SIX1 Research Articles

SIX1 expression and its clinicopathological significance: difference between classic and follicular variant papillary thyroid carcinoma

BackgroundPapillary thyroid carcinoma (PTC) is the most common type of thyroid carcinoma, representing the majority of thyroid cancer cases. Most patients with PTC have an excellent prognosis following treatment, yet approximately 10% face mortality within ten years, primarily due to lymph node metastasis (LNM) or local recurrence. The SIX1 gene, a member of the SIX gene superfamily, encodes a transcription factor integral to the development of certain tissues during embryogenesis. The impact of SIX1 in different subtypes of PTC has not been studied previously.ObjectiveThe purpose of this study was to investigate the expression of SIX1 protein in PTC and to explore its relationship with clinical behavior in two subtypes of PTC: classic PTC (C-PTC) and follicular variant PTC (FV-PTC).Materials and methodsUsing immunohistochemistry, the study analyzed 125 primary PTC cases, including 85 cases of C-PTC and 40 cases of FV-PTC.ResultsThe study found significant positive associations between high SIX1 expression and several adverse clinical features across the PTC samples. High SIX1 expression was linked with increased tumor size, multifocal tumors, LNM, high-grade tumor features, advanced tumor stage, lymphovascular invasion, perineural invasion, and extrathyroidal extension (ETE). Within the classic PTC subgroup, high SIX1 expression showed significant positive correlations with Tumor size (P = 0.04), Multifocality (P = 0.02) and High-grade features (P = 0.03). In the follicular variant subgroup, high SIX1 expression was significantly associated with Lymph node metastasis (LNM) (P = 0.001), Lymphovascular invasion (P = 0.03), ETE (P = 0.003) and tumor stage (P = 0.007).ConclusionsThe findings of this study indicate that SIX1 expression is a marker of poor prognosis in PTC, suggesting that its high expression is linked with more aggressive tumor characteristics and advanced disease stages. Importantly, the impact of SIX1 expression varies between C-PTC and FV-PTC, predicting distinct prognostic factors in each subtype. This suggests that SIX1 could be utilized not only as a prognostic biomarker but also in developing subtype-specific therapeutic strategies for PTC patients.

Multiomic factor analysis for pathologic complete response (pCR) after 12 weeks of pembrolizumab + trastuzumab + pertuzumab in HER2-enriched (HER2-E) early breast cancer (eBC) in the Keyriched-1 trial.

590 Background: pCR successfully identified candidates for (chemotherapy) de-escalation in the ADAPT HER2+ trial program. Here, we report biomarker analysis for pCR in the single arm, hypothesis-generating Keyriched-1 trial (NCT03988036) in HER2-E eBC treated with pembrolizumab and dual HER2 blockade. The trial rationale is based on high efficacy of anti-HER2 agents and potentially high immunogenicity and immune checkpoint protein expression in HER2-E eBC. Methods: 48 patients with HER2 2+ (ISH+) or 3+ eBC (stage I-III) and HER2-E subtype received pembrolizumab (200 mg), trastuzumab biosimilar (loading dose, LD 8 mg/kg, maintenance dose, MD 6 mg/kg), and pertuzumab (LD 840 mg/kg, MD 420 mg/kg) q3w for 12 weeks. Primary outcome was pCR (ypT0/is ypN0). Multiomic factor analysis was performed using different combinations of biomarker datasets: baseline BC360 single genes and gene signatures, multiplexed immunohistochemistry (mIHC), stromal tumor infiltrating lymphocytes (sTILs), somatic mutations and tumor mutational burden, and changes in circulating tumor DNA status under therapy. Factors representing combined markers developed from these pooled datasets were identified based on eigenvalue >1 criteria. Logistic regression with factors dichotomized by median score was conducted to analyze their association with pCR. Furthermore, logistic regression with elastic net regularization was performed using all single markers, factors from multiomic factor analysis, and clinical characteristics. Results: Factor involving gene expression (mainly related to immune response and tumorigenesis), mIHC markers (immune and HER2) in stroma, and sTILs datasets was significantly associated with pCR. Using the median as cutoff, higher scores increased the odds of pCR (unadj. OR 5.00, 95%CI 1.35, 18.56; p=.016). pCR rates were 66.7% and 28.6% in the high and low score groups, respectively. Effect of the factor (high vs low; OR 2.19) was also important in a model that additionally included clinical markers: grade (3 vs 2; OR 2.57), ER status (ER+ vs ER-; OR 0.89), cT (cT 2/3 vs 1; OR 0.69), cN (cN 1/2 vs 0; OR 0.51), and PR status (PR+ vs PR-; OR 0.34). When standardized values for all individual markers from gene expression, mIHC, and sTIL datasets were analyzed, markers with greatest impact on pCR vs. non-pCR were genes FNBP1, CD36, MYCN, and SIX1 (OR 1.43-1.62) and PR status (OR 0.65), with stronger impact than grade (OR 1.22) or nodal status (OR 0.90). Conclusions: Our multiomic analysis uncovered potential biomarkers for pCR in HER2-E eBC treated with immune therapy and dual-HER2 blockade alone. These results together with the results from the ADAPT translational research program support validation in larger trials investigating chemotherapy-free regimens in selected patients with HER2+ eBC. Clinical trial information: NCT03988036 .

Molecular characterization of Secreted in Xylem 1 (Six1) gene of Fusarium oxysporum causing wilt of potato (Solanum tuberosum)

AbstractDeciphering effector genes of plant‐pathogenic fungi is key to understanding their role in pathogenicity because acquisition of such genes through horizontal transfer may result in emergence of new pathogenic races. A full‐length (837 bp) Six1 gene has been cloned and sequenced from the genome of Fusarium oxysporum FPo isolated from roots of wilted potatoes in West Bengal, India. The isolate was identified based on conidial morphology and sequencing of the 28S rDNA and elongation factor 1α gene. Koch's postulates established that the isolate could incite wilting in potato plants. The Six Gene Expression 1 gene (Sge1) was amplified from the isolate and compared with that of other wilt‐causing F. oxysporum isolates. The Six1 gene had no intron and it encoded 278 amino acids, with a calculated molecular weight of 30.6 kDa, estimated isoelectric point 5.66 and theoretical extinction coefficient of 57,410 M−1 cm−1. Multiple sequence alignment of SIX1 amino acid sequences showed that the length of SIX1 varied among F. oxysporum formae speciales and different isolates of the same forma specialis. The predicted secondary structure of FPoSIX1 contained four α‐helices and 14 β‐sheets. Its predicted tertiary structure showed 92% query coverage and 67.37% identity with the template of the SIX1 protein of F. oxysporum f. sp. lycopersici PDB code: 7t69. The QMEAN score of this model was −2.53 and the model was validated using the Ramachandran Phi/Psi plot. Structure analysis of the effector protein will be helpful to identify its specific function and recognition by the host resistance protein.

Research on the toxicological prognostic significance of age-related genes in endometrial cancer unveiling key factors in patient prognosis.

This study investigates the influence of aging-related genes on endometrial cancer, a prominent gynecological malignancy with rising incidence and mortality. By analyzing gene expression differences between cancerous and normal endometrial tissues, 42 aging-related genes were identified as differentially expressed. Utilizing the TCGA-UCEC sample, consensus clustering divided the samples into two molecular subgroups, Aging low and Aging high, based on their expression profiles. These subgroups showed distinct prognoses and survival rates, with the Aging high group associated with DNA repair and cell cycle pathways, and the Aging low group showing suppressed metabolic pathways and increased immune cell infiltration, suggesting a potential for better immunotherapy outcomes. Mutation analysis did not find significant differences in mutation frequencies between the groups, but a high Tumor Mutation Burden (TMB) correlated with better prognosis. A risk score model was also developed, showcasing significant prognostic power. Further analysis of the SIX1 gene revealed its overexpression in cancer cells. Drug sensitivity tests indicated that the low-risk group might respond better to chemotherapy. This research underscores the significance of aging-related genes in endometrial cancer, offering insights into their prognostic value and therapeutic potential, which could lead to personalized treatment approaches and enhanced patient management.

Turmeric Inhibits MDA-MB-231 Cancer Cell Proliferation, Altering miR-638-5p and Its Potential Targets.

Recent research suggests curcumin extracted from the turmeric plant may inhibit the proliferation of cancer cells by controlling the expression of microRNAs (miRNAs). The effect of phenolic curcumin on miR-638-5p and potential target gene expressions in the triple negative breast cancer (TNBC) cell line MDA-MB-231 was investigated in this study. GSE154255 and GSE40525 datasets were downloaded and analyzed using GEO2R to identify dysregulated miRNAs in TNBC. To find differently expressed genes in breast cancer (BRCA), The Cancer Genome Atlas Program data was examined. Utilizing in silico tools, KEGG, GO, and other enrichment analyses were performed. The databases miRNet, miRTarBase v8.0, and TarBase v.8 were used for miRNA and mRNA matching. Real-time quantitative reverse transcription polymerase chain reaction was used to examine the levels of miRNA and its targets in miRNA mimic transfected/curcumin-treated MDA-MB-231 cultures and controls. The cell viability detection kit-8 method was used to assess cell viability, and the scratch assay was used to conduct migration assessment. Bioinformatics analysis showed that miR-638-5p was significantly reduced in TNBC patients. Experimental results showed that miR-638-5p was upregulated in MDA-MB-231 treated with curcumin, while the potential target genes of miR-638-5p, CFL1, SIX4, MAZ, and CDH1 were downregulated. Mimic miR-638-5p transfection inhibited MDA-MB-231 cell proliferation and reduced migration and expression of CFL1, SIX4, and MAZ genes was decreased in mimic miR-638-5p transfected cells. These findings suggest that curcumin exerts its anticancer effects on MDA-MB-231 cells by modulating the expression of miR-638-5p and its possible target genes.

Manzamine-A Alters In Vitro Calvarial Osteoclast Function.

Manzamine-A is a marine-derived alkaloid that has demonstrated antimalarial and antiproliferative properties and is an emerging drug lead compound as a possible intervention in certain cancers. This compound has been found to modulate SIX1 gene expression, a target that is critical for the proliferation and survival of cells via various developmental pathways. As yet, little research has focused on manzamine-A and how its use may affect tissue systems including bone. Here we hypothesized that manzamine-A, through its interaction with SIX1, would alter precursor cells that give rise to the bone cell responsible for remodeling: the osteoclast. We further hypothesized reduced effects in differentiated osteoclasts, as these cells are generally not mitotic. We interrogated the effects of manzamine-A on preosteoclasts and osteoclasts. qrtPCR, MTS cell viability, Caspase 3/7, and TRAP staining were used as a functional assay. Preosteoclasts show responsiveness to manzamine-A treatment exhibited by decreases in cell viability and an increase in apoptosis. Osteoclasts also proved to be affected by manzamine-A but only at higher concentrations where apoptosis was increased and activation was reduced. In summary, our presented results suggest manzamine-A may have significant effects on bone development and health through multiple cell targets, previously shown in the osteoblast cell lineage, the cell responsible for mineralized tissue formation, and here in the osteoclast, the cell responsible for the removal of mineralized tissue and renewal via precipitation of bone remodeling.

A genomic region associated with iteroparous spawning phenology is linked with age-at-maturity in female steelhead trout.

Age-at-maturity and iteroparity are two life history variations of steelhead trout (Oncorhynchus mykiss) that are believed to increase population resilience and stability. While repeat-spawning individuals are thought to have historically made up a substantial portion of the reproductive population in the Columbia River and the majority of females still attempt outmigration as kelts, return rates of repeat-spawner are low throughout the basin and below 1% for the furthest migrating stocks. Notably, outmigrating adults exhibit variation in rematuration phenology, displaying either "consecutive" (reproduce immediately the following season) or "skip" (delay spawning for future seasons) spawning patterns. Here, we use low coverage whole genome sequencing of consecutive versus skip spawning female Columbia River steelhead from two populations to test for genomic differences between these two iteroparous phenotypes. We identified genomic regions on several chromosomes which were associated with the phenology of iteroparity, including a region on chromosome 25 containing two genes, estradiol receptor beta (ERβ) and glycoprotein hormone beta-5 (GPHB5), which, in mammals, are estrogen-sensitive and expressed in reproductive tissues. Allele frequencies in this ERβ/GPHB5 region differed among female steelhead of different age at maturity, but not males. These genes also shared an island of linkage disequilibrium with the SIX6 gene, 600Kbp away on the same chromosome, a region of known association with age-at-maturity. These observations contribute to growing evidence that age-at-maturity and the phenology of iteroparity are determined by overlapping physiological processes and genetic pathways.

Genetic and Pharmacological Interruption of the SIX1/EYA2 Axis Impairs Leukemia Proliferation

Background: The CALM-AF10 translocation is found in 5-10% of T-cell acute lymphoblastic leukemias (T-ALL), and a subset of acute myeloid leukemias (AML). CALM-AF10 leukemias are characterized by elevated expression of proleukemic HOXA genes. Since HOXA genes are difficult to target, we sought to identify non- HOXA effector genes through RNA sequencing and Microarray analyses, and showed that SIX1 expression is increased in CALM-AF10 leukemia cells. Like HOXA genes, SIX1 is a homeobox gene involved in cell proliferation, embryogenesis, and apoptosis. SIX1 interacts with the cofactor Eyes Absent 2 (EYA2), a protein phosphatase, to transcriptionally activate developmental genes, the TGFβ pathway, and the epithelial-mesenchymal transition (EMT). SIX1 expression is elevated during development but decreases with maturation. Intriguingly, overexpression of SIX1 has been observed in numerous malignancies including breast cancer, ovarian cancer, gliomas and esophageal cancer, and SIX1 is involved in accelerating the epithelial mesenchymal transition (EMT) and metastasis. Knockdown of either SIX1 or EYA2 has been shown to reverse these effects, and two novel inhibitors - one of the SIX1/EYA2 complex (Compound 8430, “8430”) and one of the EYA2 phosphatase (Compound 9987, “9987”) - have replicated the effects of SIX1 or EYA2 knockdown. Methods: SIX1 gene and protein expression were assessed in leukemia cell lines via RT-qPCR and Western Blot. SIX1 expression vectors were transduced into fetal liver hematopoietic stem cells (HSC) and immortalization was assessed using colony assays. CALM-AF10 leukemia cells lines were derived from irradiated mice transplanted with HSC retrovirally transfected with CALM-AF10 plasmids created in our lab. The established leukemia cell lines Jurkat, MOLT16, OCI-M2, TF-1, and SHI-1 were obtained from ATCC or DSMZ. shRNAs targeting SIX1 were lentivirally transduced into CALM-AF10 and SHI1leukemia cell lines. Cell-Titer-Glo assays and liquid culture were used to assess the effects of shRNAs, 8430, or 9987 on cell proliferation and cell growth. SIX1 gene expression in leukemias was determined from The Cancer Dependency Map from The Broad Institute using R. Results: We first validated RNAseq and Microarray studies, showing that CALM-AF10 induces SIX1 expression in murine fibroblasts and murine HSC, and localizes to the SIX1 locus. Furthermore, SIX1 overexpression was sufficient to immortalize murine fetal liver HSC (FL-mHSCs), implying a role in leukemic transformation. Multiple murine derived CALM-AF10 cell lines displayed increased SIX1 expression compared to fresh murine bone marrow and isolated HSCs. shRNA knockdown of SIX1 decreased viability of murine CALM-AF10 cells in culture. In addition, both the SIX1/EYA2 complex inhibitor (8430) and the EYA2 inhibitor (9987) decreased CALM-AF10 leukemia cell proliferation in vitro. To expand the relevance of SIX1 to other leukemias, we then queried The Cancer Dependency Map from the Broad Institute and identified other leukemia cell lines with increased SIX1 expression, including Jurkat and Molt16 (T-ALL), and SHI-1, OCIM2, and TF-1 (AML). SIX1 expression in these cells was validated by immunoblot and shRNA knockdown of SIX1 slowed the proliferation of SHI-1 cells. Finally, the 8430 and 9987 inhibitors reduced the proliferation of Jurkat, OCI-M2, and SHI-1 cells at doses similar to those used in CALM-AF10 leukemias. Conclusions: We have identified involvement of the SIX1/EYA2 axis in several different leukemias, including T-ALL and AML. Furthermore, we have shown that inhibitors of the SIX1/EYA2 interaction and of EYA2 reduce the proliferation of SIX1 expressing leukemias, suggesting a potential new therapeutic target in these leukemias.

Unraveling Clonal Evolution and Mechanisms of Treatment Resistance in Murine KMT2A-Rearranged Leukemia with Subclonal FLT3 N676K

Our understanding of how individual mutations, whether present in all or just a subset of the leukemia cells, affect cellular response to therapy is limited. Herein, we investigate the impact of different therapies on survival, evolution, and resistance patterns in an acute myeloid leukemia (AML) mouse model driven by KMT2A::MLLT3 and subclonal FLT3 N676K. Leukemic bone marrow expressing KMT2A::MLLT3-mCherry in all cells and FLT3 N676K-GFP in 40% of cells was re-transplanted into sublethally irradiated recipients. Upon engraftment, recipients were subjected to different treatments, including chemotherapy (cytarabine for 5 days+doxorubicin for 3 days), the FLT3 inhibitor AC220, chemotherapy followed by AC220, or AC220+Trametinib, a MEK inhibitor. Targeted treatment was administered for 28 days, while the control group received vehicle ( Fig 1a). Each treatment prolonged survival with a median latency of 30 days for chemotherapy 37.5 days for AC220, 42 days for chemotherapy+AC220, and 45 days for AC220+Trametenib, and 25.5 days for control mice. At sacrifice, all mice displayed splenomegaly and leukocytosis. The treatment impacted the evolution of the KMT2A:: MLLT3+ FLT3 N676K cells and they expanded to clonal dominance in control and chemotherapy-treated mice. However, three distinct patterns of evolution were detected in AC220-treated mice with the FLT3 N676K-containing cells either expanding to clonal dominance (>80% of KMT2A:: MLLT3+ FLT3 N676K), the FLT3 N676K-containing cells being eradicated (>80% of KMT2A::MLLT3-alone), or dual similar sized clones expressing KMT2A:: MLLT3-alone or KMT2A::MLLT3+ FLT3 N676K(Fig1 b).Eradication of the FLT3 N676K-cells was rare, predominantly observed upon AC220+Trametinib treatment and the frequency of dual clones increased when chemotherapy was followed by AC220, in line with treatment affecting the evolution of genetically distinct clones. RNA-sequencing was used to determine altered gene expression patterns upon resistance and unveiled three major clusters including 1) mice expressing KMT2A:: MLLT3-alone, 2) control and chemotherapy-treated mice, and 3) AC220-treated mice. Notably, a subset of AC220-treated mice clustered close to the control and chemotherapy-treated mice suggesting potential resistance mechanisms through activation of the MEK/ERK-pathway. All leukemias had a myeloid Cd11b + phenotype. However, the control and chemotherapy-treated leukemias also displayed an aberrant expression of the lymphoid marker B220 and showed enrichment of gene sets correlating with stemness and oxidative phosphorylation, that suggested a switch in cellular phenotype and metabolic state. In contrast, AC220-treated leukemias lacked or had a low fraction of B220 + cells and showed enrichment of gene sets correlating with granulocyte-monocyte progenitors (GMP) and immune regulatory pathways (Fig 1 c). Acquired AC220-resistance mutations was rare (n=2), suggesting activation of alternative pathways upon resistance. Re-treatment of established cell lines from treated animals with AC220 showed that the cells were resistant. To uncover mechanisms of resistance at the cellular level, single cell RNA-sequencing was performed on four mice and revealed the emergence of distinct cellular subpopulations in AC220-treated mice, with a strong GMP signature and upregulation of the homeobox gene Six1(Fig 1d).Overexpression of Six1 in all AC220-treated leukemias was further confirmed by bulk RNA-sequencing. Interestingly, Six1 has previously been described as a regulator for leukemia stem cell maintenance in AML and under Wnt/ß-catenin signalling control. Subsequent drug assays showed AC220-treated cells exhibited sensitivity to Six1 pharmacological inhibition, suggesting a dependency on Six1, as well as sensitivity to Wnt/ß-catenin inhibition. Taken together, the treatment given affected survival and impacted evolution of the FLT3 N676K-leukemia cells. The general absence of acquired mutations in most mice suggests that target-independent mechanisms may underline acquired resistance in most mice, and we propose the Six1/Wnt/ß-catenin axis as a potential vulnerability upon AC220-resistance.

Combinatorial Atoh1, Gfi1, Pou4f3, and Six1 gene transfer induces hair cell regeneration in the flat epithelium of mature guinea pigs

Flat epithelium (FE) is a condition characterized by the loss of both hair cells (HCs) and supporting cells and the transformation of the organ of Corti into a simple flat or cuboidal epithelium, which can occur after severe cochlear insults. The transcription factors Gfi1, Atoh1, Pou4f3, and Six1 (GAPS) play key roles in HC differentiation and survival in normal ears. Previous work using a single transcription factor, Atoh1, to induce HC regeneration in mature ears in vivo usually produced very few cells and failed to produce HCs in severely damaged organs of Corti, especially those with FE. Studies in vitro suggested combinations of transcription factors may be more effective than any single factor, thus the current study aims to examine the effect of co-overexpressing GAPS genes in deafened mature guinea pig cochleae with FE. Deafening was achieved through the infusion of neomycin into the perilymph, leading to the formation of FE and substantial degeneration of nerve fibers. Seven days post neomycin treatment, adenovirus vectors carrying GAPS were injected into the scala media and successfully expressed in the FE. One or two months following GAPS inoculation, cells expressing Myosin VIIa were observed in regions under the FE (located at the scala tympani side of the basilar membrane), rather than within the FE. The number of cells, which we define as induced HCs (iHCs), was not significantly different between one and two months, but the larger N at two months made it more apparent that there were significantly more iHCs in GAPS treated animals than in controls. Additionally, qualitative observations indicated that ears with GAPS gene expression in the FE had more nerve fibers than FE without the treatment. In summary, our results showed that co-overexpression of GAPS enhances the potential for HC regeneration in a severe lesion model of FE.

The Identification of Gamma-Glutamyl Hydrolase in Uterine Corpus Endometrial Carcinoma: a Predictive Model and Machine Learning.

Poor neoplastic differentiation contributes to the rapid progression of uterine corpus endometrial carcinoma (UCEC). Thus, it is essential to identify candidate genes, clarifying the carcinogenesis and progression of UCEC. We screened genes that affect differentiation and prognosis in UCEC. Least absolute selection and shrinkage operator (LASSO) regression, univariate Cox, and multivariate Cox proportional risk regression analyses were performed to screen out γ-glutamyl hydrolase (GGH) as the candidate gene. The clinical value of GGH on prognosis was evaluated. The relationship between GGH and immune infiltration was assessed by CIBERSORT, EPIC, ssGSEA, unsupervised clustering and immunohistochemistry (IHC). Additionally, we investigated the effect of GGH knockdown in vitro. Among the GGH, CDKN2A, and SIX1 genes, the impact of GGH was predominant on immune infiltration in UCEC. A nomogram containing GGH and other clinical features showed good predictive performance via curve analysis (DCA). In the functional analysis, GGH affected differentiation, tumour proliferation, and immune regulation. The immunosuppressive components were enriched in the GGH-high group, with poor immunotherapy efficacy. The study suggests that GGH may influence the progression of UCEC by regulating the glycolytic process. GGH is closely associated with various immune cell infiltrations. Our study demonstrates the prognostic role of GGH in carcinogenesis in UCEC.

Transcriptomic analysis reveals the role of SIX1 in mouse cranial neural crest patterning and bone development.

Genetic variants of the transcription factor SIX1 and its co-factor EYA1 underlie 50% of Branchio-oto-renal syndrome (BOR) cases. BOR is characterized by craniofacial defects, including malformed middle ear ossicles leading to conductive hearing loss. In this work, we expand our knowledge of the Six1 gene regulatory network by using a Six1-null mouse line to assess gene expression profiles of E10.5 mandibular arches, which give rise to the neural crest (NC)-derived middle ear ossicles and lower jaw, via bulk RNA sequencing. Our transcriptomic analysis led to the identification of 808 differentially expressed genes that are related to translation, NC cell differentiation, osteogenesis, and chondrogenesis including components of the WNT signaling pathway. As WNT signaling is a known contributor to bone development, we demonstrated that SIX1 is required for expression of the WNT antagonist Frzb in the mandibular arch, and determined that SIX1 expression results in repression of WNT signaling. Our results clarify the mechanisms by which SIX1 regulates the development of NC-derived craniofacial elements that are altered in SIX1-associated disorders. In addition, this work identifies novel genes that could be causative to this birth defect and establishes a link between SIX1 and WNT signaling during patterning of NC cells.

Pathogenicity of Fusarium oxysporum and Fusarium proliferatum isolates from symptomless onions (Allium cepa) and onions with Fusarium basal rot

AbstractSeveral Fusarium species cause disease in onion (Allium cepa), resulting in significant yield losses. In this study, isolates of Fusarium oxysporum and Fusarium proliferatum from diseased and symptomless mature onion bulbs were tested for pathogenicity on onion seedlings and mature bulbs. For F. oxysporum isolates, the outcome of the test on mature bulbs correlated well with the symptom status of the original bulb, whereas for F. proliferatum, such a correlation was not seen, suggesting a different mechanism of symptom development. Those F. oxysporum isolates that carried the Secreted In Xylem (SIX) genes, CRX genes and C5 gene were significantly more aggressive on both seedlings and mature bulbs. However, the SIX‐negative F. oxysporum isolates also significantly reduced the emergence of onion seedlings, and thus a division into pathogenic and nonpathogenic F. oxysporum isolates was not obvious. On mature bulbs, those SIX‐negative isolates that carried the gene CRX2 were significantly more virulent than those without CRX2. The F. proliferatum isolates were all pathogenic to onion and carried one SIX2 gene homologue, SIX2‐1. The majority of F. proliferatum isolates also carried another homologue, SIX2‐2. Several isolates negative for SIX2‐2 had another potential virulence gene, CRX2, suggesting that these two genes could encode overlapping functions. The SIX2‐2 sequence was identical in all those isolates harbouring it, while SIX2‐1 showed variation that agreed with the phylogeny based on the translation elongation factor 1‐α sequence. This suggests that the two SIX2 genes of F. proliferatum might have been acquired separately.

Physiological race characterisation of Fusarium oxysporum strains infecting tomato employing candidate pathogenicity genes and host resistance.

Physiological races of 14 strains of Fusarium oxysporum f.sp. lycopersici were established by PCR profiling SIX gene expressions. No amplification of the SIX4 (Avr1) gene was observed in any of the 14 strains. Based on amplification of the SIX3 (Avr2) gene, 6 strains were distinguished as race 2. Race 2 strains are known to contain identical SIX3 sequences and differ from race 3 strains by single point mutations. Hence, based on polymorphic amplicons of the SIX3 gene detected by stringent PCR conditions, 8 strains were identified as race 3. The identity of the physiological races of the strains was validated by inoculating on three germplasm lines, EC-814916, FEB-2 and Pusa Rohini carrying I-2, I-3 and no I gene, respectively. The race 2 and race 3 strains were avirulent on EC-814916 and FEB-2 lines, respectively. All the 14 fungal strains were pathogenic on Pusa Rohini, the Fusarium wilt susceptible cultivar lacking R genes and exhibited different levels of virulence. In evaluating two other potential pathogenicity genes, Fow1 and Fow2 as markers for virulence, their expressions were observed among both the races of the Fol strains, and hence are not potential candidates for physiological race discrimination. However, strong expressions of the genes in the root tissues inoculated with the highly virulent strain, TOFU-IHBT in comparison to the uninoculated control indicated their roles in fungal pathogenicity. To understand the role of these pathogenicity genes in countering the host defence mechanisms, their expressions in response to ROS and phenolics, the earliest known defence mechanisms of host plants were assessed. In H2O2, the Fow2 gene expressed 1.4-fold greater than that of the control. On the contrary, in relation to the control, the expressions of Fow1 were strongly repressed exhibiting 0.7-to 0.8-fold lesser at 0.1 mM through 3 mM concentrations than that of the control indicating that the gene is modulated by the phenolic acid indicating the roles of Fow2 and Fow1 in alleviating oxidative stress and targeted by the phenolic acid, respectively.

A novel heterozygous SIX1 missense mutation resulted in non-syndromic unilateral hearing loss.

Familial non-syndromic unilateral hearing loss (NS-UHL) is rare and its genetic etiology has not been clearly elucidated. This study aimed to identify the genetic cause of NS-UHL in a three-generation Chinese family. Detailed medical history consultation and clinical examination were conducted. Further, whole-exome sequencing (WES) was performed to identify the genetic etiology of the proband, and the variant was verified by Sanger sequencing. A novel missense mutation, c.533G>C (p.Arg178Thr), in the SIX homeobox 1 gene (SIX1) was identified in four patients and co-segregated with NS-UHL in a three-generation Chinese family as a dominant trait. Using bioinformatics analyses, we show that this novel mutation is pathogenic and affects the structure of SIX1 protein. These data suggest that mutations in SIX1 gene are associated with NS-UHL. Our study added the NS-UHL phenotype associated with SIX1, and thereby improving the genetic counseling provided to individuals with SIX1 mutations.

Effects of transcription factor SIX2 gene on the proliferation of bovine skeletal muscle satellite cells

Objective: To investigate the effect of SIX2 gene on the proliferation of bovine skeletal muscle satellite cells. Methods: Bovine skeletal muscle satellite cells were used as experimental materials, and the expression of SIX2 gene in bovine skeletal muscle satellite cells was detected by real-time quantitative PCR at 24 h, 48 h, and 72 h of proliferation. The SIX2 gene overexpression vector was constructed by homologous recombination. The SIX2 gene overexpression plasmid and the control empty plasmid were transfected into bovine skeletal muscle satellite cells, and each group had three complex Wells. The cell viability was detected by MTT assay at 24 h, 48 h and 72 h after transfection. At 48 h after transfection, the cell cycle was detected by flow cytometry, and the expressions of cell proliferation marker genes were detected by real-time quantitative PCR (qRT-PCR) and Western blot. Results: With the proliferation of bovine skeletal muscle satellite cells, the expression of SIX2 mRNA was increased. Compared with the control group, the expressions of SIX2 mRNA and protein in the SIX2 gene overexpression plasmid group were increased by 18 and 2.6 times, respectively (P＜0.01). The cell viability of the SIX2 gene overexpression plasmid group was increased (P＜0.01), the proportion of G1 cells was decreased by 24.6%, and the proportion of S phase and G2 phase cells was increased by 20.3% and 4.31%, respectively (P＜0.01). The mRNA and protein expressions of Pax7 gene were increased by 15.84 and 1.22 times, respectively, and the mRNA and protein expressions of proliferation marker genes PCNA and CCNB1 were increased by 4.82, 2.23,1.55 and 1.46 times, respectively (P＜0.01). Conclusion: Overexpression of SIX2 gene promotes the proliferation of bovine skeletal muscle satellite cells.

Expression of SIX1b and SIX1c effector genes and banana resistance genes during Foc TR4 infection on banana cultivars

Abstract. Ulilalbab AR, Widinugraheni S, Masanto, Subandiyah S, Wibowo A. 2022. Expression of SIX1b and SIX1c effector genes and banana resistance genes during Foc TR4 infection on banana cultivars. Biodiversitas 23: 5314-5322. The relative expression SIX1 genes isolates of Foc TR4 and banana resistance genes have not been intensively studied. This study aimed to determine the expression of SIX1 genes of Foc TR4 and banana resistance genes. Twelve Foc TR4 isolates were collected from several regions in Indonesia. DSI analysis was performed to categorize their virulence levels. The representative Foc TR4 isolates from different virulence levels were artificially inoculated on the Musa acuminata Colla Cavendish subgroup and cv. Barangan and incubated for 48, 72, and 96 HPI. The expressed genes were quantitatively analyzed using the qPCR technique using primers to amplify SIX1b, SIX1c, chitinase, and PR-protein 1 genes. The results categorized the virulence of Foc TR4 isolates into moderate, virulent, and high virulent. The isolates of KJG and Batu-4 were selected for gene expression study representing moderate and high virulent groups, respectively. The results of in planta assay found that the expression of SIX1b, SIX1c, chitinase, and PR-protein1 was upregulated on the inoculated plants during the incubation period. However, the expression of these genes was increasingly upregulated in both bananas at early-stage inoculation. We assumed that plant defense genes of bananas might actively encounter the common virulence mechanisms of Foc TR4 at the initial stage of inoculation.

Manzamine-A Alters In Vitro Calvarial Osteoblast Function.

Manzamine-A is a marine-derived alkaloid which has anti-viral and anti-proliferative properties and is currently being investigated for its efficacy in the treatment of certain viruses (malaria, herpes, HIV-1) and cancers (breast, cervical, colorectal). Manzamine-A has been found to exert effects via modulation of SIX1 gene expression, a gene critical to craniofacial development via the WNT, NOTCH, and PI3K/AKT pathways. To date little work has focused on Manzamine-A and how its use may affect bone. We hypothesize that Manzamine-A, through SIX1, alters bone cell activity. Here, we assessed the effects of Manzamine-A on cells that are responsible for the generation of bone, pre-osteoblasts and osteoblasts. PCR, qrtPCR, MTS cell viability, Caspase 3/7, and functional assays were used to test the effects of Manzamine-A on these cells. Our data suggests Six1 is highly expressed in osteoblasts and their progenitors. Further, osteoblast progenitors and osteoblasts exhibit great sensitivity to Manzamine-A treatment exhibited by a significant decrease in cell viability, increase in cellular apoptosis, and decrease in alkaline phosphatase activity. In silico binding experiment showed that manzamine A potential as an inhibitor of cell proliferation and survival proteins, i.e., Iκb, JAK2, AKT, PKC, FAK, and Bcl-2. Overall, our data suggests Manzamine-A may have great effects on bone health overall and may disrupt skeletal development, homeostasis, and repair.

From clinical to molecular diagnosis: relevance of diagnostic strategy in two cases of branchio-oto-renal syndrome – case report

BackgroundBranchio-oto-renal syndrome (BOR) is an autosomal dominant disorder characterized by deafness, branchiogenic malformations and renal abnormalities. Pathogenic variants in EYA1, SIX1 and SIX5 genes cause almost half of cases; copy number variants (CNV) and complex genomic rearrangements have been revealed in about 20% of patients, but they are not routinely and commonly included in the diagnostic work-up.Case presentationWe report two unrelated patients with BOR syndrome clinical features, negative sequencing for BOR genes and the identification of a 2.65 Mb 8q13.2–13.3 microdeletion.ConclusionsWe highlight the value of CNV analyses in high level of suspicion for BOR syndrome but negative sequencing for BOR genes and we propose an innovative diagnostic flow-chart to increase current detection rate. Our report confirms a mechanism of non-allelic homologous recombination as causing this recurrent 8q13.2–13.3 microdeletion. Moreover, considering the role of PRDM14 and NCOA2 genes, both involved in regulation of fertility and deleted in our patients, we suggest the necessity of a longer follow-up to monitor fertility issues or additional clinical findings.

Association analyses of rare variants identify two genes associated with refractive error.

PurposeGenetic variants identified through population-based genome-wide studies are generally of high frequency, exerting their action in the central part of the refractive error spectrum. However, the power to identify associations with variants of lower minor allele frequency is greatly reduced, requiring considerable sample sizes. Here we aim to assess the impact of rare variants on genetic variation of refractive errors in a very large general population cohort.MethodsGenetic association analyses of non-cyclopaedic autorefraction calculated as mean spherical equivalent (SPHE) used whole-exome sequence genotypic information from 50,893 unrelated participants in the UK Biobank of European ancestry. Gene-based analyses tested for association with SPHE using an optimised SNP-set kernel association test (SKAT-O) restricted to rare variants (minor allele frequency < 1%) within protein-coding regions of the genome. All models were adjusted for age, sex and common lead variants within the same locus reported by previous genome-wide association studies. Potentially causal markers driving association at significant loci were elucidated using sensitivity analyses by sequentially dropping the most associated variants from gene-based analyses.ResultsWe found strong statistical evidence for association of SPHE with the SIX6 (p-value = 2.15 x 10−10, or Bonferroni-Corrected p = 4.41x10-06) and the CRX gene (p-value = 6.65 x 10−08, or Bonferroni-Corrected p = 0.001). The SIX6 gene codes for a transcription factor believed to be critical to the eye, retina and optic disc development and morphology, while CRX regulates photoreceptor specification and expression of over 700 genes in the retina. These novel associations suggest an important role of genes involved in eye morphogenesis in refractive error.ConclusionThe results of our study support previous research highlighting the importance of rare variants to the genetic risk of refractive error. We explain some of the origins of the genetic signals seen in GWAS but also report for the first time a completely novel association with the CRX gene.