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  1. Article ; Online: Performance of non-formalin fixed paraffin embedded samples in hybrid capture and amplicon next-generation sequencing panels.

    Meireles, Sibele Inácio / Cruz, Mariana Vargas / de Godoy, Carla Daniele / de Testagrossa, Leonardo

    Diagnostic cytopathology

    2023  Volume 52, Issue 3, Page(s) 171–182

    Abstract: Background: Genomic profiling using next-generation sequencing (NGS) is fundamental for driving prognostic and therapy in cancer. Formalin-fixed paraffin embedded (FFPE) tissue is the widely used material, whereas non-FFPE may represent an alternative. ... ...

    Abstract Background: Genomic profiling using next-generation sequencing (NGS) is fundamental for driving prognostic and therapy in cancer. Formalin-fixed paraffin embedded (FFPE) tissue is the widely used material, whereas non-FFPE may represent an alternative. However, studies comparing the NGS performance of non-FFPE materials to FFPE are still lacking in the literature. The objective of this study was to characterize in non-FFPE preparations the nucleic acid yield and NGS performance on both a capture-based and an amplicon-based NGS platform. NGS quality metrics obtained from non-FFPE preparations were compared to FFPE.
    Methods: We analyzed the cellularity and nucleic acid yield in 111 tumors from non-FFPE preparations. In addition, comprehensive hybrid capture panel sequencing metrics obtained from DNA and RNA libraries were compared between independent non-FFPE and FFPE samples. A paired comparison between non-FFPE and FFPE samples was performed to analyze concordance in mutant allele detection using an amplicon panel.
    Results: The mean target coverage from DNA libraries was 2× higher in non-FFPE samples than in FFPE. The detection of exogenous DNA was 2.5× higher in non-FFPE than in FFPE. Conversely, a lower performance was observed in non-FFPE RNA libraries in comparison to FFPE DNA libraries with no impact in minimum standard cutoffs. The variant allele detection in non-FFPE was found to be comparable to that of FFPE tumor samples in matched samples.
    Conclusions: Non-FFPE was demonstrated to be a suitable material for DNA and RNA library preparations using a comprehensive NGS panel. This is the first study reporting library quality metrics according to the TSO500 analysis pipeline.
    MeSH term(s) Humans ; Paraffin Embedding ; Formaldehyde ; Tissue Fixation ; Neoplasms/diagnosis ; Neoplasms/genetics ; DNA/genetics ; High-Throughput Nucleotide Sequencing ; RNA
    Chemical Substances Formaldehyde (1HG84L3525) ; DNA (9007-49-2) ; RNA (63231-63-0)
    Language English
    Publishing date 2023-12-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 632710-2
    ISSN 1097-0339 ; 8755-1039
    ISSN (online) 1097-0339
    ISSN 8755-1039
    DOI 10.1002/dc.25267
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 2117: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  2. Article ; Online: GPR56 Drives Colorectal Tumor Growth and Promotes Drug Resistance through Upregulation of MDR1 Expression via a RhoA-Mediated Mechanism.

    Zhang, Sheng / Chatterjee, Treena / Godoy, Carla / Wu, Ling / Liu, Qingyun J / Carmon, Kendra S

    Molecular cancer research : MCR

    2019  Volume 17, Issue 11, Page(s) 2196–2207

    Abstract: Drug resistance continues to be a major obstacle of effective therapy for colorectal cancer, leading to tumor relapse or treatment failure. Cancer stem cells (CSC) or tumor-initiating cells are a subpopulation of tumor cells which retain the capacity for ...

    Abstract Drug resistance continues to be a major obstacle of effective therapy for colorectal cancer, leading to tumor relapse or treatment failure. Cancer stem cells (CSC) or tumor-initiating cells are a subpopulation of tumor cells which retain the capacity for self-renewal and are suggested to be implicated in drug resistance. LGR5 is highly expressed in colorectal cancer and marks CSCs that drive tumor growth and metastasis. LGR5(
    MeSH term(s) ATP Binding Cassette Transporter, Subfamily B/genetics ; ATP Binding Cassette Transporter, Subfamily B/metabolism ; Cell Line, Tumor ; Colorectal Neoplasms/drug therapy ; Colorectal Neoplasms/genetics ; Colorectal Neoplasms/pathology ; Drug Resistance, Neoplasm ; Gene Expression Regulation, Neoplastic ; Humans ; Neoplastic Stem Cells/pathology ; Receptors, G-Protein-Coupled/genetics ; Receptors, G-Protein-Coupled/metabolism ; Signal Transduction ; Up-Regulation ; rhoA GTP-Binding Protein/genetics ; rhoA GTP-Binding Protein/metabolism
    Chemical Substances ABCB1 protein, human ; ADGRG1 protein, human ; ATP Binding Cassette Transporter, Subfamily B ; Receptors, G-Protein-Coupled ; RHOA protein, human (124671-05-2) ; rhoA GTP-Binding Protein (EC 3.6.5.2)
    Language English
    Publishing date 2019-08-23
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2098788-2
    ISSN 1557-3125 ; 1541-7786
    ISSN (online) 1557-3125
    ISSN 1541-7786
    DOI 10.1158/1541-7786.MCR-19-0436
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 5744: Show issues Location:
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  3. Article ; Online: Morpholino-driven blockade of Dkk-1 in osteosarcoma inhibits bone damage and tumour expansion by multiple mechanisms.

    Pan, Simin / Cesarek, Michael / Godoy, Carla / Co, Cynthia M / Schindler, Catherine / Padilla, Kelbi / Haskell, Andrew / Barreda, Heather / Story, Christopher / Poole, Roy / Dabney, Alan / Gregory, Carl A

    British journal of cancer

    2022  Volume 127, Issue 1, Page(s) 43–55

    Abstract: Background: Osteosarcoma (OS) is the most common primary bone malignancy. Chemotherapy plays an essential role in OS treatment, potentially doubling 5-year event-free survival if tumour necrosis can be stimulated. The canonical Wnt inhibitor Dickkopf-1 ( ...

    Abstract Background: Osteosarcoma (OS) is the most common primary bone malignancy. Chemotherapy plays an essential role in OS treatment, potentially doubling 5-year event-free survival if tumour necrosis can be stimulated. The canonical Wnt inhibitor Dickkopf-1 (Dkk-1) enhances OS survival in part through upregulation of aldehyde-dehydrogenase-1A1 which neutralises reactive oxygen species originating from nutritional stress and chemotherapeutic challenge.
    Methods: A vivo morpholino (DkkMo) was employed to block the expression of Dkk-1 in OS cells. Cell mitosis, gene expression and bone destruction were measured in vitro and in vivo in the presence and absence of doxorubicin (DRB).
    Results: DkkMo reduced the expression of Dkk-1 and Aldh1a1, reduced expansion of OS tumours, preserved bone volume and architecture and stimulated tumour necrosis. This was observed in the presence or absence of DRB.
    Conclusion: These results indicate that administration of DkkMo with or without chemotherapeutics can substantially improve OS outcome with respect to tumour expansion and osteolytic corruption of bone in experimental OS model.
    MeSH term(s) Bone Neoplasms/drug therapy ; Bone Neoplasms/genetics ; Bone Neoplasms/metabolism ; Cell Line, Tumor ; Humans ; Intercellular Signaling Peptides and Proteins/genetics ; Morpholinos/genetics ; Morpholinos/pharmacology ; Necrosis ; Osteosarcoma/drug therapy ; Osteosarcoma/genetics ; Osteosarcoma/metabolism
    Chemical Substances Intercellular Signaling Peptides and Proteins ; Morpholinos
    Language English
    Publishing date 2022-03-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 80075-2
    ISSN 1532-1827 ; 0007-0920
    ISSN (online) 1532-1827
    ISSN 0007-0920
    DOI 10.1038/s41416-022-01764-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Uh III Zs.142: Show issues Location:
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  4. Article: Novel Mutations in Pilomatrixoma, CTNNB1 p.s45F, and FGFR2 p.s252L: A Report of Three Cases Diagnosed by Fine-Needle Aspiration Biopsy, with Review of the Literature.

    Mitteldorf, Cristina Aparecida Troques da Silveira / Vilela, Rafael Sarlo / Fugimori, Melissa Lissae / de Godoy, Carla Daniele / Coudry, Renata de Almeida

    Case reports in genetics

    2020  Volume 2020, Page(s) 8831006

    Abstract: Pilomatrixoma ( ...

    Abstract Pilomatrixoma (
    Language English
    Publishing date 2020-08-29
    Publishing country United States
    Document type Case Reports
    ZDB-ID 2664417-4
    ISSN 2090-6552 ; 2090-6544
    ISSN (online) 2090-6552
    ISSN 2090-6544
    DOI 10.1155/2020/8831006
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  5. Article ; Online: Preemptive pain-management program is associated with reduction of opioid prescriptions after benign minimally invasive foregut surgery.

    Kim, Min P / Godoy, Carla / Nguyen, Duc T / Meisenbach, Leonora M / Chihara, Ray / Chan, Edward Y / Graviss, Edward A

    The Journal of thoracic and cardiovascular surgery

    2019  Volume 159, Issue 2, Page(s) 734–744.e4

    Abstract: Objective: The opioid crisis is partly due to opioids prescribed after elective surgery. We sought to determine if a preemptive pain-management program would be associated with opioid-free discharge after benign foregut surgery.: Methods: A ... ...

    Abstract Objective: The opioid crisis is partly due to opioids prescribed after elective surgery. We sought to determine if a preemptive pain-management program would be associated with opioid-free discharge after benign foregut surgery.
    Methods: A retrospective case-control study of prospectively collected data was conducted at a single institution of patients who underwent elective minimally invasive benign foregut surgery. We compared the outcomes among patients who were managed with standard care (control), enhanced recovery after surgery alone, or a preemptive pain-management program with enhanced recovery after surgery.
    Results: Among 414 patients, there were significantly fewer opioid medication prescriptions at discharge (9.6% vs 85.2% vs 87%, P < .001) and fewer postoperative complications (3.2% vs 14.8% vs 15.1%, P = .004) in the preemptive pain-management group (n = 94), enhanced recovery after surgery alone (n = 81), and the control group (n = 239), respectively. Multivariable logistic regression analysis showed that the preemptive pain-management program was a factor associated with a decrease in opioid medication prescriptions at discharge (odds ratio, 0.01; 95% confidence interval, 0.01-0.03; P < .001), as well as a decrease in complications after surgery (odds ratio, 0.22; 95% confidence interval, 0.06-0.79; P = .02). Moreover, in the preemptive pain-management group, average self-reported pain level in a subset of patients at 30 days after surgery was 0.9 ± 1.4 on a 0- to 10-point pain scale.
    Conclusions: The preemptive pain-management program was associated with opioid-free discharge after minimally invasive foregut surgery. This study provides a strategy to reduce opioid prescriptions after foregut surgery and, if implemented nationally, could decrease the amount of opioids used in the community.
    MeSH term(s) Aged ; Analgesics, Opioid/administration & dosage ; Analgesics, Opioid/therapeutic use ; Case-Control Studies ; Digestive System Surgical Procedures/adverse effects ; Drug Prescriptions/statistics & numerical data ; Enhanced Recovery After Surgery ; Female ; Hernia, Hiatal/surgery ; Humans ; Male ; Middle Aged ; Minimally Invasive Surgical Procedures/adverse effects ; Pain Management/methods ; Pain, Postoperative/drug therapy ; Pain, Postoperative/prevention & control ; Retrospective Studies ; Stomach/surgery
    Chemical Substances Analgesics, Opioid
    Language English
    Publishing date 2019-07-10
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3104-5
    ISSN 1097-685X ; 0022-5223
    ISSN (online) 1097-685X
    ISSN 0022-5223
    DOI 10.1016/j.jtcvs.2019.06.056
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    Uk I Zs.104: Show issues Location:
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  6. Article ; Online: Ras gene mutation is not related to tumour invasion during rat tongue carcinogenesis induced by 4-nitroquinoline 1-oxide.

    Fracalossi, Ana C C / Comparini, Larissa / Funabashi, Karina / Godoy, Carla / Iwamura, Edna S M / Nascimento, Fábio D / Nader, Helena B / Oshima, Celina T F / Ribeiro, Daniel A

    Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology

    2011  Volume 40, Issue 4, Page(s) 325–333

    Abstract: Background: The aim of this study was to investigate whether mutations in the genes H-ras and K-ras were related to the mechanism of invasion as a result of the immunoexpression of H-Ras, Ki-67, alpha-smooth muscle actin (SMA) and vascular endothelial ... ...

    Abstract Background: The aim of this study was to investigate whether mutations in the genes H-ras and K-ras were related to the mechanism of invasion as a result of the immunoexpression of H-Ras, Ki-67, alpha-smooth muscle actin (SMA) and vascular endothelial growth factor (VEGF) during 4-nitroquinoline 1-oxide (4NQO)-induced rat tongue carcinogenesis.
    Methods: Male Wistar rats were distributed into three groups of 10 animals each and treated with 50 ppm 4NQO solution through their drinking water for 4, 12 and 20 weeks. Ten animals were used as negative control.
    Results: Although no histopathological abnormalities were induced in the epithelium after 4 weeks of carcinogen exposure, Ki-67 was overexpresssed in the 'normal' oral epithelium. In pre-neoplastic lesions at 12 weeks following carcinogen exposure, the levels of Ki-67 were increased (P < 0.05) when compared to negative control. Ki-67, alpha-SMA and VEGF were also overexpressed in squamous cell carcinomas induced after 20 weeks of treatment with 4NQO. No significant statistical differences (P > 0.05) were found in H-ras protein expression for all experimental periods evaluated that corresponded to normal oral mucosa, hyperplasia, dysplasia and squamous cell carcinomas. In the same way, no mutations in H-ras or K-ras genes were found.
    Conclusions: Our results support the idea that expression of Ki-67 plays a crucial role during malignant transformation being closely related to neoplastic conversion of the oral mucosa cells. However, it seems that mutations in the ras genes are not involved to experimental tongue carcinogenesis induced by 4NQO.
    MeSH term(s) 4-Nitroquinoline-1-oxide ; Actins/biosynthesis ; Animals ; Cell Transformation, Neoplastic/metabolism ; Genes, ras/genetics ; Ki-67 Antigen/biosynthesis ; Male ; Mutation ; Neoplasm Invasiveness/genetics ; Neoplasms, Experimental/genetics ; Neoplasms, Experimental/metabolism ; Rats ; Rats, Wistar ; Tongue Neoplasms/chemically induced ; Tongue Neoplasms/genetics ; Tongue Neoplasms/metabolism ; Vascular Endothelial Growth Factor A/biosynthesis ; ras Proteins/biosynthesis
    Chemical Substances Actins ; Ki-67 Antigen ; Vascular Endothelial Growth Factor A ; 4-Nitroquinoline-1-oxide (56-57-5) ; ras Proteins (EC 3.6.5.2)
    Language English
    Publishing date 2011-04
    Publishing country Denmark
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1021270-x
    ISSN 1600-0714 ; 0904-2512
    ISSN (online) 1600-0714
    ISSN 0904-2512
    DOI 10.1111/j.1600-0714.2010.00987.x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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