Journal: bioRxiv

Article Title: OSTM1 is a ubiquitin E3 ligase that suppresses B-cell malignancy by activating the cAMP/PKA/CREB pathway

doi: 10.64898/2026.01.23.701155

Figure Lengend Snippet: (A) Genomic alterations of OSTM1 across human cancers were derived from TCGA. Shown are the top 5 cancer types with the most frequent alterations. (B) Frequency of OSTM1 genomic deletions across BCL subtypes from published datasets, including DLBCL, multiple myeloma (MM), follicular lymphoma (FL), B-CLL, and Burkitt lymphoma (BL). (C) OSTM1 log2 copy number variations (CNVs) and percent loss across BCL subtypes in the TCGA Mature B-cell Malignancies dataset (MD Anderson Cancer Center, MDACC). (D) Spearman correlations between fraction genome altered (FGA; genomic instability) and OSTM1 copy number (left) and the Kaplan–Meier survival of patients with or without OSTM1 deletion in the same dataset in mature B-cell malignancies (dataset from C). (E) Correlations between FGA and OSTM1 deletions (left) or mRNA expression levels (right) in DLBCL patients (TCGA Firehose Legacy). (F) OSTM1 mRNA expression in normal lymphoid tissues vs. BCL subtypes using published datasets. (G) qRT-PCR analysis of OSTM1 expression in cell lines from DLBCL, MCL, MM, and BL compared to PBMCs from healthy donors. (H) Kaplan–Meier survival analyses across multiple BCL datasets, stratified by median OSTM1 expression (upper median: high expression; lower median: low expression).

Article Snippet: Human DLBCL cell lines SU-DHL-4 (CRL-2957), SU-DHL-5 (CRL-2958), and SU-DHL-10 (CRL-2963), Burkitt’s lymphoma cell lines Daudi and Ramos, as well as mantle cell lymphoma cell lines Z-138 and JeKo-1 were obtained from American Type Culture Collection (ATCC, Manassas, VA).

Techniques: Derivative Assay, Expressing, Quantitative RT-PCR

Journal: bioRxiv

Article Title: OSTM1 is a ubiquitin E3 ligase that suppresses B-cell malignancy by activating the cAMP/PKA/CREB pathway

doi: 10.64898/2026.01.23.701155

Figure Lengend Snippet: (A) OSTM1 copy number variations (CNVs) were available in DLBCL patients in TCGA Firehose Legacy. While 25% patients had shallow deletion, 12.5% had deep deletion. (B) OSTM1 deletions correlated with decreased mRNA expression in the same patients. (C) RPMI-8226 cell line stably expressing OSTM1-Flag, PBMC isolated from three healthy donors, and indicated BCL cell lines were probed for ectopically expressed or endogenous OSTM1. (D) ImageJ quantification of the ratio between non-glycosylated (∼37 kDa) and glycosylated (∼60 kDa) OSTM1.

Article Snippet: Human DLBCL cell lines SU-DHL-4 (CRL-2957), SU-DHL-5 (CRL-2958), and SU-DHL-10 (CRL-2963), Burkitt’s lymphoma cell lines Daudi and Ramos, as well as mantle cell lymphoma cell lines Z-138 and JeKo-1 were obtained from American Type Culture Collection (ATCC, Manassas, VA).

Techniques: Expressing, Stable Transfection, Isolation

Journal: bioRxiv

Article Title: OSTM1 is a ubiquitin E3 ligase that suppresses B-cell malignancy by activating the cAMP/PKA/CREB pathway

doi: 10.64898/2026.01.23.701155

Figure Lengend Snippet: (A) Oncoprint visualization of OSTM1 and CDKN2A co-deletions across different BCLs as reported in the indicated studies. (B) Frequencies of CDKN2A deletions among patients with OSTM1 deletions across BCLs (left), and the frequencies of OSTM1 deletion among patients with CDKN2A deletions (right), in the indicated studies. (C) Progression-free survival of DLBCL patients stratified by the presence of chr. 6q deletion ( OSTM1 DEL), 9p21.3 deletion ( CDKN2A DEL), both ( Co-DEL ), or neither (WT). Patients with co-deletions had worse survival. ( D ) Frequencies of individual clonotypes obtained from Igh V(D)J sequencing of mouse spleen samples. Each clonotype is color-coded according to its rank of prevalence within the corresponding sample. ( E ) Comparison of the frequency of the most expanded clonotype across samples, grouped by genotype. ( F ) Percent identity between BCL Igh V(D)J sequences and their corresponding germline sequences, grouped by genotype.

Article Snippet: Human DLBCL cell lines SU-DHL-4 (CRL-2957), SU-DHL-5 (CRL-2958), and SU-DHL-10 (CRL-2963), Burkitt’s lymphoma cell lines Daudi and Ramos, as well as mantle cell lymphoma cell lines Z-138 and JeKo-1 were obtained from American Type Culture Collection (ATCC, Manassas, VA).

Techniques: Sequencing, Comparison

Journal: bioRxiv

Article Title: OSTM1 is a ubiquitin E3 ligase that suppresses B-cell malignancy by activating the cAMP/PKA/CREB pathway

doi: 10.64898/2026.01.23.701155

Figure Lengend Snippet: (A) Left: Pie chart showing the percentage of DLBCL patients with chr. 11p amplification (17.4%). Right: Pie chart showing the fraction of DLBCL patients (n = 48, TCGA Firehose Legacy) with PDE3B amplification (16.7%). (B) Percentage of patients with PDE3B gains across B-cell malignancies (TCGA, MDACC dataset), with individual log2 copy-number values overlaid. (C) Spearman correlation between PDE3B log2 copy-number value and fraction genome altered (FGA) in mature B-cell malignancies. (D) PDE3B expression across indicated BCL cohorts, comparing normal B cells with BCLs; P values were calculated by grouping all normal samples and cancer samples separately and comparing the two groups using Student’s t-test. (E) DLBCL patient samples were obtained from the Rutgers Cancer Institute. The tumor tissue lysates and PBMC from a healthy donor were probed for PDE3B expression. (F) Kaplan-Meier survival curves in DLBCL (GSE4475) and multiple myeloma (GSE2658) patients showing reduced survival in patients with high PDE3B expression, stratified by median expression. (G) PDE3B-His was stably expressed in Ba/F3 cells. Cells were cultured in the presence or absence of IL3, and cell growth was determined by counting cell numbers. ****p<0.0001. (H) PDE3B was detected by IB across cell lines from different BCL subtypes. (I) PDE3B-His was stably expressed in indicated BCL cell lines, and cell proliferation was measured. ***p<0.001. (J and K) PDE3B was silenced with 2 sgRNAs in RPMI-8226 and OPM2 cell lines. Cell proliferation was measured. P-value calculation was done using multiple t-test comparisons, one per row ***p<0.001; ****p<0.0001. (L and M) Spleens from two-month-old C -/- and DKO mice were harvested for scRNA-seq. (L) Pan-cell-type UMAP embeddings with cells from both C -/- and DKO mice combined (n=10,000 cells per mouse). (M) Dot-plot of B-cell markers stratified by sub-population. Color represents average log fold expression.

Article Snippet: Human DLBCL cell lines SU-DHL-4 (CRL-2957), SU-DHL-5 (CRL-2958), and SU-DHL-10 (CRL-2963), Burkitt’s lymphoma cell lines Daudi and Ramos, as well as mantle cell lymphoma cell lines Z-138 and JeKo-1 were obtained from American Type Culture Collection (ATCC, Manassas, VA).

Techniques: Amplification, Expressing, Stable Transfection, Cell Culture

Journal: Hereditas

Article Title: Damnacanthus giganteus extract block diffuse large b-cell lymphoma proliferation and EMT by regulating mitochondrial dysfunction and glycolysis

doi: 10.1186/s41065-025-00531-3

Figure Lengend Snippet: DGE inhibits cell proliferation and promotes DOX sensitivity in DLBCL cells. A : CCK-8 assay to detect the effect of different concentrations of DGE on the viability of GM12878 cells; B : CCK-8 assay to detect the effect of different concentrations of DGE on the viability of SU-DHL4 cells; C : EdU assay to detect the effect of different concentrations of DGE on the proliferation rate of the cells; D : Colony formation assay to detect the effect of different concentrations of DGE on the ability of the cells to form clones; E : AnnexinV-PI double staining assay to detect the effect of different concentrations of DGE on the apoptosis rate of cells; F : CCK-8 assay to detect the effect of different concentrations of DGE on the sensitivity of SU-DHL4 cells to DOX. Cells were treated with DGE or DOX for 24 h, DOX (0.5 µM, 24 h) was used as a positive control. Each group of experiments was repeated independently 3 times, * P < 0.05, ** P < 0.01, *** P < 0.001

Article Snippet: Normal human B lymphocytes (GM12878) with human DLBCL cell line SU-DHL4 (ATCC, VA, USA) were placed in Iscove’s modifed Dulbecco’s medium (Gibco, Grand Island, NY, USA) containing 10% fetal bovine serum (FBS, Gibco) and penicillin/streptomycin 100 U/mL and cultured at 37 °C, 5% CO 2 .

Techniques: CCK-8 Assay, EdU Assay, Colony Assay, Clone Assay, Double Staining, Positive Control

Journal: Hereditas

Article Title: Damnacanthus giganteus extract block diffuse large b-cell lymphoma proliferation and EMT by regulating mitochondrial dysfunction and glycolysis

doi: 10.1186/s41065-025-00531-3

Figure Lengend Snippet: DGE impairs metastasis and EMT in DLBCL cells. A - B : Transwell assay to detect the effect of different concentrations of DGE on cell migration and invasion ability; C : Western blot to detect the effect of different concentrations of DGE on the expression levels of cellular E-cadherin, N-cadherin and Vimentin. Cells were treated with DGE or DOX for 24 h, DOX (0.5 µM, 24 h) was used as a positive control. Each group of experiments was repeated independently 3 times, * P < 0.05, ** P < 0.01, *** P < 0.001

Article Snippet: Normal human B lymphocytes (GM12878) with human DLBCL cell line SU-DHL4 (ATCC, VA, USA) were placed in Iscove’s modifed Dulbecco’s medium (Gibco, Grand Island, NY, USA) containing 10% fetal bovine serum (FBS, Gibco) and penicillin/streptomycin 100 U/mL and cultured at 37 °C, 5% CO 2 .

Techniques: Transwell Assay, Migration, Western Blot, Expressing, Positive Control

Journal: Hereditas

Article Title: Damnacanthus giganteus extract block diffuse large b-cell lymphoma proliferation and EMT by regulating mitochondrial dysfunction and glycolysis

doi: 10.1186/s41065-025-00531-3

Figure Lengend Snippet: DGE and DOX synergistically inhibit DLBCL cell growth in a mouse xenograft model. A : Schematic diagram of the in vivo experiment. Mice bearing tumors were treated with vehicle control, DGE (100 mg/kg/once per day, i.g.), DOX (1.5 mg/kg/once per week, i.p. ), or DGE + DOX for 21 days. n = 3 mice per group. B : Representative pictures of transplanted tumors in nude mice; C - D : The volume and weight of transplanted tumors in nude mice; E - F : Immunohistochemical assessment of the positive expression levels of Ki67 and N-cadherin proteins in the tissues of transplanted tumors in nude mice. * P < 0.05, ** P < 0.01, *** P < 0.001

Article Snippet: Normal human B lymphocytes (GM12878) with human DLBCL cell line SU-DHL4 (ATCC, VA, USA) were placed in Iscove’s modifed Dulbecco’s medium (Gibco, Grand Island, NY, USA) containing 10% fetal bovine serum (FBS, Gibco) and penicillin/streptomycin 100 U/mL and cultured at 37 °C, 5% CO 2 .

Techniques: In Vivo, Control, Immunohistochemical staining, Expressing

Journal: Hereditas

Article Title: Damnacanthus giganteus extract block diffuse large b-cell lymphoma proliferation and EMT by regulating mitochondrial dysfunction and glycolysis

doi: 10.1186/s41065-025-00531-3

Figure Lengend Snippet: DGE regulates mitochondrial function and glycolysis in DLBCL cells. A : MitoSOX Red staining to assess the effect of different concentrations of DGE on mitochondrial ROS; B : Flow cytometry analysis of the effect of different concentrations of DGE on MMP; C : Kits to detect the effects of different concentrations of DGE on cellular ATP production; D : Western blot to detect the effect of different concentrations of DGE on the expression levels of cellular PINK1 and PRKN; E - F : Kits to detect the effects of different concentrations of DGE on cellular glucose uptake and lactate production. Cells were treated with DGE for 24 h. Each group of experiments was repeated independently 3 times, * P < 0.05, ** P < 0.01, *** P < 0.001

Article Snippet: Normal human B lymphocytes (GM12878) with human DLBCL cell line SU-DHL4 (ATCC, VA, USA) were placed in Iscove’s modifed Dulbecco’s medium (Gibco, Grand Island, NY, USA) containing 10% fetal bovine serum (FBS, Gibco) and penicillin/streptomycin 100 U/mL and cultured at 37 °C, 5% CO 2 .

Techniques: Staining, Flow Cytometry, Western Blot, Expressing

Journal: Cancer Biology & Therapy

Article Title: PDLIM1, a novel miR-3940-5p target, regulates the malignant progression of diffuse large B-cell lymphoma

doi: 10.1080/15384047.2024.2429175

Figure Lengend Snippet: PDLIM1 silencing suppresses DLBCL cell growth and induces their apoptosis. (a) Western blot analysis of PDLIM1 protein levels in four DLBCL cell lines compared to normal human B lymphocytes (GM12878). (b) Western blot confirmation of PDLIM1 knockdown efficiency using different shRNAs in TMD8 and SU-DHL-4 cells. (c) Cell proliferation analysis (CCK-8 assay) for TMD8 and SU-DHL-4 cells following PDLIM1 knockdown. (d) Apoptosis analysis (Annexin V and PI staining) of TMD8 and SU-DHL-4 cells after PDLIM1 knockdown.

Article Snippet: Four human DLBCL cell lines (SU-DHL-4, SU-DHL-10, TMD8, and U2932) were acquired from the American Type Culture Collection (ATCC, Manassas, VA, USA).

Techniques: Western Blot, Knockdown, CCK-8 Assay, Staining

Journal: Cancer Biology & Therapy

Article Title: PDLIM1, a novel miR-3940-5p target, regulates the malignant progression of diffuse large B-cell lymphoma

doi: 10.1080/15384047.2024.2429175

Figure Lengend Snippet: Knockdown of PDLIM1 inhibits tumor growth of DLBCL cells in vivo . (a) tumor growth curves of xenografts derived from SU-DHL-4 cells expressing sh-PDLIM1 or sh-nc. (b) Final tumor weights at the end of the experiment. The images of tumor samples in each group was shown. (c) Western blot analysis of PDLIM1 expression in tumor samples from sh-PDLIM1 and sh-nc groups. (d) H&E staining, ki-67 immunohistochemistry, and TUNEL assay results for tumor tissues from sh-PDLIM1 and sh-nc groups.

Article Snippet: Four human DLBCL cell lines (SU-DHL-4, SU-DHL-10, TMD8, and U2932) were acquired from the American Type Culture Collection (ATCC, Manassas, VA, USA).

Techniques: Knockdown, In Vivo, Derivative Assay, Expressing, Western Blot, Staining, Immunohistochemistry, TUNEL Assay

Journal: Cancer Biology & Therapy

Article Title: PDLIM1, a novel miR-3940-5p target, regulates the malignant progression of diffuse large B-cell lymphoma

doi: 10.1080/15384047.2024.2429175

Figure Lengend Snippet: PDLIM1 is a potential target of miR-3940-5p. (a) venn diagram showing the intersection of predicted miRNAs targeting PDLIM1 and downregulated miRNAs in DLBCL. (b) qRT-pcr analysis of PDLIM1 mRNA levels in TMD8 and SU-DHL-4 cells transfected with mimics of the four identified miRnas. (c) miR-3940-5p expression levels in DLBCL samples from GSE173080 dataset. (d) Predicted binding sites of miR-3940-5p on PDLIM1 mRNA 3‘UTR. (e) Luciferase reporter assay results for wild-type and mutated PDLIM1 3‘UTR reporters in the presence of miRNA mimic or miR-nc (negative control). (f) Western blot analysis of PDLIM1 protein levels in TMD8 and SU-DHL-4 cells transfected with miR-nc or miR-3940-5p mimic. (g) qRT-pcr analysis of miR-3940-5p expression in DLBCL cell lines compared to normal human B lymphocytes. (h) qRT-pcr analysis of miR-3940-5p levels in 76 DLBCL samples and matched non-carcinoma samples. (i) Correlation analysis between PDLIM1 and miR-3940-5p expression levels in DLBCL samples.

Article Snippet: Four human DLBCL cell lines (SU-DHL-4, SU-DHL-10, TMD8, and U2932) were acquired from the American Type Culture Collection (ATCC, Manassas, VA, USA).

Techniques: Quantitative RT-PCR, Transfection, Expressing, Binding Assay, Luciferase, Reporter Assay, Negative Control, Western Blot

Journal: Cancer Biology & Therapy

Article Title: PDLIM1, a novel miR-3940-5p target, regulates the malignant progression of diffuse large B-cell lymphoma

doi: 10.1080/15384047.2024.2429175

Figure Lengend Snippet: miR-3940-5p overexpression inhibits DLBCL cell growth and induces apoptosis by targeting PDLIM1. (a) Western blot confirmation of PDLIM1 overexpression in SU-DHL-4 and TMD8 cells. (b) Cell proliferation assay results for SU-DHL-4 and TMD8 cells transfected with miR-NC+vector, miR-3940-5p+vector, or miR-3940-5p+PDLIM1 expression vector. (c) Apoptosis analysis of SU-DHL-4 and TMD8 cells under different transfection conditions. (d) Transwell migration assay results showing cell migration under different transfection conditions. (e) Transwell invasion assay results showing cell invasion under different transfection conditions.

Article Snippet: Four human DLBCL cell lines (SU-DHL-4, SU-DHL-10, TMD8, and U2932) were acquired from the American Type Culture Collection (ATCC, Manassas, VA, USA).

Techniques: Over Expression, Western Blot, Proliferation Assay, Transfection, Plasmid Preparation, Expressing, Transwell Migration Assay, Migration, Transwell Invasion Assay