Examination of 93 cases of perianal warts and suggestion of a new classification.

PURPOSE: The anatomical distribution of perianal warts is associated with patient characteristics such as sexual orientation. The purpose of this study is to confirm this experiential knowledge using a quantitative classification system and analysis and to obtain findings useful for future treatment. METHODS: From January 2014 to December 2020, 93 patients with perianal warts presented to our hospital. Patients were analyzed for age, sex, lesion site, and recurrence type, among other factors. The lesion site was divided into skin (S) and anal epithelium (anoderm, A), and the number and degree of each were classified into grades 0 to 3. The higher grade between S and A determines its dominant type, such as type S (e.g., S3A1) and type A (e.g., S0A2). RESULTS: The average age of the patients was 39.6 years, and the percentage of patients who were not married was 54.8%. In all, 95.8% of patients were positive for low-risk human papillomavirus (HPV). Type S accounted for 80.6%, whereas type A accounted for 9.7%. Type A cases were all male and were all presumed to be men who have sex with men (MSM). This indicates that the determination of type A may be highly specific for MSM. The type at the time of recurrence was the same type at the time of the first surgery in almost all cases. CONCLUSION: In cases of perianal warts, it is useful to analyze the lesion by considering the range and grade separately for daily clinical practice on proctologist.

[A Case of Intestinal Obstruction Caused by Peritoneal Metastatic Recurrence One Year after Radical Operation for Pancreatic Cancer].

In December 20XX-1, abdominal enhanced CT of a 73-year-old female patient showed a 28mm-in-diameter pancreatic tail cancer with splenic venous invasion. She underwent neoadjuvant GEM/TS-1 combination chemotherapy but abandoned this chemotherapy due to melena and exanthema. She underwent a distal pancreatectomy with lymph node dissemination. In these pathological findings, the tumor was diagnosed as a pancreatic tail cancer with splenic venous invasion(T3, N0, M0, Stage ⅡA). She underwent adjuvant GEM chemotherapy, but she abandoned this chemotherapy due to exanthema and was managed with observation. In September 20XX, she had a postoperative bowel obstruction and was treated with natural light. However, she had a postoperative bowel obstruction again in July, 20XX+1. Fluoroscopic images revealed stenosis in the intestine located 170 cm from the nasal cavity. She underwent open surgery to manage the bowel obstruction. There was a peritoneal tumor with adhesion to each intestine serosa in 3 areas located 80 cm, 100 cm, and 150 cm from the Treitz ligament. Therefore, she underwent a small intestine resection and anastomosis 70 cm to 110 cm from the Treitz ligament. Pathological findings showed that there was a 3mm-in-diameter adenocarcinoma in this peritoneal tumor. In these findings, this final diagnosis was an adhesive intestinal obstruction caused by peritoneal metastasis. Curative resection for single peritoneal recurrent metastasis might be useful for prognosis prolongation.

[Hyperprogressive Disease during Treatment with Nivolumab for Recurrence of Gastric Cancer].

A man in his 60s with a large Type 3 gastric cancer presented with the chief complaint of epicardial discomfort. We decided to perform laparoscopy. The patient was diagnosed with cT4aN2M1(CY1), cStage Ⅳ disease and was treated with XP(capecitabine plus cisplatin[CDDP])plus trastuzumab(HER). After chemotherapy, CY0 was confirmed using laparoscopy. The patient underwent total gastrectomy and D2 lymph node dissection. Histopathological examination revealed ypT4aN3M0, ypStage ⅢC disease. Therefore, adjuvant treatment with XP plus HER was continued. Four months after surgery, liver, lung, and # 16b1latLN metastases were observed on CT. The metastatic foci were observed even after 3 courses of ramucirumab plus paclitaxel. Nivolumab was administered as the third-line treatment; after 3 courses, the liver metastasis increased markedly. Hence, our final diagnosis was hyperprogressive disease(HPD).

Some Gammaproteobacteria are enriched within CD14+ macrophages from intestinal lamina propria of Crohn's disease patients versus mucus.

Crohn's disease causes chronic inflammation in the gastrointestinal tract and its pathogenesis remains unclear. In the intestine of Crohn's disease patients, CD14+CD11+CD163low macrophages contribute to inflammation through the induction of Th17 cells and production of inflammatory cytokines; the CD14+CD11c+163high fraction is anti-inflammatory through the production of IL-10 in normal cases. In this report, the 16S rRNA gene amplicon sequencing method was used to identify bacteria that are specifically present in intestinal CD14+CD11c+ macrophages of Crohn's disease patients. Bacteria present in intestinal CD14+CD11c+ macrophages and mucus of Crohn's disease patients were separated into different clusters in principal coordinates analysis. There was a statistically significant increase in the relative composition of CD14+CD11c+ macrophages from mucus in two phyla (Proteobacteria [p = 0.01] and Actinobacteria [p = 0.02]) and two families (Moraxellaceae [p < 0.001] and Pseudomonadaceae [p = 0.01]). In addition, OTU-1: Acinetobacter and OTU-8: Pseudomonadaceae tended to concentrate in the CD14+CD11c+CD163low subset, whereas OTU-10: Proteus, OTU-15: Collinsella tended to concentrate more in the CD14+CD11c+CD163high subset than the other subset and mucus.

[A Case of Laparoscopic Assisted Resection for Small Intestinal Cancer Diagnosed Preoperatively].

A 50-year-old woman was admitted to our hospital due to intermittent epigastric pain and vomiting for 2 months. Contrast enhanced CT scan showed stenosis in the upper jejunum. She was diagnosed with small intestinal ileus. A small enteroscopy revealed a peripheral type 2 lesion in the upper jejunum, approximately 10 cm from the Treitz's ligament. Upon biopsy, she was diagnosed with a well-differentiated adenocarcinoma. A laparoscope-assisted extracorporeal operation was performed due to the ease of raising the umbilical wound. Swollen lymph nodes were found in the mesentery. A surgical margin of 5 cm on the oral side and 20 cm on the anal side was secured. We performed partial resection of the small intestine, including the mesentery with the enlarged lymph nodes. The histopathological diagnosis was a Type 2, 3×2 cm, tub2, pT4aN1aM0, pStage Ⅲb small intestinal cancer. Due to the development of small intestinal ileus, the small bowel cancer was diagnosed preoperatively. Hence, it was slightly we will report including the literature consideration of.

[A Case of Appendix Torsion with Low-Grade Appendiceal Mucinous Neoplasm].

An 84-year-old woman with a chief complaint of right lower abdominal pain was admitted to our hospital in November 20XX. Abdominal CT scan revealed a 9.6×4.1 cm diameter low density area proximal to the 13 mm diameter appendix, which led to perforated appendicitis with a huge abscess. The patient underwent an open appendectomy with partial cecum resection. The appendix was found to be twisted by 540°. The pathological diagnosis was low-grade appendiceal mucinous neoplasm(LAMN). Recent research has found that the use of laparoscopic surgery for the treatment of LAMN has been increasing. Appropriate surgical intervention should be considered for LAMN because it is a borderline malignancy. Careful treatment with laparoscopic surgery might be considered as one of the treatment options for LAMN. We hope to accumulate more cases of LAMN to confirm our results.

Inflammation-Associated Microsatellite Alterations Caused by MSH3 Dysfunction Are Prevalent in Ulcerative Colitis and Increase With Neoplastic Advancement.

OBJECTIVES: Inflammation-associated microsatellite alterations (also known as elevated microsatellite alterations at selected tetranucleotide repeats [EMAST]) result from IL-6-induced nuclear-to-cytosolic displacement of the DNA mismatch repair (MMR) protein MSH3, allowing frameshifts of dinucleotide or longer microsatellites within DNA. MSH3 also engages homologous recombination to repair double-strand breaks (DSBs), making MSH3 deficiency contributory to both EMAST and DSBs. EMAST is observed in cancers, but given its genesis by cytokines, it may be present in non-neoplastic inflammatory conditions. We examined ulcerative colitis (UC), a preneoplastic condition from prolonged inflammatory duration. METHODS: We assessed 70 UC colons without neoplasia, 5 UC specimens with dysplasia, 14 UC-derived colorectal cancers (CRCs), and 19 early-stage sporadic CRCs for microsatellite instability (MSI) via multiplexed polymerase chain reaction capable of simultaneous detection of MSI-H, MSI-L, and EMAST. We evaluated UC specimens for MSH3 expression via immunohistochemistry. RESULTS: UC, UC with dysplasia, and UC-derived CRCs demonstrated dinucleotide or longer microsatellite frameshifts, with UC showing coincident reduction of nuclear MSH3 expression. No UC specimen, with or without neoplasia, demonstrated mononucleotide frameshifts. EMAST frequency was higher in UC-derived CRCs than UC (71.4% vs 31.4%, P = 0.0045) and higher than early-stage sporadic CRCs (66.7% vs 26.3%, P = 0.0426). EMAST frequency was higher with UC duration >8 years compared with ≤8 years (40% vs 16%, P = 0.0459). DISCUSSION: Inflammation-associated microsatellite alterations/EMAST are prevalent in UC and signify genomic mutations in the absence of neoplasia. Duration of disease and advancement to neoplasia increases frequency of EMAST. MSH3 dysfunction is a potential contributory pathway toward neoplasia in UC that could be targeted by therapeutic intervention.

[A Case of Unresectable Advanced Esophageal Cancer Treated with Chemoradiotherapy Resulting in Complete Response].

A70s man was admitted to our hospital complaining of chest discomfort. Endoscopic examination showed mucosal erythema and irregularity and an area unstained by iodine in the middle esophagus 21 to 41 cm from the incisors. The biopsy specimen showed moderately differentiated squamous cell carcinoma. An abdominal computed tomographic(CT)scan revealed swelling of the lymph nodes along the celiac artery and abdominal aorta. The patient was diagnosed with unresectable advanced esophageal cancer(cT2N4M0, cStage Ⅳa). Systemic chemotherapy was initiated using a regimen of 5-FU and cisplatin(FP). After 2 courses of chemotherapy, an abdominal CT scan showed reduction of the lymph node swelling along the abdominal aorta, but the lymph node swelling remained along the celiac artery. Therefore, chemoradiotherapy(CRT; FP plus RT 60 Gy/30 Fr at the main tumor and the swelling of lymph nodes along the celiac artery)was administered. An abdominal CT scan showed reduced swelling of the lymph nodes along the abdominal aorta and the celiac artery after CRT. In addition, FP chemotherapy was also administered. APET -CT scan showed no increased FDG up take in the main tumor and swollen lymph nodes after 2 courses of chemotherapy. The complete response(CR)has been maintained for 30 months without therapy.

[Long-Term Survival after Palliative Surgery for Advanced Gastric Cancer with Bone Marrow Metastasis-A Case Report].

A 57-year-old woman was diagnosed with advanced gastric cancer with bone marrow metastasis(cT4aN1pM1[MAR], pStage Ⅳ). After 18 courses of S-1 and cisplatin and 18 courses of ramucirumab and paclitaxel, the chemotherapy was stopped because of stenosis. We performed endoscopic metallic stent placement, but stenosis reappeared after a month. Subsequently, distal gastrectomy was performed as a palliative surgery. She had no complications and improved appetite, therefore, she resumed chemotherapy after 3 postoperative months and continued for 4 years and 9 months from the first visit. In general, gastric cancer with bone marrow metastasis has a poor prognosis, however, in this case, long-term survival was achieved with palliative surgery.

Innate Myeloid Cell Subset-Specific Gene Expression Patterns in the Human Colon are Altered in Crohn's Disease Patients.

BACKGROUND/AIMS: There is a heterogeneous subset innate myeloid cells, such as macrophages and dendritic cells, in the human intestinal lamina propria. Several studies have demonstrated that these cells contribute to the maintenance of gut homeostasis through the induction of inflammatory responses and tolerance via cell type-specific mechanisms; whereas, disrupted innate immune responses are implicated in the pathogenesis of Crohn's disease (CD). However, the detailed mechanisms by which each innate myeloid subset regulates gut homeostasis and inflammation largely remain unknown. We aimed to clarify the comprehensive gene expression profiles of innate myeloid cell -subsets in the lamina propria from normal human colons (NC) and the inflamed colon sites from patients with Crohn's disease (CDi). METHODS: We performed RNA-sequencing analysis and precise bioinformatics analysis on 3 innate myeloid cell subsets, CD14-CD11c-, CD14-CD11c+, and CD14+CD11c+CD163low cells from NC and CDi. RESULTS: Transcriptional analysis of the 3 subsets from the NC showed distinct gene expression patterns and gene ontology (GO) enrichment analysis revealed the associated innate myeloid subset-specific biological process (BP) terms. In addition, changes in gene expression patterns were observed in innate myeloid subsets from CDi. Furthermore, the core GO-BP terms for the genes upregulated in the innate myeloid cells from CDi were distinct from those found in NC. CONCLUSION: Our data identified the innate myeloid cell subset-specific transcriptomes and the associated enriched GO-BP terms in the NC and found these patterns were altered in CDi.

Heme ameliorates dextran sodium sulfate-induced colitis through providing intestinal macrophages with noninflammatory profiles.

The local environment is crucial for shaping the identities of tissue-resident macrophages (Mϕs). When hemorrhage occurs in damaged tissues, hemoglobin induces differentiation of anti-inflammatory Mϕs with reparative function. Mucosal bleeding is one of the pathological features of inflammatory bowel diseases. However, the heme-mediated mechanism modulating activation of intestinal innate immune cells remains poorly understood. Here, we show that heme regulates gut homeostasis through induction of Spi-C in intestinal CX3CR1high Mϕs. Intestinal CX3CR1high Mϕs highly expressed Spi-C in a heme-dependent manner, and myeloid lineage-specific Spic-deficient (Lyz2-cre; Spicflox/flox ) mice showed severe intestinal inflammation with an increased number of Th17 cells during dextran sodium sulfate-induced colitis. Spi-C down-regulated the expression of a subset of Toll-like receptor (TLR)-inducible genes in intestinal CX3CR1high Mϕs to prevent colitis. LPS-induced production of IL-6 and IL-1α, but not IL-10 and TNF-α, by large intestinal Mϕs from Lyz2-cre; Spicflox/flox mice was markedly enhanced. The interaction of Spi-C with IRF5 was linked to disruption of the IRF5-NF-κB p65 complex formation, thereby abrogating recruitment of IRF5 and NF-κB p65 to the Il6 and Il1a promoters. Collectively, these results demonstrate that heme-mediated Spi-C is a key molecule for the noninflammatory signature of intestinal Mϕs by suppressing the induction of a subset of TLR-inducible genes through binding to IRF5.

[A Case of Chemotherapy with FOLFOXIRI plus Cetuximab for Liver Metastasis of Sigmoid Colon Cancer].

We report a case of chemotherapy with FOLFOXIRI plus cetuximab for liver metastasis of sigmoid colon cancer. The patient was a 40's man who was diagnosed with sigmoid colon cancer with liver metastasis. Colonoscopy revealed a type 2 tumor with stenosis in the sigmoid colon. He underwent sigmoidectomy under laparotomy, and after the operation, received 7 courses of chemotherapy with FOLFOXIRI plus cetuximab. The liver tumor was sufficiently reduced, and laparotomy and liver right lobectomy were performed. Histopathology revealed a modified, Grade 2 tumor regression. He has been followed for 1 year 4months after the operation.

[A Case of Primary Duodenal Cancer with Duodenocolic Fistula Treated with Pancreatoduodenectomy and Right Hemicolectomy].

A patient was 59-year-old female. She presented our hospital with weight loss, anorexia and lower abdominal bloating. Abdominal computed tomography(CT), gastrointestinal endoscopy, colonoscopy and duodenal fistulagram showed duodenal cancer or colon cancer with duodenocolic fistula and ovary metastasis. She underwent subtotal stomach preserving pancreatoduodenectomy and right hemicolectomy. In these pathological findings, tumor was diagnosed as a duodenal cancer with duodenocolic fistula. She was surviving 12 months after the last surgery. In cases of cancer with duodenocolic fistula, pancreatoduodenectomy with right hemicolectomy would be necessary for nutrition improvement and cancer treatment.

Validation of the Japanese Version of the Low Anterior Resection Syndrome Score.

BACKGROUND: The low anterior resection syndrome (LARS) score is a patient-reported outcome measure to evaluate the severity of bowel dysfunction after rectal cancer surgery by scoring the major symptoms of LARS. The aim of this study was to translate the English version of the LARS score into Japanese and to investigate the validity and reliability of the LARS score. METHODS: The LARS score was translated in Japanese following current international recommendations. A total of 149 rectal cancer patients completed the LARS score questionnaire and were also asked a single question assessing the impact of bowel function on quality of life (QoL). A total of 136 patients answered the LARS score questionnaire twice. RESULTS: The Japanese LARS score showed high convergent validity, based on its good correlation between the LARS score and QoL (p < 0.001). The LARS score was able to discriminate between patients according to the tumor distance to anal verge (p < 0.001), type of surgery (p < 0.001), and time since surgery (p = 0.001). Patients after ultra-low anterior resection and intersphincteric resection showed especially high scores. The score also had high test-retest reliability (intraclass correlation coefficient: 0.87). CONCLUSION: The Japanese LARS score is a valid and reliable tool for measuring LARS. The LARS score is appropriate for assessments in postoperative bowel function and international comparison. Using this score, patient-reported outcome measures of LARS in Japanese patients can be shared internationally. Additional validation reports from non-English speaking countries can support the LARS score as a worldwide assessment tool for postoperative bowel dysfunction.

A Refined Culture System for Human Induced Pluripotent Stem Cell-Derived Intestinal Epithelial Organoids.

Gut epithelial organoids are routinely used to investigate intestinal biology; however, current culture methods are not amenable to genetic manipulation, and it is difficult to generate sufficient numbers for high-throughput studies. Here, we present an improved culture system of human induced pluripotent stem cell (iPSC)-derived intestinal organoids involving four methodological advances. (1) We adopted a lentiviral vector to readily establish and optimize conditioned medium for human intestinal organoid culture. (2) We obtained intestinal organoids from human iPSCs more efficiently by supplementing WNT3A and fibroblast growth factor 2 to induce differentiation into definitive endoderm. (3) Using 2D culture, followed by re-establishment of organoids, we achieved an efficient transduction of exogenous genes in organoids. (4) We investigated suspension organoid culture without scaffolds for easier harvesting and assays. These techniques enable us to develop, maintain, and expand intestinal organoids readily and quickly at low cost, facilitating high-throughput screening of pathogenic factors and candidate treatments for gastrointestinal diseases.

The activated conformation of integrin ß7 is a novel multiple myeloma-specific target for CAR T cell therapy.

Cancer-specific cell-surface antigens are ideal targets for monoclonal antibody (mAb)-based immunotherapy but are likely to have previously been identified in transcriptome or proteome analyses. Here, we show that the active conformer of an integrin can serve as a specific therapeutic target for multiple myeloma (MM). We screened >10,000 anti-MM mAb clones and identified MMG49 as an MM-specific mAb specifically recognizing a subset of integrin ß7 molecules. The MMG49 epitope, in the N-terminal region of the ß7 chain, is predicted to be inaccessible in the resting integrin conformer but exposed in the active conformation. Elevated expression and constitutive activation of integrin ß7 conferred high MMG49 reactivity on MM cells, whereas MMG49 binding was scarcely detectable in other cell types including normal integrin ß7+ lymphocytes. T cells transduced with MMG49-derived chimeric antigen receptor (CAR) exerted anti-MM effects without damaging normal hematopoietic cells. Thus, MMG49 CAR T cell therapy is promising for MM, and a receptor protein with a rare but physiologically relevant conformation can serve as a cancer immunotherapy target.

CD103+ Dendritic Cell Function Is Altered in the Colons of Patients with Ulcerative Colitis.

BACKGROUND: Human intestinal innate myeloid cells can be divided into 3 subsets: HLA-DRCD14 cells, HLA-DRCD103 dendritic cells (DCs), and HLA-DRCD14CD103 cells. CD103 DCs generate Treg cells and Th17 cells in the ileum, but their function in the colon remains largely unknown. This study characterized CD103 DCs in the colon and investigated whether these cells are implicated in the pathogenesis of ulcerative colitis (UC). METHODS: Normal intestinal mucosa was obtained from intact sites of patients with colorectal cancer (n = 24). Noninflamed and inflamed colonic tissues were obtained from surgically resected specimens of patients with UC (n = 13). Among LinCD45HLA-DR intestinal lamina propria cells, CD14 cells and CD103 DCs were sorted and analyzed for microRNA expression of cytokines and toll-like receptors by quantitative real-time polymerase chain reaction. In addition, IL-4/IL-5/IL-13/IL-17/IFN-γ production and Foxp3 expression by naive T cells cultured with CD14 cells and CD103 DCs were analyzed. RESULTS: CD103 DCs in the normal colon showed lower expression of toll-like receptors and proinflammatory cytokines than CD14 cells. Coculture with naive T cells revealed that CD103 DCs generated Treg cells. CD103 DCs from patients with UC did not generate Treg cells, but they induced IFN-γ-, IL-13-, and IL-17-producing CD4 T cells and showed higher expression of IL6 (P < 0.0001), IL23A (P < 0.05), IL12p35 (P < 0.05), and TNF (P < 0.05). CONCLUSIONS: In patients with UC, CD103 DCs show the impaired ability to generate Treg cells, but exhibit a colitogenic function inducing Th1/Th2/Th17 responses. These findings show how human CD103 DCs could contribute to the pathogenesis of UC.

[Continued Chemotherapy for Advanced Gastric Cancer and Seven Year Survival after Operation].

The patient was a 66-year-old man. Total abdominal gastrectomy and D2 dissection were performed for gastric cancer (cT3N0M0P0CYXH0, cStage II A). Pathological examination confirmed a diagnosis of Stage III C mucinous adenocarcinoma (pT4pN3pM0, pStage III C). He underwent adjuvant chemotherapy with TS-1(120mg/body). One year after adjuvant chemotherapy, anastomotic stricture was caused. Although it was not possible to point out recurrent lesions on the CT image, we strongly suspected that extrinsic compression around the anastomotic portion was due to peritoneal dissemination recurrence because of symptoms and marked tumor elevation. Therefore, TS-1(120mg/body)plus cisplatin(CDDP 60mg/m2)were administered as first-line therapy for advanced gastric cancer. TS-1 plus CDDP(SP)chemotherapy resulted in marked tumor reduction and improved symptoms. However, after 33 courses of SP chemotherapy, renal function was worse due to cisplatin; thus, docetaxel(DTX 70mg/m2)was administered as second line therapy. After 8 courses of DTX, peritoneal dissemination recurrence was diagnosed, and the patient was treated with irinotecan(CPT-11 150mg/m / 2), ramucirumab(RAM 8 mg/kg) plus paclitaxel(PTX 80mg/m2 day 1, 8, 15). However, the disease worsened. The side effect of SP therapy was renal dysfunction. Nonetheless, we experienced that long-term disease control could be achieved by administering chemotherapy under strict follow-up.

Detection of Anorectal Cancer among Patients with Crohn's Disease Undergoing Surveillance with Various Biopsy Methods.

BACKGROUND/AIMS: Crohn's disease (CD) is an inflammatory bowel disease. The risk of colorectal cancer (CRC) is increased in patients with CD. In Japan, anorectal cancer accounted for >60% of CRCs associated with CD. These anorectal cancers are typically diagnosed in advanced stages, because a surveillance protocol remains to be established. This study aimed to assess various biopsy methods for detecting CRC. METHODS: This study included 72 patients (113 examinations) with CD who underwent cancer surveillance between August 2008 and October 2015. Surveillances were performed with a core needle biopsy in perianal regions (54 cases), endoscopic biopsy (90 cases), and excisional biopsy (34 cases). When it was difficult to perform colonoscopy in an outpatient setting, due to perianal pain or stricture, we employed examinations under anesthesia for surveillance. RESULTS: The total CRC detection rate was 6.19% (7 examinations). CRC detection rates were 1.85% (1 case) with core needle biopsy, 5.56% (5 cases) with endoscopic biopsy, and 5.88% (2 cases) with excisional biopsy. CONCLUSIONS: We showed that it was important to employ various biopsy methods in cancer surveillance to detect CRC among patients with CD.

MUFINS: multi-formalism interaction network simulator.

Systems Biology has established numerous approaches for mechanistic modeling of molecular networks in the cell and a legacy of models. The current frontier is the integration of models expressed in different formalisms to address the multi-scale biological system organization challenge. We present MUFINS (MUlti-Formalism Interaction Network Simulator) software, implementing a unique set of approaches for multi-formalism simulation of interaction networks. We extend the constraint-based modeling (CBM) framework by incorporation of linear inhibition constraints, enabling for the first time linear modeling of networks simultaneously describing gene regulation, signaling and whole-cell metabolism at steady state. We present a use case where a logical hypergraph model of a regulatory network is expressed by linear constraints and integrated with a Genome-Scale Metabolic Network (GSMN) of mouse macrophage. We experimentally validate predictions, demonstrating application of our software in an iterative cycle of hypothesis generation, validation and model refinement. MUFINS incorporates an extended version of our Quasi-Steady State Petri Net approach to integrate dynamic models with CBM, which we demonstrate through a dynamic model of cortisol signaling integrated with the human Recon2 GSMN and a model of nutrient dynamics in physiological compartments. Finally, we implement a number of methods for deriving metabolic states from ~omics data, including our new variant of the iMAT congruency approach. We compare our approach with iMAT through the analysis of 262 individual tumor transcriptomes, recovering features of metabolic reprogramming in cancer. The software provides graphics user interface with network visualization, which facilitates use by researchers who are not experienced in coding and mathematical modeling environments.