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Article ; Online: FHACT: the FISH-based HPV-associated cancer test that detects nonrandom gain at four genomic loci as biomarkers of disease progression.

Houldsworth, Jane

2014 Volume 14, Issue 8, Page(s) 921–934

Abstract: Despite implementation of screening programs for human papillomavirus (HPV)-associated cancers, in particular cervical, scientific studies continue to uncover viral and host biomarkers that could serve to further optimize the detection of individuals ... ...

Abstract	Despite implementation of screening programs for human papillomavirus (HPV)-associated cancers, in particular cervical, scientific studies continue to uncover viral and host biomarkers that could serve to further optimize the detection of individuals with underlying or at risk for developing precancer or cancer. Nonrandom host somatic chromosomal alterations are frequently shared across HPV-associated cancers, but with varying frequencies, potentially with functional roles. At least for 3q26 gain, there is firm preliminary evidence to support that this genomic alteration can serve as a biomarker of disease progression of cervical cancer. In the current review, the FISH-based HPV-associated cancer test is described that enables detection of genomic imbalance at four loci (3q26, 5p15, 20q13, centromere 7) in a single hybridization on a cell-by-cell basis in cytology specimens. When implemented as a secondary screening assay, the FISH-based HPV-associated cancer test could assist in the detection of clinically relevant HPV-associated disease and help guide patient management decisions.
MeSH term(s)	Chromosome Aberrations ; Cost-Benefit Analysis ; Disease Progression ; Early Detection of Cancer ; Female ; Genetic Loci ; Genomics ; Humans ; In Situ Hybridization, Fluorescence/economics ; In Situ Hybridization, Fluorescence/methods ; In Situ Hybridization, Fluorescence/standards ; Papillomaviridae/genetics ; Papillomavirus Infections/complications ; Sensitivity and Specificity ; Uterine Cervical Neoplasms/diagnosis ; Uterine Cervical Neoplasms/etiology
Language	English
Publishing date	2014-11
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2112530-2
ISSN	1744-8352 ; 1473-7159
ISSN (online)	1744-8352
ISSN	1473-7159
DOI	10.1586/14737159.2014.965685
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Article ; Online: Primary hemangioblastoma of the kidney with molecular analyses by next generation sequencing: a case report and review of the literature.

Wang, Xintong / Haines, George K / Mehrotra, Meenakshi / Houldsworth, Jane / Si, Qiusheng

Diagnostic pathology

2022 Volume 17, Issue 1, Page(s) 34

Abstract: Background: Hemangioblastoma is an indolent mesenchymal tumor most frequently occurring in the central nervous system (CNS), but can also arise extraneuraxially, as part of Von Hippel-Lindau (VHL) disease or in sporadic tumors. Extraneuraxial ... ...

Abstract	Background: Hemangioblastoma is an indolent mesenchymal tumor most frequently occurring in the central nervous system (CNS), but can also arise extraneuraxially, as part of Von Hippel-Lindau (VHL) disease or in sporadic tumors. Extraneuraxial hemangioblastomas occur outside the central nervous system. It includes tumors arising from the nervous paraneuraxial structures and visceral organs. Sporadic hemangioblastoma of the kidney, a rare subset of extraneuraxial hemangioblastomas, is an under-recognized renal neoplasm. There have been only 25 cases described to date in the English language literature. We report herein one additional sporadic tumor in a patient without VHL disease. Case presentation: A 61 year old male presenting with gross hematuria was found to have a 3.5 cm renal mass at the lateral mid to lower pole of the left kidney on computed tomography urogram. The patient underwent a partial nephrectomy for the mass. Pathological examination showed a well-circumscribed non-encapsulated tumor composed of sheets of large polygonal cells traversed by a rich vascular network. The tumor cells showed clear to eosinophilic cytoplasm and overall bland nuclei. The diagnosis of hemangioblastoma was confirmed by positive immunostaining for alpha-inhibin, S100, neuron-specific enolase, and PAX8. No significant gene mutations, including VHL gene and copy number changes were detected in the tumor using next generation sequencing supporting the diagnosis of sporadic renal hemangioblastoma. Conclusion: Sporadic renal hemangioblastoma is a rare subset of extraneuraxial hemangioblastomas. We report one such tumor in a patient without clinical or molecular evidence of VHL disease. The literature was reviewed to better understand the clinical, radiological, pathological, and molecular features of this neoplasm. The majority of renal hemangioblastomas showed positive immunostaining for PAX8, which supports the idea that the immunoprofiles of extraneuraxial hemangioblastomas can vary depending on sites of origin. Diagnosis of renal hemangioblastoma is challenging because of its rarity and overlapping microscopic and immunophenotypic features with other renal tumors, including clear cell renal cell carcinoma. In some cases, molecular or genetic studies may be necessary to obtain an accurate diagnosis. Since renal hemangioblastoma is clinically benign, recognition of this pathological entity is important to avoid unnecessary over-treatment.
MeSH term(s)	Hemangioblastoma/diagnosis ; Hemangioblastoma/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Kidney/pathology ; Kidney Neoplasms/chemistry ; Kidney Neoplasms/diagnosis ; Kidney Neoplasms/genetics ; Male ; Middle Aged ; von Hippel-Lindau Disease/complications ; von Hippel-Lindau Disease/diagnosis ; von Hippel-Lindau Disease/genetics
Language	English
Publishing date	2022-02-27
Publishing country	England
Document type	Case Reports ; Journal Article ; Review
ZDB-ID	2210518-9
ISSN	1746-1596 ; 1746-1596
ISSN (online)	1746-1596
ISSN	1746-1596
DOI	10.1186/s13000-022-01213-8
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Article ; Online: Platinum Sensitivity in

Doroshow, Deborah Blythe / Wei, Wei / Mehrotra, Meenakshi / Sia, Daniella / Eder, Joseph Paul / Bindra, Ranjit / Houldsworth, Jane / LoRusso, Patricia / Walther, Zenta

Cancer investigation

2023 Volume 41, Issue 7, Page(s) 646–655

Abstract: Preclinical data suggest ... ...

Abstract	Preclinical data suggest that
MeSH term(s)	Humans ; Retrospective Studies ; Bile Duct Neoplasms/drug therapy ; Bile Duct Neoplasms/genetics ; Bile Duct Neoplasms/pathology ; Isocitrate Dehydrogenase/genetics ; Cholangiocarcinoma/drug therapy ; Cholangiocarcinoma/genetics ; Cholangiocarcinoma/pathology ; Mutation ; Bile Ducts, Intrahepatic/pathology
Chemical Substances	Isocitrate Dehydrogenase (EC 1.1.1.41) ; IDH1 protein, human (EC 1.1.1.42.)
Language	English
Publishing date	2023-08-17
Publishing country	England
Document type	Multicenter Study ; Journal Article
ZDB-ID	604942-4
ISSN	1532-4192 ; 0735-7907
ISSN (online)	1532-4192
ISSN	0735-7907
DOI	10.1080/07357907.2023.2242957
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Article ; Online: Host Nuclear Genome Copy Number Variations Identify High-Risk Anal Precancers in People Living with HIV.

Mutetwa, Tinaye / Liu, Yuxin / Silvera, Richard / Evans, Michelle / Yurich, Michael / Tripodi, Joseph / Leonard, Issa / Houldsworth, Jane / Gümüş, Zeynep / Bowcock, Anne M / Sigel, Keith / Gaisa, Michael / Polak, Paz

Journal of acquired immune deficiency syndromes (1999)

2024

Abstract: Background: People living with HIV (PLWH) have substantially increased incidence of anal precancer and cancer. There are very little data regarding genomic disturbances in anal precancers among PLWH. Here, we identified specific chromosomal variants in ... ...

Abstract	Background: People living with HIV (PLWH) have substantially increased incidence of anal precancer and cancer. There are very little data regarding genomic disturbances in anal precancers among PLWH. Here, we identified specific chromosomal variants in anal squamous intraepithelial lesions. Methods: We collected 63 anal biopsy specimens (27 low-grade intraepithelial lesions [LSIL] and 36 high-grade intraepithelial lesions [HSIL]) from PLWH obtained as part of anal cancer screening in our NYC-based health system. Data on patient demographics, anal cytological and high-risk human papillomavirus (HR-HPV) diagnoses were collected. Specimens were tested for a panel of chromosomal alterations associated with HPV-induced oncogenesis using Fluorescence In-Situ Hybridization (FISH) and analyses compared the associations of these alterations with clinical characteristics. Results: Gains of 3q26, 5p15, 20q13 and cen7 were detected in 42%, 31%, 31%, and 19% of HSIL compared to 7%, 0%, 4%, and 0% of LSIL, respectively. Where at least one abnormality was seen, 89% had a 3q26 gain. In lesions with 5p15 gains, 20q13 gains co-occurred in 91% of cases, while cen7 gain only co-occurred with the other three alterations. Sensitivity and specificity of any alteration to predict HSIL was 47% (95% CI: 30-65%) and 93% (95% CI: 76%-99%) respectively. Conclusions: Genomic alterations seen in HPV-associated cancers may help distinguish anal LSIL from HSIL. 3q26 amplification may be an early component of anal carcinogenesis, preceding 5p16, 20q13 and/or chr7. Impact: We share insights on potential genomic biomarkers for discriminating high-risk anal precancers.
Language	English
Publishing date	2024-04-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	645053-2
ISSN	1944-7884 ; 1077-9450 ; 0897-5965 ; 0894-9255 ; 1525-4135
ISSN (online)	1944-7884 ; 1077-9450
ISSN	0897-5965 ; 0894-9255 ; 1525-4135
DOI	10.1097/QAI.0000000000003409
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Zs.A 2442: Show issues

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Article: A 24 year-old patient with no prior history of endometriosis diagnosed with bilateral ovarian endometrioid adenocarcinoma arising in endometriosis.

Tomita, Shannon / Mehrotra, Meenakshi / Chaoul, Jessica / Houldsworth, Jane / Kolev, Valentin / Kalir, Tamara

Gynecologic oncology reports

2021 Volume 36, Page(s) 100718

Language	English
Publishing date	2021-02-02
Publishing country	Netherlands
Document type	Case Reports
ZDB-ID	2818505-5
ISSN	2352-5789
ISSN	2352-5789
DOI	10.1016/j.gore.2021.100718
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Article ; Online: Solitary Peutz-Jeghers Type Polyp of Jejunum with Gastric Fundic and Antral Gland Lining Mucosa: A Case Report and Review of Literature.

Liu, Bella Lingjia / Zhou, Huifang / Risech, Martina / Ky, Alex / Houldsworth, Jane / Ward, Stephen C

International journal of surgical pathology

2021 Volume 30, Issue 5, Page(s) 539–542

Abstract: Solitary Peutz-Jeghers type polyps are characterized by a hamartomatous polyp of the gastrointestinal (GI) tract in a patient without mucocutaneous pigmentation, family history of Peutz-Jeghers syndrome, ... ...

Abstract	Solitary Peutz-Jeghers type polyps are characterized by a hamartomatous polyp of the gastrointestinal (GI) tract in a patient without mucocutaneous pigmentation, family history of Peutz-Jeghers syndrome, or
MeSH term(s)	Adult ; Gastric Mucosa/pathology ; Hamartoma/pathology ; Humans ; Intestinal Polyps/diagnosis ; Intestinal Polyps/pathology ; Intestinal Polyps/surgery ; Jejunum/pathology ; Male ; Peutz-Jeghers Syndrome/complications ; Peutz-Jeghers Syndrome/diagnosis ; Peutz-Jeghers Syndrome/genetics
Language	English
Publishing date	2021-12-27
Publishing country	United States
Document type	Case Reports ; Journal Article ; Review
ZDB-ID	1336393-1
ISSN	1940-2465 ; 1066-8969
ISSN (online)	1940-2465
ISSN	1066-8969
DOI	10.1177/10668969211067760
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Zs.A 4500: Show issues

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Article ; Online: KRAS G12C-Mutant Non-Small Cell Lung Cancer: Biology, Developmental Therapeutics, and Molecular Testing.

Veluswamy, Rajwanth / Mack, Philip C / Houldsworth, Jane / Elkhouly, Ehab / Hirsch, Fred R

The Journal of molecular diagnostics : JMD

2021 Volume 23, Issue 5, Page(s) 507–520

Abstract: Mutation in the gene that encodes Kirsten rat sarcoma viral oncogene homolog (KRAS) is the most common oncogenic driver in advanced non-small cell lung cancer, occurring in approximately 30% of lung adenocarcinomas. Over 80% of oncogenic KRAS mutations ... ...

Abstract	Mutation in the gene that encodes Kirsten rat sarcoma viral oncogene homolog (KRAS) is the most common oncogenic driver in advanced non-small cell lung cancer, occurring in approximately 30% of lung adenocarcinomas. Over 80% of oncogenic KRAS mutations occur at codon 12, where the glycine residue is substituted by different amino acids, leading to genomic heterogeneity of KRas-mutant tumors. The KRAS glycine-to-cysteine mutation (G12C) composes approximately 44% of KRAS mutations in non-small cell lung cancer, with mutant KRas
MeSH term(s)	Antineoplastic Agents/therapeutic use ; Carcinoma, Non-Small-Cell Lung/diagnosis ; Carcinoma, Non-Small-Cell Lung/drug therapy ; Carcinoma, Non-Small-Cell Lung/pathology ; Diagnostic Techniques and Procedures ; Humans ; Lung Neoplasms/diagnosis ; Lung Neoplasms/drug therapy ; Lung Neoplasms/pathology ; Molecular Targeted Therapy ; Mutation ; Proto-Oncogene Proteins p21(ras)/antagonists & inhibitors ; Proto-Oncogene Proteins p21(ras)/genetics
Chemical Substances	Antineoplastic Agents ; KRAS protein, human ; Proto-Oncogene Proteins p21(ras) (EC 3.6.5.2)
Language	English
Publishing date	2021-02-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2000060-1
ISSN	1943-7811 ; 1525-1578
ISSN (online)	1943-7811
ISSN	1525-1578
DOI	10.1016/j.jmoldx.2021.02.002
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Article: Assessing Genomic Copy Number Alterations as Best Practice for Renal Cell Neoplasia: An Evidence-Based Review from the Cancer Genomics Consortium Workgroup.

Liu, Yajuan J / Houldsworth, Jane / Emmadi, Rajyasree / Dyer, Lisa / Wolff, Daynna J

Cancer genetics

2020 Volume 244, Page(s) 40–54

Abstract: Renal cell neoplasia are heterogeneous with diverse histology, genetic alterations, and clinical behavior that are diagnosed mostly on morphologic features. The Renal Cell Neoplasia Workgroup of the Cancer Genomics Consortium systematically evaluated ... ...

Abstract	Renal cell neoplasia are heterogeneous with diverse histology, genetic alterations, and clinical behavior that are diagnosed mostly on morphologic features. The Renal Cell Neoplasia Workgroup of the Cancer Genomics Consortium systematically evaluated peer-reviewed literature on genomic studies of renal cell carcinoma (RCC), including clear cell RCC, papillary RCC, chromophobe RCC, and the translocation RCC involving TFE3, TFEB and MITF rearrangements, as well as benign oncocytoma, which together comprise about 95% of all renal cell neoplasia. The Workgroup curated recurrent copy number alterations (CNAs), copy-neutral loss-of-heterozygosity (cnLOH), rearrangements, and mutations, found in each subtype and assigned clinical relevance according to established criteria. In clear cell RCC, loss of 3p has a disease-initiating role and most likely also in progression with mutations detected in VHL and other genes mapped to this arm, and loss of 9p and/or 14q has well-substantiated prognostic utility. Gain of chromosomes 7 and 17 are hallmark CNAs of papillary RCC, but patterns of other CNAs as detected by chromosomal microarray analysis (CMA) afford sub-classification into Type 1 and 2 with prognostic value, and for further sub-stratification of Type 2. Inherent chromosome loss in chromophobe RCC as detected by CMA is useful for distinguishing the eosinophilic variant from benign oncocytoma which in contrast exhibits few CNAs or rearranged CCND1, but share mitochondrial DNA mutations. In morphologically atypical RCCs, rearrangement of TFE3 and TFEB should be considered in the differential diagnosis, portending an aggressive RCC subtype. Overall, this evidence-based review provides a validated role for assessment of CNAs in renal cell neoplasia in the clinical setting to assist in renal cell neoplasm diagnosis and sub-classification within subtypes that is integral to the management of patients, from small incidentally found renal masses to larger surgically resected specimens, and simultaneously identify the presence of key alterations portending outcome in malignant RCC subtypes.
MeSH term(s)	Carcinoma, Renal Cell/genetics ; Carcinoma, Renal Cell/pathology ; DNA Copy Number Variations ; Diagnosis, Differential ; Evidence-Based Medicine ; Genomics/methods ; Humans ; Kidney Neoplasms/genetics ; Kidney Neoplasms/pathology ; Prognosis
Language	English
Publishing date	2020-05-01
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2599227-2
ISSN	2210-7762
ISSN	2210-7762
DOI	10.1016/j.cancergen.2020.04.004
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Article ; Online: Polypoid Undifferentiated Carcinoma With Osteoclast-like Giant Cells Arising in the Distal Common Bile Duct: A Rare Case Report.

Liao, Xiaoyan / Houldsworth, Jane / Luo, Jean / Harpaz, Noam / Zhu, Hongfa

Anticancer research

2018 Volume 39, Issue 1, Page(s) 437–441

Abstract: Background: Undifferentiated carcinoma with osteoclast-like giant cells (UC-OGC) in distal common bile duct (CBD) is a rare entity.: Case report: This case report describes a 45-year-old male with a history of a choledochal cyst status post partial ... ...

Abstract	Background: Undifferentiated carcinoma with osteoclast-like giant cells (UC-OGC) in distal common bile duct (CBD) is a rare entity. Case report: This case report describes a 45-year-old male with a history of a choledochal cyst status post partial excision and cholecystectomy who presented with a mass in the remaining distal/intrapancreatic common bile duct. It was initially mistaken for post-surgery hematoma; however, the rapid growth raised concern for malignancy, and prompted a pancreaticoduodenectomy (Whipple) procedure. Macroscopic examination revealed a 5.5 cm polypoid mass grossly confined in the lumen of the distal CBD. Histology was consistent with UC-OGC, with minimal invasion into the polyp stalk and adjacent CBD wall. Immunohistochemistry demonstrated co-expression of CK7 and p40, normal/wild-type p53, and retained SMAD4 expression in tumor cells. Next-generation sequencing detected mutations at p.Q61H (c.183A>C) of KRAS and p.E545K (c.1633G>A) of PIK3CA, keeping in line with similarity to conventional cholangiocarcinoma. The patient remained disease-free after two years of follow-up without chemotherapy. Conclusion: To our knowledge, this is the first case report of UC-OGC presented as a polypoid mass in the distal CBD. It highlights the complex dynamism and controversial pathogenesis of this unique entity, which should be made aware to avoid diagnostic pitfalls.
MeSH term(s)	Carcinoma/physiopathology ; Carcinoma/surgery ; Choledochal Cyst/pathology ; Choledochal Cyst/physiopathology ; Choledochal Cyst/surgery ; Common Bile Duct/physiopathology ; Common Bile Duct/surgery ; Female ; Gene Expression Regulation, Neoplastic ; Giant Cells/pathology ; Humans ; Middle Aged ; Neoplasm Proteins/genetics ; Osteoclasts/pathology ; Pancreaticoduodenectomy ; Polyps/pathology ; Polyps/surgery
Chemical Substances	Neoplasm Proteins
Language	English
Publishing date	2018-12-11
Publishing country	Greece
Document type	Case Reports ; Journal Article
ZDB-ID	604549-2
ISSN	1791-7530 ; 0250-7005
ISSN (online)	1791-7530
ISSN	0250-7005
DOI	10.21873/anticanres.13131
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Article ; Online: Urothelial carcinoma of the graft kidney with molecular analyses: a rare case report.

Chen, Joyce M / Kenneth Haines, G / Lam, William / Reddy, Asha / Mehrotra, Meenakshi / Houldsworth, Jane / Si, Qiusheng

Diagnostic pathology

2021 Volume 16, Issue 1, Page(s) 53

Abstract: Background: Malignancy after transplantation is a leading cause of death among kidney transplant recipients. However, donor-derived malignancies are rare. We report a case of a high grade papillary urothelial carcinoma arising in a transplanted kidney.!# ...

Abstract	Background: Malignancy after transplantation is a leading cause of death among kidney transplant recipients. However, donor-derived malignancies are rare. We report a case of a high grade papillary urothelial carcinoma arising in a transplanted kidney. Case presentation: A 62-year-old female who received a kidney transplantation more than 30 years ago presented with urinary tract infection, acute renal failure, and hydronephrosis of the transplant kidney. Anterograde nephrostogram showed a large filling defect in the lower pole of the transplant kidney and in the proximal 3-4 cm of the ureter. A biopsy from the renal pelvic mass showed a high grade urothelial carcinoma. She underwent an anterior exenteration, resection of both transplant and native kidneys and bilateral pelvic lymph node dissection. Pathologic examination showed a high grade papillary urothelial carcinoma which appeared to arise in the pelvis of the graft kidney, involve the graft ureter and native urinary bladder. The tumor had metastasized to one left obturator lymph node but spared the two native kidneys and ureters. Short tandem repeat (STR) analysis confirmed the tumor to be of donor origin. Next-generation sequencing identified amplification of TERT and loss of CDKN2A/CDKN2B in the primary tumor. Conclusion: While it is known that transplant recipients have an increased risk of urothelial carcinoma compared to the general population, the lack of the well-documented risk factors, such as older age at transplantation, BK polyomavirus infection, and prolonged post-transplantation history and dissemination of the tumor in this case shed light on the de novo tumorigenesis of the graft kidney within the host microenvironment. Amplification of Telomerase reverse transcriptase (TERT) and loss of cyclin dependent kinase inhibitor 2A/2B (CDKN2A/CDKN2B) detected in the tumor by next gene sequencing suggests that they may play an important role in this case.
MeSH term(s)	Biomarkers, Tumor/deficiency ; Biomarkers, Tumor/genetics ; Carcinoma, Papillary/etiology ; Carcinoma, Papillary/genetics ; Carcinoma, Papillary/secondary ; Carcinoma, Papillary/therapy ; Cyclin-Dependent Kinase Inhibitor p15/deficiency ; Cyclin-Dependent Kinase Inhibitor p15/genetics ; Cyclin-Dependent Kinase Inhibitor p16/deficiency ; Cyclin-Dependent Kinase Inhibitor p16/genetics ; Female ; Gene Amplification ; Genetic Predisposition to Disease ; Humans ; Kidney Neoplasms/etiology ; Kidney Neoplasms/genetics ; Kidney Neoplasms/pathology ; Kidney Neoplasms/therapy ; Kidney Transplantation/adverse effects ; Middle Aged ; Neoplasm Grading ; Phenotype ; Telomerase/genetics ; Treatment Outcome ; Urothelium/pathology
Chemical Substances	Biomarkers, Tumor ; CDKN2A protein, human ; CDKN2B protein, human ; Cyclin-Dependent Kinase Inhibitor p15 ; Cyclin-Dependent Kinase Inhibitor p16 ; TERT protein, human (EC 2.7.7.49) ; Telomerase (EC 2.7.7.49)
Language	English
Publishing date	2021-06-14
Publishing country	England
Document type	Case Reports
ISSN	1746-1596
ISSN (online)	1746-1596
DOI	10.1186/s13000-021-01109-z
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