Charting oncogenicity of genes and variants across lineages via multiplexed screens in teratomas.

Deconstructing tissue-specific effects of genes and variants on proliferation is critical to understanding cellular transformation and systematically selecting cancer therapeutics. This requires scalable methods for multiplexed genetic screens tracking fitness across time, across lineages, and in a suitable niche, since physiological cues influence functional differences. Towards this, we present an approach, coupling single-cell cancer driver screens in teratomas with hit enrichment by serial teratoma reinjection, to simultaneously screen drivers across multiple lineages in vivo. Using this system, we analyzed population shifts and lineage-specific enrichment for 51 cancer associated genes and variants, profiling over 100,000 cells spanning over 20 lineages, across two rounds of serial reinjection. We confirmed that c-MYC alone or combined with myristoylated AKT1 potently drives proliferation in progenitor neural lineages, demonstrating signatures of malignancy. Additionally, mutant MEK1 S218D/S222D provides a proliferative advantage in mesenchymal lineages like fibroblasts. Our method provides a powerful platform for multi-lineage longitudinal study of oncogenesis.

Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19.

Background: SARS-CoV-2, the virus responsible for COVID-19, causes widespread damage in the lungs in the setting of an overzealous immune response whose origin remains unclear. Methods: We present a scalable, propagable, personalized, cost-effective adult stem cell-derived human lung organoid model that is complete with both proximal and distal airway epithelia. Monolayers derived from adult lung organoids (ALOs), primary airway cells, or hiPSC-derived alveolar type II (AT2) pneumocytes were infected with SARS-CoV-2 to create in vitro lung models of COVID-19. Results: Infected ALO monolayers best recapitulated the transcriptomic signatures in diverse cohorts of COVID-19 patient-derived respiratory samples. The airway (proximal) cells were critical for sustained viral infection, whereas distal alveolar differentiation (AT2→AT1) was critical for mounting the overzealous host immune response in fatal disease; ALO monolayers with well-mixed proximodistal airway components recapitulated both. Conclusions: Findings validate a human lung model of COVID-19, which can be immediately utilized to investigate COVID-19 pathogenesis and vet new therapies and vaccines. Funding: This work was supported by the National Institutes for Health (NIH) grants 1R01DK107585-01A1, 3R01DK107585-05S1 (to SD); R01-AI141630, CA100768 and CA160911 (to PG) and R01-AI 155696 (to PG, DS and SD); R00-CA151673 and R01-GM138385 (to DS), R01- HL32225 (to PT), UCOP-R00RG2642 (to SD and PG), UCOP-R01RG3780 (to P.G. and D.S) and a pilot award from the Sanford Stem Cell Clinical Center at UC San Diego Health (P.G, S.D, D.S). GDK was supported through The American Association of Immunologists Intersect Fellowship Program for Computational Scientists and Immunologists. L.C.A's salary was supported in part by the VA San Diego Healthcare System. This manuscript includes data generated at the UC San Diego Institute of Genomic Medicine (IGC) using an Illumina NovaSeq 6000 that was purchased with funding from a National Institutes of Health SIG grant (#S10 OD026929).

Regional variation in bone turnover at the iliac crest versus the greater trochanter.

BACKGROUND: Iliac crest bone biopsy with histomorphometry is the gold standard for diagnosis of abnormalities in bone turnover, yet fractures more frequently occur at the greater trochanter of the hip. Whether bone turnover is similar at these two anatomic sites within individuals is uncertain. METHODS: We collected bone biopsy samples from the ipsilateral iliac crest and greater trochanter in 9 deceased individuals undergoing autopsies at an academic medical center between March-August 2018. We measured 14 static bone histomorphometry parameters including osteoclast number (N.Oc/T.A), eroded surface (ES/BS), trabecular separation (Tb.Sp), osteoclast surface (Oc.S/BS) and osteoid volume (OV/BV) as markers of bone turnover, mineralization, and volume (TMV), and evaluated the correlation of these markers between the iliac crest and greater trochanter. RESULTS: Average age at time of death was 58 ± 15 years, 2 were women, and average time from death to autopsy was 2.9 ± 1.8 days. Overall, correlations of the markers of bone turnover across the two sites were poor, ranging from as low as 0 for Tb.Sp (p = 1.0) to as high as 0.583 for Oc.S/BS (p = 0.102). CONCLUSIONS: Static histomorphometric measures of bone turnover at the iliac crest may not provide reliable information about turnover at other anatomic sites.

Adult Stem Cell-derived Complete Lung Organoid Models Emulate Lung Disease in COVID-19.

SARS-CoV-2, the virus responsible for COVID-19, causes widespread damage in the lungs in the setting of an overzealous immune response whose origin remains unclear. We present a scalable, propagable, personalized, cost-effective adult stem cell-derived human lung organoid model that is complete with both proximal and distal airway epithelia. Monolayers derived from adult lung organoids (ALOs), primary airway cells, or hiPSC-derived alveolar type-II (AT2) pneumocytes were infected with SARS-CoV-2 to create in vitro lung models of COVID-19. Infected ALO-monolayers best recapitulated the transcriptomic signatures in diverse cohorts of COVID-19 patient-derived respiratory samples. The airway (proximal) cells were critical for sustained viral infection whereas distal alveolar differentiation (AT2→AT1) was critical for mounting the overzealous host immune response in fatal disease; ALO monolayers with well-mixed proximodistal airway components recapitulated both. Findings validate a human lung model of COVID-19 which can be immediately utilized to investigate COVID-19 pathogenesis, and vet new therapies and vaccines.

Defining the Teratoma as a Model for Multi-lineage Human Development.

We propose that the teratoma, a recognized standard for validating pluripotency in stem cells, could be a promising platform for studying human developmental processes. Performing single-cell RNA sequencing (RNA-seq) of 179,632 cells across 23 teratomas from 4 cell lines, we found that teratomas reproducibly contain approximately 20 cell types across all 3 germ layers, that inter-teratoma cell type heterogeneity is comparable with organoid systems, and teratoma gut and brain cell types correspond well to similar fetal cell types. Furthermore, cellular barcoding confirmed that injected stem cells robustly engraft and contribute to all lineages. Using pooled CRISPR-Cas9 knockout screens, we showed that teratomas can enable simultaneous assaying of the effects of genetic perturbations across all germ layers. Additionally, we demonstrated that teratomas can be sculpted molecularly via microRNA (miRNA)-regulated suicide gene expression to enrich for specific tissues. Taken together, teratomas are a promising platform for modeling multi-lineage development, pan-tissue functional genetic screening, and tissue engineering.

Intranodal palisaded myofibroblastoma of para-esophageal lymph node: Case report with cytologic and histologic findings.

Intranodal palisaded myofibroblastoma is a rare lymph node mesenchymal neoplasm that most commonly arises in inguinal lymph nodes. There is limited data about cytologic features of this tumor and its diagnostic pitfalls. The combination of bland appearing spindle cells, fibrillary matrix, and hemosiderin pigments are the characteristic features of this neoplasm in cytologic specimens.

Osteosarcomatous Divergence in Dedifferentiated Liposarcoma Presenting as a Colonic Mass.

Dedifferentiated liposarcomas most commonly arise in the retroperitoneum, accounting for 10% of liposarcomas. Heterologous differentiation occurs in 5-10% of dedifferentiated liposarcomas; however, divergent osteosarcomatous differentiation is rare. We report a rare case of initial presentation of dedifferentiated liposarcoma with osteosarcomatous component as a colonic mass in a 72-year-old man. The tumor is mainly composed of bony trabeculae with intervening highly atypical cells and adjacent high-grade mesenchymal nonlipogenic tumor, as well as areas of well-differentiated liposarcoma. Immunohistochemical studies showed diffuse positivity for SATB2 in the atypical cells and fluorescence in situ hybridization revealed high-level amplification of MDM2 gene, supporting the diagnosis of well-differentiated and dedifferentiated liposarcoma with heterologous osteosarcomatous differentiation.

Overinterpretation is common in pathological diagnosis of appendix cancer during patient referral for oncologic care.

CONTEXT: Low-grade appendiceal mucinous neoplasm (LAMN) and appendiceal adenocarcinoma are known to cause the majority of pseudomyxoma peritonei (PMP, i.e. mucinous ascites); however, recognition and proper classification of these neoplasms can be difficult despite established diagnostic criteria. OBJECTIVE: To determine the pathological diagnostic concordance for appendix neoplasia and related lesions during patient referral to an academic medical center specialized in treating patients with PMP. DESIGN: The anatomic pathology laboratory information system was searched to identify cases over a two-year period containing appendix specimens with mucinous neoplasia evaluated by an outside pathology group and by in-house slide review at a single large academic medical center during patient referral. RESULTS: 161 cases containing appendix specimens were identified over this period. Forty-six of 161 cases (28.6%) contained appendiceal primary neoplasia or lesions. Of these, the originating pathologist diagnosed 23 cases (50%) as adenocarcinoma and 23 cases (50%) as LAMN; however, the reference pathologist diagnosed 29 cases (63.0%) as LAMN, 13 cases (28.3%) as adenocarcinoma, and 4 cases (8.7%) as ruptured simple mucocele. Importantly, for cases in which the originating pathologist rendered a diagnosis of adenocarcinoma, the reference pathologist rendered a diagnosis of adenocarcinoma (56.5%, 13 of 23), LAMN (39.1%, 9 of 23), or simple mucocele (4.3%, 1 of 23). The overall diagnostic concordance rate for these major classifications was 71.7% (33 of 46) with an unweighted observed kappa value of 0.48 (95% CI, 0.27-0.69), consistent with moderate interobserver agreement. All of the observed discordance (28.3%) for major classifications could be attributed to over-interpretation. In addition, the majority of LAMN cases (65.5%) had potential diagnostic deficiencies including over-interpretation as adenocarcinoma and lacking or discordant risk stratification (i.e. documentation of extra-appendiceal neoplastic epithelium). CONCLUSIONS: Appendiceal mucinous lesions remain a difficult area for appropriate pathological classification with substantial discordance due to over-interpretation in this study. The findings highlight the critical need for recognition and application of diagnostic criteria regarding these tumors. Recently published consensus guidelines and a checklist provided herein may help facilitate improvement of diagnostic concordance and thereby reduce over-interpretation and potential overtreatment. Further studies are needed to determine the extent of this phenomenon and its potential clinical impact.

Adenocarcinoma Ex-Goblet Cell Carcinoid of the Appendix With Metastatic Peritoneal Spread to Meckel's Diverticulum and Endometriosis.

Adenocarcinoma ex-goblet cell carcinoid is a very rare and histologically unique appendiceal malignancy with dual glandular and neuroendocrine differentiation. There is a high incidence of this tumor among middle-aged women with metastasis to the gynecologic tract with the mode of metastasis following peritoneal spread rather than hematogenous distribution. Adenocarcinoma ex-goblet cell carcinoid can spread to any peritoneal site including ovaries or omentum. We report a 37-year-old healthy woman who initially presented with right lower quadrant abdominal pain and pseudomyxoma peritonei. Histopathology of the appendectomy specimen revealed an adenocarcinoma ex-goblet cell carcinoid, signet ring cell type. Follow-up right hemicolectomy, omentectomy, bilateral salpingo-oophorectomy, and regional peritoneal resections revealed metastatic involvement by adenocarcinoma ex-goblet cell carcinoid, signet ring cell type. In this report, we describe a case of appendiceal adenocarcinoma ex goblet cell carcinoid with metastases to Meckel's diverticulum and areas of pelvic endometriosis, which have not been previously reported.

Newly Diagnosed Colonic Adenocarcinoma: The Presenting Sign in a Young Woman with Undiagnosed Crohn's Disease in the Absence of Primary Sclerosing Cholangitis and a Normal Microsatellite Instability Profile.

Ulcerative colitis has long been linked with an increased risk for colonic adenocarcinoma, whereas Crohn's disease (CD) has recently been reported to pose a similar increased risk. We report a 33-year-old healthy female with no family history who presented with abdominal pain and a colon mass. Histopathology revealed a moderately differentiated adenocarcinoma extending through the muscularis propria with metastatic lymph nodes and intact mismatch repair proteins by immunohistochemical expression and gene sequencing. The nonneoplastic grossly uninvolved background mucosa showed marked crypt distortion, crypt abscesses, CD-like lymphoid hyperplasia, transmural inflammation, and reactive epithelial atypia. Additional patient questioning revealed frequent loose stools since she was a teenager leading to diagnosis of a previously undiagnosed CD without primary sclerosing cholangitis (PSC). The adenocarcinoma is suspected to be related to the underlying CD. Newly diagnosed adenocarcinoma in a young female as the presenting sign for CD in the absence of PSC is extremely rare.

Successful Treatment of Multifocal Histiocytic Sarcoma Occurring after Renal Transplantation with Cladribine, High-Dose Cytarabine, G-CSF, and Mitoxantrone (CLAG-M) Followed by Allogeneic Hematopoietic Stem Cell Transplantation.

Histiocytic sarcoma (HS) is a rare, aggressive malignancy. Lesions previously called HS were typically non-Hodgkin lymphomas, not HS. As such, chemotherapy directed at lymphoid neoplasms was frequently successful, but it is unclear if these regimens are ideal for HS. We present a 33-year-old African gentleman who underwent sequential renal transplants for glomerulonephritis. He subsequently developed HS of the upper airway and multiple cutaneous sites. The patient received cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP) followed by salvage ifosfamide, carboplatin, and etoposide (ICE) but had continuous progression of cutaneous involvement. Cladribine, high-dose cytarabine, G-CSF, and mitoxantrone (CLAG-M) yielded a partial response with near resolution of disease. Ultimately, the patient achieved a complete remission after myeloablative allogeneic hematopoietic stem cell transplant. HS occurring after solid organ transplant raises the possibility of HS as a potential posttransplant malignancy. The use of CLAG-M has not been reported in HS. In this case, histiocyte-directed chemotherapy with CLAG-M was superior to lymphoma-directed regimens.

Rapidly progressive subcutaneous metastases from gallbladder cancer: insight into a rare presentation in gastrointestinal malignancies.

BACKGROUND: Gallbladder cancer (GBCA) is the most common malignancy of the biliary tract. It has an aggressive biology that results in the ability to spread, seed and grow in disparate environments. It can metastasize via lymphatic, hematogenous, and peritoneal seeding. However, GBCA metastasis to distant subcutaneous sites is extremely rare. CASE PRESENTATION: This case report describes the presentation of metastatic GBCA with rapidly progressive subcutaneous metastases. A 58-year-old woman presented with acute onset right upper quadrant abdominal pain. Computed tomography (CT) revealed a calcified and thickened gallbladder with cholelithiasis and presumed cholecystitis. Diagnostic laparoscopy revealed a gallbladder mass. Biopsies were consistent with GBCA. The patient was referred to our cancer center for further surgical management. However, she was found to have rapidly growing subcutaneous nodules in the shoulders, chest, abdomen, and buttocks. Positron emission tomography (PET) demonstrated that these were fluorodeoxyglucose (FDG)-avid. A core needle biopsy of a chest wall lesion was consistent with metastatic GBCA. Therefore, the patient was diagnosed with stage IVB GBCA and was initiated on systemic chemotherapy. DISCUSSION: GBCA is known to have an incredible propensity to grow within the peritoneal cavity, as well as along needle biopsy tracts and at laparoscopic port sites. Several case reports have demonstrated that GBCA also has the potential to metastasize to distant subcutaneous sites, most often including breast metastases, while the current cases represents a more diffuse pattern of spread. CONCLUSIONS: GBCA belongs to the short list of solid visceral malignancies that have the potential to develop remote subcutaneous metastases.

Examination of sources of diagnostic error leading to cervical cone biopsies with no evidence of dysplasia.

At our institution, 17% of cervical conization specimens are reported as negative for dysplasia or malignancy. To identify sources of error, we reviewed 53 negative conization specimens and their prior and follow-up cytology, biopsy, and endocervical curettage specimens. Examination of deeper-level sections and p16 immunostaining were performed on all conization specimens and selected biopsy specimens. Dysplasia was detected in 26% (14/53) of conization specimens. Twenty-eight percent (15/53) of cones were truly negative, and the presurgical material had been overcalled as high-grade squamous intraepithelial lesions (HSIL). Forty-five percent (24/53) of cones were truly negative and HSIL was confirmed in the presurgical material. Of these, 11% (6/53) showed subsequent evidence of residual dysplasia and 26% (14/53) were negative on further follow-up. Deeper-level sections, p16 immunostains, and consensus review may help identify squamous dysplasia in conization specimens and may prevent the overdiagnosis of HSIL on cervical biopsies.

Fine-needle aspiration of ganglioneuroma, maturing type (a.k.a., "borderline ganglioneuroblastoma") in the mediastinum of a young man: Case report and discussion of classification.

We report a very unusual case of a posterior mediastinal tumor in a young man, which we diagnosed by fine-needle aspiration cytology as most consistent with ganglioneuroma, maturing subtype. The cytopathologic features were interpreted using the classification of neuroblastic tumors as defined by the International Neuroblastoma Pathology Committee. Neuroblastic tumors are peculiar tumors that have capacity for maturation, and hence they present as a spectrum of tumors, ranging from the undifferentiated neuroblastoma, to ganglioneuroblastoma, to the mature version ganglioneuroma. The practicing surgical pathologist or cytopathologist who does not regularly encounter pediatric specimens may experience difficulty interpreting a specimen from one of these tumors. The following case report discusses application of these criteria to cytopathologic diagnosis of these tumors.

Prognostic implications of parathyroid hormone-related protein in males and females with non--small-cell lung cancer.

BACKGROUND: Non-small-cell lung carcinoma immunoreactivity for parathyroid hormone-related protein has been associated with increased survival in female patients but not in male patients. The current investigation attempted to substantiate this finding in 2 new patient groups. METHODS: Patients were divided into groups with and without immunoreactivity for a carboxyl-terminal parathyroid hormone-related protein epitope assessed in deparaffinized sections by a blinded observer. One group included 85 female patients with stage I lung cancer, and the second group had 48 female and 66 male patients with stage I-IV lung cancer. Survival times were compared by the log-rank test between groups separated by tumor parathyroid hormone-related protein status. RESULTS: Parathyroid hormone-related protein was present in 70%-80% of the patients, independent of sex, stage, and smoking history. In the females with stage I lung cancer, parathyroid hormone-related protein increased median survival from 25 to 60 months (P < .05). In the second group, parathyroid hormone-related protein expression increased 48-month disease-free survival of female lung cancer patients from 44% to 63% (P < .05), but had no effect in male patients. Parathyroid hormone-related protein remained a significant, independent predictor when evaluated together with other covariates by Cox multivariate regression. CONCLUSION: This study verifies that parathyroid hormone-related protein is a sex-dependent survival factor for non-small-cell lung carcinoma, that it correlates with disease-free survival, and that the association with survival holds for women with early-stage disease as well as more advanced cancer. Thus, the protein could find use as a prognostic indicator and could be a target for therapy.

Reliability of Her2/neu, estrogen receptor, and progesterone receptor testing by immunohistochemistry on cell block of FNA and serous effusions from patients with primary and metastatic breast carcinoma.

The prognostic and predictive value of Her2/neu and the hormone receptors in patient with primary or metastatic breast cancer is essential for a favorable outcome of treatment. We have been experiencing increasing requests to test cytologic specimens for these markers in patients with metastatic breast carcinoma. A recent study threw some doubts on the validity of such testing using cell blocks. In this study we compared our immunohistochemical Her2/neu, ER and PR testing performed on 42 formalin-fixed, paraffin-embedded cell blocks from 27 fine needle aspirations (FNA) and 15 serous effusions of 42 patients with metastatic (n = 38) and primary (n = 4) breast carcinoma to the test results obtained on tissue sections. In seven cases the Her2/neu immunohistochemistry (IHC) results on cell blocks were also compared with Her2/neu fluorescence in situ hybridization (FISH) on tissue or cell block. The study revealed 100% correlation for positive and negative Her2/neu results. For ER testing the results showed 85.7% sensitivity, 100% specificity, 100% positive predictive value (PPV), and 85.7% negative predictive value (NPV). For PR testing the results showed 80% sensitivity, 100% specificity, 100% PPV, and 88.8% NPV respectively. In conclusion, IHC for Her2/neu, ER and PR performed on formalin-fixed, paraffin-embedded cell blocks prepared from fresh FNA and serous fluid is reliable in predicting the expression of these markers when correlated with IHC and FISH performed on the corresponding tumor tissue.

Endometrioid carcinoma with a low-grade spindle cell component: a tumor resembling an adnexal tumor of probable Wolffian origin.

Endometrioid carcinoma is known to have many histopathologic variants, which may cause diagnostic difficulty. One rare variant resembles Wolffian adnexal tumor (female adnexal tumor of probable Wolffian origin). This pattern can produce a significant solid component within the tumor. Once the true endometrioid nature of the tumor is recognized, the tumor can appear deceptively high grade by International Federation of Gynecology and Obstetrics grading criteria, which take into account the percentage of the tumor showing solid growth. The English-language literature on this variant is scant, and its behavior is not well documented. We present a case of ovarian endometrioid carcinoma with a Wolffian adnexal tumor pattern that recurred 19 years after the original surgery; and the patient continues to remain well without evidence of disease 1 year following her second surgery, that is, 20 years of indolent behavior. This long clinical course shows evidence for low-grade behavior for this tumor.