preprocessing.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Document Preprocessing"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 88,
   "metadata": {},
   "outputs": [],
   "source": [
    "import fitz  # pip install PyMuPDF\n",
    "import os\n",
    "\n",
    "# Set the directory containing PDFs\n",
    "pdf_dir = \"Papers\"  # Replace with the actual path if needed\n",
    "output_dir = \"extracted_texts\"  # Directory to store the extracted text\n",
    "\n",
    "# Create the output directory if it doesn't exist\n",
    "os.makedirs(output_dir, exist_ok=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 89,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Processed FSB2-37-e23130.pdf and saved to extracted_texts/FSB2-37-e23130.json\n",
      "Processed 13048_2019_Article_582.pdf and saved to extracted_texts/13048_2019_Article_582.json\n",
      "Processed f1000research-8-16126.pdf and saved to extracted_texts/f1000research-8-16126.json\n",
      "Processed FVVinObGyn-11-269.pdf and saved to extracted_texts/FVVinObGyn-11-269.json\n",
      "Processed hoaa002.pdf and saved to extracted_texts/hoaa002.json\n",
      "Processed 11604_2024_Article_1569.pdf and saved to extracted_texts/11604_2024_Article_1569.json\n",
      "Processed ijms-24-07503.pdf and saved to extracted_texts/ijms-24-07503.json\n",
      "Processed 404_2022_Article_6766.pdf and saved to extracted_texts/404_2022_Article_6766.json\n",
      "Processed biomolecules-12-01721.pdf and saved to extracted_texts/biomolecules-12-01721.json\n",
      "Processed dead229.pdf and saved to extracted_texts/dead229.json\n",
      "Processed AOGS-103-1634.pdf and saved to extracted_texts/AOGS-103-1634.json\n",
      "Processed ijerph-19-06162.pdf and saved to extracted_texts/ijerph-19-06162.json\n",
      "Processed hoac009.pdf and saved to extracted_texts/hoac009.json\n",
      "Processed fendo-13-1020827.pdf and saved to extracted_texts/fendo-13-1020827.json\n"
     ]
    }
   ],
   "source": [
    "import re\n",
    "import json\n",
    "# Define keywords to stop processing\n",
    "stop_keywords = [\"References\", \"REFERENCES\", \"references\", \"Conflict of interest\", \"Conflicts of Interest\"]\n",
    "\n",
    "# Iterate over all PDF files in the directory\n",
    "for pdf_filename in os.listdir(pdf_dir):\n",
    "    if pdf_filename.endswith(\".pdf\"):\n",
    "        pdf_path = os.path.join(pdf_dir, pdf_filename)\n",
    "        doc = fitz.open(pdf_path)\n",
    "        content = []\n",
    "        stop_processing = False\n",
    "\n",
    "        # Original loop to extract text and images\n",
    "        for page_num in range(len(doc)):\n",
    "            if stop_processing:\n",
    "                break  # Stop processing pages once a stop keyword is found\n",
    "            page = doc.load_page(page_num)\n",
    "            blocks = page.get_text(\"dict\")[\"blocks\"]\n",
    "\n",
    "            for block in blocks:\n",
    "                if block[\"type\"] == 0:  # text block\n",
    "                    block_text = \"\"\n",
    "                    for line in block[\"lines\"]:\n",
    "                        for span in line[\"spans\"]:\n",
    "                            block_text += span[\"text\"] + \" \"\n",
    "                    block_text = block_text.strip()\n",
    "\n",
    "                     # Check if \"References\" is in the current block text\n",
    "                    if any(keyword in block_text for keyword in stop_keywords):\n",
    "                        stop_processing = True\n",
    "                        break  # Stop further processing if any stop keyword is found\n",
    "\n",
    "                    # Clean and process text\n",
    "                    block_text = \" \".join(block_text.split())  # Remove extra spaces and newlines\n",
    "                    block_text = re.sub(r'^\\d+\\.\\s+', '', block_text)  # Remove section numbering\n",
    "                    block_text = re.sub(r'[^A-Za-z0-9\\s,.]', '', block_text)  # Keep only basic punctuation and letters\n",
    "            \n",
    "                    if len(block_text) < 10 or re.match(r'Page \\d+', block_text):\n",
    "                        continue  # Skip short blocks or page numbers\n",
    "\n",
    "                    content.append({\n",
    "                        \"type\": \"text\",\n",
    "                        \"content\": block_text,\n",
    "                        \"bbox\": block[\"bbox\"],\n",
    "                        \"page_num\": page_num\n",
    "                    })\n",
    "\n",
    "                elif block[\"type\"] == 1:  # image block\n",
    "                    image_ext = block[\"ext\"]\n",
    "                    image_filename = f\"images/image_{page_num}_{block['number']}.{image_ext}\"\n",
    "                    # Uncomment the line below if you want to save the image files\n",
    "                    # with open(image_filename, \"wb\") as img_file:\n",
    "                    #     img_file.write(block[\"image\"])\n",
    "                    content.append({\n",
    "                        \"type\": \"image\",\n",
    "                        \"content\": image_filename,\n",
    "                        \"bbox\": block[\"bbox\"],\n",
    "                        \"page_num\": page_num\n",
    "                    })\n",
    "    # Sort content by page number and y-position\n",
    "    content.sort(key=lambda x: (x[\"page_num\"], x[\"bbox\"][1]))\n",
    "\n",
    "    # Save the extracted content to a .txt or .json file\n",
    "    output_filename = os.path.splitext(pdf_filename)[0] + \".json\"\n",
    "    output_filepath = os.path.join(output_dir, output_filename)\n",
    "\n",
    "    with open(output_filepath, \"w\", encoding=\"utf-8\") as f:\n",
    "        json.dump(content, f, ensure_ascii=False, indent=4)\n",
    "\n",
    "    print(f\"Processed {pdf_filename} and saved to {output_filepath}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 90,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Text: TYPE Review\n",
      "Text: PUBLISHED 26 October 2022\n",
      "Text: DOI 10.3389fendo.2022.1020827\n",
      "Text: Endometriosisassociated infertility From pathophysiology to tailored treatment\n",
      "Image: images/image_0_9.jpeg\n",
      "Text: OPEN ACCESS\n",
      "Text: EDITED BY Lusine Aghajanova, Stanford Healthcare, United States\n",
      "Text: REVIEWED BY Michael Strug, Stanford University, United States Antonio Simone Lagan, University of Palermo, Italy\n",
      "Text: Giulia Bonavina and Hugh S. Taylor \n",
      "Text: Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, United States\n",
      "Text: CORRESPONDENCE Hugh S. Taylor hugh.tayloryale.edu\n",
      "Text: Despite the clinically recognized association between endometriosis and infertility, the mechanisms implicated in endometriosisassociated infertility are not fully understood. Endometriosis is a multifactorial and systemic disease that has pleiotropic direct and indirect effects on reproduction. A complex interaction between endometriosis subtype, pain, in  ammation, altered pelvic anatomy, adhesions, disrupted ovarian reservefunction, and compromised endometrial receptivity as well as systemic effects of the disease de  ne endometriosisassociated infertility. The population of infertile women with endometriosis is heterogeneous, and diverse patients  phenotypes can be observed in the clinical setting, thus making dif  cult to establish a precise diagnosis and a single mechanism of endometriosis related infertility. Moreover, clinical management of infertility associated with endometriosis can be challenging due to this heterogeneity. Innovative noninvasive diagnostic tools are on the horizon that may allow us to target the speci  c dysfunctional alteration in the reproduction process. Currently the treatment should be individualized according to the clinical situation and to the suspected level of impairment. Here we review the etiology of endometriosis related infertility as well as current treatment options, including the roles of surgery and assisted reproductive technologies.\n",
      "Text: SPECIALTY SECTION This article was submitted to Reproduction, a section of the journal Frontiers in Endocrinology\n",
      "Text: RECEIVED 16 August 2022\n",
      "Text: ACCEPTED 06 October 2022\n",
      "Text: PUBLISHED 26 October 2022\n",
      "Text: CITATION Bonavina G and Taylor HS 2022 Endometriosisassociated infertility From pathophysiology to tailored treatment. Front. Endocrinol. 131020827. doi 10.3389fendo.2022.1020827\n",
      "Text: COPYRIGHT  2022 Bonavina and Taylor. This is an openaccess article distributed under the terms of the Creative Commons Attribution License CC BY. The use, distribution or reproduction in other forums is permitted, provided the original authors and the copyright owners are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.\n",
      "Text: endometriosis, infertility, pathogenesis, ovarian reserve, endometrial receptivity, in vitro fertilization IVF, stem cell\n",
      "Text: Background\n",
      "Text: Endometriosis is a complex and systemic clinical syndrome that can negatively impact on women  s reproductive health and quality of life  1 . Chronic in  ammation and hormonal dependance are the main underlying pathophysiologic mechanisms that drive endometriosis, and the association of these two key biological features make the natural history of this disease distinct.\n",
      "Text: Frontiers in Endocrinology frontiersin.org 01\n",
      "Text: Bonavina and Taylor 10.3389fendo.2022.1020827\n",
      "Text: 10 . Viable endometrial tissue moves into the pelvic cavity through the fallopian tubes at the time of menses, adheres to the peritoneal mesothelial cells, proliferates, and  nally invades pelvic structures. Retrograde menstruation is a physiological event that occurs in approximately 90 of women  11  13 . Viable endometrial tissue has been identi  ed in the shed menstrual endometrium  13 . However, the differences in its morphohistological, hormonal, and biological composition compared with the eutopic endometrium of healthy women still remain matter of investigation. Endometrial re  ux seems to be enhanced in women with endometriosis and possibly driven by the action of prostaglandins that may cause disorganized myometrial contraction  14  16 . Moreover, the incidence of endometrial re  ux is much higher in women with congenital anomalies causing menstrual out  ow obstruction  17 . This theory has been well supported by animal models of endometriosis. Normal endometrial tissue placed into the peritoneal cavity recapitulates the disease, including the effects on eutopic endometrium, suggesting that an abnormal endometrium is not a prerequisite for initiation and development of endometriosis  18  21 . Early age at menarche, long duration and heavy menstrual  ow are all wellrecognized epidemiological risk factors for the development of endometriosis. The anatomical predominance of endometriosis in the right side of both hemipelvis and diaphragm, further supports this theory  22 . This asymmetry has been attributed to both a physiological process the clockwise intraperitoneal current and an anatomical factor the presence of the sigmoid colon and falciform ligament. However, the retrograde menstruation hypothesis is not suf  cient to explain the development of rare forms of the disease.\n",
      "Text: A possible relationship between endometriosis and infertility was  rst suggested in the Corpus Hippocraticum , as women suffering from dysmenorrhea were urged to conceive as quickly as possible to increase the chance of become pregnant  2 . Today, nearly 10 of women in their reproductive age suffer from endometriosis and about one third of them experience infertility, almost twice the rate observed among women without the disease  3 . Up to 50 of infertile women are found to suffer from endometriosis  4 . Despite the clinically recognized association between endometriosis and infertility, the mechanisms implicated in endometriosisassociated infertility are unclear and this condition is currently considered multifactorial. In addition, the diagnosis of endometriosis is currently underestimated due to the almost exclusive reliance on surgical  ndings, which delays diagnosis until symptoms require surgical intervention. The ability to identify endometriosis also critically depend on surgeon  s expertise and may preclude early recognition and treatment. The average time to diagnostics ranges from 4 to 11 years is reported in these patients, and this delay has a signi  cant impact on healthcare utilization and costs  5 , 6 . Indeed, the absence of macroscopic lesions or clinical features does not exclude the diagnosis of endometriosis, as infertility is often the only health concern. Furthermore, only onehalf of women with endometriosisassociated infertility show typical lesions  7 . In women with infertility, an early diagnosis of endometriosis is crucial from the perspective of fertility because the burden of the disease could be even more deleterious when compounded by the effect of increasing age on ovarian reserve. The focus of this review is to provide an update of pathophysiology of endometriosisassociated infertility. We will also discuss current medical and surgical strategies, and the role of fertility preservation and of assisted reproductive technologies ART in patients with endometriosis.\n",
      "Text: Coelomic metaplasia and mullerian remnants hypotheses\n",
      "Text: Pathogenesis of endometriosis\n",
      "Text: The coelomic metaplasia and mullerian remnants hypothesis are both based on the concept that endometriotic lesions originate insitu from embryological remnants or by metaplasia. Based on the mullerian remnants hypothesis   mullerianosis    23 , endometriosis is a consequence of the aberrant migration and differentiation of embryonic cell rests originating from the Mullerian ducts during organogenesis. This hypothesis can explain the presence of endometriosis in in adolescents before or shortly after menarche and in fetuses  24  26 . Embryological studies  24  support the presence of Mullerian remnants in the culdesac area, uterosacral ligaments, and medial broad ligaments. Alternatively, both germinal ovarian epithelium and peritoneum may undergo a Mullerian metaplasia and differentiate into endometrium  27 . This latter theory would explain the presence of endometriosis in ovary, sigmoid colon, appendix, or more distal sites such as the diaphragm and pleura  28 , although direct in  ltration through\n",
      "Text: Understanding the pathogenesis of endometriosis is crucial as it may have meaningful clinical and therapeutical implications. To date, none of the proposed theories have been able to comprehensively explain the natural history of the disease and its associated diverse clinical presentations. The common thread to all theories is a complex dysregulated hormonal signaling, enhanced proin  ammatory microenvironment that has the potential to drive the initiation, maintenance, and progression of the disease  Figure 1 .\n",
      "Text: Retrograde menstruation theory\n",
      "Text: The most widely accepted pathogenetic hypothesis is based on retrograde menstruation as proposed by Sampson in 1927  8 \n",
      "Text: Frontiers in Endocrinology frontiersin.org 02\n",
      "Text: Bonavina and Taylor 10.3389fendo.2022.1020827\n",
      "Image: images/image_2_6.jpeg\n",
      "Text: FIGURE 1 Theories of Endometriosis Pathogenesis. SF1, steroidogenic factor 1GATA6, GATA binding protein 6PGE2, Prostaglandin E 2 COX2, cyclooxygenase2ESR2, estrogen receptor alpha HOXA10, homebox protein A10PRB, progesterone receptor isoform B GATA2, GATA binding protein 2.\n",
      "Text: spread to ectopic sites  38 . In murine models of surgically induced endometriosis, endometriosisderived cells are capable of migration and micrometastasis to different extrapelvic organs including lung, spleen, liver and brain  39 . Clinically, this theory has been supported by the presence of endometrial tissue in the uterine vasculature  37  and by evidence of emboli in sentinel lymph nodes  40 .\n",
      "Text: diaphragmatic fenestrations is possible. Additionally, both hypotheses may explain rare cases of endometriosis in women with MayerRokitanskyKusterHauser syndrome and other nonobstructive Mullerian anomalies  29  31 , in the absence of menstruation menopause  32  and in men  33  36 .\n",
      "Text: Hematogenous and lymphovascular dissemination\n",
      "Text: Stem cell theory\n",
      "Text: Sampson recognized that retrograde menstruation does not explain uncommon extraperitoneal locations and diverse clinical presentations with symptoms remote form the pelvis  37 . He  rst suggested hematogenous or lymphatic dissemination of endometrial liketissue as an alternative theory. This hypothesis implies that endometrial cells enter the uterine vasculature or lymphatic system at menstruation, and they\n",
      "Text: In the last few years, it has become clear that altered stem cell traf  cking contribute to the etiology and pathophysiology of endometriosis. The  rst evidence on the contribution of bone marrow derived stem cells BMDCs in the regeneration of the endometrium was reported in 2004  41  subsequent studies have con  rmed the bone marrow contribution to endometrium\n",
      "Text: Frontiers in Endocrinology frontiersin.org 03\n",
      "Text: Bonavina and Taylor 10.3389fendo.2022.1020827\n",
      "Text: that multiple genes contribute to endometriosis is widely accepted. Studies on monozygotic twins show that endometriosis has an estimated total heritability of approximately 51  58  60 . Daughters of mothers with surgically con  rmed endometriosis have more than double risk of developing the disease  61 . Moreover, familial inherited of endometriosis tends to be more severe with an earlier onset of symptoms compared with sporadic cases  55 , 62 . Metaanalyses of genomewide association studies of diverse populations have identi  ed a robust association of endometriosis with certain risk loci involved in sex steroid hormone pathways, indicating a possible role in the development of advanced stages of endometriosis  63  68 . However, none are common and in total these genetic variants account for only a small fraction disease risk. In general, a multitude of genetic variants with only weak individual effects care likely responsible for the increased hereditary risk of endometriosis  69 . In the context of infertility associated with endometriosis, a recent crosssectional study including 213 infertile women with endometriosis who underwent IVF procedures, found that single nucleotide variants of FSHB and FSHR separately interfered with the hormonal pro  le both FSH and LH levels and ultimately with the number of oocytes retrieved in these patients at any stage of the disease  70 .\n",
      "Text:  42 , 43 . Both progenitor cells within the endometrium and multipotent cells from bone marrow contribute to endometrial homeostasis. The BMDSCs travel through the circulatory system and contribute to the composition of eutopic endometrium  41 . After travelling to endometrium these BMDSCs can become restricted to an endometrial cell lineage, contributing to the pool of both stromal and epithelial endometrial progenitor cells. Some become located in the basal layer of the eutopic endometrium and regenerate on a monthly basis under the in  uence of estrogens. Furthermore, women with endometriosis have a higher number of these pluripotential cells compared with healthy women during menses  44 . During menstruation, women with endometriosis shed more basalis cells, including progenitor cells, than healthy individuals, these cells can more easily generate endometrium in ectopic locations than differentiated cells and further expand on Sampson  s theory of retrograde menstruation  45 . BMDSCs can directly differentiate into endometrium without  rst being localized in the uterus. Ectopic differentiation of circulating stem cells has been proposed as a pathogenetic mechanism of endometriosis. Mesenchymal extrauterine stem cells derived from bone marrow and other sources may also be involved in the pathogenesis of the disease both in the peritoneal cavity as well as distant sites. Their inappropriate differentiation to endometrial cells at ectopic locations is likely the principal source of extraperitoneal endometriosis  46 , 47 . The ability of BMDSCs to contribute to endometriotic lesion and differentiate into endometrial phenotypes help to explain how ectopic tissue can occur in locations outside the peritoneal cavity and in nonperitonealderived cells, such as lungs  48  50 , central nervous system  51  and in men  33  36 . Furthermore, BMDSC are attracted by eutopic endometrium under injury and in  ammatory conditions  52 . Endometriotic lesions, through the production and release of proin  ammatory cytokines and chemokines  47  and under estrogenic in  uence  53  recruit more stem cells to further promote lesion growth. Additionally circulating endothelial progenitor cells contribute to the vascularization of endometriotic lesions. Stem cells are also capable of traf  cking between endometriotic lesions and the eutopic endometrium, and therefore likely contribute to the impaired uterine receptivity in these women  54 . These cells, derived from endometriosis, migrate as mesenchymal stem cells MSC, engraft the uterine stroma, however activation epithelial Wnt signaling that likely distorts the epithelialstromal dialog needed for optimal endometrial development and receptivity.\n",
      "Text: The epigenetic theory\n",
      "Text: There is a growing body of evidence that epigenetics has a key role in the pathogenesis of endometriosis. Epigenetic modi  cations involve dynamic and reversible changes in the chromatin structure in  uencing gene expression in a heritable fashion. Epigenetic phenomena are likely to have implications for diagnosis, prognosis and for the possibility of developing targeted therapeutic strategies. The hallmarks of epigenetic gene regulation are DNA methylation hypo and hypermethylation, histone modi  cations, and microRNA production, which lead to expression or suppression of speci  c proteins. Comparative studies of both ectopic lesions and eutopic endometrium stromal cells have provided data on the role of epigenetic factors in the etiopathogenesis of endometriosis and its related infertility  19 , 71  73 . DNA methylation is one of the most common epigenetic modi  cations and active in endometrium. Numerous studies have revealed a direct correlation with the expression of genes in  uencing the implantation process in eutopic endometrium of women with endometriosis. Homebox proteinA10 HOXA10 is a gene that has a well characterized and essential role in generating a receptive endometrium. Hypermethylation of the HOXA gene promoter has been demonstrated both in animals and in the eutopic endometrium of women with endometriosis compared to healthy controls  19 , 74 , 75 . As promoter\n",
      "Text: Genetic etiology\n",
      "Text: Familiar clusters of endometriosis have been found in humans  55  and nonhuman primates  56 , 57 . However, no distinct inheritance pattern has been established and the notion\n",
      "Text: Frontiers in Endocrinology frontiersin.org 04\n",
      "Text: Bonavina and Taylor 10.3389fendo.2022.1020827\n",
      "Text: to each lesion subtype ovarian, super  cial, and deep in  ltrating endometriosis  98 . Moreover, miRNA signatures in endometrium are likely to change with the respect of the different phases of the menstrual cycle  99 , 100 . The most frequently detected miRNA both in endometriomas and endometriotic lesions, found to be downregulated in six studies was miR200 family, known to play a crucial role in the EMT, a relevant process in the establishment of endometriotic lesions  101 , 102 . Other miRNA reported to be differentially regulated up or downregulated in endometriotic lesions in more than two studies were miR1, 29c, 34c, 100, 141, 145, 183, 196b, 200a, 200b, 200c, 202, 365, and 375  103 . Several of these are also known to be involved in EMT, as well as, cell proliferation, cell adhesion, invasion and angiogenesis and demonstrating binding to target mRNAs is an important step to validate their role in the pathogenesis of the disease. Extracellular miRNAs are found in all body  uids, including the circulation both serum and plasma  104 . Circulating microRNAs can potentially impact endometriotic lesion development by mediating intercellular communication between eutopic endometrium and ectopic implants  105 .\n",
      "Text: hypermethylation is generally associated with gene silencing, the reduced HOXA10 gene expression in the endometrium of women with endometriosis is, at least in part, responsible for the impaired uterine receptivity. Conversely, one recent study  76  found hypomethylation of the HOXA10 gene in the endometrium of women with a previous history of endometriosis and under hormonal treatment at the time of surgery, opening the possibility that longterm therapy may reverse epigenetic signatures classically seen in the disease. Aberrant DNA methylation patterns have also been found in endometriotic tissue compared with eutopic endometrium. The promoter of progesterone receptor PR isoform B gene is hypermethylated in endometriosis, with subsequent reduced PRB expression  77  79  contributing to the relatively persistent progesterone resistance. Similarly, the different level of expression and methylation hypo or hyper of certain transcriptional factors GATA6, GATA 2 and steroidogenic factor 1SF1 may account for estrogen dependency and progesterone resistance by changing the expression of both estrogen receptorbeta and progesterone receptor  80  82 . Lastly, the invasive proprieties of endometriotic cells have also found to be regulated by hypermethylation in endometriosis  83  85 . Let7 microRNA is hypermethylated in endometriosis leading to decreased Let7 expression and disinhibition of KRAS and other genes that drive endometriosis growth and invasion  86 . Little is known about the role of histone modi  cations in the pathogenesis of endometriosis, and results are often con  icting. A marked histone hypoacetylation has been shown in endometriotic stromal cells of both eutopic and ectopic tissue of affected women compared to healthy endometrium  87  and HDAC enzymes seems to play a key role in this process  88  91 . Also, acetylation levels of H3 and H4 histones are lower in ectopic lesions and eutopic endometrium of women with endometriosis compared with healthy women  92 , 93 . MicroRNAs MiRNAs are small RNA molecules of approximately 22 bases. They interact with mRNA and change gene expression by inhibiting translation or inducing mRNA degradation. Their increased expression causes repression of translation from the mRNA while decreased MiRNA expression can lead to upregulation of protein production from mRNA. They also target and regulate both methylation and acetylation processes, thereby modifying the epigenome. Unlike other epigenetic mechanisms, miRNAs regulate gene expression at a posttranscriptional level, and they are found both intra and extracellularly  94 . They target genes involved in hormone metabolism, cell cycle proliferation, migration, and invasion, immune in  ammatory response, epithelialmesenchymal transition EMT, apoptosis and angiogenesis  95 . Differential expression of more than 100 miRNAs has been found in paired endometriotic lesions and eutopic endometrium of women with and without endometriosis  96 , 97 . In addition, different expression pro  les were detected and reported as characteristic\n",
      "Text: Pathophysiology of endometriosis associated infertility\n",
      "Text: Translational animal models of endometriosis associated infertility\n",
      "Text: Considering the limited knowledge of endometriosis pathophysiology, research has long focused on  nding animal models to study suspected pathogenic mechanisms and to  nd novel targets for therapy. As with human endometriosis, animal models of endometriosis reveal an impact on fecundity in terms of impaired folliculogenesis, ovulation, fertilization, implantation or embryonic developement  106 . Nonhuman primates have been extensively used as experimental models for endometriosis because of their phylogenetic proximity to humans. They menstruate cyclically and therefore they can develop endometriosis spontaneously, resembling the human disease based on retrograde menstruation. To date, 11 species of menstruating nonhuman primates have been reported  107 . Ectopic lesions are laparoscopically and histologically identical and at a similar pelvic sites  108 . However, spontaneous endometriosis develops slowly, at a lower rate compared to humans and might be multifactorial. Therefore, alternative methods of arti  cially induced endometriosis have been introduced in these species cervical repositioning  109 , cervical occlusion  110  or surgical induction  18 , 21 . The use of the nonhuman primate model of endometriosis, either inducible or spontaneous, seems to provide an excellent tool to investigate not only the pathogenesis of disease but also its\n",
      "Text: Frontiers in Endocrinology frontiersin.org 05\n",
      "Text: Bonavina and Taylor 10.3389fendo.2022.1020827\n",
      "Text: with histologically con  rmed endometriosis reported that the severity of super  cial dyspareunia was associated with increased odds of infertility concerns  116 . Endometriosis is associated with a 9fold increased risk of deep dyspareunia mostly due to the in  ltrative form and severe stages of the disease affecting the posterior vaginal fornix, the pouch of Douglas, the uterosacral ligaments, and the rectum  117  119 . Although relatively frequent, dyspareunia, is not the exclusive sexual complaint in women with endometriosis. Systematic reviews have highlighted that about two thirds of women with endometriosis have some form of sexual dysfunction not limited to deep dyspareunia  120  122 . Chronic, nonmenstrual pelvic pain associated with the disease might in  uence sexual life by reducing desire, frequency of sexual intercourse, arousal, or orgasm. This will have a signi  cant negative impact on intimate relationships, emotional wellbeing, and quality of life in general. In this regard, a holistic approach, rather than just a mechanistic approach, is mandatory given the complex nature of human sexuality.\n",
      "Text: associated infertility and impaired endometrial function. These models offer the opportunity to investigate the effect of endometriosis on the eutopic endometrium because of their similar reproductive physiology and endometrial pattern compared to humans. However, high costs, restricted facilities and ethical challenges are limiting their use for experimental purposes. Conversely, rodents do not menstruate and therefore they do not develop endometriosis spontaneously. Only homologuos models of surgically induced endometriosis have been used so far in this setting. Heterologous mouse models consisting of immunode  cient mouses do not seem offer obvious advantages in the study of endometriosis associated infertility. Ectopic transplanted tissue grows and behaves in a hormone dependent manner, and they exhibit similar histological patterns compared with human endometriotic lesions  106 . Despite of these limitations, the rodent model offers a low cost option and the opportunity to perform studies on large homogeneous groups of genetically similar animals. Transgenerational and longterm studies can also be performed because there is no rejection of the transplanted ectopic tissue. For an accurate model of the human condition, an intact hypothalamic pituitaryovarian axis in the animal recipient is essential for the evaluation of endometriosis and its related infertility. Another challenge is the dif  culty in developing models that recapitulate all subtypes of endometriotic disease and therefore individualize and target. For example, there is a lack of speci  c in vivo models which resemble characteristics of ovarian endometriosis and its related infertility. To date, few animal models of ovarian endometriosis have been successfully implemented  108 , 111 , 112 . Spontaneous ovarian endometriosis in nonhuman primates is also not as common as in humans  108 . Lastly, a major limitation of these models is the concomitant establishment of other subtypes of the disease within the peritoneal cavity causing potential confounding effects. To capture the full extent of human disease it is possible to transplant human endometriosis into an immunode  cient mouse. This model may best recapitulate human disease  113 .\n",
      "Text: Mechanical factors Pelvic adhesions and anatomical distortion potentially affect the conception process in endometriosis. In  ammation,  brosis, adhesions, and surgical sequela are the main pathophysiologic processes involved. Anatomical distortion and mechanical factors may impair oocyte release from the ovary, inhibit tubal ovum pick up or ovum transport, andor block sperm transfer into the fallopian tube. Interestingly, no term pregnancies occurred in a nonhuman primate animal model of induced endometriosis when adnexal adhesions were noted on the same side as the ovulation occured  123 .\n",
      "Text: Ovarian reserve The ovary is the most common location of endometriosis. Ovarian reserve is one of the main prognostic factors regarding fertility and is in large part related to a woman  s age. Ovarian reserve is de  ned as the supply of nongrowing, unrecruited primordial follicles  124  currently, a clinical tool that accurately predicts ovarian reserve does not exist. Despite concerns over their role and its speci  city in clinical practice, antral follicle count AFC and serum antiMullerian hormone levels AMH are currently the most widely used indices of ovarian function  125 . AMH is best used in identifying women who may be poor responders to gonadotropin stimulation in the setting of assisted reproductive technologies ART  126 . AMH concentrations are not greatly affected by the menstrual cycle or oral contraceptives, making measurement possible at any time. At present, the pathophysiologic mechanism of diminished ovarian reserve in endometriosis remains unclear. Nevertheless, there is a growing molecular, histological, and morphological evidence that endometriomas have a detrimental effect on\n",
      "Text: Role of pain For a successful natural conception, the feasibility of sexual intercourse is an important prerequisite, and one that is often neglected, however this is a potentially relevant mechanism involved in endometriosisassociated infertility. Pain may be a factor involved in endometriosisrelated infertility when super  cial dyspareunia pain occurring in or around the vaginal introitus makes intercourse dif  cult to achieve or deep dyspareunia makes intercourse dif  cult to sustain, leading to avoidance to sexual activity. However, only a few studies have focused on the relationship between super  cial dyspareunia and endometriosis and is often concomitant with deep dyspareunia  114 , 115 . One crosssectional study conducted on 300 women\n",
      "Text: Frontiers in Endocrinology frontiersin.org 06\n",
      "Text: Bonavina and Taylor 10.3389fendo.2022.1020827\n",
      "Text: yet identi  ed. One recent study  138  found that proteins involved in apoptotic pathways were signi  cantly increased in cortical tissue surrounding small endometriotic cysts 3cm but not in those surrounding other benign cysts. Clinical  ndings con  rm this trend one recent, large, prospective cohort study including 106,633 premenopausal, laparoscopically con  rmed endometriosis patients found higher risk for early natural menopause compared to those without endometriosis, especially in nulliparous women and in those who never used oral contraceptives  139 . In two recent metaanalysis both serum AMH and AFC were found to be reduced in patients with unoperated endometriomas compared to patients with other benign ovarian cysts without endometriosis  140 , 141 . Moreover, in a prospective longitudinal study, a timedependent effect was recently where serum AMH decline in women with untreated endometriomas faster than in agematched healthy controls  142 . Five meta analyses  143  146  evaluating reproductive outcomes of women with endometrioma who had not undergone previous adnexal surgery found a reduced responsiveness to ovarian stimulation as measured by higher cycle cancellation rate, lower number of oocytes retrieved and lower number of formed embryos despite similar pregnancy and live birth rates. Besides their overall effect, important questions have been raised concerning endometrioma and the effect of size and bilaterality. Indeed, several comparative studies  147  150  in patients with unilateral endometriomas undergoing IVF showed that the affected and the healthy ovary produce a similar number of codominant follicles and oocytes perhaps indicating more than a local effect in the affected ovary a single visible endometrioma maybe a marker of bilateral disease or alternatively there may be a systemic effect of the single endometrioma on both ovaries. Women with bilateral endometriomas demonstrate an even lower response to stimulation, however clinical pregnancy rate are not affected  151  153 , likely overcome by the availability of multiple eggs and embryos Another key concern is whether surgery has a negative impact on residual ovarian function. Despite the many studies that have been performed to evaluate the impact of surgical treatment of ovarian endometrioma on ovarian reserve, the data are still inconclusive. The potential detrimental impact of adnexal surgery on ovarian reserve has been elucidated in several histological studies con  rming that cystectomy is generally associated with inadvertent removal of healthy ovarian tissue and primordial follicles adjacent to the cyst  s pseudocapsule  154 , 155  this effect increases proportionally with cyst diameter  156 , and ultimately is poorly correlated with the level of expertise in reproductive surgery  157 , 158 . Unlike other benign cysts, in which a wellde  ned capsule is present, endometrioma is not surrounded by a capsule  154  and technical dif  culties may arise due to the absence of a clear cleavage plane. However, the damage in  icted by surgery may also be due to the related local in  ammation or vascular\n",
      "Text: ovarian function. Whether the endometrioma reduces the amount of functional tissue available by spaceoccupying effect mechanical stretching damage or by a direct toxic effect remains unknown. An endometrioma is a peculiar benign cyst without a real capsule therefore, there is exchange of cysts contents with the adjacent healthy ovarian cortex. Unlikely other benign cysts, the  uid of endometriotic cyst is able to induce oxidative stress in viable cells and potentially cause damage to healthy tissue. Molecular comparative analysis of the cystic  uid revealed high concentrations of free iron which is able to mediate the production of reactive oxygen species ROS that are highly diffusible through cellular compartments. An increase in the iron concentration in the follicular  uid from follicles in contact with the endometrioma was found in comparison with the contralateral healthy ovary  127 . Moreover, proteolytic enzymes, in  ammatory and adhesion molecules were also found in the endometriotic cyst  uid microenviroment  128 . Thus, the release of toxic cysts contents in the adjacent ovarian parenchyma may lead to oxidative stress,  brosis, loss of cortical stroma, smooth muscle cell metaplasia, impaired vascularization, and, at later stage, reduced follicular maturation and atresia in early follicles  128 . Notably, the demonstration of increased oxidative stress affecting the normal ovarian cortex surrounding an endometrioma strongly suggest a ROSinduced  brogenic response, leading to inhibition of angiogenesis and to follicular damage  129 . Maneschi et al.  130   rst found a reduced follicular number and activity prior to surgery compared in histopathological specimens of endometriomas compared to other benign cysts these  ndings were later con  rmed in other similar studies evaluating follicular density  131  133 . Another histopathological study also found increased  brotic tissue surrounding endometrioma in comparison with that of other benign cysts  134 . Interestingly, focal in  ammation in the ovarian cortex of affected ovaries was suggested to cause enhanced follicular recruitment and atresia as a result of  brosis and loss of cortexspeci  c stroma that maintains the follicular niche  135 . Hence, excessive primordial follicle activation was proposed as a mechanism of  burnout  of the follicular reservoir in ovarian endometriosis  136 . Primordial follicle activation is an irreversible process and results in follicular depletion. The PI3KPTENAktFOXO3 and PI3K AktmTOR signaling pathways are the bestcharacterized regulators of primordial follicle activation during the initial recruitment. Takeuchi et al.  136  demonstrated that the number of primordial follicles was diminished, whereas primary, secondary, antral and growing follicle numbers increased in human ovaries with endometrioma, and this effect was mediated by the PI3KPTENAktFoxo3 pathway. Similarly luteinized granulosa cells of women with endometriosis are characterized by increased apoptosis  137 , however the speci  c putative mechanism leading to cell loss has not been\n",
      "Text: Frontiers in Endocrinology frontiersin.org 07\n",
      "Text: Bonavina and Taylor 10.3389fendo.2022.1020827\n",
      "Text: including 3818 embryos in cleavage stage found similar fertilization rate and embryo quality, despite a reduction in viable pregnancy rate. Conversely, one recent retrospective analysis using timelapse technology observed altered relative kinetics in embryos from patients with endometriosis, supporting poorer embryo quality  176 . Lastly, from the oocyte donation perspective, reduced pregnancy and implantation rates are observed when oocytes come from donors with endometriosis  177  179 , supporting an effect of endometriosis on embryo quality. In contrast no difference was seen in recipients of donated oocytes based on the presence or absence of endometriosis. However, the cases used in these studies do not re  ect the general population of women with endometriosis. The recipients in oocyte donation programs are relatively older compared with the majority of women with endometriosis seeking for pregnancy. With diminishing ovarian reserve and menopause endometriosis typically resolves. A history of endometriosis in a recipient of donor oocytes may not re  ect current disease status. Therefore, use of results from oocyte donation does not provide a valid model to evaluate implantation and pregnancy rates in young women with infertility related to endometriosis. Dysregulation of steroidogenesis and alterations of intrafollicular microenvironment are the main pathophysiological processes investigated in the context of endometriosis. E 2 is crucial for follicular maturation and oocyte competence follicular  uid also plays an important role in the reproductive performance of oocytes. Alterations in the normal physiology of the granulosa cells such as increased apoptosis and dysregulations of molecular pathways involved in its development and have been intensively studied. Granulosa cells of women with endometriosis are characterized by a decreased expression of P540 aromatase, a key enzyme in estrogen production. Similarly, some evidence also indicates an altered progesterone secretion from granulosa cells that might affect normal oocyte maturation  180 , 181 . Symmetrical lower E 2 levels and higher progesterone levels were found in the follicular  uid of patients with endometriosis compared to controls  182 . Moreover, follicular  uid has been shown to be subject to an important oxidative stress  183  188 . An imbalance in ROS and antioxidant systems in the oocyte microenvironment could promote abnormal oocyte development, causing DNA damage, which would result in lower oocyte quality. In another study, cryopreserved human oocytes exposed to endometriotic  uid from patients with advanced stages of the disease had excess cellular fragmentation of derived embryos that may lead to impaired embryo development by inducing apoptosis in surrounding blastomeres or by altering blastomere division  189 . An altered systemic and peritoneal immune and in  ammatory pro  le that characterize women with endometriosis has also been proposed to directly in  uence the follicular  uid composition. Altered levels of proin  ammatory\n",
      "Text: compromise secondary to excessive manipulation of the cortex with subsequent tearing, bleeding, and the need for electrosurgical coagulation  159 . Five metaanalyses showed a signi  cant reduction in serum AMH concentrations after surgical treatment of endometriomas  160  162  and this effect is persistent postoperatively up to 18 months  162  and more pronounced in case of bilateral adnexal surgery  163  165 . In contrast, two metaanalyses showed that ovarian reserve evaluated by AFC is not decreased after surgical treatment of endometriomas  162 , 166 . Concerning reproductive outcomes following IVF treatment, two recent metaanalyses  167 , 168  showed a lower number of oocytes retrieved in women who had surgical treatment for endometrioma compared to women with expectant management this  nding was previously con  rmed separately in case of unilateral treatment, compared with the contralateral normal ovary without endometrioma in the same patient  144 . However, two metaanalyses  144 , 169  concluded that women who had surgical treatment before IVFICSI had a similar live birth rate, clinical pregnancy rate, miscarriage rate, number of oocytes retrieved, and cancellation rate per cycle compared with those with untreated endometrioma. Lastly, according to a recent cohort study  170 , the SAFE surgery and ART for endometriomas trial, about 50 of women with endometrioma were able to conceive spontaneously within 6 to 12 months after surgery. On the other hand, higher FSH and LH levels between the 2 nd and the 5 th day of the cycle prior to IVF required higher doses of gonadotropins for ovarian stimulation, and lower number of oocytes were retrieved after surgery for endometrioma in the remaining cohort of patients addressed for IVF, compared with women with unexplained infertility. Despite all these efforts, further clinical analysis implementing standardization of endometrioma size, bilaterality, surgical technique, postoperative timeinterval evaluations and clinical measurements are needed to help in elucidating both contributions and the magnitude of the effect.\n",
      "Text: Oocyte quality, embryo transport, sperm function and motility, spermoocyte interaction The possible effect of ovarian endometriosis on oocyte quality is still under debate. Deeper understanding of the impact of the disease on oocyte quality is crucial as fertility preservation techniques are gaining attention in the counseling and treatment of this patients. Only few studies have investigated the impact of endometriosis on embryological competence. A recent metaanalysis including 22 studies indicate that endometriosis does not affect embryo morphology Women with endometriosis have comparable highquality embryo rate, cleavage rate, and embryo formation rate, regardless the stage of the disease  171 . Results from several metaanalyses analyzing IVF outcomes, are controversial due to the high heterogeneity of the included studies  172  175 . One recent large cohort study\n",
      "Text: Frontiers in Endocrinology frontiersin.org 08\n",
      "Text: Bonavina and Taylor 10.3389fendo.2022.1020827\n",
      "Text: con  icting  216 , 217 . Two recent reports showed similar outcomes in terms of implantation rates through ART cycles when compared to healthy controls  218 , 219 . Defective implantation could be due to a reduced endometrial receptivity or decidualization capacity in these women. The eutopic endometrium of women with endometriosis displays several molecular and functional, abnormalities compared to healthy women  s endometrium  220  223 . Gradual and profound alterations have also been detected in the endometrium of endometriosisinduced baboons  224 , 225 . However, the mechanism and speci  c signal that leads to alterations in the endometrial microenvironment of women with endometriosis is not fully characterized and is still unknown whether changes in the endometrial pattern are the cause for the infertility and for presence of ectopic lesions or vice versa. Endometrial receptivity and decidualization is dependent upon hormonally regulated molecular processes. Estradiol E 2  and progesterone P 4  responsive signaling pathways are regulated in an epithelial and stromal compartmentspeci  c manner in the endometrium. Progesterone is the main hormone responsible for the transient receptive endometrial phenotype, essential for embryo implantation. The endometrial response to P 4 is characterized by inhibition of estrogendependent proliferation of epithelial cells, secretory maturation of the glands, and transformation of stromal cells into specialized decidual cells. Functional dysregulation of steroid hormone signaling in endometriosis, such as upregulation of E 2 induced cell proliferation, in  ammation and progesterone resistance, seems to play an important role in impairing endometrial receptivity in these patients  226 , 227 . The shift toward estrogen dominance promotes in  ammation, angiogenesis, cell proliferation, and immunosuppression. Both total endometrial PR expression and PRAPRB isoforms ratios are dysregulated in the endometrium of women with endometriosis  222 , 228  230  and in mice with induced endometriosis  19 . Moreover, progesterone receptor expression levels are lower in women with endometriosis associatedinfertility  231 , whereas estrogen receptor 1 ESR 1 levels are increased in the mid secretory phase endometrium of these women compared to controls  232 , 233 . From a histological perspective, Noyes et al. in 1950 have been proposed eight morphological criteria to evaluate endometrial receptivity, and for many decades they were adopted as the main diagnostic tool for detection of endometrial receptivity defects. However, these criteria have been questioned in recent years and several randomized control trials RCT  234 , 235  have invalidated their use based on data demonstrating that histological dating of the endometrium does not discriminate between fertile and infertile women. Similarly, the negative predictive value of the endometrial thickness and the endometrial pattern as ultrasonographic parameters  236  239  in predicting endometrial receptivity are insuf  cient  240 .\n",
      "Text: cytokines and growth factors IL1B, TNFa, IL2, IL8, IL12, IL6, RANTES have been reported in the follicular  uid of women with endometriosis compared to controls  190  192 . Follicular  uid is released into the peritoneal cavity at each ovulation. Three studies have shown spindle and chromosome damage after incubating murine  193 , 194  and bovine  185 , 195  oocytes in metaphase II with both peritoneal  uid and follicular  uid derived from infertile women with endometriosis. A reduced implantation rate in normal rabbits was observed when the peritoneal  uid from rabbits with surgically induced endometriosis was transferred  196 . On the other hand, intraperitoneal injection of peritoneal  uid from women with endometriosis signi  cantly reduced implantation rates in rabbits as well as in hamsters  197 , 198 . Gamete transport is also affected by the in  ammatory microenvironment, anatomical distortions and uterotubal dysperistalsis associated with endometriosis  15 . The endometriotic proin  ammatory peritoneal  uid microenvironment may also affect sperm function  199  201  by inducing sperm DNA fragmentation  201 , disrupt sperm membrane permeability or integrity  202 , reduced sperm mobility  203 , impaired spermoocyte interaction  204  and abnormal sperm acrosome reaction  205 .\n",
      "Text: Impaired ovulation Clinical data concerning spontaneous ovulation rate in these women is poor and controversial  206 , 207 . Prolactin levels are signi  cantly higher in women with endometriosis when compared to those of women without endometriosis. Hyperprolactinemia prevents luteinizing hormone pulsatility and interferes with hypothalamic function by blocking estrogen receptors, thus producing anovulation. Another potential cause of ovulation failure in women with endometriosis is the luteinized unruptured follicle syndrome  208 , a condition challenging to estimate in clinical settings in which the dominant follicle undergoes luteinization but fails to rupture at or to release the oocyte. Altered patterns of estrogen and progesterone secretion leading to an abnormal luteal phase may also compromise ovulation in these women  209 . An association between endometriosis, luteinized unruptured follicle syndrome, and impaired fertility was observed in non human primates animal models of endometriosis  123 , 210  as well as in a mouse model of surgicallyinduced endometriosis  211 , 212 .\n",
      "Text: Endometrial receptivity The implantation rate is clearly diminished in women with endometriosis during both natural cycles and ART treatments, even in patients with minimal disease  213  215 . However, data from clinical studies suggesting that endometriosis leads to implantation defects implicating the endometrium is still\n",
      "Text: Frontiers in Endocrinology frontiersin.org 09\n",
      "Text: Bonavina and Taylor 10.3389fendo.2022.1020827\n",
      "Text: controls  250 , 251 . Several pathways have found to be aberrant in endometriosis  251  256  contributing to the unfavorable environment and promoting aberrant effects on the maternalembryo interface. Increased activation of PI3K AKT  252  pathway and decreased NOTCH signaling  256  contributes to inactivates FOXO1, an important mediator of decidualization involved in the progesterone signaling. Moreover, AKT pathway has been shown to downregulate and upregulate ESR2 and ESR1, respectively, with the net effect of promoting estrogen dominance  257 , 258 . Lastly, IGFBP1, a downstream target gene of HOXA 10 and a marker of decidualization, is reduced in the endometrium of women with endometriosis  251 , and it is also downregulated in the eutopic endometrium of mice with induced endometriosis  19 . It is still poorly understood how the immune system contributes to and in  uences the endometrial microenvironment and the implantation window. Data is con  icting on the immune cell population of both ectopic and eutopic endometrium of women with endometriosis and controls, especially regarding absolute numbers, markers, activation states and cycle dependence due to heterogeneity of studies  259 . Eutopic endometrium microenvironment of women with endometriosis seems to be more proin  ammatory than controls and aberrant functions of certain immune population may lead to an inhospitable environment for embryo implantation. Interestingly, type I classically activated macrophages, that secretes proin  ammatory factors, are the main population in eutopic endometrium of women with endometriosis, across all cycle phases, compared with normal controls  260  262 . This proin  ammatory predominance may decrease embryo nidation. The relative less cytotoxicity of natural killers together with their higher immaturity in the eutopic endometrium of women with endometriosis was signi  cantly correlated with the infertility status in the same group  263 . Concerning the role of B cells, antiendometrial antibodies may also play a role in impaired implantation by affecting directly endometrial function for embryo receptivity  264 . Finally, circulating and endometrialdecidual regulatory T cells Tregs have shown to be reduced in women with recurrent pregnancy loss, recurrent implantation failure and endometriosis  265 .\n",
      "Text: A transition from an anatomical and histological to a molecular perspective led to the genomewide screening of all transcribed genes. Transcriptomic analysis of both eutopic and ectopic endometrium from women with or without endometriosis found dysregulations of selected genes that are implicated in the implantation process  241 . Interestingly, HOXA10 is a progesterone target in the endometrium. The homebox gene family is critical in the development of the female reproductive tract during embryonic stages as well as in the regulation of endometrial receptivity during adulthood in response to steroid hormones  242 . Decreased HOXA10 and HOXA 11 expression has shown to be involved in impaired endometrial receptivity, resulting in decreased implantation rates  75 , 243 . Patients with endometriosis do not show the normal physiologic rise in HOXA10 and HOXA11 during the midluteal phase of the menstrual cycle  75 , 243 , 244 . HOX gene expression is also subjected to epigenetic modi  cations that leads to longlasting alterations in endometrial receptivity  245 . HOXA10 hypermethylation is an important mechanism responsible for its diminished expression  74 . Both murine and baboon endometriosis models showed hypermethylation of the promoter region of HOXA10 and decreased expression of HOXA10 genes in the eutopic endometrium  19 , 246 . In humans, hypermethylation of HOXA10 was also identi  ed in the endometrium of women with endometriosis  71 , 74 . Lastly, under normal conditions, high expression of the HOXA10 gene suppresses the transcription of the EMX2 gene, which is also essential in regulating endometrial receptivity and implantation. With the diminished expression of HOXA10 in endometriosis, the increased level of endometrial EMX2 directly affects endometrial cell proliferation and function during the peri implantation period, resulting in aberrant implantation  247 . Integrins are cell adhesion molecules expressed in the endometrium during the receptive window and therefore involved in successful implantation. Interestingly, B3integrin subunit is a direct downstream target gene of both HOXA10 and ESR1  248  and its aberrant expression have been described in the endometrium of women with endometriosis. Moreover, in the clinical setting, ART is less effective in patients with lower expression level of B3integrin in the eutopic endometrium  249 . Other transcriptional factors involved in regulation and mediation of progesterone signaling IGFBP1, GATA2, FOXO1, ARID1A, NOTCH1and WNT4, required for successful implantation are also reduced in endometrium of women with endometriosis. In human endometrial stromal cells, silencing of GATA2, diminishes markers of decidualization  82  and interestingly the expression level is signi  cantly reduced in the endometrium of women with endometriosis  80 . Defects in decidual response have been also investigated in the eutopic endometrium of women with endometriosis. Compromised decidualization of cultured stromal cells was found in fresh shed endometrium as well as in the eutopic endometrium of women with endometriosis compared with matched healthy\n",
      "Text: Adenomyosis and other uterine factors Endometriosis and adenomyosis often coexist, especially in infertile women  266 , 267 . Additionally, the concomitant presence of both conditions seems to worsen fertility outcomes  267 . In baboons, endometriosis was found to be statistically signi  cantly associated to adenomyosis and the latter was found to be strongly associated with primary infertility  268 . Several pathogenetic hypotheses have been postulated regarding adenomyosis and its associated infertility, including junctional zone thickness and subsequent perturbed uterine peristalsis that may alter uterotubal transport, as well as biochemical, functional\n",
      "Text: Frontiers in Endocrinology frontiersin.org 10\n",
      "Text: Bonavina and Taylor 10.3389fendo.2022.1020827\n",
      "Text: endometriosisassociated infertility is best undertaken in referral centers where a multidisciplinary approach can be offered and where both surgery and IVF services are present. From the patient perspective, a shared and informed decision is mandatory because different treatment options may involve both clinical and personal aspects. The treatment must be individualized according to the clinical situation and to the suspected level of impairment. Factors such as woman  s age, ovarian reserve, duration of infertility, additional infertility factors male, tubal, ASRM stage, previous surgical treatment for endometriosis, concomitant pain, and indications for IVF ET must be considered because they will in  uence the choice of treatment and may also have socioeconomic implications. In American and European guidelines  278 , 279 , the management of endometriosis is still based on the disease stage de  ned according to the revised American Society of Reproductive Medicine rASRM classi  cation. Despite the high consensus and multiple revisions, the currently used classi  cations system has several limitations, including failure in predicting fertility outcomes and in accounting for the different types of endometriosis. For this reason, Adamson and Pasta developed a validated and predictive endometriosis staging system, the Endometriosis Fertility Index EFI, to estimate the nonART pregnancy rate natural intercourse or IUI in women with surgically documented endometriosis  280 . This scoring system, which takes into account patientrelated factors age, length of infertility, history of previous pregnancy and surgical factors rASRM total score, endometriosis lesions and  least function score  from the tubes and ovaries, is highly accurate  281  and reproducible  282  and represents an important clinical decision tool to counsel patients on their reproductive options after surgery. While ART can correct many defects that prevent conception, implantation failure is not easily identi  ed, and in most cases, there are no available treatments. The endometrial status is rarely investigated during the standard workup of infertile women performed in infertility clinics worldwide, even prior to ART  283 . Thus, in the era of precision medicine and tailored therapy, a reliable endometrial receptivity assay would be of huge clinical and economical bene  t for the patient  s selection process. Starting from functional analysis of the endometrium, Kliman et al.  284  introduced an innovative endometrial functional diagnostic tool endometrial function test EFT   based on the use of antibodies two cyclins, as expression patterns of this type of mitotic cycle regulators have been associated with implantation success or failure. Moreover, revolutionary diagnostic tests based on transcriptomic and bioinformatic technologies, that can inform clinicians about the status of endometrial receptivity, have been proposed for diagnostic and prognostic purposes. The endometrial receptivity array ERA  285  is a and reproducible  286  microarraybased machinelearning predictive model for assessing endometrial status in the workup for infertile patients\n",
      "Text: and epigenetic alterations in both eutopic and ectopic endometrium  269 . The eutopic endometrial microenviroment in adenomyosis differs from the endometrium of unaffected women  270 , 271 . However, it remains con  icting whether these changes are of clinical signi  cance and, in particular, in the setting of assisted reproductive technologies. According to the most recent metaanalysis in the  eld  213 , 272  the presence of adenomyosis was associated with lower clinical pregnancy rate, higher risk of miscarriage following ART, and independently of the mode of conception with adverse pregnancy and neonatal outcomes. However, because of the limited number of comparative studies and their heterogeneous design, the real in  uence of adenomyosis alone on fertility is still controversial and poorly understood. One recent retrospective cohort study including more than 2000 subjects who underwent ART and by excluding those with decreased ovarian reserve and coexistence of endometriosis and  broids, found that adenomyosis has a negative effect on IVF outcomes including an increased risk of miscarriage and a reduced live birth rate  273 . There are several major limitations in investigating the impact of adenomyosis on infertility. First, there are major diagnostic limitations related with coexistence of endometriosis and adenomyosis, making the interpretation of the available literature dif  cult. Second, with the advent of 3D ultrasound and the use of magnetic resonance imaging the diagnosis of adenomyosis can now be relatively reliable without the need of histological examination of the surgical specimen  274 . However, there is no consensus regarding diagnostic features of adenomyosis using imaging making the interpretation of observational studies challenging different imaging criteria to de  ne adenomyosis are commonly used. Lastly, adenomyosis frequently coexists with other gynecological disorders and potential confounders, such as uterine leyomiomas. As with adenomyosis, uterine  broids, in particular submucous leyomiomas, has been associated with lower implantation rates and increased risk for early pregnancy loss  275 , 276 . The main pathophysiological processes implicated in endometriosis associated infertility are summarized in Figure 2 .\n",
      "Text: Management of endometriosis associated infertility\n",
      "Text: Clinical management of infertility associated with endometriosis is challenging due to lack of highquality scienti  c evidence and con  icting available guidelines  277 . The complexity in therapeutic decisionmaking is mainly related to the heterogeneous population of infertile women with endometriosis which includes diverse patient  s phenotypes. This often requires innovative diagnostic and therapeutic tools to target the speci  c dysfunctional step of the reproduction process. Therefore, care of women with\n",
      "Text: Frontiers in Endocrinology frontiersin.org 11\n",
      "Text: Bonavina and Taylor 10.3389fendo.2022.1020827\n",
      "Image: images/image_11_2.jpeg\n",
      "Text: FIGURE 2 Summary of the main pathophysiological processes implicated in endometriosis associated infertility.\n",
      "Text: based on the speci  c signature of 238 differentially expressed genes in the receptive endometrium. The ReceptivaDX  test a new screening and diagnostic test has been proposed  287  based on the  ndings that Bcelllymphoma 6 BCL6 overexpression in the secretory endometrium of these women contribute to the progesterone resistance  288  and could potentially serve as a surrogate in  ammatory marker for a dysfunctional endometrium in endometriosis associated with infertility  289 , 290 . Given the important diagnostic delay, strenuous research has been made to identify potential noninvasive diagnostic tool in endometriosis and to date, remains one of the major research priorities in this disease. Several potential biomarkers have been evaluated however, none has demonstrated suf  cient sensitivity and speci  city for clinical use. Cancer antigen125 CA125, a highmolecularweight glycoprotein antigen expressed in some derivatives of the celomic epithelium, has been previously reported to be elevated in serum of women with advanced forms of the disease  291 , 292  however, its overall sensivity is reported to be extremely low 53  293 . Based on their pivotal role in the etiopathogenesis of endometriosis, a substantial body of work has shed light on circulatingexosomal miRNAs as potential leading biomarkers for early diagnosis, prognosis, and surveillance for\n",
      "Text: endometriosis. They are they are found both intra and extracellularly, contained and released via exosomes  294 . MiRNAs are attractive due to their simple structure and their stability at the posttranslational level and in extracellular bio  uids. Conversely, their highly variable content and their low abundance in extracellular bio  uids, make detection very demanding. Real time PCR qRTPCR remains the gold standard for miRNA quanti  cation  295 . Nextgeneration sequencing platforms are also used for miRNA sequencing, and they showed high sensivity and excellent reproducibility  296 , nevertheless a great performance variation exists among the different platforms. MicroRNA have several targets in cells and each single mRNA transcript may be subjected to regulation by various miRNAs, Thus, the same pathway maybe regulated by a panel of miRNA. Many studies have investigated the role of circulating miRNA in endometriosis  104 , 297  312 . To date, more than 60 miRNAs were found to be differentially expressed in the circulation plasma andor serum of women with endometriosis  313 . Very few 20 miRNAs have been replicated in more than one study  314 . While generally miRNAs are not highly evolutionarily conserved, serum let7 family miRNA showed similar dysregulation in a murine model of endometriosis  315 . In general, serumderived miRNAs seems to yield higher sensitivity and speci  city 92 and 95,5 respectively compared\n",
      "Text: Frontiers in Endocrinology frontiersin.org 12\n",
      "Text: Bonavina and Taylor 10.3389fendo.2022.1020827\n",
      "Text: Reproductive surgery\n",
      "Text: with plasmaderived miRNAs and the highest biomarkers potential was found to be represented by a panel of serum derived miRNAs comprised of miR1255p, miR1505P, mir 3423p, miR451a, miR36135P, and let7b area under the curve AUC of 0.94  313 . Cosar et al.  302  reported a logistic regression model combining miR1255p, miR451a, and miR 36133p. Later, the same group  300  con  rmed a signi  cant diagnostic value of a combination of six miRNAs, with a  nal AUC0.9 across two independent clinical data sets. The reason for the limited consistency of results across studies is related with the dynamic naturebehavior of miRNA expression which is in  uenced by lack of standardization in the study protocols, such as sample collection menstrual phase, circadian rhythm, miRNA analysis method, casecontrol matching and subject  s background age, ethnicity, health status, stage minimalmild vs. moderatesevere and type of endometriosis ovarian, peritoneal, deep in  ltrating. In addition, different cutoff points were considered to de  ne a meaningful change in expression. An important variable is whether their expression is in  uenced by the menstrual cycle phase. Results need to be replicated on large series of well phenotyped patients and under stringent conditions of sampling. The availability of a reliable noninvasive test for endometriosis will allow more accurate and accessible diagnosis as well as the potential for identi  cation and treatment of endometriosis related infertility. Current and emerging treatment options for endometriosis associated infertility are summarized in Figure 3 .\n",
      "Text: Surgical indications should be guided by the presence or absence of pain, patient  s age, history of previous surgery for endometriosis, presence of other infertility factors, ovarian reserve, and estimated EFI. In general, it is clear that multiple surgeries should not be attempted to improve fecundity. Current guidelines suggest fertility counseling before surgery which should include AMH measurement  278 , 279 .\n",
      "Text: rASRM stages I and II\n",
      "Text: Stages I and II are not visible during the clinical and ultrasound examination and they are diagnosed mainly during diagnostic laparoscopy. A recent metaanalysis  315  of moderate quality evidence, including three RCTs on rASRM stage III endometriosis, concluded that operative laparoscopy increases natural viable intrauterine pregnancy rates compared to diagnostic laparoscopy only OR 1.89, 95 CI 1.252.86 I 2  0. Similar  ndings were later con  rmed in a networkmetanalysis by Hodgson et al.  316  comparing operative laparoscopy with placebo OR 1.63 95 CI 1.13 2.35. Only one metaanalysis  317  analyzed the live birth rate outcome and concluded that laparoscopic surgery in this disease stages has an overall advantage in improving the chances of live birth RR 1.52, 95 CI 1.261.84. Based on this evidence, operative laparoscopy is currently an option for\n",
      "Image: images/image_12_5.jpeg\n",
      "Text: FIGURE 3 Current and emerging treatment options for endometriosis related infertility.\n",
      "Text: Frontiers in Endocrinology frontiersin.org 13\n",
      "Text: Bonavina and Taylor 10.3389fendo.2022.1020827\n",
      "Text: indications for surgical management of the  asymptomatic  ovarian endometrioma in patients with infertility is to improve the accessibility of follicles and to prevent potential complications endometrioma rupture, contamination prior to ART. A recent metaanalysis  326  conducted by Alborzi et al. of eight prospective studies comparing pregnancy rate from four different approaches of OMA surgery  ART, surgery  spontaneous pregnancy, aspiration with or without sclerotherapy  ART, and ART alone found no signi  cant difference between the four study groups. Another meta analysis  167  analyzing surgical versus expectant management of endometriomas reported similar live birth rates per cycle after IVF in both groups. Surgery is generally not recommended for the sole purpose of enhancing fertility in an otherwise asymptomatic patient.\n",
      "Text: endometriosisassociated infertility in rASRM stage III  278 , 279  when is performed for other indications such as pain. The absolute bene  t is modest with a number of women needed to be treated of 12 to achieve one additional pregnancy.\n",
      "Text: rASRM stages III and IV\n",
      "Text: The situation is more complex for advanced disease where high quality evidence regarding the role of surgery for infertile patients is lacking and the risk of major complications due to the surgery itself must be considered. There are no RCT to determine whether clinical pregnancy rates are improved after surgery in patients with stage IIIIV of the disease. Women with advanced disease are normally counseled toward surgery in case of signi  cant pain symptoms, large endometriomas, or ureter and bowel clinical involvement. Apart from the deep in  ltrating endometriosis DIE induced alteration of pelvic anatomy and adhesions, evidence supporting a direct link between DIE and infertility is weak and the lack of highquality data preclude  rm conclusions on the effect of surgery. Moreover, DIE alone is found in only 6 of endometriosis patients  318  and surgeryrelated major complications in this context must be taken into account. According to three independent systematic reviews, pregnancy rate after surgery for rectovaginal endometriosis varies from 24 to 44  319  321 . An additional systematic review  322  of heterogeneous prospective and retrospective studies reported postoperative spontaneous pregnancy rates in women with DIE with and without bowel involvement of approximately 50 and 20, respectively. Lastly, a recent metaanalysis including observational studies on both rectovaginal and rectosigmoid DIE patients showed a statistically signi  cant bene  t of surgery before IVF  323  in terms of live birth and pregnancy rates per patient and per cycle. Nonetheless results need to be interpreted with caution before attributing this rate of success entirely to surgery  324 . Interestingly it has been shown in a recent study that extensive surgery in women with deep and intraperitoneal endometriosis, when compared with intraperitoneal surgery only, does not modify the fertility outcome  325 . At present, operative laparoscopy for DIE represent a wellestablished indication in endometriosis associatedpain and in case of visceral obstruction, and is a treatment option in symptomatic patients wishing to conceive  278 , 279 . Potential bene  ts and harms of adnexal surgery for endometrioma must be considered in this context because of its direct effect on ovarian reserve and the risk of recurrence. There is still no consensus regarding the optimal indication for surgery depending on cyst diameter due to the lack of comparative studies. According to guidlines  278 , 279 , key\n",
      "Text: Medically assisted reproduction IUI, ART The utility of Intrauterine Insemination IUI with or without ovarian stimulation in patients with endometriosis is supported by only one single RCT  327  including patients undergoing ovarian stimulation with gonadotrophins and IUI versus expectant management. The study found a 56 times higher live birth rate per cycle in the treatment group. IUI in combination with controlled ovarian stimulation clomiphene citrate is currently recommended only in infertile women with ASRM stage III  328 . Currently, up to 25 of in vitro fertilization IVFembryo transfer procedures are performed in patients with endometriosis  329 . Despite its high implementation, both the in  uence of endometriosis on pregnancy rates after ART, and the effectiveness of ART treatments in women with endometriosis are still a matter of debate. Main indications for ART remain tubal impairment, male factor, low EFI, and failure of other treatments. There are currently no RCTs evaluating the ef  cacy of this treatment option versus no intervention in women with endometriosis, and only indirect evidence is available from studies comparing ART outcomes in women with endometriosis to women without the disease. Several metaanalyses  172  175  have investigated ART outcomes of women with and without endometriosis, but results appear con  icting due to the low quality and the high heterogeneity of the selected studies. According to a recent metaanalysis  213 , endometriosis consistently leads to reduced oocyte yield and a reduced fertilization rate. Milder forms of endometriosis are most likely to affect fertilization and implantation processes as discussed earlier, whereas advanced stages of the disease may in  uence all stages of reproduction. Reasons for the suspected suboptimal performance of ART in endometriosis may include the affected ovarian responsiveness during the ART cycles low\n",
      "Text: Frontiers in Endocrinology frontiersin.org 14\n",
      "Text: Bonavina and Taylor 10.3389fendo.2022.1020827\n",
      "Text: is ongoing in the US with the aim to investigate for the  rst time the preIVF treatment with a GnRH antagonist Elagolix in women with endometriosis PREGnant. Compared with GnRHagonists, the rapid reversibility and recovery of the hormone secretion once the treatment is concluded using GnRH antagonist may allow for better outcomes at the time of ART. Data addressing pretreatment with continuous oral contraceptives are very limited and do not allow  rm conclusion  338 , 339 . Comparative studies between different hormonal suppression treatment strategies are lacking. Lastly, assuming that endometriosis is a chronic in  ammatory condition, the effect of several anti in  ammatory, immunomodulatory and antioxidant agents has been investigated in the context of in  ammation and altered redox balance in the follicular  uid microenvironment and of suspected impaired oocyte quality  340 . Pentoxi  lline has been the most studied antiin  ammatory and antioxidant agent in endometriosisassociated infertility, and it has also been shown to enhance sperm motility and improve semen parameters in men with oligoasthenospermia. However, according to a recent Cochrane review  341  including 5 RCT, there is no conclusive evidence on its effectiveness and safety in endometriosis associatedinfertility.\n",
      "Text: ovarian reserve, impaired endometrial receptivity, and altered folliculogenesis. Finally, a speci  c protocol of controlled ovarian stimulation for ART in women with endometriosis is not currently recommended as both antagonist and agonist protocols are still widely used and no difference in pregnancy or live birth rates has already been demonstrated  330 .\n",
      "Text: Medical approach Based on a presumed altered steroidogenesis in endometriosis associated infertility, the use hormonal suppression has been investigated. Based on current recommendations  278 , 279  ovarian suppression danazol, GnRH agonists, progestogens, OCP should not be offered alone or in combination with surgery in endometriosisrelated infertility because there is no evidence of its bene  t on pregnancy outcomes  331 . A recent Cochrane review  332 , comparing the effectiveness of different timing of hormonal suppression in the setting of surgery, concluded that postsurgical medical therapy compared with no treatment or placebo may increase pregnancy rates and reduce disease recurrence, and that it should be recommended in women who cannot, or decide not to conceive immediately after surgery. The role of downregulation with GnRH agonists prior to ART has been extensively investigated and several metaanalysis have been performed however results are still contradictory. It has been proposed that medical treatment with gonadotropins prior to IVF may result in improved fertility outcomes in terms of both oocyte quality and endometrial receptivity. An updated Cochrane review by Georgiu et al.  333  that included 8 RCT concluded that the effect of longterm GnRH agonist pretreatment for at least 3 months versus no pre treatment is uncertain in terms of live birth rate primary outcome, clinical pregnancy rate, multiple pregnancy rate, miscarriage rate, mean number of oocytes and mean number of embryos. Another more recent metaanalysis  334  investigated the effectiveness of three different downregulating protocols based on the use of GnRHagonist ultralong, long and short protocol in infertile women with endometriosis prior to ART. The authors concluded that the ultralong protocol may improve the clinical pregnancy rate especially in patients with stages III IV endometriosis based on data from two RCTs. Conversely, more recently, two RCTs  335 , 336  failed to demonstrate a bene  cial effect of the ultralong protocol in terms of live birth rate, clinical pregnancy rate, or embryo quality instead, it was associated with a longer duration of ovarian stimulation, a higher consumption of gonadotropins, and a lower ovarian estradiol production  335 . No studies have been conducted to evaluate the ef  cacy of GnRH antagonists for the treatment of endometriosisrelated infertility. A large multicenter RCT  337 \n",
      "Text: Emerging treatment strategies By elucidating the cellular and molecular mechanisms involved in endometriosisassociated infertility and based on the assumption that current hormonal suppressionbased treatment cause important side effects rather than effectively improve fertility  342 , there is a fundamental need to identify potential signaling pathways for nonhormonal targets for endometriosis associated with infertility. Noncoding RNAs ncRNAs have rapidly emerged as important regulatory molecules in cancer and several reproductive diseases such as recurrent pregnancy loss and endometriosis  95 . The use of ncRNAs as a therapeutic tool is still in its infancy however, the USFDA has recently approved three RNAi therapies  343 , 344 . In the context of impaired endometrial receptivity and progesterone resistance, Petracco et al.  345  identi  ed a putative miR135 binding site in HOXA10 gene showing that miR135a and miR135b are expressed in normal endometrium and increased in the endometrium of women with endometriosis they likely act by regulating targets of progesterone action in the endometrium. Furthermore, miR451 was found to be the most highly downregulated in the midsecretory phase of eutopic endometrium of baboons  346  and women with endometriosis  347  compared to controls, leading to an increased expression of transcription factors involved in regulation and mediation of progesterone signaling such as\n",
      "Text: Frontiers in Endocrinology frontiersin.org 15\n",
      "Text: Bonavina and Taylor 10.3389fendo.2022.1020827\n",
      "Text: GATA2 and YWHAZ. Similarly, H19 is one of the  rst long noncoding RNA identi  ed it is expressed in a menstrual cycle dependent fashion, con  ned to the stroma, and acts as a decoy for several tumorsuppressor miRNA. Moreover, it is positively regulated by E2 and negatively regulated by progesterone in the mouse. It was recently found that in the eutopic endometrium of patients with endometriosis, downregulation of H19 will increase let7 activity, contributing to a decreased proliferation of endometrial stromal cells through IGFR1 expression inhibition and contributing to the impaired endometrial preparation and receptivity through reduction of stromal cell proliferation  348 . Finally, further studies have investigated the role of certain miRNA within progesterone resistance during the luteal phase in women with endometriosis they reveal that miR 30b, miR30d, miR29c and miR1943p are upregulated whereas mi494 and miR923 are down regulated in receptive endometrium  230 , 349  of both humans and baboons  350 . Lastly, upregulation of miR196 and MEKERK signaling proteins was reported in infertile women with minimalmild endometriosis mediating downregulation of PGR expression and decidualization in eutopic endometrium  351 . MicroRNA based therapies are promising new fertility treatments. In the context of a proin  ammatory endometrium, one recent study  352  investigated the pharmacological effects of selective inhibition of prostaglandin receptors EP2EP4 by using a chimeric mouse model of endometriosis and found that endometrial functional receptivity can potentially be restored the interaction among prostaglandin E 2 PGE 2 , estrogens and progesterone. The results indicate that inhibition of EP2EP4 decreases PGE 2 , estrogen biosynthesis and signaling, pro in  ammatory cytokine production, and increases P 4 signaling in eutopic endometrium of women with endometriosis. Stem cell therapy has shown to be promising as a new therapeutic target for infertility, especially Asherman  s syndrome  353 . The interaction between BMDSC and endometrial MSC has generated considerable interest because of their tropism toward in  amed foci. Stem cell properties of selfrenewal and differentiation made attractive their use to replace potential damaged tissues and in  ammation by reducing intrauterine adhesions and  brosis  354 , 355 , improving endometrial thickness  356  and promote endometrial regeneration. To date, the use of stem cell for treating endometriosis, and in particular endometriosis associated infertility offers an attractive option because of its tropic and immunomodulatory proprieties. Endometriotic lesions recruit stem cells away from the uterus resulting in inadequate endometrial repair and regeneration as endometriosis more effective in recruiting BMDSCs than eutopic endometrium  357 . Lesions highly express CXCL12, a chemoattractant for BMDSCs expressed in many organs, as well as by endometrial stromal cells  357 . Inhibiting its receptor CXCR4was shown to impact the\n",
      "Text: migration of BMDSCs to the uterus  358 . Endometriosis relatedchronic in  ammation likely acts by continually recruiting BMDSCs to the lesions as demonstrated in animal  52 . Moreover, physiologic estradiol levels can increase CXCL12 and CXCR4 expression by endometrial stromal cells and BMDSCs respectively in vitro , thereby increasing the chemoattractiveness between the two and consequently, migration  358 . Interestingly, Badoxifene, a selective antagonist ER antagonist, showed to reduce both ectopic endometriotic lesions and the BMDCs engraftment to them, redirecting these cells to the eutopic endometrium  54 , 359 , 360 . This phenomenon might be able to create a new endometrium partially free of epigenetic defects. The route of stem cell administration will be a crucial component of any stem cell based therapy. Signi  cantly greater levels of stem cell incorporate in uteri of mice when cells were administered systemically by intravenous injection as compared with local injections into the uterus  361 . Interestingly, mice that received a systemic infusion of BMDSCs prior to uterine injury were also more likely than twice to achieve a pregnancy, suggesting functional repair of damaged endometrium was due to BMDSs activity  355 . BMDSCs maybe superior to ESC in the treatment of uterine injury they may allow a more complete repair due to their superior versatility, developing into a large number of cell types required for endometrial function  355 .\n",
      "Text: Fertility preservation The need for reproductive counseling utilizing a multidisciplinary medical team has become more evident in endometriosis not only prior to surgery but also at diagnosis, based on the assumption that fertility is likely to be compromised in these women. Several options are currently available to preserve fertility, including embryo or oocyte cryopreservation and ovarian tissue cryopreservation which are no longer considered experimental procedures  362 . Vitri  cation or planned oocyte cryopreservation technology has grown enormously during the last few years. Several metaanalyses demonstrated that clinical outcomes after vitri  cation are superior to the standard slow freezingthawing. Moreover, comparable results between vitri  cated and fresh oocytes were reported  363 , 364 . Many questions in terms of ef  ciency, effectiveness and risks remain unanswered, and the strength of evidence to support fertility preservation in endometriosis, regardless disease severity, is still limited  365 . Systematically offering FP to patients with endometriosis might have a dramatic effect on the public healthcare expenditure and may expose patient to unnecessary clinical risks  366 , 367 . In the context of ovarian endometriosis, subgroups that would particularly bene  t from\n",
      "Text: Frontiers in Endocrinology frontiersin.org 16\n",
      "Text: Bonavina and Taylor 10.3389fendo.2022.1020827\n",
      "Text: Conclusions\n",
      "Text: fertility preservation are women with bilateral endometriomas and those scheduled for surgery for contralateral recurrence after unilateral endometrioma surgery or in whom spontaneous conception is unlikely after ovarian surgery  365  368 . One of the advantages related with an earlier approach is the opportunity to preserve oocyte at a young age. However, lack of reliable data regarding the effectiveness limit full scale adoption. Women at young age may have a greater risk of recurrence, and when there is not an immediate desire for pregnancy, offering FP could be a bene  cial option. Ovarian tissue cryopreservation represents an alternative in case where ovarian hyperstimulation is contraindicated. The  rst case of autologous ovarian transplantation with cryopreserved tissue was reported in 2000 by Oktay et al.  369 . Later updates by the same group in 2010  370  and Donnez et al. in 2005  371  reported a similar successful approach in endometriosis cases and to date, other few cases have been reported  372  378 .\n",
      "Text: The mechanisms involved in endometriosisassociated infertility are still not completely understood and this condition is multifactorial. Endometriosisassociated pain and in  ammation, altered pelvic anatomy and adhesions, disrupted ovarian function, and compromised endometrial receptivity all play a major role in endometriosis infertility in women with endometriosis. Identifying innovative, noninvasive diagnostic tools in endometriosis that also predict a higher risk of infertility remains one of the major research and clinical priorities in this disease delayed diagnosis allows for disease progression which is clearly detrimental from the perspective of fertility. Treatment options of infertility associated with endometriosis are still limited. Surgery and ART remain the mainstay of effective therapy. All medical therapies currently approved for use in this disease prevent or diminish fertility and therefore are not helpful in treating this condition. Future nonhormonal medical therapies are needed that can enhance fertility by interfering with the pathways outlined above. Endometriosisassociated infertility requires a multidisciplinary, personalized, shared and holistic approach based on patient  s unique characteristics, endometriosis subtype and level of impairment.\n",
      "Text: Fertility sparing surgery\n",
      "Text: Optimizing fertility in patients with endometriosis requires reducing potential iatrogenic harm to the ovarian reserve. In this context, the role of adnexal sparing surgery, when indicated, is crucial for treating symptomatic women with endometriosis associated pain for improving accessibility of follicles prior to ART due to endometriosisassociated infertility. Thus, skilled surgeons with expertise in reproductive pathophysiology are required to avoid potential insults to the healthy parenchyma and ovarian vascular network. Decrease of normal ovarian cortex ovarian reserve and disease recurrence are the two main risks associated with surgery for endometrioma, regardless the surgical technique. Several surgical approaches for endometrioma have been proposed Excisional, ablative or a combination of both. Lower rates of spontaneous pregnancy and higher rates of recurrence are associated with ablative surgery compared with cystectomy, whereas cystectomy was found to be deleterious for residual ovarian function  162 , 379 , 380 . Since the metaanalysis of Dan et al. in 2013  380 , RCTs comparing ablative versus excisional techniques in terms of ovarian reserve markers and ovarian residual volume have been performed  381  386 . Data from animal studies  387  and RCT  381 , 382 , 388  on the use of laser and plasma energy is encouraging and may result in less inadvertent tissue removal and thermal injury compared with cystectomy and bipolar electrosurgery. Fertility sparing surgery performed in the context of endometriosisassociated infertility also requires the systematic evaluation and optimization of tubal anatomy and patency. Concomitant adhesiolysis with restoration of pelvic anatomy is also recommended when anatomical distortion is present.\n",
      "Text: Author contributions\n",
      "Text: GB and HT contributed to manuscript writing and editing. HT revised the manuscript for important intellectual content all authors approved the  nal version of the manuscript.\n",
      "Text: Con  ict of interest\n",
      "Text: The authors declare that the research was conducted in the absence of any commercial or  nancial relationships that could be construed as a potential con  ict of interest.\n",
      "Text: Publisher  s note\n",
      "Text: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their af  liated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.\n",
      "Text: Frontiers in Endocrinology frontiersin.org 17\n"
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