissues, suggesting a common progenitor cancer cell. The KIT mutated cells are likely from early embryonic development during germ cell migration. A literature search found additional eight similar cases. These diseases are characterized by pediatric‐onset, all‐female, neoplastic proliferation in both gonad and bone marrow, and a common oncogenic cause, that is, KIT mutation, constituting a clinically and genetically homogenous disease entity. Importantly, the association of germ cell tumors with hematopoietic neoplasms suggests that the primordial germ cells are the primitive hematopoietic stem cells, a much‐debated and unsettled question.

Amplification of ERBB2 (HER2) in embryonal rhabdomyosarcoma: A potential treatment target in rare cases?

AbstractThe ERBB2 gene encodes a receptor tyrosine kinase also known as HER2. The gene is amplified and overexpressed in one‐fifth of breast carcinomas; patients with such tumors benefit from targeted treatment with trastuzumab or other drugs blocking the receptor. In addition, ERBB2 has been shown to be amplified and/or overexpressed in a variety of other malignancies. Notably, both alveolar and embryonal rhabdomyosarcoma (RMS), especially in children, often show increased expression of ERBB2. Although high‐level amplification of the gene has not been described in RMS, its frequent expression at the cell surface of RMS cells has been exploited for chimeric antigen receptor T‐cell (CAR T)‐based treatment strategies. We here describe two cases of pediatric, fusion‐negative embryonal RMS with high‐level amplification of the ERBB2 gene. One patient is currently treated with conventional chemotherapy for a recently detected standard risk RMS, whereas the other patient died from metastatic disease. Both tumors displayed focal amplicons (210 and 274 Kb, respectively) in chromosome band 17q12, with proximal and distal borders corresponding to those typically seen in breast cancer. In both tumors, the ERBB2 amplicon correlated with high expression at the RNA and protein levels. Thus, breast cancer‐like ERBB2 amplification is a very rare, but recurrent feature of pediatric RMS, and should be exploited as an alternative treatment target.

Combined assessment of 3q26 amplification and promoter methylation in patients with high grade cervical lesions show age specific differences

AbstractA considerable proportion of high grade cervical intraepithelial lesions (CIN2/3) are known to resolve on their own especially among young women. However, since reliable prognostic markers are still lacking, the diagnosis “CIN3” is still an indication for surgery which may result in overtreatment. It is conceivable that a combination of different, ideally independent molecular markers may provide more reliable results. In the present cross‐sectional study two established triage markers, 3q26 amplification and a methylation signature, were evaluated in an age‐dependent manner. The patient cohort comprised 60 patients with histologically confirmed CIN2/3 in two equally sized age groups (<30 years, ≥30 years). Cervical scrapes were analyzed by interphase fluorescence in situ hybridization for 3q26 amplification and methylation specific PCR (GynTect®) for six different genome regions. Both assays showed a significantly different pattern of test outcome independent of age (P = .001). Moreover, the combination of both assays differed significantly for double positive and double negative cases when comparing the two age groups: In patients <30 years there were clearly less cases with positive methylation signature and amplification of 3q26 as in women ≥30 years (23% vs 63%, Bonferroni adjusted P = .016). Of particular interest is the finding that double negative results were exclusive for the young age group (0% vs 27%, Bonferroni adjusted P = .020). Since regression of CIN2/3 characteristically occurs among young women it is tempting to speculate that a double negative test result could be prognostic for regression of CIN2/3. This will have to be investigated further in a prospective longitudinal intervention study.