Proteostatic reactivation of the developmental transcription factor TBX3 drives BRAF/MAPK-mediated tumorigenesis

Classified as probably not a substantial claim.

Upregulation of pioneer developmental organizers such as SOX2, KLF4, β-catenin, SNAIL-1, c-MYC, TBX3, and BCL6 is reported downstream of BRAF/MAPK-driven tumor.

“Even upregulation of pioneer developmental organizers, such as SOX2, KLF4, β-catenin, SNAIL-1, c-MYC, TBX3, BCL6, et al., are reported downstream of BRAF/MAPK-driven tumor, the pathways causing lineage reprogramming are not clear12,15,30–36.”

• cites [12] Boyd, S. C. et al. Oncogenic B-RAFV600E Signaling Induces the T-Box3 transcriptional repressor to repress E-Cadherin and Enhance Melanoma Cell Invasion. J. Investig. Dermatol. 133, 1269–1277 (2013). sourceSupported
• cites [15] Zhang, P. et al. Targeting myeloid derived suppressor cells reverts immune suppression and sensitizes BRAF-mutant papillary thyroid cancer to MAPK inhibitors. Nat. Commun. 13, 1588 (2022). sourcePartly supported

  The Results section, “BRAF/MAPK directs TBX3 expression through AP-1-mediated transcriptional regulation” (page unavailable), reports that BRAF/MAPK activity increases TBX3 expression in papillary thyroid cancer cells. The cited paper supports TBX3 as an example, but the passages do not establish BRAF/MAPK-driven upregulation of the other listed factors. (LLM, conf=0.88)

  Experimental — accuracy not yet measured
• cites [30] Knauf, J. A. et al. Targeted expression of BRAFV600E in thyroid cells of transgenic mice results in papillary thyroid cancers that undergo dedifferentiation. Cancer Res. 65, 4238–4245 (2005). sourceNot checked — no full text of the source
• cites [31] Feng, L. et al. BRAFV600E dictates cell survival via c-Myc-dependent induction of Skp2 in human melanoma. Biochem. Biophys. Res. Commun. 524, 28–35 (2020). sourceNot checked — no full text of the source
• cites [32] Li, K. et al. BCL6 is regulated by the MAPK/ELK1 axis and promotes KRAS-driven lung cancer. J. Clin. Investig. 132, e161308 (2022). sourceSupported
• cites [33] Lüdtke, TimoH. et al. Tbx2 and Tbx3 Act downstream of Shh to maintain canonical wnt signaling during branching morphogenesis of the murine lung. Dev. Cell 39, 239–253 (2016). sourceNot checked — no full text of the source
• cites [34] Riverso, M., Montagnani, V. & Stecca, B. KLF4 is regulated by RAS/RAF/MEK/ERK signaling through E2F1 and promotes melanoma cell growth. Oncogene 36, 3322–3333 (2017). sourceSupported
• cites [35] Sastre-Perona, A., Riesco-Eizaguirre, G., Zaballos, M. A. & Santisteban, P. β-catenin signaling is required for RAS-driven thyroid cancer through PI3K activation. Oncotarget 7, 49435–49449 (2016). sourceDisputed

  The Results section ('RAS but not BRAF induces Wnt/β-catenin activation in thyroid cells'; page unavailable) reports that only HRAS increased nuclear β-catenin, although both HRAS and BRAF caused a minor increase in total levels. The Abstract and Discussion attribute substantial β-catenin activation to RAS and PI3K/AKT, not BRAF/MAPK. The paper therefore makes a contrary point about the β-catenin component of the cited claim; it does not establish the other listed factors as downstream of BRAF/MAPK. (LLM, conf=0.88)

  Checked by a reasoning model — may be wrong.

  Experimental — accuracy not yet measured
• cites [36] Wieczorek-Szukala, K., Kopczynski, J., Kowalska, A. & Lewinski, A. Snail-1 Overexpression Correlates with Metastatic Phenotype in BRAFV600E Positive Papillary Thyroid Carcinoma. J. Clin. Med. 9, 2701 (2020). sourcePartly supported

  The Discussion (page unavailable) reports higher Snail-1 expression specifically in metastatic papillary thyroid carcinomas with a BRAFV600E mutation, and suggests that the mutation may facilitate its overexpression. The paper does not report BRAF/MAPK-driven upregulation of SOX2, KLF4, β-catenin, c-MYC, TBX3, or BCL6, or establish the broader downstream relationship claimed. (LLM, conf=0.88)

  Experimental — accuracy not yet measured

May combine two claims.

TBX3 is often up-regulated in tumorigenesis and promotes tumor cell proliferation and metastasis, especially during BRAF/MAPK induced tumorigenesis.

“Recently, the oncogenic function of TBX3 draws attention, where TBX3 is often up-regulated in tumorigenesis and promotes tumor cell proliferation and metastasis, especially during BRAF/MAPK induced tumorigenesis12–16.”

• cites [12] Boyd, S. C. et al. Oncogenic B-RAFV600E Signaling Induces the T-Box3 transcriptional repressor to repress E-Cadherin and Enhance Melanoma Cell Invasion. J. Investig. Dermatol. 133, 1269–1277 (2013). sourcePartly supported

  The Results (‘B-RAFV600E upregulates the Tbx3 transcriptional repressor’) and Discussion report TBX3 upregulation by oncogenic B-RAF, and the invasion Results show that silencing TBX3 reduces melanoma-cell invasion. But the paper does not show that TBX3 promotes metastasis: its direct test is an invasion assay. The Discussion says TBX3 may favor proliferation when combined with loss of p16INK4a, while B-RAFV600E induces senescence in primary melanocytes despite TBX3 accumulation. (LLM, conf=0.86)

  Experimental — accuracy not yet measured
• cites [13] Willmer, T., Cooper, A., Peres, J., Omar, R. & Prince, S. The T-Box transcription factor 3 in development and cancer. Biosci. Trends 11, 254–266 (2017). sourcePartly supported

  Section 2.3 says TBX3 is overexpressed in many cancers and can promote proliferation, tumour formation and invasion; section 2.3.2 links elevated TBX3 to metastasis and describes BRAF V600E–driven TBX3 promoting melanoma-cell invasion. The paper does not establish that TBX3 especially promotes proliferation and metastasis during BRAF/MAPK-induced tumorigenesis. Section 2.3.1 also reports that TBX3 can reduce proliferation in melanoma cells. (LLM, conf=0.86)

  Experimental — accuracy not yet measured
• cites [14] Li, X. et al. TBX3 promotes proliferation of papillary thyroid carcinoma cells through facilitating PRC2-mediated p57KIP2 repression. Oncogene 37, 2773–2792 (2018). sourceNot checked — no full text of the source
• cites [15] Zhang, P. et al. Targeting myeloid derived suppressor cells reverts immune suppression and sensitizes BRAF-mutant papillary thyroid cancer to MAPK inhibitors. Nat. Commun. 13, 1588 (2022). sourceSupported
• cites [16] Mowla, S., Pinnock, R., Leaner, VirnaD., Goding, ColinR. & Prince, S. PMA-induced up-regulation of TBX3 is mediated by AP-1 and contributes to breast cancer cell migration. Biochem. J. 433, 145–153 (2010). sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing).

Proper TBX3 expression directs the embryonic formation of hypothalamus-pituitary, the heart, mammary glands, limbs, and lungs.

“Proper TBX3 expression directs the embryonic formation of hypothalamus-pituitary, the heart, mammary glands, limbs, and lungs9,10.”

• cites [9] Khan, S. F. et al. The roles and regulation of TBX3 in development and disease. Gene 726, 144223 (2020). sourcePartly supported

  The “Expression and function of TBX3 during development” section says TBX3 plays crucial roles in development of the heart, mammary glands, limbs and lungs. It reports TBX3 expression in developing pituitary glands, but does not establish that it directs formation of the hypothalamic–pituitary axis. The citation therefore supports four of the five listed developmental roles, but not the full claim. (LLM, conf=0.86)

  Experimental — accuracy not yet measured
• cites [10] Trowe, M.-O. et al. Inhibition of Sox2-dependent activation of Shh in the ventral diencephalon by Tbx3 is required for formation of the neurohypophysis. Development 140, 2299–2309 (2013). sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing).

Critical morphogenic and oncogenic signaling pathways, including BMPs, Shh, TGF-β, FGFs, Wnt/β-catenin, and BRAF/MAPK, participate in TBX3 expression regulation, mostly at the transcriptional level.

“Thus, critical morphogenic and oncogenic signaling pathways, such as BMPs17, Shh18, TGF-β19, FGFs20, Wnt/β-catenin21, as well as BRAF/MAPK pathway, participate in TBX3 expression regulation, mostly at the transcriptional level12,15.”

• cites [12] Boyd, S. C. et al. Oncogenic B-RAFV600E Signaling Induces the T-Box3 transcriptional repressor to repress E-Cadherin and Enhance Melanoma Cell Invasion. J. Investig. Dermatol. 133, 1269–1277 (2013). sourceSupported
• cites [15] Zhang, P. et al. Targeting myeloid derived suppressor cells reverts immune suppression and sensitizes BRAF-mutant papillary thyroid cancer to MAPK inhibitors. Nat. Commun. 13, 1588 (2022). sourceSupported
• cites [17] Yang, L. et al. Isl1Cre reveals a common Bmp pathway in heart and limb development. Development 133, 1575–1585 (2006). sourceSupported
• cites [18] Suzuki, T., Takeuchi, J., Koshiba-Takeuchi, K. & Ogura, T. Tbx Genes Specify Posterior Digit Identity through Shh and BMP Signaling. Dev. Cell 6, 43–53 (2004). sourceNot checked — no full text of the source

May combine two claims.

Expression levels of USP15 and TBX3 are significantly increased and positively correlated with tumor progression in thyroid cancer tissue array samples.

“Across the 152 tissue array samples composed mainly of PTC samples with adjacent tissues, as well as a small number of other types of thyroid cancer tissues, expression levels of USP15 and TBX3 are significantly increased and positively correlated with tumor progression15 (Supplementary Fig. 4a).”

• cites [15] Zhang, P. et al. Targeting myeloid derived suppressor cells reverts immune suppression and sensitizes BRAF-mutant papillary thyroid cancer to MAPK inhibitors. Nat. Commun. 13, 1588 (2022). sourcePartly supported

  The Results section reports that TBX3 was up-regulated and correlated with histological grade in 110 PTC specimens. It does not report USP15 expression or a 152-sample tissue array, so those parts of the attributed claim are unsupported by this paper. (LLM, conf=0.88)

  Experimental — accuracy not yet measured

Probably not a substantial claim: may not pass S3 (load-bearing).

MAPK pathways transduce critical mitogenic signals downstream of RTK-RAS during embryogenesis, essential for lineage progenitor reservoir maintenance and organ growth.

“Developmentally, MAPK pathways transduce critical mitogenic signals downstream of RTK-RAS during embryogenesis, which are essential for lineage progenitor reservoir maintenance and organ growth37.”

• cites [37] Hirashima, T. Live imaging approach of dynamic multicellular responses in ERK signaling during vertebrate tissue development. Biochem. J. 479, 129–143 (2022). sourcePartly supported

  The “RTK-ERK signaling pathway” section describes signaling from RTKs through RAS to ERK and says activated ERK regulates cell proliferation and growth. The “Genetic deficiency of ERK during embryonic development” section also describes ERK as essential for development. The copy does not establish the more specific claim that these signals maintain lineage progenitor reservoirs or are essential for organ growth. (LLM, conf=0.86)

  Experimental — accuracy not yet measured

Classified as probably not a substantial claim. May combine two claims.

Gene mutations of BRAF, especially BRAFV600E, and constitutively activated MAPK cascades drive multiple cancers, depriving differentiated features.

“Gene mutations of BRAF, especially BRAFV600E, and constitutively activated MAPK cascades drive multiple types of cancers, depriving differentiated features through melanoma genesis and intestine/colon carcinogenesis24–27.”

• cites [24] Śmiech, M., Leszczyński, P., Kono, H., Wardell, C. & Taniguchi, H. Emerging BRAF mutations in cancer progression and their possible effects on transcriptional networks. Genes 11, 1342 (2020). sourcePartly supported

  Section 2 (Class I BRAF Mutations; page unavailable) describes BRAF V600E as constitutively active and BRAF as an oncogenic driver in cancers including melanoma and colorectal cancer. Section 6 reports increased proliferation in BRAF-mutated colorectal cancer cells. The cited passages do not establish that these cancers lose differentiated features, so that part of the claim is unsupported. (LLM, conf=0.84)

  Experimental — accuracy not yet measured
• cites [25] Köhler, C. et al. Mouse cutaneous melanoma induced by mutant BRaf arises from expansion and dedifferentiation of mature pigmented melanocytes. Cell Stem Cell 21, 679–693.e676 (2017). sourcePartly supported

  The Introduction identifies BRAFV600E-induced melanoma in mice, and the Discussion reports that a subset of melanoma cells later loses its differentiation signature. The Discussion also says the initial expansion retains differentiated features and that what triggers the subsequent dedifferentiation remains unclear. The paper does not establish that MAPK activation causes that loss or address intestinal or colon carcinogenesis. (LLM, conf=0.87)

  Experimental — accuracy not yet measured
• cites [26] Sun, Q. et al. FOXD1 promotes dedifferentiation and targeted therapy resistance in melanoma by regulating the expression of connective tissue growth factor. Int. J. Cancer 149, 657–674 (2021). sourceNot checked — no full text of the source
• cites [27] Reischmann, N. et al. BRAFV600E drives dedifferentiation in small intestinal and colonic organoids and cooperates with mutant p53 and Apc loss in transformation. Oncogene 39, 6053–6070 (2020). sourcePartly supported

  The Introduction describes BRAFV600E as a constitutively active oncoprotein in colorectal cancer and links its signaling to reduced intestinal differentiation. The Discussion also reports a dedifferentiation-associated gene-expression pattern in intestinal organoids. These passages support the intestine/colon portion, but do not establish the claim about melanoma or multiple cancer types. (LLM, conf=0.85)

  Experimental — accuracy not yet measured

May combine two claims.

Pathologically activated BRAF/MAPK signaling, possibly by BRAFV600E, initiates and promotes tumor development through transcriptionally elevating USP15 and protecting TBX3 from degradation, in addition to directly transcriptionally up-regulating TBX3.

“Therefore, pathologically activated BRAF/MAPK signaling, possibly by BRAFV600E, initiates and promotes tumor development through transcriptionally elevating USP15 and protecting TBX3 from degradation, in addition to direct transcriptionally up-regulating TBX315.”

• cites [15] Zhang, P. et al. Targeting myeloid derived suppressor cells reverts immune suppression and sensitizes BRAF-mutant papillary thyroid cancer to MAPK inhibitors. Nat. Commun. 13, 1588 (2022). sourcePartly supported

  Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

  Experimental — accuracy not yet measured

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

The ubiquitin-proteasome system controls core signaling factor abundance by selective degradation, mediates many processes in embryonic development, and aberrant UPS-dependent degradation is involved in carcinogenesis.

“The ubiquitin-proteasome system (UPS) provides an essential way to control core signaling factor abundance by selective degradation, such that it mediates many processes in embryonic development, also aberrant regulations of UPS-dependent degradation are involved in different pathological processes especially carcinogenesis22,23.”

• cites [22] Deng, L., Meng, T., Chen, L., Wei, W. & Wang, P. The role of ubiquitination in tumorigenesis and targeted drug discovery. Signal Transduct. Target. Ther. 5, 11 (2020). sourcePartly supported

  The UPS section describes protein degradation and links UPS dysfunction to cancer; the Oct4 and Sox2 ubiquitination sections give examples of selective degradation of core regulatory factors. The CSC stemness section mentions embryonic development and UPS-regulated stem-cell processes, but it does not establish the broader claim that the UPS mediates many processes in embryonic development. (LLM, conf=0.82)

  Experimental — accuracy not yet measured
• cites [23] Harrigan, J. A., Jacq, X., Martin, N. M. & Jackson, S. P. Deubiquitylating enzymes and drug discovery: emerging opportunities. Nat. Rev. Drug Discov. 17, 57–78 (2017). sourcePartly supported

  The Main section describes selective degradation through the UPS, and “DUBs in oncology” links dysregulated ubiquitin regulation to tumorigenesis. The paper does not establish the claimed role of UPS-dependent degradation in many embryonic-development processes; its developmental examples concern specific DUBs. Page numbers are unavailable in our copy. (LLM, conf=0.85)

  Experimental — accuracy not yet measured

Probably not a substantial claim: may not pass S3 (load-bearing).

Tbx3 is a thyroid bud-specific factor as early as E10.5.

“previous microarray combined with laser capture microdissection analysis identifies Tbx3 as a thyroid bud-specific factor at early as E10.548.”

• cites [48] Fagman, H. et al. Gene expression profiling at early organogenesis reveals both common and diverse mechanisms in foregut patterning. Dev. Biol. 359, 163–175 (2011). sourcePartly supported

  In “Genes enriched in the E10.5 thyroid bud” (page not provided), the paper reports Tbx3 expression in the thyroid bud at E10.5. It also reports Tbx3 in the first pharyngeal arch and mesenchyme surrounding the lung bud and trachea, so “thyroid bud-specific” overstates its distribution. (LLM, conf=0.88)

  Experimental — accuracy not yet measured

May combine two claims.

Tbx3 knockout restores differentiation factor expression and renders re-differentiation marked by Tpo, Nis, Tg in BRAFV600E-driven tumors.

“Tbx3 knockout restored differentiation factors expression and rendered re-differentiation marked with, but not limited to Tpo, Nis, Tg15 (Fig. 7a).”

• cites [15] Zhang, P. et al. Targeting myeloid derived suppressor cells reverts immune suppression and sensitizes BRAF-mutant papillary thyroid cancer to MAPK inhibitors. Nat. Commun. 13, 1588 (2022). sourcePartly supported

  The Discussion says Tbx3 ablation ameliorates the BRAFV600E-associated reduction of thyroid lineage factors, supporting the general differentiation-factor claim. Our copy does not identify Tpo, Nis, and Tg as markers restored by knockout, and the Results report no significant relief of lineage-factor expression after later postnatal Tbx3 knockout. (LLM, conf=0.85)

  Experimental — accuracy not yet measured

• AssumptionRests on an assumption: The mouse models used (Usp15null, Tbx3Δthy, mPTC) faithfully represent human BRAFV600E-related tumorigenesis and development.

Probably not a substantial claim: may not pass S3 (load-bearing).

TBX3 has been confirmed to be highly pro-tumorigenic in melanoma.

“where TBX3 has been confirmed to be highly pro-tumorigenic46.”

• cites [46] Peres, J. & Prince, S. The T-box transcription factor, TBX3, is sufficient to promote melanoma formation and invasion. Mol. Cancer 12, 117 (2013). sourceSupported

• AssumptionRests on an assumption: BRAFV600E-induced BRAF/MAPK activation is the most dramatic carcinogenic mutation in melanoma.

May combine two claims.

Tbx3 is specifically and dynamically expressed during embryonic organogenesis and its expression is relatively low in adult organs.

“As a developmental factor, Tbx3 is specifically and dynamically expressed during embryonic organogenesis, while its expression goes relatively low in adult organs9.”

• cites [9] Khan, S. F. et al. The roles and regulation of TBX3 in development and disease. Gene 726, 144223 (2020). sourcePartly supported

  The ‘Expression and function of TBX3 during development’ section (page unavailable) lists numerous developing mouse organs that express Tbx3. The heart, limb and mammary-gland sections also describe changes in where it is expressed as development proceeds. The paper does not establish the claimed general decrease in expression across adult organs; its cancer section compares particular tumors with normal tissue, not adult organs with embryonic organs. (LLM, conf=0.86)

  Experimental — accuracy not yet measured

Probably not a substantial claim: may not pass S3 (load-bearing).

Tbx3 plays fate determination roles for other endoderm-derived organs including the lungs, the liver, and the pancreas.

“A series of genetic studies have shown Tbx3 plays fate determination roles for other endoderm-derived organs including the lungs, the liver, and the pancreas9.”

• cites [9] Khan, S. F. et al. The roles and regulation of TBX3 in development and disease. Gene 726, 144223 (2020). sourcePartly supported

  The References section cites a study reporting that Tbx3 controls hepatic progenitor-cell fate, supporting the liver part. The Lung development section describes Tbx3’s role in mesenchymal proliferation and branching morphogenesis, not fate determination; the Expression and function section lists pancreatic expression but does not establish a pancreatic fate-determination role. Page numbers are unavailable in our copy. (LLM, conf=0.85)

  Experimental — accuracy not yet measured

Probably not a substantial claim: may not pass S3 (load-bearing).

Multiple oncogenic pathways regulate TBX3 expression in melanoma, lung, thyroid, breast and other cancers.

“Multiple oncogenic pathways have been found to regulate TBX3 expression in occurrence of melanoma, lung, thyroid, breast and other types of cancers12,15,16,20,21,53,54”

• cites [12] Boyd, S. C. et al. Oncogenic B-RAFV600E Signaling Induces the T-Box3 transcriptional repressor to repress E-Cadherin and Enhance Melanoma Cell Invasion. J. Investig. Dermatol. 133, 1269–1277 (2013). sourcePartly supported

  The Results and Discussion (page unavailable) show that oncogenic B-RAFV600E upregulates TBX3 in melanocytes and melanoma cells. The Discussion also notes TBX3 overexpression in several other cancers, but it does not establish that multiple oncogenic pathways regulate TBX3 across lung, thyroid, breast and other cancers. (LLM, conf=0.88)

  Experimental — accuracy not yet measured
• cites [15] Zhang, P. et al. Targeting myeloid derived suppressor cells reverts immune suppression and sensitizes BRAF-mutant papillary thyroid cancer to MAPK inhibitors. Nat. Commun. 13, 1588 (2022). sourcePartly supported

  The Introduction reports BRAF/MAPK-induced TBX3 up-regulation in melanoma, and the Results show BRAF/MAPK regulation of TBX3 in thyroid cancer. The Discussion also describes c-Jun activating TBX3 transcription in breast cancer. Our copy does not establish regulation of TBX3 expression in lung cancer or substantiate the claim across other cancer types. (LLM, conf=0.85)

  Experimental — accuracy not yet measured
• cites [16] Mowla, S., Pinnock, R., Leaner, VirnaD., Goding, ColinR. & Prince, S. PMA-induced up-regulation of TBX3 is mediated by AP-1 and contributes to breast cancer cell migration. Biochem. J. 433, 145–153 (2010). sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

TBX3 is critical in embryonic stem cell maintenance, lineage specification, and embryogenic organ formation, and its up- or down-regulation leads to aberrant regulation of cell fate/proliferation and different malignancies.

“As a critical factor in embryonic stem cells maintenance, lineage specification, and embryogenic organ formation, TBX3 expression is finely controlled, with its up or down-regulation leading to aberrant regulation of cell fate/proliferation and different malignancies.13.”

• cites [13] Willmer, T., Cooper, A., Peres, J., Omar, R. & Prince, S. The T-Box transcription factor 3 in development and cancer. Biosci. Trends 11, 254–266 (2017). sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

USP15 shows dual effects in tumorigenesis; USP15 copy number is increased in glioblastoma, breast cancer, and ovarian cancer, but decreased in pancreatic cancer.

“Due to the conflicting functions of substrates, USP15 shows dual effects in tumorigenesis. For instance, USP15 copy number is increased in glioblastoma, breast cancer, and ovarian cancer, but decreased in pancreatic cancer40,52,55–58.”

• cites [40] Eichhorn, P. J. A. et al. USP15 stabilizes TGF-β receptor I and promotes oncogenesis through the activation of TGF-β signaling in glioblastoma. Nat. Med. 18, 429–435 (2012). sourceNot checked — no full text of the source
• cites [52] Srihari, S. & Ragan, M. A. Systematic tracking of dysregulated modules identifies novel genes in cancer. Bioinformatics 29, 1553–1561 (2013). sourceNot checked — no full text of the source
• cites [55] Padmanabhan, A. et al. USP15-dependent lysosomal pathway controls p53-R175H turnover in ovarian cancer cells. Nat. Commun. 9, 1270 (2018). sourcePartly supported

  The Results section (page unavailable) states that USP15 is amplified in ovarian cancer, glioblastoma, and breast cancer, supporting the increased-copy-number portion of the claim. The passages found do not report decreased USP15 copy number in pancreatic cancer or establish that conflicting substrate functions give USP15 dual effects in tumorigenesis. (LLM, conf=0.88)

  Experimental — accuracy not yet measured
• cites [56] Peng, Y. et al. The deubiquitylating enzyme USP15 regulates homologous recombination repair and cancer cell response to PARP inhibitors. Nat. Commun. 10, 1224 (2019). sourcePartly supported

  The Results section reports deep depletion of USP15 copy number in pancreatic cancer patients, supporting that part of the claim. It also reports USP15 gene depletion in a subset of breast cancer patients; our copy does not establish increased copy number in breast or ovarian cancer or glioblastoma, or the claimed dual effects in tumorigenesis. Page numbers were not available in the indexed passages. (LLM, conf=0.85)

  Experimental — accuracy not yet measured
• cites [57] Jiang, B. et al. Clinicopathological and prognostic significance of ubiquitin-specific peptidase 15 and its relationship with transforming growth factor-β receptors in patients with pancreatic ductal adenocarcinoma. J. Gastroenterol. Hepatol. 36, 507–515 (2021). sourceNot checked — no full text of the source
• cites [58] Sun, X. et al. Loss of the receptors ER, PR and HER2 promotes USP15-dependent stabilization of PARP1 in triple-negative breast cancer. Nat. Cancer 4, 716–733 (2023). sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Epithelial cell dedifferentiation is a critical cell state transition during tumorigenesis and confers tumor cells high proliferation capacity and progenitor-like fate through multidimensional reprogramming.

“Epithelial cell dedifferentiation is recognized as a critical cell state transition during tumorigenesis and confer tumor cells on high proliferation capacity and progenitor-like fate through multidimensional reprogramming1–3.”

• cites [1] Liu, J. The dualistic origin of human tumors. Semin. Cancer Biol. 53, 1–16 (2018). sourcePartly supported

  In “The giant cell cycle as a novel mechanism for somatic cell dedifferentiation (or reprogramming)” (page unavailable), the paper proposes that somatic-cell dedifferentiation during tumor initiation can produce embryonic-like cancer stem cells. It does not establish the claim specifically for epithelial cells or say that dedifferentiation confers high proliferation capacity; its mechanism is presented as a proposal rather than a recognized general transition. (LLM, conf=0.86)

  Experimental — accuracy not yet measured
• cites [2] Palmer, N. P., Schmid, P. R., Berger, B. & Kohane, I. S. A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers. Genome Biol. 13, R71 (2012). sourcePartly supported

  The Background describes cancers as showing stem cell-like programming and shared proliferative potential, and the Conclusions describe stem cell-specific expression in tumor samples. Neither section establishes epithelial-cell dedifferentiation as a critical transition during tumorigenesis or shows that multidimensional reprogramming confers proliferation and progenitor-like fate. Page numbers are unavailable in our copy. (LLM, conf=0.84)

  Experimental — accuracy not yet measured
• cites [3] Strauss, R., Hamerlik, P., Lieber, A. & Bartek, J. Regulation of stem cell plasticity: mechanisms and relevance to tissue biology and cancer. Mol. Ther. 20, 887–897 (2012). sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

A few kinases participate in phosphorylation of TBX3, such as AKT3 at S720, cyclin A-CDK2 at either S190 or S354, p38 MAP kinase at S692, and AKT1 is also involved.

“Moreover, a few kinases participate in phosphorylation of TBX3, such as AKT3 at S720, cyclin A-CDK2 at either S190 or S354, p38 MAP kinase at S692, and AKT1 is also involved54,59–61.”

• cites [54] Willmer, T., Peres, J., Mowla, S., Abrahams, A. & Prince, S. The T-Box factor TBX3 is important in S-phase and is regulated by c-Myc and cyclin A-CDK2. Cell Cycle 14, 3173–3183 (2015). sourcePartly supported

  The “Cyclin A-CDK2 binds and phosphorylates TBX3” section reports that CDK2 phosphorylates TBX3 within its N-terminal half, but does not identify S190 or S354 as the site. The cited paper’s text does not establish the other kinase–site claims in the sentence; its reference list names a separate AKT3 study, without giving the S720 site. (LLM, conf=0.88)

  Experimental — accuracy not yet measured
• cites [59] Peres, J., Mowla, S. & Prince, S. The T-box transcription factor, TBX3, is a key substrate of AKT3 in melanomagenesis. Oncotarget 6, 1821–1833 (2015). sourceSupported
• cites [60] Yano, T. et al. Group V secretory phospholipase A2 plays a pathogenic role in myocardial ischaemia-reperfusion injury. Cardiovasc. Res. 90, 335–343 (2011). sourceCould not verify

  Section 3.7 discusses phosphorylation of p38 and cPLA2 in ischaemic myocardium, not phosphorylation of TBX3. Searches for TBX3 and the specified kinases and phosphorylation sites found no passage addressing the claim in our copy; no page number was provided for the section. (LLM, conf=0.77)

  Experimental — accuracy not yet measured
• cites [61] Sims, D. et al. The c-Myc/AKT1/TBX3 axis is important to target in the treatment of embryonal rhabdomyosarcoma. Cancers 12, 501 (2020). sourceSupported

May combine two claims.

USP15 depletion inhibits tumor growth and elevates p21CIP1 and p57KIP2.

“In vivo, USP15 depletion indeed inhibited tumor growth, accompanied with elevated p21CIP1, p57KIP2, direct TBX3 repressing targets, thus restricted cell proliferation (Fig. 3c−e, Supplementary Fig. 2g).”

May combine two claims.

Multiple AP-1 binding motifs are located within the USP15 promoter and are transactivated by c-Jun/JunB/c-Fos over-expression.

“Indeed, multiple AP-1 binding motifs were located within USP15 promoter, which were transactivated by c-Jun/JunB/c-Fos over-expression (Fig. 4e).”

May combine two claims.

Tumors from Usp15 mutant mice, when formed, exhibit more differentiated characteristics and retain more healthy follicles compared to control.

“Histological staining showed that tumors from mutant mice, when formed, exhibited more differentiated characteristics and retained more healthy follicles compared to those from control mice (Fig. 3j).”

May combine two claims.

Ectopic TBX3 reverses the function of USP15 depletion and restores tumor growth.

“Remarkably, ectopic TBX3 reversed the function and restored tumor growth (Fig. 3c−e, Supplementary Fig. 2g).”

May combine two claims.

Induction of Usp15 expression by BRAF/MAPK is instant and dramatic, with augmented level in E16.5 embryonic thyroid from mPTC mice compared to wild-type.

“Remarkably, induction of Usp15 expression by BRAF/MAPK could be instant and dramatic, so that its level was augmented in E16.5 embryonic thyroid from mPTC mice compared to that from wild-type mice (Fig. 4f and Supplementary Fig. 3c).”

May combine two claims.

USP15 over-expression increases TBX3 levels dose-dependently, and USP15 knock-down decreases TBX3 expression without changing its mRNA levels.

“Moreover, USP15 over-expression increased TBX3 levels in a dose-dependent manner, while USP15 knock-down decreased TBX3 expression, its mRNA levels remained relatively stable (Fig. 1e, f and Supplementary Fig. 1d).”

May combine two claims.

Upon Usp15 loss, Tbx3 protein level is significantly decreased and p57KIP2 is increased in tumors.

“In these tumors, Tbx3 protein level was significantly decreased, while p57KIP2 was increased upon Usp15 loss, consistent with the cellular data (Fig. 3j and Supplementary Fig. 2j).”

May combine two claims.

Expressions of Usp15, p-Erk, and Tbx3 decline as development continues and remain low after birth and in adult thyroid.

“Their expressions decline as development continues and remain low after birth and in adult thyroid.”

• AssumptionRests on an assumption: The thyroid is a suitable model to study BRAF/MAPK-directed endoderm development and tumorigenesis.

May combine two claims.

Differentiation factors are increased in Tbx3Δthy, pointing to an over-differentiation tendency.

“Histologically and quantitatively, differentiation factors were increased in Tbx3Δthy, pointing to an over-differentiation tendency (Fig. 7a and Supplementary Fig. 5c).”

• AssumptionRests on an assumption: The mouse models used (Usp15null, Tbx3Δthy, mPTC) faithfully represent human BRAFV600E-related tumorigenesis and development.

May combine two claims.

Tbx3 is restrictedly expressed in the ventral midline of hypothalamus at E10.5, and is hardly detectable in the same position during Usp15null mutant embryogenesis despite comparable mRNA expressions.

“We have shown that Tbx3 is restrictedly expressed in the ventral midline of hypothalamus at E10.510, which was hardly detectable in the same position during Usp15null mutant embryogenesis, in spite of comparable mRNA expressions (Fig. 6c and Supplementary Fig. 5b).”

• cites [10] Trowe, M.-O. et al. Inhibition of Sox2-dependent activation of Shh in the ventral diencephalon by Tbx3 is required for formation of the neurohypophysis. Development 140, 2299–2309 (2013). sourceNot checked — no full text of the source

• AssumptionRests on an assumption: The mouse models used (Usp15null, Tbx3Δthy, mPTC) faithfully represent human BRAFV600E-related tumorigenesis and development.

May combine two claims.

Tbx3 and Usp15 deficiency both lead to differentiation augmentation, exemplified with excessive Tpo, Nis, and Tg in thyroid folliculogenesis and regain the same factors in BRAFV600E-driven thyroid tumor development.

“Tbx3 and Usp15 deficiency both lead to differentiation augmentation, exemplified with excessive Tpo, Nis, and Tg in thyroid folliculogenesis and regain the same factors in BRAFV600E-driven thyroid tumor development.”

May combine two claims.

Usp15 removal dramatically abrogates Tbx3 protein expression from E14.5 thyroid without affecting the mRNA level.

“Strikingly, Usp15 removal dramatically abrogated Tbx3 protein expression from E14.5 thyroid without affecting the mRNA level (Fig. 6c and Supplementary Fig. 5b)”

• AssumptionRests on an assumption: The mouse models used (Usp15null, Tbx3Δthy, mPTC) faithfully represent human BRAFV600E-related tumorigenesis and development.

Probably not a substantial claim: may not pass S3 (load-bearing).

USP15 and TBX3 transcriptional expressions show a positive correlation tendency, although not statistically significant.

“USP15 and TBX3 transcriptional expressions also show positively correlated tendency, although not statistically significant (Supplementary Fig. 4g, h).”

May combine two claims.

Hormone secretion function and T3/T4 levels are damaged in Tbx3Δthy.

“The hormone secretion function and T3/T4 levels were thus damaged (Fig. 7c).”

• AssumptionRests on an assumption: The mouse models used (Usp15null, Tbx3Δthy, mPTC) faithfully represent human BRAFV600E-related tumorigenesis and development.

May combine two claims.

BRAFV600E-induced mPTC is re-differentiated by Usp15 knockout, largely due to reduced Tbx3.

“BRAFV600E-induced mPTC was also re-differentiated by Usp15 knockout, largely due to reduced Tbx3 (Fig, 7d, e and Supplementary Fig. 5d).”

• AssumptionRests on an assumption: The mouse models used (Usp15null, Tbx3Δthy, mPTC) faithfully represent human BRAFV600E-related tumorigenesis and development.

May combine two claims.

Both USP15 and TBX3 highly correlate with BRAFV600E signature and poor tumor prognosis.

“The clinical relevance is highlighted in that both USP15 and TBX3 highly correlates with BRAFV600E signature and poor tumor prognosis.”

May combine two claims.

Tbx3Δthy mutants are born normally but have disrupted and irregular follicles.

“Tbx3Δthy mutants were born normally, but with disrupted and irregular follicles (Fig. 7a).”

• AssumptionRests on an assumption: The mouse models used (Usp15null, Tbx3Δthy, mPTC) faithfully represent human BRAFV600E-related tumorigenesis and development.

May combine two claims.

Deleting Tbx3 or Usp15 leads to tumor redifferentiation, paralleling their overdifferentiation tendency during development, exemplified by disrupted thyroid folliculogenesis and elevated differentiation factors Tpo, Nis, and Tg.

“Deleting Tbx3 or Usp15 leads to tumor redifferentiation, which parallels their overdifferentiation tendency during development, exemplified by disrupted thyroid folliculogenesis and elevated differentiation factors such as Tpo, Nis, Tg.”

• Also stated in: § Introduction · plain

  “Tbx3 and Usp15 deficiency both lead to differentiation augmentation, exemplified with excessive Tpo, Nis, and Tg in thyroid folliculogenesis and regain the same factors in BRAFV600E-driven thyroid tumor development.”

May combine two claims.

Genetic knockout of Usp15 leads to disrupted organ development and tumorigenesis comparable to Tbx3 mutants.

“Activated BRAF/MAPK pathway functions partially through USP15-mediated TBX3 stabilization, thus genetic knockout of Usp15 leads to disrupted organ development and tumorigenesis comparable to Tbx3 mutants.”

May combine two claims.

USP15 deficiency inhibits melanoma tumor cell proliferation and xenografted tumor growth in a TBX3-dependent manner.

“Consequently, USP15 deficiency inhibits melanoma tumor cell proliferation and xenografted tumor growth in the TBX3-dependent manner”

• AssumptionRests on an assumption: BRAFV600E-induced BRAF/MAPK activation is the most dramatic carcinogenic mutation in melanoma.

May combine two claims.

USP15 and TBX3 show high expression in TPC-1 cells with RET rearrangement and Cal-62 cells with KRAS mutation.

“Additionally, USP15 and TBX3 also showed high expression within TPC-1 and Cal-62 cells with RET rearrangement or KRAS mutation respectively”

May combine two claims.

In THCA transcriptome data from TCGA, USP15 expression is positively correlated with TBX3 and BRAF.

“Based on THCA transcriptome data from The Cancer Genome Atlas (TCGA), USP15 expression is positively correlated with TBX3, even BRAF”

May combine two claims.

Tbx3 is significantly and specifically reduced at the protein level across various tissues in Usp15null mutants, defining Usp15 as a critical post-translational modifier of Tbx3 through physiological processes.

“Here we find Tbx3 is significantly and specifically reduced at the protein level across various tissues in Usp15null mutants, defining Usp15 as a critical post-translation modifier of Tbx3 through physiological processes.”

• AssumptionRests on an assumption: The mouse models used (Usp15null, Tbx3Δthy, mPTC) faithfully represent human BRAFV600E-related tumorigenesis and development.

Probably not a substantial claim: may not pass S2 (checkable).

TBX3 expression level needs to be tightly controlled.

“Considering the mal-development in the absence of TBX3 and the tumorigenic risk of high TBX3 levels, its expression level needs to be tightly controlled.”

Probably not a substantial claim: may not pass S3 (load-bearing).

Loss-of-function mutations in human TBX3 lead to ulnar-mammary syndrome, characterized by mammary and apocrine gland hypoplasia and defects of the upper limb, areola, dental structures, heart and genitalia.

“Accordingly, loss-of-function mutations in human TBX3 lead to ulnar-mammary syndrome which is characterized by mammary and apocrine glands hypoplasia, as well as defects of the upper limb, areola, dental structures, heart and genitalia11.”

• cites [11] Bamshad, M. et al. The spectrum of mutations in TBX3: genotype/phenotype relationship in ulnar-mammary syndrome. Am. J. Hum. Genet. 64, 1550–1562 (1999). sourceNot checked — no full text of the source

May combine two claims.

Nthy/BRAFV600E cells gain the capability to form thyroid tumors in vivo, with high metastasis potential and ATC-like transcriptome.

“Nthy/BRAFV600E cells gain the capability to form thyroid tumors in vivo, with high metastasis potential and ATC-like transcriptome44.”

• cites [44] Kim, M. et al. BRAFV600E Transduction of an SV40-Immortalized normal human thyroid cell line induces dedifferentiated thyroid carcinogenesis in a mouse Xenograft Model. Thyroid 30, 487–500 (2020). sourceNot checked — no full text of the source

May combine two claims.

USP15, downstream of activated BRAF/MAPK pathway, functions as the proteostatic controller of TBX3 and determines its ultimate abundance.

“Together, USP15, downstream of activated BRAF/MAPK pathway, functions as the proteostatic controller of TBX3 and determines the ultimate abundance.”

May combine two claims.

Tbx3 level is subject to Usp15 regulation from embryonic development, organ formation, and to tumorigenesis, likely responding to BRAF/MAPK cascade.

“These data suggest that Tbx3 level is subjected to Usp15 regulation from embryonic development, organ formation, and to tumorigenesis, likely responding to BRAF/MAPK cascade.”

• AssumptionRests on an assumption: The mouse models used (Usp15null, Tbx3Δthy, mPTC) faithfully represent human BRAFV600E-related tumorigenesis and development.

May combine two claims.

USP15 is transcriptionally activated by BRAF/MAPK pathway during melanoma genesis and controls TBX3 stability.

“USP15 is also transcriptionally activated by BRAF/MAPK pathway during melanoma genesis and controls TBX3 stability (Fig. 5i, j and Supplementary Fig. 4f).”

• AssumptionRests on an assumption: BRAFV600E-induced BRAF/MAPK activation is the most dramatic carcinogenic mutation in melanoma.

Probably not a substantial claim: may not pass S3 (load-bearing).

p-Erk participates in early embryonic endoderm foregut specification.

“phosphorylated Erks (p-Erk) participate in early embryonic endoderm foregut specification47”

• cites [47] Corson, L. B., Yamanaka, Y., Lai, K.-M. V. & Rossant, J. Spatial and temporal patterns of ERK signaling during mouse embryogenesis. Development 130, 4527–4537 (2003). sourceNot checked — no full text of the source

May combine two claims.

High USP15 expression level could predict higher tumor progression and poorer overall survival in BRAFV600E-related malignancies.

“These analyses indicate that high USP15 expression level could predict higher tumor progression and poorer overall survival, in BRAFV600E related malignancies”

• AssumptionRests on an assumption: BRAFV600E-induced BRAF/MAPK activation is the most dramatic carcinogenic mutation in melanoma.

May combine two claims.

USP15 maintains TBX3 expression through physiological development and pathological tumor progression, and both confine differentiation progression (more USP15/TBX3, less differentiation, and vice versa).

“Therefore, USP15 maintains TBX3 expression through physiological development and pathological tumor progression where both confine the differentiation progression, as the more USP15/TBX3, the less differentiation, and vice versa.”

• Also stated in: § Discussion · boosted

  “Our study provides compelling evidence that TBX3 homeostasis is also regulated by the UPS mediator, DUB USP15, during the development and tumorigenesis.”

• AssumptionRests on an assumption: The mouse models used (Usp15null, Tbx3Δthy, mPTC) faithfully represent human BRAFV600E-related tumorigenesis and development.

Probably not a substantial claim: may not pass S3 (load-bearing).

USP7 promotes PTC progression by directly binding and deubiquitylating TBX3 biochemically in vitro.

“Xie et al. reported that USP7 promoted PTC progression through directly binding and deubiquitylating TBX3 biochemically in vitro62.”

• cites [62] Xie, P. et al. USP7 promotes proliferation of papillary thyroid carcinoma cells through TBX3-mediated p57KIP2 repression. Mol. Cell. Endocrinol. 518, 111037 (2020). sourceNot checked — no full text of the source

Classified as probably not a substantial claim.

A total of 93 cases of pathological sections were obtained.

“A total of 93 cases of pathological sections were obtained in Tianjin Medical University Cancer Institute and Hospital to distinguish whether BRAF is mutated or not, including 37 cases of BRAFWT and 56 cases of BRAFV600E mutation.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Of the 93 cases, 37 were BRAFWT and 56 were BRAFV600E mutation.

“A total of 93 cases of pathological sections were obtained in Tianjin Medical University Cancer Institute and Hospital to distinguish whether BRAF is mutated or not, including 37 cases of BRAFWT and 56 cases of BRAFV600E mutation.”

Probably not a substantial claim: may not pass S2 (checkable). May combine two claims.

The findings shed light on targeting strategies for USP15-TBX3 axis related developmental and oncogenic diseases and provide more thoughts for BRAF/MAPK related therapy designs.

“Translationally, the findings shed light on targeting strategies for USP15-TBX3 axis related developmental and oncogenic diseases and provide more thoughts for BRAF/MAPK related therapy designs.”

Classified as probably not a substantial claim.

Current findings open up the possibility to modulate TBX3 expression through intervening the enzyme activity of USP15 or the physiological molecular binding.

“the current findings open up the possibility to modulate TBX3 expression through intervening the enzyme activity of USP15 or the physiological molecular binding.”

Probably not a substantial claim: may not pass S3 (load-bearing).

Multiple DUBs may participate in TBX3 stability regulation.

“the situation that multiple DUBs participate in TBX3 stability regulation cannot be ruled out.”

Probably not a substantial claim: may not pass S3 (load-bearing).

The human PTC tissue arrays were mostly PTC and included a small amount of other thyroid cancer.

“The human PTC tissue arrays were purchased from Shanghai Outdo Biotech company included 152 thyroid cancer and adjacent tissues, mostly PTC and with a small amount of other thyroid cancer.”

Probably not a substantial claim: may not pass S3 (load-bearing).

The human PTC tissue arrays included 152 thyroid cancer and adjacent tissues.

“The human PTC tissue arrays were purchased from Shanghai Outdo Biotech company included 152 thyroid cancer and adjacent tissues, mostly PTC and with a small amount of other thyroid cancer.”

Probably not a substantial claim: may not pass S3 (load-bearing).

The study was approved by the Ethics Committee (Approval number: bc2022062).

“the study was approved by the Ethics Committee (Approval number: bc2022062).”

May combine two claims.

At differentiating cell state, postnatal tissue and initial transformation, low BRAF/MAPK/USP15 depletes TBX3.

“While at differentiating cell state, postnatal tissue and initial transformation, low BRAF/MAPK/USP15 depletes TBX3 respectively.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

All mice experiment procedures and protocols were evaluated and authorized by the Regulations of Tianjin Laboratory Animal Management and strictly followed the guidelines under the Institutional Animal Care and Use Committee of Tianjin Medical University (Approval number: SYXK-(Jin) 2019-0004).

“All mice experiment procedures and protocols were evaluated and authorized by the Regulations of Tianjin Laboratory Animal Management and strictly followed the guidelines under the Institutional Animal Care and Use Committee of Tianjin Medical University (Approval number: SYXK-(Jin) 2019-0004).”

May combine two claims.

Usp15 global knockout mice display growth retardation and average weights 20% less compared with wild-type littermates.

“Usp15 global knock-out mice display growth retardation, and the average weights are 20% less compared with wild-type littermates52.”

• cites [52] Srihari, S. & Ragan, M. A. Systematic tracking of dysregulated modules identifies novel genes in cancer. Bioinformatics 29, 1553–1561 (2013). sourceNot checked — no full text of the source

May combine two claims.

Reactivation of developmental transcription factors drives carcinogenesis, with TBX3 as a paradigmatic illustration.

“Importantly, our study supports TBX3 as a paradigmatic illustration on how reactivation of developmental transcription factors drives carcinogenesis.”